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Publisher: AIP   (Total: 27 journals)   [Sort by number of followers]

Showing 1 - 27 of 27 Journals sorted alphabetically
Acoustics Today     Hybrid Journal   (Followers: 8)
AIP Advances     Open Access   (Followers: 11, SJR: 0.472, CiteScore: 1)
AIP Conference Proceedings     Full-text available via subscription   (Followers: 4)
American J. of Physics     Full-text available via subscription   (Followers: 54, SJR: 0.456, CiteScore: 1)
APL Bioengineering     Open Access  
APL Materials     Open Access   (Followers: 14, SJR: 1.63, CiteScore: 4)
APL Photonics     Open Access   (Followers: 1)
Applied Physics Letters     Hybrid Journal   (Followers: 38, SJR: 1.382, CiteScore: 3)
Applied Physics Reviews     Hybrid Journal   (Followers: 10, SJR: 4.156, CiteScore: 12)
Biointerphases     Open Access   (Followers: 1, SJR: 0.558, CiteScore: 2)
Biomicrofluidics     Open Access   (Followers: 5, SJR: 0.592, CiteScore: 2)
Chaos : An Interdisciplinary J. of Nonlinear Science     Hybrid Journal   (Followers: 3, SJR: 0.716, CiteScore: 2)
Chinese J. of Chemical Physics     Hybrid Journal   (Followers: 1, SJR: 0.24, CiteScore: 1)
J. of Applied Physics     Hybrid Journal   (Followers: 79, SJR: 0.739, CiteScore: 2)
J. of Chemical Physics     Hybrid Journal   (Followers: 31, SJR: 1.252, CiteScore: 2)
J. of Laser Applications     Full-text available via subscription   (Followers: 13, SJR: 0.741, CiteScore: 2)
J. of Mathematical Physics     Hybrid Journal   (Followers: 23, SJR: 0.644, CiteScore: 1)
J. of Physical and Chemical Reference Data     Hybrid Journal   (Followers: 3, SJR: 1.046, CiteScore: 3)
J. of Renewable and Sustainable Energy     Hybrid Journal   (Followers: 14, SJR: 0.44, CiteScore: 1)
Low Temperature Physics     Hybrid Journal   (Followers: 5, SJR: 0.264, CiteScore: 1)
Physics of Fluids     Hybrid Journal   (Followers: 37, SJR: 1.19, CiteScore: 3)
Physics of Plasmas     Hybrid Journal   (Followers: 8, SJR: 0.576, CiteScore: 1)
Physics Today     Hybrid Journal   (Followers: 80, SJR: 0.66, CiteScore: 1)
Review of Scientific Instruments     Hybrid Journal   (Followers: 20, SJR: 0.585, CiteScore: 1)
Scilight     Full-text available via subscription  
Structural Dynamics     Open Access   (Followers: 5, SJR: 1.625, CiteScore: 4)
Surface Science Spectra     Hybrid Journal   (Followers: 1, SJR: 0.416, CiteScore: 1)
Journal Cover
Journal of Chemical Physics
Journal Prestige (SJR): 1.252
Citation Impact (citeScore): 2
Number of Followers: 31  
 
  Hybrid Journal Hybrid journal (It can contain Open Access articles)
ISSN (Print) 0021-9606 - ISSN (Online) 1089-7690
Published by AIP Homepage  [27 journals]
  • Trapped and non-trapped polymer translocations through a spherical pore
    • Authors: Li-Zhen Sun, Chang-Hui Wang, Meng-Bo Luo, Haibin Li
      Abstract: The Journal of Chemical Physics, Volume 150, Issue 2, January 2019.
      The polymer translocation through a spherical pore is studied using the Langevin dynamics simulation. The translocation events are classified into two types: one is the trapped translocation in which the entire polymer is trapped in the pore and the other is the non-trapped translocation where the pore cannot hold the whole polymer. We find that the trapped translocation is favored at large spheres and small external voltages. However, the monomer-pore attraction would lead to the non-monotonic behavior of the trapped translocation possibility out of all translocation events. Moreover, both the trapped and non-trapped translocation times are dependent on the polymer length, pore size, external voltage, and the monomer-pore attraction. There exist two pathways for the polymer in the trapped translocation: an actively trapped pathway for the polymer trapped in the pore before the head monomer arrives at the pore exit, and a passively trapped pathway for the polymer trapped in the pore while the head monomer is struggling to move out of the pore. The studies of trapped pathways can provide a deep understanding of the polymer translocation behavior.
      Citation: The Journal of Chemical Physics
      PubDate: 2019-01-14T08:58:24Z
      DOI: 10.1063/1.5063331
       
  • Erratum: “Effect of the chemical environment of the DNA guanine
           quadruplex on the free energy of binding of Na and K ions” [J. Chem.
           Phys. 149, 225102 (2018)]
    • Authors: Mahmoud Sharawy, Styliani Consta
      Abstract: The Journal of Chemical Physics, Volume 150, Issue 2, January 2019.

      Citation: The Journal of Chemical Physics
      PubDate: 2019-01-14T08:58:20Z
      DOI: 10.1063/1.5086679
       
  • Enhancing the signal strength of surface sensitive 2D IR spectroscopy
    • Authors: Megan K. Petti, Joshua S. Ostrander, Vivek Saraswat, Erin R. Birdsall, Kacie L. Rich, Justin P. Lomont, Michael S. Arnold, Martin T. Zanni
      Abstract: The Journal of Chemical Physics, Volume 150, Issue 2, January 2019.
      Spectroscopic techniques that are capable of measuring surfaces and interfaces must overcome two technical challenges: one, the low coverage of molecules at the surface, and two, discerning between signals from the bulk and surface. We present surface enhanced attenuated reflection 2D infrared (SEAR 2D IR) spectroscopy, a method that combines localized surface plasmons with a reflection pump-probe geometry to achieve monolayer sensitivity. The method is demonstrated at 6 µm with the amide I band of a model peptide, a cysteine terminated α-helical peptide tethered to a gold surface. Using SEAR 2D IR spectroscopy, the signal from this sample is enhanced 20 000-times over a monolayer on a dielectric surface. Like attenuated total reflection IR spectroscopy, SEAR 2D IR spectroscopy can be applied to strongly absorbing solvents. We demonstrated this capability by solvating a peptide monolayer with H2O, which cannot normally be used when measuring the amide I band. SEAR 2D IR spectroscopy will be advantageous for studying chemical reactions at electrochemical surfaces, interfacial charge transfer in photovoltaics, and structural changes of transmembrane proteins in lipid membranes.
      Citation: The Journal of Chemical Physics
      PubDate: 2019-01-14T08:58:18Z
      DOI: 10.1063/1.5065511
       
  • Development of ultrafast broadband electronic sum frequency generation for
           charge dynamics at surfaces and interfaces
    • Authors: Gang-Hua Deng, Yuqin Qian, Yi Rao
      Abstract: The Journal of Chemical Physics, Volume 150, Issue 2, January 2019.
      Understandings of population and relaxation of charges at surfaces and interfaces are essential to improve charge collection efficiency for energy conversion, catalysis, and photosynthesis. Existing time-resolved surface and interface tools are limited to either under ultrahigh vacuum or in a narrow wavelength region with the loss of spectral information. There lacks an efficient time-resolved surface/interface-specific electronic spectroscopy under ambient conditions for the ultrafast surface/interface dynamics. Here we developed a novel technique for surface/interface-specific broadband electronic sum frequency generation (ESFG). The broadband ESFG was based on a stable two-stage BiB3O6 crystal-based optical parametric amplifier, which generates a strong broadband short-wave infrared (SWIR) from 1200 nm to 2400 nm. A resultant surface spectrum covers almost all visible light from 480 nm to 760 nm, combined a broadband electronic second harmonic generation (ESHG) with the ESFG from the SWIR laser source. We further developed the steady-state and transient broadband ESFG and ESHG techniques to investigate the structure and dynamics of charges at oxidized p-type GaAs (100) semiconductor surfaces, as an example. Both the steady-state and transient experiments have shown that two surface states exist inside the bandgap of the GaAs. The kinetic processes at the GaAs surface include both the population and recombination of the surface states after photoexcitation, in addition to the build-up of the space photo-voltage (SPV). The build-up SPV occurs with a rate of 0.56 ± 0.07 ps−1, while the population rate of the surface states exhibits a two-body behavior with a rate constant of (0.012 ± 0.002) × 1012 s−1 cm2. The photo-generated electron-hole pairs near the surface recombine with a rate of 0.002 ± 0.0002 ps−1 for the oxidized p-type GaAs (100). All the methodologies developed here are readily applied to any optically accessible interfaces and surfaces, in particular buried interfaces under ambient conditions.
      Citation: The Journal of Chemical Physics
      PubDate: 2019-01-14T08:58:17Z
      DOI: 10.1063/1.5063458
       
  • Rheological investigation of gels formed by competing interactions: A
           numerical study
    • Authors: José Ruiz-Franco, Nicoletta Gnan, Emanuela Zaccarelli
      Abstract: The Journal of Chemical Physics, Volume 150, Issue 2, January 2019.
      A transition from solid-like to liquid-like behavior occurs when colloidal gels are subjected to a prolonged exposure to a steady shear. This phenomenon, which is characterized by a yielding point, is found to be strongly dependent on the packing fraction. However, it is not yet known how the effective inter-particle potential affects this transition. To this aim, we present a numerical investigation of the rheology of equilibrium gels in which a short-range depletion is complemented by a long-range electrostatic interaction. We observe a single yielding event in the stress-strain curve, occurring at a fixed strain. The stress overshoot is found to follow a power-law dependence on the Péclet number, with an exponent larger than that found in depletion gels, suggesting that its value may depend systematically on the underlying colloid-colloid interactions. We also establish a mapping between equilibrium states and steady states under shear, which allows us to identify the structural modifications induced by the presence of the shear. Remarkably, we find that steady states corresponding to the same Péclet number, obtained by different combinations of shear rate and solvent viscosity, show identical structural and rheological properties. Our results highlight the importance of understanding the coupling between colloidal interactions, solvent effects, and flow to be able to describe the microscopic organization of colloidal particles under shear.
      Citation: The Journal of Chemical Physics
      PubDate: 2019-01-14T08:58:14Z
      DOI: 10.1063/1.5052317
       
  • Dynamics of a polymer under multi-gradient fields
    • Authors: Sadhana Singh, Sanjay Kumar
      Abstract: The Journal of Chemical Physics, Volume 150, Issue 2, January 2019.
      Effects of multi-gradient fields on the transport of a polymer chain are investigated using Langevin dynamics simulations. We observe that the natural frequency of tumbling follows Wi0.66 scaling, where Wi is the Weissenberg number. The distribution of angular tumbling time has exponentially decaying tails, and at high Wi, it deviates from Poisson behavior. Competition between the velocity gradient, which results in a shear flow in the system, and the solvent quality gradient arising due to the interaction among monomers reveals that there is another scaling associated with the angular tumbling time distribution. Moreover, at low temperature, we observe unusual behavior that at intermediate shear rates, the decay rate ν decreases with Wi.
      Citation: The Journal of Chemical Physics
      PubDate: 2019-01-14T08:58:13Z
      DOI: 10.1063/1.5052219
       
  • Predictive collective variable discovery with deep Bayesian models
    • Authors: Markus Schöberl, Nicholas Zabaras, Phaedon-Stelios Koutsourelakis
      Abstract: The Journal of Chemical Physics, Volume 150, Issue 2, January 2019.
      Extending spatio-temporal scale limitations of models for complex atomistic systems considered in biochemistry and materials science necessitates the development of enhanced sampling methods. The potential acceleration in exploring the configurational space by enhanced sampling methods depends on the choice of collective variables (CVs). In this work, we formulate the discovery of CVs as a Bayesian inference problem and consider the CVs as hidden generators of the full-atomistic trajectory. The ability to generate samples of the fine-scale atomistic configurations using limited training data allows us to compute estimates of observables as well as our probabilistic confidence on them. The methodology is based on emerging methodological advances in machine learning and variational inference. The discovered CVs are related to physicochemical properties which are essential for understanding mechanisms especially in unexplored complex systems. We provide a quantitative assessment of the CVs in terms of their predictive ability for alanine dipeptide (ALA-2) and ALA-15 peptide.
      Citation: The Journal of Chemical Physics
      PubDate: 2019-01-14T08:58:06Z
      DOI: 10.1063/1.5058063
       
  • Glycerol confined in zeolitic imidazolate frameworks: The
           temperature-dependent cooperativity length scale of glassy freezing
    • Authors: M. Uhl, J. K. H. Fischer, P. Sippel, H. Bunzen, P. Lunkenheimer, D. Volkmer, A. Loidl
      Abstract: The Journal of Chemical Physics, Volume 150, Issue 2, January 2019.
      In the present work, we employ broadband dielectric spectroscopy to study the molecular dynamics of the prototypical glass former glycerol confined in two microporous zeolitic imidazolate frameworks (ZIF-8 and ZIF-11) with well-defined pore diameters of 1.16 and 1.46 nm, respectively. The spectra reveal information on the modified α relaxation of the confined supercooled liquid, whose temperature dependence exhibits clear deviations from the typical super-Arrhenius temperature dependence of the bulk material, depending on the temperature and pore size. This allows assigning well-defined cooperativity length scales of molecular motion to certain temperatures above the glass transition. We relate these and previous results on glycerol confined in other host systems to the temperature-dependent length scale deduced from nonlinear dielectric measurements. The combined experimental data can be consistently described by a critical divergence of this correlation length as expected within theoretical approaches assuming that the glass transition is due to an underlying phase transition.
      Citation: The Journal of Chemical Physics
      PubDate: 2019-01-14T08:58:03Z
      DOI: 10.1063/1.5080334
       
  • Non-monotonic effect of additive particle size on the glass transition in
           polymers
    • Authors: Elias M. Zirdehi, Fathollah Varnik
      Abstract: The Journal of Chemical Physics, Volume 150, Issue 2, January 2019.
      Effect of small additive molecules on the structural relaxation of polymer melts is investigated via molecular dynamics simulations. At a constant external pressure and a fixed number concentration of added molecules, the variation of the particle diameter leads to a non-monotonic change of the relaxation dynamics of the polymer melt. For non-entangled chains, this effect is rationalized in terms of an enhanced added-particle-dynamics which competes with a weaker coupling strength upon decreasing the particle size. Interestingly, cooling simulations reveal a non-monotonic effect on the glass transition temperature also for entangled chains, where the effect of additives on polymer dynamics is more intricate. This observation underlines the importance of monomer-scale packing effects on the glass transition in polymers. In view of this fact, size-adaptive thermosensitive core-shell colloids would be a promising candidate route to explore this phenomenon experimentally.
      Citation: The Journal of Chemical Physics
      PubDate: 2019-01-11T07:24:30Z
      DOI: 10.1063/1.5063476
       
  • Equations of motion for position-dependent coarse-grain mappings obtained
           with Mori-Zwanzig theory
    • Authors: Hudson Lynn, Mark Thachuk
      Abstract: The Journal of Chemical Physics, Volume 150, Issue 2, January 2019.
      A position-dependent transformation is introduced for mapping a system of atomistic particles to a system of coarse-grained (CG) variables, which under some circumstances might be considered particles. This CG mapping allows atomistic particles to simultaneously contribute to more than a single CG particle and to change in time the CG particle they are associated with. That is, the CG mapping is dynamic. Mori-Zwanzig theory is then used to obtain the equations of motion for this CG mapping, resulting in conservative, dissipative, and random force terms in generalized, non-Markovian Langevin equations. In addition to the usual forces arising from the effective CG potential derived from atomistic interactions, new forces arise from the dynamic changes in the CG mapping itself. These new forces effectively account for changes arising from fluxes of atomistic particles into and out of CG ones as time progresses. Several examples are given showing the range of problems that can be addressed with this new CG mapping. These range from the usual case where atomistic particles are grouped into large molecular-like chunks, with mappings that remain fixed in time and for which an atomistic particle is part of only a single CG one, to the case where CG particles resemble fluid elements, containing many hundreds of independent atomistic particles. The new CG mapping also allows for hybrid descriptions, in which a part of the system remains atomistic or molecular-like and a part is highly coarse-grained to mesoscopic fluid element-like particles, for example. In the latter case, the equations of motion then provide the correct formalism for determining the forces, beyond the usual conservative ones. This provides a theoretical foundation upon which approximate equations of motion can be formulated to thus build numerical algorithms for expanded applications of accurate CG molecular dynamics.
      Citation: The Journal of Chemical Physics
      PubDate: 2019-01-11T07:24:27Z
      DOI: 10.1063/1.5058061
       
  • Active escape dynamics: The effect of persistence on barrier crossing
    • Authors: Lorenzo Caprini, Umberto Marini Bettolo Marconi, Andrea Puglisi, Angelo Vulpiani
      Abstract: The Journal of Chemical Physics, Volume 150, Issue 2, January 2019.
      We study a system of non-interacting active particles, propelled by colored noises, characterized by an activity time τ, and confined by a double-well potential. A straightforward application of this system is the problem of barrier crossing of active particles, which has been studied only in the limit of small activity. When τ is sufficiently large, equilibrium-like approximations break down in the barrier crossing region. In the model under investigation, it emerges as a sort of “negative temperature” region, and numerical simulations confirm the presence of non-convex local velocity distributions. We propose, in the limit of large τ, approximate equations for the typical trajectories which successfully predict many aspects of the numerical results. The local breakdown of detailed balance and its relation with a recent definition of non-equilibrium heat exchange is also discussed.
      Citation: The Journal of Chemical Physics
      PubDate: 2019-01-11T07:24:27Z
      DOI: 10.1063/1.5080537
       
  • Context in synthetic biology: Memory effects of environments with
           mono-molecular reactions
    • Authors: Johannes Falk, Leo Bronstein, Maleen Hanst, Barbara Drossel, Heinz Koeppl
      Abstract: The Journal of Chemical Physics, Volume 150, Issue 2, January 2019.
      Synthetic biology aims at designing modular genetic circuits that can be assembled according to the desired function. When embedded in a cell, a circuit module becomes a small subnetwork within a larger environmental network, and its dynamics is therefore affected by potentially unknown interactions with the environment. It is well-known that the presence of the environment not only causes extrinsic noise but also memory effects, which means that the dynamics of the subnetwork is affected by its past states via a memory function that is characteristic of the environment. We study several generic scenarios for the coupling between a small module and a larger environment, with the environment consisting of a chain of mono-molecular reactions. By mapping the dynamics of this coupled system onto random walks, we are able to give exact analytical expressions for the arising memory functions. Hence, our results give insights into the possible types of memory functions and thereby help to better predict subnetwork dynamics.
      Citation: The Journal of Chemical Physics
      PubDate: 2019-01-10T06:33:32Z
      DOI: 10.1063/1.5053816
       
  • Machine learning model for non-equilibrium structures and energies of
           simple molecules
    • Authors: E. Iype, S. Urolagin
      Abstract: The Journal of Chemical Physics, Volume 150, Issue 2, January 2019.
      Predicting molecular properties using a Machine Learning (ML) method is gaining interest among research as it offers quantum chemical accuracy at molecular mechanics speed. This prediction is performed by training an ML model using a set of reference data [mostly Density Functional Theory (DFT)] and then using it to predict properties. In this work, kernel based ML models are trained (using Bag of Bonds as well as many body tensor representation) against datasets containing non-equilibrium structures of six molecules (water, methane, ethane, propane, butane, and pentane) to predict their atomization energies and to perform a Metropolis Monte Carlo (MMC) run with simulated annealing to optimize molecular structures. The optimized structures and energies of the molecules are found to be comparable with DFT optimized structures, energies, and forces. Thus, this method offers the possibility to use a trained ML model to perform a classical simulation such as MMC without using any force field, thereby improving the accuracy of the simulation at low computational cost.
      Citation: The Journal of Chemical Physics
      PubDate: 2019-01-10T06:33:27Z
      DOI: 10.1063/1.5054968
       
  • Two-body intermolecular potentials from second virial coefficient
           properties
    • Authors: Richard J. Sadus
      Abstract: The Journal of Chemical Physics, Volume 150, Issue 2, January 2019.
      A method is reported that enables second virial coefficient properties to be used to obtain relatively simple two-body intermolecular potentials. Generic n-m Lennard-Jones/Mie potentials are transformed into two-body potentials for neon, argon, krypton, and xenon. Comparison with results from highly accurate ab initio potentials indicates good agreement. A complete potential for real fluids is obtained by combining the two-body potentials with a density-dependent term for three-body interactions. Vapor-liquid equilibria molecular simulation data for the new potentials are compared with the experiment, which demonstrates the effectiveness of the two- and three-body contributions. The combination of the two-body 10-8 Lennard-Jones/Mie potential and three-body term is a good overall choice for the noble gases.
      Citation: The Journal of Chemical Physics
      PubDate: 2019-01-10T06:33:23Z
      DOI: 10.1063/1.5080308
       
  • Revisiting the Stokes-Einstein relation without a hydrodynamic diameter
    • Authors: Lorenzo Costigliola, David M. Heyes, Thomas B. Schrøder, Jeppe C. Dyre
      Abstract: The Journal of Chemical Physics, Volume 150, Issue 2, January 2019.
      We present diffusion coefficient and shear viscosity data for the Lennard-Jones fluid along nine isochores above the critical density, each involving a temperature variation of roughly two orders of magnitude. The data are analyzed with respect to the Stokes-Einstein (SE) relation, which breaks down gradually at high temperatures. This is rationalized in terms of the fact that the reduced diffusion coefficient [math] and the reduced viscosity [math] are both constant along the system’s lines of constant excess entropy (the isomorphs). As a consequence, [math] is a function of T/TRef(ρ) in which T is the temperature, ρ is the density, and TRef(ρ) is the temperature as a function of the density along a reference isomorph. This allows one to successfully predict the viscosity from the diffusion coefficient in the studied region of the thermodynamic phase diagram.
      Citation: The Journal of Chemical Physics
      PubDate: 2019-01-10T06:33:20Z
      DOI: 10.1063/1.5080662
       
  • Transferable density functional tight binding for carbon, hydrogen,
           nitrogen, and oxygen: Application to shock compression
    • Authors: M. J. Cawkwell, R. Perriot
      Abstract: The Journal of Chemical Physics, Volume 150, Issue 2, January 2019.
      A new parameterization for density functional tight binding (DFTB) theory, lanl31, has been developed for molecules containing carbon, hydrogen, nitrogen, and oxygen. Optimal values for the Hubbard Us, on-site energies, and the radial dependences of the bond integrals and repulsive potentials were determined by numerical optimization using simulated annealing to a modest database of ab initio-calculated atomization energies and interatomic forces. The transferability of the optimized DFTB parameterization has been assessed using the CHNO subset of the QM-9 database [R. Ramakrishnan et al., Sci. Data 1, 140022 (2014)]. These analyses showed that the errors in the atomization energies and interatomic forces predicted by our model are small and in the vicinity of the differences between density functional theory calculations with different basis sets and exchange-correlation functionals. Good correlations between the molecular dipole moments and HOMO-LUMO gaps predicted by lanl31 and the QM-9 data set are also found. Furthermore, the errors in the atomization energies and forces derived from lanl31 are significantly smaller than those obtained from the ReaxFF-lg reactive force field for organic materials [L. Liu et al., J. Phys. Chem. A 115, 11016 (2011)]. The lanl31 DFTB parameterization for C, H, N, and O has been applied to the molecular dynamics simulation of the principal Hugoniot of liquid nitromethane, liquid benzene, liquid nitrogen, pentaerythritol tetranitrate, trinitrotoluene, and cyclotetramethylene tetranitramine. The computed and measured Hugoniot loci are in excellent agreement with experiment, and we discuss the sensitivity of the loci to the underestimated shock heating that is a characteristic of classical molecular dynamics simulations.
      Citation: The Journal of Chemical Physics
      PubDate: 2019-01-10T06:33:18Z
      DOI: 10.1063/1.5063385
       
  • An AIMD study of dissociative chemisorption of methanol on Cu(111) with
           implications for formaldehyde formation
    • Authors: Nick Gerrits, Geert-Jan Kroes
      Abstract: The Journal of Chemical Physics, Volume 150, Issue 2, January 2019.
      An important industrial process is methanol steam reforming, which is typically used in conjunction with copper catalysts. However, little agreement exists on the reaction mechanisms involved on a copper catalyst. Therefore, we have performed research yielding additional insight into the reaction mechanism for dissociative chemisorption of methanol on Cu(111) using ab initio molecular dynamics, supported by static calculations of the molecule-surface interaction with density functional theory. Our work predicts that after the initial dissociation, formaldehyde is formed through three different mechanisms. Additionally, it is observed that at high energy, CH cleavage is the dominant pathway instead of the formerly presumed OH cleavage pathway. Finally, in order to describe the interaction of methanol with the metal surface, the SRP32-vdW functional is used, which has been previously developed and tested for CHD3 on Ni(111), Pt(111), and Pt(211) using the Specific Reaction Parameter (SRP) approach. In this work, the SRP32-vdW functional is applied to methanol on Cu(111) as well, in the hope that future experiments can validate the transferability of the SRP32-vdW functional to chemically related molecule-metal surface systems.
      Citation: The Journal of Chemical Physics
      PubDate: 2019-01-10T06:33:16Z
      DOI: 10.1063/1.5070129
       
  • Phononic heat transport in molecular junctions: Quantum effects and
           vibrational mismatch
    • Authors: Roya Moghaddasi Fereidani, Dvira Segal
      Abstract: The Journal of Chemical Physics, Volume 150, Issue 2, January 2019.
      Problems of heat transport are ubiquitous to various technologies such as power generation, cooling, electronics, and thermoelectrics. In this paper, we advocate for the application of the quantum self-consistent reservoir method, which is based on the generalized quantum Langevin equation, to study phononic thermal conduction in molecular junctions. The method emulates phonon-phonon scattering processes while taking into account quantum effects and far-from-equilibrium (large temperature difference) conditions. We test the applicability of the method by simulating the thermal conductance of molecular junctions with one-dimensional molecules sandwiched between solid surfaces. Our results satisfy the expected behavior of the thermal conductance in anharmonic chains as a function of length, phonon scattering rate, and temperature, thus validating the computational scheme. Moreover, we examine the effects of vibrational mismatch between the solids’ phonon spectra on the heat transfer characteristics in molecular junctions. Here, we reveal the dual role of vibrational anharmonicity: It raises the resistance of the junction due to multiple scattering processes, yet it promotes energy transport across a vibrational mismatch by enabling phonon recombination and decay processes.
      Citation: The Journal of Chemical Physics
      PubDate: 2019-01-10T06:33:13Z
      DOI: 10.1063/1.5075620
       
  • Contour forward flux sampling: Sampling rare events along multiple
           collective variables
    • Authors: Ryan S. DeFever, Sapna Sarupria
      Abstract: The Journal of Chemical Physics, Volume 150, Issue 2, January 2019.
      Many rare event transitions involve multiple collective variables (CVs), and the most appropriate combination of CVs is generally unknown a priori. We thus introduce a new method, contour forward flux sampling (cFFS), to study rare events with multiple CVs simultaneously. cFFS places nonlinear interfaces on-the-fly from the collective progress of the simulations, without any prior knowledge of the energy landscape or appropriate combination of CVs. We demonstrate cFFS on analytical potential energy surfaces and a conformational change in alanine dipeptide.
      Citation: The Journal of Chemical Physics
      PubDate: 2019-01-09T07:14:41Z
      DOI: 10.1063/1.5063358
       
  • Linear and sublinear scaling computation of the electronic g-tensor at the
           density functional theory level
    • Authors: Michael Glasbrenner, Sigurd Vogler, Christian Ochsenfeld
      Abstract: The Journal of Chemical Physics, Volume 150, Issue 2, January 2019.
      We present an efficient and low-scaling implementation of a density functional theory based method for the computation of electronic g-tensors. It allows for an accurate description of spin-orbit coupling effects by employing the spin-orbit mean-field operator. Gauge-origin independence is ensured by the use of gauge-including atomic orbitals. Asymptotically linear scaling with molecule size is achieved with an atomic orbital based formulation, integral screening methods, and sparse linear algebra. In addition, we introduce an ansatz that exploits the locality of the contributions to the g-tensor for molecules with local spin density. For such systems, sublinear scaling is obtained by restricting the magnetic field perturbation to the relevant subspaces of the full atomic orbital space; several criteria for selecting these subspaces are discussed and compared. It is shown that the computational cost of g-tensor calculations with the local approach can fall below the cost of the self-consistent field calculation for large molecules. The presented methods thus enable efficient, accurate, and gauge-origin independent computations of electronic g-tensors of large molecular systems.
      Citation: The Journal of Chemical Physics
      PubDate: 2019-01-09T07:14:35Z
      DOI: 10.1063/1.5066266
       
  • Adsorption of water, methanol, and their mixtures in slit graphite pores
    • Authors: Paulina Pršlja, Enrique Lomba, Paula Gómez-Álvarez, Tomaz Urbič, Eva G. Noya
      Abstract: The Journal of Chemical Physics, Volume 150, Issue 2, January 2019.
      The behavior of water, methanol, and water-methanol mixtures confined in narrow slit graphite pores as a function of pore size was investigated by Monte Carlo, hybrid Monte Carlo, and Molecular Dynamics simulations. Interactions were described using TIP4P/2005 for water, OPLS/2016 for methanol, and cross interactions fitted to excess water/methanol properties over the whole range of concentrations, which provide a rather accurate description of water-methanol mixtures. As expected for hydrophobic pores, whereas pure methanol is adsorbed already from the gas phase, pure water only enters the pore at pressures well beyond bulk saturation for all pore sizes considered. When adsorbed from a mixture, however, water adsorbs at much lower pressures due to the formation of hydrogen bonds with previously adsorbed methanol molecules. For all studied compositions and pore sizes, methanol adsorbs preferentially over water at liquid-vapor equilibrium conditions. In pure components, both water and methanol are microscopically structured in layers, the number of layers increasing with pore size. This is also the case in adsorbed mixtures, in which methanol has a higher affinity for the walls. This becomes more evident as the pore widens. Diffusion of pure water is higher than that of pure methanol for all pore sizes due to the larger size of the methyl group. In mixtures, both components present similar diffusivities at all pore sizes, which is explained in terms of the coupling of molecular movements due to strong hydrogen bonding between methanol and water molecules. This is particularly evident in very narrow pores, in which pure methanol diffusion is completely impeded on the time scale of our simulations, but the presence of a small amount of water molecules facilitates alcohol diffusion following a single-file mechanism. Additionally, our results indicate that pure water diffusivities display a non-monotonous dependence of pore size, due to effects of confinement (proximity to a fluid-solid-fluid transition induced by confinement as reported in previous work) and the dynamic anomalies of water.
      Citation: The Journal of Chemical Physics
      PubDate: 2019-01-09T07:14:32Z
      DOI: 10.1063/1.5078603
       
  • A modified generalized Langevin oscillator model for activated gas-surface
           reactions
    • Authors: Xueyao Zhou, Bin Jiang
      Abstract: The Journal of Chemical Physics, Volume 150, Issue 2, January 2019.
      Surface motion has proven to influence the gas-surface reactions in various ways. An adequate model to describe the complex lattice effects in a relatively simple way is therefore highly desirable. In this work, we have modified the widely used Generalized Langevin Oscillator (GLO) model to incorporate the molecule-surface coupling that plays an important role in activated dissociation of polyatomic molecules on metal surfaces. To this end, taking the well-studied CHD3+Ni(111) system as an example, we add a coupling potential linearly dependent on the surface oscillating coordinate, which becomes essential in predicting the dissociative sticking coefficients for reactive scattering. We further scale the mass of the surface oscillator on the basis of a mechanic coupling parameter, which has significantly improved the description of the molecule-surface energy transfer for nonreactive scattering. This so-called modified GLO (MGLO) model retains the simplicity and advantages of the original GLO, while yields much more accurate dynamics results that are in remarkably good agreement with the benchmark data calculated using ab initio molecular dynamics. We argue that the MGLO model is applicable to these highly activated gas-surface reactions with strong molecule-surface couplings.
      Citation: The Journal of Chemical Physics
      PubDate: 2019-01-09T07:14:27Z
      DOI: 10.1063/1.5078541
       
  • Ballistic and diffusive vibrational energy transport in molecules
    • Authors: Igor V. Rubtsov, Alexander L. Burin
      Abstract: The Journal of Chemical Physics, Volume 150, Issue 2, January 2019.
      Energy transport in molecules is essential for many areas of science and technology. Strong covalent bonds of a molecular backbone can facilitate the involvement of the molecule’s high-frequency modes in energy transport, which, under certain conditions, makes the transport fast and efficient. We discuss such conditions and describe various transport regimes in molecules, including ballistic, diffusive, directed diffusion, and intermediate regime cases, in light of recently developed experimental and theoretical approaches.
      Citation: The Journal of Chemical Physics
      PubDate: 2019-01-09T07:14:21Z
      DOI: 10.1063/1.5055670
       
  • Effect of molecular size and hydrogen bonding on three surface-facilitated
           processes in molecular glasses: Surface diffusion, surface crystal growth,
           and formation of stable glasses by vapor deposition
    • Authors: Yinshan Chen, Zhenxuan Chen, Michael Tylinski, M. D. Ediger, Lian Yu
      Abstract: The Journal of Chemical Physics, Volume 150, Issue 2, January 2019.
      Recent work has shown that diffusion and crystal growth can be much faster on the surface of molecular glasses than in the interior and that the enhancement effect varies with molecular size and intermolecular hydrogen bonds (HBs). In a related phenomenon, some molecules form highly stable glasses when vapor-deposited, while others (notably those forming extensive HBs) do not. Here we examine all available data on these phenomena for quantitative structure-property relations. For the systems that form no HBs, the surface diffusion coefficient Ds decreases with increasing molecular size d (d = Ω1/3, where Ω is the molecular volume); when evaluated at the glass transition temperature Tg, Ds decreases ∼5 orders of magnitude for 1 nm of increase in d. Assuming that center-of-mass diffusion is limited by the deepest part of the molecule in the surface-mobility gradient, these data indicate a mobility gradient in reasonable agreement with the Elastically Collective Nonlinear Langevin Equation theory prediction for polystyrene as disjointed Kuhn monomers. For systems of similar d, the Ds value decreases with the extent of intermolecular HB, x (HB), defined as the fraction of vaporization enthalpy due to HB. For both groups together (hydrogen-bonded and otherwise), the Ds data collapse when plotted against d/[1 − x(HB)]; this argues that the HB effect on Ds can be described as a narrowing of the surface mobility layer by a factor [1 − x(HB)] relative to the van der Waals systems. Essentially the same picture holds for the surface crystal growth rate us. The kinetic stability of a vapor-deposited glass decreases with x(HB) but is not better organized by the combined variable d/[1 − x(HB)]. These results indicate that surface crystal growth depends strongly on surface diffusion, whereas the formation of stable glasses by vapor deposition may depend on other factors.
      Citation: The Journal of Chemical Physics
      PubDate: 2019-01-09T07:14:19Z
      DOI: 10.1063/1.5079441
       
  • The electronic complexity of the ground-state of the FeMo cofactor of
           nitrogenase as relevant to quantum simulations
    • Authors: Zhendong Li, Junhao Li, Nikesh S. Dattani, C. J. Umrigar, Garnet Kin-Lic Chan
      Abstract: The Journal of Chemical Physics, Volume 150, Issue 2, January 2019.
      We report that a recent active space model of the nitrogenase FeMo cofactor, proposed in the context of simulations on quantum computers, is not representative of the electronic structure of the FeMo cofactor ground-state. A more representative model does not affect much certain resource estimates for a quantum computer such as the cost of a Trotter step, while strongly affecting others such as the cost of adiabatic state preparation. Thus, conclusions should not be drawn from the complexity of quantum or classical simulations of the electronic structure of this system in this active space. We provide a different model active space for the FeMo cofactor that contains the basic open-shell qualitative character, which may be useful as a benchmark system for making resource estimates for classical and quantum computers.
      Citation: The Journal of Chemical Physics
      PubDate: 2019-01-08T06:47:36Z
      DOI: 10.1063/1.5063376
       
  • Shockwave compression and dissociation of ammonia gas
    • Authors: Dana M. Dattelbaum, John M. Lang, Peter M. Goodwin, Lloyd L. Gibson, William P. Gammel, Joshua D. Coe, Christopher Ticknor, Jeffery A. Leiding
      Abstract: The Journal of Chemical Physics, Volume 150, Issue 2, January 2019.
      We performed a series of plate impact experiments on NH3 gas initially at room temperature and at a pressure of ∼100 psi. Shocked states were determined by optical velocimetry and the temperatures by optical pyrometry, yielding compression ratios of ∼5–10 and second shock temperatures in excess of 7500 K. A first-principles statistical mechanical (thermochemical) approach that included chemical dissociation yielded reasonable agreement with experimental results on the principal Hugoniot, even with interparticle interactions neglected. Theoretical analysis of reshocked states, which predicts a significant degree of chemical dissociation, showed reasonable agreement with experimental data for higher temperature shots; however, reshock calculations required the use of interaction potentials. We rationalize the very different shock temperatures obtained, relative to previous results for argon, in terms of atomic versus molecular heat capacities.
      Citation: The Journal of Chemical Physics
      PubDate: 2019-01-08T06:47:31Z
      DOI: 10.1063/1.5063012
       
  • Breaking dynamic inversion symmetry in a racemic mixture using simple
           trains of laser pulses
    • Authors: Esben F. Thomas, Niels E. Henriksen
      Abstract: The Journal of Chemical Physics, Volume 150, Issue 2, January 2019.
      Recent advances in ultrafast laser technology hint at the possibility of using shaped pulses to generate deracemization via selective enantiomeric conversion; however, experimental implementation remains a challenge and has not yet been achieved. Here, we describe an experiment that can be considered an accessible intermediate step on the road towards achieving laser induced deracemization in a laboratory. Our approach consists of driving a racemic mixture of 3D oriented 3,5-difluoro-3′, 5′-dibromobiphenyl (F2H3C6–C6H3Br2) molecules with a simple train of Gaussian pulses with alternating polarization axes. We use arguments related to the geometry of the field/molecule interaction to illustrate why this will increase the amplitude of the torsional oscillations between the phenyl rings while simultaneously breaking the inversion symmetry of the dynamics between the left- and right-handed enantiomeric forms, two crucial requirements for achieving deracemization. We verify our approach using numerical simulations and show that it leads to significant and experimentally measurable differences in the internal enantiomeric structures when detected by Coulomb explosion imaging.
      Citation: The Journal of Chemical Physics
      PubDate: 2019-01-08T06:47:30Z
      DOI: 10.1063/1.5063536
       
  • Multimode quantum dynamics with multiple Davydov D2 trial states:
           Application to a 24-dimensional conical intersection model
    • Authors: Lipeng Chen, Maxim F. Gelin, Wolfgang Domcke
      Abstract: The Journal of Chemical Physics, Volume 150, Issue 2, January 2019.
      The ultrafast nonadiabatic dynamics of a two-electronic-state four-vibrational-mode conical intersection coupled to a finite bath with up to 20 harmonic oscillators has been investigated by employing the multiple Davydov D2 ansatz. It is demonstrated, using the multi-configuration time-dependent Hartree method as a benchmark, that this approach provides an efficient and robust description of the internal conversion process at multimode conical intersections. Thanks to the Gaussian nature of the Davydov ansatz, it allows for numerically accurate simulations of time-dependent diabatic and (for the first time for a 24-mode system) adiabatic populations of the electronic states and reduced probability densities of the tuning and coupling modes. The obtained adiabatic populations and wave packets can be used as benchmarks for the testing of various simulation methods, in particular, surface-hopping methods.
      Citation: The Journal of Chemical Physics
      PubDate: 2019-01-08T06:47:24Z
      DOI: 10.1063/1.5066022
       
  • Copper atomic contacts exposed to water molecules
    • Authors: Firuz Demir, Kevin Dean
      Abstract: The Journal of Chemical Physics, Volume 150, Issue 2, January 2019.
      Monatomic and molecular hydrogen and also oxygen, as well as water molecules and OH that are exposed to atomic copper in intimate contact, have been studied theoretically using computational methods. The authors optimized moderately large structures of Cu/H/Cu, Cu/HCuH/Cu, Cu/H2/Cu, Cu/H2O/Cu, Cu/OH/Cu, Cu/O/Cu, and Cu/O2/Cu and calculated appropriate values for conductance and inelastic tunneling spectroscopy (IETS) properties of the contact junctions, elucidating them as being a possible outcome resulting from the exposure of copper electrodes to the atomic/molecular contaminant species. Here we also demonstrate the IETS properties, by means of ab initio calculations, which can determine the form of the junction geometries. Furthermore, we identify the bonding geometries at the interfaces of the copper electrodes that directly give rise to the specific IETS signatures that have been observed in recent experiments. Based on low-bias conductance and IETS calculations, for the specific case of water exposure of copper electrodes, it was concluded that a single hydrogen or a single oxygen atom bridging the copper electrodes is not responsible for the high conductance peak measurements. Regarding Model 4, where an individual water molecule is considered to be the bridging constituent, our computational results suggest that it has a relatively low probability of being an appropriate candidate. Based upon current computational results, the two hydrogens in Model 3 appear to be in molecular form, although they still form a bond with the adjacent copper atoms. Comparing computational with experimental results indicates that Model 3 is in acceptable agreement with available data.
      Citation: The Journal of Chemical Physics
      PubDate: 2019-01-08T06:47:22Z
      DOI: 10.1063/1.5080803
       
  • Chemical signatures of surface microheterogeneity on liquid mixtures
    • Authors: Shinichi Enami, Shinnosuke Ishizuka, Agustín J. Colussi
      Abstract: The Journal of Chemical Physics, Volume 150, Issue 2, January 2019.
      Many chemical reactions in Nature, the laboratory, and chemical industry occur in solvent mixtures that bring together species of dissimilar solubilities. Solvent mixtures are visually homogeneous, but are not randomly mixed at the molecular scale. In the all-important binary water-hydrotrope mixtures, small-angle neutron and dynamic light scattering experiments reveal the existence of short-lived (
      Citation: The Journal of Chemical Physics
      PubDate: 2019-01-08T06:47:22Z
      DOI: 10.1063/1.5055684
       
  • A transient bond model for dynamic constraints in meso-scale
           coarse-grained systems
    • Authors: Takashi Uneyama
      Abstract: The Journal of Chemical Physics, Volume 150, Issue 2, January 2019.
      The dynamical properties of entangled polymers originate from the dynamic constraints due to the uncrossability between polymer chains. We propose a highly coarse-grained simulation model with transient bonds for such dynamically constrained systems. Based on the ideas of the responsive particle dynamics (RaPiD) model [P. Kindt and W. J. Briels, J. Chem. Phys. 127, 134901 (2007)] and the multi-chain slip-spring model [T. Uneyama and Y. Masubuchi, J. Chem. Phys. 137, 154902 (2012)], we construct the RaPiD type transient bond model as a coarse-grained slip-spring model. In our model, a polymer chain is expressed as a single particle, and particles are connected by transient bonds. The transient bonds modulate the dynamics of particles, but they do not affect static properties in equilibrium. We show the relation between parameters for the entangled polymer systems and those for the transient bond model. By performing simulations based on the transient bond model, we show how model parameters affect the linear viscoelastic behavior and the diffusion behavior. We also show that the viscoelastic behavior of entangled polymer systems can be well reproduced by the transient bond model.
      Citation: The Journal of Chemical Physics
      PubDate: 2019-01-08T06:47:19Z
      DOI: 10.1063/1.5062495
       
  • Total and partial electron impact ionization cross sections of
           fusion-relevant diatomic molecules
    • Authors: Stefan E. Huber, Andreas Mauracher, Daniel Süß, Ivan Sukuba, Jan Urban, Dmitry Borodin, Michael Probst
      Abstract: The Journal of Chemical Physics, Volume 150, Issue 2, January 2019.
      We report calculations of total (and absolute) electron-impact ionization cross sections (EICSs) for the fusion-relevant diatomic molecular species BeH, BeN, BeO, WH, WBe, WN, WO, O2, and N2 by means of the Deutsch-Märk and the binary-encounter-Bethe methods in the energy range from threshold to 10 keV. In addition, we discuss an empirical scheme to estimate partial cross sections from the total ones based on reaction energetics and empirical threshold laws and explore its accuracy by assessing available experimental data on total and partial EICSs. Finally, we also report parameters obtained by fitting the calculated cross sections to an expression commonly used in fusion edge plasma modeling.
      Citation: The Journal of Chemical Physics
      PubDate: 2019-01-08T06:47:06Z
      DOI: 10.1063/1.5063767
       
  • Observation of the shallow [math] state of NaH
    • Authors: Chia-Ching Chu, Hsien-Yu Huang, Hsiang-Chin Lin, Yi-Hsiang Hsiao, Thou-Jen Whang, Chin-Chun Tsai
      Abstract: The Journal of Chemical Physics, Volume 150, Issue 2, January 2019.
      The 2 1Π state of NaH has been observed up to the last bound vibrational level using pulsed optical-optical double resonance fluorescence depletion spectroscopy. A total of 20 rovibrational energy levels ([math] = 2–4 and J = 1–9) were assigned to this electronic state by means of comparing the successive rovibrational spectra to the eigenvalues of the ab initio potential energy curve. The decrease of background fluorescence near the atomic asymptotic limit Na(3d) + H(1s) is an indication of reaching the dissociation limit of the NaH 2 1Π state. Unobserved rovibrational levels ([math] = 0 and 1) are due to poor Franck-Condon overlap of 2 1Π ← A 1Σ+ transition within the accessible rovibrational levels of intermediate A 1Σ+ state of this work.
      Citation: The Journal of Chemical Physics
      PubDate: 2019-01-08T06:47:03Z
      DOI: 10.1063/1.5065460
       
  • Reactive SINDy: Discovering governing reactions from concentration data
    • Authors: Moritz Hoffmann, Christoph Fröhner, Frank Noé
      Abstract: The Journal of Chemical Physics, Volume 150, Issue 2, January 2019.
      The inner workings of a biological cell or a chemical reactor can be rationalized by the network of reactions, whose structure reveals the most important functional mechanisms. For complex systems, these reaction networks are not known a priori and cannot be efficiently computed with ab initio methods; therefore, an important goal is to estimate effective reaction networks from observations, such as time series of the main species. Reaction networks estimated with standard machine learning techniques such as least-squares regression may fit the observations but will typically contain spurious reactions. Here we extend the sparse identification of nonlinear dynamics (SINDy) method to vector-valued ansatz functions, each describing a particular reaction process. The resulting sparse tensor regression method “reactive SINDy” is able to estimate a parsimonious reaction network. We illustrate that a gene regulation network can be correctly estimated from observed time series.
      Citation: The Journal of Chemical Physics
      PubDate: 2019-01-08T06:47:02Z
      DOI: 10.1063/1.5066099
       
  • Optical properties of semiconducting zigzag carbon nanotubes with and
           without defects
    • Authors: Jinglin Mu, Yuchen Ma, Huichun Liu, Tian Zhang, Shuping Zhuo
      Abstract: The Journal of Chemical Physics, Volume 150, Issue 2, January 2019.
      The excited states of a series of semiconducting zigzag (n, 0) tubes are studied using the GW method and the Bethe-Salpeter equation within the ab initio many-body perturbation theory. The optical variation rule of the excitation energy with the tube diameter exhibits a family pattern, which arises from the electronic structure of the pristine tube and depends on the value of n mod 3. The introduction of single vacancy and Stone-Wales defects with different orientations affords an effective route for modulating the band structures and optical spectra, resulting in the variation of the selection rules of the excitons and turning dipole-forbidden excitons into dipole-allowed ones. The new localized impurity states in defected tubes will provide additional optically allowed transitions and give rise to pronounced satellite red-shifted peaks. These findings provide inspiration for the tune of optical properties of carbon nanotubes in the future for applications in optoelectronics.
      Citation: The Journal of Chemical Physics
      PubDate: 2019-01-08T06:47:00Z
      DOI: 10.1063/1.5055271
       
  • Magnetic field effect on ion pair dynamics upon bimolecular photoinduced
           electron transfer in solution
    • Authors: Serguei V. Feskov, Marina V. Rogozina, Anatoly I. Ivanov, Alexander Aster, Marius Koch, Eric Vauthey
      Abstract: The Journal of Chemical Physics, Volume 150, Issue 2, January 2019.
      The dynamics of the ion pairs produced upon fluorescence quenching of the electron donor 9,10-dimethylanthracene (DMeA) by phthalonitrile have been investigated in acetonitrile and tetrahydrofuran using transient absorption spectroscopy. Charge recombination to both the neutral ground state and the triplet excited state of DMeA is observed in both solvents. The relative efficiency of the triplet recombination pathway decreases substantially in the presence of an external magnetic field. These results were analyzed theoretically within the differential encounter theory, with the spin conversion of the geminate ion pairs described as a coherent process driven by the hyperfine interaction. The early temporal evolution of ion pair and triplet state populations with and without magnetic field could be well reproduced in acetonitrile, but not in tetrahydrofuran where fluorescence quenching involves the formation of an exciplex. A description of the spin conversion in terms of rates, i.e., incoherent spin transitions, leads to an overestimation of the magnetic field effect.
      Citation: The Journal of Chemical Physics
      PubDate: 2019-01-08T06:46:57Z
      DOI: 10.1063/1.5064802
       
  • Electron density topological and adsorbate orbital analyses of water and
           carbon monoxide co-adsorption on platinum
    • Authors: Nicholas Dimakis, Isaiah Salas, Luis Gonzalez, Neili Loupe, Eugene S. Smotkin
      Abstract: The Journal of Chemical Physics, Volume 150, Issue 2, January 2019.
      The electron density topology of carbon monoxide (CO) on dry and hydrated platinum is evaluated under the quantum theory of atoms in molecules (QTAIM) and by adsorbate orbital approaches. The impact of water co-adsorbate on the electronic, structural, and vibrational properties of CO on Pt are modelled by periodic density functional theory (DFT). At low CO coverage, increased hydration weakens C–O bonds and strengthens C–Pt bonds, as verified by changes in bond lengths and stretching frequencies. These results are consistent with QTAIM, the 5σ donation-2π* backdonation model, and our extended π-attraction σ-repulsion model (extended π-σ model). This work links changes in the non-zero eigenvalues of the electron density Hessian at QTAIM bond critical points to changes in the π and σ C–O bonds with systematic variation of CO/H2O co-adsorbate scenarios. QTAIM invariably shows bond strengths and lengths as being negatively correlated. For atop CO on hydrated Pt, QTAIM and phenomenological models are consistent with a direct correlation between C–O bond strength and CO coverage. However, DFT modelling in the absence of hydration shows that C–O bond lengths are not negatively correlated to their stretching frequencies, in contrast to the Badger rule: When QTAIM and phenomenological models do not agree, the use of the non-zero eigenvalues of the electron density Hessian as inputs to the phenomenological models, aligns them with QTAIM. The C–O and C–Pt bond strengths of bridge and three-fold bound CO on dry and hydrated platinum are also evaluated by QTAIM and adsorbate orbital analyses.
      Citation: The Journal of Chemical Physics
      PubDate: 2019-01-08T06:46:51Z
      DOI: 10.1063/1.5046183
       
  • Automated detection of many-particle solvation states for accurate
           characterizations of diffusion kinetics
    • Authors: Joseph F. Rudzinski, Marc Radu, Tristan Bereau
      Abstract: The Journal of Chemical Physics, Volume 150, Issue 2, January 2019.
      Discrete-space kinetic models, i.e., Markov state models, have emerged as powerful tools for reducing the complexity of trajectories generated from molecular dynamics simulations. These models require configuration-space representations that accurately characterize the relevant dynamics. Well-established, low-dimensional order parameters for constructing this representation have led to widespread application of Markov state models to study conformational dynamics in biomolecular systems. On the contrary, applications to characterize single-molecule diffusion processes have been scarce and typically employ system-specific, higher-dimensional order parameters to characterize the local solvation state of the molecule. In this work, we propose an automated method for generating a coarse configuration-space representation, using generic features of the solvation structure—the coordination numbers about each particle. To overcome the inherent noisy behavior of these low-dimensional observables, we treat the features as indicators of an underlying, latent Markov process. The resulting hidden Markov models filter the trajectories of each feature into the most likely latent solvation state at each time step. The filtered trajectories are then used to construct a configuration-space discretization, which accurately describes the diffusion kinetics. The method is validated on a standard model for glassy liquids, where particle jumps between local cages determine the diffusion properties of the system. Not only do the resulting models provide quantitatively accurate characterizations of the diffusion constant, but they also reveal a mechanistic description of diffusive jumps, quantifying the heterogeneity of local diffusion.
      Citation: The Journal of Chemical Physics
      PubDate: 2019-01-08T06:46:46Z
      DOI: 10.1063/1.5064808
       
 
 
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