Quantum Chemistry on Graphical Processing Units. 3. Analytical Energy Gradients, Geometry Optimization, and First Principles Molecular DynamicsClick to copy article linkArticle link copied!
Abstract
We demonstrate that a video gaming machine containing two consumer graphical cards can outpace a state-of-the-art quad-core processor workstation by a factor of more than 180× in Hartree−Fock energy + gradient calculations. Such performance makes it possible to run large scale Hartree−Fock and Density Functional Theory calculations, which typically require hundreds of traditional processor cores, on a single workstation. Benchmark Born−Oppenheimer molecular dynamics simulations are performed on two molecular systems using the 3-21G basis set - a hydronium ion solvated by 30 waters (94 atoms, 405 basis functions) and an aspartic acid molecule solvated by 147 waters (457 atoms, 2014 basis functions). Our GPU implementation can perform 27 ps/day and 0.7 ps/day of ab initio molecular dynamics simulation on a single desktop computer for these systems.
Cited By
Smart citations by scite.ai include citation statements extracted from the full text of the citing article. The number of the statements may be higher than the number of citations provided by ACS Publications if one paper cites another multiple times or lower if scite has not yet processed some of the citing articles.
This article is cited by 762 publications.
- Abdelazim M. A. Abdelgawwad, Antonio Francés-Monerris. easyPARM: Automated, Versatile, and Reliable Force Field Parameters for Metal-Containing Molecules with Unique Labeling of Coordinating Atoms. Journal of Chemical Theory and Computation 2025, Article ASAP.
- Vyshnavi Vennelakanti, Mugyeom Jeon, Heather J. Kulik. Computational Investigation of the Role of Metal Center Identity in Cytochrome P450 Enzyme Model Reactivity. Biochemistry 2025, 64
(3)
, 678-691. https://doi.org/10.1021/acs.biochem.4c00594
- Angel Ivan Rodriguez-Leon, Cristian Ordóñez, Ruben Santamaria. Simulating the Helicase Enzymatic Action on ds-DNA: A First-Principles Molecular Dynamics Study. ACS Omega 2025, 10
(4)
, 3627-3639. https://doi.org/10.1021/acsomega.4c08555
- Jan A. Meissner, Jan Meisner. Acceleration of Diffusion in Ab Initio Nanoreactor Molecular Dynamics and Application to Hydrogen Sulfide Oxidation. Journal of Chemical Theory and Computation 2025, 21
(1)
, 218-229. https://doi.org/10.1021/acs.jctc.4c00826
- Eleftherios Mainas, Gregory M. Curtin, Shaena D. Riddles, Elisa Pieri. Biliverdin’s Propionic Chains Influence Oligomerization in Sandercyanin. The Journal of Physical Chemistry B 2024, 128
(50)
, 12443-12455. https://doi.org/10.1021/acs.jpcb.4c06722
- Elise Palethorpe, Ryan Stocks, Giuseppe M. J. Barca. Advanced Techniques for High-Performance Fock Matrix Construction on GPU Clusters. Journal of Chemical Theory and Computation 2024, 20
(23)
, 10424-10442. https://doi.org/10.1021/acs.jctc.4c00994
- Abhishek Bera, Pritish Joshi, Niladri Patra. Delving into Macrolide Binding Affinities and Associated Structural Modulations in Erythromycin Esterase C: Insights into the Venus Flytrap Mechanism. Journal of Chemical Information and Modeling 2024, 64
(23)
, 8892-8908. https://doi.org/10.1021/acs.jcim.4c01523
- Anne Germann, Jan Meisner. Force-Assisted Orbital Crossing in Mechanochemical Oxirane Ring Opening. The Journal of Physical Chemistry A 2024, 128
(47)
, 10224-10233. https://doi.org/10.1021/acs.jpca.4c06204
- Cheng Qian, Yuanhao Liu, Wenting Meng, Yaoyukun Jiang, Sijian Wang, Lu Wang. Modeling Infrared Spectroscopy of Nucleic Acids: Integrating Vibrational Non-Condon Effects with Machine Learning Schemes. Journal of Chemical Theory and Computation 2024, 20
(22)
, 10080-10094. https://doi.org/10.1021/acs.jctc.4c01130
- Calum Snowdon, Giuseppe M. J. Barca. An Efficient RI-MP2 Algorithm for Distributed Many-GPU Architectures. Journal of Chemical Theory and Computation 2024, 20
(21)
, 9394-9406. https://doi.org/10.1021/acs.jctc.4c00814
- Nathan D. Yoshino, Lee-Ping Wang. Two P, Ten P, White P, Red P: Mechanistic Exploration of the Oligomerization of Red Phosphorus from Diphosphorus with the Ab Initio Nanoreactor. Inorganic Chemistry 2024, 63
(41)
, 19074-19086. https://doi.org/10.1021/acs.inorgchem.4c02299
- Sommer L. Johansen, Heejune Park, Lee-Ping Wang, Kyle N. Crabtree. Reactant Discovery with an Ab Initio Nanoreactor: Exploration of Astrophysical N-Heterocycle Precursors and Formation Pathways. ACS Earth and Space Chemistry 2024, 8
(9)
, 1771-1783. https://doi.org/10.1021/acsearthspacechem.4c00120
- Ryan Stocks, Elise Palethorpe, Giuseppe M. J. Barca. Multi-GPU RI-HF Energies and Analytic Gradients─Toward High-Throughput Ab Initio Molecular Dynamics. Journal of Chemical Theory and Computation 2024, 20
(17)
, 7503-7515. https://doi.org/10.1021/acs.jctc.4c00877
- Rakesh Kumar Roy, Abhishek Bera, Niladri Patra. Insights into Allosteric Inhibition of the AcrB Efflux Pump: Role of Distinct Binding Pockets, Protomer Preferences, and Crosstalk Disruption. Journal of Chemical Information and Modeling 2024, 64
(15)
, 5964-5976. https://doi.org/10.1021/acs.jcim.4c00306
- Himanshu Sharma, Kumar Vanka. In Silico Discovery of a Neutral 2π Aromatic Silicon Aluminum Compound. Organometallics 2024, 43
(14)
, 1583-1592. https://doi.org/10.1021/acs.organomet.4c00151
- Soumya Ranjan Dash, Kumar Vanka. Unveiling the Inverse Sandwich Complexes of XeO3: A Computational Exploration. Inorganic Chemistry 2024, 63
(29)
, 13585-13593. https://doi.org/10.1021/acs.inorgchem.4c01744
- Avigyan Naskar, Rakesh K. Roy, Diship Srivastava, Niladri Patra. Decoding Inhibitor Egression from Wild-Type and G2019S Mutant LRRK2 Kinase: Insights into Unbinding Mechanisms for Precision Drug Design in Parkinson’s Disease. The Journal of Physical Chemistry B 2024, 128
(28)
, 6657-6669. https://doi.org/10.1021/acs.jpcb.4c00335
- Jack T. Taylor, David J. Tozer, Basile F. E. Curchod. On the Topological Phase around Conical Intersections with Tamm–Dancoff Linear-Response Time-Dependent Density Functional Theory. The Journal of Physical Chemistry A 2024, 128
(27)
, 5314-5320. https://doi.org/10.1021/acs.jpca.4c02503
- Dayana Bashirova, Tim J. Zuehlsdorff. First-Principles Modeling of the Absorption Spectrum of Crystal Violet in Solution: The Importance of Environmentally Driven Symmetry Breaking. The Journal of Physical Chemistry A 2024, 128
(27)
, 5229-5242. https://doi.org/10.1021/acs.jpca.4c00389
- Elisa Pieri, Alice R. Walker, Mingning Zhu, Todd J. Martínez. Conical Intersection Accessibility Dictates Brightness in Red Fluorescent Proteins. Journal of the American Chemical Society 2024, 146
(26)
, 17646-17658. https://doi.org/10.1021/jacs.4c00458
- Gibson Kirui, Widana Kaushalya, S. Sameera Perera, Alice R. Walker, Cláudio N. Verani. Influence of Peripheral and Ancillary Changes on the Electron Transport of HS3d5 FeIII Metallosurfactants – Substituents, Chain Length, Subphase Polarity, and Junction Electrodes. The Journal of Physical Chemistry C 2024, 128
(25)
, 10668-10681. https://doi.org/10.1021/acs.jpcc.4c02249
- Jaewoon Jung, Kiyoshi Yagi, Cheng Tan, Hiraku Oshima, Takaharu Mori, Isseki Yu, Yasuhiro Matsunaga, Chigusa Kobayashi, Shingo Ito, Diego Ugarte La Torre, Yuji Sugita. GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and Free-Energy Calculations for Atomistic, Coarse-Grained, and Quantum Mechanics/Molecular Mechanics Models. The Journal of Physical Chemistry B 2024, 128
(25)
, 6028-6048. https://doi.org/10.1021/acs.jpcb.4c02096
- Ankit Pandey, Bill Poirier, Ruibin Liang. Development of Parallel On-the-Fly Crystal Algorithm for Global Exploration of Conical Intersection Seam Space. Journal of Chemical Theory and Computation 2024, 20
(11)
, 4778-4789. https://doi.org/10.1021/acs.jctc.4c00292
- Jakub K. Sowa, Danielle M. Cadena, Arshad Mehmood, Benjamin G. Levine, Sean T. Roberts, Peter J. Rossky. IR Spectroscopy of Carboxylate-Passivated Semiconducting Nanocrystals: Simulation and Experiment. The Journal of Physical Chemistry C 2024, 128
(21)
, 8724-8731. https://doi.org/10.1021/acs.jpcc.4c01988
- Matteo Capone, Marco Romanelli, Davide Castaldo, Giovanni Parolin, Alessandro Bello, Gabriel Gil, Mirko Vanzan. A Vision for the Future of Multiscale Modeling. ACS Physical Chemistry Au 2024, 4
(3)
, 202-225. https://doi.org/10.1021/acsphyschemau.3c00080
- Duccio Di Prima, Peter Reinholdt, Jacob Kongsted. Color Tuning in Bovine Rhodopsin through Polarizable Embedding. The Journal of Physical Chemistry B 2024, 128
(12)
, 2864-2873. https://doi.org/10.1021/acs.jpcb.3c07891
- Ryan Stocks, Elise Palethorpe, Giuseppe M. J. Barca. High-Performance Multi-GPU Analytic RI-MP2 Energy Gradients. Journal of Chemical Theory and Computation 2024, 20
(6)
, 2505-2519. https://doi.org/10.1021/acs.jctc.3c01424
- Haojun Jia, Chenru Duan, Ilia Kevlishvili, Aditya Nandy, Mingjie Liu, Heather J. Kulik. Computational Discovery of Codoped Single-Atom Catalysts for Methane-to-Methanol Conversion. ACS Catalysis 2024, 14
(5)
, 2992-3005. https://doi.org/10.1021/acscatal.3c05506
- Colin Gallagher, Wali Siddiqui, Tyler Arnold, Carmen Cheng, Eric Su, Qing Zhao. Benchmarking a Molecular Flake Model on the Road to Programmable Graphene-Based Single-Atom Catalysts. The Journal of Physical Chemistry C 2024, 128
(7)
, 2876-2883. https://doi.org/10.1021/acs.jpcc.3c07681
- Shavkat Mamatkulov, Jakub Polák, Jamoliddin Razzokov, Lukáš Tomaník, Petr Slavíček, Joachim Dzubiella, Matej Kanduč, Jan Heyda. Unveiling the Borohydride Ion through Force-Field Development. Journal of Chemical Theory and Computation 2024, 20
(3)
, 1263-1273. https://doi.org/10.1021/acs.jctc.3c01020
- Diptarka Hait, Todd J. Martínez. Predicting the X-ray Absorption Spectrum of Ozone with Single Configuration State Functions. Journal of Chemical Theory and Computation 2024, 20
(2)
, 873-881. https://doi.org/10.1021/acs.jctc.3c01035
- Nicole Spanedda, Chandler Martin, Kevin Mesta, Arindam Chakraborty. Enhancement of Spontaneous Photon Emission in Inverse Photoemission Transitions in Semiconductor Quantum Dots. The Journal of Physical Chemistry Letters 2024, 15
(2)
, 364-370. https://doi.org/10.1021/acs.jpclett.3c02934
- Martin Melčák, Filip Šebesta, Jan Heyda, Harry B. Gray, Stanislav Záliš, Antonín Vlček. Tryptophan to Tryptophan Hole Hopping in an Azurin Construct. The Journal of Physical Chemistry B 2024, 128
(1)
, 96-108. https://doi.org/10.1021/acs.jpcb.3c06568
- Evgeniy G. Gordeev, Djamaladdin G. Musaev, Valentine P. Ananikov. Comparative Study of Pd-Mediated Carbon–Carbon, Carbon–Heteroatom, and Heteroatom–Heteroatom Bond Formation/Breakage (C ═ Csp3, Csp2, Csp; X = B, N, O, Si, P, S, Se, Te). Organometallics 2024, 43
(1)
, 1-13. https://doi.org/10.1021/acs.organomet.3c00367
- Lieyang Chen, Yujie Wu, Chuanjie Wu, Ana Silveira, Woody Sherman, Huafeng Xu, Emilio Gallicchio. Performance and Analysis of the Alchemical Transfer Method for Binding-Free-Energy Predictions of Diverse Ligands. Journal of Chemical Information and Modeling 2024, 64
(1)
, 250-264. https://doi.org/10.1021/acs.jcim.3c01705
- Caitlin V. Hetherington, Nila Mohan T. M., Ryan W. Tilluck, Warren F. Beck, Benjamin G. Levine. Origin of Vibronic Coherences During Carrier Cooling in Colloidal Quantum Dots. The Journal of Physical Chemistry Letters 2023, 14
(51)
, 11651-11658. https://doi.org/10.1021/acs.jpclett.3c02384
- Gustavo J. Costa, Abel Egbemhenghe, Ruibin Liang. Computational Characterization of the Reactivity of Compound I in Unspecific Peroxygenases. The Journal of Physical Chemistry B 2023, 127
(51)
, 10987-10999. https://doi.org/10.1021/acs.jpcb.3c06311
- Yaoyukun Jiang, Ning Ding, Qianzhen Shao, Sebastian L. Stull, Zihao Cheng, Zhongyue J. Yang. Substrate Positioning Dynamics Involves a Non-Electrostatic Component to Mediate Catalysis. The Journal of Physical Chemistry Letters 2023, 14
(50)
, 11480-11489. https://doi.org/10.1021/acs.jpclett.3c02444
- Kousik K. Bhanja, Madhur Sharma, Niladri Patra. Uncovering the Structural and Binding Insights of Dual Inhibitors Simultaneously Targeting Two Distinct Sites on EGFR Kinase. The Journal of Physical Chemistry B 2023, 127
(50)
, 10749-10765. https://doi.org/10.1021/acs.jpcb.3c04337
- Ilia Kevlishvili, Chenru Duan, Heather J. Kulik. Classification of Hemilabile Ligands Using Machine Learning. The Journal of Physical Chemistry Letters 2023, 14
(49)
, 11100-11109. https://doi.org/10.1021/acs.jpclett.3c02828
- Jiří Janoš, Petr Slavíček. What Controls the Quality of Photodynamical Simulations? Electronic Structure Versus Nonadiabatic Algorithm. Journal of Chemical Theory and Computation 2023, 19
(22)
, 8273-8284. https://doi.org/10.1021/acs.jctc.3c00908
- Zhengyi Bian, Alison Wallum, Arshad Mehmood, Eric Gomez, Ziwen Wang, Subhendu Pandit, Shuming Nie, Stephan Link, Benjamin G. Levine, Martin Gruebele. Properties of Carbon Dots versus Small Molecules from “Bottom-up” Synthesis. ACS Nano 2023, 17
(22)
, 22788-22799. https://doi.org/10.1021/acsnano.3c07486
- Ernst Dennis Larsson, Peter Reinholdt, Erik Donovan Hedegård, Jacob Kongsted. Accuracy of One- and Two-Photon Intensities with the Extended Polarizable Density Embedding Model. The Journal of Physical Chemistry B 2023, 127
(46)
, 9905-9914. https://doi.org/10.1021/acs.jpcb.3c05029
- Lanhai He, Lukáš Tomaník, Sebastian Malerz, Florian Trinter, Sebastian Trippel, Michal Belina, Petr Slavíček, Bernd Winter, Jochen Küpper. Specific versus Nonspecific Solvent Interactions of a Biomolecule in Water. The Journal of Physical Chemistry Letters 2023, 14
(46)
, 10499-10508. https://doi.org/10.1021/acs.jpclett.3c01763
- Jiří Janoš, Ivo S. Vinklárek, Jozef Rakovský, Deb Pratim Mukhopadhyay, Basile F. E. Curchod, Michal Fárník, Petr Slavíček. On the Wavelength-Dependent Photochemistry of the Atmospheric Molecule CF3COCl. ACS Earth and Space Chemistry 2023, 7
(11)
, 2275-2286. https://doi.org/10.1021/acsearthspacechem.3c00196
- Jacob Stamm, Sung Kwon, Shawn Sandhu, Moaid Shaik, Rituparna Das, Jesse Sandhu, Bradley Curenton, Clayton Wicka, Benjamin G. Levine, Liangliang Sun, Marcos Dantus. The Surprising Dynamics of the McLafferty Rearrangement. The Journal of Physical Chemistry Letters 2023, 14
(44)
, 10088-10093. https://doi.org/10.1021/acs.jpclett.3c02102
- Christina H. McCulley, Alice R. Walker. Dimer Interface Destabilization of Photodissociative Dronpa Driven by Asymmetric Monomer Dynamics. The Journal of Physical Chemistry B 2023, 127
(43)
, 9248-9257. https://doi.org/10.1021/acs.jpcb.3c03798
- Federico Zahariev, Peng Xu, Bryce M. Westheimer, Simon Webb, Jorge Galvez Vallejo, Ananta Tiwari, Vaibhav Sundriyal, Masha Sosonkina, Jun Shen, George Schoendorff, Megan Schlinsog, Tosaporn Sattasathuchana, Klaus Ruedenberg, Luke B. Roskop, Alistair P. Rendell, David Poole, Piotr Piecuch, Buu Q. Pham, Vladimir Mironov, Joani Mato, Sam Leonard, Sarom S. Leang, Joe Ivanic, Jackson Hayes, Taylor Harville, Karthik Gururangan, Emilie Guidez, Igor S. Gerasimov, Christian Friedl, Katherine N. Ferreras, George Elliott, Dipayan Datta, Daniel Del Angel Cruz, Laura Carrington, Colleen Bertoni, Giuseppe M. J. Barca, Melisa Alkan, Mark S. Gordon. The General Atomic and Molecular Electronic Structure System (GAMESS): Novel Methods on Novel Architectures. Journal of Chemical Theory and Computation 2023, 19
(20)
, 7031-7055. https://doi.org/10.1021/acs.jctc.3c00379
- Mark A. Hix, Alice R. Walker. AutoParams: An Automated Web-Based Tool To Generate Force Field Parameters for Molecular Dynamics Simulations. Journal of Chemical Information and Modeling 2023, 63
(20)
, 6293-6301. https://doi.org/10.1021/acs.jcim.3c01049
- Sung Kwon, Shawn Sandhu, Moaid Shaik, Jacob Stamm, Jesse Sandhu, Rituparna Das, Caitlin V. Hetherington, Benjamin G. Levine, Marcos Dantus. What is the Mechanism of H3+ Formation from Cyclopropane?. The Journal of Physical Chemistry A 2023, 127
(41)
, 8633-8638. https://doi.org/10.1021/acs.jpca.3c05442
- Gustavo J. Costa, Ruibin Liang. Understanding the Multifaceted Mechanism of Compound I Formation in Unspecific Peroxygenases through Multiscale Simulations. The Journal of Physical Chemistry B 2023, 127
(41)
, 8809-8824. https://doi.org/10.1021/acs.jpcb.3c04589
- Abigail Cousino, Lanka D. Wickramasinghe, Widana Kaushalya, S. Sameera Perera, Habib Baydoun, Alice R. Walker, Cláudio N. Verani. Studies on Monolayer Formation and Electron Transport in Au|LB|Au Junctions Containing 3d4 MnIII Metallosurfactants. The Journal of Physical Chemistry C 2023, 127
(33)
, 16654-16667. https://doi.org/10.1021/acs.jpcc.3c03616
- Soren Holm, Pablo A. Unzueta, Keiran Thompson, Todd J. Martínez. Single-Point Extrapolation to the Complete Basis Set Limit through Deep Learning. Journal of Chemical Theory and Computation 2023, 19
(14)
, 4474-4483. https://doi.org/10.1021/acs.jctc.2c01298
- Pratip Chakraborty, Rafael C. Couto, Nanna H. List. Deciphering Methylation Effects on S2(ππ*) Internal Conversion in the Simplest Linear α,β-Unsaturated Carbonyl. The Journal of Physical Chemistry A 2023, 127
(25)
, 5360-5373. https://doi.org/10.1021/acs.jpca.3c02582
- Tianyi Yu, Xubo Luo, David Prendergast, Glenn L. Butterfoss, Behzad Rad, Nitash P. Balsara, Ronald N. Zuckermann, Xi Jiang. Structural Elucidation of a Polypeptoid Chain in a Crystalline Lattice Reveals Key Morphology-Directing Role of the N-Terminus. ACS Nano 2023, 17
(5)
, 4958-4970. https://doi.org/10.1021/acsnano.2c12503
- Justin Villard, Murat Kılıç, Ursula Rothlisberger. Surrogate Based Genetic Algorithm Method for Efficient Identification of Low-Energy Peptide Structures. Journal of Chemical Theory and Computation 2023, 19
(3)
, 1080-1097. https://doi.org/10.1021/acs.jctc.2c01078
- Madushanka Manathunga, Hasan Metin Aktulga, Andreas W. Götz, Kenneth M. Merz, Jr.. Quantum Mechanics/Molecular Mechanics Simulations on NVIDIA and AMD Graphics Processing Units. Journal of Chemical Information and Modeling 2023, 63
(3)
, 711-717. https://doi.org/10.1021/acs.jcim.2c01505
- Yorick Lassmann, Daniel Hollas, Basile F. E. Curchod. Extending the Applicability of the Multiple-Spawning Framework for Nonadiabatic Molecular Dynamics. The Journal of Physical Chemistry Letters 2022, 13
(51)
, 12011-12018. https://doi.org/10.1021/acs.jpclett.2c03295
- Xim Bokhimi. Effect of Pressure on the Distribution of Electrons in a Cluster of H2S. ACS Omega 2022, 7
(46)
, 42499-42504. https://doi.org/10.1021/acsomega.2c05726
- Siddharth Sundararaman, David M. Halat, Jeffrey A. Reimer, Nitash P. Balsara, David Prendergast. Understanding the Impact of Multi-Chain Ion Coordination in Poly(ether-Acetal) Electrolytes. Macromolecules 2022, 55
(21)
, 9880-9889. https://doi.org/10.1021/acs.macromol.2c01897
- K. Grace Johnson, Seema Mirchandaney, Ellis Hoag, Alan Heirich, Alex Aiken, Todd J. Martínez. Multinode Multi-GPU Two-Electron Integrals: Code Generation Using the Regent Language. Journal of Chemical Theory and Computation 2022, 18
(11)
, 6522-6536. https://doi.org/10.1021/acs.jctc.2c00414
- Richard Jacobi, David Hernández-Castillo, Novitasari Sinambela, Julian Bösking, Andrea Pannwitz, Leticia González. Computation of Förster Resonance Energy Transfer in Lipid Bilayer Membranes. The Journal of Physical Chemistry A 2022, 126
(43)
, 8070-8081. https://doi.org/10.1021/acs.jpca.2c04524
- Christina Yeo, Minh Nguyen, Lee-Ping Wang. Benchmarking Density Functionals, Basis Sets, and Solvent Models in Predicting Thermodynamic Hydricities of Organic Hydrides. The Journal of Physical Chemistry A 2022, 126
(42)
, 7566-7577. https://doi.org/10.1021/acs.jpca.2c03072
- Philipp Pracht, Christoph Bannwarth. Fast Screening of Minimum Energy Crossing Points with Semiempirical Tight-Binding Methods. Journal of Chemical Theory and Computation 2022, 18
(10)
, 6370-6385. https://doi.org/10.1021/acs.jctc.2c00578
- Lisa Oh, Yang Ji, Wanqing Li, Ajit Varki, Xi Chen, Lee-Ping Wang. O-Acetyl Migration within the Sialic Acid Side Chain: A Mechanistic Study Using the Ab Initio Nanoreactor. Biochemistry 2022, 61
(18)
, 2007-2013. https://doi.org/10.1021/acs.biochem.2c00343
- D. Vale Cofer-Shabica, Maximilian F. S. J. Menger, Qi Ou, Yihan Shao, Joseph E. Subotnik, Shirin Faraji. INAQS, a Generic Interface for Nonadiabatic QM/MM Dynamics: Design, Implementation, and Validation for GROMACS/Q-CHEM simulations. Journal of Chemical Theory and Computation 2022, 18
(8)
, 4601-4614. https://doi.org/10.1021/acs.jctc.2c00204
- Chenru Duan, Adriana J. Ladera, Julian C.-L. Liu, Michael G. Taylor, Isuru R. Ariyarathna, Heather J. Kulik. Exploiting Ligand Additivity for Transferable Machine Learning of Multireference Character across Known Transition Metal Complex Ligands. Journal of Chemical Theory and Computation 2022, 18
(8)
, 4836-4845. https://doi.org/10.1021/acs.jctc.2c00468
- Chey M. Jones, Nanna H. List, Todd J. Martínez. Steric and Electronic Origins of Fluorescence in GFP and GFP-like Proteins. Journal of the American Chemical Society 2022, 144
(28)
, 12732-12746. https://doi.org/10.1021/jacs.2c02946
- Jianhong Yang, Yong Li, Qiang Qiu, Ruihan Wang, Wei Yan, Yamei Yu, Lu Niu, Heying Pei, Haoche Wei, Liang Ouyang, Haoyu Ye, Dingguo Xu, Yuquan Wei, Qiang Chen, Lijuan Chen. Small Molecules Promote Selective Denaturation and Degradation of Tubulin Heterodimers through a Low-Barrier Hydrogen Bond. Journal of Medicinal Chemistry 2022, 65
(13)
, 9159-9173. https://doi.org/10.1021/acs.jmedchem.2c00379
- Joshua Finkelstein, Emanuel H. Rubensson, Susan M. Mniszewski, Christian F. A. Negre, Anders M. N. Niklasson. Quantum Perturbation Theory Using Tensor Cores and a Deep Neural Network. Journal of Chemical Theory and Computation 2022, 18
(7)
, 4255-4268. https://doi.org/10.1021/acs.jctc.2c00274
- Yuanheng Wang, Stefan Seritan, Dean Lahana, Jason E. Ford, Alessio Valentini, Edward G. Hohenstein, Todd J. Martínez. InteraChem: Exploring Excited States in Virtual Reality with Ab Initio Interactive Molecular Dynamics. Journal of Chemical Theory and Computation 2022, 18
(6)
, 3308-3317. https://doi.org/10.1021/acs.jctc.2c00005
- In Seong Lee, Seung Kyu Min. Generalized Formulation of the Density Functional Tight Binding-Based Restricted Ensemble Kohn–Sham Method with Onsite Correction to Long-Range Correction. Journal of Chemical Theory and Computation 2022, 18
(6)
, 3391-3409. https://doi.org/10.1021/acs.jctc.2c00037
- Azadeh Nazemi, Adam H. Steeves, David W. Kastner, Heather J. Kulik. Influence of the Greater Protein Environment on the Electrostatic Potential in Metalloenzyme Active Sites: The Case of Formate Dehydrogenase. The Journal of Physical Chemistry B 2022, 126
(22)
, 4069-4079. https://doi.org/10.1021/acs.jpcb.2c02260
- Yael Cytter, Aditya Nandy, Akash Bajaj, Heather J. Kulik. Ligand Additivity and Divergent Trends in Two Types of Delocalization Errors from Approximate Density Functional Theory. The Journal of Physical Chemistry Letters 2022, 13
(20)
, 4549-4555. https://doi.org/10.1021/acs.jpclett.2c01026
- Aditya Nandy, Chenru Duan, Conrad Goffinet, Heather J. Kulik. New Strategies for Direct Methane-to-Methanol Conversion from Active Learning Exploration of 16 Million Catalysts. JACS Au 2022, 2
(5)
, 1200-1213. https://doi.org/10.1021/jacsau.2c00176
- Dewi Yokelson, Nikolay V. Tkachenko, Robert Robey, Ying Wai Li, Pavel A. Dub. Performance Analysis of CP2K Code for Ab Initio Molecular Dynamics on CPUs and GPUs. Journal of Chemical Information and Modeling 2022, 62
(10)
, 2378-2386. https://doi.org/10.1021/acs.jcim.1c01538
- Rakesh Kumar Roy, Niladri Patra. Prediction of COMT Inhibitors Using Machine Learning and Molecular Dynamics Methods. The Journal of Physical Chemistry B 2022, 126
(19)
, 3477-3492. https://doi.org/10.1021/acs.jpcb.1c10278
- Zhongyue Yang, Natalia Hajlasz, Heather J. Kulik. Computational Modeling of Conformer Stability in Benenodin-1, a Thermally Actuated Lasso Peptide Switch. The Journal of Physical Chemistry B 2022, 126
(18)
, 3398-3406. https://doi.org/10.1021/acs.jpcb.2c00762
- Ruibin Liang, Amirhossein Bakhtiiari. Effects of Enzyme–Ligand Interactions on the Photoisomerization of a Light-Regulated Chemotherapeutic Drug. The Journal of Physical Chemistry B 2022, 126
(12)
, 2382-2393. https://doi.org/10.1021/acs.jpcb.1c10819
- Roberto López, Natalia Díaz, Evelio Francisco, Angel Martín-Pendás, Dimas Suárez. QM/MM Energy Decomposition Using the Interacting Quantum Atoms Approach. Journal of Chemical Information and Modeling 2022, 62
(6)
, 1510-1524. https://doi.org/10.1021/acs.jcim.1c01372
- Ming Zhang, Zhengning Guo, Xiaoyu Mi, Zheng Li, Yunquan Liu. Ultrafast Imaging of Molecular Dynamics Using Ultrafast Low-Frequency Lasers, X-ray Free Electron Lasers, and Electron Pulses. The Journal of Physical Chemistry Letters 2022, 13
(7)
, 1668-1680. https://doi.org/10.1021/acs.jpclett.1c03916
- Ian E. Jacobs, Gabriele D’Avino, Vincent Lemaur, Yue Lin, Yuxuan Huang, Chen Chen, Thomas F. Harrelson, William Wood, Leszek J. Spalek, Tarig Mustafa, Christopher A. O’Keefe, Xinglong Ren, Dimitrios Simatos, Dion Tjhe, Martin Statz, Joseph W. Strzalka, Jin-Kyun Lee, Iain McCulloch, Simone Fratini, David Beljonne, Henning Sirringhaus. Structural and Dynamic Disorder, Not Ionic Trapping, Controls Charge Transport in Highly Doped Conducting Polymers. Journal of the American Chemical Society 2022, 144
(7)
, 3005-3019. https://doi.org/10.1021/jacs.1c10651
- Andrew S. Durden, Benjamin G. Levine. Floquet Time-Dependent Configuration Interaction for Modeling Ultrafast Electron Dynamics. Journal of Chemical Theory and Computation 2022, 18
(2)
, 795-806. https://doi.org/10.1021/acs.jctc.1c01009
- Gustavo J. R. Aroeira, Matthew M. Davis, Justin M. Turney, Henry F. Schaefer, III. Fermi.jl: A Modern Design for Quantum Chemistry. Journal of Chemical Theory and Computation 2022, 18
(2)
, 677-686. https://doi.org/10.1021/acs.jctc.1c00719
- Daniel R. Harper, Heather J. Kulik. Computational Scaling Relationships Predict Experimental Activity and Rate-Limiting Behavior in Homogeneous Water Oxidation. Inorganic Chemistry 2022, 61
(4)
, 2186-2197. https://doi.org/10.1021/acs.inorgchem.1c03376
- Mingjie Liu, Azadeh Nazemi, Michael G. Taylor, Aditya Nandy, Chenru Duan, Adam H. Steeves, Heather J. Kulik. Large-Scale Screening Reveals That Geometric Structure Matters More Than Electronic Structure in the Bioinspired Catalyst Design of Formate Dehydrogenase Mimics. ACS Catalysis 2022, 12
(1)
, 383-396. https://doi.org/10.1021/acscatal.1c04624
- Giuseppe M. J. Barca, Melisa Alkan, Jorge L. Galvez-Vallejo, David L. Poole, Alistair P. Rendell, Mark S. Gordon. Faster Self-Consistent Field (SCF) Calculations on GPU Clusters. Journal of Chemical Theory and Computation 2021, 17
(12)
, 7486-7503. https://doi.org/10.1021/acs.jctc.1c00720
- David M. Sanchez, Umberto Raucci, Todd J. Martínez. In Silico Discovery of Multistep Chemistry Initiated by a Conical Intersection: The Challenging Case of Donor–Acceptor Stenhouse Adducts. Journal of the American Chemical Society 2021, 143
(48)
, 20015-20021. https://doi.org/10.1021/jacs.1c06648
- Maryann Laboe, Jurick Lahiri, Nila Mohan T. M., Fangchun Liang, Benjamin G. Levine, Warren F. Beck, Marcos Dantus. Linear and Nonlinear Optical Processes Controlling S2 and S1 Dual Fluorescence in Cyanine Dyes. The Journal of Physical Chemistry A 2021, 125
(45)
, 9770-9784. https://doi.org/10.1021/acs.jpca.1c05772
- Alice R. Walker, Boning Wu, Jan Meisner, Michael D. Fayer, Todd J. Martínez. Proton Transfer from a Photoacid to a Water Wire: First Principles Simulations and Fast Fluorescence Spectroscopy. The Journal of Physical Chemistry B 2021, 125
(45)
, 12539-12551. https://doi.org/10.1021/acs.jpcb.1c07254
- Kevin J. Naidoo, Tomás Bruce-Chwatt, Tharindu Senapathi, Malcolm Hillebrand. Multidimensional Free Energy and Accelerated Quantum Library Methods Provide a Gateway to Glycoenzyme Conformational, Electronic, and Reaction Mechanisms. Accounts of Chemical Research 2021, 54
(22)
, 4120-4130. https://doi.org/10.1021/acs.accounts.1c00477
- Edward G. Hohenstein, Jimmy K. Yu, Christoph Bannwarth, Nanna Holmgaard List, Alexander C. Paul, Sarai D. Folkestad, Henrik Koch, Todd J. Martínez. Predictions of Pre-edge Features in Time-Resolved Near-Edge X-ray Absorption Fine Structure Spectroscopy from Hole–Hole Tamm–Dancoff-Approximated Density Functional Theory. Journal of Chemical Theory and Computation 2021, 17
(11)
, 7120-7133. https://doi.org/10.1021/acs.jctc.1c00478
- Beomchang Kang, Chaok Seok, Juyong Lee. MOLGENGO: Finding Novel Molecules with Desired Electronic Properties by Capitalizing on Their Global Optimization. ACS Omega 2021, 6
(41)
, 27454-27465. https://doi.org/10.1021/acsomega.1c04347
- Joshua Finkelstein, Justin S. Smith, Susan M. Mniszewski, Kipton Barros, Christian F. A. Negre, Emanuel H. Rubensson, Anders M. N. Niklasson. Quantum-Based Molecular Dynamics Simulations Using Tensor Cores. Journal of Chemical Theory and Computation 2021, 17
(10)
, 6180-6192. https://doi.org/10.1021/acs.jctc.1c00726
- Ryan W. Tilluck, Nila Mohan
T. M., Caitlin V. Hetherington, Chase H. Leslie, Sourav Sil, Jared Frazier, Mengliang Zhang, Benjamin G. Levine, P. Gregory Van Patten, Warren F. Beck. Vibronic Excitons and Conical Intersections in Semiconductor Quantum Dots. The Journal of Physical Chemistry Letters 2021, 12
(39)
, 9677-9683. https://doi.org/10.1021/acs.jpclett.1c02630
- Rimsha Mehmood, Vyshnavi Vennelakanti, Heather J. Kulik. Spectroscopically Guided Simulations Reveal Distinct Strategies for Positioning Substrates to Achieve Selectivity in Nonheme Fe(II)/α-Ketoglutarate-Dependent Halogenases. ACS Catalysis 2021, 11
(19)
, 12394-12408. https://doi.org/10.1021/acscatal.1c03169
- Siddharth Sundararaman, David M. Halat, Youngwoo Choo, Rachel L. Snyder, Brooks A. Abel, Geoffrey W. Coates, Jeffrey A. Reimer, Nitash P. Balsara, David Prendergast. Exploring the Ion Solvation Environments in Solid-State Polymer Electrolytes through Free-Energy Sampling. Macromolecules 2021, 54
(18)
, 8590-8600. https://doi.org/10.1021/acs.macromol.1c01417
- Maximilian L. Hupfer, Robert Meyer, Tanja Deckert-Gaudig, Soumik Ghosh, Artem Skabeev, Kalina Peneva, Volker Deckert, Benjamin Dietzek, Martin Presselt. Supramolecular Reorientation During Deposition Onto Metal Surfaces of Quasi-Two-Dimensional Langmuir Monolayers Composed of Bifunctional Amphiphilic, Twisted Perylenes. Langmuir 2021, 37
(37)
, 11018-11026. https://doi.org/10.1021/acs.langmuir.1c01525
- Maximilian L. Hupfer, Beata Koszarna, Soumik Ghosh, Daniel T. Gryko, Martin Presselt. Langmuir–Blodgett Films of Diketopyrrolopyrroles with Tunable Amphiphilicity. Langmuir 2021, 37
(34)
, 10272-10278. https://doi.org/10.1021/acs.langmuir.1c01113
- Aditya Nandy, Chenru Duan, Michael G. Taylor, Fang Liu, Adam H. Steeves, Heather J. Kulik. Computational Discovery of Transition-metal Complexes: From High-throughput Screening to Machine Learning. Chemical Reviews 2021, 121
(16)
, 9927-10000. https://doi.org/10.1021/acs.chemrev.1c00347
Article Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.
Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.
The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated.