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Yang L.,Institute of Theoretical and Computational Chemistry | Yang L.,Peking University | Liu C.-E.,Institute of Theoretical and Computational Chemistry | Shao Q.,CAS Shanghai Institute of Materia Medica | And 4 more authors.
Accounts of Chemical Research | Year: 2015

Conspectus Despite great advances in molecular dynamics simulations, there remain large gaps beteen the simulations and experimental observations in terms of the time and length scales that can be approached. Developing fast and accurate algorithms and methods is of ultimate importance to bridge these gaps. In this Account, e briefly summarize recent efforts in such directions. In particular, e focus on integrated tempering sampling. The efficiency of this sampling method has been demonstrated by applications to a range of chemical and biological problems: protein folding, molecular cluster structure searches, and chemical reactions. The combination of integrated tempering sampling and a trajectory sampling method allos the calculation of rate constants and reaction pathays ithout predefined collective coordinates. © 2015 American Chemical Society.

Wang X.,Sichuan University | Wu S.,Sichuan University | Xu D.,Sichuan University | Xie D.,Institute of Theoretical and Computational Chemistry | Guo H.,University of New Mexico
Journal of Chemical Information and Modeling | Year: 2011

Angiotensin-converting enzyme (ACE) is an important zinc-dependent hydrolase responsible for converting the inactive angiotensin I to the vasoconstrictor angiotensin II and for inactivating the vasodilator bradykinin. However, the substrate binding mode of ACE has not been completely understood. In this work, we propose a model for an ACE Michaelis complex based on two known X-ray structures of inhibitor-enzyme complexes. Specifically, the human testis angiotensin-converting enzyme (tACE) complexed with two clinic drugs were first investigated using a combined quantum mechanical and molecular mechanical (QM/MM) approach. The structural parameters obtained from the 550 ps molecular dynamics simulations are in excellent agreement with the X-ray structures, validating the QM/MM approach. Based on these structures, a model for the Michaelis complex was proposed and simulated using the same computational protocol. Implications to ACE catalysis are discussed. (Figure presented). © 2011 American Chemical Society.

Shen J.,Institute of Theoretical and Computational Chemistry | Li S.H.,Institute of Theoretical and Computational Chemistry
Science China Chemistry | Year: 2010

The performances of several multireference electronic structure methods including complete active space self-consistent field (CASSCF)-based second-order perturbation theory (CASPT2), multireference configuration interaction with single and double excitations (MR-CISD), MR-CISD with the Davidson correction (MR-CISD+Q), and the CASSCF-based block-correlated coupled cluster method (CAS-BCCC4) we developed recently are compared by applying them to study several different chemical problems involving computation of ground state potential energy surfaces, the singlet-triplet gaps in diradicals, reaction barriers, and the excitation energies of low-lying excited states. Comparison with the results from other highly accurate theoretical methods or the available experimental data demonstrate that for all the problems studied, the overall performance of CAS-BCCC4 is competitive with that of MR-CISD+Q, and better than that of CASPT2 and MR-CISD methods. Thus the CAS-BCCC4 approach is expected to be a promising theoretical method for quantitative descriptions of the electronic structures of molecules with noticeable multireference character. © Science China Press and Springer-Verlag Berlin Heidelberg 2010.

Xie C.,Institute of Theoretical and Computational Chemistry | Hu X.,Institute of Theoretical and Computational Chemistry | Zhou L.,Institute of Theoretical and Computational Chemistry | Xie D.,Institute of Theoretical and Computational Chemistry | Guo H.,University of New Mexico
Journal of Chemical Physics | Year: 2013

Three-dimensional potential energy surfaces for the two lowest singlet (Ã1B1 and B̃1A2) and two lowest triplet (ã3B1 and b̃3A 2) states of SO2 have been determined at the Davidson corrected internally contracted multi-reference configuration interaction level with the augmented correlation-consistent polarized triple-zeta basis set (icMRCI+Q/AVTZ). The non-adiabatically coupled singlet states, which are responsible for the complex Clements bands of the B band, are expressed in a 2 × 2 quasi-diabatic representation. The triplet state potential energy surfaces, which are responsible for the weak A band, were constructed in the adiabatic representation. The absorption spectrum spanning both the A and B bands, which is calculated with a three-state non-adiabatic coupled Hamil-tonian, is in good agreement with experiment, thus validating the potential energy surfaces and their couplings. © 2013 AIP Publishing LLC.

Lin S.,Institute of Theoretical and Computational Chemistry | Lin S.,University of New Mexico | Johnson R.S.,Institute of Theoretical and Computational Chemistry | Johnson R.S.,University of New Mexico | And 6 more authors.
ACS National Meeting Book of Abstracts | Year: 2011

Methanol steam reforming (MSR) has gained considerable interest lately as a potential solution to hydrogen storage and distribution problems in mobile fuel cell applications. We present results of a plane-wave density functional theory study in which we explore the possible MSR pathways on the Cu(111) surface. We focus on various intermediary reactions from adsorbed formaldehyde (CH 2O), an intermediate of methanol decomposition, and adsorbed hydroxyl (OH) formed from water decomposition, through to the final products carbon dioxide (CO 2) and adsorbed hydrogen (H). Three possible pathways have been identified and the lowest two paths through the formate (CHOO) intermediate. Adsorption energies and geometries of all intermediates, as well as the characterization of transition states are reported. Additionally, the effect of hydroxyl assisted disproportionation reactions are shown to drastically reduce barriers for RO-H bond cleavage but have little effect on C-H breaking. These results provide vital information for determining the mechanism of MSR on Cu(111).

Lin S.Y.,University of New Mexico | Guo H.,University of New Mexico | Jiang B.,Institute of Theoretical and Computational Chemistry | Zhou S.,Institute of Theoretical and Computational Chemistry | Xie D.,Institute of Theoretical and Computational Chemistry
Journal of Physical Chemistry A | Year: 2010

This publication examines the influence of electronically nonadiabatic Renner-Teller coupling between the two lowest-lying electronic states of NH 2 on state-to-state reaction dynamics. The fully Coriolis coupled quantum mechanical calculations were carried out on the recently developed NH2 potential energy surfaces of both the X̄2A and Ā2A states. It is shown that the Renner-Teller coupling has a dramatic effect on the low-lying ro-vibrational states on the excited Ā2A potential, but its impact on the differential and integral cross sections of the N(2D) + H2 → NH(X̄3Σ-) + H reaction is relatively minor. © 2010 American Chemical Society.

Zhu Y.,Jiangsu University | Xia C.-K.,Jiangsu University | Meng S.-C.,Jiangsu University | Meng S.-C.,Institute of Theoretical and Computational Chemistry | And 2 more authors.
Polyhedron | Year: 2013

Five new compounds constructed with bzimpy, namely [Zn(bzimpy)(H 2O)2(NO3)]NO3 (1), [Co(bzimpy) (bipy)(H2O)]·CH3OH·ClO4· NO3 (2), [Ni(bzimpy)(bipy)Cl]ClO4 (3), [Ce(bzimpy) 2 (NO3)2]·bipy·CH 3OH·ClO4 (4) and [Pr(bzimpy)2(NO 3)2]'bipy·CH3OHClO4 (5) (bzimpy = 2,6-bis (benzimidazolyl)pyridine, bipy = 2,2′-dipyridine), have been synthesized and characterized by elemental analysis, IR and fluorescence spectra, electrochemical analysis and single crystal X-ray diffraction. For 1, DFT and TD-DFT calculations have been performed to obtain its UV-Vis absorption spectrum, and a satisfactory theoretical-experimental agreement was achieved. These compounds are all ionic complexes and are stabilized in the solid state by complicated networks of hydrogen bonds between the crystallized cationic complexes and anionic fragments, as well as solvent molecules. Moreover, hydrogen bonds, π-π and C-H···π stacking interactions seem to be effective in stabilizing the crystal structures. Electrochemical investigations indicate metal centered reduction couples. The fluorescence properties were studied in solvents with different dipole moments. The different shifts between different solvents provide information for the application as luminescent materials in further studies. © 2013 Elsevier Ltd. All rights reserved.

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