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  • 更新日期:2020-01-17
  • Unfolding the complexity of phonon quasi-particle physics in disordered materials
    npj Comput. Mater. (IF 9.200) Pub Date : 2020-01-17
    Sai Mu; Raina J. Olsen; Biswanath Dutta; Lucas Lindsay; German D. Samolyuk; Tom Berlijn; Eliot D. Specht; Ke Jin; Hongbin Bei; Tilmann Hickel; Bennet C. Larson; George M. Stocks
    更新日期:2020-01-17
  • 更新日期:2020-01-17
  • Releasing the hidden shift current in the TTF-CA organic molecular solid via symmetry lowering
    npj Comput. Mater. (IF 9.200) Pub Date : 2020-01-17
    Bumseop Kim; Jeongwoo Kim; Dongbin Shin; Min Choi; Junhee Lee; Noejung Park
    更新日期:2020-01-17
  • Real-space quasi-relativistic quantum chemistry
    Comput. Theor. Chem. (IF 1.344) Pub Date : 2020-01-17
    Joel Anderson; Robert J. Harrison; Bryan Sundahl; W. Scott Thornton; Gregory Beylkin
    更新日期:2020-01-17
  • Anion Effect on Gas Absorption in Imidazolium-Based Ionic Liquids
    J. Chem. Inf. Model. (IF 3.966) Pub Date : 2020-01-17
    Jessé G. Neumann; Hubert Stassen
    更新日期:2020-01-17
  • 更新日期:2020-01-17
  • Bidirectional Molecule Generation with Recurrent Neural Networks
    J. Chem. Inf. Model. (IF 3.966) Pub Date : 2020-01-16
    Francesca Grisoni; Michael Moret; Robin Lingwood; Gisbert Schneider
    更新日期:2020-01-17
  • Systematically Scrutinizing the Impact of Substitution Sites on Thermostability and Detergent Tolerance for Bacillus subtilis Lipase A
    J. Chem. Inf. Model. (IF 3.966) Pub Date : 2020-01-16
    Christina Nutschel; Alexander Fulton; Olav Zimmermann; Ulrich Schwaneberg; Karl-Erich Jaeger; Holger Gohlke
    更新日期:2020-01-17
  • Evaluating QM/MM free energy surfaces for ranking cysteine protease covalent inhibitors
    J. Chem. Inf. Model. (IF 3.966) Pub Date : 2020-01-16
    Clauber Costa; Vinícius Bonatto; Alberto Santos; Jeronimo Lameira; Andrei Leitao; Carlos A. Montanari

    One tactic for cysteine protease inhibition is to form a covalent bond between an electrophilic atom of the inhibitor and the thiol of the catalytic cysteine. In this study, we evaluate the reaction free energy obtained from a hybrid Quantum Mechanical/Molecular Mechanical (QM/MM) free energy profile as a predictor of affinity for reversible, covalent inhibitors of rhodesain. We demonstrate that the reaction free energy calculated with the PM6/MM potential is in agreement with the experimental data and suggest that the free energy profile for covalent bond formation in a protein environment may be a useful tool for the inhibitor design.

    更新日期:2020-01-17
  • Why Purine Nucleoside Phosphorylase Ribosylates 2,6-diamino-8-azapurine in non-Canonical Positions? A Molecular Modeling Study
    J. Chem. Inf. Model. (IF 3.966) Pub Date : 2020-01-16
    Maciej Pyrka; Maciej Maciejczyk

    Protein Nucleoside Phosphorylase (PNP) is an enzyme, which catalyzes reversible conversion process (ribosylation and phosphorolysis) between nucleobases (purines) and their nucleosides. Experimental studies showed that calf PNP ribosylates purine analogs in specific positions – 2,6-diamino-8-azapurine in positions 7 or 8 and 8-azaguanine in position 9 of the triazole ring. The reason of this phenomena can be a result of different exposition of purine substrates to the channel leading to the binding site. This hypothesis was verified by application of molecular modelling techniques to two complexes of purine analogs 2,6-diamino-azapurine – calf PNP (pdb-code: 1LVU) and 8-azaguanine – calf PNP (pdb-code: 2AI1). The results obtained with combination of quantum chemistry, docking and molecular dynamics methods showed qualitative validity of our hypothesis. Binding free energies of protein-ligand systems showed that most probable binding poses expose N8 nitrogen for 2,6-diamino-8-azapurine and N9 nitrogen for 8-azaguanine into the binding channel and ruled out exposition of N9 for 2,6-diamino-8-azapurine and N7 for 8-azaguanine, partially in agreement with the experimental data. The other important result obtained in this study is a significantly higher population of protonated form of crucial residue Glu-201 present in the binding pocket, compared to the standard protonation of free glutamic acid in solution. This result combined with populations of tautomeric forms of both investigated systems strongly suggests that 2,6-diamino-8-azaguanine and 8-azaguanine is recognized by proteins with deprotonated and protonated Glu-201 residue, respectively. Comparison of computed binding poses of the investigated ligands to the inhibitors present in crystal structures suggests that modification of (S)-PMPDAP inhibitor, in which 2-(phosphonomethoxy)propyl chain is attached at position 8 instead of position 9, might increase its binding affinity.

    更新日期:2020-01-17
  • Identification of highest-affinity binding sites of yeast transcription factor families
    J. Chem. Inf. Model. (IF 3.966) Pub Date : 2020-01-16
    Zongyu Wang; Wenying He; Jijun Tang; Fei Guo

    Transcription factors (TFs) play the key role in the process of major regulators that control critical cellular processes and response to environmental conditions. Yeast is a single-cell fungal organism that is an important model organism in understanding fundamental biological pathways and transcriptional regulatory networks. The transcriptional regulation in yeast has been studied extensively both computationally and experimentally using traditional methods and high-throughput technologies. However, the identities of transcription factors that regulate major functional categories of genes remain unknown. Due to the avalanche of biological data in the post-genomic era, it is an urgent need to develop automated computational methods to enable accurate identification of efficient transcription factor binding sites from the large number of candidates. In this paper, we analyze high-resolution DNA-binding profiles and motifs for TFs, covering all possible contiguous 8-mers. First, we divide all 8-mers motifs into 16 various categories, and select all sorts of samples from each category by setting the threshold of E-score. Then, we employ five feature representation methods. Also, we adopt a total of three feature selection methods to filter out useless features. Finally, we use Extreme Gradient Boosting (XGBoost) as the base classifier, and adopt the one-vs-rest strategy to construct 16 binary classifiers to solve this multi-classification problem. In the experiment, our method achieves the best performance with the overall Acc of 79.72% and the MCC of 0.77. We find the similarity relationship among each category from different TF families and obtain sequence motif schematic diagram via multiple sequence alignment. The complexity of DNA recognition may act as an important role in the evolution of gene regulatory.

    更新日期:2020-01-17
  • Molecular Determinants for the Activation/Inhibition of Bak Protein by BH3 Peptides
    J. Chem. Inf. Model. (IF 3.966) Pub Date : 2020-01-16
    Guillem Vila-Julià; Jose Manuel Granadino-Roldan; Juan Jesus Perez; Jaime Rubio Martinez

    Apoptosis is a key cell death pathway in mammalian cells. Understanding this process and its regulation has been a subject of study in the last three decades. Members of the Bcl-2 family of proteins are involved in the regulation of apoptosis through mitochondrial poration with the subsequent initiation of apoptosis. Deregulation of pro-apoptotic proteins contributes to the progression of many tumour processes. Understanding how these pore-forming Bcl-2 proteins Bak and Bax are activated is key to find new anti-cancer treatments. Since no drug capable of activating Bak has been disclosed yet, the study of the structural features of BH3 peptides -known Bak activators- relevant for binding along with its binding energy decomposition analysis, results essential for designing novel small molecule mimics of BH3. Interestingly, a BH3 Bim analogue inactivating Bak has recently been discovered, opening a question on the molecular features that determine the function of BH3 peptides. Therefore, the present work is aimed at understanding the way BH3 peptides activate or inactivate Bak in order to identify differential structural features that can be used in drug design. For this purpose, complexes of Bak with an activator and an inhibitor have been subjected to a molecular dynamics study. Structural differences were assessed by means of the fluctuations of the corresponding Principal Components. Moreover, the MMPB/GBSA approach was used to compute the binding free energy of the diverse complexes to identify those residues of the BH3 peptide that exhibit the larger contributions to complex formation. The results obtained in this work show differences between activators and inhibitors, both in structural and energetic terms, which can be used in the design of new molecules that can activate or inactivate pro-apoptotic Bak.

    更新日期:2020-01-17
  • Molecular Insight into the Interaction between Camptothecin and Acyclic Cucurbit[4]urils as Efficient Nanocontainers in Comparison with Cucurbit[7]uril: Molecular Docking and Molecular Dynamics Simulation
    J. Chem. Inf. Model. (IF 3.966) Pub Date : 2020-01-16
    Nasim Ahmadian; Faramarz Mehrnejad; Mehriar Amininasab

    Cucurbit[n]urils (CB[n], n = 5, 6, 7, 8, 10, 14) and their derivatives due to the hydrophobic cavities and polar carbonyl portals have been considerably explored for their potential uses as drug delivery systems. It is important to understand how these macrocyclic compounds interact with guests. Camptothecin (CPT), as a natural alkaloid, is a topoisomerase inhibitor with antitumor activity against breast, pancreas and lung cancers. The application of this drug in cancer therapy is restricted due to its low aqueous solubility and high toxicity. Recently, the complex formation between the cucurbit[7]uril (CB[7]) / acyclic cucurbit[4]uril (aCB[4]) nanocontainers and CPT have been evaluated to overcome the potential drawbacks of the related drug. Herein, using computational methods, we identified the interaction mechanism of CPT with CB[7]/aCB[4]s consist of benzene and naphthalene sidewalls (aCB[4]benzene and aCB[4]naphthalene, respectively), since the experimental approaches have not completely provided information at the molecular level. Our molecular docking and molecular dynamics (MD) simulations show that CB[7] and its two acyclic derivatives form stable inclusion complexes with CPT especially through hydrophobic interactions. We also found that aCB[4]s with the aromatic sidewalls can attach to CPT through π-π interactions. This investigation highlights aCB[4]s due to the structural properties and flexible nature as a better nanocontainers for controlled release delivery of pharmaceutical agents in comparison with CB[7] nanocontainer.

    更新日期:2020-01-17
  • A New Strategy for Atomic Flexible Fitting in Cryo-EM Maps by Molecular Dynamics with Excited Normal Modes (MDeNM-EMfit)
    J. Chem. Inf. Model. (IF 3.966) Pub Date : 2020-01-16
    Mauricio G.S. Costa; Charline Fagnen; Catherine Vénien-Bryan; David Perahia

    Previous studies demonstrated the efficiency of the Molecular Dynamics with excited Normal modes (MDeNM) method on the characterization of large structural changes at a low computational cost. We present here MDeNM-EMfit, an extension of the original method designed to the flexible fit of structures into cryo-EM maps. Here, instead of a uniform exploration of the collective motions described by normal modes, sampling is directed towards conformations with increased correlations with the experimental map. Future perspectives to improve the accuracy of fitting and speed of calculations are discussed in light of the results.

    更新日期:2020-01-17
  • A Combined Computational and Structural Approach into Understanding the Role of Peptide Binding and Activation of the Melanocortin Receptor 4
    J. Chem. Inf. Model. (IF 3.966) Pub Date : 2020-01-16
    Julian Zachmann; Eftichia Kritsi; Anthi Tapeinou; Panagiotis Zoumpoulakis; Theodore Tselios; Minos-Timotheos Matsoukas

    The melanocortin receptor 4 (MC4R), is expressed predominantly in the central nervous system and regulates food intake, sexual function and is also thought to be responsible for effects on mood and cognition. It belongs to the melanocortin receptors subfamily of G protein-coupled receptors (GPCRs). Here, we have synthesized and structurally characterized three peptides that bind to MC4R, producing different signaling events. AgRP, a naturally occurring antagonist, HLWNRS, the minimal sequence of the N-terminal with partial agonist activity and aMSH, a full agonistic peptide. By implementing molecular dynamics simulations on the different peptide-receptor complexes, we propose their molecular basis of binding, in order to investigate their differential molecular properties regarding the activation states of the receptor. Our analysis shows that the agonist and partially agonist induce a rotation in transmembrane helix 3, which is known to be involved in the key events occurring during GPCR activation, and this movement is impacted by certain aromatic residues and their positioning in the orthosteric binding site of the receptor.

    更新日期:2020-01-17
  • Understanding Beam-Induced Electronic Excitations in Materials
    J. Chem. Theory Comput. (IF 5.313) Pub Date : 2020-01-17
    David B. Lingerfelt; Panchapakesan Ganesh; Jacek Jakowski; Bobby G. Sumpter
    更新日期:2020-01-17
  • Characterizing Protein–Ligand Binding Using Atomistic Simulation and Machine Learning: Application to Drug Resistance in HIV-1 Protease
    J. Chem. Theory Comput. (IF 5.313) Pub Date : 2020-01-16
    Troy W. Whitfield; Debra A. Ragland; Konstantin B. Zeldovich; Celia A. Schiffer
    更新日期:2020-01-17
  • 更新日期:2020-01-17
  • 更新日期:2020-01-17
  • Accelerating Convergence in Fock Space Quantum Monte Carlo Methods
    J. Chem. Theory Comput. (IF 5.313) Pub Date : 2020-01-16
    Verena Andrea Neufeld; Alex J.W. Thom

    The convergence of full configuration interaction quantum Monte Carlo (FCIQMC) is accelerated using a quasi-Newton propagation (QN) which can also be applied to coupled cluster Monte Carlo (CCMC). The computational scaling of this optimised propagation is O(1), keeping the additional computational cost to a bare minimum. Its effects are investigated deterministically and stochastically on a model system, the uniform electron gas, with Hilbert space size up to 1040 and shown to accelerate convergence of the instantaneous projected energy by over an order of magnitude in the FCIQMC test case. Its capabilities are then demonstrated with FCIQMC on an archetypical quantum chemistry problem, the chromium dimer, in an all-electron basis set with Hilbert space size of about 1022 yielding highly accurate FCI energies.

    更新日期:2020-01-17
  • Using density matrix quantum Monte Carlo for calculating exact-on-average energies for ab-initio Hamiltonians in a finite basis set
    J. Chem. Theory Comput. (IF 5.313) Pub Date : 2020-01-16
    Hayley R Petras; Sai Kumar Ramadugu; Fionn D. Malone; James J. Shepherd

    We here apply the recently-developed initiator density matrix quantum Monte Carlo (i-DMQMC) to a variety of atoms and molecules in vacuum. i-DMQMC samples the exact density matrix of a Hamiltonian at finite temperature and combines the accuracy of full configuration interaction quantum Monte Carlo (FCIQMC)---full configuration interaction (FCI) or exact energies in a finite basis set---with finite temperature. In order to explore the applicability of i-DMQMC for molecular systems, we choose to study a recently-developed test set by Rubenstein and coworkers: Be, H2O, and H10 at near-equilibrium and stretched geometries. We find that, for Be and H2O, i-DMQMC delivers energies with sub-millihartree accuracy when compared with finite temperature FCI. For H2O and both geometries of H10, we examine the difference between FT-AFQMC and i-DMQMC, which, in turn, estimates the difference in canonical versus grand canonical energies. We close with two discussions: one of simulation settings (initiator error, the interaction picture, and different basis sets), and another of energy difference calculations in the form of specific heat capacity and ionization potential calculations.

    更新日期:2020-01-17
  • Boron arsenide heterostructures: lattice-matched heterointerfaces and strain effects on band alignments and mobility
    npj Comput. Mater. (IF 9.200) Pub Date : 2020-01-16
    Kyle Bushick; Sieun Chae; Zihao Deng; John T. Heron; Emmanouil Kioupakis
    更新日期:2020-01-16
  • 更新日期:2020-01-16
  • Coevolved Positions Represent Key Functional Properties in the Trypsin-Like Serine Proteases Protein Family
    J. Chem. Inf. Model. (IF 3.966) Pub Date : 2020-01-16
    Marcelo Querino Lima Afonso; Neli J. da Fonseca, Jr.; Lucas Carrijo de Oliveira; Francisco Pereira Lobo; Lucas Bleicher
    更新日期:2020-01-16
  • 更新日期:2020-01-16
  • 更新日期:2020-01-15
  • Theoretical investigation of exciplex generation under X-ray irradiation of non-polar solutions
    J. Math. Chem. (IF 1.81) Pub Date : 2020-01-14
    Alexander B. Doktorov, Alexander A. Kipriyanov

    Abstract Theoretical investigation of exciplex generation under X-ray irradiation of the reacting system of non-polar solutions is consistently performed. The scheme of multistage reaction of ion-radical pairs generated under X-ray irradiation is improved as compared to that proposed in the literature previously. The possibility of excited state of electron donor formation, as well as additional channel of exciplex generation is taken into account. Formulation of the modified multistage process of exciplex generation in the framework of the theoretical approach of “effective particles” allows consistent derivation of the kinetic equations for the mean concentrations of reactants and on their basis calculation of the quantum yield of luminescence. Computations predict the change of exciplex generation efficiency under X-ray irradiation in comparison with the reaction under optical excitation. General properties of inhomogeneous sources of the obtained kinetic equations are established. A special case of the absence of excited donor generation is considered in detail, as well as the dependence of the studied values on the concentration of the electronic donor with some model simplifications.

    更新日期:2020-01-15
  • 更新日期:2020-01-15
  • PiNN: A Python Library for Building Atomic Neural Networks of Molecules and Materials
    J. Chem. Inf. Model. (IF 3.966) Pub Date : 2020-01-14
    Yunqi Shao; Matti Hellström; Pavlin D. Mitev; Lisanne Knijff; Chao Zhang

    Atomic neural networks (ANNs) constitute a class of machine learning methods for predicting potential energy surfaces and physico-chemical properties of molecules and materials. Despite many successes, developing interpretable ANN architectures and implementing existing ones efficiently are still challenging. This calls for reliable, general-purpose and open-source codes. Here, we present a python library named PiNN as a solution toward this goal. In PiNN, we designed a new interpretable and high-performing graph convolutional neural network variant, PiNet, as well as implemented the established Behler-Parrinello high-dimensional neural network. These implementations were tested using datasets of isolated small molecules, crystalline materials, liquid water and an aqueous alkaline electrolyte. PiNN comes with a visualizer called PiNNBoard to extract chemical insight ``learned'' by ANNs, provides analytical stress tensor calculations and interfaces to both the Atomic Simulation Environment and a development version of the Amsterdam Modeling Suite. Moreover, PiNN is highly modularized which makes it useful not only as a standalone package but also as a chain of tools to develop and to implement novel ANNs. The code is distributed under a permissive BSD license and is freely accessible at \href{https://github.com/Teoroo-CMC/PiNN/}{https://github.com/Teoroo-CMC/PiNN/} with full documentation and tutorials.

    更新日期:2020-01-15
  • Exploring methamphetamine non-enantioselectively targeting Toll-like receptor 4/myeloid differentiation protein 2 by in silico simulations and wet-lab techniques
    J. Chem. Inf. Model. (IF 3.966) Pub Date : 2020-01-14
    Xiaozheng Zhang; Yibo Wang; Hongshuang Wang; Hongyuan Li; Tianshu Zhang; Yinghua Peng; Xiaohui Wang

    Methamphetamine (METH) is one of the highly addictive non-opioid psychostimulants, acting as a xenobiotic-associated molecular pattern to target TLR4 and activate microglia. However, the molecule recognition of METH by innate immune receptor TLR4/MD-2 is not well understood. METH exists in two enantiomeric forms and it is unclear whether the TLR4 innate immune recognition with METH is stereoselective. Herein molecular dynamics simulations were performed to dissect the recognition of (+)-METH and (-)-METH by TLR4/MD-2 at the atomic level. Amphetamine (AMPH), which is an analog of METH, was also investigated for comparison. Computational simulations indicate METH binds into the interaction interface between MD-2 as well as TLR4* that is from the adjacent copy of TLR4-MD-2, therefore stabilizing the active heterotetramer (TLR4/MD-2)2 complex. The calculated binding free energies and potential of mean force values show (−)-METH and (+)-METH have similar TLR4/MD-2 binding affinity. Further dynamics analyses of bindings with TLR4/MD-2 indicate that (−)-METH and (+)-METH behave similarly. Unlike the stereo-selective neuron stimulating activities of METH, no enantioselectivity was observed for METH interacting with TLR4/MD-2 complex as well as activating TLR4 signaling. Compared to METH, AMPH showed much weaker interactions with TLR4/MD-2, indicating that the substituted methyl group is critical in the molecular recognition of METH by TLR4/MD-2. In all, this study provides a molecular insight into the innate immune recognition of METH, which demonstrates that METH could be non-enantioselectively sensed by TLR4/MD-2.

    更新日期:2020-01-15
  • A Dynamic View of Allosteric Regulation in the Hsp70 Chaperones by J-Domain Cochaperone and Post-Translational Modifications: Computational Analysis of Hsp70 Mechanisms by Exploring Conformational Landscapes and Residue Interaction Networks
    J. Chem. Inf. Model. (IF 3.966) Pub Date : 2020-01-14
    Lindy Astl; Gennady M. Verkhivker

    Structural and biochemical studies of the Hsp70 chaperones have provided the molecular view of the chaperone biochemical cycle by revealing a complex interplay between allosteric conformational states that controls the feedback loop between stimulation of the ATPase activity and the substrate release. Allosteric regulation in the Hsp70 chaperones and efficient substrate targeting are mediated by J-domain cochaperones through a dynamic interaction network controlled by the regulatory hotspots. In the current work, we have simulated conformational landscapes and residue interaction networks in the open, closed and cochaperone-bound DnaK structures. The results of this work have shown that J-domain can selectively enhance direction-specific signal propagation from the substrate binding domain to the catalytic center and promote structural environment required for ATP hydrolysis. By employing different network-based approaches, we examined the role and contribution of post-translational modifications sites in allosteric regulation of human Hsp70. The central finding of this analysis indicated that conserved phosphorylation sites localized preferentially in the nucleotide-binding domain regions are often aligned with the allosteric control points and serve as effector centers in the Hsp70. We have found that cooperation of post-translational modifications sites is based on the governing role of phosphorylation sites in dictating regulatory switching functions, while the bulk of acetylation sites can be involved in sensing the long-range signals and executing allosteric changes during the ATPase cycle. The results of this study highlight the important role of phosphorylation sites in exerting control over allosteric changes in the Hsp70. The network-centric framework for analysis of conformational dynamics and chaperone landscapes can explain a range of structural and functional experiments, providing a robust dynamic model of Hsp70 regulation by cochaperones and sites of post-translational modifications.

    更新日期:2020-01-15
  • Determination of the Free Energies of Mixing of Organic Solutions through a Combined Molecular Dynamics and Bayesian Statistics Approach
    J. Chem. Inf. Model. (IF 3.966) Pub Date : 2020-01-14
    Shi Li; Balaji Sesha Sarath Pokuri; Sean Ryno; Asare Nkansah; Camron De'vine; Baskar Ganapathysubramanian; Chad Risko

    As new generations of thin-film semiconductors are moving towards solution-based processing, the development of printing formulations will require information pertaining to the free energies of mixing of complex mixtures. From the standpoint of in silico materials design, this move necessitates the development of methods that can accurately and quickly evaluate these formulations in order to maximize processing speed and reproducibility. Here, we make use of molecular dynamics (MD) simulations in combination with the two-phase thermodynamic (2PT) model to explore the free energy of mixing surfaces for a series of halogenated solvents and high boiling point solvent additives used in the development of thin-film organic semiconductors. While the combined methods generally show good agreement with available experimental data, the computational cost to traverse the free-energy landscape is considerable. Hence, we demonstrate how a Bayesian optimization scheme, coupled with the MD and 2PT approaches, can drastically reduce the number of simulations required, in turn shrinking dramatically both the computational cost and time.

    更新日期:2020-01-15
  • Linear-Response Time-Dependent Density Functional Theory with Stochastic Range-Separated Hybrids
    J. Chem. Theory Comput. (IF 5.313) Pub Date : 2020-01-14
    Xu Zhang; Gang Lu; Roi Baer; Eran Rabani; Daniel Neuhauser
    更新日期:2020-01-15
  • OPUS-Refine: A Fast Sampling-based Framework for Refining Protein Backbone Torsion Angles and Global Conformation
    J. Chem. Theory Comput. (IF 5.313) Pub Date : 2020-01-14
    Gang Xu; Qinghua Wang; Jianpeng Ma

    Protein backbone torsion angles (Phi and Psi) are crucial for protein local conformation description. In this paper, we propose a general post-processing method for all prediction methods, namely OPUS-Refine, which may contribute to the field in a different way. OPUS-Refine is a sampling-based method, therefore, the results of other prediction methods can be used as its constraints. After OPUS-Refine refinement, for instance, the accuracy of Phi/Psi predicted by SPIDER3 and SPOT-1D are both increased. In addition, to facilitate the sampling efficiency, we construct a neighbor-dependent statistical torsion angles sampling database, namely OPUS-TA, which may be useful for other sampling-based methods. Furthermore, we also introduce the contact map predicted by RaptorX to OPUS-Refine as a global structural constraint. After refinement, comparing to the predicted structures obtained from RaptorX online server, the accuracy of both global structural configurations (measured by TM-score and RMSD) and local structural configurations (measured by Phi/Psi) results are improved. OPUS-Refine is a highly efficient framework, it takes only about 4s to refine the torsion angles and 30s to refine the global structural of a protein with 100 residues in length on a typical desktop personal computer. Therefore, the sampling-based feature and the efficiency of OPUS-Refine offer greater potentiality for it to takes advantage of any other method to achieve a better performance.

    更新日期:2020-01-15
  • Iterative Qubit Coupled Cluster approach with efficient screening of generators
    J. Chem. Theory Comput. (IF 5.313) Pub Date : 2020-01-14
    Ilya G. Ryabinkin; Robert A Lang; Scott N Genin; Artur F. Izmaylov

    An iterative version of the qubit coupled cluster (QCC) method [I.G. Ryabinkin et al., J. Chem. Theory Comput. 14, 6317 (2019)] is proposed. The new method seeks to find ground electronic energies of molecules on noisy intermediate-scale quantum (NISQ) devices. Each iteration involves a canonical transformation of the Hamiltonian and employs constant-size quantum circuits at the expense of increasing the Hamiltonian size. We numerically studied the convergence of the method on ground-state calculations for LiH, H2O, and N2 molecules and found that the exact ground-state energies can be systematically approached only if the generators of the QCC ansatz are sampled from a specific set of operators. We report an algorithm for constructing this set that scales linearly with the size of the Hamiltonian.

    更新日期:2020-01-15
  • Transient absorption microscopy: Technological innovations and applications in materials science and life science
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-09
    Yifan Zhu, Ji-Xin Cheng

    Transient absorption (TA) spectroscopy has been extensively used in the study of excited state dynamics of various materials and molecules. The transition from TA spectroscopy to TA microscopy, which enables the space-resolved measurement of TA, is opening new investigations toward a more complete picture of excited state dynamics in functional materials, as well as the mapping of crucial biopigments for precision diagnosis. Here, we review the recent instrumental advancement that is pushing the limit of spatial resolution, detection sensitivity, and imaging speed. We further highlight the emerging application in materials science and life science.

    更新日期:2020-01-14
  • Near-unity photoluminescence quantum yield in inorganic perovskite nanocrystals by metal-ion doping
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-09
    Ghada H. Ahmed, Jun Yin, Osman M. Bakr, Omar F. Mohammed

    The luminescence and charge transport properties of inorganic CsPbX3 perovskite nanocrystals (NCs) make them attractive candidates for various optoelectronic applications, such as lasing, X-ray imaging, light communication, and light-emitting diodes (LEDs). However, to realize cutting-edge device performance, high-quality NCs with high photoluminescence quantum yields (PLQYs) are essential. Therefore, substantial efforts and progress have been made to attain superior design/engineering and optimization of the inorganic NCs with a focus on surface quality, reduced nonradiative charge carrier recombination centers, and improved colloidal stabilities. Metal-ion doping has been proven to have a robust influence on the electronic band structure, PL behavior, and charge carrier recombination dynamics. Thus, in this perspective, we summarize the recent progress of the significant impact of metal cation doping on the optical properties, including the PL enhancement of CsPbCl3, CsPbBr3, and CsPbI3 perovskite NCs. Moreover, we shed light on the mechanism behind such improved properties. We conclude by recommending possible aspects and strategies to be further explored and considered for better utilization of these doped NCs in thin-film optoelectronic and energy conversion devices.

    更新日期:2020-01-14
  • Ultrafast excited-state proton transfer dynamics in dihalogenated non-fluorescent and fluorescent GFP chromophores
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-13
    Cheng Chen, Liangdong Zhu, Sean A. Boulanger, Nadezhda S. Baleeva, Ivan N. Myasnyanko, Mikhail S. Baranov, Chong Fang

    Green fluorescent protein (GFP) has enabled a myriad of bioimaging advances due to its photophysical and photochemical properties. To deepen the mechanistic understanding of such light-induced processes, novel derivatives of GFP chromophore p-HBDI were engineered by fluorination or bromination of the phenolic moiety into superphotoacids, which efficiently undergo excited-state proton transfer (ESPT) in aqueous solution within the short lifetime of the excited state, as opposed to p-HBDI where efficient ESPT is not observed. In addition, we tuned the excited-state lifetime from picoseconds to nanoseconds by conformational locking of the p-HBDI backbone, essentially transforming the nonfluorescent chromophores into highly fluorescent ones. The unlocked superphotoacids undergo a barrierless ESPT without much solvent activity, whereas the locked counterparts exhibit two distinct solvent-involved ESPT pathways. Comparative analysis of femtosecond transient absorption spectra of these unlocked and locked superphotoacids reveals that the ESPT rates adopt an “inverted” kinetic behavior as the thermodynamic driving force increases upon locking the backbone. Further experimental and theoretical investigations are expected to shed more light on the interplay between the modified electronic structure (mainly by dihalogenation) and nuclear motions (by conformational locking) of the functionalized GFP derivatives (e.g., fluorescence on and off).

    更新日期:2020-01-14
  • Analytical classical density functionals from an equation learning network
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-14
    S.-C. Lin, G. Martius, M. Oettel

    We explore the feasibility of using machine learning methods to obtain an analytic form of the classical free energy functional for two model fluids, hard rods and Lennard–Jones, in one dimension. The equation learning network proposed by Martius and Lampert [e-print arXiv:1610.02995 (2016)] is suitably modified to construct free energy densities which are functions of a set of weighted densities and which are built from a small number of basis functions with flexible combination rules. This setup considerably enlarges the functional space used in the machine learning optimization as compared to the previous work [S.-C. Lin and M. Oettel, SciPost Phys. 6, 025 (2019)] where the functional is limited to a simple polynomial form. As a result, we find a good approximation for the exact hard rod functional and its direct correlation function. For the Lennard–Jones fluid, we let the network learn (i) the full excess free energy functional and (ii) the excess free energy functional related to interparticle attractions. Both functionals show a good agreement with simulated density profiles for thermodynamic parameters inside and outside the training region.

    更新日期:2020-01-14
  • Turing instability conditions in confined systems with an effective position-dependent diffusion coefficient
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-08
    G. Chacón-Acosta, M. Núñez-López, I. Pineda

    We study a reaction-diffusion system within a long channel in the regime in which the projected Fick-Jacobs-Zwanzig operator for confined diffusion can be used. We found that under this approximation, Turing instability conditions can be modified due to the channel geometry. The dispersion relation, range of unstable modes where pattern formation occurs, and spatial structure of the patterns itself change as functions of the geometric parameters of the channel. This occurs for the three channels analyzed, for which the values of the projected operators can be found analytically. For the reaction term, we use the well-known Schnakenberg kinetics.

    更新日期:2020-01-14
  • Large-scale excited-state calculation using dynamical polarizability evaluated by divide-and-conquer based coupled cluster linear response method
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-08
    Takeshi Yoshikawa, Jyunya Yoshihara, Hiromi Nakai

    This study attempted to propose an efficient scheme at the coupled cluster linear response (CCLR) level to perform large-scale excited-state calculations of not only local excitations but also nonlocal ones such as charge transfers and transitions between delocalized orbitals. Although standard applications of fragmentation techniques to the excited-state calculations brought about the limitations that could only deal with local excitations, this study solved the problem by evaluating the excited states as the poles of dynamical polarizability. Because such an approach previously succeeded at the time-dependent density functional theory level [H. Nakai and T. Yoshikawa, J. Chem. Phys. 146, 124123 (2017)], this study was considered as an extension to the CCLR level. To evaluate the dynamical polarizability at the CCLR level, we revisited three equivalent formulas, namely, coupled-perturbed self-consistent field (CPSCF), random phase approximation (RPA), and Green’s function (GF). We further extended these formulas to the linear-scaling methods based on the divide-and-conquer (DC) technique. We implemented the CCLR with singles and doubles (CCSDLR) program for the six schemes, i.e., the standard and DC-type CPSCF, RPA, and GF. Illustrative applications of the present methods demonstrated the accuracy and efficiency. Although the standard three treatments could exactly reproduced the conventional frequency-domain CCSDLR results, their computational costs were commonly higher than that of the conventional ones due to large amount of computations for individual frequencies of the external electric field. The DC-type treatments, which approximately reproduced the conventional results, could achieve quasilinear scaling computational costs. Among them, DC-GF was found to exhibit the best performance.

    更新日期:2020-01-14
  • Adaptive Markov state model estimation using short reseeding trajectories
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-08
    Hongbin Wan, Vincent A. Voelz

    In the last decade, advances in molecular dynamics (MD) and Markov State Model (MSM) methodologies have made possible accurate and efficient estimation of kinetic rates and reactive pathways for complex biomolecular dynamics occurring on slow time scales. A promising approach to enhanced sampling of MSMs is to use “adaptive” methods, in which new MD trajectories are “seeded” preferentially from previously identified states. Here, we investigate the performance of various MSM estimators applied to reseeding trajectory data, for both a simple 1D free energy landscape and mini-protein folding MSMs of WW domain and NTL9(1–39). Our results reveal the practical challenges of reseeding simulations and suggest a simple way to reweight seeding trajectory data to better estimate both thermodynamic and kinetic quantities.

    更新日期:2020-01-14
  • Dissipation and dynamics in ultrafast intersystem crossings
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-08
    Michel van Veenendaal

    The effects of dynamics and dissipation on ultrafast intersystem crossings are studied for a dissipative two-level system coupled to a local vibronic mode. A method of amplitude damping of the wave packet is presented that accounts better for the position of the wave packet and avoids spurious transitions between potential wells. It is demonstrated that Fermi’s golden rule, the typical semiquantitative approach to extract population transfer rates from potential landscapes, only holds under limited conditions. Generally, the effects of dynamics and dissipation lead to deviations from the expected exponential population transfer, strong changes in transfer times and total population transfer, and significant recurrence or “spill back” of the wave packet.

    更新日期:2020-01-14
  • Use of the complete basis set limit for computing highly accurateab initiodipole moments
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-08
    Eamon K. Conway, Iouli E. Gordon, Oleg L. Polyansky, Jonathan Tennyson

    Calculating dipole moments with high-order basis sets is generally only possible for the light molecules, such as water. A simple, yet highly effective strategy of obtaining high-order dipoles with small, computationally less expensive basis sets is described. Using the finite field method for computing dipoles, energies calculated with small basis sets can be extrapolated to produce dipoles that are comparable to those obtained in high order calculations. The method reduces computational resources by approximately 50% (allowing the calculation of reliable dipole moments for larger molecules) and simultaneously improves the agreement with experimentally measured infrared transition intensities. For atmospherically important molecules, which are typically too large to consider the use of large basis sets, this procedure will provide the necessary means of improving calculated spectral intensities by several percent.

    更新日期:2020-01-14
  • Quantum momentum distribution and quantum entanglement in the deep tunneling regime
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-08
    Yantao Wu, Roberto Car

    In this paper, we consider the momentum operator of a quantum particle directed along the displacement of two of its neighbors. A modified open-path path integral molecular dynamics is presented to sample the distribution of this directional momentum distribution, where we derive and use a new estimator for this distribution. Variationally enhanced sampling is used to obtain this distribution for an example molecule, malonaldehyde, in the very low temperature regime where deep tunneling happens. We find no secondary feature in the directional momentum distribution and that its absence is due to quantum entanglement through a further study of the reduced density matrix.

    更新日期:2020-01-14
  • Coarse-grained simulations of diffusion controlled release of drugs from neutral nanogels: Effect of excluded volume interactions
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-08
    José Alberto Maroto-Centeno, Manuel Quesada-Pérez

    The primary goal of this work is to assess the effect of excluded volume interactions on the diffusion controlled release of drug molecules from a spherical, neutral, inert, and cross-linked device of nanometric size. To this end, coarse-grained simulations of the release process were performed. In this way, the inner structure and topology of the polymer network can be explicitly taken into account as well. Our in silico experiments reveal that the boundary condition of constant surface concentration is not appropriate for nanogels. In particular, the predictions based on the perfect sink condition clearly overestimate the fraction of drug released. In addition, these simulations provide values for the release exponent that depends on both the diameter of drug molecules and the number of drug molecules loaded in the matrix, which clearly contrasts with the classical prediction of a constant release exponent. Consequently, the widely used classification of drug release mechanisms based on this kinetic exponent must be extended to include new situations.

    更新日期:2020-01-14
  • Transforming high-dimensional potential energy surfaces into a canonical polyadic decomposition using Monte Carlo methods
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-09
    Markus Schröder

    A Monte Carlo method is proposed for transforming high-dimensional potential energy surfaces evaluated on discrete grid points into a sum-of-products form, more precisely into a Canonical Polyadic Decomposition form. To this end, a modified existing ansatz based on the alternating least squares method is used, in which numerically exact integrals are replaced with Monte Carlo integrals. This largely reduces the numerical cost by avoiding the evaluation of the potential on all grid points and allows the treatment of surfaces with many degrees of freedom. Calculations on the 15D potential of the protonated water dimer (Zundel cation) in a sum-of-products form are presented and compared to the results obtained in a previous work [M. Schröder and H.-D. Meyer, J. Chem. Phys. 147, 064105 (2017)], where a sum-of-products form of the potential was obtained in the Tucker format.

    更新日期:2020-01-14
  • Algorithms to apply dihedral-angle constraints in molecular or stochastic dynamics simulations
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-09
    Maria Pechlaner, Wilfred F. van Gunsteren

    Various algorithms to apply dihedral-angle constraints in molecular dynamics or stochastic dynamics simulations of molecular systems are presented, investigated, and tested. They use Cartesian coordinates and determine the Lagrangian multipliers necessary for maintaining the constraints iteratively. The most suitable algorithm to maintain a dihedral-angle constraint is numerically compared to the alternative to use distance constraints to this end. It can easily be used to obtain a potential of mean force along a dihedral-angle coordinate.

    更新日期:2020-01-14
  • Bayesian counting of photobleaching steps with physical priors
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-09
    Jon Garry, Yuchong Li, Brandon Shew, Claudiu C. Gradinaru, Andrew D. Rutenberg

    Counting fluorescence photobleaching steps is commonly used to infer the number n0 of monomeric units of individual oligomeric protein complexes or misfolded protein aggregates. We present a principled Bayesian approach for counting that incorporates the statistics of photobleaching. Our physics-based prior leads to a simple and efficient numerical scheme for maximum a posteriori probability (MAP) estimates of the initial fluorophore number n^0. Our focus here is on using a calibration to precisely estimate n^0, though our approach can also be used to calibrate the photophysics. Imaging noise increases with n^0, while bias is often introduced by temporal averaging. We examine the effects of fluorophore number n^0 of the oligomer or aggregate, lifetime photon yield μeff of an individual fluorophore, and exposure time Δt of each image frame in a time-lapse experiment. We find that, in comparison with standard ratiometric approaches or with a “change-point” step-counting algorithm, our MAP approach is both more precise and less biased.

    更新日期:2020-01-14
  • An accelerated linear method for optimizing non-linear wavefunctions in variational Monte Carlo
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-10
    Iliya Sabzevari, Ankit Mahajan, Sandeep Sharma

    Although the linear method is one of the most robust algorithms for optimizing nonlinearly parametrized wavefunctions in variational Monte Carlo, it suffers from a memory bottleneck due to the fact that at each optimization step, a generalized eigenvalue problem is solved in which the Hamiltonian and overlap matrices are stored in memory. Here, we demonstrate that by applying the Jacobi-Davidson algorithm, one can solve the generalized eigenvalue problem iteratively without having to build and store the matrices in question. The resulting direct linear method greatly lowers the cost and improves the scaling of the algorithm with respect to the number of parameters. To further improve the efficiency of optimization for wavefunctions with a large number of parameters, we use the first order method AMSGrad far from the minimum as it is very inexpensive and only switch to the direct linear method near the end of the optimization where methods such as AMSGrad have long convergence tails. We apply this improved optimizer to wavefunctions with real and orbital space Jastrow factors applied to a symmetry-projected generalized Hartree-Fock reference. Systems addressed include atomic systems such as beryllium and neon, molecular systems such as the carbon dimer and iron(ii) porphyrin, and model systems such as the Hubbard model and hydrogen chains.

    更新日期:2020-01-14
  • Compressed intramolecular dispersion interactions
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-10
    Cameron J. Mackie, Jérôme F. Gonthier, Martin Head-Gordon

    The feasibility of the compression of localized virtual orbitals is explored in the context of intramolecular long-range dispersion interactions. Singular value decomposition (SVD) of coupled cluster doubles amplitudes associated with the dispersion interactions is analyzed for a number of long-chain systems, including saturated and unsaturated hydrocarbons and a silane chain. Further decomposition of the most important amplitudes obtained from these SVDs allows for the analysis of the dispersion-specific virtual orbitals that are naturally localized. Consistent with previous work on intermolecular dispersion interactions in dimers, it is found that three important geminals arise and account for the majority of dispersion interactions at the long range, even in the many body intramolecular case. Furthermore, it is shown that as few as three localized virtual orbitals per occupied orbital can be enough to capture all pairwise long-range dispersion interactions within a molecule.

    更新日期:2020-01-14
  • Intermediate state representation approach to physical properties of molecular electron-detached states. I. Theory and implementation
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-10
    Adrian L. Dempwolff, Alexander C. Paul, Alexandra M. Belogolova, Alexander B. Trofimov, Andreas Dreuw

    The third-order non-Dyson algebraic-diagrammatic construction approach to the electron propagator [IP-ADC(3)] is extended using the intermediate state representation (ISR) formalism, allowing the wave functions and properties of molecular states with detached electron to be studied. The second-order ISR equations [ISR(2)] for the one-particle (transition) density matrix have been derived and implemented in the Q-CHEM program. The approach is completely general and enables evaluation of arbitrary one-particle operators and interpretation of electron detachment processes in terms of density-based quantities. The IP-ADC(3)/ISR(2) equations were implemented for Ŝz-adapted intermediate states, allowing open-shell molecules to be studied using unrestricted Hartree-Fock references. As a first test for computations of ground state properties, dipole moments of various closed- and open-shell molecules have been computed by means of electron detachment from the corresponding anions. The results are in good agreement with experimental data. The potential of IP-ADC(3)/ISR(2) for the interpretation of photoelectron spectra is demonstrated for the galvinoxyl free radical.

    更新日期:2020-01-14
  • Shadow Hamiltonian in classical NVE molecular dynamics simulations: A path to long time stability
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-10
    K. D. Hammonds, D. M. Heyes

    The shadow energy, Es, is the conserved quantity in microcanonical ensemble (NVE) molecular dynamics simulations carried out with the position Verlet central-difference algorithm. A new methodology for calculating precise and accurate values of Es is presented. It is shown for the first time that Es rather than E is constant during structural changes occurring within a supercooled liquid. It is also explained how to prepare and conduct microsecond range bulk-phase NVE simulations with essentially zero energy drift without the need for thermostating. The drift is analyzed with block averaging and new drift functions of the shadow energy. With such minimal drift, extremely small and accurate standard errors in the mean for quantities like Es, E, and temperature, T, can be obtained. Values of the standard error for Es of ≈10−10 in molecule-based reduced units can be routinely achieved for simulations of 108 time steps. This corresponds to a simulation temperature drift of ≈10−6 K/μs, six orders of magnitude smaller than generally considered to be acceptable for protein simulations. We also show for the first time how these treatments can be extended with no loss of accuracy to polyatomic systems with both flexible degrees of freedom and arbitrary geometric constraints imposed via the SHAKE algorithm. As a bonus, estimates of simulation-average kinetic and total energies from high order velocity expressions can be obtained to a good approximation from 2nd order velocities and the average mean square force (for polyatomics, this refers to per site, including any constraint forces).

    更新日期:2020-01-14
  • Binuclear Mn oxo complex as a self-contained photocatalyst in water-splitting cycle: Role of additional Mn oxides as a buffer of electrons and protons
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-10
    Kentaro Yamamoto, Kazuo Takatsuka

    We theoretically propose a photoinduced water-splitting cycle catalyzed by a binuclear Mn oxo complex. In our “bottom-up approach” to this problem, we once proposed a working minimal model of water-splitting cycle in terms of a mononuclear Mn oxo complex as a catalyst along with water clusters [K. Yamamoto and K. Takatsuka, Phys. Chem. Chem. Phys. 20, 6708 (2018)]. However, this catalyst is not self-contained in that the cycle additionally needs buffering molecules for electrons and protons in order to reload the Mn complex with electrons and protons, which are lost by photoinduced charge separation processes. We here show that a binuclear Mn oxo complex works as a self-contained photocatalyst without further assistant of additional reagents and propose another catalytic cycle in terms of this photocatalyst. Besides charge separation and proton relay transfer, the proposed cycle consists of other fundamental chemical dynamics including electron–proton reloading, radical relay-transfer, and Mn reduction. The feasibility of the present water-splitting cycle is examined by means of full dimensional nonadiabatic electron–wavepacket dynamics based on multireference electronic wavefunctions and energy profiles estimated with rather accurate quantum chemical methods for all the metastable states appearing in the cycle.

    更新日期:2020-01-14
  • Linear scaling perturbative triples correction approximations for open-shell domain-based local pair natural orbital coupled cluster singles and doubles theory [DLPNO-CCSD(T0/T)]
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-10
    Yang Guo, Christoph Riplinger, Dimitrios G. Liakos, Ute Becker, Masaaki Saitow, Frank Neese

    The coupled cluster method with single-, double-, and perturbative triple excitations [CCSD(T)] is considered to be one of the most reliable quantum chemistry theories. However, the steep scaling of CCSD(T) has limited its application to small or medium-sized systems for a long time. In our previous work, the linear scaling domain based local pair natural orbital CCSD variant (DLPNO-CCSD) has been developed for closed-shell and open-shell. However, it is known from extensive benchmark studies that triple-excitation contributions are important to reach chemical accuracy. In the present work, two linear scaling (T) approximations for open-shell DLPNO-CCSD are implemented and compared: (a) an algorithm based on the semicanonical approximation, in which off-diagonal Fock matrix elements in the occupied space are neglected [referred to as DLPNO-(T0)]; and (b) an improved algorithm in which the triples amplitudes are computed iteratively [referred to as DLPNO-(T)]. This work is based on the previous open-shell DLPNO-CCSD algorithm [M. Saitow et al., J. Chem. Phys. 146, 164105 (2017)] as well as the iterative (T) correction for closed-shell systems [Y. Guo et al., J. Chem. Phys. 148, 011101 (2018)]. Our results show that the new open-shell perturbative corrections, DLPNO-(T0/T), can predict accurate absolute and relative correlation energies relative to the canonical reference calculations with the same basis set. The absolute energies from DLPNO-(T) are significantly more accurate than those of DLPNO-(T0). The additional computational effort of DLPNO-(T) relative to DLPNO-(T0) is a factor of 4 on average. We report calculations on systems with more than 4000 basis functions.

    更新日期:2020-01-14
  • Evaluation of the AMOEBA force field for simulating metal halide perovskites in the solid state and in solution
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-13
    P. V. G. M. Rathnayake, Stefano Bernardi, Asaph Widmer-Cooper

    In this work, we compare the existing nonpolarizable force fields developed to study the solid or solution phases of hybrid organic-inorganic halide perovskites with the AMOEBA polarizable force field. The aim is to test whether more computationally expensive polarizable force fields like AMOEBA offer better transferability between solution and solid phases, with the ultimate goal being the study of crystal nucleation, growth, and other interfacial phenomena involving these ionic compounds. In the context of hybrid perovskites, AMOEBA force field parameters already exist for several elements in solution, and we decided to leave them unchanged and to only parameterize the missing ones (Pb2+ and CH3NH3+ ions) in order to maximize transferability and avoid overfitting to the specific examples studied here. Overall, we find that AMOEBA yields accurate hydration free energies (within 5%) for typical ionic species while showing the correct ordering of stability for the different crystal polymorphs of CsPbI3 and CH3NH3PbI3. Although the existing parameters do not accurately reproduce all transition temperatures and lattice parameters, AMOEBA offers better transferability between solution and solid states than existing nonpolarizable force fields.

    更新日期:2020-01-14
  • Orbital localization error of density functional theory in shear properties of vanadium and niobium
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-13
    Yi X. Wang, Hua Y. Geng, Q. Wu, Xiang R. Chen

    It is believed that the density functional theory (DFT) describes most elements with s, p, and d orbitals very well, except some materials that have strongly localized and correlated valence electrons. In this work, we find that the widely employed exchange-correlation (XC) functionals, including local-density approximation (LDA), generalized gradient approximation (GGA), and meta-GGA, underestimate the shear modulus and phase stability of V and Nb greatly. The advanced hybrid functional that is usually better for correlated systems, on the other hand, completely fails in these two simple metals. This striking failure is revealed due to the orbital localization error in GGA, which is further deteriorated by hybrid functionals. This observation is corroborated by a similar failure of DFT+U and van der Waals functionals when applied to V and Nb. To remedy this problem, a semiempirical approach of DFT+J is proposed, which can delocalize electrons by facilitating the on-site exchange. Furthermore, it is observed that including density derivatives slightly improves the performance of the semilocal functionals, with meta-GGA outperforms GGA, and the latter is better than LDA. This discovery indicates the possibility and necessity to include higher-order density derivatives beyond the Laplacian level for the purpose of removing the orbital localization error (mainly from d orbitals) and delocalization error (mainly from s and p orbitals) completely in V and Nb so that a better description of their electronic structures is achieved. The same strategy can be applied to the other d electron system and f electron system.

    更新日期:2020-01-14
  • Quantum mechanical/molecular mechanical trajectory surface hopping molecular dynamics simulation by spin-flip time-dependent density functional theory
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-13
    Noriyuki Minezawa, Takahito Nakajima

    This paper presents the nonadiabatic molecular dynamics simulation in the solution phase using the spin-flip time-dependent density functional theory (SF-TDDFT). Despite the single-reference level of theory, the SF-TDDFT method can generate the correct topology of S0/S1 crossing points, thus providing a natural S1 → S0 nonadiabatic transition. We extend the gas-phase trajectory surface hopping simulation with the SF-TDDFT [N. Minezawa and T. Nakajima, J. Chem. Phys. 150, 204120 (2019)] to the hybrid quantum mechanical/molecular mechanics (QM/MM) scheme. To this end, we modify the code to evaluate the electrostatic interaction between the QM and MM atoms and to extract the classical MM energy and forces from the MM program package. We apply the proposed method to the photoisomerization reaction of aqueous E-azomethane and anionic green fluorescent protein chromophore in water and compare the results with those of the previous simulation studies based on the multireference methods.

    更新日期:2020-01-14
  • The nuclear Overhauser Effect (NOE) as a tool to study macromolecular confinement: Elucidation and disentangling of crowding and encapsulation effects
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-13
    Philipp Honegger, Othmar Steinhauser

    We propose a methodology to capture short-lived but biophysically important contacts of biomacromolecules using the biomolecule-water nuclear Overhauser effect as an indirect microscope. Thus, instead of probing the direct correlation with the foreign biomolecule, we detect its presence by the disturbance it causes in the surrounding water. In addition, this information obtained is spatially resolved and can thus be attributed to specific sites. We extend this approach to the influence of more than one change in chemical environment and show a methodological way of resolution. This is achieved by taking double differences of corresponding σNOE/σROE ratios of the systems studied and separating specific, unspecific, and intermediate influence. While applied to crowding and encapsulation in this study, this method is generally suitable for any combination of changes in chemical environment.

    更新日期:2020-01-14
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