Diabatic Population Matrix Formalism for Performing Molecular Mechanics Style Simulations with Multiple Electronic States (Unknown)
- New search for: Park, Jae Woo
- New search for: Rhee, Young Min
- New search for: Park, Jae Woo
- New search for: Rhee, Young Min
In:
Journal of Chemical Theory and Computation
;
10
, 12
;
5238-5253
;
2014
- Article (Journal) / Electronic Resource
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Title:Diabatic Population Matrix Formalism for Performing Molecular Mechanics Style Simulations with Multiple Electronic States
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Additional title:J. Chem. Theory Comput.
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Contributors:Park, Jae Woo ( author ) / Rhee, Young Min ( author )
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Published in:Journal of Chemical Theory and Computation ; 10, 12 ; 5238-5253
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Publisher:
- New search for: American Chemical Society
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Publication date:2014-12-09
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ISSN:
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Coden:
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DOI:
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Type of media:Article (Journal)
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Type of material:Electronic Resource
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Language:Unknown
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Source:
Table of contents – Volume 10, Issue 12
The tables of contents are generated automatically and are based on the data records of the individual contributions available in the index of the TIB portal. The display of the Tables of Contents may therefore be incomplete.
- 5217
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Automatic Selection of Order Parameters in the Analysis of Large Scale Molecular Dynamics SimulationsSultan, Mohammad M. / Kiss, Gert / Shukla, Diwakar / Pande, Vijay S. et al. | 2014
- 5224
-
Optical Signature of Formation of Protein Corona in the Firefly Luciferase-CdSe Quantum Dot ComplexElward, Jennifer M. / Irudayanathan, Flaviyan Jerome / Nangia, Shikha / Chakraborty, Arindam et al. | 2014
- 5229
-
Quantifying Computational Effort Required for Stochastic AveragesSchultz, Andrew J. / Kofke, David A. et al. | 2014
- 5235
-
Assignment of Electronic Bands in the Photoelectron Spectrum of the VO2 – AnionKim, Jongjin B. / Weichman, Marissa L. / Neumark, Daniel M. et al. | 2014
- 5238
-
Diabatic Population Matrix Formalism for Performing Molecular Mechanics Style Simulations with Multiple Electronic StatesPark, Jae Woo / Rhee, Young Min et al. | 2014
- 5254
-
Infinite Boundary Terms of Ewald Sums and Pairwise Interactions for Electrostatics in Bulk and at InterfacesHu, Zhonghan et al. | 2014
- 5265
-
The Theory of Ultra-Coarse-Graining. 2. Numerical ImplementationDavtyan, Aram / Dama, James F. / Sinitskiy, Anton V. / Voth, Gregory A. et al. | 2014
- 5276
-
Multiple-Replica Strategies for Free-Energy Calculations in NAMD: Multiple-Walker Adaptive Biasing Force and Walker Selection RulesComer, Jeffrey / Phillips, James C. / Schulten, Klaus / Chipot, Christophe et al. | 2014
- 5286
-
Spin Density Distribution in Open-Shell Transition Metal Systems: A Comparative Post-Hartree–Fock, Density Functional Theory, and Quantum Monte Carlo Study of the CuCl2 MoleculeCaffarel, Michel / Giner, Emmanuel / Scemama, Anthony / Ramírez-Solís, Alejandro et al. | 2014
- 5297
-
Analytic Gradient for Density Functional Theory Based on the Fragment Molecular Orbital MethodBrorsen, Kurt R. / Zahariev, Federico / Nakata, Hiroya / Fedorov, Dmitri G. / Gordon, Mark S. et al. | 2014
- 5308
-
Efficient Implementation of Local Excitation Approximation for Treating Excited States of Molecules in Condensed PhaseZhang, Chenyang / Yuan, Dandan / Guo, Yang / Li, Shuhua et al. | 2014
- 5318
-
Binding and Diffusion of Lithium in Graphite: Quantum Monte Carlo Benchmarks and Validation of van der Waals Density Functional MethodsGanesh, P. / Kim, Jeongnim / Park, Changwon / Yoon, Mina / Reboredo, Fernando A. / Kent, Paul R. C. et al. | 2014
- 5324
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Variational, Self-Consistent Implementation of the Perdew–Zunger Self-Interaction Correction with Complex Optimal OrbitalsLehtola, Susi / Jónsson, Hannes et al. | 2014
- 5338
-
Molecular Binding in Post-Kohn–Sham Orbital-Free DFTBorgoo, Alex / Green, James A. / Tozer, David J. et al. | 2014
- 5346
-
Accurate Excited State Geometries within Reduced Subspace TDDFT/TDARobinson, David et al. | 2014
- 5353
-
Nucleic Acid Quadruplexes Based on 8‑Halo-9-deazaxanthines: Energetics and Noncovalent Interactions in Quadruplex StemsYurenko, Yevgen P. / Novotný, Jan / Mitoraj, Mariusz P. / Sklenář, Vladimir / Michalak, Artur / Marek, Radek et al. | 2014
- 5366
-
Ab Initio Implementation of the Frenkel–Davydov Exciton Model: A Naturally Parallelizable Approach to Computing Collective Excitations in Crystals and AggregatesMorrison, Adrian F. / You, Zhi-Qiang / Herbert, John M. et al. | 2014
- 5377
-
Expanding the Scope of Density Derived Electrostatic and Chemical Charge Partitioning to Thousands of AtomsLee, Louis P. / Limas, Nidia Gabaldon / Cole, Daniel J. / Payne, Mike C. / Skylaris, Chris-Kriton / Manz, Thomas A. et al. | 2014
- 5391
-
Computation of the Density Matrix in Electronic Structure Theory in Parallel on Multiple Graphics Processing UnitsCawkwell, M. J. / Wood, M. A. / Niklasson, Anders M. N. / Mniszewski, S. M. et al. | 2014
- 5397
-
Local Hybrid QM/QM Calculations of Reaction Pathways in MetallobiositesAndrejić, Milica / Mata, Ricardo A. et al. | 2014
- 5405
-
Distributed Multipoles from a Robust Basis-Space Implementation of the Iterated Stockholder Atoms ProcedureMisquitta, Alston J. / Stone, Anthony J. / Fazeli, Farhang et al. | 2014
- 5419
-
Stable and Efficient Linear Scaling First-Principles Molecular Dynamics for 10000+ AtomsArita, Michiaki / Bowler, David R. / Miyazaki, Tsuyoshi et al. | 2014
- 5426
-
Getting down to the Fundamentals of Hydrogen Bonding: Anharmonic Vibrational Frequencies of (HF)2 and (H2O)2 from Ab Initio Electronic Structure ComputationsHoward, J. Coleman / Gray, Jessica L. / Hardwick, Amanda J. / Nguyen, Linh T. / Tschumper, Gregory S. et al. | 2014
- 5436
-
Halogen Bonding from Dispersion-Corrected Density-Functional Theory: The Role of Delocalization ErrorOtero-de-la-Roza, A. / Johnson, Erin R. / DiLabio, Gino A. et al. | 2014
- 5448
-
Ab Initio QM/MM Study Shows a Highly Dissociated SN2 Hydrolysis Mechanism for the cGMP-Specific Phosphodiesterase‑5Li, Zhe / Wu, Yinuo / Feng, Ling-Jun / Wu, Ruibo / Luo, Hai-Bin et al. | 2014
- 5458
-
Catalytic Mechanism of Retroviral Integrase for the Strand Transfer Reaction Explored by QM/MM CalculationsAraújo, Ana R. / Ribeiro, António J. M. / Fernandes, Pedro A. / Ramos, Maria J. et al. | 2014
- 5467
-
Finding Chemical Reaction Paths with a Multilevel Preconditioning ProtocolKale, Seyit / Sode, Olaseni / Weare, Jonathan / Dinner, Aaron R. et al. | 2014
- 5476
-
Benchmarks for Characterization of Minima, Transition States, and Pathways in Atomic, Molecular, and Condensed Matter SystemsChill, Samuel T. / Stevenson, Jacob / Ruehle, Victor / Shang, Cheng / Xiao, Penghao / Farrell, James D. / Wales, David J. / Henkelman, Graeme et al. | 2014
- 5483
-
Treatment of Ionic Strength in Biomolecular Simulations of Charged Lipid BilayersVila-Viçosa, Diogo / Teixeira, Vitor H. / Santos, Hugo A. F. / Baptista, António M. / Machuqueiro, Miguel et al. | 2014
- 5493
-
Systematic Improvement of Potential-Derived Atomic Multipoles and Redundancy of the Electrostatic Parameter SpaceJakobsen, Sofie / Jensen, Frank et al. | 2014
- 5505
-
AMBER-DYES: Characterization of Charge Fluctuations and Force Field Parameterization of Fluorescent Dyes for Molecular Dynamics SimulationsGraen, Timo / Hoefling, Martin / Grubmüller, Helmut et al. | 2014
- 5513
-
Efficient Handling of Gaussian Charge Distributions: An Application to Polarizable Molecular ModelsKiss, Péter T. / Sega, Marcello / Baranyai, András et al. | 2014
- 5520
-
Mode Robustness in Raman Optical ActivityTommasini, Matteo / Longhi, Giovanna / Mazzeo, Giuseppe / Abbate, Sergio / Nieto-Ortega, Belén / Ramírez, Francisco J. / Casado, Juan / López Navarrete, Juan Teodomiro et al. | 2014
- 5528
-
Solvent Effects on Excited-State Structures: A Quantum Monte Carlo and Density Functional StudyGuareschi, Riccardo / Floris, Franca Maria / Amovilli, Claudio / Filippi, Claudia et al. | 2014
- 5538
-
Describing Excited State Relaxation and Localization in TiO2 Nanoparticles Using TD-DFTBerardo, Enrico / Hu, Han-Shi / van Dam, Hubertus J. J. / Shevlin, Stephen A. / Woodley, Scott M. / Kowalski, Karol / Zwijnenburg, Martijn A. et al. | 2014
- 5549
-
Assessment of Franck–Condon Methods for Computing Vibrationally Broadened UV–vis Absorption Spectra of Flavin Derivatives: Riboflavin, Roseoflavin, and 5‑ThioflavinKarasulu, Bora / Götze, Jan Philipp / Thiel, Walter et al. | 2014
- 5567
-
Equation-of-Motion Coupled-Cluster Theory for Excitation Energies of Closed-Shell Systems with Spin–Orbit CouplingWang, Zhifan / Tu, Zheyan / Wang, Fan et al. | 2014
- 5577
-
Computational Protocol for Modeling Thermochromic Molecular Crystals: Salicylidene Aniline As a Case StudyPresti, Davide / Labat, Fréderic / Pedone, Alfonso / Frisch, Michael J. / Hratchian, Hrant P. / Ciofini, Ilaria / Menziani, Maria Cristina / Adamo, Carlo et al. | 2014
- 5586
-
Computational Chemistry Meets Experiments for Explaining the Behavior of Bibenzyl: A Thermochemical and Spectroscopic (Infrared, Raman, and NMR) InvestigationLatouche, Camille / Barone, Vincenzo et al. | 2014
- 5593
-
Actinoid(III) HydrationFirst Principle Gibbs Energies of Hydration Using High Level Correlation MethodsHeinz, Norah / Zhang, Jun / Dolg, Michael et al. | 2014
- 5599
-
Superposition-Enhanced Estimation of Optimal Temperature Spacings for Parallel Tempering SimulationsBallard, Andrew J. / Wales, David J. et al. | 2014
- 5606
-
Order Parameters and Algorithmic Approaches for Detection and Demarcation of Interfaces in Hydrate–Fluid and Ice–Fluid SystemsSæthre, Bjørn Steen / Hoffmann, Alex C. / van der Spoel, David et al. | 2014
- 5616
-
Surface Adsorption in Nonpolarizable Atomic ModelsWhitmer, Jonathan K. / Joshi, Abhijeet A. / Carlton, Rebecca J. / Abbott, Nicholas L. / de Pablo, Juan J. et al. | 2014
- 5625
-
Benchmarking the AK13 Exchange Functional: Ionization Potentials and Electron AffinitiesCerqueira, Tiago F. T. / Oliveira, Micael J. T. / Marques, Miguel A. L. et al. | 2014
- 5630
-
Two-Photon Absorption of Metal-Assisted ChromophoresLi, Xin / Rinkevicius, Zilvinas / Ågren, Hans et al. | 2014
- 5640
-
Modeling the Partial Atomic Charges in Inorganometallic Molecules and Solids and Charge Redistribution in Lithium-Ion CathodesWang, Bo / Li, Shaohong L. / Truhlar, Donald G. et al. | 2014
- 5651
-
Generation of Well-Relaxed All-Atom Models of Large Molecular Weight Polymer Melts: A Hybrid Particle-Continuum Approach Based on Particle-Field Molecular Dynamics SimulationsDe Nicola, Antonio / Kawakatsu, Toshihiro / Milano, Giuseppe et al. | 2014
- 5668
-
Assessment of a Cost-Effective Approach to the Calculation of Kinetic and Thermodynamic Properties of Methyl Methacrylate Homopolymerization: A Comprehensive Theoretical StudyZhang, Guozhen / Konstantinov, Ivan A. / Arturo, Steven G. / Yu, Decai / Broadbelt, Linda J. et al. | 2014
- 5677
-
Mechanisms of Differential Allosteric Modulation in Homologous Proteins: Insights from the Analysis of Internal Dynamics and Energetics of PDZ DomainsMorra, Giulia / Genoni, Alessandro / Colombo, Giorgio et al. | 2014
- 5690
-
Accelerating All-Atom MD Simulations of Lipids Using a Modified Virtual-Sites TechniqueLoubet, Bastien / Kopec, Wojciech / Khandelia, Himanshu et al. | 2014
- 5696
-
Role of Desolvation in Thermodynamics and Kinetics of Ligand Binding to a KinaseMondal, Jagannath / Friesner, Richard A. / Berne, B. J. et al. | 2014
- 5706
-
Reparameterized United Atom Model for Molecular Dynamics Simulations of Gel and Fluid Phosphatidylcholine BilayersTjörnhammar, Richard / Edholm, Olle et al. | 2014
- 5716
-
Surprisal Metrics for Quantifying Perturbed Conformational Dynamics in Markov State ModelsVoelz, Vincent A. / Elman, Brandon / Razavi, Asghar M. / Zhou, Guangfeng et al. | 2014
- 5729
-
cluster: Searching for Unique Low Energy Minima of Structures Using a Novel Implementation of a Genetic AlgorithmKanters, René P. F. / Donald, Kelling J. et al. | 2014
- 5738
-
Correction to An Explicit Consideration of Desolvation is Critical to Binding Free Energy Calculations of Charged Molecules at Ionic SurfacesMori, Toshifumi / Hamers, Robert J. / Pedersen, Joel A. / Cui, Qiang et al. | 2014