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1

Generalized Hybrid-Orbital Method for Combining Density Functional Theory with Molecular Mechanicals

Jingzhi Pu, Jiali Gao, Donald G. Truhlar

Journal:

Year:

2005

Language:

english

File:

PDF, 198 KB

english, 2005

2

Development of a Polarizable Intermolecular Potential Function (PIPF) for Liquid Amides and Alkanes

Xie, Wangshen, Pu, Jingzhi, MacKerell,, Alexander D., Gao, Jiali

Journal:

Journal of Chemical Theory and Computation

Year:

2007

Language:

english

File:

PDF, 290 KB

english, 2007

3

Chemical Synthesis, Crystal Structure and Enzymatic Evaluation of a Dinucleotide Spore Photoproduct Analogue Containing a Formacetal Linker

Dr. Gengjie Lin, Dr. Chun-Hsing Chen, Dr. Maren Pink, Prof. Dr. Jingzhi Pu, Prof. Dr. Lei Li

Journal:

Chemistry - A European Journal

Year:

2011

Language:

english

File:

PDF, 815 KB

english, 2011

4

Use of Block Hessians for the Optimization of Molecular Geometries

Pu, Jingzhi, Truhlar, Donald G.

Journal:

Journal of Chemical Theory and Computation

Year:

2005

Language:

english

File:

PDF, 75 KB

english, 2005

5

Expanding the Horizon of the Thymine Isostere Biochemistry: Unique Cyclobutane Dimers Formed by Photoreaction between a Thymine and a Toluene Residue in the Dinucleotide Framework

Dr. Degang Liu, Dr. Yan Zhou, Prof. Dr. Jingzhi Pu, Prof. Dr. Lei Li

Journal:

Chemistry - A European Journal

Year:

2012

Language:

english

File:

PDF, 542 KB

english, 2012

6

Mechanisms and Free Energies of Enzymatic Reactions

Gao, Jiali, Ma, Shuhua, Major, Dan T., Nam, Kwangho, Pu, Jingzhi, Truhlar, Donald G.

Journal:

Chemical Reviews

Year:

2006

Language:

english

File:

PDF, 526 KB

english, 2006

7

Multidimensional Tunneling, Recrossing, and the Transmission Coefficient for Enzymatic Reactions

Pu, Jingzhi, Gao, Jiali, Truhlar, Donald G.

Journal:

Chemical Reviews

Year:

2006

Language:

english

File:

PDF, 330 KB

english, 2006

8

Benchmark Results for Hydrogen Atom Transfer between Carbon Centers and Validation of Electronic Structure Methods for Bond Energies and Barrier Heights

Dybala-Defratyka, Agnieszka, Paneth, Piotr, Pu, Jingzhi, Truhlar, Donald G.

Journal:

Journal of Physical Chemistry A

Year:

2004

Language:

english

File:

PDF, 144 KB

english, 2004

9

Nonperfect Synchronization of Reaction Center Rehybridization in the Transition State of the Hydride Transfer Catalyzed by Dihydrofolate Reductase

Pu, Jingzhi, Ma, Shuhua, Garcia-Viloca, Mireia, Gao, Jiali, Truhlar, Donald G., Kohen, Amnon

Journal:

Journal of the American Chemical Society

Year:

2005

Language:

english

File:

PDF, 170 KB

english, 2005

10

Multicoefficient Gaussian-3 Calculation of the Rate Constant for the OH + CH 4 Reaction and Its 12 C/ 13 C Kinetic Isotope Effect with Emphasis on the Effects of Coordinate System and Torsional Treatment

Ellingson, Benjamin A., Pu, Jingzhi, Lin, Hai, Zhao, Yan, Truhlar, Donald G.

Journal:

Journal of Physical Chemistry A

Year:

2007

Language:

english

File:

PDF, 239 KB

english, 2007

11

Tests of potential energy surfaces for H+CH[sub 4]↔CH[sub 3]+H[sub 2]: Deuterium and muonium kinetic isotope effects for the forward and reverse reaction

Pu, Jingzhi, Truhlar, Donald G.

Journal:

The Journal of Chemical Physics

Year:

2002

Language:

english

File:

PDF, 288 KB

english, 2002

12

Replica exchange molecular dynamics simulations of an α/β-type small acid soluble protein (SASP)

Ojeda-May, P., Pu, Jingzhi

Journal:

Biophysical Chemistry

Year:

2013

Language:

english

File:

PDF, 774 KB

english, 2013

13

Combining Self-Consistent-Charge Density-Functional Tight-Binding (SCC-DFTB) with Molecular Mechanics by the Generalized Hybrid Orbital (GHO) Method

Pu, Jingzhi, Gao, Jiali, Truhlar, Donald G.

Journal:

Journal of Physical Chemistry A

Year:

2004

Language:

english

File:

PDF, 106 KB

english, 2004

14

Hydride Transfer Reaction Catalyzed by Hyperthermophilic Dihydrofolate Reductase Is Dominated by Quantum Mechanical Tunneling and Is Promoted by Both Inter- and Intramonomeric Correlated Motions

Pang, Jiayun, Pu, Jingzhi, Gao, Jiali, Truhlar, Donald G., Allemann, Rudolf K.

Journal:

Journal of the American Chemical Society

Year:

2006

Language:

english

File:

PDF, 467 KB

english, 2006

15

Temperature Dependence of Carbon-13 Kinetic Isotope Effects of Importance to Global Climate Change

Lin, Hai, Zhao, Yan, Ellingson, Benjamin A., Pu, Jingzhi, Truhlar, Donald G.

Journal:

Journal of the American Chemical Society

Year:

2005

Language:

english

File:

PDF, 51 KB

english, 2005

16

Efficient Molecular Mechanics for Chemical Reactions: Multiconfiguration Molecular Mechanics Using Partial Electronic Structure Hessians

Lin, Hai, Pu, Jingzhi, Albu, Titus V., Truhlar, Donald G.

Journal:

Journal of Physical Chemistry A

Year:

2004

Language:

english

File:

PDF, 137 KB

english, 2004

17

Searching for Saddle Points by Using the Nudged Elastic Band Method: An Implementation for Gas-Phase Systems

González-García, Núria, Pu, Jingzhi, González-Lafont, Àngels, Lluch, José M., Truhlar, Donald G.

Journal:

Journal of Chemical Theory and Computation

Year:

2006

Language:

english

File:

PDF, 145 KB

english, 2006

18

Isotropic Periodic Sum Treatment of Long-Range Electrostatic Interactions in Combined Quantum Mechanical and Molecular Mechanical Calculations

Ojeda-May, Pedro, Pu, Jingzhi

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 1.54 MB

english, 2014

19

A Coupled Polarization-Matrix Inversion and Iteration Approach for Accelerating the Dipole Convergence in a Polarizable Potential Function †

Xie, Wangshen, Pu, Jingzhi, Gao, Jiali

Journal:

Journal of Physical Chemistry A

Year:

2009

Language:

english

File:

PDF, 310 KB

english, 2009

20

Benchmark Calculations of Reaction Energies, Barrier Heights, and Transition-State Geometries for Hydrogen Abstraction from Methanol by a Hydrogen Atom

Pu, Jingzhi, Truhlar, Donald G.

Journal:

Journal of Physical Chemistry A

Year:

2005

Language:

english

File:

PDF, 59 KB

english, 2005

21

Small Temperature Dependence of the Kinetic Isotope Effect for the Hydride Transfer Reaction Catalyzed by Escherichia c oli Dihydrofolate Reductase

Pu, Jingzhi, Ma, Shuhua, Gao, Jiali, Truhlar, Donald G.

Journal:

Journal of Physical Chemistry B

Year:

2005

Language:

english

File:

PDF, 195 KB

english, 2005

22

Generalized Hybrid Orbital (GHO) Method for Combining Ab Initio Hartree−Fock Wave Functions with Molecular Mechanics

Pu, Jingzhi, Gao, Jiali, Truhlar, Donald G.

Journal:

Journal of Physical Chemistry A

Year:

2004

Language:

english

File:

PDF, 203 KB

english, 2004

23

Reaction Path Force Matching: A New Strategy of Fitting Specific Reaction Parameters for Semiempirical Methods in Combined QM/MM Simulations

Zhou, Yan, Pu, Jingzhi

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 3.56 MB

english, 2014

24

Tests of second-generation and third-generation density functionals for thermochemical kineticsElectronic supplementary information (ESI) available: Mean errors for pure and hybrid DFT methods. See http://www.rsc.org/suppdata/cp/b3/b316260e/

Zhao, Yan, Pu, Jingzhi, Lynch, Benjamin J., Truhlar, Donald G.

Journal:

Physical Chemistry Chemical Physics

Year:

2004

Language:

english

File:

PDF, 92 KB

english, 2004

25

H-loop histidine catalyzes ATP hydrolysis in the E. coli ABC-transporter HlyB

Zhou, Yan, Ojeda-May, Pedro, Pu, Jingzhi

Journal:

Physical Chemistry Chemical Physics

Year:

2013

Language:

english

File:

PDF, 1.53 MB

english, 2013

26

Lateral confinement of image electron wave function by an interfacial dipole lattice

Dutton, Gregory, Pu, Jingzhi, Truhlar, Donald G., Zhu, X.-Y.

Journal:

The Journal of Chemical Physics

Year:

2003

Language:

english

File:

PDF, 413 KB

english, 2003

27

Parametrized direct dynamics study of rate constants of H with CH[sub 4] from 250 to 2400 K

Pu, Jingzhi, Truhlar, Donald G.

Journal:

The Journal of Chemical Physics

Year:

2002

Language:

english

File:

PDF, 401 KB

english, 2002

28

Trapping the ATP binding state leads to a detailed understanding of the F 1 -ATPase mechanism

Nam, Kwangho, Pu, Jingzhi, Karplus, Martin

Journal:

Proceedings of the National Academy of Sciences

Year:

2014

Language:

english

File:

PDF, 1.34 MB

english, 2014

29

Validation of variational transition state theory with multidimensional tunneling contributions against accurate quantum mechanical dynamics for H+CH[sub 4]→H[sub 2]+CH[sub 3] in an extended temperature interval

Pu, Jingzhi, Truhlar, Donald G.

Journal:

The Journal of Chemical Physics

Year:

2002

Language:

english

File:

PDF, 259 KB

english, 2002

30

[IEEE 2011 International Conference on Consumer Electronics, Communications and Networks (CECNet) - Xianning, China (2011.04.16-2011.04.18)] 2011 International Conference on Consumer Electronics, Communications and Networks (CECNet) - An identification method of stiffness of mechanical joint

Jinjuan, Zhao, Shijun, Wang, Jingzhi, Ma, Pu, Guo

Year:

2011

Language:

english

File:

PDF, 288 KB

english, 2011

31

Assessing the accuracy of the isotropic periodic sum method through Madelung energy computation

Ojeda-May, Pedro, Pu, Jingzhi

Journal:

The Journal of Chemical Physics

Year:

2014

Language:

english

File:

PDF, 371 KB

english, 2014

32

Test of variational transition state theory with multidimensional tunneling contributions against an accurate full-dimensional rate constant calculation for a six-atom system

Pu, Jingzhi, Corchado, José C., Truhlar, Donald G.

Journal:

The Journal of Chemical Physics

Year:

2001

Language:

english

File:

PDF, 255 KB

english, 2001

33

Multiscale QM/MM Simulations of ATP Hydrolysis Mechanism in ABC-Transporters

Journal:

Biophysical Journal

Year:

2015

Language:

english

File:

PDF, 40 KB

english, 2015

34

Epitaxial growth of Y 3 Fe 5 O 12 thin films with perpendicular magnetic anisotropy

Fu, Jianbo, Hua, Muxin, Wen, Xin, Xue, Mingzhu, Ding, Shilei, Wang, Meng, Yu, Pu, Liu, Shunquan, Han, Jingzhi, Wang, Changsheng, Du, Honglin, Yang, Yingchang, Yang, Jinbo

Journal:

Applied Physics Letters

Year:

2017

Language:

english

File:

PDF, 1.85 MB

english, 2017

35

Treating electrostatics with Wolf summation in combined quantum mechanical and molecular mechanical simulations

Ojeda-May, Pedro, Pu, Jingzhi

Journal:

The Journal of Chemical Physics

Year:

2015

Language:

english

File:

PDF, 470 KB

english, 2015

36

Elucidating the role of surface passivating ligand structural parameters in hole wave function delocalization in semiconductor cluster molecules

Teunis, Meghan B, Mulpuri, Nagaraju, Dutta, Poulami, Pu, Jingzhi, Muhoberac, Barry B, Sardar, Rajesh, Agarwal, Mangilal

Journal:

Year:

2017

Language:

english

File:

PDF, 1.87 MB

english, 2017

37

Exploring Cycloreversion Reaction of Cyclobutane Pyrimidine Dimers Quantum Mechanically

Huang, Donglian, Chen, Shanfeng, Pu, Jingzhi, Tan, Xuecai, Zhou, Yan

Journal:

Journal of Physical Chemistry A

Year:

2019

Language:

english

File:

PDF, 1.81 MB

english, 2019

38

Accelerated Computation of Free Energy Profile at ab Initio Quantum Mechanical/Molecular Mechanics Accuracy via a Semi-Empirical Reference Potential. II. Recalibrating Semi-Empirical Parameters with Force Matching

Pan, Xiaoliang, Li, Pengfei, Ho, Junming, Pu, Jingzhi, Mei, Ye, Shao, YIhan

Journal:

Physical Chemistry Chemical Physics

Year:

2019

Language:

english

File:

PDF, 2.78 MB

english, 2019

39

EXPRESS: Identifying Thermal Decomposition Products of Nitrate Ester Explosives Using Gas ChromatographyâVacuum Ultraviolet Spectroscopy: An Experimental and Computational Study

Cruse, Courtney, Pu, Jingzhi, Goodpaster, John Vincent

Journal:

Applied Spectroscopy

Year:

2020

Language:

english

File:

PDF, 1.25 MB

english, 2020