Molecular dynamics simulations of the melting of 1,3,3-trinitroazetidine

Physical properties of condensed-phase 1,3,3-trinitroazetidine (TNAZ) have been computed with molecular dynamics (MD) and a nonreactive, fully flexible force field formulated by combining the intramolecular interactions obtained from the Generalized AMBER Force Field and the rigid-molecule force field developed by Sorescu-Rice-Thompson [J. Phys. Chem. B 1997, 101, 798] (AMBER-SRT). The results are compared with MD calculations, using the AMBER force field. The predicted densities of crystalline TNAZ from both force fields are about 10% lower than the experimental value. The calculated thermodynamic melting point at 1 atm from the AMBER-SRT force field is 390 K, in good agreement with the measured value of 374 K, while the AMBER force field predicts a thermodynamic melting point of 462 K. The lattice parameters and the molecular and crystal structures calculated with the AMBER-SRT force field are in excellent agreement with experiment. Simulations with the AMBER-SRT force field were also used to generate the isotherm of TNAZ up to 4 GPa and the bulk modulus and its pressure derivative.     

Molecular dynamics simulations of hexahydro-1,3,5-trinitro-1,3,5-s-triazine (RDX) using a combined Sorescu-Rice-Thompson AMBER force field

We present the results of molecular dynamics simulations of crystalline hexahydro-1,3,5-trinitro-1,3,5-s-triazine (RDX) using the SRT-AMBER force field (P. M. Agrawal et al., J. Phys. Chem. B 2006, 110, 5721), which combines the rigid-molecule force field developed by Sorescu-Rice-Thompson (D. C. Sorescu, B. M. Rice, and D. L. Thompson, J. Phys. Chem. B 1997, 101, 798) with the intramolecular interactions obtained from the Generalized AMBER Force Field (Wang et al., J. Comput. Chem. 2004, 25, 1157). The calculated crystal density at room conditions is about 10% lower than the measured value, while the lattice parameters and thermodynamic melting point are within about 5% at ambient pressure. The chair and inverted chair conformation, bond lengths, and bond angles of the RDX molecule are accurately predicted; however, there are some inaccuracies in the calculated orientations of the NO2 groups. The SRT-AMBER force field predicts overall reasonable results, but modifications, probably in the torsional parameters, are needed for a more accurate force field.     

Molecular dynamics simulations of the thermal conductivity of methane hydrate

Nonequilibrium molecular dynamics simulations with the nonpolarizable SPC/E (Berendsen et al., J. Phys. Chem. 1987, 91, 6269) and the polarizable COS/G2 (Yu and van Gunsteren, J. Chem. Phys. 2004, 121, 9549) force fields have been employed to calculate the thermal conductivity and other associated properties of methane hydrate over a temperature range from 30 to 260 K. The calculated results are compared to experimental data over this same range. The values of the thermal conductivity calculated with the COS/G2 model are closer to the experimental values than are those calculated with the nonpolarizable SPC/E model. The calculations match the temperature trend in the experimental data at temperatures below 50 K; however, they exhibit a slight decrease in thermal conductivity at higher temperatures in comparison to an opposite trend in the experimental data. The calculated thermal conductivity values are found to be relatively insensitive to the occupancy of the cages except at low (T相似文献   

Simulations of the solid, liquid, and melting of 1-n-butyl-4-amino-1,2,4-triazolium bromide

Molecular dynamics simulations are used to study the solid and liquid properties and to predict the melting point of 1-n-propyl-4-amino-1,2,4-triazolium bromide ([patr][Br]) using a force field based on the one developed by Canongia Lopes et al. (J. Phys. Chem. B 2004, 108, 2038) for dialkyl substituted imidazolium salts, which was modified by including terms from the general AMBER force field. Electrostatic charges for the intermolecular interactions were determined from gas-phase ab initio electron structure calculations of the triazolium cation. Simulations of the solid state at 100 K reproduced the experimental density to within 4%. Simulations from 100 K to the melting point and the liquid from 333 to 500 K were performed to determine the temperature dependence of the densities of the two phases. The structures of the solid and liquid phases are characterized with radial distribution functions, which show that there are strong spatial correlations among neighboring ion pairs in liquid [patr][Br]. The dynamic behavior of the ions in the liquid state is also studied by computing velocity autocorrelation functions and the mean-square displacements between the ions. The melting point is determined by simulating void-induced melting. Changes in the density, intermolecular energy, and Lindemann index are used as indicators of the melting transition. The computed melting point is 360 +/- 10 K, which is within 10% of the experimental value 333 K.     

Molecular dynamics simulations of surface-initiated melting of nitromethane

The melting of nitromethane initiated at solid-vacuum interfaces has been investigated using molecular dynamics nvt simulations with a realistic force field [D. C. Sorescu et al., J. Phys. Chem. B 104, 8406 (2000)]. The calculated melting point (251+/-5 K) is in good agreement with experiment (244.73 K) and values obtained previously (approximately 255.5 and 266.5+/-8 K) using other simulation methods [P. M. Agrawal et al., J. Chem. Phys. 119, 9617 (2003)]. Analyses of the molecular orientations and diffusion during the simulations as functions of the distance from the exposed surfaces show that the melting is a direct crystal-to-liquid transition, in which the molecules first gain rotational freedom, then mobility. There is a slight dependence of the melting temperature on the exposed crystallographic face.     

Molecular dynamics simulations of melting and the glass transition of nitromethane

Molecular dynamics simulations have been used to investigate the thermodynamic melting point of the crystalline nitromethane, the melting mechanism of superheated crystalline nitromethane, and the physical properties of crystalline and glassy nitromethane. The maximum superheating and glass transition temperatures of nitromethane are calculated to be 316 and 160 K, respectively, for heating and cooling rates of 8.9 x 10(9) Ks. Using the hysteresis method [Luo et al., J. Chem. Phys. 120, 11640 (2004)] and by taking the glass transition temperature as the supercooling temperature, we calculate a value of 251.1 K for the thermodynamic melting point, which is in excellent agreement with the two-phase result [Agrawal et al., J. Chem. Phys. 119, 9617 (2003)] of 255.5 K and measured value of 244.73 K. In the melting process, the nitromethane molecules begin to rotate about their lattice positions in the crystal, followed by translational freedom of the molecules. A nucleation mechanism for the melting is illustrated by the distribution of the local translational order parameter. The critical values of the Lindemann index for the C and N atoms immediately prior to melting (the Lindemann criterion) are found to be around 0.155 at 1 atm. The intramolecular motions and molecular structure of nitromethane undergo no abrupt changes upon melting, indicating that the intramolecular degrees of freedom have little effect on the melting. The thermal expansion coefficient and bulk modulus are predicted to be about two or three times larger in crystalline nitromethane than in glassy nitromethane. The vibrational density of states is almost identical in both phases.     

Melting temperature of ice Ih calculated from coexisting solid-liquid phases

We carried out molecular-dynamics simulations by using the two-phase coexistence method with the constant pressure, particle number, and enthalpy ensemble to compute the melting temperature of proton-disordered hexagonal ice I(h) at 1-bar pressure. Four models of water were considered, including the widely used TIP4P [W. L. Jorgensen, J. Chandrasekha, J. D. Madura, R. W. Impey, and M. L. Klein, J. Chem. Phys.79, 926 (1983)] and TIP5P [M. W. Mahoney and W. L. Jorgensen J. Chem. Phys.112, 8910 (2000)] models, as well as recently improved TIP4P and TIP5P models for use with Ewald techniques-the TIP4P-Ew [W. Horn, W. C. Swope, J. W. Pitera, J. C. Madura, T. J. Dick, G. L. Hura, and T. Head-Gordon, J. Chem. Phys.120, 9665 (2004)] and TIP5P-Ew [S. W. Rick, J. Chem. Phys.120, 6085 (2004)] models. The calculated melting temperature at 1 bar is T(m) = 229 +/- 1 K for the TIP4P and T(m) = 272.0 +/- 0.6 K for the TIP5P ice I(h), both are consistent with previous simulations based on free-energy methods. For the TIP4P-Ew and TIP5P-Ew models, the calculated melting temperature is T(m) = 257.0 +/- 1.1 K and T(m) = 253.9 +/- 1.1 K, respectively.     

Molecular dynamics simulations of melting of perfect crystalline hexahydro-1,3,5-trinitro-1,3,5-s-triazine

The melting mechanism of superheated perfect crystalline hexahydro-1,3,5-trinitro-1,3,5-s-triazine (alpha-RDX) has been investigated using molecular dynamics simulations with the fully flexible force field developed by Smith and Bharadwaj [J. Phys. Chem. B 103, 3570 (1999)]. Sequential 50 ps equilibration simulations of the constant stress-constant temperature ensemble were performed at 10 K intervals over the range of 300-650 K, corresponding to a heating rate of 2.0 x 10(11) Ks. A solid-solid phase transition is observed between 480 and 490 K, followed by melting, which occurs between 500 and 510 K. The solid-solid phase transition, both displacive and rotational, is characterized by an abrupt decrease in the lengths of the unit cell edges a and b and an increase of the length of edge c. The molecular conformation in the new phase is AAE, although the axial nitro groups have different changes: one shift is more axial and the other is more equatorial. Phases other than alpha-RDX have been observed experimentally, however, there are insufficient data for comparisons to ascertain that the new phase observed here corresponds to a real phase. At the high heating rate (2.0 x 10(11) Ks) used in the simulations, the melted RDX reaches full orientational disorder at about 540 K and translational freedom at around 580 K. If the simulation at the melting temperature (510 K) is run sufficiently long complete rotational freedom is achieved in a few hundreds of picoseconds, while complete translational freedom requires much longer. These results show that given a sufficiently high heating rate, the system can exist for significant periods of time in a near-liquid state in which the molecules are not as free to rotate and diffuse as in the true liquid state. The bond lengths and bond angles undergo little change upon melting, while there are significant changes in the dihedral angles. The molecular conformation of RDX changes from AAE to EEE upon melting. The ramification of this for formulating force fields that accurately describe melting is that it is important that the torsional motions are accurately described.     

Melting points and thermal expansivities of proton-disordered hexagonal ice with several model potentials

A method of free energy calculation is proposed, which enables to cover a wide range of pressure and temperature. The free energies of proton-disordered hexagonal ice (ice Ih) and liquid water are calculated for the TIP4P [J. Chem. Phys. 79, 926 (1983)] model and the TIP5P [J. Chem. Phys. 112, 8910 (2000)] model. From the calculated free energy curves, we determine the melting point of the proton-disordered hexagonal ice at 0.1 MPa (atmospheric pressure), 50 MPa, 100 MPa, and 200 MPa. The melting temperatures at atmospheric pressure for the TIP4P ice and the TIP5P ice are found to be about T(m)=229 K and T(m)=268 K, respectively. The melting temperatures decrease as the pressure is increased, a feature consistent with the pressure dependence of the melting point for realistic proton-disordered hexagonal ice. We also calculate the thermal expansivity of the model ices. Negative thermal expansivity is observed at the low temperature region for the TIP4P ice, but not for the TIP5P ice at the ambient pressure.     

Effects of pressure and temperature on the carrier transports in organic crystal: a first-principles study

By employing density-functional theory coupled with Holstein-Peierls model, we investigate the pressure and temperature dependence of the hole and electron mobilities in naphthalene single crystal from atmospheric pressure up to 2.1 GPa (at room temperature) and from 5 to 296 K (at ambient pressure). It is found that the pressure reduces the electron-phonon coupling strength and enhances the mobilities. Importantly, we point out that only when temperature-dependent structure modifications are taken into account can one better describe the temperature-dependent transport behavior. Especially, the band to hopping crossover transition temperature for the electron transport in the c'-axis is calculated to be around 153 K, which is close to the experimental result of between 100 and 150 K. If this temperature-dependent structure modifications were neglected, the transition temperature would be only about 23 K, as previously obtained [L. J. Wang et al., J. Chem. Phys. 127, 044506 (2007)].     

Simulation of the thermodynamics of folding and unfolding of the Trp-cage mini-protein TC5b using different combinations of force fields and solvation models

Molecular dynamics simulations based on AMBER force fields(ff96 and ff03) and generalized Born models(igb1 and igb5) have been carried out in order to study folding/unfolding of the Trp-cage mini-protein TC5b.The thermodynamic properties of TC5b were found to be sensitive to the specific version of the solvation model and force field employed.When the ff96/igb5 combination was used,the predicted melting temperature from unfolding simulations was in good agreement with the experimental value of 315 K,but the...     

Terahertz spectrum and normal-mode relaxation in pentaerythritol tetranitrate: effect of changes in bond-stretching force-field terms

Terahertz (THz) active normal-mode relaxation in crystalline pentaerythritol tetranitrate (PETN) was studied using classical molecular dynamics simulations for energy and density conditions corresponding to room temperature and atmospheric pressure. Two modifications to the fully flexible non-reactive force field due to Borodin et al. [J. Phys. Chem. B 112, 734 (2008)] used in a previous study of THz-active normal-mode relaxation in PETN [J. Chem. Phys. 134, 014513 (2011)] were considered to assess the sensitivity of the earlier predictions to details of the covalent bond-stretching terms in the force field. In the first modification the harmonic bond-stretching potential was replaced with the Morse potential to study the effect of bond anharmonicity on the THz-region mode relaxation. In the second modification the C-H and nitro-group N-O bond lengths were constrained to constant values to mimic lower quantum occupation numbers for those high-frequency modes. The results for relaxation times of the initially excited modes were found to be insensitive to either force-field modification. Overall time scales for energy transfer to other modes in the system were essentially unaffected by the force-field modifications, whereas the detailed pathways by which the energy transfer occurs are more complicated for the Morse potential than for the harmonic-bond and fixed-bond cases. Terahertz infrared absorption spectra constructed using calculated normal-mode frequencies, transition dipoles, and relaxation times for THz-active modes were compared to the spectra obtained from the Fourier transform of the dipole-dipole time autocorrelation function (DDACF). Results from the two approaches are in near agreement with each other and with experimental results in terms of main peak positions. Both theoretical methods yield narrower peaks than observed experimentally and in addition predict a weaker peak at ω ～ 50 cm(-1) that is weak or absent experimentally. Peaks obtained using the DDACF approach are broader than those obtained from the normal-mode relaxation method.     

Assessment of standard force field models against high‐quality ab initio potential curves for prototypes of π–π, CH/π, and SH/π interactions

Several popular force fields, namely, CHARMM, AMBER, OPLS‐AA, and MM3, have been tested for their ability to reproduce highly accurate quantum mechanical potential energy curves for noncovalent interactions in the benzene dimer, the benzene‐CH₄ complex, and the benzene‐H₂S complex. All of the force fields are semi‐quantitatively correct, but none of them is consistently reliable quantitatively. Re‐optimization of Lennard‐Jones parameters and symmetry‐adapted perturbation theory analysis for the benzene dimer suggests that better agreement cannot be expected unless more flexible functional forms (particularly for the electrostatic contributions) are employed for the empirical force fields. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

Molecular dynamics studies of melting and some liquid-state properties of 1-ethyl-3-methylimidazolium hexafluorophosphate [emim][PF6

Molecular dynamics simulations are used to study the liquid-state properties and melting of 1-ethyl-3-methylimidazolium hexafluorosphosphate [emim][PF6] using the force field of Canongia Lopes et al. [J. Phys. Chem. B 108, 2038 (2004)] and geometric constants from crystallographic data. The structures of the solid and liquid states are characterized by carbon-carbon, carbon-phosphorous, and phosphorous-phosphorous radial distribution functions. Spatial correlations among the ions are strong in the liquid state. The cohesive energy density and the temperature dependences of the molar volume and density of the liquid have been computed. The melting point is determined by equilibrating the solid-state supercells in which void defects have been introduced to eliminate the free-energy barrier for the formation of a solid-liquid interface. The computed melting point is 375+/-10 K, which is approximately 10% higher than the experimental value of 333 K.     

Assessment of biomolecular force fields for molecular dynamics simulations in a protein crystal

Different biomolecular force fields (OPLS‐AA, AMBER03, and GROMOS96) in conjunction with SPC, SPC/E and TIP3P water models are assessed for molecular dynamics simulations in a tetragonal lysozyme crystal. The root mean square deviations for the C_a atoms of lysozymes are about 0.1 to 0.2 nm from OPLS‐AA and AMBER03, smaller than 0.4 nm from GROMOS96. All force fields exhibit similar pattern in B‐factors, whereas OPLS‐AA and AMBER03 accurately reproduce experimental measurements. Despite slight variations, the primary secondary structures are well conserved using different force fields. Water diffusion in the crystal is approximately ten‐fold slower than in bulk phase. The directional and average water diffusivities from OPLS‐AA and AMBER03 along with SPC/E model match fairly well with experimental data. Compared to GROMOS96, OPLS‐AA and AMBER03 predict larger hydrophilic solvent‐accessible surface area of lysozyme, more hydrogen bonds between lysozyme and water, and higher percentage of water in hydration shell. SPC, SPC/E and TIP3P water models have similar performance in most energetic and structural properties, but SPC/E outperforms in water diffusion. While all force fields overestimate the mobility and electrical conductivity of NaCl, a combination of OPLS‐AA for lysozyme and the Kirkwood‐Buff model for ions is superior to others. As attributed to the steric restraints and surface interactions, the mobility and conductivity in the crystal are reduced by one to two orders of magnitude from aqueous solution. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Vibronic coupling in asymmetric bichromophores: Theory and application to diphenylmethane

The theory for modeling vibronic interactions in bichromophores was introduced in sixties by Witkowski and Moffitt [J. Chem. Phys. 33, 872 (1960)] and extended by Fulton and Gouterman [J. Chem. Phys. 35, 1059 (1961)]. The present work describes extension of this vibronic model to describe bichromophores with broken vibrational symmetry such as partly deuterated molecules. Additionally, the model is extended to include inter-chromophore vibrational modes. The model can treat multiple vibrational modes by employing Lanczos diagonalization procedure of sparse matrices. The developed vibronic model is applied to simulation of vibronic spectra of flexible bichromophore diphenylmethane and compared to high-resolution experimental spectra [J. A. Stearns, N. R. Pillsbury, K. O. Douglass, C. W. Mu?ller, T. S. Zwier, and D. F. Plusquellic, J. Chem. Phys. 129, 224305 (2008)].     

Molecular dynamics studies of melting and solid-state transitions of ammonium nitrate

Molecular dynamics simulations are used to calculate the melting point and some aspects of high-temperature solid-state phase transitions of ammonium nitrate (AN). The force field used in the simulations is that developed by Sorescu and Thompson [J. Phys. Chem. A 105, 720 (2001)] to describe the solid-state properties of the low-temperature phase-V AN. Simulations at various temperatures were performed with this force field for a 4 x 4 x 5 supercell of phase-II AN. The melting point of AN was determined from calculations on this supercell with voids introduced in the solid structure to eliminate superheating effects. The melting temperature was determined by calculating the density and the nitrogen-nitrogen radial distribution functions as functions of temperature. The melting point was predicted to be in the range 445 +/- 10 K, in excellent agreement with the experimental value of 442 K. The computed temperature dependences of the density, diffusion, and viscosity coefficient for the liquid are in good agreement with experiment. Structural changes in the perfect crystal at various temperatures were also investigated. The ammonium ions in the phase-II structure are rotationally disordered at 400 K. At higher temperatures, beginning at 530 K, the nitrate ions are essentially rotationally unhindered. The density and radial distribution functions in this temperature range show that the AN solid is superheated. The rotational disorder is qualitatively similar to that observed in the experimental phase-II to phase-I solid-state transition.     

Reparameterizations of the χ Torsion and Lennard‐Jones σ Parameters Improve the Conformational Characteristics of Modified Uridines

The currently available force field parameters for modified RNA residues in AMBER show significant deviations in conformational properties from experimental observations. The examination of the transferability of the recently revised torsion parameters revealed that there was an overall improvement in the conformational properties for some of the modifications but the improvements were still insufficient in describing the sugar pucker preferences (J. Chem. Inf. Model. 2014, 54, 1129–1142). Here, we report an approach for the development and fine tuning of the AMBER force field parameters for 2‐thiouridine, 4‐thiouridine, and pseudouridine with diverse conformational preferences. The χ torsion parameters were reparameterized at the individual nucleoside level. The effect of combining the revised γ torsion parameter and modifying the Lennard‐Jones σ parameters were also tested by directly comparing the conformational preferences obtained from our extensive molecular dynamics simulations with those from experimental observations. © 2016 Wiley Periodicals, Inc.     

Temperature dependence of the mean autodetachment lifetime of the p-benzoquinone molecular radical anion

Experimental data previously published from this laboratory (Asfandiarov NL, Pshenichnyuk SA, Fokin AI, Nafikova EP. Chem. Phys. 2004; 298: 263), on the temperature dependence of the mean autodetachment lifetime of the p-benzoquinone molecular radical anion, were analyzed in the framework of a simple statistical model. This model is a simplification of the well-known semiempirical approach elaborated by Christophorou et al. (Christophorou LG, Hadjiantoniou A, Carter JG. J. Chem. Soc., Faraday Trans. II 1973; 69: 1722). Evaluation of the vibrational energy storage of the target molecule and anion was made in a quantum approximation following a published procedure (Matejcik S, M?rk TD, Spanel P, Smith D, Jaffke T, Illenberger E. J. Chem. Phys. 1994; 102: 2516). The results obtained are in reasonable agreement with the experimental data.     

Hydration thermodynamic properties of amino acid analogues: a systematic comparison of biomolecular force fields and water models

We present an extensive study on hydration thermodynamic properties of analogues of 13 amino acid side chains at 298 K and 1 atm. The hydration free energies DeltaG, entropies DeltaS, enthalpies DeltaH, and heat capacities Deltac(P)() were determined for 10 combinations of force fields and water models. The statistical sampling was extended such that precisions of 0.3, 0.8, 0.8 kJ/mol and 25 J/(mol K) were reached for DeltaG, TDeltaS, DeltaH, and Deltac(P)(), respectively. The three force fields used in this study are AMBER99, GROMOS 53A6, and OPLS-AA; the five water models are SPC, SPC/E, TIP3P, TIP4P, and TIP4P-Ew. We found that the choice of water model strongly influences the accuracy of the calculated hydration entropies, enthalpies, and heat capacities, while differences in accuracy between the force fields are small. On the basis of an analysis of the hydrophobic analogues of the amino acid side chains, we discuss what properties of the water models are responsible for the observed discrepancies between computed and experimental values. The SPC/E water model performs best with all three biomolecular force fields.