The parametrization and testing of the OPLS all-atom force field for organic molecules and peptides are described. Parameters for both torsional and nonbonded energetics have been derived, while the bond stretching and angle bending parameters have been adopted mostly from the AMBER all-atom force field. The torsional parameters were determined by fitting to rotational energy profiles obtained from ab initio molecular orbital calculations at the RHF/6-31G*//RHF/6-31G* level for more than 50 organic molecules and ions. The quality of the fits was high with average errors for conformational energies of less than 0.2 kcal/mol. The force-field results for molecular structures are also demonstrated to closely match the ab initio predictions. The nonbonded parameters were developed in conjunction with Monte Carlo statistical mechanics simulations by computing thermodynamic and structural properties for 34 pure organic liquids including alkanes, alkenes, alcohols, ethers, acetals, thiols, sulfides, disulfides, a...

https://sakai.rutgers.edu/access/content/user/kparis/biomaps_513_references/02_B_01_JACS118_11225_OPLS.pdf

Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids

Successive parameterizations of the GROMOS force field have been used successfully to simulate biomolecular systems over a long period of time. The continuing expansion of computational power with time makes it possible to compute ever more properties for an increasing variety of molecular systems with greater precision. This has led to recurrent parameterizations of the GROMOS force field all aimed at achieving better agreement with experimental data. Here we report the results of the latest, extensive reparameterization of the GROMOS force field. In contrast to the parameterization of other biomolecular force fields, this parameterization of the GROMOS force field is based primarily on reproducing the free enthalpies of hydration and apolar solvation for a range of compounds. This approach was chosen because the relative free enthalpy of solvation between polar and apolar environments is a key property in many biomolecular processes of interest, such as protein folding, biomolecular association, membrane formation, and transport over membranes. The newest parameter sets, 53A5 and 53A6, were optimized by first fitting to reproduce the thermodynamic properties of pure liquids of a range of small polar molecules and the solvation free enthalpies of amino acid analogs in cyclohexane (53A5). The partial charges were then adjusted to reproduce the hydration free enthalpies in water (53A6). Both parameter sets are fully documented, and the differences between these and previous parameter sets are discussed.

/pdf/a-biomolecular-force-field-based-on-the-free-enthalpy-of-1chefjehkc.pdf

A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6.

VOLUME I Introduction The Incentive Physical-Chemical Properties Experimental Methods Quantitative Structure-Property Relationships (QSPRs) Mass Balance Models of Chemical Fate Data Sources and Presentation Illustrative QSPR Plots and Fate Calculations References Aliphatic and Cyclic Hydrocarbons Lists of Chemicals and Data Compilations Summary Tables and QSPR plots References Mononuclear Aromatic Hydrocarbons Lists of Chemicals and Data Compilations Summary Tables and QSPR plots References Polynuclear Aromatic Hydrocarbons (PAHs) and Related Aromatic Hydrocarbons Lists of Chemicals and Data Compilations Summary Tables and QSPR plots References VOLUME II * Halogenated Aliphatic Hydrocarbons Chlorobenzenes and Other Halogenated Mononuclear Aromatics Polychlorinated Biphenyls (PCBs) Chlorinated Dibenzop-dioxins Chlorinated Dibenzofurans VOLUME III * Ethers Alcohols Aldehydes and Ketones Carboxylic Acids Phenolic Compounds Esters VOLUME IV Nitrogen and Sulfur Compounds Lists of Chemicals and Data Compilations Summary Tables References Herbicides Lists of Chemicals and Data Compilations Summary Tables References Insecticides Lists of Chemicals and Data Compilations Summary Tables References Fungicides Lists of Chemicals and Data Compilations Summary Tables References APPENDICES List of Symbols and Abbreviations Alphabetical Index CAS Registry Index Molecular Formula Index * Each chapter contains lists of chemicals and data compilations, summary tables, QSPR plots, and references

Handbook of Physical-Chemical Properties and Environmental Fate for Organic Chemicals

The diffusion characteristics of several substrates of varying molecular sizes into and from Ca-alginate gel beads in well-stirred solutions were investigated. The values of the diffusion coefficient (D) of substrates such as glucose, L-tryptophan, and alpha-lactoalbumin [with molecular weight (MW) less than 2 x 10(4)] into and from the gel beads agreed with those in the water system. Their substrates could diffuse freely into and from the gel beads without disturbance by the pores in the gel beads. The diffusion of their substrates into and from the gel beads was also not disturbed by increasing the Ca-alginate concentration in the beads and the CaCl(2) concentration used in the gel preparation. In the case of higher molecular weight substances such as albumin (MW = 6.9 x 10(4)), gamma-globulin (MW = 1.54 x 10(5)) and fibrinogen (MW = 3.41 x 10(5)), the diffusion behaviors of the substrates into and from the gel beads were very different. No diffusion of their substrates into the gel beads from solutions was observed, and only albumin was partly absorbed on the surface of the gel beads. The values of D of their substrates from the gel beads into their solutions were smaller than their values in the water system, but all their substrates could diffuse from the gel beads. The diffusion of high molecular weight substrates was limited more strongly by the increase of Ca-alginate concentration in the gel beads than by the increase of the CaCl(2) concentration used in the gel preparation. Using these results, the capacity of Ca-alginate gel as a matrix of immobilization was discussed.

Diffusion characteristics of substrates in Ca-alginate gel beads.

In a preceding project, functional forms for “short” Helmholtz energy equations of state for typical nonpolar and weakly polar fluids and for typical polar fluids were developed using simultaneous optimization. In this work, the coefficients of these short forms for the equations of state have been fitted for the fluids acetone, carbon monoxide, carbonyl sulfide, decane, hydrogen sulfide, 2-methylbutane (isopentane), 2,2-dimethylpropane (neopentane), 2-methylpentane (isohexane), krypton, nitrous oxide, nonane, sulfur dioxide, toluene, xenon, hexafluoroethane (R-116), 1,1-dichloro-1-fluoroethane (R-141b), 1-chloro-1,1-difluoroethane (R-142b), octafluoropropane (R-218), 1,1,1,3,3-pentafluoropropane (R-245fa), and fluoromethane (R-41). The 12 coefficients of the equations of state were fitted to substance specific data sets. The results show that simultaneously optimized functional forms can be applied to other fluids out of the same class of fluids for which they were optimized without significant loss of a...

Short Fundamental Equations of State for 20 Industrial Fluids

Low-temperature Thermal Data for the Nine Normal Paraffin Hydrocarbons from Octane to Hexadecane

From determinations of the low temperature thermal properties and vapor pressure of cycloheptane, cyclooctane and 1,3,5-cycloheptatriene, values of the entropy in the liquid and vapor states and the heat of vaporization, all at 298.16/sup 0/K, were obtained. These results and values of the heats of formation derivable from literature data were used to compute values of ..delta..Hf/sup 0/, ..delta..Ff/sup 0/, ..delta..Sf/sup 0/ and log/sub 10/ Kf for all three compounds in the liquid and vapor states at 298.16/sup 0/K. In the solid state the thermal behavior of each substance is complex; there are transitions between four different crystalline forms of cycloheptane, three of cyclooctane and two of 1,3,5-cycloheptatriene.

Cycloheptane, Cycloöctane and 1,3,5-Cycloheptatriene. Low Temperature Thermal Properties, Vapor Pressure and Derived Chemical Thermodynamic Properties

The heat capacity of 2,3-dithiabutane has been measured over the temperature range 13 to 350/sup 0/K The triple point (188.44/sup 0/K) and heat of fusion (2197.1 = 0.1 cal./mole) were determined. The vapor pressure has been measured over the temperature range 0 to 130/sup 0/ and the following equation was found to fit the vapor pressure data: log/sub 10/ p (mm.) = 6.97792 - 1346.342/(l + 218.863). The normal boiling point is 109.75/sup 0/; the heat of vaporization calculated from the vapor pressure data is 9,181 = 75 cal./mole at 298.16/sup 0/K. The entropy of the liquid is 56.26 = 0.10 cal./deg./mole and the entropy of the ideal gas at one atmosphere pressure is 80.54 = 0.30 cal./deg./mole, both at 298.16/sup 0/K. A vibrational assignment has been made for 2,3-dithiabutane with the aid of normal coordinate calculations. Internal rotation about the S--S bond is highly restricted; a 9500 cal./mole twofold potential barrier was used for thermodynamic calculations. The barrier height for methyl rotation was found to be 1140 cal./mole. Values of the free energy function, heat content, entropy, and heat capacity were calculated by the methods of statistical mechanics for selected temperatures up to 1000/sup 0/K.

2,3-Dithiabutane: Low Temperature Heat Capacity, Heat of Fusion, Heat of Vaporization, Vapor Pressure, Entropy and Thermodynamic Functions1,2

Detailed studies were made of the thermodynamic properties of thiacyclobutane. The properties determined experimentally included: heat capacity of the solid and the liquid between 12 and 321/sup 0/K, transition temperature (176.7/sup 0/K), heat of transition (159.8 cal. mole/sup -1/), triple point (199.91/sup 0/K), heat of fusion (1971 cal. mole/sup -1/), vapor pressure between 48 and 132/sup 0/ (log/sub 10/ p = 701667--1321.331/(t + 224.513) (p in mm. and t in /sup 0/C)), heat of vaporization (8234 cal. mole/sup -1/ at 327.53/sup 0/K), heat capacity of the vapor (C/sup 0//sub p/ = 20.7 cal. deg./sup -1/ mole/sup -1/ at 377.20/sup 0/K.), entropy of the liquid (44.72 and 47.32 cal. deg./sup -1/ mole/sup -1/ at 298.16 and 327.53/sup 0/K., respectively), entropy of the vapor (S/sup 0/ = 68.17 and 69.75 cal. deg./sup -1/ mole/sup -1/ at 298.16 and 327.53/sup 0/K., respectively) and heat of formation (for the reaction: 3C(graphite) + 3H/sub 2/(g) + S(rhombic) = C/sub 9/H/sub 6/S(1), ..delta..H/sup 0//sub 298.16/ = 6.20 kcal. mole/sup -1/). The functions -(F/sup 0/ - H/sup 0//sub 0/)/T, (H/sup 0/- H/sup 0//sub 0/)/T, H/sup 0/ - H/sup 0//sub 0/, S/sup 0/ and C/sup 0//sub p/ were computed by the methods of statistical mechanics for selected temperaturesmore » up to 1000/sup 0/K. Values of the standard heat, standard free energy and common logarithm of the equilibrium constant of formation were obtained for the same temperatures. Spectroscopic and calorimetric data were shown to favor a planar-ring structure of C/sub 2//sub v/ symmetry for the thiacyclobutane molecule.« less

H. L. Finke

Papers

Low-temperature Thermal Data for the Nine Normal Paraffin Hydrocarbons from Octane to Hexadecane

Cycloheptane, Cycloöctane and 1,3,5-Cycloheptatriene. Low Temperature Thermal Properties, Vapor Pressure and Derived Chemical Thermodynamic Properties

2,3-Dithiabutane: Low Temperature Heat Capacity, Heat of Fusion, Heat of Vaporization, Vapor Pressure, Entropy and Thermodynamic Functions1,2

Thiacyclobutane: Heat Capacity, Heats of Transition, Fusion and Vaporization, Vapor Pressure, Entropy, Heat of Formation and Thermodynamic Functions1

3,4-Dithiahexane: Heat Capacity, Heats of Fusion and Vaporization, Vapor Pressure, Entropy, and Thermodynamic Functions1