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DISCLAIMER
This document is intended for internal Agency use only. Mention of trade names or
commercial products does not constitute endorsement or recommendation for use.
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ABSTRACT
This report describes the development of computational methodologies and computer
programs that may be employed to estimate aromatic organic solute solubility in miscible
polar solvent/water mixtures. This information is used to predict the sorption partition
coefficient for sorption of aromatic solutes onto soils or sediments in aqueous systems
containing miscible polar solvent These procedures assist in the prediction of facilitated,
near-source, solute transport in soil or sediment in the event of spill or discharge of
organic waste containing water-soluble solvents.
The chemical thermodynamic basis for estimating organic solute solubility in water and in
solvent/water mixtures is reviewed. This information is synthesized and employed in the
design of a computer program, named AROSOL, to aid prediction of aromatic solubility in
water and in miscible organic solvent/water mixtures. The program AROSOL is formulated
to accommodate various levels of input data and physical constants. The program utilizes
four techniques to predict solute solubility in solvent/water mixtures:
(i) Log linear,
(ii) UNIFAC, -"
(iii) Excess free energy, and
(iv) Molecular surface area
The user may select any or all of these techniques to evaluate solubility depending on the
availability of data, physical constants, and other specific information required for each
approach.
The solubility prediction is then used in conjunction with a chemical thermodynamic sorption
model to estimate solute sorption partition coefficient, K , in water and in solvent/water
mixtures.
This report also describes the development of a general purpose program, named
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Ill
\
MOLACCS, to compute molecular surface area The program MOLACCS is used to estimate
molecular surface area for use in solute solubility predictions. Three types of surface
areas are computed:
(i) The solvent accessible area,
(ii) The contact surface area, and
(iii) The van der Waals area
The program allows for specification of solvent, or probe radius, and individual atomic
parameters including degree of hydrophobicity. The contribution of each atom to the
surface area is displayed, as well as the net value of the individually estimated atomic
group contributions to hydrophobic and polar surface area. The program is designed for
use by the non-expert, in which molecules are constructed from existing atomic groups
and molecular fragments. The user may construct new molecules and molecular fragments
through the program operations comprising: building, perturbing, replacing, adding, and
combining.
The report presents various sample calculations for both AROSOL and MOLACCS. Program
listings are also included.
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IV
TABLE OF CONTENTS
Chapter 1. Introduction 1
Chapter 2. Solute Solubility and Sorption onto Soil in Water and
Miscible Solvent-Water Systems 4
Phase Equilibria and Activity 4
Estimation of Infinite Dilution Activity Coefficient 6
Solubility Prediction by an Excess Free
Energy Approach 8
Solubility Prediction by Log-Linear Relationships 11
Solubility Prediction by a
Molecular Surface Area Approach 12
Calculation of Molecular Surface Area
and Its Use in Predicting Solubility 13
Molecular Surface Area 14
Calculation of Surface Area 18
Problem of Determining Hydrogen-Atom
van der Waals Radius 22
Correlation of Hydrocarbon Solubility
with Solute Surface Area 23
Effect of Organic Solvent on Sorption of
Aromatic Solutes onto Soil 26
Partition Coefficients 28
Koc and Solute Solubility 29
Solvent Effect on Solute Sorption 30
Partition Coefficient in Solvent-Water Mixtures 33
Chapter 3. Description of the Computational Programs 34
AROSOL Program Organization 34
Estimation of Solubility and Sorption
Partition Coefficient 36
Molecular Surface Area Calculations 51
Program Description 51
Program Structure 52
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Molecular Fragment Library File 56
Manipulation and Generation of
Molecular Fragments 57
Testing and Initial Results 61
Example Calculations 63
References 80
Appendix 1. AROSOL Program Listing 86
Appendix 2. MOLACCS Program Listing 107
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1
Chapter One
INTRODUCTION
The purpose of this investigation is to develop computational procedures which can be
used to estimate the solubility of aromatic solutes in miscible solvent/water mixtures. This
information can then be employed to predict the partition coefficient for sorption of
aromatic solutes onto soils or sediments.
The effect of miscible solvents, e.g. low molecular weight polar sovents, on solubility of
aromatic solutes would be evident wherever water, miscible solvents, and solutes are
comingled, such as in concentrated wastewaters or in waste liquids from chemical
manufacturing. The effect of miscible solvents on sorption of aromatic solutes onto soils
would be manifested when concentrated waste liquids contact soil or sediment material.
Understanding the combined effects of solvents on solubility and sorption will aid the
assessment of the tendency for aromatic solutes to undergo facilitated transport in
soil/sediment systems in the presence of miscible polar solvents. This will allow for
prediction of near-source contaminant transport in soils in the event of spillage or
discharge of organic waste containing wateisoluble solvents.
The following chapter describes the general methodologies employed in the computational
procedures for estimation of solute solubility in water and in miscible solvent/water
systems. Also described are the effects of organic solvents on sorption of aromatic
solutes onto soil, and the calculation of molecular surface area and its use in predicting
solubility. This is followed by a discussion of the use of the computer programs and
example calculations. An appendix contains a listing of the computer programs. A
summary of the organization and content of this report is presented below.
The chemical thermodynamic basis for estimating organic solute solubility in water and in
solvent/water mixtures is reviewed. This information is synthesized and employed in the
design of a computer program, named AROSOL, to aid prediction of aromatic solute
solubility in water and in miscible organic solvent/water mixtures. The program has been
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specifically designed to aid the prediction of aromatic solute solubility; however, the general
methodologies and procedures are also applicable for other organic compounds as well.
The program AROSOL is formulated to accommodate various levels of input data and
physical constants. The program utilizes four techniques to predict solute solubility in
solvent/water mixtures:
(i) Log linear,
(ii) UNIFAC,
(iii) Excess free energy, and
(iv) Molecular surface area
The user may select any or all of these techniques to evaluate solubility depending on the
availability of data, physical constants, and other specific information required for each
approach.
The solubility prediction is then used in conjunction with a chemical thermodynamic
sorption model to estimate solute sorption partition coefficient, K, in water and in
solvent/water mixtures.
The report then describes the development of a general purpose program, named
MOLACCS, to compute molecular surface area. The program MOLACCS Is used to estimate
molecular surface area for use in solute solubility predictions. Three types of surface
areas are computed:
(i) The solvent accessible area,
(ii) The contact surface area, and
(iii) The van der Waals area
This program allows for specification of solvent, or probe radius, and individual atomic
parameters including degree of hydrophobicity. The contribution of each atom to the
surface area is displayed, as well as the net value of the individually estimated atomic
groups contributions to hydrophobic and polar surface area. The program is designed for
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use by the non-expert, in which molecules are constructed from existing atomic groups
and molecular fragments. The user may construct new molecules and molecular fragments
through operations comprising: building, perturbing, replacing, adding, and combining.
The report presents various sample calculations for both AROSOL and MOLACCS.
Program listings are also included.
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Chapter Two
SOLUTE SOLUBILITY AND SORPTION ONTO SOIL
IN WATER AND MISCIBLE SOLVENT-WATER SYSTEMS
The following is a synthesis of current chemical thermodynamic techniques that may be
used to estimate solute solubility in miscible solvent/water systems. This information is
used in conjunction with a chemical thermodynamic sorption model to describe a
methodology by which the sorption of aromatic solutes onto soils may be predicted for
liquid phases comprised of miscible solvent-water systems. This discussion is adapted in
part from the methodological procedures presented in Fu and and Luthy (1986 a and b)
with additional information being provided on the subject of molecular surface area
calculations. The techniques described below have been incorporated in the computer
program named AROSOL for estimation of aromatic compound solubility in miscible
solvent/water mixtures, and for prediction of aromatic solute sorption onto soils and
sediments in solvent/water mixtures. This chapter also explains techniques for molecular
surface area calculations and their use in predicting solubility.
Phase Equilibria and Activity
Expressions that relate solute activity coefficient and mole fraction _are employed in
several techniques to estimate solute solubility in solvent/water systems. The relationship
between activity and solubility are described below.
The solubility of a liquid or solid non-electrolyte solute in aqueous solution can be
described by the thermodynamics of phase equlibria. The solute chemical potential can be
expressed in terms of fugacity, and the aqueous solubility of a hydrophobic organic
compound in water or water/miscible solvent mixture can be expressed in terms of
fugacity and activity using the Raoult's law convention. For liquid components the
relationship between mole fraction solubility, X, and activity coefficient, y, is
X = - (1)
7
Both terms in this equation are dimensionless. For solid solutes (e.g., naphthalene) the
relationship between mole fraction and activity is
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(2)
rR
f 7
in which fs = the pure solid fugacity, or vapor pressure; and fR = the reference or
standard state fugacity, which is usually defined as an extrapolated pure component liquid
vapor pressure below the triple point As explained below, the ratio (fs/fR) can be
estimated by several standard procedures.
The conventional definition of the reference state for a solvent identified as component
1, is y -» 1 as X -» 1. For a solute, identified as component 2, the reference state is
the infinitely dilute solution. In general, y2 > 1 for a dilute solution of a given component
in a given solvent As the solution becomes increasingly dilute, the value of y2 approaches
a limiting value, y °°, known as the infinite dilution activity coefficient (Prausnitz, 1969).
Knowledge of the infinite dilution activity coefficient can be used to estimate solute
solubility in water and in solvent/water mixtures, as well as other physico-chemical
properties important to the environmental scientist, such as solvent/water partition
coefficients and Henry's law constants (Campbell and Luthy, 1985; Grain, 1982).
A simplified expression for (fs/fR) employs heat of fusion of the solid, AHfm, cal/mole, at
the melting point (Prausnitz, 1969)
AHf.m r T i f*
in (y2X2> - L - - 1 J = «n - (3)
m T
in which T = system temperature, °K; T = melting temperature of pure solid, °K; and R =
the gas constant, 1.987 cal/mole-°K. Eq. 2 neglects certain correction terms including
those depending on the difference of specific heat between solid and liquid, AC ,
cal/mole-°K. Hildebrand and Scott (1950) proposed that the heat of fusion of a solid at a
temperature, T, can be calculated from the heat of fusion at the melting point:
AH = AH - AC (T - T) (4)
f f,m p m
in which AH( = heat of fusion at the system temperature. This expression can be used to
compensate in part for some of the error introduced by omission of the AC term in the
simplified fugacity ratio expression. Heat capacity data are available for relatively few solid
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solutes, and thus it is fortunate that the correction is usually small compared to the AHfm
term, as well as compared to other uncertainties in estimating activity coefficient (Gmehling
et al., 1978; Prausnitz, 1969).
In the case of solid solutes for which heat of fusion data are not available, heat of
fusion may be calculated from entropy of fusion, ASf (cal/mole-°K)
AH = T AS (5)
f m f
For many moderately-sized organic molecules, including substituted aromatic hydrocarbons,
the entropy of fusion is reported to be nearly constant at about 13 - 13.5 cal/mole-°K
(Tsonopoulus and Prausnitz, 1971; Yalkowsky, 1979). Then, Eqs. 3 and 5 reduce to the
following relation, assuming ASf is constant at 13 cal/mole-°K
r T "T i
In (y2X2) = 6.56 L -J ' <6)
The AROSOL computer program which was developed for the project allows for the
determination of the fugacity ratio expression as follows. AHfm is employed according to
Eq. 3 if heat of fusion data are available. If AH is not available, then Eq. 5 is used in
f,m
conjunction with Eq. 3 as the fugacity ratio expression, which reduces to Eq. 6.
Estimation of Infinite Dilution Activity Coefficient
The solute infinite dilution activity coefficient, and the solvent and water activity
coefficients, are estimated in the computer program by a group contribution method using
the Universal Quasi-Chemical Functional Group Activity Coefficient (UNIFAC) approach. This
approach computes the activity coefficients from knowledge of the molecular structure of
the solute and the solvents through equations that employ a data base comprising functional
group size and interaction parameters. This represents an especially utilitarian technique for
prediction of chemical properties of mixtures, as no specific experimental data or
correlation coefficients are required.
The UNIFAC approach is a group contribution method for predicting activity coefficients
of nonelectrolytes in liquid mixtures (Fredenslund et al., 1975). The model assumes that the
logarithm of the activity coefficient is comprised of two parts
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In y = In yc + In y (7)
Herein, yc is a combinatorial part due to the difference in molecular size and shape of the
molecules in a mixture, and yR is a residual part due to molecular interactions. The
computational procedures employed in the UNIFAC model are described in Fredenslund et al.
(1975) and Gmehling et al. (1978). The most current tabulation of group size and
interaction parameters is given by Gmehling et al. (1982).
The UNIFAC approach has been applied to various problems for estimation of solution
properties including estimating activity coefficients in organic solvent mixtures (Fredenslund
et al., 1979), estimating the solubility of a solid in a solvent (Martin et al., 1981), estimation
of octanol/water partition coefficient (Arbuckle, 1983), predicting the solubility of organic
compounds in water (Banerjee, 1984, 1985), estimating aromatic solute distribution
coefficients for both polar and nonpolar organic compounds (Campbell and Luthy, 1985),
and estimating solute solubility in solvent/water mixtures (Fu and Luthy, 1985). The
calculation of solvent and water activity coefficients, and solute infinite dilution activity
coefficient, was facilitated by the adaptation of a computer program developed by
Fredenslund et al. (1975) and updated by Anderson (1983). Examples of the computational
methodology for predicting activity coefficients are provided by Grain (1982) and Fu and
Luthy (1985).
The UNIFAC approach was adapted in this investigation in order to estimate solute infinite
dilution activity coefficient (y°°) in pure solvent and pure water, and in solvent/water
mixtures. The methodology entailed treating the solvent/water system as one component
and the solute as a second component The solvent/water system was treated as a single
component to facilitate estimation of solute solubility from y°°. In this approach the
solvent/water system may be envisioned as comprised of a "molecule" of water and solvent
in proportion to the mole fraction solvent/water composition of interest. It does not
matter if the "molecule" is comprised of water and solvent in noninteger ratios when using
a solution-of-groups approach to estimate activity coefficients.
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8
For the case of liquid solutes, mole fraction solubility can be estimated from y°° using
Eq. 1, provided y°° is sufficiently large, i.e., y°° > 1,000. If y°° is < 1,000, then the
mole fraction solubility calculation must account for the fact that at infinite dilution there is
appreciable solubility of solute, and that the solvent system mole fraction does not
approach unity. In these cases, mole fraction solubility is estimated according to
procedures described by Lyman (1982), which includes an evaluation to determine if the
component is completely miscible. For solid solutes, mole fraction solubility can be
estimated from y°° with Eq. 3 if y°° is > 100. If y°° is < 100 then the mole fraction
solubility is estimated according to Lyman (1982) to account for the solvent system mole
fraction being less than unity.
It is useful for purposes of practical environmental engineering calculations to be able to
express solute concentration in terms of molar concentration (moles per liter) or mass
concentration (mg or g per liter). This introduces a small difficulty because in computing
molar or mass composition from mole fractions, it is necessary to incorporate a value for
the volume of the solute/solvent/water mixture. In using the activity coefficient data to
compute solute molar or mass concentration, it was assumed that the separate volumetric
contributions of the solute, solvent, and water are conserved. This assumption is often
made in theories pertaining to thermodynamic properties of mixtures of nonelectrolytes
(Hildebrand et al., 1970). This assumption was addressed in experiments and discussion by
Fu and Luthy (1985) for the case of methanol/water and acetone/water mixtures. In these
cases the conservation of volume assumption generally resulted in errors less than about
5%, and often less than 1 or 2%.
Solubility Prediction by an Excess Free Energy Approach
Williams and Amidon (1984a) derived relationships between solute activity coefficient,
solute Henry's law constant in pure solvent, and solute-free solvent and water volume
fractions. These relationships were then used with an expression for the excess Gibbs
free energy of mixing to estimate the solubility of a solute in a binary solvent system. The
resulting expression was
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q2 q2
In X = z In X + z In X - A z z (2z - 1) + 2A z 2z + C z z (8)
2 1 s 3 w 1-3131 n 3-1 1 3a 213
H1 M3
in which the subscripts 1, 2, and 3 refer to solvent solute, and water, respectively; z. =
solute-free volume fraction of solvent or water; q. = molar volume for component i; A^
and A = solvent/water interaction constants (dimensionless). The first two terms in Eq. 8
represent proportional solubility of solute in pure solvent and water. The next two terms
represent the contribution of solvent/water interactions, and the last term accounts for the
interactions between solute and solvent/water. This last term, C2, is essentially a ternary
correction parameter. The solvent-water interaction constants may be estimated from the
molar excess free energy of mixing for solute-free systems (Williams and Amidon, 1984b)
A A
xi ln r, + x3 ln r3 « -^V,'0^, + W + IT ^iV^i + X3S>] <9)
H1 H3
X1 and X = solvent and water mole fraction, respectively; and y1 and y3 = solvent and
water activity coefficients, respectively. Williams and Amidon (1984b) determined A1_3 and
A for a solvent/water mixture from estimation of y1 and y3 through use of experimental
partial pressure data . In the present AROSOL program, y1 and y3 are estimated for
different solvent/water compositions by the UNIFAC method. The constants AI 3 and A
are then obtained by a two-parameter statistical regression of Eq. 9. The statistical
regression procedure is performed according to the techniques described by Ryan et al.
(1981).
Williams and Amidon (1984b) employed Eqs. 8 and 9 to describe the solubility in
ethanol/water mixtures for ten compounds of interest in pharmaceutical science, where C
was estimated by linear regression of the difference between experimental solubility and
calculated solubility without the C2 term using Eq. 8. It was noted that the C term was
correlated with the solute octanol-water partition coefficient, K . This suggested that it
may be possible to estimate C2 from octanol-water partition coefficient data, and then use
an estimated C2 term in conjunction with the solvent-water terms and pure solvent
solubilities to predict the solute solubility-solvent/water composition profile. In additional
work, Williams and Amidon (1984c) concluded that Eq. 8 predicted a semi-logarithmic
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10
increase in solute solubility with volume fraction solvent when the solvent/water interactions
were small compared to the interaction between the solute and the mixture.
In summary, three parameters must be determined in order to use the excess free energy
approach: the solvent interaction parameters A and A3 ^ and the solute-solvent
interaction parameter, C . The solvent interaction parameters are determined in the AROSOL
program from estimation of activity coefficients for the solvent and water using the
UNIFAC procedure with Eq. 9 and a two-parameter statistical regression technique. The
results of this technique for four solvent-water systems have shown that the parameters,
A and A . are constants for the binary solvent systems being considered (Fu and Luthy,
1986a). The computer program developed for this investigation uses Eq. 9 to determine
A and A3 v and considered these parameters as constants, as found previously Fu and
Luthy (1986a) and Williams and Amidon (1984b, 1984c).
The solute-solvent interaction parameter, C , was estimated from the experimental data of
Fu and Luthy (1985). Statistical analysis of the data for eighteen aromatic
solute/solvent/water systems investigated by Fu and Luthy (1985) showed that C may be
correlated with aromatic solute octanol-water partition coefficient, K , by
C = -2.69 - 1.22 log K r2 = 0.86 (10)
2 ow
For comparison, Williams and Amidon (1984b) found that the correlation for eight solutes
and ethanol-water was
C = 3.96 - 2.66 log K r2 = 0.90 (11)
2 ow
The AROSOL computer program employs Eq. 10 for prediction of solubility by the excess
free energy approach. This is because it is desired to employ an expression for C that is
more appropriate for aromatic solutes, rather than a more general, but less precise
regression equation. Nonetheless, the user of the program has the flexibility to modify the
expression for C as conditions may warrant Fu and Luthy (1986a) have shown that
statistical analysis of the combined eighteen aromatic solute/solvent/water systems
investigated by Fu and Luthy (1985), plus the eight solute/ethanol/water systems reported
by Williams and Amidon (1984b), results in a correlation for C2 with r2 = 0.69. The poor
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11
correlation for the larger data set suggests that the expression for C2 is either system-
specific, or that the expression for C2 must be expanded to include additional terms.
Solubility Prediction by Log-Linear Relationships
Yalkowsky et al. (1972) reported on the solubility of alkyl p-aminobenzoates in water-
propylene glycol mixtures, and found that the solubility could be described by a semi-
logarithmic relationship,
log S = log S + o-z (12)
2 ° w 1
in which S, = the solute solubility in the mixture, moles/L; S = the solute solubility in
2 w
water, moles/L; z = the volume fraction of solvent; and a = a parameter that was
characteristic of the system under study. Later it was reported by Yalkowsky and Flynn
(1974) that the solubility of certain compounds in solvent/water mixtures required Eq. 12
to be expanded to a fifth-degree polynomial in z in order to account for non-linearity of
solubility with increasing fraction of solvent Eq. 12 has been examined by Martin et al.
(1982) where it was noted that it was applicable to systems where the polarity of the
compound was significantly less than either of the solvents in the binary mixtures. It was
shown (Martin et al., 1982) that the linear dependence of logarithmic solubility on volume
fraction of the solvent was applicable when the Hildebrand solubility parameter of solvent
was larger than the solubility parameter of the solute. The Hildebrand solubility parameter,
<5, in units of (cal/cm3)1'2, is defined as the square root of the pure liquid component
cohesive energy density. Weast (1983) and Barton (1983) provide tabulations of 5 for
various compounds. These values typically range from less than ten (e.g., 5 = 7.3 for
hexane) to over 20, as that for water (5 = 23.45). Eq. 12 is related to the Hildebrand
solubility theory (Martin et al., 1982), where it can be shown that the mole fraction
solubility of solute may be given as a power series in terms of solvent volume fraction, z ,
and constants
log X = log X + log v - K + K z - K z 2 + ... (13)
323w3/wo1121
in which the subscript w refers to water; and KQ, K , and K , etc., are the polynomial
regression constants. Martin et al. (1982) showed that the solubility of semi-polar drugs
in solvent/water systems could be described by a simplified expression
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12
log X = log X + log y - K + K z (14)
a 2 a w a 'w o 11
If regression analysis of Eq. 14 was performed with perfect accuracy then the log yw
and the K terms would cancel in order that X, = X as z -» 0. Thus, Eq. 14 would
o 2 w ~
reduce to
log X = log X + K z = log X +
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13
mole fraction solute solubility in water; zl = the solute- free volume fraction of solvent; k
= the Boltzman constant; and T = the system temperature. A*H describes the microscopic
interfacial free energy between hydrocarbonaceous surface area and the solvent, and A* is
an analogous interfacial free energy term, which is dependent upon the interaction between
the solvent and the polar portion of the solute. For the case of relatively nonpolar
compounds, the hydrophobic interactions are dominant relative to polar interactions. This is
equivalent to assuming that the term (A*H HSA) is much greater than the term (A« PSA).
Under these conditions Eq. 17 can be reduced to
r
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14
the use of molecular surface area for correlation with aqueous solubility and partition
coefficient
The purpose of this review is to provide the user with appropriate background
information on the execution and use of molecular surface area calculations. This will help
the user in making judicious selection of atomic and molecular input parameters, as well as
»,
providing a reference base from which to make rational comparisons.
Molecular Surface Area
Richards (1977) has reviewed the procedures for calculation of molecular surface area,
and he has discussed some of the applications of this parameter in the field of protein
chemistry. Richards notes that there is an intuitive appeal with being able to correlate
thermodynamic properties of condensed phases with the packing of groups of atoms in a
molecule and the area of the molecule. This appeal derives in part from geometrical
concepts being generally easy to grasp, as well as from the success with which correlation
with molecular surface area and molecular volume may describe phase partitioning and
solubility, as well as other molecular properties that may relate to exposed surface and the
nature of the exposed groups.
The calculation of molecular surface area is usually made by assigning to each atom in a
molecule a bond length and bond angle, and a van der Waals radius. It is well understood
that the surface of a molecule must relate to the radial distribution of electrons
surrounding the molecule, and for atoms in a molecule the distribution of electrons is not
spherically symmetric nor isotropic. Nonetheless, as summarized by Richards (1977), the
hard sphere model of chemically bonded atoms has a long and successful record for
explanation of molecular properties. Richards's view is that more realistic and complex
models have improved the explanation of certain details not provided by the hard sphere
model, but these approaches have not altered the principal characteristics ascribed by hard
sphere models. This view has remained essentially unchanged, as summarized in the review
by Pearlman (1986) which concludes that even though the electron cloud surrounding the
nucleus of an atom has no well-defined surface, the intuitive appeal and empirical success
of the hard sphere or van der Waals radius concept is widely recognized.
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15
The van der Waals surface, A of a molecule may be envisioned as shown in Figure 1-a
Each atom in a molecule is represented as a sphere centered at the nucleus and having a
radius equal to the van der Waals radius of the atom, r . The van der Waals surface is
~ w
defined as the exterior surface of the union of all the van der Waals spheres in the
molecule (Pearlman, 1986). The van der Waals surface area of a molecule represents the
boundary surface of the molecular electronic distribution, and hence the van der Waals
surface is one type of descriptor of molecular surface area that may be used in estimating
solute-solvent interactions.
Hermann (1972) and Richards (1977) recognized that not all of the van der Waals surface
is accessible to the solvent, depending upon the size of a solvent molecule. This is
illustrated in Figure 1-b and Figure 2. These figures show a trace of the van der Waals
surface of some atoms in which a spherical solvent molecule with radius rso|v, or probe
with radius R , is allowed to trace the van der Waals surface by rolling on the outside of
the van der Waals surface. Figure 2 illustrates that atoms 3, 4 and 11 are never
contacted by the probe, and as such these atoms may be considered as interior atoms
which are not part of the surface of the molecule. For this reason alternate definitions of
molecular surface have been proposed which attempt to account for surface in actual
contact with solvent
One procedure for defining the surface of a molecule which is in contact with solvent is
to use the continuous sheet described by the locus of the center of the probe as the
probe rolls over the van der Waals surface. This is termed the accessible surface by '
Richards (1977) and Pearlman (1986). Another procedure is to consider those parts of the
molecular van der Waals surface that can actually be in contact with the surface of the
probe. This is termed the contact surface by Richards (1977), and it is illustrated by the
heavy line in Figure 2 for a probe of radius RV The definition of contact surface results
in a series of disconnected patches. The patches in contact with the probe are separated
by a segment given by the interior-facing part of the probe when it is simultaneously in
contact with more than one atom. These interior-facing segments are termed the reentrant
surface by Richards (1977). Taken together, the contact surface and the reentrant surface
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16
[a]
^
/.
"^-.i-^
*.
Figure 1. Molecular surface area definitions, after Pearlman (1986)
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17
OUTSIDE
Schematic representation of possible molecular surface definitions. A section
through part of the van der Waals envelope of a hypothetical protein is shown with the atom
centers numbered.
Figure 2. Molecular surface area definitions and features,
after Richards (1977)
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18
represent a continuous sheet that is termed molecular surface by Richards (1977); this
continuous sheet is termed contact surface by Pearlman (1986). Hence, there is a
conceptual difference in definition of contact surface among these authors. Pearlman's
definition of contact surface includes the reentrant surface as defined by Richards.
Richards (1977) explains, as in Figure 2 by the nature of the geometrical construction, that
the accessible surface has no reentrant sections.
Note that as the size of the probe, or solvent radius, approaches zero the accessible
surface area approaches the van der Waals surface area Also, small changes in the choice
of solvent radius can have a relatively large effect on the accessible surface area Figure
2 shows for a change in probe size from RI to R2, that the accessible surface becomes
much smoother and the number of interior atoms increases. It is generally agreed that the
smallest reasonable probe is a water molecule, which is considered as a sphere with a
radius of 1.4 or 1.5 A
Calculation of Surface Area
For covalently bonded-atoms the van der Waal hard shell spheres are normally truncated
by a plane perpendicular to the interatomic bond, with the plane chosen to divide the bond
into two segments proportional to the radii of the bonded atoms. Another normal
approximation is to specifically include the contribution of hydrogen atoms to the van der
Waals surface. This technique incorporates the radius of the hydrogen atoms into that of
the heavy atoms to which they are bonded. This is because the bond length and van der
Waal radii for atoms of carbon and higher atomic number result in the hydrogen being
"buried" to a great extent within the radii of the larger atom. Hence, a common procedure
is to expand the heavy atoms, and C,N,0 and S, into a series of groups with zero, one,
two or three hydrogen atoms attached, with each one of these groups considered to be
spherically symmetrical (Richards, 1977). This procedure is termed an extended atom
approach, in which the radius for each atomic group attempts to account for the
contribution of hydrogen to the surface area. Figure 3 illustrates this concept as applied
to a terminal methyl group, -CH3 with three tetrahedral hydrogens (Valvani et al., 1976).
The van der Waal radii for aliphatic carbon was taken as 1.6, and that for hydrogen as 1.2,
-------
19
with the C-H interatomic bond length of 1.09 A The solid curve shows the planar view of
the terminal methyl group without solvent radius with three tetrahedral hydrogens, while the
dotted curve shows the methyl group as single sphere with radius of 2.0 A
Valvani et al. (1976) evaluated procedures for calculation of surface area for various
aliphatic alcohols and hydrocarbons. Three methods for computation of surface area were
compared:
Method- A: Hermann's procedure (1972) for van der Waals surface area, which has been
adopted by Pearlman (1986), where the calculation considers the
molecule as comprised of intersecting spheres with hydrogen assigned
a specific van der Waals radius. The accessible surface also was
computed with a solvent radius of 1.5 °A (water).
Method B: An extended atom approach was used in the calculation with methyl, ~CH ,
methylene, ~CH2~, and the hydroxyl groups in alcohols, -OH,
considered as a spherical group rather than as individual atoms. The
accessible surface was computed with a solvent radius of 1.5 °A.
Method C: An extended atom procedure was used to compute the van der Waals surface
area, i.e. the computation was similar to Method B_with the solvent
radius excluded. -
Some of the conclusions from comparison of these procedures for computation of
surface area were:
1. Accessible surface areas calculated by the extended atom approach. Method
B, were generally very comparable to Method A.
2. Surface area was correlated with mole fraction aqueous solubility for 51
alcohols that are liquid at 25°C, plus four alcohols that are solids at 25°C for
which the solubility of the pure subcooled liquid was used. The correlation
showed for the 55 compounds that an expression of the form:
-------
20
A planar view of a terminal methyl group. The solid curves
show a carbon atom in the center with van der Waals radius of 1.6
A and, three hydrogen atoms with van der Waals radius 1.2 A. The
broken curve shows the whole methyl group treated as a single
sphere with radius of 2.0 A.
Figure 3. Definition of extended atom approach for a terminal
methyl group, after Valvani et al. (1976)
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21
log (X) = ft Surface Area + a
correlated the data equally well by Method A, B or C with a correlation
coefficient in the range 0.986-0.989. A similar conclusion was made for
correlation of surface area with aqueous solubility for seventeen hydrocarbons
(r = 0.980).
3. Another correlation with aqueous solubility was performed in which the total
surface area for the alcoholic molecules was partitioned between
hydrocarbonaceous surface area (HSA), and the polar surface area (PSA)
associated with the exposed portion of the hydroxyl group. The correlating
equation had the form:
log (X) = ft HSA + r PSA+«
where a. ft and y were correlating coefficients. This correlating equation
was used to evaluate the three methods for computation of surface area
This evaluation gave essentially similar results (r ~ 0.99). Although the
correlation coefficient was similar to that found in No. 2 above, the authors
judged from these results that the extended atom approach was able to
account for the contribution of the hydroxyl group to the solubility of the
alcohol.
4. The extended atom approach (Method B) afforded several computational
advantages over the single atom approach: (a) the extended atom technique
allowed one to eliminate the arbitrary selection of a specific arrangement of
hydrogen atoms in the molecule, (b) the simplest standard geometrical
representation of a molecule compared to within about 2% of that calculated
by Hermann's procedure which accounted for exact conformation, or weighted
average when several conformations were possible, and (c) the extended atom
approach offered considerable advantages in terms of computation time and
costs. In summary, Valvani et al. (1976) concluded that the extended atom
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22
approach can give at least as good, or slightly better, correlation with
solubility than the single atom approach, and that the extended atom approach
can be consistently utilized in solubility-surface area calculations. It was also
discussed for the case of alcohols that the extended atom approach for
calculation of surface area tended to eliminate from the surface area
calculations the inaccessible portions of the molecule. Although somewhat
inconsistent the authors claimed that the use of extended atoms without
solvent radius had much the same effect as inclusion of a solvent radius term.
For this reason, method C gave comparable correlation coefficient as Method
B. The authors preferred use of Method C (i.e., zero solvent radius or van der
Waals surface area) as a method for estimating surface area, since this
eliminated the need to arbitrarily select a solvent radius, which may vary
somewhat from solvent to solvent
Problem of Determining Hydrogen-Atom van der Waals Radius
Another fundamental reason for use of the extended atom approach relates to the
experimental difficulty in determining the van der Waals radius of the hydrogen atom.
Unlike interatomic bond lengths and bond angles, van der Waals radii are less well defined.
Further, the parameterization with explicit hydrogen atomic parameters seems to unduely
complicate the process of building and manipulation of molecules from fragments for
purposes of surface area calculation. In addition, extracting explicit hydrogen van der
Waals parameters is, at best, speculative. Most of the current molecular force fields
models, which are used describe the interactions between molecules, use an extended atom
representation (Brooks et al. 1983; Jorgensen and Swenson, 1985 and references therein),
and we have adapted this procedure in the current program. The difficulty associated with
extracting van der Waals parameters from standard transport data and viscosity
measurements arises because the hydrogen electron density is often buried within the heavy
atom to which it is attached, and consequently it is not "seen" by the experiments.
Therefore, these parameters have often been either empirically adjusted to fit some set of
experimental measurements or inferred from data on H2, in which case the heavy atom
parameters require empirical adjustment.
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23
Richards (1977) concludes that "within limits the choice of van der Waals radii is arbitrary,
with each author having his favorite list for the different atoms. The most appropriate
values for successful predictions may vary with the problem."
Correlation of Hydrocarbon Solubility with Solute Surface Area
Various investigators have proposed relationships between molecular surface area, or
molecular volume, and aqueous solubility or partition coefficient, such as octanol/water
partition coefficient These relationships derive from the earlier work of Langmuir who
proposed in 1925 that the logarithm of organic compound aqueous solubility should be
linearly proportional to molecular surface area. The relationship between solubility and
molecular volume was proposed in Scatchard's regular solution theory in 1931 in which the
logarithm of aqueous solubility is linearly proportional to molecular volume (Pearlman, 1986;
Richards, 1977).
Herman (1972) explained that the number of water molecules that can be packed around a
given hydrocarbon solute molecule is an important quantity in predicting solute solubility in
aqueous solution. This is because there is a decrease in entropy due to the tendency of
the water dipoles in the layer of water adjacent to the hydrocarbon to orient with respect
to the water molecules in the next water layer. This does not happen in the bulk liquid
away from the surface of a hydrocarbon molecule. The number of~water molecules that
can be packed around a hydrocarbon is related to the surface area of the solvent cavity if
the surface area is defined as that which passes through the centers of the water
molecules adjacent to the solute. This is analogous to the definition of accessible surface
area
The relationship between molar solubility, S, and accessible surface area, A , was given
by Hermann (1972) as
b A = -kT In (S) - c (19)
ace
where b and c are temperature dependent constants, and k is the Boltzmann constant This
type of relationship may consider different molecular confirmations by defining A as a
flCC
weighted average of the various confirmations, although this was shown by Valvani et al.
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24
(1976) not to be necessary for alphatic alcohols and various hydrocarbons. Hermann found
for single conformation hydrocarbon compounds that b = 0.033 kcal mole"' A2 at 25°C,
while b = 0.030 kcal mol"1 ft2 for alkylbenzenes.
Amidon et at. (1975) correlated the aqueous solubilities and molecular surface areas for
the following classes of monofunctional organic nonelectrolytes: hydrocarbons, alcohols,
ethers, ketones/aldehydes, esters, carboxylic acids, and olefins. Molecular surface areas
were calculated by Hermann's procedure with a solvent radius of 1.5 A Amidon et al.
(1975) summarized that the use of the surface area approach to explain solubility results
from consideration of the following steps in transfer of a solute from pure liquid to
aqueous solution: removal of solute from its pure liquid, creation of a cavity in water, and
placement of the solute into the cavity. These sequence of steps give the result at
equilibrium that the logarithm of the mole fraction solubility is proportional to the total
surface area in the organic solute. The total surface area may be divided into
hydrocarbonaceous (HYSA) and functional group surface area (FGSA), and the effects of
these contributions to total surface area may be determined by regression analysis assuming
that the hydrocarbonaceous and functional group portions of surface area contribute
independently to solubility. Amidon et al. (1975) showed for the different classes of
aliphatic hydrocarbons that the logarithm of organic compound aqueous molal solubility
could be correlated almost equally well with HYSA and FGSA, as with total surface area
The effects of the functional group (except for olefins) seemed to make the same
contribution to solubility for the case of pure liquid being chosen as the standard state.
The sign on the regression equations which employed an FGSA term indicated that among
any class of monofunctional aliphatic compounds, decreasing the functional group surface
area increased compound aqueous solubility.
Amidon et al. (1975) showed that the relationship between the logarithm of the aqueous
solubility and molecular surface area for all 227 solutes being considered (alkanes, alcohols,
ethers, ketones, aldehydes, esters and carboxylic acids) was 0.988, which was almost as
high as the average of the correlation coefficients obtained from separate regression
equations for each class of solutes. This suggested to Amidon et al. (1975) and Pearlman
-------
25
(1986) that the aqueous solubility of the organic solutes depends almost entirely on
molecular surface area and was seemingly independent of the chemical nature of the solute.
However, it must be recognized that this conclusion was based on monofunctional
substituted compounds. The conclusions from the discussions of Amidon et al. (1975) and
Pearlman (1986) are not necessarily broadly applicable to a variety of solute types; also,
these discussions are somewhat inconsistent with solubility theories which attempt to
account for interactions between polar and nonpolar entities.
x ^
In subsequent work, Yalkowsky and Valvani (1979) showed relationships between molecular
surface area and aqueous solubility and octanol/water partition coefficient for rigid aromatic
hydrocarbons. The surface areas were computed with zero solvent radius and using an
extended atom approach for methyl and methylene groups. For thirty-two components
having melting points equal to or greater than 25°C, the logarithm of the molar solubility
was related to TSA and melting point as
log Sw = a (TSA) + yff(mp) + 5 (20)
The relationship was derived from the recognition that the molar solubility for poorly
soluble solutes is proportional to the mole fraction solubility, which is inversely proportional
to the activity coefficient with a temperature dependent crystal energy term. The
agreement between calculated surface areas and solubilities was .judged to reflect the
concept that the molecular interactions were determined by the molecular area of contact
It was not necessary to specifically correct for structural features such as branching and
proximity effects because it was judged that these effects were reflected in the surface
area calculation and manifested as the amount of contact between the hydrocarbon
molecule and the aqueous solution. Yalkowsky and Amidon (1979) also showed that TSA
was linearly correlated with the logarithm of calculated values of octanol-water partition
coefficient for rigid aromatic solutes.
Pearlman (1980, 1986) observed for typical hydrocarbons, including normal and branched
alkanes and alkyl substituted aromatics, that molecular surface area and total molecular
volume are linearly related. The linear relationship would not be expected for a series of
essentially spherical molecules nor for globular entities such as proteins in which case
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26
*
molecular surface area and volume would vary as molecular radius to the two-thirds
power.
Pearlman (1986) explains for partitioning that Amidon's et al. (1975) observation that, the
correlation of molecular surface area with aqueous solubility for all solutes combined was
almost as high as the average of correlation coefficients obtained from separate
regressions for each type of solute, may lead to the supposition that the free energy of
solute-solvent interaction is essentially the same for all solvents. However, Pearlman
suggests that as solvents (and presumably solutes) become increasingly different,
differences in solute-solvent interaction energy are expected. Nonetheless, a weak solute-
solvent interaction in the enthalpic sense (i.e. weak "bonds"), is more favored entropically (i.e.
solvent molecules near the solute cavity surface are more asymmetric and less structured
than when solute-solvent interactions are stronger). Hence, while the enthalpy of solute-
solvent interaction may differ between solutes and solvents, the free energy of solute-
solvent interaction will differ to a lesser extent This type of argument is employed by
Pearlman (1986) to explain why a single parameter equation involving either the total
surface area or the total volume of the solute provides an adequate correlation for
partitioning for a variety of solutes. An analogus argument also may hold for aqueous
solubility, whereas although some functional groups can "interact more strongly with water
than others, they also interact with themselves more strongly, with the net difference being
nearly the same (Amidon et al., 1975; Pearlman, 1986). As a result of these explanations,
and the success of single-parameter surface area regression equations, it was concluded
by Pearlman (1986) for the case of 64 alkyl- and halo-substituted aromatics that
correlation of aqueous solubility with ISA was satisfactory, while an equation which
explicitly accounted for group-dependent differences in solute-solvent interactions was not
particularly advantageous.
Effect of Organic Solvent on Sorption of Aromatic Solutes onto Soil
The following describes the mathematical formulations that are employed in AROSOL to
describe the effect of miscible organic solvent in water on sorption of aromatic solutes
onto soil. The theoretical development for these formulations have been presented in Fu
and Luthy (1986b).
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27
The role of soil organic matter in the sorption of uncharged organic solutes has been
studied extensively, and it has been found that the organic matter in soil/sediments is
primarily responsible for sorption (Karickhoff, 1981). In studies of hydrophobic organic
solutes at low loadings, a linear correlation is often observed between solute partition
coefficient, K (L/kg), and soil/sediment organic carbon content The dependence of the
linear partition coefficient on organic carbon content can be expressed as
K = K OC (21)
p oc
where OC is the fraction organic carbon content; and K is the normalized organic carbon
partition coefficient Hamaker and Thompson (1972) suggested that KQC is highly soil or
sediment independent and is constant for a particular organic solute. A similar conclusion
is made by Karickhoff (1984) in his review of sorption of uncharged organic solutes of
limited aqueous solubility « 10"3 m/L) that are not susceptible to special interactions with
soil organic carbon.
Karickhoff (1984), following Mackay (1979), explains that sorption equilibrium may be
defined as the state in which sorbate fugacities are the same in the aqueous and sorbed
phases. For systems in which sorption to organic matter dominates over sorption to
mineral matter, the organic carbon normalized-partition coefficient may be envisioned as
being proportional to the ratio of the compound's activity coefficient in the aqueous phase,
y^ and in the organic phase, yoc, i.e. "
y«
K oc (22)
OC y
'
OC
In Eq. 22 the proportionality constant contains the reference state fugacities and
appropriate unit conversion factors. The activity coefficients "contrast" interactions of the
solute in a given phase with the cohesive interactions in the reference state (i.e., pure liquid
or subcooled liquid). Thus it may be expected for relatively hydrophobic organic solutes
that yw would be highly variable, as are variations in aqueous solubility, while y , reflecting
cohesive interactions in the organic carbon phase, should be similar to that for the
reference state and therefore much less variable. Hence, K should be dominated bv
OC '
variations in y , and as a first approximation
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28
K « y (23)
'v
OC ' W
Partition Coefficients
The octanol/water partition coefficient, K , like K , describes the partitioning of a solute
r ow oc ~ s
between an aqueous phase and a relatively immiscible hydrophobic phase. For a solute in
equilibrium with octanol and water, the fugacity is the same in each phase, and K is given
as the ratio of the mass concentration in each phase. Thus,
c r
K =-^=?^ (24)
ow
in which C = solute concentration in octanol; C = solute concentration in water; and y
oct w ' oct
= solute activity coefficient in octanol. In Eq. 24 the proportionality constant, J3, is a
conversion factor which entails the ratio of the molar volumes of water and octanol. The
same standard state is chosen for the solute in each phase (i.e., pure liquid or subcooled
liquid).
Since K and K both describe organic solute partitioning between water and a
OC OW
hydrophobic organic phase, it may be expected that these parameters would be related
K oc K "" (25)
ow oc
The concept embodied in Eq. 25 entails correlation of a partition coefficient for a given
system with that for a reference solvent/water system. This has been termed a linear free
energy relationship (Leo et al., 1971). Linear free energy correlations with K have been
used to describe aqueous solubility (Chiou et al., 1982), bioaccumulation (Chiou et al., 1977;
Neely and MacKay, 1982), and sorption of organics onto soils (Dzombak and Luthy, 1984;
Lambert, 1967).
Various investigations have developed empirical expressions to describe the relationship
between K and K . These investigations have reported excellent correlation between K
P ow OC
and K for hydrophobic solute sorption, with a linear regression equation usually given in
the form
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29
*
log K = a log K + b (26)
3 oc 3 ow
where a and b are regression coefficients. Karickhoff (1984) concluded from these results
that the correlation between K and K was "a somewhat divergent group of
relationships." This was attributed to various factors including hydrophilic contribution to
sorption, as well as kinetic or steric effects.
KQC and Solute Solubility
Organic solute solubility in water can be related to the solute's activity coefficient, y, as
explained previously. For hydrophobic solutes that are liquid at ambient temperature and
which have sufficiently large values of y, mole fraction solute solubility, X, can be
expressed as the reciprocal of the activity coefficient For hydrophobic solutes that are
solid at ambient temperature, a crystal energy term must be taken into account, and if y is
sufficiently large, the mole fraction solute solubility can be expressed as in Eq. 3. Entropy
of fusion, ASf, may be incorporated into Eq. 3 for heat of fusion, then the relationship
between solid solute activity and mole fraction solubility can be expressed as
ASf(T - T)
log y = -log X -" (27)
2.303 RT
For hydrophobic liquid solutes, the system temperature is greater than the melting
temperature, and T is set equal to T and the crystal term vanishes. Yalkowsky and Valvani
(1980) have reviewed ASf data for "rigid" organic solutes which are solids "at 25°C, and
found that AS( is not highly variable and is in the range of 12-15 cal/mol-°K. "Rigid"
solutes included cyclic compounds (aliphatic or aromatic) and molecules with less than five
atoms in a flexible chain (Yalkowsky and Valvani, 1980). It is recognized by chemical
thermodynamicists that the value of AS is in the range of 13 cal/mole-°K for solid organic
compounds (Prausnitz, 1969), and this average value of AS( was employed in this
investigation.
Eq. 23 suggests that K should be proportional to the solute activity coefficient, y.
Hence by combining Eqs. 23 and 27, an empirical equation of the following type may be
expected to fit observed sorption data
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30
i
AS,
log K = -a log X (T - T) + B (28)
2.303 RT m
in which a and ft are regression-fitted parameters. Karickhoff (1981) performed an
evaluation of Eq. 28 for condensed ring aromatic compounds using KQC data of Hassett et
al. (1980) for benzene and polycyclic aromatic hydrocarbon (PAH) compounds, with ASf
assumed to be 13.0 cal/mole-°K and system temperature T at 298 °K (25 °C). The
empirical equation was given as
log K = 0.921 log X - 0.00953 (T - 298) - 1.405 (29)
w oc "* m
This equation was evaluated for other families of hydrophobic organic solutes (triazines,
carbamates, organophosphates, and chlorinated hydrocarbons), and was found to estimate
KQC usually within a factor of 2 to 3 of measured values (Karickhoff, 1984). It was found
that Eq. 29 worked well for low molecular weight compounds but tended to overestimate
sorption of highly chlorinated, high molecular weight compounds. It was concluded that a
values for these type of compounds may be in the range of 0.7-0.8 which is considerably
less than that for polycyclic aromatic hydrocarbons. The sorption literature values for 47
organic compounds gave an a value of 0.83 and a /3 value of -0.93 (Karickhoff, 1984).
Solvent Effect on Solute Sorption
The theory behind Eqs. 21-25 and Eq. 28 is summarized by Fu and Luthy (1986b) as
follows. Linear partition coefficients are often observed for hydrophobic organic solute
sorption onto soil or sediments. The sorption partition coefficient may be normalized for
soils and sediments on the basis of fraction organic carbon, and normalized for various
solutes on the basis of octanol/water partition coefficient or aqueous solubility. Hence for
a given soil or sediment, organic solute sorption is inversely proportional to aqueous
solubility. The following explains a theoretical approach for predicting the observed effect
of a miscible organic solvent in the aqueous phase on organic solute sorption onto soil or
sediment. This approach is based on the linkage between K and aqueous solubility, and
the effect of solvent on solubility.
It has been demonstrated in Fu and Luthy (1985, 1986a) that aromatic solute solubility in a
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31
solvent/water mixture generally increases semi-logarithmically with increase of volume
fraction of solvent Using a simple log-linear solubility model (1986a), the mole fraction
solubility of the solute in the solvent/water mixture can be expressed as
log X = log X +
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32
However, for the case of solvent/water mixtures, the total number of moles per liter is
not constant and the partition coefficient must be expressed in units of mole/kg. Thus, in
order to use Eq. 34, the ratio of the experimentally determined sorption coefficients must
be expressed on the basis of total moles per unit mass of soil
r / V V v n
I / water solvent \ , ' I
log |_Kp \ + // KpJ55.34) J = - aaz (35)
water solvent
where V refers to the solute-free volume of water or solvent in the mixture, and q
x
represents the molar" volume of water or solvent
Eq. 35 indicates that K for a solvent/water mixture decreases semi-logarithmically with
the increase of solvent volume fraction. The semi-logarithmic relationship predicted by Eq.
35 can be shown on a semi-logarithmic plot with volume fraction solvent on the abscissa
and K (mole/kg) on the ordinate. The slope of this plot represents the combined .effect
of both a and a. The a term represents the effect of solvent on increase of solute
solubility, while the a term relates to the dominance of y in K among various solutes.
The a term should approach unity if the fugacity coefficient for solute in soil/sediment
organic carbon is relatively independent of solute (Karickhoff, 1984), and if the soil organic
carbon properties are independent of change in solution phase composition.
Soil sorption partition coefficient data were presented by Fu and iuthy (1986b) for
various lower molecular weight, aromatic solutes in solvent/water systems."'"From these
data it was possible to determine experimental values of the solvent volume fraction-
coefficient in Eq. 35, (a
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33
Partition Coefficient in Solvent Water Mixtures
The effect of solvent on organic solute sorption partitioning was examined by Fu and
Luthy (1985, 1986a, 1986b) using Eq. 35 and experimental solubility and sorption data Eq.
35 was examined using experimental sorption data for seven systems in conjunction with
the respective a values. The observed a values showed that the aobs values were in the
range of 0.41-0.63. The average
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34
Chapter Three
DESCRIPTION OF THE COMPUTATIONAL PROGRAMS
AND EXAMPLE CALCULATIONS
This chapter discusses the general features of the computer programs, named AROSOL
and MOLACCS. The program AROSOL is designed to aid prediction of aromatic solute
solubility in water, and in miscible organic solvent-water mixtures, and to estimate the
effect of miscible organic solvent in water on sorption of aromatic solutes on to
soils/sediments. The program MOLACCS computes MOLecular Accessible Surface area A
molecular surface area approach is one technique by which organic solute aqueous
solubility and solubility in miscible solvent/water mixtures may be predicted, and the
MOLACCS program provides surface area parameters for this approach. The theoretical
approaches and the computational methodologies employed in AROSOL and MOLACCS have
been described in the previous chapter. The use of the programs is described in turn
below.
AROSOL Program Organization
Figure 4 is an outline of the computational methodology employed in the AROSOL
program. The program utilizes four techniques to predict solubility: (i) log linear, (ii)
UNIFAC, (iii) excess free energy, and (iv) molecular surface area The user may select any
or all of these techniques to evaluate solubility depending on the availability of data,
physical constants, and other specific information required for each approach. The
program was developed to accommodate a variety of input parameters to predict solubility.
The program consists of the following subroutines:
(a) INPUT: Input data are read from this subroutine
(b) SETUP: Reads input data from the console and stores input into a data file
(c) UNIFAC: Calculates activity coefficients for each component
(d) REG1: Linear least-square regression for the log-linear procedure
(e) REG2: Two parameter least-square regression for the excess free energy procedure
(f) SOLCAL: Calculates solute solubility
-------
35
Figure 4. AROSOL Program Structure
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36
(g) LOGNR: Log-linear approach subroutine calculations
(h) UIMIEST: Numerical estimation technique for estimating solute
solubility mole fraction from activity coefficient
(i) MSA: Molecular surface area approach calculations
(j) EXFREN: Excess free energy approach calculations
(k) ADS: Calculates solute sorption partition coefficient
The AROSOL computer program is written in FORTRAN-77, and it can be run on any IBM
or IBM-compatible personal computer with at least 256 K internal memory. A listing of
the program is presented in Appendix A
The following examples illustrate the use of the program. These examples illustrate the
calculation approach employed in the log-linear, UNIFAC, excess free energy, and molecular
surface area approaches.
Estimation of Solubility and Sorption Partition Coefficient
Example Calculation I: No Input File
Quinoline in Methanol-Water
Figure 5 shows an example of calculation of quinoline solubility in methanol-water
mixtures by the log-linear, UNIFAC, and excess free energy approaches. In this example
the user inputs data from the terminal.
The program begins with a RETURN key stroke. The user is asked if there is an input
file, for which in this example the response is "no". The user enters a response that an
input file is to be established, and in this example the input file is named Q.I (for quinoline
input). The user is then asked to type in the name of the solvent (methanol, component 1)
and solute (quinoline, component 2), using twenty characters or less for each name. The
user is then asked to input the molecular weight of solvent, solute, and water. The format
for input is free format, in which a space or comma between the data entry identifies the
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37
appropriate molecular weight in the order solvent, solute, and water. The user is then
asked to input the densities of the components in the order solvent, solute, and water
using the same free input format
The user is then asked to input known solubility for the solute in the solvent The data
are input in the order per cent by volume solvent, followed by solubility in mg/L in the
mixture, using the free format with a separate line being used for each data pair. The last
data entry is followed by the input of -1 -1 on a separate line to indicate completion of
the data entry file.
The user now specifies which of the four calculation approaches are to be employed.
Each of the four approaches are employed in this example.
The user is then asked if K for the mixed solvent system is to be calculated 'In this
example the response is "yes;" and the user will be asked later to input the fraction
organic carbon content of the soil or sediment As explained later, if the organic carbon
content of the soil or sediment is unknown, the program computes KQC by inputting OC =
100%.
The user now inputs solute heat of fusion in cal/mole, solute melting temperature (K), and
system temperature (K) using the free format If solute heat of fusion is not known, then
the user is to enter zero (0) as the value, in which case the fugacity ratio expression will
be computed by Eq. 6.
The user is now asked if it is desired to see the secondary group listing for the UNIFAC
calculations. The listing is requested in this example, and the 89 secondary groups are
displayed The user is asked how many secondary groups appear in the solvent
component, in this example there is only one solvent secondary group. Similarly the user
is asked how many secondary groups appear in the solute, in this example the solute may
be constructed from two subgroups. The user now enters the number of times each
secondary group appears in the solvent, and the identification number of the secondary
group. In this example the solvent is comprised of one secondary group, number 16
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38
Figure 5. Example Calculation I: No Input
C:\JKF > File-Quinoline Solubility in Methanol/Water
C:\JKF >aro3ol
* AROSOL *
* Aromatic Solute Solubility *
* in Solvent/Water Mixtures *
* *
* by *
* Jaw-Kwei Fu *
* Charles Brooks *
* Richard G. Luthy *
* Carnegie-Mellon University *
* Pittsburgh, Pennsylvania *
* *
* August, 1986 *
Hit RETURN key to continue
This program estimates aromatic solute solubility in
solvent/water mixtures. This program is designed to
utilize different levels of input parameters to estimate
aromatic solute solubility. This program employes four
approaches: LOG-LINEAR, UNIFAC, EXCESS FREE ENERGY, and
MOLECULAR SURFACE AREA. The input parameters can be read
from either an existing input file or from the terminal.
The program estimates solute solubility via approaches
specified by the user, and stores the results into an
output file.
Hit RETURN key to continue
DO YOU HAVE INPUT FILE? (Y OR N)
n
DO YOU WANT TO SET UP AN INPUT FILE? (Y OR N)
y
GIVE THE FILE NAME IN WHICH INPUT DATA ARE TO BE STORED
q.i
INPUT THE NAME OF COMPONENT 1 IN 20 CHARACTERS 1 -SOLVENT-. 2-SOLUTE
METHANOL
INPUT THE NAME OF COMPONENT 2 IN 20 CHARACTERS 1-SOLVENT, 2-SOLUTE
QUINOLINE
INPUT MOLECULAR WEIGHT OF SOLVENT, SOLUTE, WATER
32.04 129.16 18.02
INPUT DENSITIES OF SOLVENT. SOLUTE AND WATER
.7914 1.0929 .9971
INPUT KNOWN SOLUTE SOLUBILITY IN % SOLVENT, AND SOLUTE SOLUBILITY IN MG/L,
FINISHED AS -1 -1. DATA INPUT IN PAIRS WITH ONE PAIR PER LINE
0 6832
10 14603
20 34048
30 75358
40 125493
50 251189
-1 -1
DO YOU WANT TO ESTIMATE SOLUTE SOLUBILITY BY THE LOG-LINEAR APPROACH?
(Y OR N)
y
DO YOU WANT TO ESTIMATE SOLUTE SOLUBILITY BY THE UNIFAC APPROACH? (Y OR N)
y
DO YOU WANT TO ESTIMATE SOLUTE SOLUBILITY BY THE EXCESS FREE ENERGY APPROACH?
(Y OR N)
y
DO YOU WANT TO ESTIMATE SOLUTE SOLUBILITY BY
THE MOLECULAR SURFACE AREA APPROACH? (Y OR N)
y
DO YOU WANT TO ESTIMATE ADSORPTION PARTITION COEFFICIENT? (Y OR N)
y
ENTER SOLUTE HEAT OF FUSION (CAL/MOLE), SOLUTE MELTING TEMPERATURE (K), AND
SYSTEM TEMPERATURE (K), IF HEAT OF FUSION IS NOT AVAILABLE USE 0 AS THE VALUE
3751.8 288.6 298
DO YOU WANT TO SEE THE UNIFAC SECONDARY GROUP LISTING? (Y OR N)
y
-------
39
Figure 5. Example Calculation I (continued)
1 CH3
6 CH=CH
11 AC
16 CH30H
21 CHO
26 CH2O
31 CHNH2
36 CH2N
41 CH3CN
46 CHCL
51 CHCL3
56 CH2N02
61 CH2SH
66 CH-TRIP-C
71 ACF
76 CF
81 SI
86 AMIDE
2 CH2
7 CH2=C
12 ACCH3
17 H20
22 CH3COO
27 CH-0
32 CH3NH
37 ACNH2
42 CH2CN
47 CCL
52 CCL3
57 CHN02
62 FURFURAL
67 C-TRIP-C
72 DMF-1
77 COO
82 SIH20
87 CON(ME)2
3 CH
8 CH=C
13 ACCH2
18 ACOH
23 CH2COO
28 FCH20
33 CH2NH
38 C5H5N
43 COOH
48 CH2CL2
53 CCL4
58 ACN02
63 (CH20H)2
68 ME2SO
73 DMF-2
78 SIH3
83 SIHO
88 CONMECH2
4 C
9 C=C
14 ACCH
19 CH3CO
24 HCCO
29 CH3NH2
34 CHNH
39 C5H4N
44 HCOOH
49 CHCL2
54 ACCL
59 CS2
64 I
69 ACRY
74 CF3
79 SIH2
84 SIO
89 CON(CH2)2
5 CH2=CH
10 ACH.
15 OH
20 CH2CO
25 CH30
30 CH2NH2
35 CH3N
40 C5H3N
45 CH2CL
50 CCL2
55 CH3N02
60 CH3SH
65 BR
70 CL(C=C)
75 CF2
80 SIH
85 TERT-N
INPUT THE NUMBER OF SECONDARY GROUPS IN COMPONENT METHANOL
INPUT THE NUMBER OF SECONDARY GROUPS IN COMPONENT QUINOLINE
1
INPUT NUMBER OF TIMES SECONDARY GROUP i APPEARS IN COMPONENT METHANOL
REPEAT n TIMES UNTIL n = NUMBER OF SECONDARY GROUPS
1 16
INPUT NUMBER OF TIMES SECONDARY GROUP i APPEARS IN COMPONENT QUINOLINE
REPEAT n TIMES UNTIL n = NUMBER OF SECONDARY GROUPS
4 10 1 40
INPUT LOG OCTANOL/WATER PARTITION COEFFICIENT
OF SOLUTE FOR THE EXCESS FREE ENERGY CALCULATION
2.04
INPUT SOLUTE HYDROPHOBIC SURFACE AREA AND POLAR SURFACE AREA.
INPUT IN UNITS A**2
142.877 9.078
INPUT SOLVENT MICROSCOPIC INTERFACIAL FREE ENERGY BETWEEN HSA AND PSA,
INPUT IN UNITS OF DYNE/CM**2
24.6 47.7
INPUT ORGANIC CARBON CONTENT OF ADSORBENT. IN X
2
GIVE THE OUTPUT FILE NAME IN WHICH THE SOLUBILITY
CALCULATION DATA WILL BE STORED
q.o . ~
INPUT PERCENT VOLUME SOLVENT IN THE MIXTURE TO BE EVALUATED
0 -
LOG-LINEAR REGRESSION INTERCEPT -3.0002 SLOPE .03573
LOG-LINEAR ESTIMATION METHOD
SOLVENT FRACTION [X VOL] .00
LOG LINEAR ESTIMATION SOLUBILITY [MOLE FRACTION]
LOG LINEAR ESTIMATION SOLUBILITY [MG/L] . 710E+04
. 100E-02
UNIFAC ACTIVITY COEFFICIENT ESTIMATION
COMPONENT MOLE FRAC LN ACTCF
ACTCF
QUINOLINE
METHANOL
.0000
.0000
7.51707
.00000
1839.1690
1.0000
UNIFAC ESTIMATION
METHANOL FRACTION [X VOL] .00
QUINOLINE SOLUBILITY [MOLE FRACTION] 544E-03
QUINOLINE SOLUBILITY [MG/L] .387E+04
THE SOLVENT-SOLVENT INTERACTION PARAMETERS ARE .7644 AND .4566
EXCESS FREE ENERGY ESTIMATION METHOD
SOLVENT FRACTION [X VOL] .00
EXCESS FREE ENERGY ESTIMATION SOLUBILITY [MOLE FRACTION] 961E-03
EXCESS FREE ENERGY ESTIMATION SOLUBILITY [MG/L] 683E+04
MOLECULAR SURFACE AREA APPROACH
SOLVENT FRACTION [X VOL] .00
MOLECULAR SURFACE AREA APPROACH SOLUBILITY [MOLE FRACTION]
MOLECULAR SURFACE AREA APPROACH SOLUBILITY [MG/L] .683E+04
.961E-03
-------
40
Figure 5. Example Calculation I (continued)
ADSORPTION COEFFICIENT OF QUINOLINE IN WATER/METHANOL
MIXTURES IS .515E+02
ANOTHER CALCULATION? (Y=1,N=2)
i.
INPUT PERCENT VOLUME SOLVENT IN THE MIXTURE TO BE EVALUATED
20
LOG-LINEAR ESTIMATION METHOD
SOLVENT FRACTION [X VOL] 20.00
LOG LINEAR ESTIMATION SOLUBILITY [MOLE FRACTION] .518E-02
LOG LINEAR ESTIMATION SOLUBILITY [MG/L] .321E+05
UNIFAC ACTIVITY COEFFICIENT ESTIMATION
COMPONENT MOLE FRAC LN ACTCF ACTCF
QUINOLINE .0000 5.84863 346.7577
METHANOL .1004 .00000 1.0000
UNIFAC ESTIMATION
METHANOL FRACTION [X VOL] 20.00
QUINOLINE SOLUBILITY [MOLE FRACTION] .309E-02
QUINOLINE SOLUBILITY [MG/L] .194E+05
EXCESS FREE ENERGY ESTIMATION METHOD
SOLVENT FRACTION [X VOL] 20.00
EXCESS FREE ENERGY ESTIMATION SOLUBILITY [MOLE FRACTION] .253E-02
EXCESS FREE ENERGY ESTIMATION SOLUBILITY [MG/L] .159E+05
MOLECULAR SURFACE AREA APPROACH
SOLVENT FRACTION [X VOL] 20.00
MOLECULAR SURFACE AREA APPROACH SOLUBILITY [MOLE FRACTION] .655E-02
MOLECULAR SURFACE AREA APPROACH SOLUBILITY [MG/L] .404E+05
ADSORPTION COEFFICIENT OF QUINOLINE IN WATER/METHANOL
MIXTURES IS .223E+02
ANOTHER CALCULATION? (Y=1.N=2)
2
Stop - Program terminated.
C:\JKF >
-------
41
Figure 5. Example Calculation I (continued)
C:\JKF >
C:\JKF >type q.i
METHANOL
QUINOLINE
32.0400000
7.914000E-001
.0000000
10.0000000
20.0000000
30.0000000
40.0000000
50.0000000
-1.0000000
y
y
y
y
y
3751.8000000
1
2
1.0000000
4.0000000
2.0400000
142.8770000
24.6000000
2.0000000
C:\JKF >
129.1600000 18.0200000
1.0929000 9.971000E-001
6832.0000000
14603.0000000
34048.0000000
75358.0000000
125493.0000000
251189.0000000
-1.0000000
288.6000000
16
10
9.0780000
47.7000000
298.0000000
1.0000000
40
C:\JKF >
C:\JKF >type q.o
SOLUTE USED IN THE CALCULATION IS
SOLVENT USED IN THE CALCULATION IS
PARAMETER
MOLECULAR WEIGHT
DENSITY
MOLAR VOLUME
METHANOL
32.04
.7914
40.49
QUINOLINE
METHANOL
QUINOLINE
129.16
1.0929
118.18
WATER
18.02
.9971
.-18.07
OCTANOL/WATER PARTITION COEFFICIENT .110E+03
SOLUTE SOLUBILITY PREDICTIONS IN MIXED SOLVENT SYSTEM
VOLUME LOG-LINEAR
SOLVENT APPROACH
MOLE SOL.
* [-] [MG/L]
UNIFAC
APPROACH
MOLE SOL.
[-] [MG/L]
EXCESS FREE MOLECULAR SURFACE
ENERGY APPROACH AREA APPROACH
MOLE SOL. MOLE SOL
[-] [MG/L] [-] [MG/L]
.00 .10E-02 .71E+04 .54E-03 .39E+04 .96E-03 .68E+04 .96E-03 68E+04
20.00 .52E-02 .32E+05 .31E-02 .19E+05 .25E-02 . 16E+05 .66E-02 .40E+05
*******
SOLUTE SORPTION PARTITION COEFFICIENT ESTIMATION
METHANOL
[X]
.00
20.00
OC OF ADSORBENT
[X]
2.00
2.00
KP OF SOLUTE
[MOLE/KG]
51.53
22.26
C:\JKF >
-------
42
(methanol). The user now inputs the number of times each secondary group appears in the
solute, and the identification number of each secondary group. This is repeated using free
floating format until all the secondary groups have been specified. In this example,
quinoline is constructed from a pyridine-type derivative and aromatic -CH groups (ACH).
Thus four (4) secondary group ACH, number (10), and one (1) secondary group C5H3N,
number (40), comprise the molecule quinoline.
Next the user inputs the logarithm of the solute octanol/water partition coefficient; this
value is used in the excess free energy calculation.
The user is then asked to input the solute hydrophobic surface area and the polar surface
area in units of & The data are input in their respective order using the free format
These data are obtained from the MOLACCS program, as demonstrated in a latter example
calculation. The user is then asked to input the solvent microscopic interfacial free
energies for the hydrophobic surface area and the polar surface area in units of dynes per
cm2.
The user is then asked to input the percent organic carbon content of the soil or
sediment In this example the calculation is performed for a soil having 2% organic carbon
content If the organic carbon content is unknown, the user should specify a value of
100%, in which case K becomes equal to K . _-
p oc
The user is then asked to name the output file in which the results of the calculations will
be stored. In this example the output file is named Q.O, for quinoline output The user is
then asked to specify a solvent/water volume composition to be evaluated. In this example
the user has requested calculation for 0% by volume methanol (i.e. 100% water).
The output for the various calculations are now presented, for which the program
computes and displays firstly the slope and the intercept values for the log-linear method;
the solvent volume fraction specified is also shown. The log-linear computation method
employs Eq. 15, in which the log-linear solute solubility relationship is computed in terms
of mole fraction solute in conjunction with volume fraction solvent. The log-linear
-------
43
solubility output is shown as mole fraction, for which quinoline solubility in pure water is
estimated from the input data as 1.0 x 10"3. The predicted mole fraction solute solubility
is then converted by procedures described in Chapter 2 to customary solubility units of
mg/L of solution, or 7100 mg/L in this example.
Next the results for the UNIFAC calculation procedure are presented First, the solute and
solvent activity coefficients are shown. The specified volume fraction solvent is shown,
followed by the presentation of the solute mole fraction solubility. The solute activity
coefficient is related to mole fraction by procedures discussed in Chapter 2, which is then
converted and displayed in units of mg/L, i.e. 3870 mg/L in this example.
Next, the results for the excess free energy calculation procedure are presented in units
of both mole fraction and mg/L. The regression coefficients for determinatibn of the
solvent-water interaction parameters, A and A3 ^ are also shown.
The results from the molecular surface area calculation are presented next
The solute sorption partition coefficient is then calculated by procedures described in
Chapter 2.
The user is then asked if another calculation is to be performed. In this example the user
inputs a "1" for yes, and specifies 20% by volume methanol for the next calculation.
The results for the new solvent volume fraction calculation are presented in the same
order as in the previous discussion. The regression coefficients for the log-linear and
excess free energy calculations are not repeated, however. At the conclusion of this
calculation the user terminates the calculation by inputing the number "2".
The manner in which data in the input and output files may be listed is shown at the end
of the example.
Example calculation II: No Solubility Data
Solubility of Monochlorobenzene in Acetone-Water
-------
44
In this example the user has no solubility information, hence the only calculation approach
which may be employed is the UNIFAC technique. The user is asked to input the solvent
solute, and water properties. This is done according to the procedures described in the
previous example. The user does not request that the calculations be performed by the
the log-linear, or the excess free energy approach, or the molecular surface area approach
because of lack of data Normally one would desire some data from which to establish a
correlation for the log-linear approach, and in the case of the excess free energy
approach one would normally desire at least pure solvent solute solubility as an input
parameter.
For the case of the UNIFAC approach, the solvent, acetone, is recognized as being
comprised of two secondary groups: one ~CH (secondary group 1) and one CH3CO-
(secondary group 19). The solute is comprised of two secondary groups: Five - aromatic
CH (secondary group 10), and one - aromatic C-CI (secondary group 54). The user
requests that the solubility prediction calculation be performed for the case of 0% and 20%
by volume solvent The results are displayed in the same fashion as in the previous
example, with the input and output files shown also at the end of the calculation.
Example Calculation III: Read from an Input File,
Naphthalene Solubility in Methanol-Water
In this example the user has an input data file and requests the program to estimate
solubility and sorption partition coefficient in 0, 10, and 50% by volume solvent The
results from the example calculation are shown in Figure 7. In this example the input file
is shown at the end of the calculation. The necessary solvent solute, and water
parameters are entered, as well as the solubility data The necessary data are entered
according to the format explained in Example I. Note for purposes of the UNIFAC
calculation that naphthalene is comprised of eight aromatic-CH secondary groups, and two
aromatic-C secondary groups. The calculation proceeds as described previously, and the
results are displayed in an output file.
-------
45
Figure 6. Example Calculation II: No Solubility
Data - Monochlorobenze Solubility in Acetone/Water
C:\JKF >
C:\JKF >arosol
*****************************************
* AROSOL *
* Aromatic Solute Solubility *
* in Solvent/Water Mixtures *
* *
* by *
* Jaw-Kwei Fu *
* Charles Brooks *
* Richard G. Luthy *
* Carnegie-Mellon University *
* Pittsburgh, Pennsylvania *
* *
* August, 1986 *
ft***********************************.*****
Hit RETURN key to continue
This program estimates aromatic solute solubility in
solvent/water mixtures. This program is designed to
utilize different levels of input parameters to estimate
aromatic solute solubility. This program employes four
approaches: LOG-LINEAR, UNIFAC, EXCESS FREE ENERGY, and
MOLECULAR SURFACE AREA. The input parameters can be read
from either an existing input file or from the terminal.
The program estimates solute solubility via approaches
specified by the user, and stores the results into an
output file.
Hit RETURN key to continue
DO YOU HAVE INPUT FILE? (Y OR N)
n
DO YOU WANT TO SET UP AN INPUT FILE? (Y OR N)
y
GIVE THE FILE NAME IN WHICH INPUT DATA ARE TO BE STORED
cbace.i
INPUT THE NAME OF COMPONENT 1 IN 20 CHARACTERS 1-SOLVENT, 2-SOLUTE
ACETONE
INPUT THE NAME OF COMPONENT 2 IN 20 CHARACTERS 1-SOLVENT, 2-SOLUTE
1CHLOROBENZENE
INPUT MOLECULAR WEIGHT OF SOLVENT, SOLUTE. WATER
58.08 112.56 18.02
INPUT DENSITIES OF SOLVENT, SOLUTE AND WATER
.7899 .9630 .9971
INPUT KNOWN SOLUTE SOLUBILITY IN * SOLVENT, AND SOLUTE SOLUBILITY IN MG/L,
FINISHED AS -1 -1, DATA INPUT IN PAIRS WITH ONE PAIR PER LINE
-1 -1
DO YOU WANT TO ESTIMATE SOLUTE SOLUBILITY BY THE LOG-LINEAR APPROACH?
(Y OR N)
n
DO YOU WANT TO ESTIMATE SOLUTE SOLUBILITY BY THE UNIFAC APPROACH? (Y OR N)
K
DO YOU WANT TO ESTIMATE SOLUTE SOLUBILITY BY THE EXCESS FREE ENERGY APPROACH?
(Y OR N)
n
DO YOU WANT TO ESTIMATE SOLUTE SOLUBILITY BY
THE MOLECULAR SURFACE AREA APPROACH? (Y OR N)
n
DO YOU WANT TO ESTIMATE ADSORPTION PARTITION COEFFICIENT? (Y OR N)
n
ENTER SOLUTE HEAT OF FUSION (CAL/MOLE). SOLUTE MELTING TEMPERATURE (K), AND
SYSTEM TEMPERATURE (K), IF HEAT OF FUSION IS NOT AVAILABLE USE 0 AS THE VALUE
0 295.74 298
DO YOU WANT TO SEE THE UNIFAC SECONDARY GROUP LISTING?(Y OR N)
y
-------
46
Figure 6. Example Calculation II (continued)
1 CH3
6 CH=CH
11 AC
16 CH30H
21 CHO
26 CH2O
31 CHNH2
36 CH2N
41 CH3CN
46 CHCL
51 CHCL3
56 CH2N02
61 CH2SH
66 CH-TRIP-C
71 ACF
76 CF
81 SI
86 AMIDE
2 CH2
7 CH2=C
12 ACCH3
17 H20
22 CH3COO
27 CH-0
32 CH3NH
37 ACNH2
42 CH2CN
47 CCL
52 CCL3
57 CHNO2
62 FURFURAL
67 C-TRIP-C
72 DMF-1
77 COO
82 SIH20
87 CON(ME)2
3 CH
8 CH=C
13 ACCH2
18 ACOH
23 CH2COO
28 FCH20
33 CH2NH
38 C5H5N
43 COOH
48 CH2CL2
53 CCL4
58 ACN02
63 (CH20H)2
68 ME2SO
73 DMF-2
78 SIH3
83 SIHO
88 CONMECH2
4 C
9 C=C
14 ACCH
19 CH3CO
24 HCOO
29 CH3NH2
34 CHNH
39 C5H4N
44 HCOOH
49 CHCL2
54 ACCL
59 CS2
64 I
69 ACRY
74 CF3
79 SIH2
84 SIO
89 CON(CH2)2
INPUT THE NUMBER OF SECONDARY GROUPS IN COMPONENT ACETONE
5 CH2=CH
10 ACH
15 OH
20 CH2CO
25 CH30
30 CH2NH2
35 CH3N
40 C5H3N
45 CH2CL
50 CCL2
55 CH3NO2
60 CH3SH
65 BR
70 CL(C=C)
75 CF2
80 SIH
85 TERT-N
INPUT THE NUMBER OF SECONDARY GROUPS IN COMPONENT 1CHLOROBENZENE
2
INPUT NUMBER OF TIMES SECONDARY GROUP i APPEARS IN COMPONENT ACETONE
REPEAT n TIMES UNTIL n = NUMBER OF SECONDARY GROUPS
1 1 1 19
INPUT NUMBER OF TIMES SECONDARY GROUP i APPEARS IN COMPONENT 1CHLOROBENZENE
REPEAT n TIMES UNTIL n = NUMBER OF SECONDARY GROUPS
5 10 1 54
GIVE THE OUTPUT FILE NAME IN WHICH THE SOLUBILITY
CALCULATION DATA WILL BE STORED
cbace.o
INPUT PERCENT VOLUME SOLVENT IN THE MIXTURE TO BE EVALUATED
0
UNIFAC ACTIVITY COEFFICIENT ESTIMATION
COMPONENT MOLE FRAC LN ACTCF
1CHLOROBENZENE
ACETONE
.0000
.0000
9.86048
.00000
ACTCF
19158.0400
1.0000
UNIFAC ESTIMATION
ACETONE FRACTION [X VOL] .00
1CHLOROBENZENE SOLUBILITY [MOLE FRACTION] .522E-04
1CHLOROBENZENE SOLUBILITY [MG/L] .325E+03
ANOTHER CALCULATION? (Y=1,N=2)
1
INPUT PERCENT VOLUME SOLVENT IN THE MIXTURE TO BE EVALUATED
20
UNIFAC ACTIVITY COEFFICIENT ESTIMATION
COMPONENT MOLE FRAC LN ACTCF
1CHLOROBENZENE
ACETONE
.0000
.0579
8.46858
.00000
ACTCF
4762.7260
1.0000
UNIFAC ESTIMATION
ACETONE FRACTION [X VOL] 20.00
1CHLOROBENZENE SOLUBILITY [MOLE FRACTION]
1CHLOROBENZENE SOLUBILITY [MG/L] .111E+04
ANOTHER CALCULATION? (Y=1.N=2)
2
Stop - Program terminated.
.210E-03
C:\JKF >
-------
47
Figure 6. Example Calculation II (continued)
C:\JKF >
C:\JKF >type cbace.i
ACETONE
1CHLOROBENZENE
58.0800000 112.5600000 18.0200000
7.899000E-001 9.630000E-001 9.971000E-001
-1.0000000 -1.0000000
n
Y
n
n
n
3844.6200000
2
2
1.0000000
5.0000000
C:\JKF >
C:\JKF >
C:\JKF >type cbace.o
295.7400000
298.0000000
1 - 1.0000000
10 1.0000000
19
54
SOLUTE USED IN THE CALCULATION IS
SOLVENT USED IN THE CALCULATION IS
PARAMETER
MOLECULAR WEIGHT
DENSITY
MOLAR VOLUME
ACETONE
58.08
.7899
73.53
1CHLOROBENZENE
ACETONE
1CHLOROBENZENE
112.56
.9630
116.88
WATER
18.02
.9971
18.07
SOLUTE SOLUBILITY PREDICTIONS IN MIXED SOLVENT SYSTEM
VOLUME LOG-LINEAR
SOLVENT APPROACH
MOLE SOL.
* [-] [MG/L]
UNIFAC
APPROACH
MOLE SOL.
[-] [MG/L]
EXCESS FREE MOLECULAR SURFACE
ENERGY APPROACH AREA APPROACH
MOLE SOL. MOLE---SOL.
[-] [MG/L] [-] [MG/L]
.00 .OOE-t-00 .OOE-t-00 .52E-04 .33E+03 .OOE+00 .OOE+00 .OOE+00 .OOE+00
20.00 .OOE+00 .OOE+00 .21E-03 .11E+04 .OOE+00 .OOE+00 .OOE+00 .OOE+00
C:\JKF >
-------
48
Figure 7. Example Calculation III: Read from
an Input File - Naphthalene Solubility in Methanol/Water
*****************************************
* AROSOL *
* Aromatic Solute Solubility *
* in Solvent/Water Mixtures *
* *
* by *
* Jaw-Kwei Fu *
* Charles Brooks *
* Richard G. Luthy *
* Carnegie-Mellon University *
* Pittsburgh, Pennsylvania *
* *
* August, 1986 *
*****************************************
Hit RETURN key to continue
This program estimates aromatic solute solubility in
solvent/water mixtures. This program is designed to
utilize different levels of input parameters to estimate
aromatic solute solubility. This program employes four
approaches: LOG-LINEAR, UNIFAC, EXCESS FREE ENERGY, and
MOLECULAR SURFACE AREA. The input parameters can be read t
from either an existing input file or from the terminal.
The program estimates solute solubility via approaches
specified by the user, and stores the results into an
output file.
Hit RETURN key to continue
DO YOU HAVE- INPUT FILE? (Y OR N)
y
INPUT FILE NAME=
name.i
GIVE THE OUTPUT FILE NAME IN WHICH THE SOLUBILITY
CALCULATION DATA WILL BE STORED
name.o
INPUT PERCENT VOLUME SOLVENT IN THE MIXTURE TO BE EVALUATED"
0
LOG-LINEAR REGRESSION INTERCEPT -5.4287 SLOPE .03724 -
LOG-LINEAR ESTIMATION METHOD
SOLVENT FRACTION [X VOL] .00
LOG LINEAR ESTIMATION SOLUBILITY [MOLE FRACTION] .373E-05
LOG LINEAR ESTIMATION SOLUBILITY [MG/L] .264E+02
UNIFAC ACTIVITY COEFFICIENT ESTIMATION
COMPONENT MOLE FRAC LN ACTCF ACTCF
NAPHTHALENE .0000 11.84144 138890.8000
METHANOL .0000 .00000 1.0000
UNIFAC ESTIMATION
METHANOL FRACTION [X VOL] .00
NAPHTHALENE SOLUBILITY [MOLE FRACTION] .216E-05
NAPHTHALENE SOLUBILITY [MG/L] .153E+02
THE SOLVENT-SOLVENT INTERACTION PARAMETERS ARE .7644 AND .4566
EXCESS FREE ENERGY ESTIMATION METHOD
SOLVENT FRACTION [X VOL] .00
EXCESS FREE ENERGY ESTIMATION SOLUBILITY [MOLE FRACTION] .437E-05
EXCESS FREE ENERGY ESTIMATION SOLUBILITY [MG/L] .310E+02
MOLECULAR SURFACE AREA APPROACH
SOLVENT FRACTION [X VOL] .00
MOLECULAR SURFACE AREA APPROACH SOLUBILITY [MOLE FRACTION] .437E-05
MOLECULAR SURFACE AREA APPROACH SOLUBILITY [MG/L] .310E+02
ADSORPTION COEFFICIENT OF NAPHTHALENE IN WATER/METHANOL
MIXTURES IS . 102E+-04
-------
4y
.
_0000 1U
-0473
E.
!
Of
-
Q000
-3086
50.00
..c t*
"
oo
;-05
OE
_
-------
50
Figure 7. Example Calculation III (continued)
C:\JKF >
C:\JKF >type name.i
METHANOL
NAPHTHALENE
32.0400000
128.1900000
7.914000E-001 9.625000E-001 9.971000E-001
18.0200000
Y
Y
Y
.0000000
1.0000000
5.0000000
10.0000000
20.0000000
30.0000000
40.0000000
50.0000000
62.0000000
71.0000000
75.0000000
84.0000000
92.0000000
100.0000000
100.0000000
-1.0000000
31.
39.
46.
58.
104.
243.
9961
19831
36591
66200
71093
-1
0000000
1000000
5000000
3000000
0000000
0000000
468.0000000
1230.0000000
2956.0000000
6362.0000000
0000000
0000000
0000000
0000000
0000000
0000000
4540
1
8,
3.
155.
24.
0000000
1
2
0000000
0000000
3400000
8000000
6000000
353.5000000
16
10
298,0000000
2.0000000
11
47
0000000
7000000
2.0000000
C:\JKF~ >
C:\JKF >type name.o
SOLUTE USED IN THE CALCULATION IS
SOLVENT USED IN THE CALCULATION IS
PARAMETER
MOLECULAR WEIGHT
DENSITY
MOLAR VOLUME
METHANOL
32.04
.7914
40.49
NAPHTHALENE
METHANOL
NAPHTHALENE
128.19
.9625
133.18
WATER
18.02
.9971
18.07
OCTANOL/WATER PARTITION COEFFICIENT .219E+04
SOLUTE SOLUBILITY PREDICTIONS IN MIXED SOLVENT SYSTEM
VOLUME LOG-LINEAR
SOLVENT APPROACH
MOLE SOL.
% [-] [MG/L]
UNIFAC
APPROACH
MOLE SOL.
[-] [MG/L]
EXCESS FREE MOLECULAR SURFACE
ENERGY APPROACH AREA APPROACH
MOLE SOL. MOLE SOL.
[-] [MG/L] [-] [MG/L]
.00 .37E-05 .26E+02 .22E-05 .15E+02 .44E-05 .31E+02 .44E-05 .31E+02
10.00 .88E-05 .59E+02 .52E-05 .35E+02 .72E-05 .48E-I-02 . 11E-04 .74E-t-02
50.00 .27E-03 .14E+04 .20E-03 .10E+04 .14E-03 .70E+03 .46E-03 .24E+04
SOLUTE SORPTION PARTITION COEFFICIENT ESTIMATION
METHANOL
[X]
.00
10.00
50.00
OC OF ADSORBENT
[X]
2.00
2.00
2.00
KP OF SOLUTE
[MOLE/KG]
1016.51
656,44
114.16
C:\JKF >
-------
51
Molecular Surface Area Calculations
The program MOLACCS calculates MOLecular Accessible Surface. The program MOLACCS
is presently written in standard FORTRAN-77 and requires minor modifications for use on a
personal computer. The following explains the general features of the program. This is
followed by the presentation of several example calculations.
Program Description
The FORTRAN-77 program MOLACCS is a general purpose program to compute molecular
surfaces of molecules using the Richards algorithm (1977). Three types of surface areas
are computed: (1) The solvent accessible area as defined by addition of a solvent radius to
each solute atom, which is the surface accessibility algorithm referred by Richards as the
accessible area; (2) The contact surface area, which is the accessible area without the
solvent radius as computed using the Richards algorithm and does not include the re-
entrant surface area; and (3) The van der Waals surface area is that corresponding to the
accessible area for a solvent probe of zero radius. Note that the areas computed by
procedures (1) and (2) are dependent on solvent radius, as explained previously in Chapter
2, while the area computed by procedure (3), the van der Waals area, is not dependent on
probe, or solvent, radius.
The program contains several features which permit ease of preparation, manipulation or
generation of molecular structures for surface area calculations. These features include the
ability to read in existing Cartesian coordinates for a molecule and then calculate the
surface areas; the ability to build linear and simply connected molecules; and the ability to
add atoms onto existing molecules or to replace atoms in an existing molecule. The ability
to add and replace atoms in a molecule is collectively known in MOLACCS as perturbing
the existing structure. Finally the program has the ability to combine two existing
molecules to create a new molecule.
In order to permit this flexibility, MOLACCS maintains two internal files. These are a
-------
52
i
parameter file and a molecular fragment library file. These files are read and written as
binary files in MOLACCS, and thus to maintain portability, a utility program CONVERT is
provided to change files from binary to formatted, and vice versa
The molecular fragment library may be manipulated as described above. Additional
features are also included which permit the modification of the atomic parameter file.
These include (1) addition of new atom types, and (2) changing existing types.
Program Structure
The overall structure of MOLACCS is diagrammed in Figure 8. The program exists as a
collection of three modules and a task router. The task router is the main program
MOLACCS. In MOLACCS the user is prompted with regard to the specific task to be
performed. The options are:
1. PARAMeters - this option routes to the parameter manipulation module,
NEWPARAM.
2. FRAGment - this option routes to the molecular fragment manipulation module
(task router NEWFRAG).
3. SURFACE - this option calculates surface areas for particular fragments.
4. QUIT - allows for finishing the program and exiting.
Parameter and Fragment Library File Structure
Parameter File:
The parameter file contains all the information required to compute atomic surface areas
or to construct molecular fragments. The information associated with each atom type is:
NAME - this is a 4 character identifier.
TYPE - the number of the atom as it appears in the file.
BOND - the bonding radius for an atom.
-------
53
Figure 8.
MOLACCS Program Structure
.MOLECULAR .ACCESSIBLE SURFACE AREA
(MOLACCS)
CALCULA TION PROGRAM
TASK ROUTER
CALCULATION OF
SURFACE AREAS
MANIPULATE MOLECULAR
FRAGMENT FILE
DHAN
DELETE} ' ' {PERTURB
' N
COMBINE
MANIPULATE ATOMIC
PARAMETER FILE
-I
CS7493
-------
54
ANGLE - the standard bond angle associated with a valence bond angle in which the atom
is central.
HYDROPHOBICITY - an integer value between 0 (polar) and 100 (nonpolar) indicating the
degree of hydrophobic character. This is used in partitioning total
surface areas between polar and hydrophobic surface areas.
van der Waals RADIUS - the van der Waals radius associated with an atom.
A list of the parameters currently resident in the file parameter.bin (for binary version) or
parameter.fmt (for formatted version) is given in Table I. Atom type numbers 3 and 4 are
to be used if the user desires to develop polycyclic aromatic hydrocarbon fragments in a
non-extended atom format using an aromatic-type carbon and an aromatic-type hydrogen
atom.
All of the H, C, N, 0 and S bond lengths, bond angles, and van der Waals radii reported
in Table I are taken from the data base employed in CHARMM (Brooks et al., 1983). These
parameters are considered to represent an internally consistent and reliable set of atomic
parameters. This data base was developed from the analysis of spectroscopic data, for
bond and valence angle parameters, and ab-initio quantum chemical calculations, for van der
Waals parameters, for use in molecular mechanics calculations on macromolecules (Brooks
et al., 1983).
The values for the bond lengths, bond angles, and van der Waals radii reported in Table I
for the halogens, i.e. F, Cl, Br, and I, were obtained from: (1) stanadard bond length
information, (2) standard hybridization angles, and (3) van der Waal radii based on nearest
nobel gas (i.e. crf =
-------
55
Table I
Atom Parameters for Surface Area Calculations
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
11.
Atom Type
(Name & Number)
Csp3 (aliphatic,
tetrahedral, etc.)
Csp2 (aromatic,
hybrid, etc.)
CARO
HARO
Nsp3
Osp3
S
F
Cl
Br
I
Bonding
Radius
1.53
1.35
1.39
0.6
1.4
1.35
2.00
1.3
2.0
2.3
2.7
Angle
111.0
120.0
120.0
120.0
120.0
110.0
110.0
111.0
111.0
111.0
111.0
VDW Radius Hydr
2.0
2.0
1.7
1.2
1.7
1.7
1.9
1.65
1.9
2.0
2.1
100
100
100
100
0
0
80
90
90
90
~ "100
Note: Atom type numbers 3 and 4 are to be used if the user
desires to build aromatic molecular fragments without the use
of the extended atom approach.
-------
56
The van der Waals radii values for the non-extended atom format for the aromatic
carbon (No. 3) and the hydrogen atom (No. 4) agree with average values reported by Bondi
(1968), 1.7 A and 1.2 A respectively. These tabulated values are also reasonably close to
those chosen by Hermann, 1.77 A and 1.0 A respectively. The bonding radii and van der
Waals radii reported in Table I are consistent with Valvani et al. (1976) as employed in their
"Method B" calculation procedure which used an extended atom format for methyl,
methylene, and the hydroxyl group in alcohols; the respective bond lengths and van der
Waals radii were: 1.54/2.0, 1.54/2.0, and 1.43/1.7 A These values are the same as shown
in Table I for atom type Nos. 1 and 6. except for a slightly smaller bond distance for the
oxygen bond.
Yalkowsky and Valvani (1979) computed the van der Waals surface areas of rigid aromatic
hydrocarbons using an extended atom format for methyl and methylene groups, The
following respective interatomic distances and van der Waals radii were used: aromatic C-
C, 1.40/1.70 A and aromatic C-H, 1.08/1.20 A The bonding radius of the aliphatic-
aromatic C-C was taken as 1.54 A and the methyl or methylene group was assigned a van
der Waals radius of 2.0 A These values are consistent with the parameters in Table I,
except for the choice of aromatic C-H bonding radius.
Molecular Fragment Library File:
This file contains the cartesian coordinates of molecular fragments plus all the identifiers
necessary for surface area calculation or structure manipulation. Specifically, the file
contains:
NAME - an 8 character name identifying the fragment
NUMBER of ATOMS - an integer specifying the number of atoms in a fragment
ATOM TYPES - an array containing a list of the atom types for all atoms in a fragment
COORDINATES - the cartesian coordinates for each atom in the fragment
One fragment library file is included, it is called fragmentbin (for binary version) or
fragment.fmt (for formatted version).
-------
57
Manipulation and Generation of Molecular Fragments
The fragment module permits the manipulation of existing fragments, and the creation or
deletion, of fragments in the library file. A brief description of the various options is
given below.
READ - the read option reads a new fragment into the library file. The user is prompted
for the name of the file from which to read the single fragment This file is in a specific
format and contains the following:
* FRAGMENT_NAME 2X, A8 (fragment name)
* A2
NATOM 15 (# atoms in fragment)
XI Y1 Z1 Typel (20X, 3F10.5, 10X, F10.5)
X NATOM . . (Cartesian coordinates plus
atom type for all atoms)
Appendix 2 shows the existing fragment file; this provides an example of the input
format for creation of a new fragment
BUILD - This routine builds a simple unbranched chain given a user-specified sequence of
atom types and dihedral angles. Judicious choice of dihedral angles
allows for the building of aromatic (planer) ring structures.
PERTURB - This routine executes a simple modification of existing fragment with two
options ADD and REPLACE
ADD - This attaches single atom substituents to an existing molecular fragment This
routine allows fragments like BENZENE to be perturbed to toluene, or
phenol, or chlorobenzene, or to 1,2-dichlorobenzene, etc. The user is
asked to specify the three atom sequence indicating where the
addition is to take place. The atom is added trans to the first atom
specified, e.g., for a final atomic sequence i - j - k - I, it is taken
that the atomic sequence i, j, and k are existing atoms with the new
atom, I, being added trans to atom i.
-------
58
REPLACE - This affects single atom replacements in existing fragment by substituting atom
type identifiers with no adjustment of geometries. For example, a
fragment like BENZENE may be perturbed to PYRIDINE by perturbing a
carbon to a nitrogen. If the perturbation is viewed as too dramatic,
the replacement is ignored. For example, the replacement of an sp2
carbon by an sp3 carbon is not permitted.
COMBINE - This combines two existing fragments to form a new one. This subroutine
combines a parent and a secondary fragment (order of specification)
into a third. The user is prompted for a three atom sequence on the
parent fragment which indicates where the bond is to be formed and
a two atom sequence on the secondary fragment to indicate point of
attachment For example, to combine benzene and butane one would
specify 6,1,2 on the parent fragment, benzene, in order to add butane
at the 2 position. The sequence 1, 2 is specified for the secondary
fragment, butane, to indicate that atom 1 on butane is to join benzene
at the specified location.
DELETE - This deletes a fragment from the library.
CHOOSE - This chooses a fragment for a surface calculation. - --
Additional Notes and Options
Other options are available in this program, including LOG which sets up a log file to
which all surface area calculations are saved. There is also included a facility which crudely
draws the molecular fragments. This is a crude 40 x 20 bit map to be displayed on the
terminal screen and is intended only to guide the user in building or combining molecular
fragments.
The aromatic molecular compounds, and related molecules, currently resident in the
fragment file are shown in Figure 9. Functional group substituents in the fragment file are
shown in Figure 10.
-------
59
Figure 9. Aromatic and Related Molecules
in the MOLACCS Fragment File
BASE MOLECULAR FRAGMENTS
Aromatics
OJ BENZENE
IT 1 I ^1 ^1 1
OJOJ NAPHTHALene IO1OIOJ ANTHRACEne
PHENANTHrene
0
ii
Oj BENZOPHEnone
OJ DIPHENME
(diphenylmethane)
H
,N.
Oj [Oj DIPHENAN
(diphenylanaline)
Ol lO
DIOXIN
C TRIAZINE
V
N
) IMIDAZOLe
H
O
PYRROLE
'N
H
N
H
INDOLE
N4BENZ
(naphthacene)
S4BENZ
T4BENZ
C4BENZ
/-\ ]{benzo(a)anthracene)
CHRYSENE
-------
60
Figure 10. Functional Group Substituents
in the MOLACCS Fragment File
BASE MOLECULAR FRAGMENTS
Branched Sidechains
-C-OH ACID
-C.
0
//
0
N'
KETONE
NITRO
CxNHg AMID
-C
0
S-o
S0
ISOPROPY
SULFATE
-------
61
Testing and Initial Results
A number of compounds have been used for evaluative purposes in initial surface area
calculations in order to make comparisons with existing literature data Using the current
atomic parameters listed in Table I, calculations of the van der Waals surface areas have
been performed Some of the results are tabulated in Table II along with comparison of
results from Pearlman (1986) and Yalkowsky and Valvani (1979) for benzene and several
polycyclic aromatic hydrocarbons, and Pearlman (1986) and Valvani et al. (1976) for normal
alkanes and alcohols.
The comparisons with the results of Valvani et al. (1976) on straight chain hydrocarbons
and alcohols, as computed by "Method C" in their paper, are all very good. A slightly
smaller total area is found with the MOLACCS extended atom approach and this is most
probably due to a small difference in assumed bond angles. Valvani et al. (1976) did not
specify what bond angles were used. Nonetheless, the values computed by the extended
atom approach and those of Valvani et al. (1976) agree very well, as the two methods
agree within about 1%.
It is noted that calculated values of surface areas for the n-alkanes reported by Pearlman
(1986) are not in general agreement with either the current extended atom approach, or the
calculations of Valvani et al. (1976). The values reported by Pearlman are about 15%
greater than those obtained by either the MOLACCS extended atom approach or by Valvani
et al. (1976). Pearlman (1986) did not report assumed values of bond length, or bond
angle, or van der Waals radii. Thus the explicit reason for the descrepancy cannot be
stated. Nonetheless, this points to the difficulty with making comparisons among different
sets of surface area calculations for which the atomic parameters employed for the
surface area calculation are unknown.
Table II also shows comparison of van der Waals surface area calculation for benzene
and various polycyclic aromatic hydrocarbons and aliphatic-substituted polycyclic aromatic
hydrocarbons. The results show comparison of the MOLACCS extended atom approach
-------
62
Table II
Comparison of van der Waals
Molecular Surface Area Calculations
Aromatic
Compounds
Benzene
Naphthalene
1 -Methylnaphthalene
1 -Ethylnaphthalene
Anthracene
Biphenyl
Phenanthrene
2-Methylanthracene
Pyrene
Chrysene
Naphthacene
n-Aliphatic
Compounds
Butane
Butanol
Pentane
Pentanol
hexane
Hexanol
Heptane
heptanol
Substituted
Benzene
Toluene
Benzoic Acid
Nitrobenzene
Benzamide
Aniline
Fluorobenzene
Chlorobenzene
Bromobenzene
MOLACCS
111.7
155.0
169.4
184.4
198.2
183.2
196.1
214.8
208.04
236.0
240.1
MOLACCS
104.6
114.6
122.5
132.3
140.3
150.2
158.2
168.1
MOLACCS
128.5
140.1
140.5
139.0
120.5
119.5
129.0
133.5
Pearlman
(1986)
110.0
156.8
203.5
199.4
Pearlman
(1986)
116.1
138.8
161.5
184.2
Yalkowsky
and Valvani
(1979)
155.8
172.5
187.4
202.2
182.0
198.0
226.6
213.0
241.0
248.0
Valvani
et al. (1976)
105.9
115.8
124.0
134.0
142.1
152.1
160.3
170.3
Pearlman (pers. comm.)
131.2
140.0
133.0
141.9
125.0
1 14.4
127.1
134.5
-------
63
with data reported by Pearlman (1986) for four compounds, and data reported by
Yalkowsky and Valvani (1979) for ten compounds. Pearlman's (1986) data are slightly larger
than those of Yalkowsky and Valvani (1979). Yalkowsky and Valvani (1979) calculated
molecular van der Waals surface areas according to "Method C" of Valvani et al. (1976), as
described earlier. The current extended atcm approach agrees within about 1-2% of the
van der Waals surface areas reported by Yalkowsky and Valvani (1979) for most
compounds.
Additional comparison of results from MOLACCS is given in Table II for surface area
computation data provided by Pearlman (personal communication) for purposes of this
investigation. This comparison is made for eight substituted benzene compounds. This
comparison shows good agreement of van der Waals area between the method of
Pearlman (1986) and MOLACCS for the eight substituted benzene derivatives. Although
there appears to be a small difference in selection of atomic parameters for F and N. Also,
the comparison depends upon an assumed value of the dihedral angle between the plane of
the parent fragment benzene, and the plane of the branched fragment, such as for the
carboxylic or nitro substituent
Example Calculations _._ .._
Figure 11 shows example surface area calculations. The presentation in Figure 11 shows
how to initiate the program and how to use the various features. The example calculations
show listings of accessible and contact surface area with respect to a probe radius of 1.5
A and the van der Waals surface area The listings also show the contribution of each
atom to the surface area Also shown is the net value of the individually estimated atomic
group contributions to the hydrophobic and polar surface areas.
Reading the Parameter and Fragment Files
Figure 11 shows the initiation of the program in which the user is first presented with a
question regarding the use of the prompt which is indicated by the arrow. The first task
the user must perform is either input an atomic parameter file, or read from the existing
-------
64
atomic parameter file. The user has indicated "p" for input atomic parameters, and "o" to
read the "old" file of existing atomic parameters. The atomic parameters are in the file
"parambin", and after typing the file name the user is asked if the atomic parameters
should be displayed. After entering "y", for yes, the atomic parameters are shown; these
data are the same as shown previously in Table II. The user is asked if any of these
parameters should be changed or if any new parameters are to be added to this file.
Next the user asks to have the program read the existing molecular fragment file by
entering "f", and "o". The molecular fragment file name is entered, i.e. "fragmentbin." The
fragment file is opened, and now the user is presented with a list of options.
List
The first option the user chooses is to list the existing fragments by entering "I." The
fragments are shown, and the user is then presented with the several program options.
Choose - Example of Surface Area of Molecular Fragment
The first option the user selects is "choose", which performs a surface area calculation
on one of the molecular fragments. The user sets up a file, "surface.o", in which to store
the calculation, and again requests a listing of the fragments, and chooses fragment No. 1,
"BENZENE". The user is then asked to input a probe radius, and 1.5 A' is selected. The
results of the calculation are given for the accessible, contact, and van der Waals surface
area, as well as the individual atomic contributions to these surface area values.
Build - Example of Construction of a New Molecular Fragment from Atomic
Parameters
After this calculation, the user is presented again with the various options, and the user
selects to build a new, unbranched molecular fragment from the existing atomic parameters.
The user enters "build", and decides to build "HEXANE". The current atom types and their
numbers are presented, and the user enters the sequence of atomic members (six atomic
fragments No. 1) for the molecular fragment hexane. The fragment is constructed in the
standard trans configuration, and a schematic drawing of the fragment is given.
-------
65
Figure 11.
Examples of Molecular Surface Area Calculations
$ run molaccs
MOLACCS
MOLecular Accessible Surface
Version May-86
Author Charles L. Brooks III
Department of Chemistry
Carnegie-Mellon University-
Pittsburgh, PA 15213
This program will compute molecular surface areas using the
Richards algorithm with varying solvent probe radii.
Prompts are given by the symbol ==>, and default
answer is given in parenthesis, e.g.,
Do you want to input parameters? (n) ==>
Do you understand? (n) ==>
y
Congratulations, you got it!
Now onto more interesting things.
Do you want to input atomic parameters ,
set-up a molecular fragment , calculate
a surface area or quit ? (surface) ==>
P
Current parameter file is empty or non-existent
Do you want to create a new file , Reading the Parame
or read an old one ? (new) ==>
o
What is file name, ? (for090.dat) = = > an(j Fragment Files
param.bin
File parara.bin status=old will be opened and read
Do you want to list current atom parameters? (n) ==>
y
Atom 8 Name Bond Angle vdW_radius Hydrophobicity
1 CSP3 1.530 111.000 2.000 100
2 CSP2 1.350 120.000 2.000 100
3 CARO 1.390 120.000 1.700 100_
4 HARD 0.600 120.000 1.200 100
5 NSP3 1.400 120.000 1.700 0
6 OSP3 1.350 110.000 1.700 0
7 S 2.000 110.000 1.900 80
8 F 1.300 111.000 1.650 90
9 CL 2.000 111.000 1.900 90
10 BR 2.300 111.000 2.000 90
11 I 2.700 111.000 2.100 100
Do you want to input parameters? (n) ==>
Do you want to change existing parameters? (n) ==>
Do you want to input atomic parameters ,
set-up a molecular fragment , calculate
a surface area or quit ? (surface) ==>
f
Current fragment file is empty or non-existent
Do you want to create a new file ,
or read an old one ? (new) ==>
o
What is file name, ? (for091.dat) ==>
fragment.bin
File fragment.bin status=old will be opened and read
24 fragments read from fragment file
List existing fragments ,
build new fragment ,
read in new fragment ,
perturb an existing fragment ,
combine two existing fragments ,
delete an existing fragment
or choose fragment for surface calculation 7 (choose) ==>
1
-------
66
Figure 11. Example of Molecular Surface Area Calculations (continued)
3 ANTHRAC
7 DIPHENAN
11 S4BENZ
15 PYRIDINE
19 ACID
23 NITRO
4 PHENANTH
8 DIOXIN
12 T4BENZ
16 IMIDAZOL
20 AMIDE
24 SULFATE
1 BENZENE 2 NAPHTHAL
5 BENZOPHE 6 DIPHENHE
9 TRIAZINE 10 N4BENZ
13 C4BENZ 14 CHRYSENE
17 PYRROLE 18 INDOLE
21 KETONE 22 ISOPROPY
build new fragment ,
read in new fragment ,
perturb an existing fragment ,
combine two existing fragments ,
delete an existing fragment
or choose fragment for surface calculation
Do you want to set up a LOG file to store
the surface area calculations? (n) ==>
List
? (choose) ==>
? (for093.dat) ==>
Choose
What is file name,
surf ace. o
File surf ace. o status=new will be opened
Which molecular fragment do you want?
list identifiers or input fragment
1
2 NAPHTHAL
6 DIPHENME
10 N4BENZ
14 CHRYSENE
18 INDOLE
22 ISOPROPY
(input) ==>
1 BENZENE
5 BENZOPHE
9 TRIAZINE
13 C4BENZ
17 PYRROLE
21 KETONE
Input fragment
3 ANTHRAC
7 DIPHENAN
11 S4BENZ
15 PYRIDINE
19 ACID
23 NITRO
4 PHENANTH
8 DIOXIN
12 T4BENZ
16 IMIDAZOL
20 AMIDE
24 SULFATE
8 = =
1
= = >
Input solvent probe radius.
1.5
Surface areas for fragment BENZENE
computed with respect to probe of radius
1.500
ACCESSIBLE
Hydrophobia 246.697
Polar 0.000
CSP2
CSP2
CSP2
CSP2
CSP2
6 CSP2
41
41
41
41
41
41
116
116
116
116
.116
.116
CONTACT
80.554
0.000
Atomic Breakdown
13.426
13.426
13.426
13.426
13.426
13.426
van der Waals
111.714
0.000
18.619_.
18.619
18.619
18.619
18.619
18.619
Do you want to input atomic parameters ,
set-up a molecular fragment , calculate
a surface area or quit ? (surface)
= = >
List existing fragments ,
build new fragment .
read in new fragment ,
perturb an existing fragment ,
combine two existing fragments ,
delete an existing fragment
or choose fragment for surface calculation ? (choose)
b
A single unbranched molecular fragment will be built.
Is that what you want? (yes) ==>
What is new fragment name, only 8 characters? ==>
HEXANE
New molecular fragment HEXANE will be built
Number of atoms in linear chain? ==>
6
Now specify atom types, do you want them listed? (n) ==>
y
==>
Build
-------
67
Figure 11. Example of Molecular Surface Area Calculations (continued)
Current atom type names and their numbers
CSP3 1 CSP2 2
CARD 3 HARO 4
NSP3 5 OSP3 6
S 7 F 8
CL 9 BR 10
I 11
Input sequence of atom type numbers in assending order
111111
The chain will be built in an all trans configuration
unless otherwise specified.
Do you want other dihedral angles? (n) ==>
Molecular fragment HEXANE will be drawn
1 2
Return to continue
Save fragment in the library file? (n) ==>
Fragment 25 to be used in surface calculation
Is that what you want? (y) ==>
Input solvent probe radius. ==>
1.5
Surface areas for fragment HEXANE
computed with respect to probe of radius 1^500
ACCESSIBLE CONTACT van der Waals
Hydrophobic 298.781 97.561 140.323
Polar 0.000 0.000 0.000
Atomic Breakdown
1 CSP3 83.258 27.186 33 003
2 CSP3 37.597 12.276 19.319
3 CSP3 28.536 9.318 17 840
4 CSP3 28.536 9.318 17 840
5 CSP3 37.597 12.276 19 319
6 CSP3 83.258 27.186 33.003
Do you want to input atomic parameters ,
set-up a molecular fragment , calculate
a surface area or quit ? (surface)
f
-------
68 »
Figure 1 1. Example of Molecular Surface Area Calculations (continued)
List existing fragments ,
build new fragment ,
read in new fragment . Perturb and Replace
perturb an existing fragment ,
combine two existing fragments ,
delete an existing fragment
or choose fragment for surface calculation ? (choose) ==>
P
Do you want to replace atoms in existing fragment
or add single atom substituents ? (add) ==>
r
Which molecular fragment do you want to perturb?
list identifiers or input fragment J* (input) ==>
1
1 BENZENE 2 NAPHTHAL 3 ANTHRAC 4 PHENANTH
5 BENZOPHE 6 DIPHENME 7 DIPHENAN 8 DIOXIN
9 TRIAZINE 10 N4BENZ 11 S4BENZ 12 T4BENZ
13 C4BENZ 14 CHRYSENE 15 PYRIDINE 16 IMIDAZOL
17 PYRROLE 18 INDOLE 19 ACID 20 AMIDE
21 KETONE 22 ISOPROPY 23 NITRO 24 SULFATE
Input fragment # ==>
2
Atoms will be replaced in fragment NAPHTHAL
What is new fragment name, only 8 characters? ==>
QUINOLINE
New molecular fragment QUINOLINE will be built from perturbation of NAPHTHAL
How many atoms to be replaced in fragment
1
Molecular fragment NAPHTHAL will be drawn
1 2
10
Return to continue
Atoms will be replaced one at a time
List atom to be replaced on fragment NAPHTHAL
1
Now specify new atom type, do you want them listed? (n) ==>
y
Current atom type names and their numbers
CSP3 1 CSP2 2
CARD 3 HARD 4
NSP3 5 OSP3 6
S 7 F 8
CL 9 BR 10
I 11
Number for new atom type?
5
Atom type CSP2 at site 1
replaced by atom type NSP3
-------
69
Figure 11. Example of Molecular Surface Area Calculations (continued)
Molecular fragment QUINOLIN will be drawn
1 2
10
Return to continue
Save fragment in the library file? (n) ==> ,
Fragment 25 to be used in surface calculation
Is that what you want? (y) ==>
Input solvent probe radius. ==>
1.5
Surface areas for fragment QUINOLIN
computed with respect to probe of radius 1.500
ACCESSIBLE CONTACT van der Waals
Hydrophobia 295.527 96.499 142.877
Polar 16.920 4.775 9.078
Atomic Breakdown '
1 NSP3 16.920 4.775 9.0-78
2 CSP2 50.698 16.555 21.855
3 CSP2 41.859 13.668 18.531
4 CSP2 34.574 11.289 17.470
5 CSP2 7.480 2.442 7.146
6 CSP2 4.419 1.443 5.011
7 CSP2 38.203 12.474 18.332
8 CSP2 41.859 13.668 18.531
9 CSP2 41.859 13.668 18.531
10 CSP2 34.574 11.290 17.470
Do you want to input atomic parameters ,
set-up a molecular fragment . calculate
a surface area or quit ? (surface) ">
f
-------
70
Figure 11. Example of Molecular Surface Area Calculations (continued)
List existing fragments ,
build new fragment ,
read in new fragment . D _«..._.
perturb an existing fragment . Kerturt)
combine two existing fragments ,
delete an existing fragment
or choose fragment for surface calculation ? (choose) ==>
P
Do you want to replace atoms in existing fragment
or add single atom subatituents ? (add) ==>
a
Which molecular fragment do you want to perturb?
list identifiers or input fragment tf (input) ==>
Input fragment & ==>
1
Atoms will be added to fragment BENZENE
What is new fragment name, only 8 characters? ==>
13DICLBENZ
Name greater than 8 characters, truncated.
New molecular fragment 13DICLBEN will be built by addition to BENZENE
How many atoms to add to fragment
2
Molecular fragment BENZENE will be drawn
1 2
Return to continue
Atoms will be added one at a time
Atom added where on fragment BENZENE
List 1,J and k, where k la the bond to add
atom to and j and i are the k-1, k-2 atoms
bonded to k
541
Now specify atom type to be added
Do you want them listed? (n) ==>
y
Current atom type names and their numbera
CSP3 i CSP2 2
CARD 3 HASO 4
NSP3 5 OSP3 6
S 7 F 8
CL 9 BR 10
I 11
Number of atom type to be added?
9
Atom added where on fragment BENZENE
List i,J and k, where k in the bond to add
atom to and J and i are the k-1, k-2 atoms
bonded to k
123
Now specify atom type to be added
Do you want them listed? (n) ==>
-------
71
Figure 11. Example of Molecular Surface Area Calculations (continued)
Number of atom type to be added?
3
Molecular fragment 13DICLBE will be drawn
7
5 6
Return to continue
Save fragment in the library file? (n) ==>
Fragment 25 to be used in surface calculation
Is that what you want? (y) ==>
Input solvent probe radius. ==>
1.5
Surface areas for fragment 13DICLBE
computed with respect to probe of radius 1.500
ACCESSIBLE
Hydrophobia 289.659
Polar 15.178
CONTACT
92.637
4.740
Atomic Breakdown
van der Waals
140.400
6.074
1 CSP2 5.905 1.928
2 CSP2 29.192 9.532
3 CSP2 5.905 1.928
4 CSP2 35.312 11.531
5 CSP2 41.432 13.529
6 CSP2 35.312 11.531
7 CL 75.889 23.699
8 CL 75.889 23.699
Do you want to input atomic parameters ,
set-up a molecular fragment , calculate
a surface area or quit ? (surface)
6.719
17.557
6.719
18.075
18.593
18.075
30.368
30.368
= = >
List existing fragments ,
build new fragment ,
read in new fragment ,
perturb an existing fragment ,
combine two existing fragments ,
delete an existing fragment
or choose fragment for surface calculation ? (choose) ==>
P
Do you want to replace atoms in existing fragment
or add single atom substituents ? (add) ==>
Which molecular fragment do you want to perturb?
list identifiers or input fragment # (input) ==>
Perturb and Add
-------
72
Figure 11. Example of Molecular Surface Area Calculations (continued)
Input fragment * = = >
Atoms mil be added to fragnent NAPHTHA!.
"hat i, new fragment name, only a characters? >
ethylna
New molecular fraoient ETHYINA will be built by addition to HAPHTHAL
How many atoms to add to fragment nnrninAu
Molecular (rafnent NAPHIHAL will be drawn
1 2
Return to continue
Atoras will be added one at a tine
Aton added where on fragment NAPHTHAL
List l.J and k. where k is the bond to add
atoia to and J and I are the k I, k-2 etons
bonded to k
6 5 1
Now specify atom type to be added
Do you want them listed? (n) ==>
Number of atom type to be added?
1
Aton added where on fragment HAPHTHAL
List i.J and k, where k la the bond to add
aton to and j and 1 are the k-1, k-Z atoms
bonded to k
5 1 11
Now specify atom type to be added
Do you want then listed? (n) ==>
Nunber of atom type to be added?
1
Molecular frataent ZTBYLNA will be drawn
Return to continue
Sive frel»«nt in the library file? (a) ">
Do you want to set up a LOG file to store
the surface area calculations? (n) ">
y
What 1> file name, (filename. ext>? (for093.dat) ::>
ethyna. sur
File ethyna.sur atatuaznew will be opened
fragment 2& to be uaed in surface calculation
Is that what you want? (y) ==>
Input solvent probe radius. =x>
l.S
Surface ereaa for fracment ETHYLNA
computed with reapect to probe of radiua 1 . 500
ACCESS I Bt-t
Hydropheblc 349.253
Polar 0.000
CONTACT
114.035
0.000
van dar Weals
184.428
0.000
Atomic Breakdown
1 CSP2
2 CSP2
3 CSPZ
« CSP2
5 CSP2
6 CSP2
7 CSP2
« CSP2
9 CSP2
10 CSP2
11 CSP3
12 CSF3
3,
21.
41.
33.
3
3.
23
41.
4).
33.
29.
72.
.933
.494
.116
.(34
.717
.71?
.865
.ill
.116
635
.273
417
1.
7.
13
11.
1
I
7
13
13.
11.
3.
23.
.2(4
.019
.426
.048
.214
.214
.727
.428
428
046
.559
646
5.258
14.724
It.619
17.558
5.130
S.130
15.451
18.619
16.819
17 556
17.355
30 407
surface area or quit ? (aurfece)
-------
73
Figure 1 1. Example of Molecular Surface Area Calculations (continued)
Perturb and Add
Perturb and Ad
List existing fragments .
build new fragment .
read in new fragment .
perturb an existing fragment .
combine two existing fragments ,
delete an existing fragment
or choose fragnent for surface calculation ? (choose) ==>
P
Do you want to replace atoms in existing fragment
or add single aton substltuenti ? (add) = =>
Which molecular fragment do you want to perturb?
List Identifiers or input fragment * (input) ==>
1 BENZENE
5 BENZOPHE
9 TRIAZINX
13 C4BENZ
17 PYRROLS
21 KETONE
2 HAPHTHAL
6 DIPKENME
10 H4BEHZ
3 ANTHRAC
7 DIPHENAH
11 S4BENZ
14 CHRYSENE 15 PYRIDINE
IB INDOLE
22 ISOPROPY
19 ACID
23 NITRO
4 PHZNANTH
8 DIOXIN
12 T4BEHZ
16 IMIDAZOL
20 AMIDE
24 SULFAT*
Input fragment I =->
4
Atoms will be added to fragment PHENANTH
What is new fragment name, only 6 characters? ==>
PYRENE
Sew moleculer fragment PYRENE will be built by addition to PHENANTH
Kow many atoms to add to fragment
2
Molecular fragment PKENANTH will be drawn
12 11 12
Save fragment in the library file? (n) = = >
Fragment 25 to be used in surface calculation
la that what you want? (y) = = >
Input solvent probe radius. ==>
1.5
Surface areas for fragment PYRENE
computed with respect to probe of radius 1.500
ACCESSIBLE
Hydrophoblc 374.701
Polar 0.000
1 CSP2
2 CSP2
3 CSP2
4 CSP2
5 CSP2
6 CSP2
7 CSP2
8 CSP2
9 CSP2
1O CSP2
11 CSP2
12 CSP2
13 CSP2
14 CSP2
15 CSP2
16 CSP2
3.564
33.854
41.116
33 934
3.714
3.717
3.714
33.835
3.717
33.834
3. 564
33.854
41.116
33.834
33.717
33.717
van der Waa
122.351
0.000
Atomic Breakdown
1.164
11.054
13.426
11.048
1.213
1.214
1,213
11.048
1.214
11.048
1.164
11.054
13.426
11.048
11.010
11.010
208.039
0.000
5.019
17.538
18.619
17.558
5.130
5.130
5.130
17.558
5.130
17.558
S.019
17.536
18.819
17.558
17.470
17.470
Return to continue
Atoms will be added one at a time
Atom added where on fragment PHENANTH
List l,j and k. where k la the bond to add
atom to and j and 1 are the k-1. k-2 atoms
bonded to k
3 2 1
How specify atom type to be added
Do you want them Hated? (n) ss>
y
Current atom type names and their numbera
CSP3 1 CSPZ 2
CARO 3 HAXO 4
NSP3 5 OS?3 6
S 7 T 8
CL 9 BR 10
I 11
Suaber of atom type to be added?
2 '
Aton added
List i.J ft
mitoa to «n
bonded to
13 12 11
Now sp«clf
Do you w»n
wh*r* on fr..r»nt PHENAHTH
d k. wh«r« k Is the bond to add
3 and 1 ar* tha k-1. k-2 «to»»
atow type to be added
the* listed? (n) -=>
Nuaber of atom type to be added?
Molecular fragment PYRCNE will be drawn
16 15
12
U
Return to coatlnue
-------
74
Figure 11. Example of Molecular Surface Area Calculations (continued)
Llat existing fragments .
build new fragment ,
read in new fragment .
perturb an existing fragment ,
combine two existing fragments (
delete an existing fragment
or choose fragment for surface calculation ? (choose) ==>
con
Which molecular fragments do you want to combine?
list identifiers r input fragment (input) ==>
1
3 ANTHRAC
7 DIPHENAN
11 S4BENZ
15 PYRIDINE
19 ACID
23 NITHO
Combine
1 BENZENE
5 BENZOPHE
9 TR1AZINE
13 C4BENZ
17 PYRROLE
21 KETONE
Input fragment « ==>
1 23
Molecular fragment NITRO will be added to fragment BENZENE
What is new fragment name, only 8 characters? ==>
NITROBENZ
Hew molecular fragment NITROBENZ will be built by combining BENZENE and NITRO
2 NAPHTHAL
6 OIPHENHE
10 N4BENZ
14 CHRYSENE
18 INDOLE
22 ISOPROPY
4 PHENANTH
8 DIOXIN
12 T4BENZ
16 IMIDAZOL
20 AMIDE
24 SULFATE
Mole
ula
fragments BENZENE
Fragment A
2
and NITRO
will be drawn
Fragment B
5 6
Return to continue
Fragment B added where on fragment A
List l.J and k. where k la the bond to add
atom to and J and i are the k-1. Jc-2 atons
bonded to k
632
Now specify aton on fragment B wher* bond la forned
and the aton Its bonded to
1 3
Current dihedral value around bond connecting
fragments Is 180.0000
What dihedral do you want? ==>
180
Current dihedral value around bond connecting
fragments is 180.0000
Molecular fragment NITROBEN will be drawn
9
la this the configuration you went? (ye«)
Save fragment in the library filet (o) ==
n
Do you want to set up a LOG file to store
the aurface area calculations? (n) -->
What la file name. ? (for093.dat) ==>
com log
File com.log status=new will be opened
Fragment 25 to be used in surface calculatlo
Ii that what you want? (y) ==>
Input solvent probe radius. ==>
l.i
Surface areas for fragment NITROBEN
computed with respect to probe of radius
l.SOO
ACCESSIBLE
Hydrophoblc 191 3S4
Polar 105.289
1 CSP2
2 CSP2
3 CSP2
4 CSP2
S CSP2
6 CSP2
1 NSP3
OSP3
9 OSP3
29.286
7.937
28.553
41.859
41.859
41.059
1.670
50.787
52.632
van der Waals
62.483
29.71S
Atomic Breakdown
9.563
2.592
9.323
13.666
13.668
13.668
0.471
14 333
14.911
9S 772
44.770
16.649
7.207
16.322
18.631
18.531
11.531
J.77Z
20.671
21.327
-------
75
Figure 11. Example of Molecular Surface Area Calculations (continued)
List existing fragments ,
build n«» fragment ,
read in new fragment .
perturb »n existing fragment ,
combine two existing fragments ,
delete an existing fragment
or choose fragment for surface calculation ? (choose) ==>
Combine
list Identifier!
1
1
5
9
13
17
21
BENZENE
BENZOPHE
TRUZINE
C4BENZ
PYRROLE
KETONE
Input fragment
1
1
Molecular fragm«
2
S
10
U
18
22
t
>nt
or
NAPHTHAL
DIPHENME
N4BENZ
CHRYSENE
INDOLE
ISOPROPY
= = >
BENZENE
input fragment * (input) = = >
3
7
11
IS
19
23
Kill
ANTHRAC
DIFHENAN
S4BENZ
PYRIDINE
ACID
NITRO
be added
4
8
12
16
20
24
to
PHENANTH
DIOXIN
T4BENZ
IMIDAZOL
AMIDE
SULFATE
fragment BE1
What 13 new fragment name, only B characters? ">
BIPHENYL
New molecular fragment BIPHENYL fill be built by combining BENZENE
Molecular fragments BENZENE and BENZENE will be drawn
Fragment A Fragment B
12 12
and BENZENE
S 6
Return to continue
Fragment B added where on fragment A
List 1,J and k. where k la the bond to add
atom to and j and 1 are the k-1. k-2 atoma
bonded to k
632
Now specify atom on fragment B where bond li formed
and the atom its bonded to
S 6
Current dihedral value around bond connecting
fragments is -1.9792342E-02
What dihedral do you want? =*>
0.0
Current dihedral value around bond connecting
fragments is -1.9782342E-02
Molecular fragment BIPHENYL will be drawn
? 6
12
Surface areaa for fragment BIPHENYL
computed with respect to probe of radius
1.500
Return to continue
Is thla the configuration you want** (yea) = = >
Save fragment in the library file? (n) ">
Fragment 25 to be use
Is that what you want? (y) ">
illation
Input
1.5
ACCESSIBLE
Hydrophoblc 358.596
Polar 0.000
CONTACT
116.439
0.000
van der Haala
183.268
0.000
Atomic Breakdown
I CSP2
2 CSP2
3 CSP2
4 CSP2
5 CSP2
6 CSP2
7 CSP2
6 CSP2
9 CSP2
10 CSP2
11 CSP2
12 CSP2
24.
4
24.
41.
41.
41.
41.
41.
41.
24.
4
23.
Do you want to
set-up a
a surface
q
510
346
510
696
.696
898
916
699
117
528
.347
.726
input atomic
molecular fragment
area
or
8.003
1.419
8.003
13-. 681
13.681
13.681
13.667
13.681
13.428
6.009
1.420
7.748
parameters .
i calculate
quit ? (aurface)
IS.
5.
15.
16.
16.
18.
18.
18.
16.
IS.
S
IS
ss:
.369
024
.369
624
.624
624
.629
624
.619
.374
.024
.363
MOLACCS normal termination
t
-------
76
This fragment is assigned a number in the event that the user may wish to save it, then a
probe radius of 1.5 A is selected, and the accessible, contact, and van der Waals surface
areas are calculated
Perturb and Replace - Example of Replacement of an Atom in a Fragment
The next example shows use of "perturb" and "replace", in which the molecular fragment
naphthalene is used to construct quinoline. The user selects "p" for perturb and then "r"
for replace. The molecular fragments are listed; fragment No. 2 is selected; the new
fragment is named; and the molecular fragment "NAPHTHAL" is drawn. Atom number 1 in
IMAPHTHAL is selected for replacement; the atom types are listed; atom number 5 is
selected from the list; and the new molecular fragment is drawn. The surface area
calculations are then performed for a probe radius of 1.5 A
The weighted proportion of the total surface area comprised of hydrophobic and polar
atomic entities is shown, as in the other examples. These values for hydrophobic and polar
surface area for quinoline were used in the AROSOL program Example Calculation I as
shown previously in Figure 5.
*
Perturb and Add - Example of Addition of an Atom to a Fragment
The next calculation shows an example of "perturb" and "add" in which two chlorine atoms
are added to benzene to form 1,3-dichlorobenzene. The user enters "p* and "a" for
perturb and add; and molecular fragment No. 1, "BENZENE", is selected for perturbation.
The user then inputs the number "2" to indicate the addition of two atoms to benzene.
The molecular fragment is drawn. The sequence of atoms 5,4,1 on benzene are specified,
the atom types are listed, and atom type No. 9 (CD is selected. Chlorine is added at the
one position, and the steps are repeated to add chlorine at the 3 position by specifying
the atomic sequence 1,2,3 on the aromatic ring. The molecule 1,3-dichlorobenzene is
drawn, and the surface area calculations are performed for a probe radius of 1.5 A
-------
77
Perturb and Add - Example of Addition of an Atom to a Fragment
The next example illustrates the construction and surface area calculation for 1-
ethylnaphthalene. The calculation proceeds as in the above example with the atomic
sequence 6,5,1 indicated to identify the location of the atomic addition. The atoms are
added one at a time, and an aliphatic carbon is first added at the 1-position and the
second carbon is added to the new carbon atom by specifying the sequence 5,1,11. The
map shows that first additional carbon, labled number 11 was added at the 1 -position, and
the example continues with the additional carbon being added at the 11-position. The
second carbon atom is labled No. 12.
Perturb and Add - Example of Addition for an Atom to a Fragment
The next example illustrates the construction of pyrene from phenanthrene. As before,
the user inputs "p" and "a", and the molecular fragments are shown. Molecular fragment
number 4, "PHENANTH," is specified, the new fragment is named. The new fragment will
be constructed by addition of two aromatic carbon atoms. The location of the first atom
to be added is given as 3, 2, 1 for addition at the 1-position. The atom type is selected,
i.e. atom type 2 for aromatic-CH. This procedure is repeated with the next atom being
added at position 11 by specifying 13, 12, 11. The calculation then proceeds as in the
previous examples.
Combine - Example of Combining a Functional Group Substituent to a Fragment
The next example illustrates the construction of nitrobenzene from the molecular fragment
benzene and the nitro functional group substituent The user enters "c" for combine, and
then enters the fragment numbers 1 and 23 for "BENZENE" and "NITRO", respectively. The
fragment numbers are entered with the parent fragment identification first, followed by the
secondary fragment identificatioa The new fragment is named, and then the parent and
secondary fragments are displayed. Atoms "6, 3, 2" are specified on the parent fragment
to indicate the point of attachment at atom number 2 on benzene. The two atom sequence
"1, 3" is specified for the secondary fragment to indicate the orientation and attachment of
the nitrogen atom, which is atom number 1 in the NITRO functional group. The program
then indicates that the dihedral angle between the plane containing benzene and the plane
-------
78
containing the nitro group is 180°. This value of the dihedral angle is accepted for
calulation. The configuration is checked, and the surface area calculation is performed.
NOTE: The fragment atomic numbering system is shown in the appendix in the fragment
file. This numbering system must be used to ensure that the fragments are combined in
the manner desired.
The combine operation may have to executed at one or two different locations around a
symmetric aromatic ring until the desired atomic configuration is achieved. This requirement
results from the manner in which the combine operation is performed. The combining of
two molecular fragments to form a daughter fragment is accomplished by a series of three
operations. The first step entails the atattachment of the principal atom (i.e. atom number
1) of the secondary fragment to the parent fragment with the correct bond angle. The
computer program then translocates the secondary fragment over the attached atom to
achieve superposition of the principal atoms. This translocation is executed by moving the
secondary fragment to the attached atom on the parent fragment without rotation. This
translocation is performed by superimposing the fragments in the orientation shown in the
orginal presentation of fragment A and B. The computer program then rotates the branched
atoms on the secondary fragment to achieve the correct bond angle between the branched
atoms and the principal atom on the secondary fragment This rotation is restricted to
about plus or minus 45°. Therefore, the correct strategy for combining fragments is to
select a location on the parent fragment for which a direct lateral translocation of the
secondary group results in approximately the correct orientation of the branched atoms.
The third step of the combine operation is the rotation of attacheded secondary fragment
to the specified dihedral angle between the parent fragment and secondary fragment The
dihedral angle is the angle formed by the plane containing the primary fragment and the
plane containing the secondary fragment A dihedral angle of 0° or 180° means that both
fragments lie in the same plane, while a dihedral angle of 90° means that the two
fragments lie in planes perpendicular to each other.
-------
79
Combine - Example of Combining Two Fragments
The last example shows the combination of benzene and benzene to form biphenyl.
Again, the user selects combine, and the fragment benzene is taken for both parent and
secondary fragment. The user specifies the sequence "6, 3, 2" for attachment at location
number 2 on the parent fragment, and "5, 6" for attachment of the secondary fragment at
location 5. The molecular fragment is drawn, and the calculation is performed for a
dihedral angle of 0° (actually 0.02° owing to runoff error).
The "combine" operation permits only one bond to be formed between fragments. As
indicated above, the operation may have to be executed several times at different locations
around the parent ring in order to achieve the correct symmetry and orientation for the
new molecule.
-------
80
REFERENCES
Anderson, RE, "Supplement to Program UNIFAC," 3rd revision, Dept of Chemical
Engineering, Univ. of California, Berkeley, CA, 1983.
Arbuckle, W.B., "Estimating Activity Coefficients for Use in Calculating Environmental
Parameters," Environmental Science and Technology. Vol. 17, No.9, 1983, pp.
537-542.
Barton, A.F. M., Handbook of Solubility Parameters and Other Cohesion Parameters CRC
Press Inc., Boca Raton, FL, 1983.
Benerjee, S., "Solubility of Organic Mixtures in Water," Environmental Science and
Technology, Vol. 18, 1984, pp. 587-591.
Benerjee, S., "Calculation of Water Solubility of Organic Compounds with UNIFAC-Derived
Parameters," Environmental Science and Technology. Vol. 19, No. 4, 1985, pp.
364-369.
Brooks, B.R., Bruccoleri, R., Olafson, B., States, D., Swaminathan, S., and Karplus, M.,
"Chemistry at Harvard - CHARMM: A Program for Macromolecular Energy, Minimization,
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81
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84
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85
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Aromatic Hydrocarbons," Journal of Chemical and Engineering Data, Vol. 24, No. 2,
1979, pp. 127-129.
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86
APPENDIX 1: AROSOL PROGRAM LISTING
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C
^
c
a.
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rt w -<
-" U *J X
*d^1
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ri vi u U
u -> w
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41 3
CT u
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^
.12+Rnl (i)*Rn2(
rml+Rnl {i) »Rnl (
n o o
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c c: Q
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c a. c
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-> c
w o o
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3
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1 1 t
o o n ^ o fv
f-» * (Nt~«CM*CM
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0 0 «
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OIOIO 1 0 1 O 1
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3
-ot (3) "rot (3)
(1) /Sqrt (Rotn)
c o
O . 1
O CM O *J
M TJ a c
CO O
u a u
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oc
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Q U
-------
125
a\
in
u
o
H
H
M
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n
o
U
-------
125
vo
CO
en
r-
H
in
o
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rl
M
Cu
M
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f-* *-« M M X >i
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' -^ «fl U U U U
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* X *J
r * «9 M 4 i-»
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> i »M a *j c ai c
> vi * *fl ui ua oc ui
-------
126
type param. f mt
11
1
2
3
4
5
6
7
8
9
10
11
$
CSP3
CSP2
CARO
HARD
NSP3
OSP3
S
F
CL
BR
I
1.530
1.350
1.390
0.600
1.400
1.350
2.000
1.300
2.000
2.300
2.700
111.000
120.000
120.000
120.000
120.000
110.000
110.000
111.000
111.000
111.000
111.000
2.000 100
2.000 100
1.700 100
1.200 100
1.700 0
1.700 0
1.900 80
1.650 90
1.900 90
2.000 90
2.100 100
-------
127
$ type fragment. fmt
24
BENZENE
6
1 2
2 2
3 2
4 2
5 2
6 2
NAPHTHALEN
10
1 2
2 2
3 2
4 2
5 2
6 2
7 2
8 2
9 2
10 2
ANTHRAC
14
1 2
2 2
3 2
4 2
5 2
6 2
7 2
8 2
9 2
10 2
11 2
12 2
13 2
14 2
PHENANTH
14
1 2
2 2
3 2
4 2
5 2
6 2
7 2
8 2
9 2
10 2
11 2
12 2
13 2
14 2
BEHZOPHE
14
1 2
2 2
3 2
4 2
5 2
6 2
0.00000
1.38000
2.07000
-0.69000
0.00000
1.38000
0.00000
1.38000
2.07000
1.38000
-0.69000
0.00000
-2.07000
-2.76000
-2.07000
-0.69000
0.00000
1.38000
2.07000
1.38000
-0.69000
0.00000
-2.07000
-0.69000
-2.76000
-2.07000
-4.14000
-4.83000
-4.14000
-2.76000
0.00000
1.36000
2.07000
1.38000
-0.69000
0.00000
-2.07000
-0.69000
-2.76000
-2.07000
-2.76000
-4.14000
-4.83000
-4.14000
0.00000
1.38000
2.07000
-0.69000
0.00000
1.38000
0.00000
0.00000
,19512
,19512
.39023
1.
1.
2.
2.39023
0.00000
0.00000
19512
.39023
.19512
.39023
19511
2.39023
3.58534
3.58535
0.00000
0.00000
1.19512
2.39023
1.19512
2.39023
1.19511
3.58535
2.39023
3.58534
2.39023
3.58534
.78046
4.78048
0.00000
0.00000
1.19512
2.39023
1.19512
2.39023
1.19511
3.58535
2.39023
3.58534
0.00000
0.00000
1.19511
2.39023
0.00000
0.00000
1.19512
1.19512
2.39023
2.39023
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
-------
128
V V
8 7
9 2
10 2
11 2
12 2
13 2
14 2
DIPHENME
13
1 2
2 2
3 2
4 2
5 2
6 2
7 1
8 2
9 2
10 2
11 2
12 2
13 2
DIPHENAN
13
1 2
2 2
3 2
4 2
5 2
6 2
7 5
8 2
9 2
10 2
11 2
12 2
13 2 '
DIOXIN
14
1 2
2 2
3 2
4 2
5 2
6 2
7 6
8 2
9 2
10 2
11 2
12 2
13 2
14 6
TRIAZINE
6
1 2
2 5
3 2
4 5
5 2
6 5
N4BENZ
10
1 2
2 2
-^.ubava
-2.67547
-4.17063
-2.79084
-2.18589
-4.83967
-4.12891
-2.95757
0.00000
1.38000
2.07000
-0.69000
0.00000
1.38000
-2.06979
-4.17063
-2.79084
-2.18589
-4.83967
-4.12891
-2.95757
0.00000
1.38000
2.07000
-0.69000
0.00000
1.38000
-2.06979
-4.17063
-2.79084
-2.18589
-4.83967
-4.12891
-2.95757
0.00000
1.38000
2.07000
-0.69000
0.00000
1.38000
-2.06979
-4.17063
-2.79084
-2.18589
-4.83967
-4.12891
-2.95757
-0.83918
0.00000
1.37500
2.06250
1.37500
0.00000
-0.68750
0.00000
1.38000
1. 21920
0. 14866
2.41993
2.39584
3.63618
3.62690
4.80979
4.78025
0.00000
0.00000
1.19512
1.19512
2.39023
2.39023
1.21920
2.41993
2.39584
3.63618
3.62690
4.80979
4.78025
0.00000
0.00000
1.19512
1.19512
2.39023
2.39023
1.21920
2.41993
2.39584
3.63618
3.62690
4.80979
4.78025
0.00000
0.00000
1.19512
1.19512
2.39023
2.39023
1.21920
2.41993
2.39584
3.63618
3.62690
4.80979
4.78025
3.73035
0.00000
0.00000
1.19079
2.38157
2.38157
1.19079
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
-------
129
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
S4BENZ
16
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2.07000
1.38000
-0.69000
0.00000
-2.07000
-0.69000
-2.76000
-2.07000
-4.14000
-4.83000
-4.14000
-2.76000
2.05500
3.42000
3.40500
4.09500
0.00000
1.38000
2.07000
1.38000
-0.69000
0.00000
-2.07000
-2.76000
-2.07000
-0.69000
-4.11000
-2.74500
-4.78500
-4.09500
-2.07000
-0.67500
1. 19512
2. 39023
1.19512
2.39023
1. 19511
3.58535
2.39023
3.58534
2.39023
3.58534
4.78046
4.78046
-1. 16913
1. 19512
-1.16913
0.02599
0.00000
0.00000
1.19512
2.39023
1.19512
2.39023
1.19511
2.39023
3.58534
3.58535
2.39023
0.02598
1.22110
0.02598
-1.14316
-1.16913
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
T4BENZ
17
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
0.00000
1.38000
2.07000
1.38000
-0.69000
0.00000
-2.07000
-0.69000
-2.76000
-2.07000
-4.14000
-4.83000
-4.14000
-2.76000
-4.81500
-2.74500
-4.14000
0.00000
0.00000
-.1.19512
2.39023
1.19512
2.39023
1.19511
3.58535
2.39023
3.58534
2.39023
3.58534
4.78046
4.78046
1.22109
0.02598
0.05196
C4BENZ
18
1
2
3
4
5
6
7
8
9
10
11
2
2
2
2
2
2
2
2
2
2
2
0.00000
1.38000
2.07000
1.38000
-0.69000
0.00000
-2.07000
-0.69000
-2.76000
-2.07000
-4.14000
0.00000
0.00000
1.19512
2.39023
1.19512
2.39023
1.19511
3.58535
2.39023
3.58534
2.39023
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
. 0.00000
-------
130
iZ Z
13 2
14 2
15 2
16 2
17 2
18 2
CHRYSENE
18
1 2
2 2
3 2
4 2
5 2
6 2
7 2
8 2
9 2
10 2
11 2
12 2
13 2
14 2
15 2
16 2
17 2
18 2
PYRIDINE
6
1 5
2 2
3 2
4 2
5 2
6 2
IMIDAZOL
5
1 2
2 2
3 5
4 2
5 5
PYRROLE
5
1 2
2 2
3 2
4 2
5 5
INDOLE
9
1 2
2 2
3 2
4 2
5 2
6 5
7 2
8 2
9 2
ACID
3
1 2
2 6
3 6
-4 . 83000
-4. 14000
-2.76000
3.42000
2.05500
4.09500
3.40500
0.00000
1.38000
2.07000
1.38000
-0.69000
0.00000
-2.07000
-0.69000
-2.76000
-2.07000
-2.76000
-4.14000
-4.83000
-4.14000
3.42000
2.05500
4.09500
3.40500
0.00000
1.37500
2.05000
1.37500
0.02500
-0.65000
0.36674
1.20085
0.33166
-0.95564
-0.94361
0.36674
1.20085
0.33166
-0.95564
-0.94361
-1.53762
-0.21879
-0.28479
0.97047
-2.35104
-1.54495
0.81957
2.11023
2.03692
0.00000
1.09102
-1.09102
3.58534
4.78046
4.78046
1.19512
3.55936
2.36426
3.55936
0.00000
0.00000
1.19512
2.39023
1.19512
2.39023
1.19511
3.58535
2.39023
3.58534
0.00000
0.00000
1.19511
2.39023
1.19512
3.55936
2.36426
3.55936
0.00000
0.00000
1.16913
2.33827
2.33827
1.16913
1.06526
-0.01815
-1.05777
0.66545
-0.65479
1.06526
-0.01815
-1.05777
0.66545
-0.65479
1.09831
0.73748
-0.61601
1.42322
-0.01833
-1.06399
-1.42878
0.63072
-0.76262
0.37863
-0.18932
-0.18932
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
AMIDE
-------
131
3
1 2
2 6
3 5
KETONE
3
1 1
2 6
3 1
ISOPROPY
3
1 1
2 1
3 1
NITRO
3
1 5
2 6
3 6
SULFATE
4
-0.04283
-1.09284
1.13568
0.00000
1.09102
1.22476
0.00000
-1.22476
1.22476
0.00000
1.09102
-1.09102
0.00000
-0.96361
-0.96361
-0.96361
0.41902
-0.22159
-0.19743
0.60013
-0.56795
-0.90020
0.60013
-0.30007
-0.30007
0.37863
-0.18932
-0.18932
0.00000
1.37618
-1.37618
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
1.37618
------- |