702 results match your criteria Chinese Journal Of Chemical Physics[Journal]


Polymorphism of polymeric nitrogen at high pressures.

J Chem Phys 2020 Jun;152(24):244502

Key Laboratory of Materials Physics, Institute of Solid State Physics, Chinese Academy of Sciences, Hefei, Anhui 230031, China.

Polymeric nitrogen at 120 GPa-180 GPa is known in two monatomic crystalline cubic gauche (cg-N) and layered polymeric (LP-N) phases and one amorphous modification (η-N), and all these high-pressure phases attract considerable attention for their potential application as a high energy density material. Here, we investigated the stability of these modifications at high pressures in the laser heated diamond anvil cell upon decompression from 161 GPa. Pure LP-N was synthesized above 152 GPa upon laser heating of η-N to 2500 K, while cg-N forms below 150 GPa. Read More

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http://dx.doi.org/10.1063/5.0007453DOI Listing

Reinvestigation of the Rydberg WΠ(ν = 1) level of CO, CO, and CO through rotationally dependent photodissociation branching ratio measurements.

J Chem Phys 2020 Jun;152(23):234308

Beijing National Laboratory for Molecular Sciences (BNLMS), Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.

A recent high resolution photoabsorption study revealed that the Rydberg WΠ(ν = 1) level of carbon monoxide (CO) is perturbed by the valence E″Π(ν = 0) level, and the predissociation linewidth shows drastic variation at the crossing point due to the interference effect [Heays et al., J. Chem. Read More

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http://dx.doi.org/10.1063/5.0009931DOI Listing

Polymeric liquid layer densified by surface acoustic wave.

J Chem Phys 2020 Jun;152(22):224901

Beijing National Research Center for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.

Creating densified and stable liquid is a straightforward strategy for the fabrication of strong and ultra-stable amorphous or glassy materials. The current study has discovered that a liquid polymeric thin film is densified under the application of a high frequency surface acoustic wave (SAW). The experimental evidence is the decrease in film thickness and the increase in refractive index, measured by ellipsometry, of polyisobutylene thin films deposited on the solid substrates, when a high frequency SAW (39. Read More

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http://dx.doi.org/10.1063/5.0010869DOI Listing

Plasmonic hot electrons for sensing, photodetection, and solar energy applications: A perspective.

J Chem Phys 2020 Jun;152(22):220901

Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, Massachusetts 01003-9303, USA.

In plasmonic metals, surface plasmon resonance decays and generates hot electrons and hot holes through non-radiative Landau damping. These hot carriers are highly energetic, which can be modulated by the plasmonic material, size, shape, and surrounding dielectric medium. A plasmonic metal nanostructure, which can absorb incident light in an extended spectral range and transfer the absorbed light energy to adjacent molecules or semiconductors, functions as a "plasmonic photosensitizer. Read More

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http://dx.doi.org/10.1063/5.0005334DOI Listing

Full-dimensional quantum mechanical calculations of the reaction probability of the H + CH reaction based on a mixed Jacobi and Radau description.

J Chem Phys 2020 May;152(20):201101

State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People's Republic of China.

A full-dimensional time-dependent wave packet study using mixed polyspherical Jacobi and Radau coordinates for the title reaction has been reported. The non-reactive moiety CH has been described using three Radau vectors, whereas two Jacobi vectors have been used for the bond breaking/formation process. A potential-optimized discrete variable representation basis has been employed to describe the vibrational coordinates of the reagent CH. Read More

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http://dx.doi.org/10.1063/5.0009721DOI Listing

Fitting potential energy surfaces with fundamental invariant neural network. II. Generating fundamental invariants for molecular systems with up to ten atoms.

J Chem Phys 2020 May;152(20):204307

State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People's Republic of China.

Symmetry adaptation is crucial in representing a permutationally invariant potential energy surface (PES). Due to the rapid increase in computational time with respect to the molecular size, as well as the reliance on the algebra software, the previous neural network (NN) fitting with inputs of fundamental invariants (FIs) has practical limits. Here, we report an improved and efficient generation scheme of FIs based on the computational invariant theory and parallel program, which can be readily used as the input vector of NNs in fitting high-dimensional PESs with permutation symmetry. Read More

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http://dx.doi.org/10.1063/5.0010104DOI Listing

NWChem: Past, present, and future.

J Chem Phys 2020 May;152(18):184102

Institute for Advanced Computational Science, Stony Brook University, Stony Brook, New York 11794, USA.

Specialized computational chemistry packages have permanently reshaped the landscape of chemical and materials science by providing tools to support and guide experimental efforts and for the prediction of atomistic and electronic properties. In this regard, electronic structure packages have played a special role by using first-principle-driven methodologies to model complex chemical and materials processes. Over the past few decades, the rapid development of computing technologies and the tremendous increase in computational power have offered a unique chance to study complex transformations using sophisticated and predictive many-body techniques that describe correlated behavior of electrons in molecular and condensed phase systems at different levels of theory. Read More

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http://dx.doi.org/10.1063/5.0004997DOI Listing

Bias induced spin state transition mediated by electron excitations.

J Chem Phys 2020 Apr;152(13):134301

Key Laboratory of Materials Physics, Institute of Solid State Physics, Chinese Academy of Sciences, Hefei 230031, China.

Recent experiments reported that spin state transitions were realized by applying bias voltages. However, these bias-induced transitions are not fully understood, especially the mechanism. It is well established in experiments that the metal-to-ligand charge transfer (MLCT) excitation activated by light radiation can lead to the transition from low spin (LS) to high spin (HS), and the transition from HS to LS can be achieved by light due to the metal-centered (MC) excitation. Read More

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http://dx.doi.org/10.1063/1.5126968DOI Listing

Long-range interactions of the ground state muonium with atoms.

J Chem Phys 2020 Mar;152(12):124304

State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.

The scaling relations for the dispersion coefficients of long-range interactions between the Mu(1s)-Mu(1s, 2s, or 2p) systems and the H(1s)-H(1s, 2s, or 2p) systems are obtained using analytical properties of hydrogenic wavefunctions, which allows us to obtain the dispersion coefficients for Mu(1s)-Mu(1s, 2s, or 2p) systems from the corresponding H(1s)-H(1s, 2s, or 2p) systems. Additionally, the dispersion coefficients of long-range interactions of Mu(1s) with the ground-state H, noble gas atoms He, Ne, Ar, Kr, and Xe, alkali-metal atoms Li, Na, K, and Rb, alkaline-earth atoms Be, Mg, Ca, and Sr, and Cu, Ag, F, and Cl atoms are calculated. Read More

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http://dx.doi.org/10.1063/1.5144977DOI Listing

Coherent phonon generation in laser-heated gold nanofilm.

J Chem Phys 2020 Mar;152(12):124704

Physics Department and National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, USA.

We have studied the mechanism of coherent acoustic phonon generation in gold nanofilm induced by ultrafast laser-heating. Under the non-equilibrium condition when the lattice heating time is much longer than the film vibration period, we clearly identified the contribution of electronic thermal stress to drive the lattice motion and successfully measured the electronic Grüneisen parameter γ to be 1.6 ± 0. Read More

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http://dx.doi.org/10.1063/1.5137818DOI Listing

A novel multiscale scheme to accelerate atomistic simulations of bio-macromolecules by adaptively driving coarse-grained coordinates.

J Chem Phys 2020 Mar;152(11):114115

School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.

All-atom molecular dynamics (MD) simulations of bio-macromolecules can yield relatively accurate results while suffering from the limitation of insufficient conformational sampling. On the other hand, the coarse-grained (CG) MD simulations efficiently accelerate conformational changes in biomolecules but lose atomistic details and accuracy. Here, we propose a novel multiscale simulation method called the adaptively driving multiscale simulation (ADMS)-it efficiently accelerates biomolecular dynamics by adaptively driving virtual CG atoms on the fly while maintaining the atomistic details and focusing on important conformations of the original system with irrelevant conformations rarely sampled. Read More

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http://dx.doi.org/10.1063/1.5135309DOI Listing

Magnetic quantification of single-crystalline Fe and Co nanowires via off-axis electron holography.

J Chem Phys 2020 Mar;152(11):114202

Beijing National Laboratory for Condensed Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing 100190, People's Republic of China.

Investigating the local micromagnetic structure of ferromagnetic nanowires (NWs) at the nanoscale is essential to study the structure-property relationships and can facilitate the design of nanostructures for technology applications. Herein, we synthesized high-quality iron and cobalt NWs and investigated the magnetic properties of these NWs using off-axis electron holography. The Fe NWs are about 100 nm in width and a few micrometers in length with a preferential growth direction of [100], while the Co NWs have a higher aspect-ratio with preferential crystal growth along the [110] direction. Read More

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http://dx.doi.org/10.1063/1.5145337DOI Listing

Vacuum ultraviolet photodynamics of the methyl peroxy radical studied by double imaging photoelectron photoion coincidences.

J Chem Phys 2020 Mar;152(10):104301

Synchrotron SOLEIL, L'Orme des Merisiers, St. Aubin, BP 48, 91192 Gif sur Yvette, France.

The vacuum ultraviolet photoionization of the methyl peroxy radical, CHO, and unimolecular dissociation of internal energy selected CHO cations were investigated in the 9.7-12.0 eV energy range by synchrotron-based double imaging photoelectron photoion coincidence. Read More

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http://dx.doi.org/10.1063/5.0002109DOI Listing

Probing surface defects of ZnO using formaldehyde.

J Chem Phys 2020 Feb;152(7):074714

State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.

The catalytic properties of metal oxides are often enabled by surface defects, and their characterization is thus vital to the understanding and application of metal oxide catalysts. Typically, surface defects for metal oxides show fingerprints in spectroscopic characterization. However, we found that synchrotron-radiation photoelectron spectroscopy (SRPES) is difficult to probe surface defects of ZnO. Read More

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http://dx.doi.org/10.1063/1.5138372DOI Listing
February 2020

Entire crystallization process of Lennard-Jones liquids: A large-scale molecular dynamics study.

J Chem Phys 2020 Feb;152(5):054903

Key Laboratory of Microgravity (National Microgravity Laboratory), Institute of Mechanics, Chinese Academy of Sciences, Beijing 100190, China.

By using a graphics processing unit-accelerated parallel algorithm on a compute unified device architecture platform, we perform large-scale molecular dynamics simulations in a Lennard-Jones system to observe the entire crystallization process, including metastable stage, critical nuclei formation, and the stage of crystal growth. Although the intermediated precursors that play a role in determining the polymorphs are predominantly bcc ordered, the polymorph selection is rather different at different stages. The precursors that have a relatively high orientational order will be on average in a denser region than uniform liquids, but microscopically the crystal nucleation happens without a density change. Read More

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http://dx.doi.org/10.1063/1.5139574DOI Listing
February 2020

Implementation of three-qubit quantum computation with pendular states of polar molecules by optimal control.

J Chem Phys 2020 Jan;152(4):044303

The Key Laboratory of Quantum Optics, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai 201800, China.

Ultracold polar molecules have been considered as the possible candidates for quantum information processing due to their long coherence time and strong dipole-dipole interaction. In this paper, we consider three coupled polar molecules arranged in a linear chain and trapped in an electric field with gradient. By employing the pendular states of polar molecules as qubits, we successfully realize three-qubit quantum gates and quantum algorithms via the multi-target optimal control theory. Read More

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http://dx.doi.org/10.1063/1.5139688DOI Listing
January 2020

An investigation of the anomalous asymptotic behavior of elastic electron scattering of helium.

J Chem Phys 2020 Jan;152(3):034304

Hefei National Laboratory for Physical Sciences at Microscale and Department of Modern Physics, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China.

For the inelastic electron scattering of atoms and molecules, a consensus has been reached that the first Born approximation is easily approached by decreasing the momentum transfer at the same impact electron energy or increasing the impact electron energy at the same momentum transfer. Although this consensus is applicable for the elastic electron scattering of most atoms and molecules, it is violated for helium where the experimental differential cross sections deviate from the first Born approximation prediction gradually with the decrease of squared momentum transfer at the same impact electron energy. Since this anomalous phenomenon was observed more than 40 years ago, the intrinsic mechanism is not explicit. Read More

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http://dx.doi.org/10.1063/1.5128947DOI Listing
January 2020

Structures and bonding properties of CPt and CPtH: Anion photoelectron spectroscopy and quantum chemical calculations.

J Chem Phys 2019 Dec;151(22):224303

Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.

We present a combined anion photoelectron spectroscopic and quantum chemical investigation on the structures and bonding properties of CPt and CPtH. The experimental vertical detachment energies of CPt and CPtH are measured to be 1.91 ± 0. Read More

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http://dx.doi.org/10.1063/1.5130589DOI Listing
December 2019

Coherent charge-phonon correlations and exciton dynamics in orthorhombic CHNHPbI measured by ultrafast multi-THz spectroscopy.

J Chem Phys 2019 Dec;151(21):214201

Department of Physics, McGill University, Montreal, Quebec H3A 2T8, Canada.

We use time-resolved multi-terahertz spectroscopy for the range 4-40 meV to probe coherent and incoherent ultrafast charge carrier and exciton dynamics in the low temperature orthorhombic phase of the hybrid metal halide perovskite CHNHPbI. Time- and energy-resolved terahertz reflectivity maps reveal strongly damped but coherent oscillations in the 2-4 THz reststrahlen band, indicating charge coupling to a distribution of low energy phonon modes centered at 0.9 THz (3. Read More

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http://dx.doi.org/10.1063/1.5127992DOI Listing
December 2019

Ultrafast dissociative ionization and large-amplitude vibrational wave packet dynamics of strong-field-ionized di-iodomethane.

J Chem Phys 2019 Dec;151(21):214308

Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.

We employ few-cycle pulses to strong-field-ionize di-iodomethane (CHI) and femtosecond extreme ultraviolet (XUV) transient absorption spectroscopy to investigate the subsequent ultrafast dissociative ionization and vibrational wave packet dynamics. Probing in the spectral region of the I 4d core-level transitions, the time-resolved XUV differential absorption spectra reveal the population of several electronic states of CHI by strong-field ionization. Global analysis reveals three distinct time scales for the observed dynamics: 20 ± 2 fs, 49 ± 6 fs, and 157 ± 9 fs, ascribed to relaxation of the CHI parent ion from the Franck-Condon region, dissociation of high-lying excited states of CHI to I (P), CHI, and I (Π), and dissociation of CHI to I (P) and CHI, respectively. Read More

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http://dx.doi.org/10.1063/1.5132967DOI Listing
December 2019

Interface-confined triangular FeO nanoclusters on Pt(111).

J Chem Phys 2019 Dec;151(21):214704

State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.

Under the oxidizing condition, the cheap metal component of bimetallic catalysts often segregates to the surface and forms oxide nanoclusters (NCs) supported on the metal surface, which exhibit unique structures and catalytic properties drastically different from the corresponding bulk materials. Here, density functional theory calculations are employed to describe the atomic and electronic structures of a series of triangular FeO NCs confined on Pt(111) with the size ranging from ∼0.3 nm to ∼2. Read More

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http://dx.doi.org/10.1063/1.5129266DOI Listing
December 2019
5 Reads

Picosecond electron trapping limits the emissivity of CsPbCl perovskite nanocrystals.

J Chem Phys 2019 Nov;151(19):194701

State Key Laboratory of Molecular Reaction Dynamics and Dynamics Research Center for Energy and Environmental Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China.

Lead halide perovskite nanocrystals (NCs) have emerged as enabling materials for optoelectronics and photonics. A parameter essential for these applications is the photoluminescence quantum yield (PL QY) of these NCs. Despite being generally conceived as "defect-tolerant," perovskite NCs often have PL QYs significantly lower than unity, particularly for CsPbCl NCs with QYs typically lower than 10%. Read More

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http://dx.doi.org/10.1063/1.5127887DOI Listing
November 2019

Dynamics studies of the H + HBr reaction: Based on a new potential energy surface.

J Chem Phys 2019 Nov;151(18):185102

Center for Theoretical and Computational Chemistry and State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.

The initial state specific quantum wave packet dynamics studies of the H + HBr (v = 0, j = 0-2) reaction were performed using a new global potential energy surface (PES) of the ground state of the BrH system for the collision energy ranging from 0.01 to 2.0 eV. Read More

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http://dx.doi.org/10.1063/1.5124834DOI Listing
November 2019

Universal nature of dynamic heterogeneity in glass-forming liquids: A comparative study of metallic and polymeric glass-forming liquids.

J Chem Phys 2019 Nov;151(18):184503

Material Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA.

Glass-formation is a ubiquitous phenomenon that is often observed in a broad class of materials ranging from biological matter to commonly encountered synthetic polymer, as well as metallic and inorganic glass-forming (GF) materials. Despite the many regularities in the dynamical properties of GF materials, the structural origin of the universal dynamical properties of these materials has not yet been identified. Recent simulations of coarse-grained polymeric GF liquids have indicated the coexistence of clusters of mobile and immobile particles that appear to be directly linked, respectively, to the rate of molecular diffusion and structural relaxation. Read More

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http://dx.doi.org/10.1063/1.5125641DOI Listing
November 2019

Size dependence of photocatalytic hydrogen generation for CdTe quantum dots.

J Chem Phys 2019 Nov;151(17):174707

Department of Chemistry, University of Rochester, Rochester, New York 14627, USA.

CdTe quantum dots (QDs) are attractive photosensitizers for photocatalytic proton reduction due to their broad absorbance profile that can extend from the ultraviolet to near-infrared regions, providing access to a larger portion of the solar spectrum than possible with analogous CdSe and CdS QD photosensitizers. Here, the photocatalytic hydrogen (H) generation from various sizes of dihydrolipoic acid (DHLA)-capped CdTe QDs, ranging from 2.5 to 7. Read More

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http://dx.doi.org/10.1063/1.5125000DOI Listing
November 2019

Asymmetric and long range interactions in shaken granular media.

J Chem Phys 2019 Oct;151(16):164903

Departament de Física de la Matèria Condensada, Universitat de Barcelona, C. Martí i Franquès 1, Barcelona 08028, Spain.

We use a computational model to investigate the emergence of interaction forces between pairs of intruders in a horizontally vibrated granular fluid. The time evolution of a pair of particles shows a maximum of the likelihood to find the pair at contact in the direction of shaking. This relative interaction is further studied by fixing the intruders in the simulation box where we identify effective mechanical forces and torques between particles and quantify an emergent long range attractive force as a function of the shaking relative angle, the amplitude, and the packing density of grains. Read More

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http://dx.doi.org/10.1063/1.5123304DOI Listing
October 2019

Six-dimensional potential energy surfaces for the dissociative chemisorption of HCl on rigid Ag(100) and Ag(110) surfaces.

J Chem Phys 2019 Oct;151(14):144707

State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People's Republic of China.

The dependence of reactivity on different facets of a surface is an interesting subject in dynamics at gas-surface interfaces. Here, we constructed new six-dimensional (6D) potential energy surfaces (PESs) for the dissociative chemisorption of HCl on rigid Ag(100) and Ag(110) surfaces, using the neural network method based on extensive density functional theory (DFT) calculations with the Perdew-Burke-Ernzerhof (PBE) functional, and compared the two PESs with the previously fitted PES of HCl/Ag(111). Time-dependent wave packet calculations show that the new PESs are very well converged with respect to the fitting procedure as well as to the number of DFT data points. Read More

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http://dx.doi.org/10.1063/1.5122218DOI Listing
October 2019

Morphology independent triplet formation in pentalene films: Singlet fission as the triplet formation mechanism.

J Chem Phys 2019 Sep;151(12):124701

Beijing Key Laboratory for Optical Materials and Photonic Devices, Department of Chemistry, Capital Normal University, Beijing 100048, China.

Singlet fission (SF), a spin-allowed multiexciton generation process, experienced renewed interest in the last decade due to its potential to increase the efficiency of photovoltaic devices. The hurdles now lie in the limited range of SF-capable materials and demanding morphology requirement for an efficient fission process. Although primary fission to yield triplet pair (TT) can occur independently of film morphology in intramolecular singlet fission (iSF) materials, the separation of the TT state has been shown to be highly dependent on the packing motif and morphologies. Read More

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http://dx.doi.org/10.1063/1.5097192DOI Listing
September 2019

Ultrafast carrier and phonon dynamics in few-layer 2H-MoTe.

J Chem Phys 2019 Sep;151(11):114704

Beijing National Laboratory for Condensed Matter Physics, CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.

By using femtosecond pump-probe spectroscopy with broadband detection from near-infrared to midinfrared, the carrier and phonon dynamics in few-layer 2H-MoTe after ultrafast excitation have been investigated in detail. Immediately following the photoexcitation, an ultrafast relaxation of the generated hot carriers by releasing phonons is observed within hundreds of femtoseconds. The subsequent electron-hole recombination with a time constant of ∼1. Read More

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http://dx.doi.org/10.1063/1.5115467DOI Listing
September 2019

Femtosecond real-time probing of the excited-state intramolecular proton transfer reaction in methyl salicylate.

J Chem Phys 2019 Sep;151(9):094302

Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China.

The excited-state intramolecular proton transfer (ESIPT) process and subsequent electronic relaxation dynamics in methyl salicylate have been investigated using femtosecond time-resolved ion yield spectroscopy combined with time-resolved photoelectron imaging. Excitation with a tunable pump pulse populates the keto tautomer in the first excited electronic state S(ππ). As a hydrogen atom transfers from the phenolic group to the carbonyl group within 100 fs, the molecular geometry changes gradually, leading to a variation in the electronic photoionization channel. Read More

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http://dx.doi.org/10.1063/1.5115307DOI Listing
September 2019
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Like-charge polymer-membrane complexation mediated by multivalent cations: One-loop-dressed strong coupling theory.

J Chem Phys 2019 Sep;151(9):094902

School of Physical Sciences and Kavli Institute for Theoretical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.

We probe the electrostatic mechanism driving adsorption of polyelectrolytes onto like-charged membranes upon the addition of tri- and tetravalent counterions to a bathing monovalent salt solution. We develop a one-loop-dressed strong coupling theory that treats the monovalent salt at the electrostatic one-loop level and the multivalent counterions within a strong-coupling approach. It is shown that the adhesive force of the multivalent counterions mediating the like-charge adsorption arises from their strong condensation at the charged membrane. Read More

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http://dx.doi.org/10.1063/1.5109637DOI Listing
September 2019

Prediction of amyloid aggregation rates by machine learning and feature selection.

J Chem Phys 2019 Aug;151(8):084106

Zhou Pei-Yuan Center for Applied Mathematics, Tsinghua University, Beijing 100084, China.

A novel data-based machine learning algorithm for predicting amyloid aggregation rates is reported in this paper. Based on a highly nonlinear projection from 16 intrinsic features of a protein and 4 extrinsic features of the environment to the protein aggregation rate, a feedforward fully connected neural network (FCN) with one hidden layer is trained on a dataset composed of 21 different kinds of amyloid proteins and tested on 4 rest proteins. FCN shows a much better performance than traditional algorithms, such as multivariable linear regression and support vector regression, with an average accuracy higher than 90%. Read More

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http://dx.doi.org/10.1063/1.5113848DOI Listing

Enhanced sampling in molecular dynamics.

J Chem Phys 2019 Aug;151(7):070902

Institute of Systems Biology, Shenzhen Bay Laboratory, Shenzhen 518055, Guangdong, China.

Although molecular dynamics simulations have become a useful tool in essentially all fields of chemistry, condensed matter physics, materials science, and biology, there is still a large gap between the time scale which can be reached in molecular dynamics simulations and that observed in experiments. To address the problem, many enhanced sampling methods were introduced, which effectively extend the time scale being approached in simulations. In this perspective, we review a variety of enhanced sampling methods. Read More

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http://dx.doi.org/10.1063/1.5109531DOI Listing

Temperature regulation of the contact angle of water droplets on the solid surfaces.

J Chem Phys 2019 Jun;150(23):234703

School of Physics, Shandong University, Jinan 250100, China.

We investigate theoretically the stability of the wetting property, i.e., the contact angle values, as a function of the temperature. Read More

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http://dx.doi.org/10.1063/1.5090529DOI Listing
June 2019
1 Read

Theoretical study of charge carrier transport in organic molecular crystals using the Nakajima-Zwanzig-Mori generalized master equation.

J Chem Phys 2019 Jun;150(23):234101

Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China; and Physical Science Laboratory, Huairou National Comprehensive Science Center, Beijing 101407, China.

There has been a long history of applying the generalized master equation (GME) to study charge carrier and exciton transport in molecular systems. Yet exact memory kernels in the GME are generally difficult to obtain. In this work, exact memory kernels of the Nakajima-Zwanzig-Mori GME for a one dimensional Holstein type of model are calculated by employing the Dyson relation for the exact memory kernel, combined with the hierarchical equations of motion method. Read More

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http://dx.doi.org/10.1063/1.5096214DOI Listing
June 2019
10 Reads

Full dimensional quantum mechanical calculations of the reaction probability of the H + NH collision based on a mixed Jacobi and Radau description.

J Chem Phys 2019 May;150(20):204301

State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People's Republic of China.

The collision between hydrogen and ammonia is a benchmark system to study chemical elementary reactions with five atoms. In this work, we present a description of the system based on mixed Jacobi and Radau coordinates combined with the time-dependent wave packet method to study the H + NH reaction. The Radau coordinates are used to describe the reactive moiety NH. Read More

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http://dx.doi.org/10.1063/1.5096047DOI Listing
May 2019
2 Reads

Using Pauli energy to appraise the quality of approximate semilocal non-interacting kinetic energy density functionals.

J Chem Phys 2019 May;150(20):204106

Research Computing Center, University of North Carolina, Chapel Hill, North Carolina 27599-3420, USA.

It is well-known that the kinetic energy density (KED) functional is the most difficult to approximate in density functional theory (DFT), yet to take full advantage of DFT with its density-based descriptive capability of molecular properties, an accurate account of KED is a must. To have a better idea of how an approximate KED formula behaves and where we should focus in the future development of better approximate KEDs, in this work we propose to employ the Pauli energy to assess their quality. We tested the performance of a total of 22 approximate semilocal noninteracting KED functionals from the literature for 18 neutral atoms and 20 small molecules. Read More

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http://dx.doi.org/10.1063/1.5095072DOI Listing
May 2019
15 Reads

Ultrafast intramolecular vibrational energy transfer in carbon nitride hydrocolloid examined by femtosecond two-dimensional infrared spectroscopy.

J Chem Phys 2019 May;150(19):194703

Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.

In this work, ultrafast vibrational and structural processes in a graphitic carbon nitride hydrocolloid system were studied using a combination of linear infrared and nonlinear two-dimensional infrared (2D IR) spectroscopies. The experimentally observed three IR line shapes in the C=N stretching vibration frequency region were analyzed and attributed to the rigid and conjugated molecular frame of the prepared g-CN molecular species, which is believed to be a dimeric tris-s-triazine, as well as attributed to insignificant solvent influence on the delocalized C=N vibrations. Vibrational transition density cubes were also computed for the proposed g-CN dimer, confirming the heterocyclic C=N stretching nature of the three IR absorption peaks. Read More

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http://dx.doi.org/10.1063/1.5093542DOI Listing
May 2019
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Heterogeneous dynamics of unentangled chains in polymer nanocomposites.

J Chem Phys 2019 May;150(18):184903

State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China.

We present a systematic investigation on the effect of adding nanoparticles on the dynamics of polymer chains by using coarse-grained molecular dynamics simulation. The dynamics is characterized by three aspects: molecular motion, relaxation at different length scales, and dynamical heterogeneity. It is found that the motion of polymer chains slows down and the deviation from Gaussian distribution becomes more pronounced with increasing nanoparticle volume fractions. Read More

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http://dx.doi.org/10.1063/1.5089816DOI Listing
May 2019
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Investigating the influence of intramolecular bond lengths on the intermolecular interaction of H-AgCl complex: Binding energy, intermolecular vibrations, and isotope effects.

J Chem Phys 2019 Apr;150(16):164301

Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China.

In this paper, we performed a theoretical study on the influence of intramolecular bond lengths on the intermolecular interactions between H and AgCl molecules. Using four sets of bond lengths for the monomers of H and AgCl, four-dimensional intermolecular potential energy surfaces (PESs) were constructed from ab initio data points at the level of single and double excitation coupled cluster method with noniterative perturbation treatment of triple excitations. A T-shaped global minimum was found on the PES. Read More

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http://dx.doi.org/10.1063/1.5085751DOI Listing
April 2019
1 Read

Optimization of band-selective homonuclear dipolar recoupling in solid-state NMR by a numerical phase search.

J Chem Phys 2019 Apr;150(15):154201

Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China.

Spin polarization transfers among aliphatic C nuclei, especially Cα-Cβ transfers, permit correlations of their nuclear magnetic resonance (NMR) frequencies that are essential for signal assignments in multidimensional solid-state NMR of proteins. We derive and demonstrate a new radio-frequency (RF) excitation sequence for homonuclear dipolar recoupling that enhances spin polarization transfers among aliphatic C nuclei at moderate magic-angle spinning (MAS) frequencies. The phase-optimized recoupling sequence with five π pulses per MAS rotation period (denoted as PR5) is derived initially from systematic numerical simulations in which only the RF phases are varied. Read More

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http://aip.scitation.org/doi/10.1063/1.5092986
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http://dx.doi.org/10.1063/1.5092986DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6474779PMC
April 2019
25 Reads

Erratum: "Homogeneous and inhomogeneous broadenings and the Voigt line shapes in the phase-resolved and intensity sum-frequency generation vibrational spectroscopy" [J. Chem. Phys. 144, 034704 (2016)].

J Chem Phys 2019 04;150(14):149901

William R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, Richland, Washington 99352, USA.

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http://dx.doi.org/10.1063/1.5096906DOI Listing
April 2019
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Two-body dissociation of CH isomers investigated by 50 keV/u Ne impact.

J Chem Phys 2019 Apr;150(14):144311

Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China.

The fragmentation of two isomers of CH, propyne (CHCCH) and allene (CHCCH), is investigated by 50 keV/u Ne impact. Obvious isomer effects are observed by comparing the time-of-flight spectra generated from the two isomers. Six two-body fragmentation channels of CH dications are identified for each isomer. Read More

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http://dx.doi.org/10.1063/1.5097413DOI Listing
April 2019
3 Reads

An interaction-asymptotic region decomposition method for general state-to-state reactive scatterings.

J Chem Phys 2019 Apr;150(13):134105

State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People's Republic of China and Center for Advanced Chemical Physics and 2011 Frontier Centre for Quantum Science and Technology, University of Science and Technology of China, 96 Jinzhai Road, Hefei 230026, China.

A single set of coordinates, which is optimal for both asymptotic product and reactant, is difficult to find in a state-to-state reactive scattering calculation using the quantum wave packet method. An interaction-asymptotic region decomposition (IARD) method was proposed in this work to solve this "coordinate problem." In the method, the interaction region and asymptotic regions are applied with the local optimal coordinate system, i. Read More

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http://dx.doi.org/10.1063/1.5085651DOI Listing
April 2019
3 Reads

Assessing the utility of structure in amorphous materials.

J Chem Phys 2019 Mar;150(11):114502

School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia.

This paper presents a set of general strategies for the analysis of structure in amorphous materials and a general approach to assessing the utility of any selected structural description. Two measures of structure are defined, "diversity" and "utility," and applied to two model glass forming binary atomic alloys, CuZr and a Lennard-Jones AB mixture. We show that the change in diversity associated with selecting Voronoi structures with high localization or low energy, while real, is too weak to support claims that specific structures are the prime cause of these local physical properties. Read More

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http://dx.doi.org/10.1063/1.5064531DOI Listing
March 2019
2 Reads

Helium-hydrogen immiscibility at high pressures.

J Chem Phys 2019 Mar;150(11):114504

Key Laboratory of Materials Physics and Center for Energy Matter in Extreme Environments, Institute of Solid State Physics, Chinese Academy of Sciences, Hefei, Anhui 230031, China.

Hydrogen and helium are the most abundant elements in the universe, and they constitute the interiors of gas giant planets. Thus, their equations of states, phase, chemical state, and chemical reactivity at extreme conditions are of great interest. Applying Raman spectroscopy, visual observation, and synchrotron X-ray diffraction in diamond anvil cells, we performed experiments on H-He 1:1 and D-He 1:10 compressed gas mixtures up to 100 GPa at 300 K. Read More

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http://dx.doi.org/10.1063/1.5086270DOI Listing
March 2019
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A first-principles study on magnetic properties of the intrinsic defects in wurtzite ZnO.

J Chem Phys 2019 Mar;150(9):094704

Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, Gansu 730000, People's Republic of China.

Since the origin of magnetism in ZnO-based diluted magnetic semiconductors (DMSs) is still controversial, in this work, we presented a detailed study on the magnetic, structural, and electronic properties of wurtzite ZnO-based DMS systems with point and complex intrinsic defects. Two outer electrons from neutral oxygen vacancy (V) occupy the a orbital, making the inducted magnetic moment to be zero, while a cluster including three Vs leads to a magnetic moment of ∼1 μ. The magnetic moment of the system with a Zn vacancy (V) is 1. Read More

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http://dx.doi.org/10.1063/1.5063953DOI Listing
March 2019
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Size-selected anion photoelectron spectroscopy and density functional theory study of MnC (n = 3-10): Odd-even alternation and linear-cyclic structure competition.

J Chem Phys 2019 Feb;150(7):074304

Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.

The structural and electronic properties of MnC (n = 3-10) clusters have been investigated using size-selected photoelectron spectroscopy and density functional theory calculations. The vertical detachment energies of MnC exhibit a strong odd-even alternation with increasing number of carbon atoms: the vertical detachment energies of MnC containing even number of carbon atoms are higher than those of adjacent ones containing odd number of carbon atoms. The theoretical analyses indicate that the spin multiplicities and relative stabilities of MnC also exhibit odd-even alternations. Read More

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http://dx.doi.org/10.1063/1.5084310DOI Listing
February 2019
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Flexible high-resolution broadband sum-frequency generation vibrational spectroscopy for intrinsic spectral line widths.

J Chem Phys 2019 Feb;150(7):074702

State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, People's Republic of China.

The difficulty in achieving high spectral resolution and accurate line shape in sum-frequency generation vibrational spectroscopy (SFG-VS) has restricted its use in applications requiring precise detection and quantitative analysis. Recently, the development of high-resolution broadband sum-frequency generation vibrational spectroscopy (HR-BB-SFG-VS) with sub-wavenumber resolution generated by synchronizing two independent amplifier lasers have opened new opportunities for probing an intrinsic SFG response. Here, we present a new flexible approach to achieve HR-BB-SFG-VS. Read More

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http://dx.doi.org/10.1063/1.5066580DOI Listing
February 2019

Unusual self-diffusion behaviors of polymer adsorbed on rough surfaces.

J Chem Phys 2019 Feb;150(6):064902

State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China.

We investigate the diffusion dynamics of a single polymer strongly adsorbed on surfaces in an extremely broad chain length and surface roughness by means of molecular dynamics simulations. Our simulations demonstrate that with the increase in chain length, the diffusion dynamics of polymer chains exhibits three regimes: the Rouse dynamics with D ∼ N when the lateral size of polymer chains is smaller than a half of distance between obstacles on rough surfaces; the reptationlike dynamics with D ∼ N and τ ∼ N when the obstacles inhibit the freely Rouse behavior of polymer chains; and the quasi-Rouse dynamics with D ∼ N and τ ∼ N when the height of obstacles is smaller than twice the vertical size of polymer chains, where D, N, and τ are the diffusion coefficient, chain length, and end-to-end vector relaxation time of polymer chains, respectively. The long chains have sufficient conformation entropy to form loops to hop over short obstacles, which could dramatically reduce the confinement from obstacles on the rough surfaces and changes the diffusion and relaxation dynamics of polymer chains from the reptationlike dynamics to the quasi-Rouse dynamics. Read More

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http://dx.doi.org/10.1063/1.5085178DOI Listing
February 2019
1 Read
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