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

Publisher details

American Institute of Physics

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    • Author can archive a pre-print version
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    • Author can archive a post-print version
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    • 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

  • [Show abstract] [Hide abstract]
    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: De Gennes model for Knudsen diffusion and strong surface trapping kinetics is applied to slit, capillary, and spherical pores. The exact analytical survival probability-time expressions obtained for each case, which scale with the average pore diameter, are compared with numerical simulation curves for a densely packed hard sphere model porous bed.
    The Journal of Chemical Physics 12/2014; 141(12):124708.
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    ABSTRACT: The article presents a study of the strongly spin-orbit coupled singlet A(1)Σ(+) and triplet b(3)Π states of the RbCs molecule, which provide an efficient optical path to transfer ultracold molecules to their rovibrational ground state. Fourier-transform A(1)Σ(+) - b(3)Π → X(1)Σ(+) and (4)(1)Σ(+) → A(1)Σ(+) - b(3)Π laser-induced fluorescence (LIF) spectra were recorded for the natural mixture of the (85)Rb(133)Cs and (87)Rb(133)Cs isotopologues produced in a heat pipe oven. Overall 8730 rovibronic term values of A(1)Σ(+) and b(3)Π states were determined with an uncertainty of 0.01 cm(-1) in the energy range [9012, 14087] cm(-1), covering rotational quantum numbers J ∈ [6, 324]. An energy-based deperturbation analysis performed in the framework of the four A(1)Σ(+) - b(3)ΠΩ = 0, 1, 2 coupled-channels approach reproduces 97% of the experimental term values of both isotopologues with a standard deviation of 0.0036 cm(-1). The reliability of the deperturbed mass-invariant potentials and spin-orbit coupling functions of the interacting A(1)Σ(+) and b(3)Π states is additionally proved by a good reproduction of the A - b → X and (4)(1)Σ(+) → A - b relative intensity distributions. The achieved accuracy of the A - b complex description allowed us to use the latter to assign the observed (5)(1)Σ(+) → A - b and (3)(1)Π → A - b transitions. As is demonstrated, LIF to the A - b complex becomes as informative as to the ground X(1)Σ(+) state, which is confirmed by comparing the results of (4)(1)Σ(+) state analysis based on (4)(1)Σ(+) → A - b LIF with the data from V. Zuters et al. [Phys. Rev. A 87, 022504 (2013)] based on (4)(1)Σ(+) → X LIF.
    The Journal of Chemical Physics 11/2014; 141(18):184309.
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    ABSTRACT: We report on the ordering and dynamics of interacting colloidal particles confined by a parabolic potential. By means of Brownian dynamics simulations, we find that by varying the magnitude of the trap stiffness, it is possible to control the dimension of the system and, thus, explore both the structural transitions and the long-time self-diffusion coefficient as a function of the degree of confinement. We particularly study the structural ordering in the directions perpendicular and parallel to the confinement. Further analysis of the local distribution of the first-neighbors layer allows us to identify and understand the different structural phases induced by the parabolic potential. These results are summarized in a structural state diagram that describes the way in which the colloidal suspension undergoes a structural re-ordering while increasing the confinement. To fully understand the particle dynamics, we take into account hydrodynamic interactions between colloids; the parabolic potential constricts the available space for the colloids, but it does not act on the solvent. Our findings show a non-monotonic long-time self-diffusion, which can be associated to the structural transitions induced by the external field.
    The Journal of Chemical Physics 11/2014;
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    ABSTRACT: Chloride anions permeate the bacterial NanC porin in physiological processes. Here we present a DFT-based QM/MM study of this porin in the presence of these anions. Comparison is made with classical MD simulations on the same system. In both QM/MM and classical approaches, the anions are almost entirely solvated by water molecules. However, the average water–Cl− distance is significantly larger in the first approach. Polarization effects of protein groups close to Cl− anion are sizeable. These effects might modulate the anion-protein electrostatic interactions, which in turn play a central role for selectivity mechanisms of the channel.
    The Journal of Chemical Physics 11/2014; 141(22):22D521.
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    ABSTRACT: McMillan and Mayer (MM) proved two remarkable theorems in their paper on the equilibrium statistical mechanics of liquid solutions. They first showed that the grand canonical partition function for a solution can be reduced to one with an effectively solute-only form, by integrating out the solvent degrees of freedom. The total effective solute potential in the effective solute grand partition function can be decomposed into components which are potentials of mean force for isolated groups of one, two, three, etc., solute molecules. Second, from the first result, now assuming low solute concentration, MM derived an expansion for the osmotic pressure in powers of the solute concentration, in complete analogy with the virial expansion of gas pressure in powers of the density at low density. The molecular expressions found for the osmotic virial coefficients have exactly the same form as the corresponding gas virial coefficients, with potentials of mean force replacing vacuum potentials. In this paper, we restrict ourselves to binary liquid solutions with solute species A and solvent species B and do three things: (a) By working with a semi-grand canonical ensemble (grand with respect to solvent only) instead of the grand canonical ensemble used by MM, and avoiding graphical methods, we have greatly simplified the derivation of the first MM result, (b) by using a simple nongraphical method developed by van Kampen for gases, we have greatly simplified the derivation of the second MM result, i.e., the osmotic pressure virial expansion; as a by-product, we show the precise relation between MM theory and Widom potential distribution theory, and (c) we have extended MM theory by deriving virial expansions for other solution properties such as the enthalpy of mixing. The latter expansion is proving useful in analyzing ongoing isothermal titration calorimetry experiments with which we are involved. For the enthalpy virial expansion, we have also changed independent variables from semi-grand canonical, i.e., fixed {NA,μB,V,T} , to those relevant to the experiment, i.e., fixed {N A , N B , p, T}, where μ denotes chemical potential, N the number of molecules, V the volume, p the pressure, and T the temperature.
    The Journal of Chemical Physics 10/2014; 141:154501.
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    ABSTRACT: Absorption spectra of Ag 20 and Agq55 (q = +1, −3) nanoclusters are investigated in the framework of the time-dependent density functional theory in order to analyse the role of the d electrons in plasmon-like band of silver clusters. The description of the plasmon-like band from calculations using density functionals containing an amount of Hartree-Fock exchange at long range, namely, hybrid and range-separated hybrid (RSH) density functionals, is in good agreement with the classical interpretation of the plasmon-like structure as a collective excitation of valence s-electrons. In contrast, using local or semi-local exchange functionals (generalized gradient approximations (GGAs) or meta-GGAs) leads to a strong overestimation of the role of d electrons in the plasmon-like band. The semi-local asymptotically corrected model potentials also describe the plasmon as mainly associated to d electrons, though calculated spectra are in fairly good agreement with those calculated using the RSH scheme. Our analysis shows that a portion of non-local exchange modifies the description of the plasmon-like band.
    The Journal of Chemical Physics 10/2014; 141:144302.
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    ABSTRACT: This paper reports femtosecond RIKES study of (acetamide + electrolyte) deep eutectics for the first time.
    The Journal of Chemical Physics 10/2014; 141:134506.