The Journal of Chemical Physics

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ISSN / EISSN : 0021-9606 / 1089-7690
Published by: AIP Publishing (10.1063)
Total articles ≅ 141,618
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Aixi Zhang, Alex R. Moore, Haoqiang Zhao, Shivajee Govind, Sarah E. Wolf, Yi Jin, , Robert A. Riggleman,
The Journal of Chemical Physics, Volume 156; https://doi.org/10.1063/5.0087600

Abstract:
Stable glasses (SGs) are formed through surface-mediated equilibration (SME) during physical vapor deposition (PVD). Unlike intermolecular interactions, the role of intramolecular degrees of freedom in this process remains unexplored. Here, using experiments and coarse-grained molecular dynamics simulations, we demonstrate that varying dihedral rotation barriers of even a single bond, in otherwise isomeric molecules, can strongly influence the structure and stability of PVD glasses. These effects arise from variations in the degree of surface mobility, mobility gradients, and mobility anisotropy, at a given deposition temperature ( T dep). At high T dep, flexible molecules have access to more configurations, which enhances the rate of SME, forming isotropic SGs. At low T dep, stability is achieved by out of equilibrium aging of the surface layer. Here, the poor packing of rigid molecules enhances the rate of surface-mediated aging, producing stable glasses with layered structures in a broad range of T dep. In contrast, the dynamics of flexible molecules couple more efficiently to the glass layers underneath, resulting in reduced mobility and weaker mobility gradients, producing unstable glasses. Independent of stability, the flattened shape of flexible molecules can also promote in-plane orientational order at low T dep. These results indicate that small changes in intramolecular relaxation barriers can be used as an approach to independently tune the structure and mobility profiles of the surface layer and, thus, the stability and structure of PVD glasses.
Tao Xing, Tianchu Li, Yaming Yan, ,
The Journal of Chemical Physics, Volume 156; https://doi.org/10.1063/5.0095790

Abstract:
We investigate the application of the imaginary time hierarchical equations of motion method to calculate real time quantum correlation functions. By starting from the path integral expression for the correlated system–bath equilibrium state, we first derive a new set of equations that decouple the imaginary time propagation and the calculation of auxiliary density operators. The new equations, thus, greatly simplify the calculation of the equilibrium correlated initial state that is subsequently used in the real time propagation to obtain the quantum correlation functions. It is also shown that a periodic decomposition of the bath imaginary time correlation function is no longer necessary in the new equations such that different decomposition schemes can be explored. The applicability of the new method is demonstrated in several numerical examples, including the spin-Boson model, the Holstein model, and the double-well model for proton transfer reaction.
A. Katts,
The Journal of Chemical Physics, Volume 156; https://doi.org/10.1063/5.0092703

Abstract:
In this work, we study the global isomorphism between the liquid–vapor equilibrium of the hardcore attractive Yukawa fluid (HCAYF) and that of the Lattice Gas (LG) model of the Ising-like type. The applicability of the global isomorphism transformation and the dependence of its parameters on the screening length of the Yukawa potential are discussed. These parameters determine both the slope of the rectilinear diameter of the liquid–vapor binodal and the Zeno-element, which are the core ingredients of the fluid–LG isomorphism. We compare the Zeno-element parameters with the virial Zeno-line parameters, which are commonly used in the literature for the formulation of generalized law of the correspondent states. It is demonstrated that the Zeno-element parameters appear to be sensitive to the liquid state instability when the interaction potential becomes too short-ranged, while the virial ones do not show any peculiarities connected with this specific of the HCAYF.
Ida Bochert, , , Günter Majer
The Journal of Chemical Physics, Volume 156; https://doi.org/10.1063/5.0092568

Abstract:
We report on the diffusion mechanism of short, single-stranded DNA molecules with up to 100 nucleobases in agarose gels with concentrations of up to 2.0% with the aim to characterize the DNA–agarose interaction. The diffusion coefficients were measured directly, i.e., without any model assumptions, by pulsed field gradient nuclear magnetic resonance (PFG-NMR). We find that the diffusion coefficient decreases, as expected, with an increase in both DNA strand length and gel concentration. In addition, we performed Monte Carlo simulations of particle diffusion in a model network of polymer chains, considering our experimental conditions. Together, the Monte Carlo simulations and the PFG-NMR results show that the decrease in diffusion coefficients in the presence of the agarose gel is due to a temporary adhesion of the DNA molecules to the surface of gel fibers. The average adhesion time to a given gel fiber increases with the length of the DNA strands but is independent of the number of gel fibers. The corresponding magnitude of the binding enthalpies of DNA strands to gel fibers indicates that a mixture of van der Waals interactions and hydrogen bonding contributes to the decreased diffusion of DNA in agarose gels.
The Journal of Chemical Physics, Volume 156; https://doi.org/10.1063/5.0093441

Abstract:
Quantifying the correlation between the complex structures of amorphous materials and their physical properties has been a longstanding problem in materials science. In amorphous Si, a representative covalent amorphous solid, the presence of a medium-range order (MRO) has been intensively discussed. However, the specific atomic arrangement corresponding to the MRO and its relationship with physical properties, such as thermal conductivity, remains elusive. We solved this problem by combining topological data analysis, machine learning, and molecular dynamics simulations. Using persistent homology, we constructed a topological descriptor that can predict thermal conductivity. Moreover, from the inverse analysis of the descriptor, we determined the typical ring features correlated with both the thermal conductivity and MRO. The results could provide an avenue for controlling material characteristics through the topology of the nanostructures.
, O. Chitarra, J.-T. Spaniol, , ,
The Journal of Chemical Physics, Volume 156; https://doi.org/10.1063/5.0095242

Abstract:
The (sub-)millimeter wave spectrum of the non-rigid CH2OH radical is investigated both experimentally and theoretically. Ab initio calculations are carried out to quantitatively characterize its potential energy surface as a function of the two large amplitude ∠H1COH and ∠H2COH dihedral angles. It is shown that the radical displays a large amplitude torsional-like motion of its CH2 group with respect to the OH group. The rotation–torsion levels computed with the help of a 4D Hamiltonian accounting for this torsional-like motion and for the overall rotation exhibit a tunneling splitting, in agreement with recent experimental investigations, and a strong rotational dependence of this tunneling splitting on the rotational quantum number K a due to the rotation–torsion Coriolis coupling. Based on an internal axis method approach, a fitting Hamiltonian accounting for tunneling effects and for the fine and hyperfine structure is built and applied to the fitting of the new (sub)-millimeter wave transitions measured in this work along with previously available high-resolution data. 778 frequencies and wavenumbers are reproduced with a unitless standard deviation of 0.79 using 27 parameters. The N = 0 tunneling splitting, which could not be determined unambiguously in the previous high-resolution investigations, is determined based on its rotational dependence.
, , Rajsekhar Das,
The Journal of Chemical Physics, Volume 156; https://doi.org/10.1063/5.0087815

Abstract:
The growth of a tissue, which depends on cell–cell interactions and biologically relevant processes such as cell division and apoptosis, is regulated by a mechanical feedback mechanism. We account for these effects in a minimal two-dimensional model in order to investigate the consequences of mechanical feedback, which is controlled by a critical pressure, p c. A cell can only grow and divide if its pressure, due to interaction with its neighbors, is less than p c. Because temperature is not a relevant variable, the cell dynamics is driven by self-generated active forces (SGAFs) that arise due to cell division. We show that even in the absence of intercellular interactions, cells undergo diffusive behavior. The SGAF-driven diffusion is indistinguishable from the well-known dynamics of a free Brownian particle at a fixed finite temperature. When intercellular interactions are taken into account, we find persistent temporal correlations in the force–force autocorrelation function (FAF) that extends over a timescale of several cell division times. The time-dependence of the FAF reveals memory effects, which increases as p c increases. The observed non-Markovian effects emerge due to the interplay of cell division and mechanical feedback and are inherently a non-equilibrium phenomenon.
Zhenfeng Pang, Sheetal Jain, Chen Yang, , Kong Ooi Tan
The Journal of Chemical Physics, Volume 156; https://doi.org/10.1063/5.0092265

Abstract:
Polarization transfers are crucial building blocks in magnetic resonance experiments, i.e., they can be used to polarize insensitive nuclei and correlate nuclear spins in multidimensional nuclear magnetic resonance (NMR) spectroscopy. The polarization can be transferred either across different nuclear spin species or from electron spins to the relatively low-polarized nuclear spins. The former route occurring in solid-state NMR can be performed via cross polarization (CP), while the latter route is known as dynamic nuclear polarization (DNP). Despite having different operating conditions, we opinionate that both mechanisms are theoretically similar processes in ideal conditions, i.e., the electron is merely another spin-1/2 particle with a much higher gyromagnetic ratio. Here, we show that the CP and DNP processes can be described using a unified theory based on average Hamiltonian theory combined with fictitious operators. The intuitive and unified approach has allowed new insights into the cross-effect DNP mechanism, leading to better design of DNP polarizing agents and extending the applications beyond just hyperpolarization. We explore the possibility of exploiting theoretically predicted DNP transients for electron–nucleus distance measurements—such as routine dipolar-recoupling experiments in solid-state NMR.
S. Seyedraoufi,
The Journal of Chemical Physics, Volume 156; https://doi.org/10.1063/5.0095128

Abstract:
Proton-transfer (PT) between organic complexes is a common and important biochemical process. Unfortunately, PT energy barriers are difficult to accurately predict using density functional theory (DFT); in particular, using the generalized gradient approximation (GGA) tends to underestimate PT barriers. Moreover, PT typically occurs in environments where dispersion forces contribute to the cohesion of the system; thus, a suitable exchange-correlation functional should accurately describe both dispersion forces and PT barriers. This paper provides benchmark results for the PT barriers of several density functionals, including several variants of the van der Waals density functional (vdW-DF). The benchmark set comprises small organic molecules with inter- and intra-molecular PT. The results show that replacing GGA correlation with a fully non-local vdW-DF correlation increases the PT barriers, making it closer to the quantum chemical reference values. In contrast, including non-local correlations with the Vydrov-Voorhis method or dispersion-corrections at the DFT-D3 or the Tkatchenko–Scheffler level has barely any impact on the PT barriers. Hybrid functionals also increase and improve the energies, resulting in an excellent performance of hybrid versions of vdW-DF-cx and vdW-DF2-B86R. For the formic acid dimer PT system, we analyzed the GGA exchange and non-local correlation contributions. The analysis shows that the repulsive part of the non-local correlation kernel plays a key role in the PT energy barriers predicted with vdW-DF.
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