Volume 11; Issue 3

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Journal of Chemical Theory and Computation
Volume 11; Issue 3

Journal of Chemical Theory and Computation

Volume 11; Issue 3

1

Multiple-Time Step Ab Initio Molecular Dynamics Based on Two-Electron Integral Screening

Fatehi, Shervin, Steele, Ryan P.

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 1.02 MB

english, 2015

2

Can We Execute Stable Microsecond-Scale Atomistic Simulations of Protein–RNA Complexes?

Krepl, M., Havrila, M., Stadlbauer, P., Banas, P., Otyepka, M., Pasulka, J., Stefl, R., Sponer, J.

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 2.40 MB

english, 2015

3

Acidic C–H Bond as a Proton Donor in Excited State Intramolecular Proton Transfer Reactions

Stasyuk, Anton J., Cyrański, Michał K., Gryko, Daniel T., Solà, Miquel

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 1.39 MB

english, 2015

4

Decoding the Mobility and Time Scales of Protein Loops

Gu, Yina, Li, Da-Wei, Brüschweiler, Rafael

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 1.09 MB

english, 2015

5

Improved cryoEM-Guided Iterative Molecular Dynamics–Rosetta Protein Structure Refinement Protocol for High Precision Protein Structure Prediction

Lindert, Steffen, McCammon, J. Andrew

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 5.55 MB

english, 2015

6

Tree Tensor Network State with Variable Tensor Order: An Efficient Multireference Method for Strongly Correlated Systems

Murg, V., Verstraete, F., Schneider, R., Nagy, P. R., Legeza, Ö.

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 999 KB

english, 2015

7

Applicability of Quantum Thermal Baths to Complex Many-Body Systems with Various Degrees of Anharmonicity

Hernández-Rojas, Javier, Calvo, Florent, Noya, Eva Gonzalez

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 1.20 MB

english, 2015

8

Quantum Monte Carlo Treatment of the Charge Transfer and Diradical Electronic Character in a Retinal Chromophore Minimal Model

Zen, Andrea, Coccia, Emanuele, Gozem, Samer, Olivucci, Massimo, Guidoni, Leonardo

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 1.25 MB

english, 2015

9

One-Electron Energies from the Two-Component GW Method

Kühn, Michael, Weigend, Florian

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 272 KB

english, 2015

10

A Kinetic Monte Carlo Study of Fullerene Adsorption within a Pc-PBBA Covalent Organic Framework and Implications for Electron Transport

Koo, Brian T., Berard, Philip G., Clancy, Paulette

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 1.62 MB

english, 2015

11

Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering

Gil-Ley, Alejandro, Bussi, Giovanni

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 1.92 MB

english, 2015

12

Conserve Water: A Method for the Analysis of Solvent in Molecular Dynamics

Harrigan, Matthew P., Shukla, Diwakar, Pande, Vijay S.

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 2.18 MB

english, 2015

13

Hierarchical Biomolecular Dynamics: Picosecond Hydrogen Bonding Regulates Microsecond Conformational Transitions

Buchenberg, Sebastian, Schaudinnus, Norbert, Gerhard Stock,

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 927 KB

english, 2015

14

Energy Minimization on Manifolds for Docking Flexible Molecules

Mirzaei, Hanieh, Zarbafian, Shahrooz, Villar, Elizabeth, Mottarella, Scott, Beglov, Dmitri, Vajda, Sandor, Paschalidis, Ioannis Ch., Vakili, Pirooz, Kozakov, Dima

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 672 KB

english, 2015

15

A Collective Variable for the Rapid Exploration of Protein Druggability

Cuchillo, Rémi, Pinto-Gil, Kevin, Michel, Julien

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 2.45 MB

english, 2015

16

Infrared and Raman Spectroscopy of Liquid Water through “First-Principles” Many-Body Molecular Dynamics

Medders, Gregory R., Paesani, Francesco

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 518 KB

english, 2015

17

Accurate Treatment of Large Supramolecular Complexes by Double-Hybrid Density Functionals Coupled with Nonlocal van der Waals Corrections

Calbo, Joaquín, Ortí, Enrique, Sancho-García, Juan C., Aragó, Juan

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 432 KB

english, 2015

18

Disfavoring Mechanochemical Reactions by Stress-Induced Steric Hindrance

Krupička, Martin, Marx, Dominik

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 1.20 MB

english, 2015

19

Density-Difference-Driven Optimized Embedding Potential Method To Study the Spectroscopy of Br 2 in Water Clusters

Roncero, Octavio, Aguado, Alfredo, Batista-Romero, Fidel A., Bernal-Uruchurtu, Margarita I., Hernández-Lamoneda, Ramón

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 2.67 MB

english, 2015

20

Opsin Effect on the Electronic Structure of the Retinylidene Chromophore in Rhodopsin

Sproviero, Eduardo M.

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 751 KB

english, 2015

21

Co–C Bond Dissociation Energies in Cobalamin Derivatives and Dispersion Effects: Anomaly or Just Challenging?

Qu, Zheng-wang, Hansen, Andreas, Grimme, Stefan

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 1.07 MB

english, 2015

22

The Energy Difference between the Triply-Bridged and All-Terminal Structures of Co 4 (CO) 12 , Rh 4 (CO) 12 , and Ir 4 (CO) 12 : A Difficult Test for Conventional Density Functional Methods

Ding, Hairong, Lu, Yunxiang, Xie, Yaoming, Liu, Honglai, Schaefer, Henry F.

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 537 KB

english, 2015

23

Evaluation of Energy Gradients and Infrared Vibrational Spectra through Molecules-in-Molecules Fragment-Based Approach

Jose, K. V. Jovan, Raghavachari, Krishnan

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 2.33 MB

english, 2015

24

Independent Metrics for Protein Backbone and Side-Chain Flexibility: Time Scales and Effects of Ligand Binding

Fuchs, Julian E., Waldner, Birgit J., Huber, Roland G., von Grafenstein, Susanne, Kramer, Christian, Liedl, Klaus R.

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 1.37 MB

english, 2015

25

Photodissociation Dynamics of Homonuclear Diatomic Molecules in Helium Nanodroplets. The Case of Cl 2 @( 4 He) N

Vilà, Arnau, González, Miguel, Mayol, Ricardo

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 3.30 MB

english, 2015

26

Excitation Energies from Real-Time Propagation of the Four-Component Dirac–Kohn–Sham Equation

Repisky, Michal, Konecny, Lukas, Kadek, Marius, Komorovsky, Stanislav, Malkin, Olga L., Malkin, Vladimir G., Ruud, Kenneth

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 1.17 MB

english, 2015

27

Coupled-Perturbed SCF Approach for Calculating Static Polarizabilities and Hyperpolarizabilities with Nonorthogonal Localized Molecular Orbitals

Li, Shaopeng, Hu, Linping, Peng, Liang, Yang, Weitao, Gu, Feng Long

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 717 KB

english, 2015

28

Early Events in the Nonadiabatic Relaxation Dynamics of 4-( N , N -Dimethylamino)benzonitrile

Kochman, Michał A., Tajti, Attila, Morrison, Carole A., Miller, R. J. Dwayne

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 2.18 MB

english, 2015

29

Open-Ended Recursive Approach for the Calculation of Multiphoton Absorption Matrix Elements

Friese, Daniel H., Beerepoot, Maarten T. P., Ringholm, Magnus, Ruud, Kenneth

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 2.43 MB

english, 2015

30

Stalking Higher Energy Conformers on the Potential Energy Surface of Charged Species

Brites, Vincent, Cimas, Alvaro, Spezia, Riccardo, Sieffert, Nicolas, Lisy, James M., Gaigeot, Marie-Pierre

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 2.92 MB

english, 2015

31

Calculating High Energy Charge Transfer States Using Optimally Tuned Range-Separated Hybrid Functionals

Manna, Arun K., Lee, Myeong H., McMahon, Kayla L., Dunietz, Barry D.

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 1.79 MB

english, 2015

32

Spin Adapted versus Broken Symmetry Approaches in the Description of Magnetic Coupling in Heterodinuclear Complexes

Costa, Ramon, Valero, Rosendo, Mañeru, Daniel Reta, Moreira, Ibério de P. R., Illas, Francesc

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 1.93 MB

english, 2015

33

Probing the Unfolded Configurations of a β-Hairpin Using Sketch-Map

Ardevol, Albert, Tribello, Gareth A., Ceriotti, Michele, Parrinello, Michele

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 11.95 MB

english, 2015

34

Why is Benzene Soluble in Water? Role of OH/π Interaction in Solvation

Takahashi, Hideaki, Suzuoka, Daiki, Morita, Akihiro

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 6.83 MB

english, 2015

35

Molecular Dynamics Simulations of 441 Two-Residue Peptides in Aqueous Solution: Conformational Preferences and Neighboring Residue Effects with the Amber ff99SB-ildn-NMR Force Field

Li, Shuxiang, Andrews, Casey T., Frembgen-Kesner, Tamara, Miller, Mark S., Siemonsma, Stephen L., Collingsworth, Timothy D., Rockafellow, Isaac T., Ngo, Nguyet Anh, Campbell, Brady A., Brown, Reid F.,

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 3.56 MB

english, 2015

36

Comparison of Real-Time and Linear-Response Time-Dependent Density Functional Theories for Molecular Chromophores Ranging from Sparse to High Densities of States

Tussupbayev, Samat, Govind, Niranjan, Lopata, Kenneth, Cramer, Christopher J.

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 1.19 MB

english, 2015

37

Third-Order Incremental Dual-Basis Set Zero-Buffer Approach for Large High-Spin Open-Shell Systems

Zhang, Jun, Dolg, Michael

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 920 KB

english, 2015

38

Potential Application of Alchemical Free Energy Simulations to Discriminate GPCR Ligand Efficacy

Lee, Hui Sun, Seok, Chaok, Im, Wonpil

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 2.98 MB

english, 2015

39

Diffusion Monte Carlo Study of Para -Diiodobenzene Polymorphism Revisited

Hongo, Kenta, Watson, Mark A., Iitaka, Toshiaki, Aspuru-Guzik, Alán, Maezono, Ryo

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 937 KB

english, 2015

40

Removing External Degrees of Freedom from Transition-State Search Methods using Quaternions

Melander, Marko, Laasonen, Kari, Jónsson, Hannes

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 2.02 MB

english, 2015

41

Reassessment of the Thermodynamic, Kinetic, and Spectroscopic Features of Cyanomethanimine Derivatives: A Full Anharmonic Perturbative Treatment

Vazart, Fanny, Calderini, Danilo, Skouteris, Dimitrios, Latouche, Camille, Barone, Vincenzo

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 878 KB

english, 2015

42

Biasing Potential Replica Exchange Multisite λ-Dynamics for Efficient Free Energy Calculations

Armacost, Kira A., Goh, Garrett B., Brooks, Charles L.

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 2.28 MB

english, 2015

43

High-Resolution Coarse-Grained Modeling Using Oriented Coarse-Grained Sites

Haxton, Thomas K.

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 11.25 MB

english, 2015

44

Excited-State Vibrations of Solvated Molecules: Going Beyond the Linear-Response Polarizable Continuum Model

Mennucci, Benedetta, Scalmani, Giovanni, Jacquemin, Denis

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 417 KB

english, 2015

45

Understanding the ε and ζ High-Pressure Solid Phases of Oxygen. Systematic Periodic Density Functional Theory Studies Using Localized Atomic Basis

Ochoa-Calle, A. J., Zicovich-Wilson, C. M., Hernández-Lamoneda, R., Ramírez-Solís, A.

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 736 KB

english, 2015

46

Calculated Nuclear Magnetic Resonance Spectra of Polytwistane and Related Hydrocarbon Nanorods

Maryasin, Boris, Olbrich, Martin, Trauner, Dirk, Ochsenfeld, Christian

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 2.20 MB

english, 2015

47

Preselective Screening for Linear-Scaling Exact Exchange-Gradient Calculations for Graphics Processing Units and General Strong-Scaling Massively Parallel Calculations

Kussmann, Jörg, Ochsenfeld, Christian

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 563 KB

english, 2015

48

Correction to Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations

Mobley, David L., Bayly, Christopher I., Cooper, Matthew D., Shirts, Michael R., Dill, Ken A.

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 117 KB

english, 2015

49

Bottom-Up Coarse-Graining of Peptide Ensembles and Helix–Coil Transitions

Rudzinski, Joseph F., Noid, William G.

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 4.29 MB

english, 2015