Volume 10; Issue 4

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Journal of Chemical Theory and Computation
Volume 10; Issue 4

Journal of Chemical Theory and Computation

Volume 10; Issue 4

1

Variational Approach to Molecular Kinetics

Nüske, Feliks, Keller, Bettina G., Pérez-Hernández, Guillermo, Mey, Antonia S. J. S., Noé, Frank

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 3.82 MB

english, 2014

2

Protocol To Make Protein NMR Structures Amenable to Stable Long Time Scale Molecular Dynamics Simulations

Li, Da-Wei, Brüschweiler, Rafael

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 3.71 MB

english, 2014

3

Geometry Optimization in Polarizable QM/MM Models: The Induced Dipole Formulation

Caprasecca, Stefano, Jurinovich, Sandro, Viani, Lucas, Curutchet, Carles, Mennucci, Benedetta

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 1.67 MB

english, 2014

4

Parameterization of DFTB3/3OB for Sulfur and Phosphorus for Chemical and Biological Applications

Gaus, Michael, Lu, Xiya, Elstner, Marcus, Cui, Qiang

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 1.46 MB

english, 2014

5

Performance of an Optimally Tuned Range-Separated Hybrid Functional for 0–0 Electronic Excitation Energies

Jacquemin, Denis, Moore, Barry, Planchat, Aurélien, Adamo, Carlo, Autschbach, Jochen

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 1.10 MB

english, 2014

6

Quantum Mechanical Calculation of Noncovalent Interactions: A Large-Scale Evaluation of PMx, DFT, and SAPT Approaches

Li, Amanda, Muddana, Hari S., Gilson, Michael K.

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 854 KB

english, 2014

7

Predicting the Impact of Missense Mutations on Protein–Protein Binding Affinity

Li, Minghui, Petukh, Marharyta, Alexov, Emil, Panchenko, Anna R.

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 1.73 MB

english, 2014

8

Multiscale Free Energy Simulations: An Efficient Method for Connecting Classical MD Simulations to QM or QM/MM Free Energies Using Non-Boltzmann Bennett Reweighting Schemes

König, Gerhard, Hudson, Phillip S., Boresch, Stefan, Woodcock, H. Lee

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 1.12 MB

english, 2014

9

Application of Automated Reaction Path Search Methods to a Systematic Search of Single-Bond Activation Pathways Catalyzed by Small Metal Clusters: A Case Study on H–H Activation by Gold

Gao, Min, Lyalin, Andrey, Maeda, Satoshi, Taketsugu, Tetsuya

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 393 KB

english, 2014

10

GEM*: A Molecular Electronic Density-Based Force Field for Molecular Dynamics Simulations

Duke, Robert E., Starovoytov, Oleg N., Piquemal, Jean-Philip, Cisneros, G. Andrés

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 649 KB

english, 2014

11

General Multiobjective Force Field Optimization Framework, with Application to Reactive Force Fields for Silicon Carbide

Jaramillo-Botero, Andres, Naserifar, Saber, Goddard, William A.

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 2.85 MB

english, 2014

12

Transmembrane Permeation Mechanism of Charged Methyl Guanidine

Wang, Yukun, Hu, Dan, Wei, Dongqing

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 420 KB

english, 2014

13

Exploring the Conformational Dynamics of Alanine Dipeptide in Solution Subjected to an External Electric Field: A Nonequilibrium Molecular Dynamics Simulation

Wang, Han, Schütte, Christof, Ciccotti, Giovanni, Delle Site, Luigi

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 2.08 MB

english, 2014

14

Force-Field Development from Electronic Structure Calculations with Periodic Boundary Conditions: Applications to Gaseous Adsorption and Transport in Metal–Organic Frameworks

Lin, Li-Chiang, Lee, Kyuho, Gagliardi, Laura, Neaton, Jeffrey B., Smit, Berend

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 3.01 MB

english, 2014

15

Toward QM/MM Simulation of Enzymatic Reactions with the Drude Oscillator Polarizable Force Field

Boulanger, Eliot, Thiel, Walter

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 429 KB

english, 2014

16

Dipeptide Aggregation in Aqueous Solution from Fixed Point-Charge Force Fields

Götz, Andreas W., Bucher, Denis, Lindert, Steffen, McCammon, J. Andrew

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 2.78 MB

english, 2014

17

A Practical Computational Approach to Study Molecular Instability Using the Pseudo-Jahn–Teller Effect

García-Fernández, Pablo, Aramburu, Jose Antonio, Moreno, Miguel, Zlatar, Matija, Gruden-Pavlović, Maja

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 1.34 MB

english, 2014

18

Development of a “First Principles” Water Potential with Flexible Monomers. II: Trimer Potential Energy Surface, Third Virial Coefficient, and Small Clusters

Babin, Volodymyr, Medders, Gregory R., Paesani, Francesco

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 1.26 MB

english, 2014

19

Determination of Signaling Pathways in Proteins through Network Theory: Importance of the Topology

Ribeiro, Andre A. S. T., Ortiz, Vanessa

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 4.23 MB

english, 2014

20

A Comparative Study of Transferable Aspherical Pseudoatom Databank and Classical Force Fields for Predicting Electrostatic Interactions in Molecular Dimers

Kumar, Prashant, Bojarowski, Sławomir A., Jarzembska, Katarzyna N., Domagała, Sławomir, Vanommeslaeghe, Kenno, MacKerell, Alexander D., Dominiak, Paulina M.

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 3.11 MB

english, 2014

21

Enthalpy–Entropy Tuning in the Adsorption of Nucleobases at the Au(111) Surface

Rosa, Marta, Corni, Stefano, Di Felice, Rosa

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 1.61 MB

english, 2014

22

Solv-ccCA: Implicit Solvation and the Correlation Consistent Composite Approach for the Determination of p K a

Riojas, Amanda G., Wilson, Angela K.

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 2.27 MB

english, 2014

23

Erratum: “The Variationally Orbital-Adapted Configuration Interaction Singles (VOA-CIS) Approach to Electronically Excited States”

Liu, Xinle, Subotnik, Joseph E.

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 119 KB

english, 2014

24

Improvement of DNA and RNA Sugar Pucker Profiles from Semiempirical Quantum Methods

Huang, Ming, Giese, Timothy J., Lee, Tai-Sung, York, Darrin M.

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 4.88 MB

english, 2014

25

Origin of the Red Shift for the Lowest Singlet π → π* Charge-Transfer Absorption of p -Nitroaniline in Supercritical CO 2

Hidalgo, Marcelo, Rivelino, Roberto, Canuto, Sylvio

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 1.84 MB

english, 2014

26

Variational Implicit Solvation with Poisson–Boltzmann Theory

Zhou, Shenggao, Cheng, Li-Tien, Dzubiella, Joachim, Li, Bo, McCammon, J. Andrew

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 4.06 MB

english, 2014

27

Surface Hopping Dynamics with Correlated Single-Reference Methods: 9H-Adenine as a Case Study

Plasser, Felix, Crespo-Otero, Rachel, Pederzoli, Marek, Pittner, Jiri, Lischka, Hans, Barbatti, Mario

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 2.39 MB

english, 2014

28

First Multireference Correlation Treatment of Bulk Metals

Voloshina, Elena, Paulus, Beate

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 2.30 MB

english, 2014

29

Static Dielectric Constant from Simulations Revisited: Fluctuations or External Field?

Kolafa, Jiří, Viererblová, Linda

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 858 KB

english, 2014

30

Mechanism of Stapled Peptide Binding to MDM2: Possible Consequences for Peptide Design

Sim, Adelene Y. L., Joseph, Thomas, Lane, David P., Verma, Chandra

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 2.07 MB

english, 2014

31

Simple Link Atom Saccharide Hybrid (SLASH) Treatment for Glycosidic Bonds at the QM/MM Boundary

Crous, Werner, Field, Martin J., Naidoo, Kevin J.

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 5.57 MB

english, 2014

32

Assessing the Reliability of the Dynamics Reconstructed from Metadynamics

Salvalaglio, Matteo, Tiwary, Pratyush, Parrinello, Michele

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 876 KB

english, 2014

33

Data Filtering for Effective Analysis of Crystal–Solution Interface Molecular Dynamics Simulations

Elts, Ekaterina, Greiner, Maximilian M., Briesen, Heiko

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 6.09 MB

english, 2014

34

The R –7 Dispersion Interaction in the General Effective Fragment Potential Method

Xu, Peng, Zahariev, Federico, Gordon, Mark S.

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 1.36 MB

english, 2014

35

Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: I. Toward Massively Parallel Direct Space Computations

Lipparini, Filippo, Lagardère, Louis, Stamm, Benjamin, Cancès, Eric, Schnieders, Michael, Ren, Pengyu, Maday, Yvon, Piquemal, Jean-Philip

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 1.57 MB

english, 2014

36

Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme

Mlýnský, Vojtěch, Banáš, Pavel, Šponer, Jiří, van der Kamp, Marc W., Mulholland, Adrian J., Otyepka, Michal

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 6.03 MB

english, 2014

37

Erratum to Molecular Dynamics Simulations of Highly Crowded Amino Acid Solutions: Comparisons of Eight Different Force Field Combinations with Experiment and with Each Other

Andrews, Casey T., Elcock, Adrian H.

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 107 KB

english, 2014

38

Efficient Calculation of Free Energy Differences Associated with Isotopic Substitution Using Path-Integral Molecular Dynamics

Marsalek, Ondrej, Chen, Pei-Yang, Dupuis, Romain, Benoit, Magali, Méheut, Merlin, Bačić, Zlatko, Tuckerman, Mark E.

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 1.64 MB

english, 2014

39

Introducing Charge Hydration Asymmetry into the Generalized Born Model

Mukhopadhyay, Abhishek, Aguilar, Boris H., Tolokh, Igor S., Onufriev, Alexey V.

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 1.41 MB

english, 2014

40

Energy Landscapes and Global Optimization of Self-Assembling Cyclic Peptides

Oakley, Mark T., Johnston, Roy L.

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 1.84 MB

english, 2014

41

How Small Can a Catenane Be?

Feng, Xuejun, Gu, Jiande, Chen, Qun, Lii, Jenn-Huei, Allinger, Norman L., Xie, Yaoming, Schaefer, Henry F.

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 2.73 MB

english, 2014

42

Nonadiabatic and Time-Resolved Photoelectron Spectroscopy for Molecular Systems

Flick, Johannes, Appel, Heiko, Rubio, Angel

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 2.65 MB

english, 2014

43

Audibilization: Data Analysis by Ear

Jallouk, Andrew P., Cummings, Peter T.

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 2.59 MB

english, 2014

44

Mechanism of Spin–Orbit Effects on the Ligand NMR Chemical Shift in Transition-Metal Complexes: Linking NMR to EPR

Vícha, Jan, Straka, Michal, Munzarová, Markéta L., Marek, Radek

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 1.82 MB

english, 2014

45

Cooperativity Assisted Shortening of Hydrogen Bonds in Crystalline Oxalic Acid Dihydrate: DFT and NBO Model Studies

Stare, Jernej, Hadži, Dušan

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 1.02 MB

english, 2014

46

Multisurface Adiabatic Reactive Molecular Dynamics

Nagy, Tibor, Yosa Reyes, Juvenal, Meuwly, Markus

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 2.71 MB

english, 2014