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

SummaryOn the basis of statistical mechanics, it is shown that the following rules concerning the relative stability of different polymorphic modifications are usually obeyed. (1) The enthalpy of transition of two enantiotropic forms is always positive at temperatures above their transition point, and negative at temperatures below the transition point or between monotropic forms (heat-of-transition rule). (2) Instead of the heat of transition, the difference in the heats of fusion may generally be used (heat-of-fusion rule). (3) If a modification is less dense, it is less stable at absolute zero. (4) For hydrogen-bonded crystals, the modification for which the first absorption band in the infrared spectrum is at higher frequencies has the larger entropy. The possibility of exceptions is discussed.ZusammenfassungMit Argumenten der statistischen Mechanik wird gezeigt, daß im Hinblick auf die relative Stabilität polymorpher Modifikationen von Molekülkristallen im allgemeinen folgende Regeln gelten. 1. Die Umwandlungsenthalpie zweier enantiotroper Formen ist über ihrem Umwandlungspunkt immer positiv, unter dem Umwandlungspunkt oder zwischen monotropen Formen negativ (Umwandlungswärme-Regel). 2. Statt der Umwandlungswärme kann meist auch die Differenz der Schmelzwärmen verwendet werden (Schmelzwärme-Regel). 3. Eine Modifikation von geringerer Dichte weist am absoluten Nullpunkt die geringere Stabilität auf. 4. Bilden zwei Modifikationen Kristalle mit Wasserstoffbrücken, so hat diejenige die größere Entropie, deren erste Bande im IR-Spektrum bei höheren Frequenzen liegt. Auf mögliche Ausnahmen von diesen Regeln wird hingewiesen.

On the polymorphism of pharmaceuticals and other molecular crystals. II@@@ber die Polymorphie von Arzneistoffen und anderen Moleklkristallen. II: Applicability of thermodynamic rules

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

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

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

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

M. E. Gross

Papers

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

Thermodynamic Properties of Furan

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

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