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Journal of Chemical Physics

Jianfeng Lu, Zhennan Zhou
In this work, a novel ring polymer representation for a multi-level quantum system is proposed for thermal average calculations. The proposed representation keeps the discreteness of the electronic states: besides position and momentum, each bead in the ring polymer is also characterized by a surface index indicating the electronic energy surface. A path integral molecular dynamics with surface hopping (PIMD-SH) dynamics is also developed to sample the equilibrium distribution of the ring polymer configurational space...
April 21, 2017: Journal of Chemical Physics
Johannes Ingenmey, Michael von Domaros, Barbara Kirchner
The quantum cluster equilibrium method is applied to model binary systems of molecular solvents. We minimize the computational effort as well as the experimental input and present the results obtained for the completely miscible acetonitrile/acetone, benzene/acetone, and water/acetone systems, as well as for the hardly miscible water/benzene system. Only clusters of sizes up to n = 3 are applied and these are optimized employing the low-cost functional PBEh-3c. The thermodynamic functions of the pure liquids are in reasonable agreement with experiments...
April 21, 2017: Journal of Chemical Physics
Sheida Ahmadi, Richard K Bowles
Particles confined to a single file, in a narrow quasi-one-dimensional channel, exhibit a dynamic crossover from single file diffusion to Fickian diffusion as the channel radius increases and the particles begin to pass each other. The long time diffusion coefficient for a system in the crossover regime can be described in terms of a hopping time, which measures the time it takes for a particle to escape the cage formed by its neighbours. In this paper, we develop a transition state theory approach to the calculation of the hopping time, using the small system isobaric-isothermal ensemble to rigorously account for the volume fluctuations associated with the size of the cage...
April 21, 2017: Journal of Chemical Physics
Elad Harel
The correlations between different quantum-mechanical degrees of freedom of molecular species dictate their chemical and physical properties. Generally, these correlations are reflected in the optical response of the system but in low-order or low-dimensionality measurement the signals are highly averaged. Here, we describe a novel four-dimensional coherent spectroscopic method that directly correlates within and between the manifold of electronic and vibrational states. The optical response theory is developed in terms of both resonant and non-resonant field-matter interactions...
April 21, 2017: Journal of Chemical Physics
Yurii A Makhnovskii, Sheh-Yi Sheu, Dah-Yen Yang, Sheng Hsien Lin
The motion of a spherical Brownian particle in an asymmetric periodic channel is considered. Under an external periodic stimulus, the particle switches between two states with different particle radius, every half-period. Using Brownian dynamics simulations, we show that the particle size oscillation, combined with the asymmetry of the channel, induces a drift along the channel axis, directed towards the steeper wall of the channel. The oscillation of the particle size is accompanied by a time variation of the space accessible to the particle and by an oscillation of its diffusion coefficient...
April 21, 2017: Journal of Chemical Physics
M H Motevaselian, N R Aluru
We present an empirical potential-based quasi-continuum theory (EQT) to predict the structure and thermodynamic properties of confined fluid mixtures. The central idea in the EQT is to construct potential energies that integrate important atomistic details into a continuum-based model such as the Nernst-Planck equation. The EQT potentials can be also used to construct the excess free energy functional, which is required for the grand potential in the classical density functional theory (cDFT). In this work, we use the EQT-based grand potential to predict various thermodynamic properties of a confined binary mixture of hydrogen and methane molecules inside graphene slit channels of different widths...
April 21, 2017: Journal of Chemical Physics
Nishith K Das, Wissam A Saidi
Nickel-based alloys are widely applied materials in high-temperature applications because they exhibit superior corrosion resistance and mechanical properties. The effects of sulfur, which is invariably present in industrial atmospheres, on the early stages of oxidation of Ni-based surfaces are not well understood. Here we use density functional theory to investigate the interactions of sulfur, SO, and SO2 with the Ni(111) and Cr-doped Ni(111) surface and elucidate their electronic interactions and potential energy surfaces...
April 21, 2017: Journal of Chemical Physics
Camilla Terenzi, Sabine Bouguet-Bonnet, Daniel Canet
At ambient temperature, conversion from 100% enriched para-hydrogen (p-H2; singlet state) to ortho-hydrogen (o-H2; triplet state) leads necessarily to the thermodynamic equilibrium proportions: 75% of o-H2 and 25% of p-H2. When p-H2 is dissolved in a diamagnetic organic solvent, conversion is very slow and can be considered as arising from nuclear spin relaxation phenomena. A first relaxation mechanism, specific to the singlet state and involving a combination of auto-correlation and cross correlation spectral densities, can be retained: randomly fluctuating magnetic fields due to inter-molecular dipolar interactions...
April 21, 2017: Journal of Chemical Physics
Tina Hecksher, Niels Boye Olsen, Jeppe C Dyre
This paper presents data for supercooled squalane's frequency-dependent shear modulus covering frequencies from 10 mHz to 30 kHz and temperatures from 168 K to 190 K; measurements are also reported for the glass phase down to 146 K. The data reveal a strong mechanical beta process. A model is proposed for the shear response of the metastable equilibrium liquid phase of supercooled liquids. The model is an electrical equivalent-circuit characterized by additivity of the dynamic shear compliances of the alpha and beta processes...
April 21, 2017: Journal of Chemical Physics
Rajib Biswas, William Carpenter, Joseph A Fournier, Gregory A Voth, Andrei Tokmakoff
The local environmental sensitivity of infrared (IR) spectroscopy to a hydrogen-bonding structure makes it a powerful tool for investigating the structure and dynamics of excess protons in water. Although of significant interest, the line broadening that results from the ultrafast evolution of different solvated proton-water structures makes the assignment of liquid-phase IR spectra a challenging task. In this work, we apply a normal mode analysis using density functional theory of thousands of proton-water clusters taken from reactive molecular dynamics trajectories of the latest generation multistate empirical valence bond proton model (MS-EVB 3...
April 21, 2017: Journal of Chemical Physics
G Lanaro, G N Patey
We employ lattice energy calculations and molecular dynamics simulations to compare the stability of wurtzite and rock salt crystal structures of four lithium halides (LiF, LiCl, LiBr, and LiI) modeled using the Tosi-Fumi and Joung-Cheatham potentials, which are models frequently used in simulation studies. Both infinite crystals and finite clusters are considered. For the Tosi-Fumi model, we find that all four salts prefer the wurtzite structure both at 0 K and at finite temperatures, in disagreement with experiments, where rock salt is the stable structure and wurtzite exists as a metastable state...
April 21, 2017: Journal of Chemical Physics
Debarati Sarkar, Snigdha Thakur
We simulate a semi-flexible active filament that exhibits spontaneous oscillations on clamping and show self-propulsion when left free. The activity on the filament relies on the nano-dimers distributed at regular intervals along the chain. With an emphasis on the spontaneous beating of a clamped filament, we demonstrate that the two competing forces necessary for oscillation are the elastic forces due to polymer rigidity and the active forces due to chemical activity. In addition, we also study the synchronization of two extensile filaments and the role played by non-local hydrodynamic interactions...
April 21, 2017: Journal of Chemical Physics
M Giani, W K den Otter, W J Briels
The self-assembly process of clathrin coated pits during endocytosis has been simulated by combining and extending coarse grained models of the clathrin triskelion, the adaptor protein AP2, and a flexible network membrane. The AP2's core, upon binding to membrane and cargo, releases a motif that can bind clathrin. In conditions where the core-membrane-cargo binding is weak, the binding of this motif to clathrin can result in a stable complex. We characterize the conditions and mechanisms resulting in the formation of clathrin lattices that curve the membrane, i...
April 21, 2017: Journal of Chemical Physics
Masumeh Gharabaghi, Shant Shahbazian
The quantum theory of atoms in molecules (QTAIM) is based on the clamped nucleus paradigm and solely working with the electronic wavefunctions, so does not include nuclear vibrations in the AIM analysis. On the other hand, the recently extended version of the QTAIM, called the multi-component QTAIM (MC-QTAIM), incorporates both electrons and quantum nuclei, i.e., those nuclei treated as quantum waves instead of clamped point charges, into the AIM analysis using non-adiabatic wavefunctions. Thus, the MC-QTAIM is the natural framework to incorporate the role of nuclear vibrations into the AIM analysis...
April 21, 2017: Journal of Chemical Physics
Yuan Lyu, Ning Xiang, Xiao Zhu, Ganesan Narsimhan
Antimicrobial peptides (AMPs) inactivate microorganisms by forming transmembrane pores in a cell membrane through adsorption and aggregation. Energetics of addition of an AMP to a transmembrane pore is important for evaluation of its formation and growth. Such information is essential for the characterization of pore forming ability of peptides in cell membranes. This study quantifies the potential of mean force through molecular dynamics (MD) simulation for the addition of melittin, a naturally occurring AMP, into a DOPC/DOPG mixed bilayer, a mimic of bacterial membrane, for different extents of insertion into either a bilayer or a pore consisting of three to six transmembrane peptides...
April 21, 2017: Journal of Chemical Physics
Hao Wu, Feliks Nüske, Fabian Paul, Stefan Klus, Péter Koltai, Frank Noé
Markov state models (MSMs) and master equation models are popular approaches to approximate molecular kinetics, equilibria, metastable states, and reaction coordinates in terms of a state space discretization usually obtained by clustering. Recently, a powerful generalization of MSMs has been introduced, the variational approach conformation dynamics/molecular kinetics (VAC) and its special case the time-lagged independent component analysis (TICA), which allow us to approximate slow collective variables and molecular kinetics by linear combinations of smooth basis functions or order parameters...
April 21, 2017: Journal of Chemical Physics
Gurmeet Singh, Apurba Nandi, Shridhar R Gadre, Takashi Chiba, Asuka Fujii
Structures and vibrational spectra of phenol-(acetylene)n (Ph(Ac)n) clusters are studied by a combination of theoretical calculations and infrared (IR) spectroscopy. The molecular electrostatic potential features are utilized for generating trial geometries of the medium-sized Ph(Ac)n (n = 1, 2, 4, 6, and 7) clusters. These initial geometries are subjected to geometry optimization within the second-order Møller-Plesset (MP2) theory, employing correlation consistent aug-cc-pVDZ (aVDZ) basis set. Minimal nature of the reported structures is confirmed by doing vibrational frequency run at MP2/aVDZ level of theory using full calculations for n = 1 and 2 and employing grafting based molecular tailoring approach for the n = 4, 6, and 7...
April 21, 2017: Journal of Chemical Physics
Pep Español, Patrick B Warren
Dissipative particle dynamics (DPD) belongs to a class of models and computational algorithms developed to address mesoscale problems in complex fluids and soft matter in general. It is based on the notion of particles that represent coarse-grained portions of the system under study and allow, therefore, reaching time and length scales that would be otherwise unreachable from microscopic simulations. The method has been conceptually refined since its introduction almost twenty five years ago. This perspective surveys the major conceptual improvements in the original DPD model, along with its microscopic foundation, and discusses outstanding challenges in the field...
April 21, 2017: Journal of Chemical Physics
Takayuki Kamihara, K Takegoshi
Rotational resonance (R2) is one of the widely applied techniques in solid-state NMR for recoupling a homonuclear dipolar interaction under magic-angle spinning (MAS). R2 occurs as the result of interference between the difference of the chemical shifts and MAS. In this work, we extend R2 to a heteronuclear dipolar interaction in the interaction frame of RF irradiation. Based on the average Hamiltonian theory, we show that the recoupling of the heteronuclear dipolar (I-S) interaction occurs at the recoupling conditions written as ΩI(')±ΩS(')=kωr (k=0,±1,±2), where ΩX(') is the RF offset for spin-X (X = I or S) scaled by RF irradiation...
April 21, 2017: Journal of Chemical Physics
Andreas Reindl, Markus Bier, S Dietrich
Density functional theory is used to describe electrolyte solutions in contact with electrodes of planar or spherical shape. For the electrolyte solutions, we consider the so-called civilized model, in which all species present are treated on equal footing. This allows us to discuss the features of the electric double layer in terms of the differential capacitance. The model provides insight into the microscopic structure of the electric double layer, which goes beyond the mesoscopic approach studied in Paper I...
April 21, 2017: Journal of Chemical Physics
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