The Journal of Chemical Physics (J Chem Phys )

Publisher: American Institute of Physics, American Institute of Physics


The purpose of The Journal of Chemical Physics is to bridge a gap between journals of physics and journals of chemistry by publishing quantitative research based on physical principles and techniques, as applied to "chemical" systems. Just as the fields of chemistry and physics have expanded, so have chemical physics subject areas, which include polymers, materials, surfaces/interfaces, and biological macromolecules, along with the traditional small molecule and condensed phase systems. The Journal of Chemical Physics (JCP) is published four times per month (48 issues per year) by the American Institute of Physics.

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  • 5-year impact
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  • Article influence
  • Website
    Journal of Chemical Physics, The website
  • Other titles
    Journal of chemical physics (Online), Journal of chemical physics online
  • ISSN
  • OCLC
  • Material type
    Document, Periodical, Internet resource
  • Document type
    Internet Resource, Computer File, Journal / Magazine / Newspaper

Publisher details

American Institute of Physics

  • Pre-print
    • Author can archive a pre-print version
  • Post-print
    • Author can archive a post-print version
  • Conditions
    • Publishers version/PDF may be used on author's personal website or institutional website
    • Authors own version of final article on e-print servers
    • Must link to publisher version or journal home page
    • Publisher copyright and source must be acknowledged
    • NIH-funded articles are automatically deposited with PubMed Central with open access after 12 months
    • For Medical Physics see AAPM policy
    • This policy does not apply to Physics Today
    • Publisher last contacted on 27/09/2013
  • Classification
    ​ green

Publications in this journal

  • The Journal of Chemical Physics 12/2014; 121(24).
  • [Show abstract] [Hide abstract]
    ABSTRACT: We report a molecular-dynamics simulation of a single-component system of particles interacting via a spherically symmetric potential that is found to form, upon cooling from a liquid state, a low-density porous crystalline phase. Its structure analysis demonstrates that the crystal can be described by a net with a topology that belongs to the class of topologies characteristic of the metal-organic frameworks (MOFs). The observed net is new, and it is now included in the Reticular Chemistry Structure Resource database (RCSR). The observation that a net topology characteristic of MOF crystals, which are known to be formed by a coordination-driven self-assembly process, can be reproduced by a thermodynamically stable configuration of a simple single-component system of particles opens a possibility of using these models in studies of MOF nets. It also indicates that structures with MOF topology, as well as other low-density porous crystalline structures can possibly be produced in colloidal systems of spherical particles, with an appropriate tuning of interparticle interaction.
    The Journal of Chemical Physics 12/2014; 141(21):234503.
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    ABSTRACT: We study the equilibrium dynamics of a symmetrical binary Lennard-Jones fluid mixture near its consolute criticality. Molecular dynamics simulation results for the shear viscosity, η, from a microcanonical ensemble are compared with those from a canonical ensemble with various thermostats. It is observed that the Nosé-Hoover thermostat is a good candidate for this purpose, and is therefore adopted for the quantification of the critical singularity of η, to avoid the temperature fluctuations (or even drifts) that are often encountered in microcanonical simulations. Via a finite-size scaling analysis of our simulation data we have been able to confirm that the shear viscosity exhibits a weak critical singularity in agreement with the theoretical predictions.
    The Journal of Chemical Physics 12/2014; 141(234502).
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    ABSTRACT: A new method is introduced to compute X-ray solution scattering profiles from atomic models of macromolecules. The three-dimensional version of the Reference Interaction Site Model (RISM) from liquid-state statistical mechanics is employed to compute the solvent distribution around the solute, including both water and ions. X-ray scattering profiles are computed from this distribution together with the solute geometry. We describe an efficient procedure for performing this calculation employing a Lebedev grid for the angular averaging. The intensity profiles (which involve no adjustable parameters) match experiment and molecular dynamics simulations up to wide angle for two proteins (lysozyme and myoglobin) in water, as well as the small-angle profiles for a dozen biomolecules taken from the database. The RISM model is especially well-suited for studies of nucleic acids in salt solution. Use of fiber-diffraction models for the structure of duplex DNA in solution yields close agreement with the observed scattering profiles in both the small and wide angle scattering (SAXS and WAXS) regimes. In addition, computed profiles of anomalous SAXS signals (for Rb+ and Sr2+) emphasize the ionic contribution to scattering and are in reasonable agreement with experiment. In cases where an absolute calibration of the experimental data at q=0 is available, one can extract a count of the excess number of waters and ions; computed values depend on the closure that is assumed in the solution of the Ornstein-Zernike equations, with results from the Kovalenko-Hirata (KH) closure being closest to experiment for the cases studied here.
    The Journal of Chemical Physics 12/2014; 141(22).
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    ABSTRACT: Adenine and cytosine methylation are two important epigenetic modifications of DNA sequences at the levels of the genome and transcriptome. To characterize the differential roles of methylating adenine or cytosine with respect to their hydration properties, we performed conventional MD simulations and free energy perturbation calculations for two particular DNA sequences, namely the BDNF promoter and the R.DpnI-bound DNA that are known to undergo methylation of C5-methyl cytosine and N6-methyl adenine, respectively. We found that a single methylated cytosine has a clearly favorable hydration free energy over cytosine since the attached methyl group has a slightly polar character. In contrast, capping the strongly polar N6 of adenine with a methyl group gives a slightly unfavorable contribution to its free energy of solvation. Performing the same demethylation in the context of a DNA double-strand gave quite similar results for the more solvent-accessible cytosine, but much more unfavorable results for the rather buried adenine. Interestingly, the same demethylation reactions are far more unfavorable when performed in the context of the opposite (BDNF or R.DpnI target) sequence. This suggests a natural preference for methylation in a specific sequence context. In addition, free energy calculations for demethylating adenine or cytosine in the context of B-DNA vs. Z-DNA suggest that the conformational B-Z transition of DNA transition is rather a property of cytosine methylated sequences but is not preferable for the adenine-methylated sequences investigated here.
    The Journal of Chemical Physics 12/2014; 141.
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    ABSTRACT: Ionic sulfophosphate liquids of the type ZnO-Na2O-Na2SO4-P2O5 exhibit surprising glass forming ability, even at slow or moderate cooling rate. As a concept, they also provide high solubility of transition metal ions which could act as cross-linking sites between the sulfate and phosphate entities. It is therefore investigated how the replacement of ZnO by MnO and/or FeO affects the glass structure and the glass properties. Increasing manganese levels are found to result in a monotonic increase of the transition temperature Tg and most of the mechanical properties. This trend is attributed to the change of metal-ion coordination from four-fold around Zn2+ to six-fold around Mn2+ ions. The higher coordination facilitates cross-linking of the ionic structural entities and subsequently increases Tg. Raman and infrared spectroscopy show that the structure of these glasses involves only SO42− and PO43− monomers as well as P2O74- dimers. Replacement of ZnO by MnO is found to favour PO43− over P2O74- species, a trend which is enhanced by co-doping with FeO. Both transition metal ions show, like Zn2+, a preference to selectively coordinate to phosphate anionic species, as opposed to sodium ions which coordinate mainly to sulfate anions. EPR spectroscopy finally shows that divalent Mn2+ ions are present primarily in MnO6-clusters, which, in the studied sulfophosphate glasses, convert upon increasing MnO content from corner-sharing to edge-sharing entities.
    The Journal of Chemical Physics 12/2014; 141:224509.