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Static polarizabilities at the basis set limit: A benchmark of 124 species. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-06-16 Anders Brakestad,Stig Rune Jensen,Peter Wind,Marco D'Alessandro,Luigi Genovese,Kathrin H Hopmann,Luca Frediani
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Reliable computational prediction of supramolecular ordering of complex molecules under electrochemical conditions. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-06-14 Benedikt Hartl,Shubham Sharma,Oliver Brügner,Stijn F L Mertens,Michael Walter,Gerhard Kahl
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Varying electronic configurations in compressed atoms: from the role of the spatial extension of atomic orbitals to the change of electronic configuration as an isobaric transformation. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-06-18 Roberto Cammi,Martin Rahm,Roald Hoffmann,Neil W Ashcroft
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Simulation of Excitation by Sunlight in Mixed Quantum-Classical Dynamics J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-06-24 Mario Barbatti
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Conformational free energy differences of large solvated systems with the focused confinement method. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-06-19 Paul B Orndorff,Sang T Le Phan,Ka Ho Li,Arjan van der Vaart
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Repulsive soft-core potentials for efficient alchemical free energy calculations. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-06-19 Yaozong Li,Kwangho Nam
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A modified interaction-strength interpolation method as an important step towards self-consistent calculations. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-06-19 Szymon Śmiga,Lucian A Constantin
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Coupling Coarse-Grained to Fine-Grained Models via Hamiltonian Replica Exchange. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-06-22 Yang Liu,Weria Pezeshkian,Jonathan Barnoud,Alex H De Vries,Siewert J Marrink
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Bayesian active learning for optimization and uncertainty quantification in protein docking. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-06-19 Yue Cao,Yang Shen
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Pair Potentials as Machine Learning Features. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-06-19 Jun Pei,Lin Frank Song,Kenneth M Merz
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Mechanism of fully-reversible, pH-sensitive inhibition of human glutamine synthetase by tyrosine nitration. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-06-17 Benedikt Frieg,Boris Goerg,Natalia Qvartskhava,Thomas Jeitner,Nadine Homeyer,Dieter Häussinger,Holger Gohlke
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MR-MCTDH[n]: Flexible configuration spaces and non-adiabatic dynamics within the MCTDH[n] framework. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-06-16 Niels Kristian Madsen,Mads B Oslash Ttger Hansen,Graham A Worth,Ove Christiansen
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Statistically optimal continuous free energy surfaces from biased simulations and multistate reweighting. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-06-04 Michael R Shirts,Andrew L Ferguson
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An Efficient Algorithm for Topological Characterisation of Worm-Like and Branched Micelle Structures from Simulations. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-06-16 Breanndan O Conchuir,Kirk Gardner,Kirk Edmond Jordan,David J Bray,Richard L Anderson,Michael Andrew Johnston,William C Swope,Alex Harrison,Donald R Sheehy,Thomas J Peters
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Data-Driven Approaches Can Overcome the Cost-Accuracy Trade-off in Multireference Diagnostics. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-06-14 Chenru Duan,Fang Liu,Aditya Nandy,Heather J Kulik
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AdaptiveBandit: A multi-armed bandit framework for adaptive sampling in molecular simulations. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-06-15 Adrià Pérez,Pablo Herrera-Nieto,Stefan Doerr,Gianni De Fabritiis
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Improved Parameterization of Protein-DNA Interactions for Molecular Dynamics Simulations of PCNA Diffusion on DNA. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-06-16 Seonju You,Hongeun Lee,Kimoon Kim,Jejoong Yoo
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Reduced density matrix driven CASSCF corrected for dynamic correlation from the adiabatic connection. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-06-14 Elvis Maradzike,Michal Hapka,Katarzyna Pernal,A Eugene DePrince
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Trajectory Surface Hopping Nonadiabatic Molecular Dynamics with Kohn–Sham ΔSCF for Condensed-Phase Systems J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-06-30 Momir Mališ; Sandra Luber
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Correction to “An Efficient Analytic Approach for Calculation of Multi-Dimensional Franck–Condon Factors and Associated Photoelectron Spectra” J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-06-30 Tosaporn Sattasathuchana; Riccardo Murri; Kim K. Baldridge
The variable definitions for eq 14 in Table 1 should read as follows: The definition of F1 component in eq 18 should read as follows: The erratum does not alter results or conclusion in this paper. This article has not yet been cited by other publications.
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Systematic Parameterization of Divalent Metal Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-06-08 Zhen Li,Lin Frank Song,Pengfei Li,Kenneth M Merz
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Halogen Bonds in Protein Nucleic Acid Recognition J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-06-24 Antonio Frontera; Antonio Bauzá
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Extending the applicability of the ANI deep learning molecular potential to Sulfur and Halogens. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-06-16 Christian Devereux,Justin S Smith,Kate K Davis,Kipton Barros,Roman Zubatyuk,Olexandr Isayev,Adrian E Roitberg
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Performance of Coupled-Cluster Singles and Doubles on Modern Stream Processing Architectures. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-06-20 B Scott Fales,Ethan R Curtis,K Grace Johnson,Dean Lahana,Stefan Seritan,Yuanheng Wang,Hayley Weir,Todd J Martínez,Edward G Hohenstein
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Compact Basis Sets for Optical Rotation Calculations. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-06-11 Tal Aharon,Marco Caricato
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Spin Splitting Energy of Transition Metals: A New, More Affordable Wave Function Benchmark Method and Its Use to Test Density Functional Theory. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-06-11 Dayou Zhang,Donald G Truhlar
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The remarkable accuracy of an O(N6) perturbative correction to opposite-spin CCSD: are triples necessary for chemical accuracy in coupled cluster? J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-06-18 David W Small
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Generalized Analytic Approach for Determination of Multidimensional Franck–Condon Factors: Simulated Photoelectron Spectra of Polynuclear Aromatic Hydrocarbons J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-06-26 Tosaporn Sattasathuchana; Jay S. Siegel; Kim K. Baldridge
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Multidimensional Global Optimization and Robustness Analysis in the Context of Protein-Ligand Binding. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-05-25 Negin Forouzesh,Abhishek Mukhopadhyay,Layne T Watson,Alexey V Onufriev
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Parallel Implementation of Density Functional Theory Methods in the Quantum Interaction Computational Kernel Program. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-06-08 Madushanka Manathunga,Yipu Miao,Dawei Mu,Andreas W Götz,Kenneth M Merz
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Visualization of dynamics effect: projection of on-the-fly trajectories to the subspace spanned by the static reaction path network. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-06-11 Takuro Tsutsumi,Yuriko Ono,Zin Arai,Tetsuya Taketsugu
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ALTRUISM: A Higher Calling. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-06-08 Terri E Field-Theodore,Peter R Taylor
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A New Benchmark Set for Excitation Energy of Charge Transfer States: Systematic Investigation of Coupled-Cluster Type Methods. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-06-05 Balázs Kozma,Attila Tajti,Baptiste Demoulin,Robert Izsak,Marcel Nooijen,Péter G Szalay
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A real-time time-dependent density functional tight-binding implementation for semiclassical excited state electron-nuclear dynamics and pump-probe spectroscopy simulations. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-06-08 Franco P Bonafé,Bálint Aradi,Ben Hourahine,Carlos R Medrano,Federico J Hernandez,Thomas Frauenheim,Cristian G Sanchez
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Incorporating Electronic Information into Machine Learning Potential Energy Surfaces via Approaching the Ground-State Electronic Energy as a Function of Atom-Based Electronic Populations. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-06-05 Xiaowei Xie,Kristin A Persson,David W Small
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General Approach for Reducing Continuous Translational Symmetry Errors in Finite Difference Real-Space Calculations. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-05-26 Tian Qiu,Leeor Kronik,Andrew M Rappe
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Unveiling the Finite Temperature Physics of Hydrogen Chains via Auxiliary Field Quantum Monte Carlo. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-05-26 Yuan Liu,Tong Shen,Hang Zhang,Brenda Rubenstein
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Capturing the Flexibility of a Protein-Ligand Complex: Binding Free Energies from Different Enhanced Sampling Techniques. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-06-04 Sebastian Wingbermühle,Lars V Schäfer
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Confronting Racism in Chemistry Journals. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-06-19 Cynthia J Burrows,Jiaxiang Huang,Shu Wang,Hyun Jae Kim,Gerald J Meyer,Kirk Schanze,T Randall Lee,Jodie L Lutkenhaus,David Kaplan,Christopher Jones,Carolyn Bertozzi,Laura Kiessling,Mary Beth Mulcahy,Craig W Lindsley,M G Finn,Joel D Blum,Prashant Kamat,Wonyong Choi,Shane Snyder,Courtney C Aldrich,Stuart Rowan,Bin Liu,Dennis Liotta,Paul S Weiss,Deqing Zhang,Krishna N Ganesh,Harry A Atwater,J Justin Gooding
The following joint Editorial was originally published in ACS Applied Materials & Interfaces (DOI: 10.1021/acsami.0c10979). We confront the terrible reality that systemic racism and discrimination impacts the daily personal and professional lives of many members of the scientific community and broader society. In the U.S., the brutal killing of George Floyd while in police custody is one of the most
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Charge and Exciton Transfer Simulations Using Machine-Learned Hamiltonians. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-06-03 Mila Krämer,Philipp M Dohmen,Weiwei Xie,Daniel Holub,Anders S Christensen,Marcus Elstner
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General Density-Based Index to Analyze Charge Transfer Phenomena: From Models to Butterfly Molecules. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-05-14 Léon Huet,Anna Perfetto,Francesco Muniz-Miranda,Marco Campetella,Carlo Adamo,Ilaria Ciofini
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Effect of Protein Flexibility from Coarse-Grained Elastic Network Parameterizations on the Calculation of Free Energy Profiles of Ligand Binding. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-06-04 Hugo A L Filipe,Margarida I M Esteves,César A Henriques,Filipe E Antunes
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A Geometric Measure Theory Approach to Identify Complex Structural Features on Soft Matter Surfaces. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-06-01 Enrique Alvarado,Zhu Liu,Michael J Servis,Bala Krishnamoorthy,Aurora E Clark
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Accelerating Auxiliary-Field Quantum Monte Carlo Simulations of Solids with Graphical Processing Units. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-05-21 Fionn D Malone,Shuai Zhang,Miguel A Morales
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Correction to Reconciling Work Functions and Adsorption Enthalpies for Implicit Solvent Models: A Pt (111)/Water Interface Case Study. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-06-16 Gabriel Bramley,Manh-Thuong Nguyen,Vassiliki-Alexandra Glezakou,Roger Rousseau,Chris-Kriton Skylaris
The correct version of the Acknowledgments is shown below. G.B. (partial support), V.-A.G., M.-T.N., and R.R. were supported by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division. Computer resources were provided by Research Computing at Pacific Northwest National Laboratory (PNNL) and the National Energy Research Scientific
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Correction to Norm-Conserving Pseudopotentials and Basis Sets To Explore Lanthanide Chemistry in Complex Environments. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-06-15 Jun-Bo Lu,David C Cantu,Manh-Thuong Nguyen,Jun Li,Vassiliki-Alexandra Glezakou,Roger Rousseau
The paragraphs for the Funding Sources and Acknowledgments listed below now contain the correct information. V.-A.G. was supported by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division. R.R. and M.-T.N. were supported by the Laboratory Directed Research and Development Program at Pacific Northwest National Laboratory (PNNL)
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Small Matrix Path Integral for System-Bath Dynamics. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-06-15 Nancy Makri
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Correction to "Probing the Accuracy of Explicit Solvent Constant pH Molecular Dynamics Simulations for Peptides". J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-06-05 Plamen Dobrev,Sahithya Phani Babu Vemulapalli,Nilamoni Nath,Christian Griesinger,Gerrit Groenhof,Helmut Grubmüller
Equations 1 and 5 were wrong. The correct equations are(1)and(5)The respective explanation, following eq 1 now reads as follows: “In the present work, f(λ) is further enhanced to serve as a pH correction potential, which provides the free energy difference (given by RT ln 10(pKa,ref – pH)) between the protonation forms of the titrated compound reference state by setting different depths for the two
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Exploring Mechanisms of Communication Switching in the Hsp90-Cdc37 Regulatory Complexes with Client Kinases through Allosteric Coupling of Phosphorylation Sites: Perturbation-Based Modeling and Hierarchical Community Analysis of Residue Interaction Networks. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-06-03 Gabrielle Stetz,Lindy Astl,Gennady M Verkhivker
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Extrapolating Unconverged GW Energies up to the Complete Basis Set Limit with Linear Regression. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-06-03 Fabien Bruneval,Ivan Maliyov,Clovis Lapointe,Mihai-Cosmin Marinica
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Development of a New Coarse-Grained Model to Simulate Assembly of Cellulose Chains Due to Hydrogen Bonding. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-06-02 Zijie Wu,Daniel J Beltran-Villegas,Arthi Jayaraman
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NCIPLOT4: Fast, Robust, and Quantitative Analysis of Noncovalent Interactions. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-05-29 Roberto A Boto,Francesca Peccati,Rubén Laplaza,Chaoyu Quan,Alessandra Carbone,Jean-Philip Piquemal,Yvon Maday,Julia Contreras-Garcı A
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Improved Basis-Set Incompleteness Potentials for Accurate Density-Functional Theory Calculations in Large Systems. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-05-29 A Otero-de-la-Roza,Gino A DiLabio
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First-Principles Simulations of X-ray Transient Absorption for Probing Attosecond Electron Dynamics. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-05-29 Min Chen,Kenneth Lopata
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Construction of Two-Dimensional Potential Energy Surfaces of Reactions with Post-Transition-State Bifurcations. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-05-29 Hsiao-Han Chuang,Dean J Tantillo,Chao-Ping Hsu
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Comparison of Reaction Field Schemes for Coupling Continuum Solvation Models with Wave Function Methods for Excitation Energies. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-05-29 Sarah Karbalaei Khani,Alireza Marefat Khah,Christof Hättig
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pKa Calculations with the Polarizable Drude Force Field and Poisson-Boltzmann Solvation Model. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-05-28 Alexey Aleksandrov,Benoît Roux,Alexander D MacKerell
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Solubility Advantage of Amorphous Ketoprofen. Thermodynamic and Kinetic Aspects by Molecular Dynamics and Free Energy Approaches. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-05-28 D Gobbo,P Ballone,S Decherchi,A Cavalli
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Multistate QM/QM Extrapolation of UV/Vis Absorption Spectra with Point Charge Embedding. J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-05-27 Kaihua Zhang,Sijin Ren,Marco Caricato
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Canonical and DLPNO-Based G4(MP2)XK-Inspired Composite Wave Function Methods Parametrized against Large and Chemically Diverse Training Sets: Are They More Accurate and/or Robust than Double-Hybrid DFT? J. Chem. Theory Comput. (IF 5.011) Pub Date : 2020-05-26 Emmanouil Semidalas,Jan M L Martin
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