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.

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

Ammonia and related chemicals as potential indirect hydrogen storage materials

The heat-of-transition rule, heat-of-fusion rule, infrared rule and density rule, which concern the relative stability of polymorphic molecular crystals, have been checked experimentally. Among the 228 transitions examined, there are only few exceptions, and these mainly concern the infrared and density rules. The heat-of-transition and heat-of-fusion rules, however, give the right result in more than 99% of cases. If certain restrictions are observed, the other rules are also fairly reliable. By their means the stability relations in polymorphic systems can easily be clarified. Data are given for 113 polymorphic substances.

On the polymorphism of pharmaceuticals and other molecular crystals. II

The Heat Capacity, Heat of Fusion and Entropy of Benzene1

Thermodynamic Properties of Thiophene

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

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

Low Temperature Thermal Data on Eight C8H16 Alkylcyclohexanes

The heat capacity of solid 2,2,3,3-tetramethylbutane was studied between 12/sup 0/K, and the melting point, 373.97 +- 0.05/sup 0/K. The transition temperature (152.5 +- 0.2/sup 0/K), heat of transition (478 cal./mole/sup -1/), and heat of fusion (1802 cal./mole/sup -0/) were determined. The entropy of the solid at 298.16/sup 0/K was found to be 65.43 +- 0.15 cal./deg/sup -1//mole/sup -1/. The vapor pressure was measured from 0 to 65/sup 0/ and the following equation was selected to represent the data: log/sub 10/p = 7.92864 - 1709.428/(t + 233.634). The heat of sublimation calculated from the vapor pressure data is 10.365 +- 50 cal./mole/sup -1/. The standard entropy of the vapor at 298.16/sup 0/K was found to be 93.05 +- 0.30 cal./deg/sup -1//mole/sup -1/. By utilizing the results of relatively detailed normal coordinate calculations as a guide in interpreting the spectra, a vibrational assignment adequate for purposes of thermodynamic computations was obtained. The average height of the potential barriers hindering internal rotation that is required to give agreement with the observed value of the entropy is 4700 cal./mole/sup -1/. Using this value of the average barrier height, the vibrational assignment, and other pertinent molecular-structure data, the thermodynamic functions -(F/sup 0/ - H/supmore » 0//sub 0/)/T, H/sup 0/ - H/sub 0//sup 0/, S/sup 0/, and C/sup 0//sub p/ for 2,2,3,3-tetramethylbutane were computed for selected temperatures up to 1500/sup 0/K.« less

George D. Oliver

Papers

The Heat Capacity, Heat of Fusion and Entropy of Benzene1

Thermodynamic Properties of Thiophene

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

Low Temperature Thermal Data on Eight C8H16 Alkylcyclohexanes

2,2,3,3-tetramethylbutane: heat capacity, heats of transition, fusion, and sublimation, vapor pressure, entropy, and thermodynamic functions