Journal of Physical Chemistry A
American Chemical Society
About: Journal of Physical Chemistry A is an academic journal published by American Chemical Society. The journal publishes majorly in the area(s): Ab initio & Excited state. It has an ISSN identifier of 1089-5639. Over the lifetime, 36636 publications have been published receiving 1173070 citations. The journal is also known as: Stereodynamics of chemical reactions & Dynamics, kinetics, environmental chemistry, spectroscopy, structure, theory.
Papers published on a yearly basis
TL;DR: In this paper, a new implementation of the conductor-like screening solvation model (COSMO) in the GAUSSIAN94 package is presented, which allows Hartree−Fock (HF), density functional (DF) and post-HF energy, and HF and DF gradient calculations: the cavities are modeled on the molecular shape, using recently optimized parameters, and both electrostatic and nonelectrostatic contributions to energies and gradients are considered.
Abstract: A new implementation of the conductor-like screening solvation model (COSMO) in the GAUSSIAN94 package is presented. It allows Hartree−Fock (HF), density functional (DF) and post-HF energy, and HF and DF gradient calculations: the cavities are modeled on the molecular shape, using recently optimized parameters, and both electrostatic and nonelectrostatic contributions to energies and gradients are considered. The calculated solvation energies for 19 neutral molecules in water are found in very good agreement with experimental data; the solvent-induced geometry relaxation is studied for some closed and open shell molecules, at HF and DF levels. The computational times are very satisfying: the self-consistent energy evaluation needs a time 15−30% longer than the corresponding procedure in vacuo, whereas the calculation of energy gradients is only 25% longer than in vacuo for medium size molecules.
TL;DR: In this paper, a force field for large-scale reactive chemical systems (1000s of atoms) is proposed. But the force field does not have Coulomb and Morse potentials to describe nonbond interactions between all atoms.
Abstract: To make practical the molecular dynamics simulation of large scale reactive chemical systems (1000s of atoms), we developed ReaxFF, a force field for reactive systems. ReaxFF uses a general relationship between bond distance and bond order on one hand and between bond order and bond energy on the other hand that leads to proper dissociation of bonds to separated atoms. Other valence terms present in the force field (angle and torsion) are defined in terms of the same bond orders so that all these terms go to zero smoothly as bonds break. In addition, ReaxFF has Coulomb and Morse (van der Waals) potentials to describe nonbond interactions between all atoms (no exclusions). These nonbond interactions are shielded at short range so that the Coulomb and van der Waals interactions become constant as Rij → 0. We report here the ReaxFF for hydrocarbons. The parameters were derived from quantum chemical calculations on bond dissociation and reactions of small molecules plus heat of formation and geometry data for...
TL;DR: In this paper, the potential energy surface is transformed into a collection of interpenetrating staircases, and the lowest known structures are located for all Lennard-Jones clusters up to 110 atoms, including a number that have never been found before in unbiased searches.
Abstract: We describe a global optimization technique using “basin-hopping” in which the potential energy surface is transformed into a collection of interpenetrating staircases. This method has been designed to exploit the features that recent work suggests must be present in an energy landscape for efficient relaxation to the global minimum. The transformation associates any point in configuration space with the local minimum obtained by a geometry optimization started from that point, effectively removing transition state regions from the problem. However, unlike other methods based upon hypersurface deformation, this transformation does not change the global minimum. The lowest known structures are located for all Lennard-Jones clusters up to 110 atoms, including a number that have never been found before in unbiased searches.
TL;DR: A near-linear relationship between the magnitude of the scale factor and the proportion of exact exchange is revealed and hybrid DFT calculations using a modified B3-LYP functional are probed.
Abstract: Scale factors for obtaining fundamental vibrational frequencies, low-frequency vibrational frequencies, zeropoint vibrational energies (ZPVEs), and thermal contributions to enthalpy and entropy have been derived through a least-squares approach from harmonic frequencies determined at more than 100 levels of theory. Wave function procedures (HF, MP2, QCISD, QCISD(T), CCSD, and CCSD(T)) and a large and representative range of density functional theory (DFT) approaches (B3-LYP, BMK, EDF2, M05-2X, MPWB1K, O3-LYP, PBE, TPSS, etc.) have been examined in conjunction with basis sets such as 6-31G(d), 6-31+G(d,p), 6-31G(2df,p), 6-311+G(d,p), and 6-311+G(2df,p). The vibrational frequency scale factors were determined by a comparison of theoretical harmonic frequencies with the corresponding experimental fundamentals utilizing a standard set of 1066 individual vibrations. ZPVE scale factors were generally obtained from a comparison of the computed ZPVEs with experimental ZPVEs for a smaller standard set of 39 molecules, though the effect of expansion to a 48 molecule data set was also examined. In addition to evaluating the scale factors for a wide range of levels of theory, we have also probed the effect on scale factors of varying the percentage of incorporated exact exchange in hybrid DFT calculations using a modified B3-LYP functional. This has revealed a near-linear relationship between the magnitude of the scale factor and the proportion of exact exchange. Finally, we have investigated the effect of basis set size on HF, MP2, B3-LYP, and BMK scale factors by deriving values with basis sets ranging from 6-31G(d) up to 6-311++G(3df,3pd) as well as with basis sets in the cc-pVnZ and aug-cc-pVnZ series and with the TZV2P basis.
TL;DR: In this paper, the effects of velocity rescaling on the self-diffusion coefficient D and radial distribution functions, gOO, gOH, and gHH for all five water models were determined and compared to experimental data.
Abstract: Molecular dynamics simulations of five water models, the TIP3P (original and modified), SPC (original and refined), and SPC/E (original), were performed using the CHARMM molecular mechanics program. All simulations were carried out in the microcanonical NVE ensemble, using 901 water molecules in a cubic simulation cell furnished with periodic boundary conditions at 298 K. The SHAKE algorithm was used to keep water molecules rigid. Nanosecond trajectories were calculated with all water models for high statistical accuracy. The characteristic self-diffusion coefficients D and radial distribution functions, gOO, gOH, and gHH for all five water models were determined and compared to experimental data. The effects of velocity rescaling on the self-diffusion coefficient D were examined. All these empirical water models used in this study are similar by having three interaction sites, but the small differences in their pair potentials composed of Lennard-Jones (LJ) and Coulombic terms give significant difference...