Publisher: AIP   (Total: 28 journals)   [Sort alphabetically]

Showing 1 - 27 of 27 Journals sorted by number of followers
Physics Today     Hybrid Journal   (Followers: 77, SJR: 0.66, CiteScore: 1)
J. of Applied Physics     Hybrid Journal   (Followers: 69, SJR: 0.739, CiteScore: 2)
Physics of Fluids     Hybrid Journal   (Followers: 58, SJR: 1.19, CiteScore: 3)
Applied Physics Letters     Hybrid Journal   (Followers: 52, SJR: 1.382, CiteScore: 3)
J. of Chemical Physics     Hybrid Journal   (Followers: 37, SJR: 1.252, CiteScore: 2)
J. of Mathematical Physics     Hybrid Journal   (Followers: 26, SJR: 0.644, CiteScore: 1)
Review of Scientific Instruments     Hybrid Journal   (Followers: 21, SJR: 0.585, CiteScore: 1)
Applied Physics Reviews     Hybrid Journal   (Followers: 15, SJR: 4.156, CiteScore: 12)
J. of Laser Applications     Full-text available via subscription   (Followers: 14, SJR: 0.741, CiteScore: 2)
J. of Renewable and Sustainable Energy     Hybrid Journal   (Followers: 14, SJR: 0.44, CiteScore: 1)
Physics of Plasmas     Hybrid Journal   (Followers: 11, SJR: 0.576, CiteScore: 1)
Acoustics Today     Hybrid Journal   (Followers: 10)
APL Materials     Open Access   (Followers: 10, SJR: 1.63, CiteScore: 4)
AIP Advances     Open Access   (Followers: 7, SJR: 0.472, CiteScore: 1)
Biomicrofluidics     Open Access   (Followers: 6, SJR: 0.592, CiteScore: 2)
Low Temperature Physics     Hybrid Journal   (Followers: 6, SJR: 0.264, CiteScore: 1)
Structural Dynamics     Open Access   (Followers: 6, SJR: 1.625, CiteScore: 4)
Chaos : An Interdisciplinary J. of Nonlinear Science     Hybrid Journal   (Followers: 4, SJR: 0.716, CiteScore: 2)
J. of Physical and Chemical Reference Data     Hybrid Journal   (Followers: 3, SJR: 1.046, CiteScore: 3)
Virtual J. of Quantum Information     Hybrid Journal   (Followers: 3)
AIP Conference Proceedings     Full-text available via subscription   (Followers: 2)
Biointerphases     Open Access   (Followers: 1, SJR: 0.558, CiteScore: 2)
Chinese J. of Chemical Physics     Hybrid Journal   (Followers: 1, SJR: 0.24, CiteScore: 1)
Surface Science Spectra     Hybrid Journal   (Followers: 1, SJR: 0.416, CiteScore: 1)
APL Photonics     Open Access   (Followers: 1)
Scilight     Full-text available via subscription  
APL Bioengineering     Open Access  
Similar Journals
Journal Cover
Journal of Chemical Physics
Journal Prestige (SJR): 1.252
Citation Impact (citeScore): 2
Number of Followers: 37  
 
  Hybrid Journal Hybrid journal (It can contain Open Access articles)
ISSN (Print) 0021-9606 - ISSN (Online) 1089-7690
Published by AIP Homepage  [28 journals]
  • The origin of the density scaling exponent for polyatomic molecules and
           the estimation of its value from the liquid structure

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      Authors: F. Kaśkosz, K. Koperwas, A. Grzybowski, M. Paluch
      Abstract: The Journal of Chemical Physics, Volume 158, Issue 14, April 2023.
      In this article, we unravel the problem of interpreting the density scaling exponent for the polyatomic molecules representing the real van der Waals liquids. Our studies show that the density scaling exponent is a weighted average of the exponents of the repulsive terms of all interatomic interactions that occur between molecules, where the potential energy of a given interaction represents its weight. It implies that potential energy is a key quantity required to calculate the density scaling exponent value for real molecules. Finally, we use the well-known method for potential energy estimation and show that the density scaling exponent could be successfully predicted from the liquid structure for fair representatives of the real systems.
      Citation: The Journal of Chemical Physics
      PubDate: 2023-04-14T10:21:59Z
      DOI: 10.1063/5.0141975
       
  • Assessment of random phase approximation and second-order
           Møller–Plesset perturbation theory for many-body interactions in solid
           ethane, ethylene, and acetylene

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      Authors: Khanh Ngoc Pham, Marcin Modrzejewski, Jiří Klimeš
      Abstract: The Journal of Chemical Physics, Volume 158, Issue 14, April 2023.
      The relative energies of different phases or polymorphs of molecular solids can be small, less than a kilojoule/mol. A reliable description of such energy differences requires high-quality treatment of electron correlations, typically beyond that achievable by routinely applicable density functional theory (DFT) approximations. At the same time, high-level wave function theory is currently too computationally expensive. Methods employing an intermediate level of approximations, such as Møller–Plesset (MP) perturbation theory and the random phase approximation (RPA), are potentially useful. However, their development and application for molecular solids has been impeded by the scarcity of necessary benchmark data for these systems. In this work, we employ the coupled-cluster method with singles, doubles, and perturbative triples to obtain a reference-quality many-body expansion of the binding energy of four crystalline hydrocarbons with a varying π-electron character: ethane, ethene, and cubic and orthorhombic forms of acetylene. The binding energy is resolved into explicit dimer, trimer, and tetramer contributions, which facilitates the analysis of errors in the approximate approaches. With the newly generated benchmark data, we test the accuracy of MP2 and non-self-consistent RPA. We find that both of the methods poorly describe the non-additive many-body interactions in closely packed clusters. Using different DFT input states for RPA leads to similar total binding energies, but the many-body components strongly depend on the choice of the exchange–correlation functional.
      Citation: The Journal of Chemical Physics
      PubDate: 2023-04-14T10:21:54Z
      DOI: 10.1063/5.0142348
       
  • Binuclear spin-crossover [Fe(bt)(NCS)2]2(bpm) complex: A study using first
           principles calculations

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      Authors: Koussai Lazaar, Fatma Aouaini, Saber Gueddida
      Abstract: The Journal of Chemical Physics, Volume 158, Issue 14, April 2023.
      The spin-crossover [Fe(bt)(NCS)2]2(bpm) complex is studied using spin-polarized density functional theory within the generalized gradient approximation, the Hubbard U and the weak van der Waals interactions in conjunction with the projector augmented wave method in its molecular and periodic arrangements. It is shown that the considered complex has three magnetic configurations [high spin state (HS)–HS, HS–low spin state (LS), and LS–LS] corresponding to those observed experimentally after two transition temperatures [math] of 163 K and [math] of 197 K. For the HS–HS magnetic state, we found that the two Fe centers are antiferromagnetically coupled for both molecular and periodic structures in good agreement with the experimental observations. Our results show that the computed total energy difference between the magnetic state configurations of the considered Fe2 complex is significantly smaller compared to those reported in the literature for other mono- or binuclear compounds.
      Citation: The Journal of Chemical Physics
      PubDate: 2023-04-14T10:21:53Z
      DOI: 10.1063/5.0147313
       
  • Electrochemical hydrogen evolution on Pt-based catalysts from a
           theoretical perspective

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      Authors: Ke-Xiang Zhang, Zhi-Pan Liu
      Abstract: The Journal of Chemical Physics, Volume 158, Issue 14, April 2023.
      Hydrogen evolution reaction (HER) by splitting water is a key technology toward a clean energy society, where Pt-based catalysts were long known to have the highest activity under acidic electrochemical conditions but suffer from high cost and poor stability. Here, we overview the current status of Pt-catalyzed HER from a theoretical perspective, focusing on the methodology development of electrochemistry simulation, catalytic mechanism, and catalyst stability. Recent developments in theoretical methods for studying electrochemistry are introduced, elaborating on how they describe solid–liquid interface reactions under electrochemical potentials. The HER mechanism, the reaction kinetics, and the reaction sites on Pt are then summarized, which provides an atomic-level picture of Pt catalyst surface dynamics under reaction conditions. Finally, state-of-the-art experimental solutions to improve catalyst stability are also introduced, which illustrates the significance of fundamental understandings in the new catalyst design.
      Citation: The Journal of Chemical Physics
      PubDate: 2023-04-14T10:21:50Z
      DOI: 10.1063/5.0142540
       
  • Kinetic reconstruction of free energies as a function of multiple order
           parameters

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      Authors: Yagyik Goswami, Srikanth Sastry
      Abstract: The Journal of Chemical Physics, Volume 158, Issue 14, April 2023.
      A vast array of phenomena, ranging from chemical reactions to phase transformations, are analyzed in terms of a free energy surface defined with respect to a single or multiple order parameters. Enhanced sampling methods are typically used, especially in the presence of large free energy barriers, to estimate free energies using biasing protocols and sampling of transition paths. Kinetic reconstructions of free energy barriers of intermediate height have been performed, with respect to a single order parameter, employing the steady state properties of unconstrained simulation trajectories when barrier crossing is achievable with reasonable computational effort. Considering such cases, we describe a method to estimate free energy surfaces with respect to multiple order parameters from a steady state ensemble of trajectories. The approach applies to cases where the transition rates between pairs of order parameter values considered is not affected by the presence of an absorbing boundary, whereas the macroscopic fluxes and sampling probabilities are. We demonstrate the applicability of our prescription on different test cases of random walkers executing Brownian motion in order parameter space with an underlying (free) energy landscape and discuss strategies to improve numerical estimates of the fluxes and sampling. We next use this approach to reconstruct the free energy surface for supercooled liquid silicon with respect to the degree of crystallinity and density, from unconstrained molecular dynamics simulations, and obtain results quantitatively consistent with earlier results from umbrella sampling.
      Citation: The Journal of Chemical Physics
      PubDate: 2023-04-14T10:21:48Z
      DOI: 10.1063/5.0144338
       
  • Positioning of grid points for spanning potential energy surfaces—How
           much effort is really needed'

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      Authors: Moritz Schneider, Daniel Born, Johannes Kästner, Guntram Rauhut
      Abstract: The Journal of Chemical Physics, Volume 158, Issue 14, April 2023.
      The positions of grid points for representing a multidimensional potential energy surface (PES) have a non-negligible impact on its accuracy and the associated computational effort for its generation. Six different positioning schemes were studied for PESs represented by n-mode expansions as needed for the accurate calculation of anharmonic vibrational frequencies by means of vibrational configuration interaction theory. A static approach, which has successfully been used in many applications, and five adaptive schemes based on Gaussian process regression have been investigated with respect to the number of necessary grid points and the accuracy of the fundamental modes for a small set of test molecules. A comparison with a related, more sophisticated, and consistent approach by Christiansen et al. is provided. The impact of the positions of the ab initio grid points is discussed for multilevel PESs, for which the computational effort of the individual electronic structure calculations decreases for increasing orders of the n-mode expansion. As a result of that, the ultimate goal is not the maximal reduction of grid points but rather the computational cost, which is not directly related.
      Citation: The Journal of Chemical Physics
      PubDate: 2023-04-13T10:20:05Z
      DOI: 10.1063/5.0146020
       
  • Relation between microscopic structure and macroscopic properties in
           polyacrylonitrile-based lithium-ion polymer gel electrolytes

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      Authors: Jeramie C. Rushing, Anit Gurung, Daniel G. Kuroda
      Abstract: The Journal of Chemical Physics, Volume 158, Issue 14, April 2023.
      Polymer gel electrolytes (PGE) have seen a renewed interest in their development because they have high ionic conductivities but low electrochemical degradation and flammability. PGEs are formed by mixing a liquid lithium-ion electrolyte with a polymer at a sufficiently large concentration to form a gel. PGEs have been extensively studied, but the direct connection between their microscopic structure and macroscopic properties remains controversial. For example, it is still unknown whether the polymer in the PGE acts as an inert, stabilizing scaffold for the electrolyte or it interacts with the ionic components. Here, a PGE composed of a prototypical lithium-carbonate electrolyte and polyacrylonitrile (PAN) is pursued at both microscopic and macroscopic levels. Specifically, this study focused on describing the microscopic and macroscopic changes in the PGE at different polymer concentrations. The results indicated that the polymer-ion and polymer–polymer interactions are strongly dependent on the concentration of the polymer and the lithium salt. In particular, the polymer interacts with itself at very high PAN concentrations (10% weight) resulting in a viscous gel. However, the conductivity and dynamics of the electrolyte liquid components are significantly less affected by the addition of the polymer. The observations are explained in terms of the PGE structure, which transitions from a polymer solution to a gel, containing a polymer matrix and disperse electrolyte, at low and high PAN concentrations, respectively. The results highlight the critical role that the polymer concentration plays in determining both the macroscopic properties of the system and the molecular structure of the PGE.
      Citation: The Journal of Chemical Physics
      PubDate: 2023-04-13T10:20:04Z
      DOI: 10.1063/5.0135631
       
  • Computing vibrational spectra using a new collocation method with a pruned
           basis and more points than basis functions: Avoiding quadrature

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      Authors: Jesse Simmons, Tucker Carrington
      Abstract: The Journal of Chemical Physics, Volume 158, Issue 14, April 2023.
      We present a new collocation method for computing the vibrational spectrum of a polyatomic molecule. Some form of quadrature or collocation is necessary when the potential energy surface does not have a simple form that simplifies the calculation of the potential matrix elements required to do a variational calculation. With quadrature, better accuracy is obtained by using more points than basis functions. To achieve the same advantage with collocation, we introduce a collocation method with more points than basis functions. Critically important, the method can be used with a large basis because it is incorporated into an iterative eigensolver. Previous collocation methods with more points than functions were incompatible with iterative eigensolvers. We test the new ideas by computing energy levels of molecules with as many as six atoms. We use pruned bases but expect the new method to be advantageous whenever one uses a basis for which it is not possible to find an accurate quadrature with about as many points as there are basis functions. For our test molecules, accurate energy levels are obtained even using non-optimal, simple, equally spaced points.
      Citation: The Journal of Chemical Physics
      PubDate: 2023-04-13T10:19:58Z
      DOI: 10.1063/5.0146703
       
  • KIF—Key Interactions Finder: A program to identify the key molecular
           interactions that regulate protein conformational changes

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      Authors: Rory M. Crean, Joanna S. G. Slusky, Peter M. Kasson, Shina Caroline Lynn Kamerlin
      Abstract: The Journal of Chemical Physics, Volume 158, Issue 14, April 2023.
      Simulation datasets of proteins (e.g., those generated by molecular dynamics simulations) are filled with information about how a non-covalent interaction network within a protein regulates the conformation and, thus, function of the said protein. Most proteins contain thousands of non-covalent interactions, with most of these being largely irrelevant to any single conformational change. The ability to automatically process any protein simulation dataset to identify non-covalent interactions that are strongly associated with a single, defined conformational change would be a highly valuable tool for the community. Furthermore, the insights generated from this tool could be applied to basic research, in order to improve understanding of a mechanism of action, or for protein engineering, to identify candidate mutations to improve/alter the functionality of any given protein. The open-source Python package Key Interactions Finder (KIF) enables users to identify those non-covalent interactions that are strongly associated with any conformational change of interest for any protein simulated. KIF gives the user full control to define the conformational change of interest as either a continuous variable or categorical variable, and methods from statistics or machine learning can be applied to identify and rank the interactions and residues distributed throughout the protein, which are relevant to the conformational change. Finally, KIF has been applied to three diverse model systems (protein tyrosine phosphatase 1B, the PDZ3 domain, and the KE07 series of Kemp eliminases) in order to illustrate its power to identify key features that regulate functionally important conformational dynamics.
      Citation: The Journal of Chemical Physics
      PubDate: 2023-04-13T10:19:55Z
      DOI: 10.1063/5.0140882
       
  • Nanoscopic jets and filaments of superfluid 4He at zero temperature: A DFT
           study

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      Authors: Francesco Ancilotto, Manuel Barranco, Martí Pi
      Abstract: The Journal of Chemical Physics, Volume 158, Issue 14, April 2023.
      The instability of a cryogenic 4He jet exiting through a small nozzle into vacuum leads to the formation of 4He drops, which are considered ideal matrices for spectroscopic studies of embedded atoms and molecules. Here, we present a He-density functional theory (DFT) description of droplet formation resulting from jet breaking and contraction of superfluid 4He filaments. Whereas the fragmentation of long jets closely follows the predictions of linear theory for inviscid fluids, leading to droplet trains interspersed with smaller satellite droplets, the contraction of filaments with an aspect ratio larger than a threshold value leads to the nucleation of vortex rings, which hinder their breakup into droplets.
      Citation: The Journal of Chemical Physics
      PubDate: 2023-04-13T10:19:40Z
      DOI: 10.1063/5.0143399
       
  • Effects of electrostatic coupling and surface polarization on
           polyelectrolyte brush structure

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      Authors: Igor M. Telles, Muhammad Arfan, Alexandre P. dos Santos
      Abstract: The Journal of Chemical Physics, Volume 158, Issue 14, April 2023.
      In this work, we perform molecular dynamics simulations to study a spherical polyelectrolyte brush. We explore the effects of surface polarization and electrostatic coupling on brush size and distribution of counterions. The method of image charges is considered to take into account surface polarization, considering a metallic, an unpolarizable, and a dielectric nano-core. It is observed that, for all cases, a moderate shrinking–swelling effect appears with an increase in the electrostatic coupling parameter. This effect occurs under high Manning ratios. The curves relating the average size of polyelectrolyte brush as a function of coupling show a minimum. The results show that the grafting density of polyelectrolytes on the nano-core surface plays an important role in the polarization effect. We consider a modified Poisson–Boltzmann theory to describe the counterion profiles around the brush in the case of unpolarizable nano-cores and weak electrostatic coupling.
      Citation: The Journal of Chemical Physics
      PubDate: 2023-04-13T10:19:38Z
      DOI: 10.1063/5.0147056
       
  • Near-thermo-neutral electron recombination of titanium oxide ions

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      Authors: Naman Jain, Ábel Kálosi, Felix Nuesslein, Daniel Paul, Patrick Wilhelm, Shaun G. Ard, Manfred Grieser, Robert von Hahn, Michael C. Heaven, Evangelos Miliordos, Dominique Maffucci, Nicholas S. Shuman, Albert A. Viggiano, Andreas Wolf, Oldřich Novotný
      Abstract: The Journal of Chemical Physics, Volume 158, Issue 14, April 2023.
      While the dissociative recombination (DR) of ground-state molecular ions with low-energy free electrons is generally known to be exothermic, it has been predicted to be endothermic for a class of transition-metal oxide ions. To understand this unusual case, the electron recombination of titanium oxide ions (TiO+) with electrons has been experimentally investigated using the Cryogenic Storage Ring. In its low radiation field, the TiO+ ions relax internally to low rotational excitation (≲100 K). Under controlled collision energies down to [math] meV within the merged electron and ion beam configuration, fragment imaging has been applied to determine the kinetic energy released to Ti and O neutral reaction products. Detailed analysis of the fragment imaging data considering the reactant and product excitation channels reveals an endothermicity for the TiO+ dissociative electron recombination of (+4 ± 10) meV. This result improves the accuracy of the energy balance by a factor of 7 compared to that found indirectly from hitherto known molecular properties. Conversely, the present endothermicity yields improved dissociation energy values for D0(TiO) = (6.824 ± 0.010) eV and D0(TiO+) = (6.832 ± 0.010) eV. All thermochemistry values were compared to new coupled-cluster calculations and found to be in good agreement. Moreover, absolute rate coefficients for the electron recombination of rotationally relaxed ions have been measured, yielding an upper limit of 1 × 10−7 cm3 s−1 for typical conditions of cold astrophysical media. Strong variation of the DR rate with the TiO+ internal excitation is predicted. Furthermore, potential energy curves for TiO+ and TiO have been calculated using a multi-reference configuration interaction method to constrain quantum-dynamical paths driving the observed TiO+ electron recombination.
      Citation: The Journal of Chemical Physics
      PubDate: 2023-04-13T10:19:34Z
      DOI: 10.1063/5.0146365
       
  • Isotope study of the nonlinear pressure shifts of 85Rb and 87Rb hyperfine
           resonances in Ar, Kr, and Xe buffer gases

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      Authors: B. H. McGuyer
      Abstract: The Journal of Chemical Physics, Volume 158, Issue 14, April 2023.
      Measurements of the 0–0 hyperfine resonant frequencies of ground-state 85Rb atoms show a nonlinear dependence on the pressure of the buffer gases Ar, Kr, and Xe. The nonlinearities are similar to those previously observed with 87Rb and 133Cs and presumed to come from alkali-metal–noble-gas van der Waals molecules. However, the shape of the nonlinearity observed for Xe conflicts with previous theory, and the nonlinearities for Ar and Kr disagree with the expected isotopic scaling of previous 87Rb results. Improving the modeling alleviates most of these discrepancies by treating rotation quantum mechanically and considering additional spin interactions in the molecules. Including the dipolar-hyperfine interaction allows simultaneous fitting of the linear and nonlinear shifts of both 85Rb and 87Rb in either Ar, Kr, or Xe buffer gases with a minimal set of shared, isotope-independent parameters. To the limit of experimental accuracy, the shifts in He and N2 were linear with pressure. The results are of practical interest to vapor-cell atomic clocks and related devices.
      Citation: The Journal of Chemical Physics
      PubDate: 2023-04-13T10:19:30Z
      DOI: 10.1063/5.0145919
       
  • Topological Data analysis of Ion Migration Mechanism

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      Authors: Ryuhei Sato, Kazuto Akagi, Shigeyuki Takagi, Kartik Sau, Kazuaki Kisu, Hao Li, Shin-ichi Orimo
      Abstract: The Journal of Chemical Physics, Volume 158, Issue 14, April 2023.
      Topological data analysis based on persistent homology has been applied to the molecular dynamics simulation for the fast ion-conducting phase (α-phase) of AgI to show its effectiveness on the ion migration mechanism analysis. Time-averaged persistence diagrams of α-AgI, which quantitatively record the shape and size of the ring structures in the given atomic configurations, clearly showed the emergence of the four-membered rings formed by two Ag and two I ions at high temperatures. They were identified as common structures during the Ag ion migration. The averaged potential energy change due to the deformation of the four-membered ring during Ag migration agrees well with the activation energy calculated from the conductivity Arrhenius plot. The concerted motion of two Ag ions via the four-membered ring was also successfully extracted from molecular dynamics simulations by our approach, providing new insight into the specific mechanism of the concerted motion.
      Citation: The Journal of Chemical Physics
      PubDate: 2023-04-13T10:19:29Z
      DOI: 10.1063/5.0143387
       
  • High-pressure and temperature neural network reactive force field for
           energetic materials

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      Authors: Brenden W. Hamilton, Pilsun Yoo, Michael N. Sakano, Md Mahbubul Islam, Alejandro Strachan
      Abstract: The Journal of Chemical Physics, Volume 158, Issue 14, April 2023.
      Reactive force fields for molecular dynamics have enabled a wide range of studies in numerous material classes. These force fields are computationally inexpensive compared with electronic structure calculations and allow for simulations of millions of atoms. However, the accuracy of traditional force fields is limited by their functional forms, preventing continual refinement and improvement. Therefore, we develop a neural network-based reactive interatomic potential for the prediction of the mechanical, thermal, and chemical responses of energetic materials at extreme conditions. The training set is expanded in an automatic iterative approach and consists of various CHNO materials and their reactions under ambient and shock-loading conditions. This new potential shows improved accuracy over the current state-of-the-art force fields for a wide range of properties such as detonation performance, decomposition product formation, and vibrational spectra under ambient and shock-loading conditions.
      Citation: The Journal of Chemical Physics
      PubDate: 2023-04-13T10:19:26Z
      DOI: 10.1063/5.0146055
       
  • Excited-state dynamics of o-nitrophenol studied with UV pump–VUV probe
           time-resolved photoelectron and photoion spectroscopy

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      Authors: Samuel McClung, Dakshitha Abeygunewardane, Spiridoula Matsika, Thomas Weinacht
      Abstract: The Journal of Chemical Physics, Volume 158, Issue 14, April 2023.
      Time-resolved photoionization measurements were performed on o-nitrophenol pumped with UV laser pulses at a central wavelength of 255 nm (4.9 eV) and probed with vacuum ultraviolet (VUV) pulses at 153 nm (8.1 eV). The photoelectron spectrum and time of flight mass spectrum for ions were recorded at each pump–probe delay. The measurements are interpreted with the aid of electronic structure calculations for both the neutral and ionic states. Evidence is found for the formation of a bicyclic intermediate followed by NO dissociation through a process of internal conversion and intersystem crossing. The combination of photoelectron and photoion spectroscopy, together with computational results, provides strong evidence of intersystem crossing that is difficult to establish with only a single technique.
      Citation: The Journal of Chemical Physics
      PubDate: 2023-04-13T10:19:25Z
      DOI: 10.1063/5.0146399
       
  • SchNetPack 2.0: A neural network toolbox for atomistic machine learning

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      Authors: Kristof T. Schütt, Stefaan S. P. Hessmann, Niklas W. A. Gebauer, Jonas Lederer, Michael Gastegger
      Abstract: The Journal of Chemical Physics, Volume 158, Issue 14, April 2023.
      SchNetPack is a versatile neural network toolbox that addresses both the requirements of method development and the application of atomistic machine learning. Version 2.0 comes with an improved data pipeline, modules for equivariant neural networks, and a PyTorch implementation of molecular dynamics. An optional integration with PyTorch Lightning and the Hydra configuration framework powers a flexible command-line interface. This makes SchNetPack 2.0 easily extendable with a custom code and ready for complex training tasks, such as the generation of 3D molecular structures.
      Citation: The Journal of Chemical Physics
      PubDate: 2023-04-12T11:16:47Z
      DOI: 10.1063/5.0138367
       
  • A theory of chemical reactions in biomolecules in solution: Generalized
           Langevin mode analysis (GLMA)

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      Authors: Fumio Hirata
      Abstract: The Journal of Chemical Physics, Volume 158, Issue 14, April 2023.
      The generalized Langevin mode analysis (GLMA) is applied to chemical reactions in biomolecules in solution. The theory sees a chemical reaction in solution as a barrier-crossing process, similar to the Marcus theory. The barrier is defined as the crossing point of two free-energy surfaces that are attributed to the reactant and product of the reaction. It is assumed that both free-energy surfaces are quadratic or harmonic. The assumption is based on the Kim-Hirata theory of structural fluctuation of protein, which proves that the fluctuation around an equilibrium structure is quadratic with respect to the structure or atomic coordinates. The quadratic surface is a composite of many harmonic functions with different modes or frequencies. The height of the activation barrier will be dependent on the mode or frequency—the less the frequency, the lower the barrier. Hence, it is essential to decouple the fluctuational modes into a hierarchical order. GLMA is impeccable for this purpose. It is essential for a theoretical study of chemical reactions to choose a reaction coordinate along which the reaction proceeds. We suppose that the mode whose center of coordinate and/or the frequency changes most before and after the reaction is the one relevant to the chemical reaction and choose the coordinate as the reaction coordinate. The rate of reaction along the reaction coordinate is [math], which is similar to the Marcus expression for the electron transfer reaction. In the equation, ΔF(†) is the activation barrier defined by [math], where [math] and [math] denote the free energies at equilibrium [math] and the crossing point Q†, respectively, both on the free energy surface of the reactant.
      Citation: The Journal of Chemical Physics
      PubDate: 2023-04-12T11:16:45Z
      DOI: 10.1063/5.0143849
       
  • Pulse overlap artifacts and double quantum coherence spectroscopy

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      Authors: Albin Hedse, Alex Arash Sand Kalaee, Andreas Wacker, Tõnu Pullerits
      Abstract: The Journal of Chemical Physics, Volume 158, Issue 14, April 2023.
      The double quantum coherence (DQC) signal in nonlinear spectroscopy gives information about the many-body correlation effects not easily available by other methods. The signal is short-lived, consequently, a significant part of it is generated during the pulse overlap. Since the signal is at two times the laser frequency, one may intuitively expect that the pulse overlap-related artifacts are filtered out by the Fourier transform. Here, we show that this is not the case. We perform explicit calculations of phase-modulated two-pulse experiments of a two-level system where the DQC is impossible. Still, we obtain a significant signal at the modulation frequency, which corresponds to the DQC, while the Fourier transform over the pulse delay shows a double frequency. We repeat the calculations with a three-level system where the true DQC signal occurs. We conclude that with realistic dephasing times, the pulse-overlap artifact can be significantly stronger than the DQC signal. Our results call for great care when analyzing such experiments. As a rule of thumb, we recommend that only delays larger than 1.5 times the pulse length should be used.
      Citation: The Journal of Chemical Physics
      PubDate: 2023-04-12T11:16:43Z
      DOI: 10.1063/5.0146148
       
  • Testing Koopmans spectral functionals on the analytically solvable
           Hooke’s atom

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      Authors: Yannick Schubert, Nicola Marzari, Edward Linscott
      Abstract: The Journal of Chemical Physics, Volume 158, Issue 14, April 2023.
      Koopmans spectral functionals are a class of orbital-density-dependent functionals designed to accurately predict spectroscopic properties. They do so markedly better than their Kohn–Sham density-functional theory counterparts, as demonstrated in earlier works on benchmarks of molecules and bulk systems. This work is a complementary study where—instead of comparing against real, many-electron systems—we test Koopmans spectral functionals on Hooke’s atom, a toy two-electron system that has analytical solutions for particular strengths of its harmonic confining potential. As these calculations clearly illustrate, Koopmans spectral functionals do an excellent job of describing Hooke’s atom across a range of confining potential strengths. This work also provides broader insights into the features and capabilities of Koopmans spectral functionals more generally.
      Citation: The Journal of Chemical Physics
      PubDate: 2023-04-12T11:16:40Z
      DOI: 10.1063/5.0138610
       
  • Enhancing the accuracy of density functional tight binding models through
           ChIMES many-body interaction potentials

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      Authors: Nir Goldman, Laurence E. Fried, Rebecca K. Lindsey, C. Huy Pham, R. Dettori
      Abstract: The Journal of Chemical Physics, Volume 158, Issue 14, April 2023.
      Semi-empirical quantum models such as Density Functional Tight Binding (DFTB) are attractive methods for obtaining quantum simulation data at longer time and length scales than possible with standard approaches. However, application of these models can require lengthy effort due to the lack of a systematic approach for their development. In this work, we discuss the use of the Chebyshev Interaction Model for Efficient Simulation (ChIMES) to create rapidly parameterized DFTB models, which exhibit strong transferability due to the inclusion of many-body interactions that might otherwise be inaccurate. We apply our modeling approach to silicon polymorphs and review previous work on titanium hydride. We also review the creation of a general purpose DFTB/ChIMES model for organic molecules and compounds that approaches hybrid functional and coupled cluster accuracy with two orders of magnitude fewer parameters than similar neural network approaches. In all cases, DFTB/ChIMES yields similar accuracy to the underlying quantum method with orders of magnitude improvement in computational cost. Our developments provide a way to create computationally efficient and highly accurate simulations over varying extreme thermodynamic conditions, where physical and chemical properties can be difficult to interrogate directly, and there is historically a significant reliance on theoretical approaches for interpretation and validation of experimental results.
      Citation: The Journal of Chemical Physics
      PubDate: 2023-04-12T11:16:34Z
      DOI: 10.1063/5.0141616
       
  • 2D-IR spectroscopy of carbohydrates: Characterization of
           thiocyanate-labeled β-glucose in CHCl3 and H2O

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      Authors: P. Gasse, T. Stensitzki, Y. Mai-Linde, T. Linker, H. M. Müller-Werkmeister
      Abstract: The Journal of Chemical Physics, Volume 158, Issue 14, April 2023.
      Carbohydrates constitute one of the four key classes of biomacromolecules but have not been studied by 2D-IR spectroscopy so far. Similarly as for proteins, a lack of native vibrational reporter groups, combined with their huge structural diversity, leads to spectrally congested infrared spectra already for single carbohydrates. Biophysical studies are further impeded by the strong overlap between water modes and carbohydrate modes. Here, we demonstrate the application of the known vibrational reporter group thiocyanate (SCN) as a label in glucose. In this first study, we are able to perform IR and 2D-IR spectroscopy of β-glucose with SCN at the C2 position in chloroform. Upon improved synthesis and the removal of all protecting groups, we successfully performed 2D-IR spectroscopy of β-glucose in H2O. All experimental results are compared to those of methyl-thiocyanate as a reference sample. Overall, we show that the concept of using site-specific vibrational reporter groups can be transferred to carbohydrates. Thus, biophysical studies with 2D-IR spectroscopy can now expand to glycoscience.
      Citation: The Journal of Chemical Physics
      PubDate: 2023-04-12T11:16:31Z
      DOI: 10.1063/5.0139166
       
  • Large barrier behavior of the rate constant from the diffusion equation

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      Authors: Pierpaolo Pravatto, Barbara Fresch, Giorgio J. Moro
      Abstract: The Journal of Chemical Physics, Volume 158, Issue 14, April 2023.
      Many processes in chemistry, physics, and biology depend on thermally activated events in which the system changes its state by surmounting an activation barrier. Examples range from chemical reactions to protein folding and nucleation events. Parameterized forms of the mean field potential are often employed in the stochastic modeling of activated processes. In this contribution, we explore the alternative of employing parameterized forms of the equilibrium distribution by means of symmetric linear combination of two Gaussian functions. Such a procedure leads to flexible and convenient models for the landscape and the energy barrier whose features are controlled by the second moments of these Gaussian functions. The rate constants are examined through the solution of the corresponding diffusion problem, that is, the Fokker–Planck–Smoluchowski equation specified according to the parameterized equilibrium distribution. Numerical calculations clearly show that the asymptotic limit of large barriers does not agree with the results of the Kramers theory. The underlying reason is that the linear scaling of the potential, the procedure justifying the Kramers theory, cannot be applied when dealing with parameterized forms of the equilibrium distribution. A different kind of asymptotic analysis is then required and we introduce the appropriate theory when the equilibrium distribution is represented as a symmetric linear combination of two Gaussian functions: first in the one-dimensional case and afterward in the multidimensional diffusion model.
      Citation: The Journal of Chemical Physics
      PubDate: 2023-04-12T11:16:28Z
      DOI: 10.1063/5.0143522
       
  • Fast conformational clustering of extensive molecular dynamics simulation
           data

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      Authors: Simon Hunkler, Kay Diederichs, Oleksandra Kukharenko, Christine Peter
      Abstract: The Journal of Chemical Physics, Volume 158, Issue 14, April 2023.
      We present an unsupervised data processing workflow that is specifically designed to obtain a fast conformational clustering of long molecular dynamics simulation trajectories. In this approach, we combine two dimensionality reduction algorithms (cc_analysis and encodermap) with a density-based spatial clustering algorithm (hierarchical density-based spatial clustering of applications with noise). The proposed scheme benefits from the strengths of the three algorithms while avoiding most of the drawbacks of the individual methods. Here, the cc_analysis algorithm is applied for the first time to molecular simulation data. The encodermap algorithm complements cc_analysis by providing an efficient way to process and assign large amounts of data to clusters. The main goal of the procedure is to maximize the number of assigned frames of a given trajectory while keeping a clear conformational identity of the clusters that are found. In practice, we achieve this by using an iterative clustering approach and a tunable root-mean-square-deviation-based criterion in the final cluster assignment. This allows us to find clusters of different densities and different degrees of structural identity. With the help of four protein systems, we illustrate the capability and performance of this clustering workflow: wild-type and thermostable mutant of the Trp-cage protein (TC5b and TC10b), NTL9, and Protein B. Each of these test systems poses their individual challenges to the scheme, which, in total, give a nice overview of the advantages and potential difficulties that can arise when using the proposed method.
      Citation: The Journal of Chemical Physics
      PubDate: 2023-04-12T11:16:25Z
      DOI: 10.1063/5.0142797
       
  • Nucleation and growth of crystalline ices from amorphous ices

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      Authors: Christina M. Tonauer, Lilli-Ruth Fidler, Johannes Giebelmann, Keishiro Yamashita, Thomas Loerting
      Abstract: The Journal of Chemical Physics, Volume 158, Issue 14, April 2023.
      We here review mostly experimental and some computational work devoted to nucleation in amorphous ices. In fact, there are only a handful of studies in which nucleation and growth in amorphous ices are investigated as two separate processes. In most studies, crystallization temperatures Tx or crystallization rates RJG are accessed for the combined process. Our Review deals with different amorphous ices, namely, vapor-deposited amorphous solid water (ASW) encountered in many astrophysical environments; hyperquenched glassy water (HGW) produced from μm-droplets of liquid water; and low density amorphous (LDA), high density amorphous (HDA), and very high density amorphous (VHDA) ices produced via pressure-induced amorphization of ice I or from high-pressure polymorphs. We cover the pressure range of up to about 6 GPa and the temperature range of up to 270 K, where only the presence of salts allows for the observation of amorphous ices at such high temperatures. In the case of ASW, its microporosity and very high internal surface to volume ratio are the key factors determining its crystallization kinetics. For HGW, the role of interfaces between individual glassy droplets is crucial but mostly neglected in nucleation or crystallization studies. In the case of LDA, HDA, and VHDA, parallel crystallization kinetics to different ice phases is observed, where the fraction of crystallized ices is controlled by the heating rate. A key aspect here is that in different experiments, amorphous ices of different “purities” are obtained, where “purity” here means the “absence of crystalline nuclei.” For this reason, “preseeded amorphous ice” and “nuclei-free amorphous ice” should be distinguished carefully, which has not been done properly in most studies. This makes a direct comparison of results obtained in different laboratories very hard, and even results obtained in the same laboratory are affected by very small changes in the preparation protocol. In terms of mechanism, the results are consistent with amorphous ices turning into an ultraviscous, deeply supercooled liquid prior to nucleation. However, especially in preseeded amorphous ices, crystallization from the preexisting nuclei takes place simultaneously. To separate the time scales of crystallization from the time scale of structure relaxation cleanly, the goal needs to be to produce amorphous ices free from crystalline ice nuclei. Such ices have only been produced in very few studies.
      Citation: The Journal of Chemical Physics
      PubDate: 2023-04-12T11:16:04Z
      DOI: 10.1063/5.0143343
       
  • Massively parallel GPU enabled third-order cluster perturbation excitation
           energies for cost-effective large scale excitation energy calculations

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      Authors: Andreas Erbs Hillers-Bendtsen, Dmytro Bykov, Ashleigh Barnes, Dmitry Liakh, Hector H. Corzo, Jeppe Olsen, Poul Jørgensen, Kurt V. Mikkelsen
      Abstract: The Journal of Chemical Physics, Volume 158, Issue 14, April 2023.
      We present here a massively parallel implementation of the recently developed CPS(D-3) excitation energy model that is based on cluster perturbation theory. The new algorithm extends the one developed in Baudin et al. [J. Chem. Phys., 150, 134110 (2019)] to leverage multiple nodes and utilize graphical processing units for the acceleration of heavy tensor contractions. Furthermore, we show that the extended algorithm scales efficiently with increasing amounts of computational resources and that the developed code enables CPS(D-3) excitation energy calculations on large molecular systems with a low time-to-solution. More specifically, calculations on systems with over 100 atoms and 1000 basis functions are possible in a few hours of wall clock time. This establishes CPS(D-3) excitation energies as a computationally efficient alternative to those obtained from the coupled-cluster singles and doubles model.
      Citation: The Journal of Chemical Physics
      PubDate: 2023-04-12T02:59:07Z
      DOI: 10.1063/5.0142780
       
  • Hidden singularities in spontaneously polarized molecular solids

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      Authors: Andrew Cassidy, Frank P. Pijpers, David Field
      Abstract: The Journal of Chemical Physics, Volume 158, Issue 14, April 2023.
      Films of dipolar molecules formed by physical vapor deposition are, in general, spontaneously polarized, with implications ranging from electron transfer in molecular optoelectronic devices to the properties of astrochemical ices in the interstellar medium. Polarization arises from dipole orientation, which should intuitively decrease with increasing deposition temperature, T. However, it is experimentally found that minimum or maximum values in polarization vs T may be observed for cis-methyl formate, 1-propanol, and ammonia. A continuous analytic form of polarization vs T is developed, which has the property that it is not differentiable at all T. The minima and maxima in polarization vs T are marked by singularities in the differential of this analytic form. This exotic behavior is presently unique to films of dipolar species and has not been reported, for example, in the related magnetic phases of spin glasses.
      Citation: The Journal of Chemical Physics
      PubDate: 2023-04-11T11:06:21Z
      DOI: 10.1063/5.0138642
       
  • Embedding vertex corrections in GW self-energy: Theory, implementation,
           and outlook

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      Authors: Guorong Weng, Rushil Mallarapu, Vojtěch Vlček
      Abstract: The Journal of Chemical Physics, Volume 158, Issue 14, April 2023.
      The vertex function (Γ) within the Green’s function formalism encapsulates information about all higher-order electron–electron interaction beyond those mediated by density fluctuations. Herein, we present an efficient approach that embeds vertex corrections in the one-shot GW correlation self-energy for isolated and periodic systems. The vertex-corrected self-energy is constructed through the proposed separation–propagation–recombination procedure: the electronic Hilbert space is separated into an active space and its orthogonal complement denoted as the “rest;” the active component is propagated by a space-specific effective Hamiltonian different from the rest. The vertex corrections are introduced by a rescaled time-dependent nonlocal exchange interaction. The direct Γ correction to the self-energy is further updated by adjusting the rescaling factor in a self-consistent post-processing cycle. Our embedding method is tested mainly on donor–acceptor charge-transfer systems. The embedded vertex effects consistently and significantly correct the quasiparticle energies of the gap-edge states. The fundamental gap is generally improved by 1–3 eV upon the one-shot GW approximation. Furthermore, we provide an outlook for applications of (embedded) vertex corrections in calculations of extended solids.
      Citation: The Journal of Chemical Physics
      PubDate: 2023-04-11T10:56:02Z
      DOI: 10.1063/5.0139117
       
  • Non-equilibrium dynamics at the gas–liquid interface: State-resolved
           studies of NO evaporation from a benzyl alcohol liquid microjet

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      Authors: Mikhail Ryazanov, David J. Nesbitt
      Abstract: The Journal of Chemical Physics, Volume 158, Issue 14, April 2023.
      First measurements of internal quantum-state distributions for nitric oxide (NO) evaporating from liquid benzyl alcohol are presented over a broad range of temperatures, performed by liquid-microjet techniques in an essentially collision-free regime, with rotational/spin–orbit populations in the 2Π1/2,3/2 manifolds measured by laser-induced fluorescence. The observed rotational distributions exhibit highly linear (i.e., thermal) Boltzmann plots but notably reflect rotational temperatures (Trot) as much as 30 K lower than the liquid temperature (Tjet). A comparable lack of equilibrium behavior is also noted in the electronic degrees of freedom but with populations corresponding to spin–orbit temperatures (TSO) consistently higher than Trot by ∼15 K. These results unambiguously demonstrate evaporation into a non-equilibrium distribution, which, by detailed-balance considerations, predict quantum-state-dependent sticking coefficients for incident collisions of NO at the gas–liquid interface. Comparison and parallels with previous experimental studies of NO thermal desorption and molecular-beam scattering in other systems are discussed, which suggests the emergence of a self-consistent picture for the non-equilibrium dynamics.
      Citation: The Journal of Chemical Physics
      PubDate: 2023-04-11T10:56:01Z
      DOI: 10.1063/5.0143254
       
  • Molecular-level understanding of the rovibrational spectra of N2O in
           gaseous, supercritical, and liquid SF6 and Xe

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      Authors: Kai Töpfer, Debasish Koner, Shyamsunder Erramilli, Lawrence D. Ziegler, Markus Meuwly
      Abstract: The Journal of Chemical Physics, Volume 158, Issue 14, April 2023.
      The transition between the gas-, supercritical-, and liquid-phase behavior is a fascinating topic, which still lacks molecular-level understanding. Recent ultrafast two-dimensional infrared spectroscopy experiments suggested that the vibrational spectroscopy of N2O embedded in xenon and SF6 as solvents provides an avenue to characterize the transitions between different phases as the concentration (or density) of the solvent increases. The present work demonstrates that classical molecular dynamics (MD) simulations together with accurate interaction potentials allows us to (semi-)quantitatively describe the transition in rotational vibrational infrared spectra from the P-/R-branch line shape for the stretch vibrations of N2O at low solvent densities to the Q-branch-like line shapes at high densities. The results are interpreted within the classical theory of rigid-body rotation in more/less constraining environments at high/low solvent densities or based on phenomenological models for the orientational relaxation of rotational motion. It is concluded that classical MD simulations provide a powerful approach to characterize and interpret the ultrafast motion of solutes in low to high density solvents at a molecular level.
      Citation: The Journal of Chemical Physics
      PubDate: 2023-04-11T10:55:58Z
      DOI: 10.1063/5.0143395
       
  • Topological aspects of system-bath Hamiltonians and a vector model for
           multisite systems coupled to local, correlated, or common baths

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      Authors: Nancy Makri
      Abstract: The Journal of Chemical Physics, Volume 158, Issue 14, April 2023.
      Some topological features of multisite Hamiltonians consisting of harmonic potential surfaces with constant site-to-site couplings are discussed. Even in the absence of Duschinsky rotation, such a Hamiltonian assumes the system-bath form only if severe constraints exist. The simplest case of a common bath that couples to all sites is realized when the potential minima are collinear. The bath reorganization energy increases quadratically with site distance in this case. Another frequently encountered situation involves exciton-vibration coupling in molecular aggregates, where the intramolecular normal modes of the monomers give rise to local harmonic potentials. In this case, the reorganization energy accompanying excitation transfer is independent of site-to-site separation, thus this situation cannot be described by the usual system-bath Hamiltonian. A vector system-bath representation is introduced, which brings the exciton-vibration Hamiltonian in system-bath form. In this, the system vectors specify the locations of the potential minima, which in the case of identical monomers lie on the vertices of a regular polyhedron. By properly choosing the system vectors, it is possible to couple each bath to one or more sites and to specify the desired initial density. With a collinear choice of system vectors, the coupling reverts to the simple form of a common bath. The compact form of the vector system-bath coupling generalizes the dissipative tight-binding model to account for local, correlated, and common baths. The influence functional for the vector system-bath Hamiltonian is obtained in a compact and simple form.
      Citation: The Journal of Chemical Physics
      PubDate: 2023-04-11T10:55:55Z
      DOI: 10.1063/5.0147135
       
  • Generation of entangled-photons by a quantum dot cascade source in
           polarized cavities: Using cavity resonances to boost signals and preserve
           the entanglements

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      Authors: K. Nasiri Avanaki, George C. Schatz
      Abstract: The Journal of Chemical Physics, Volume 158, Issue 14, April 2023.
      Motivated by recent advances in the development of single photon emitters for quantum information sciences, here we design and formulate a quantum cascade model that describes cascade emission by a quantum dot (QD) in a cavity structure while preserving entanglement that stores information needed for single photon emission. The theoretical approach is based on a photonic structure that consists of two orthogonal cavities in which resonance with either the first or second of the two emitted photons is possible, leading to amplification and rerouting of the entangled light. The cavity–QD scheme uses a four-level cascade emitter that involves three levels for each polarization, leading to two spatially entangled photons for each polarization. By solving the Schrodinger equation, we identify the characteristic properties of the system, which can be used in conjunction with optimization techniques to achieve the “best” design relative to a set of prioritized criteria or constraints in our optical system. The theoretical investigations include an analysis of emission spectra in addition to the joint spectral density profile, and the results demonstrate the ability of the cavities to act as frequency filters for the photons that make up the entanglements and to modify entanglement properties. The results provide new opportunities for the experimental design and engineering of on-demand single photon sources.
      Citation: The Journal of Chemical Physics
      PubDate: 2023-04-11T10:55:54Z
      DOI: 10.1063/5.0144364
       
  • Effects of the 10B/11B isotopic substitution on shear relaxation in
           supercooled B2O3 liquid: A validation of the elastic model of viscous flow
           

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      Authors: Jacob M. Lovi, Sabyasachi Sen
      Abstract: The Journal of Chemical Physics, Volume 158, Issue 14, April 2023.
      The effects of atomic mass in terms of its zero-point vibrational energy, on molar volume, glass transition temperature Tg, and viscosity are studied in glassy and supercooled B2O3 liquids using boron isotope substitutions. The molar volume decreases and Tg and isothermal viscosity increase on the substitution of lighter 10B isotopes with the heavier 11B isotopes. These effects are argued to be a manifestation of the higher zero-point vibrational energy of the lighter isotope, which along with the anharmonicity of the potential well, results in a longer equilibrium inter-atomic distance and larger mean-square displacement with respect to that for the heavier isotope. The isotope effect on viscosity is increasingly enhanced as the temperature approaches Tg, which is shown to be consistent with the prediction of the elastic models of viscous flow and shear relaxation.
      Citation: The Journal of Chemical Physics
      PubDate: 2023-04-11T10:55:53Z
      DOI: 10.1063/5.0147333
       
  • Fast-release kinetics of a pH-responsive polymer detected by dynamic
           contact angles

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      Authors: Xiaomei Li, Krisada Auepattana-Aumrung, Hans-Jürgen Butt, Daniel Crespy, Rüdiger Berger
      Abstract: The Journal of Chemical Physics, Volume 158, Issue 14, April 2023.
      Polymers conjugated with active agents have applications in biomedicine, anticorrosion, and smart agriculture. When the active agent is used as a drug, corrosion inhibitor, or pesticide, it can be released upon a specific stimulus. The efficiency and the sustainability of active agents are determined by the released kinetics. In this work, we study the fast-release kinetics of 8-hydroxyquinoline (8HQ) from a pH-responsive, random copolymer of methyl methacrylate and 8-quinolinyl-sulfide-ethyl acrylate [P(MMA-co-HQSEA)] by hydrolysis of the β-thiopropionate groups. We used contact angle measurements of sliding drops as an elegant way to characterize the release kinetics. Based on the results gained from 1H nuclear magnetic resonance measurement, fluorescent intensity measurement, and velocity-dependent contact angle measurement, we found that both the hydrolysis rate and polymer conformation affect the release kinetics of 8HQ from a P(MMA-co-HQSEA) film. Polymer chains collapse and further suppress the release from the inner layer in acidic conditions, while polymer chains in a stretched condition further facilitate the release from the inner layer. As a result, the cumulative release rate of 8HQ is higher in the basic condition than in the acidic condition.
      Citation: The Journal of Chemical Physics
      PubDate: 2023-04-11T10:55:53Z
      DOI: 10.1063/5.0142928
       
  • Structural, mechanical, and electronic properties of Ni–Co-based layered
           transition metal oxide LiNixCo1−xO2 for Li-ion batteries from first
           principles

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      Authors: Wenjing Qin, Sanqiu Liu, Shuying Zhong, Bo Xu
      Abstract: The Journal of Chemical Physics, Volume 158, Issue 14, April 2023.
      The structural, mechanical, and electronic properties of Ni–Co-based layered transition oxide LiNixCo1−xO2 (x = 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, and 0.9) (LNCO) have been investigated using the first-principles method. The results show that the effect of Ni/Co mixing on the structural property is slight. For the case of the mechanical property, the elastic constant, elastic modulus, such as Young’s modulus (Y), Poisson’s ratio (v), Pugh’s ratio (B/G), and Cauchy pressure (C′) of LNCO have been carefully analyzed based on the strain-energy method. The results demonstrate that the mechanical strength of LNCO materials is weaker than that of pure LiCoO2 (LCO) and LiNiO2 (LNO). However, the B/G ratio and Poisson’s ratio of LNCO are greater than that of the pure LCO and LNO, which means that Ni/Co mixing can improve the ductility of pure LCO and LNO. In addition, Cauchy pressure and anisotropy are also discussed, and as cathode materials, LNCO still exhibits good electrical conductivity. Our results provide a feasible way to realize mechanical property modulation by Ni–Co-based layered transition metal oxides LCO. Furthermore, our study is also helpful to reveal the formation mechanism of intra-lattice microcracks in electrode materials.
      Citation: The Journal of Chemical Physics
      PubDate: 2023-04-11T10:55:51Z
      DOI: 10.1063/5.0142614
       
  • Quantum version of the integral equation theory-based dielectric scheme
           for strongly coupled electron liquids

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      Authors: Panagiotis Tolias, Federico Lucco Castello, Tobias Dornheim
      Abstract: The Journal of Chemical Physics, Volume 158, Issue 14, April 2023.
      A novel dielectric scheme is proposed for strongly coupled electron liquids, which handles quantum mechanical effects beyond the random phase approximation level and treats electronic correlations within the integral equation theory of classical liquids. The self-consistent scheme features a complicated dynamic local field correction functional and its formulation is guided by ab initio path integral Monte Carlo simulations. Remarkably, our scheme is capable of providing unprecedently accurate results for the static structure factor with the exception of the Wigner crystallization vicinity, despite the absence of adjustable or empirical parameters.
      Citation: The Journal of Chemical Physics
      PubDate: 2023-04-11T10:55:42Z
      DOI: 10.1063/5.0145687
       
  • On the potentially transformative role of auxiliary-field quantum Monte
           Carlo in quantum chemistry: A highly accurate method for transition metals
           and beyond

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      Authors: James Shee, John L. Weber, David R. Reichman, Richard A. Friesner, Shiwei Zhang
      Abstract: The Journal of Chemical Physics, Volume 158, Issue 14, April 2023.
      Approximate solutions to the ab initio electronic structure problem have been a focus of theoretical and computational chemistry research for much of the past century, with the goal of predicting relevant energy differences to within “chemical accuracy” (1 kcal/mol). For small organic molecules, or in general, for weakly correlated main group chemistry, a hierarchy of single-reference wave function methods has been rigorously established, spanning perturbation theory and the coupled cluster (CC) formalism. For these systems, CC with singles, doubles, and perturbative triples is known to achieve chemical accuracy, albeit at [math](N7) computational cost. In addition, a hierarchy of density functional approximations of increasing formal sophistication, known as Jacob’s ladder, has been shown to systematically reduce average errors over large datasets representing weakly correlated chemistry. However, the accuracy of such computational models is less clear in the increasingly important frontiers of chemical space including transition metals and f-block compounds, in which strong correlation can play an important role in reactivity. A stochastic method, phaseless auxiliary-field quantum Monte Carlo (ph-AFQMC), has been shown to be capable of producing chemically accurate predictions even for challenging molecular systems beyond the main group, with relatively low [math](N3 − N4) cost and near-perfect parallel efficiency. Herein, we present our perspectives on the past, present, and future of the ph-AFQMC method. We focus on its potential in transition metal quantum chemistry to be a highly accurate, systematically improvable method that can reliably probe strongly correlated systems in biology and chemical catalysis and provide reference thermochemical values (for future development of density functionals or interatomic potentials) when experiments are either noisy or absent. Finally, we discuss the present limitations of the method and where we expect near-term development to be most fruitful.
      Citation: The Journal of Chemical Physics
      PubDate: 2023-04-10T02:00:41Z
      DOI: 10.1063/5.0134009
       
  • Simple and efficient algorithms based on Volterra equations to compute
           memory kernels and projected cross-correlation functions from molecular
           dynamics

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      Authors: Amaël Obliger
      Abstract: The Journal of Chemical Physics, Volume 158, Issue 14, April 2023.
      Starting from the orthogonal dynamics of any given set of variables with respect to the projection variable used to derive the Mori–Zwanzig equation, a set of coupled Volterra equations is obtained that relate the projected time correlation functions between all the variables of interest. This set of equations can be solved using standard numerical inversion methods for Volterra equations, leading to a very convenient yet efficient strategy to obtain any projected time correlation function or contribution to the memory kernel entering a generalized Langevin equation. Using this strategy, the memory kernel related to the diffusion of tagged particles in a bulk Lennard–Jones fluid is investigated up to the long-term regime to show that the repulsive–attractive cross-contribution to memory effects represents a small but non-zero contribution to the self-diffusion coefficient.
      Citation: The Journal of Chemical Physics
      PubDate: 2023-04-10T02:00:40Z
      DOI: 10.1063/5.0143707
       
  • Natural virtual orbitals for the GW method in the random-phase
           approximation and beyond

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      Authors: Laurenz Monzel, Christof Holzer, Wim Klopper
      Abstract: The Journal of Chemical Physics, Volume 158, Issue 14, April 2023.
      The increasingly popular GW method is becoming a convenient tool to determine vertical ionization energies in molecular systems. However, depending on the formalism used and the range of orbitals investigated, it may be hampered by a steep computational scaling. To alleviate this issue, correlated natural virtual orbitals (NVOs) based on second-order Møller–Plesset (MP2) and direct MP2 correlation energies are implemented, and the resulting correlated NVOs are tested on GW quasiparticle energies. Test cases include the popular GW variants G0W0 and evGW0 as well as more elaborate vertex corrections. We find that for increasingly larger molecular systems and basis sets, NVOs considerably improve efficiency. Furthermore, we test the performance of the truncated (frozen) NVO ansatz on the GW100 test set. For the latter, it is demonstrated that, using a carefully chosen truncation threshold, NVOs lead to a negligible loss in accuracy while providing speedups of one order of magnitude. Furthermore, we compare the resulting quasiparticle energies to very accurate vertical ionization energies obtained from coupled-cluster theory with singles, doubles, and noniterative triples [CCSD(T)], confirming that the loss in accuracy introduced by truncating the NVOs is negligible compared to the methodical errors in the GW approximation. It is also demonstrated that the choice of basis set impacts results far more than using a suitably truncated NVO space. Therefore, at the same computational expense, more accurate results can be obtained using NVOs. Finally, we provide improved reference CCSD(T) values for the GW100 test set, which have been obtained using the def2-QZVPP basis set.
      Citation: The Journal of Chemical Physics
      PubDate: 2023-04-10T02:00:37Z
      DOI: 10.1063/5.0144469
       
  • Transient absorption spectroscopy based on uncompressed hollow core fiber
           white light proves pre-association between a radical ion photocatalyst and
           substrate

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      Authors: Ajeet Kumar, Pavel Malevich, Lars Mewes, Shangze Wu, Joshua P. Barham, Jürgen Hauer
      Abstract: The Journal of Chemical Physics, Volume 158, Issue 14, April 2023.
      We present a hollow-core fiber (HCF) based transient absorption experiment, with capabilities beyond common titanium:sapphire based setups. By spectral filtering of the HCF spectrum, we provide pump pulses centered at 425 nm with several hundred nJ of pulse energy at the sample position. By employing the red edge of the HCF output for seeding CaF2, we obtain smooth probing spectra in the range between 320 and 900 nm. We demonstrate the capabilities of our experiment by following the ultrafast relaxation dynamics of a radical cationic photocatalyst to prove its pre-association with an arene substrate, a phenomenon that was not detectable previously by steady-state spectroscopic techniques. The detected preassembly rationalizes the successful participation of radical ionic photocatalysts in single electron transfer reactions, a notion that has been subject to controversy in recent years.
      Citation: The Journal of Chemical Physics
      PubDate: 2023-04-10T02:00:34Z
      DOI: 10.1063/5.0142225
       
  • Fluorescence in quantum dynamics: Accurate spectra require post-mean-field
           approaches

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      Authors: Carlos M. Bustamante, Esteban D. Gadea, Tchavdar N. Todorov, Andrew Horsfield, Lorenzo Stella, Damian A. Scherlis
      Abstract: The Journal of Chemical Physics, Volume 158, Issue 14, April 2023.
      Real time modeling of fluorescence with vibronic resolution entails the representation of the light–matter interaction coupled to a quantum-mechanical description of the phonons and is therefore a challenging problem. In this work, taking advantage of the difference in timescales characterizing internal conversion and radiative relaxation—which allows us to decouple these two phenomena by sequentially modeling one after the other—we simulate the electron dynamics of fluorescence through a master equation derived from the Redfield formalism. Moreover, we explore the use of a recent semiclassical dissipative equation of motion [C. M. Bustamante et al., Phys. Rev. Lett. 126, 087401 (2021)], termed coherent electron electric-field dynamics (CEED), to describe the radiative stage. By comparing the results with those from the full quantum-electrodynamics treatment, we find that the semiclassical model does not reproduce the right amplitudes in the emission spectra when the radiative process involves the de-excitation to a manifold of closely lying states. We argue that this flaw is inherent to any mean-field approach and is the case with CEED. This effect is critical for the study of light–matter interaction, and this work is, to our knowledge, the first one to report this problem. We note that CEED reproduces the correct frequencies in agreement with quantum electrodynamics. This is a major asset of the semiclassical model, since the emission peak positions will be predicted correctly without any prior assumption about the nature of the molecular Hamiltonian. This is not so for the quantum electrodynamics approach, where access to the spectral information relies on knowledge of the Hamiltonian eigenvalues.
      Citation: The Journal of Chemical Physics
      PubDate: 2023-04-10T02:00:31Z
      DOI: 10.1063/5.0142094
       
  • Machine learning and polymer self-consistent field theory in two spatial
           dimensions

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      Authors: Yao Xuan, Kris T. Delaney, Hector D. Ceniceros, Glenn H. Fredrickson
      Abstract: The Journal of Chemical Physics, Volume 158, Issue 14, April 2023.
      A computational framework that leverages data from self-consistent field theory simulations with deep learning to accelerate the exploration of parameter space for block copolymers is presented. This is a substantial two-dimensional extension of the framework introduced in the work of Xuan et al. [J. Comput. Phys. 443, 110519 (2021)]. Several innovations and improvements are proposed. (1) A Sobolev space-trained, convolutional neural network is employed to handle the exponential dimension increase of the discretized, local average monomer density fields and to strongly enforce both spatial translation and rotation invariance of the predicted, field-theoretic intensive Hamiltonian. (2) A generative adversarial network (GAN) is introduced to efficiently and accurately predict saddle point, local average monomer density fields without resorting to gradient descent methods that employ the training set. This GAN approach yields important savings of both memory and computational cost. (3) The proposed machine learning framework is successfully applied to 2D cell size optimization as a clear illustration of its broad potential to accelerate the exploration of parameter space for discovering polymer nanostructures. Extensions to three-dimensional phase discovery appear to be feasible.
      Citation: The Journal of Chemical Physics
      PubDate: 2023-04-10T02:00:30Z
      DOI: 10.1063/5.0142608
       
  • Photoinduced electron transfer across the polymer-capped CsPbBr3 interface
           in a polar medium

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      Authors: Anthony Kipkorir, Xiuyu Jin, Haifeng Gao, Prashant V. Kamat
      Abstract: The Journal of Chemical Physics, Volume 158, Issue 14, April 2023.
      In-situ polymer capping of cesium lead bromide (CsPbBr3) nanocrystals with polymethyl acrylate is an effective approach to improve the colloidal stability in the polar medium and thus extends their use in photocatalysis. The photoinduced electron transfer properties of polymethyl acrylate (PMA)-capped CsPbBr3 nanocrystals have been probed using surface-bound viologen molecules with different alkyl chains as electron acceptors. The apparent association constant (Kapp) obtained for the binding of viologen molecules with PMA-capped CsPbBr3 was 2.3 × 107 M−1, which is an order of magnitude greater than that obtained with oleic acid/oleylamine-capped CsPbBr3. Although the length of the alkyl chain of the viologen molecule did not show any impact on the electron transfer rate constant, it influenced the charge separation efficiency and net electron transfer quantum yield. Viologen moieties with a shorter alkyl chain length exhibited a charge separation efficiency of 72% compared with 50% for the longer chain alkyl chain length viologens. Implications of polymer-capped CsPbBr3 perovskite nanocrystals for carrying out photocatalytic reduction in the polar medium are discussed.
      Citation: The Journal of Chemical Physics
      PubDate: 2023-04-10T02:00:30Z
      DOI: 10.1063/5.0143920
       
  • Approximating constant potential DFT with canonical DFT and electrostatic
           corrections

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      Authors: Fabiola Domínguez-Flores, Marko M. Melander
      Abstract: The Journal of Chemical Physics, Volume 158, Issue 14, April 2023.
      The complexity of electrochemical interfaces has led to the development of several approximate density functional theory (DFT)-based schemes to study reaction thermodynamics and kinetics as a function of electrode potential. While fixed electrode potential conditions can be simulated with grand canonical ensemble DFT (GCE-DFT), various electrostatic corrections on canonical, constant charge DFT are often applied instead. In this work, we present a systematic derivation and analysis of the different electrostatic corrections on canonical DFT to understand their physical validity, implicit assumptions, and scope of applicability. Our work highlights the need to carefully address the suitability of a given model for the problem under study, especially if physical or chemical insight in addition to reaction energetics is sought. In particular, we analytically show that the different corrections cannot differentiate between electrostatic interactions and covalent or charge-transfer interactions. By numerically testing different models for CO2 adsorption on a single-atom catalyst as a function of the electrode potential, we further show that computed capacitances, dipole moments, and the obtained physical insight depend sensitively on the chosen approximation. These features limit the scope, generality, and physical insight of these corrective schemes despite their proven practicality for specific systems and energetics. Finally, we suggest guidelines for choosing different electrostatic corrections and propose the use of conceptual DFT to develop more general approximations for electrochemical interfaces and reactions using canonical DFT.
      Citation: The Journal of Chemical Physics
      PubDate: 2023-04-10T02:00:26Z
      DOI: 10.1063/5.0138197
       
  • A Zn-based catalyst with high oxygen reduction activity and anti-poisoning
           property for stable seawater batteries

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      Authors: Yingxin Liu, Xin Jiang, Li Wang, Rongwei Meng, Quanjun Tang, Yong Guo, Zishan Han, Guowei Ling, Chen Zhang, Quan-Hong Yang
      Abstract: The Journal of Chemical Physics, Volume 158, Issue 14, April 2023.
      Seawater batteries (SWBs) are a key part of the future underwater energy network for maritime safety and resource development due to their high safety, long lifespan, and eco-friendly nature. However, the complicated seawater composition and pollution, such as the S2−, usually poison the catalyst and lead to the degradation of the battery performance. Here, Zn single-atom catalysts (SACs) were demonstrated as effective oxygen reduction reaction catalysts with high anti-poisoning properties by density functional theory calculation and the Zn SACs anchoring on an N, P-doped carbon substrate (Zn-SAC@PNC) was synthesized by a one-pot strategy. Zinc active sites ensure the anti-poisoning property toward S2−, and N, P-doped carbon helps improve the activity. Therefore, Zn-SAC@PNC exhibits superior activity (E1/2: 0.87 V, Tafel slope: 69.5 mV dec−1) compared with Pt/C and shows a lower decay rate of the voltage after discharge in lean-oxygen natural seawater. In the presence of S2−, Zn-SAC@PNC can still maintain its original catalytic activity, which ensures the stable operation of SWBs in the marine environment with sulfur-based pollutants. This study provides a new strategy to design and develop efficient cathode materials for SWBs.
      Citation: The Journal of Chemical Physics
      PubDate: 2023-04-10T02:00:24Z
      DOI: 10.1063/5.0142794
       
  • NAl4X4+ (X = S, Se, Te): Clusters with a planar tetracoordinate nitrogen
           and significantly improved stability

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      Authors: Rui Sun, Caixia Yuan, Hua-Jin Zhai, Yan-Bo Wu
      Abstract: The Journal of Chemical Physics, Volume 158, Issue 14, April 2023.
      The design of clusters featuring non-classical planar hypercoordinate atoms (phAs) often depends on the delocalized multicenter bonds involving reactive electron-deficient elements, which both destabilize the clusters and lead to difficulty in achieving the phA arrangement for electronegative elements such as nitrogen due to their preference for localized bonds. In this work, we computationally designed a series of aluminum chalcogenide clusters NAl4X4+ (X = S, Se, Te) with a desired planar tetracoordinate nitrogen and meaningfully improved chemical stability, as evidenced by the wide gaps (6.51–7.23 eV) between their highest occupied molecular orbitals and lowest unoccupied molecular orbitals, high molecular rigidity (dynamically stable up to 1500 K), and exclusively low global energy minima nature (their isomers locate at least 51.2 kcal/mol higher). Remarkably, these clusters are stabilized by peripheral chalcogen atoms, which not only sterically protect the NAl4 core moiety but also electronically compensate for the electron-deficient aluminum atoms via X → Al π back bonds, meeting the description of our recently proposed “electron-compensation” strategy.
      Citation: The Journal of Chemical Physics
      PubDate: 2023-04-10T02:00:17Z
      DOI: 10.1063/5.0143021
       
 
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Publisher: AIP   (Total: 28 journals)   [Sort alphabetically]

Showing 1 - 27 of 27 Journals sorted by number of followers
Physics Today     Hybrid Journal   (Followers: 77, SJR: 0.66, CiteScore: 1)
J. of Applied Physics     Hybrid Journal   (Followers: 69, SJR: 0.739, CiteScore: 2)
Physics of Fluids     Hybrid Journal   (Followers: 58, SJR: 1.19, CiteScore: 3)
Applied Physics Letters     Hybrid Journal   (Followers: 52, SJR: 1.382, CiteScore: 3)
J. of Chemical Physics     Hybrid Journal   (Followers: 37, SJR: 1.252, CiteScore: 2)
J. of Mathematical Physics     Hybrid Journal   (Followers: 26, SJR: 0.644, CiteScore: 1)
Review of Scientific Instruments     Hybrid Journal   (Followers: 21, SJR: 0.585, CiteScore: 1)
Applied Physics Reviews     Hybrid Journal   (Followers: 15, SJR: 4.156, CiteScore: 12)
J. of Laser Applications     Full-text available via subscription   (Followers: 14, SJR: 0.741, CiteScore: 2)
J. of Renewable and Sustainable Energy     Hybrid Journal   (Followers: 14, SJR: 0.44, CiteScore: 1)
Physics of Plasmas     Hybrid Journal   (Followers: 11, SJR: 0.576, CiteScore: 1)
Acoustics Today     Hybrid Journal   (Followers: 10)
APL Materials     Open Access   (Followers: 10, SJR: 1.63, CiteScore: 4)
AIP Advances     Open Access   (Followers: 7, SJR: 0.472, CiteScore: 1)
Biomicrofluidics     Open Access   (Followers: 6, SJR: 0.592, CiteScore: 2)
Low Temperature Physics     Hybrid Journal   (Followers: 6, SJR: 0.264, CiteScore: 1)
Structural Dynamics     Open Access   (Followers: 6, SJR: 1.625, CiteScore: 4)
Chaos : An Interdisciplinary J. of Nonlinear Science     Hybrid Journal   (Followers: 4, SJR: 0.716, CiteScore: 2)
J. of Physical and Chemical Reference Data     Hybrid Journal   (Followers: 3, SJR: 1.046, CiteScore: 3)
Virtual J. of Quantum Information     Hybrid Journal   (Followers: 3)
AIP Conference Proceedings     Full-text available via subscription   (Followers: 2)
Biointerphases     Open Access   (Followers: 1, SJR: 0.558, CiteScore: 2)
Chinese J. of Chemical Physics     Hybrid Journal   (Followers: 1, SJR: 0.24, CiteScore: 1)
Surface Science Spectra     Hybrid Journal   (Followers: 1, SJR: 0.416, CiteScore: 1)
APL Photonics     Open Access   (Followers: 1)
Scilight     Full-text available via subscription  
APL Bioengineering     Open Access  
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