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.

Electron spin resonance methods have been used to observe alkyl radicals in liquid hydrocarbon systems during irradiation with 2.8‐MeV electrons. These investigations provide detailed structural, radiation chemical, and kinetic information about a large number of radicals.In general, in these studies the ESR lines are found to be narrow; considerable fine structure is observable, permitting positive assignment of the radical species. Accurate hyperfine constants are reported for 21 alkyl and cycloalkyl radicals (including several deuterated species), vinyl, 1‐methylvinyl, 3‐butenyl, allyl, and cyclohexadienyl radicals, and hydrogen and deuterium atoms. Except for cyclopropyl radical, all the alkyl and cycloalkyl radicals have α coupling constants in the range 21–23 G. The β coupling constants in cases where they have been rotationally averaged isotropically are found to decrease with increasing substitution of alkyl groups on the α carbon atom. In general the values for primary, secondary, and tertiary ra...

Electron spin resonance studies of transient alkyl radicals

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

A New Method for Extrapolating Specific Heat Curves of Organic Compounds below the Temperatures of Liquid Air

The heat capacity of spiropentane in the solid and liquid states was measured over the temperature range 12 to 298/sup 0/K. The melting point (166.14 +- 0.05/sup 0/K) and heat of fusion (1538 cal./mole) were determined. The heat of vaporization was measured at three temperatures, and the values found were 6753, 6572 and 6393 cal./mole, at 10.00, 25.00 and 38.98/sup 0/, respectively. The heat capacity of the vapor was measured at five different temperatures in the range 318 to 487/sup 0/K. The experimental values of C/sub p/, the heat capacity in the ideal gas state, may be represented by the equation: C/sup 0//sub p/ = -7.078 + 0.10850T - 4.799 x 10/sup -5/T/sup 2/. The vapor pressure was measured over the temperature range from 3 to 71/sup 0/, and the following equation was found to fit the vapor-pressure data: log/sub 10/p = 6.91794 - 1090.589/(t + 231.165). An equation for the second virial coefficient, B, in the equation of state PV = RT + BP was obtained from thermal data. This equation is B(cc.) = -57 - 136.7 exp(650/T). The entropy of liquid spiropentane is 46.29 = 0.10 cal./deg./mole, and the entropy of the vapor in the ideal gas statemore » at one atmosphere pressure is 67.45 = 0.15 cal./deg./mole, both at 298.16/sup 0/K. A vibrational assignment was made for spiropentane with the aid of detailed normal coordinate calculations. Using this vibrational assignment and other molecular structure data, values of the functions (H/sub 0//sup 0/ - F/sup 0//sub T/)/T H/sup 0//sub T/ - H/sub 0//sup 0/, S/sup 0/ and Cp/sup 0/ were computed for selected temperatures up to 1500/sup 0/K.« less

Hugh M. Huffman

Papers

A New Method for Extrapolating Specific Heat Curves of Organic Compounds below the Temperatures of Liquid Air

Hydrazine: Heat Capacity, Heats of Fusion and Vaporization, Vapor Pressure, Entropy and Thermodynamic Functions

Thermal Data on Organic Compounds. XI. The Heat Capacities, Entropies and Free Energies of Ten Compounds Containing Oxygen or Nitrogen

The Heat Capacities, Heats of Transition, Heats of Fusion and Entropies of Cyclopentane, Methylcyclopentane and Methylcyclohexane1

Low Temperature Thermal Data on Eight C8H16 Alkylcyclohexanes