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

https://www.umsl.edu/~chickosj/JSCPUBS/dsccal.pdf

Reference materials for calorimetry and differential thermal analysis

The thermal conductivities of H2O and D2O vapors were measured in a modified thick hot wire cell between 358 and 386 K at pressures ranging from 100 to 1000 Torr. Analysis of the data indicates that molecular association to form a dimeric species is the main source of enhancement of the thermal conductivity of both vapors. The enthalpy and entropy of association of the H2O dimer are −3.59 kcal mol−1 and −18.59 cal deg−1 mol−1, respectively. The enthalpy and entropy of association of the D2O dimer are −3.66 kcal mol−1 and −18.67 cal deg−1 mol−1, respectively. The measured enthalpy of association of the H2O dimer is in agreement with recently reported ab initio molecular orbital calculations on the H2O dimer. The entropies of association of the H2O and D2O dimers are calculated theoretically and are found to be in agreement with the measured values.

Studies of molecular association in H2O and D2O vapors by measurement of thermal conductivity

A sample of furan was purified and used for calorimetric studies and for measurement of vapor pressure, density, refractive index, infrared spectrum (2 to 15..mu..) and mass spectrum. The heat of formation of liquid furan (-..delta..H/sub t/ = 14.90 kcal mole/sup -1/) was derived from heat of combustion measurements. Low temperature thermal studies included measurement of the heat capacity of the solid, transition temperature (150.0/sup 0/K), heat of transition (489.2 cal. mole/sup -1/), triple point (187.55/sup 0/K), heat of fusion (908.8 cal. mole/sup -1/) and heat capacity of the liquid. The entropy of the liquid at 298.16/sup 0/K, calculated from these data is 42.22 cal. deg./sup -1/ mole/sup -1/. The observed vapor pressures between 2 and 62/sup 0/ are represented by the equation log/sub 10/p (mm) = 6.97523 - 1060.851 (t + 227.740). The heat of vaporization at the normal boiling point (31.36/sup 0/) is 6474 cal. mole/sup -1/. The vapor heat capacity, measured at five temperatures between 317 and 488/sup 0/K, is given by the equation C/sup 0/psub p/ = -7.55 + 9.352 x 9.352 x 10/sup -2/T - 5.287 x 10/sup -6/ T/sup 2/ cal. deg./sup -1/ mole/sup -1/. The equation B = -279 - 22.6 exp(950/T) ccmore » mole/sup -1/ was derived for the second virial coefficient from calorimetric data. A vibrational assignment which was partly empirical was made and used with molecular structure data to compute thermodynamic functions of the ideal gas to 1500/sup 0/K. The heat, free energy and equilibrium constant of formation at temperatures to 1500/sup 0/ were calculated using appropriate calorimetric data and thermodynamic functions.« less

Thermodynamic Properties of Furan

Thermodynamic Properties of Thiophene

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

Guy Waddington

Papers

Thermodynamic Properties of Furan

Thermodynamic Properties of Thiophene

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

Thiophene: Heat of Combustion and Chemical Thermodynamic Properties1

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