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                 for Complex Molecular Systems Reaction Dynamics

 
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Youth's a stuff that will not endure.


• 2nd March, 2011  

Molecular dynamics simulation reveals preorganization of the chloroplast FtsY towards complex formation induced by GTP binding

Ming-Jun Yang, Xue-Qin Pang, Xin Zhang and Ke-Li Han.
J. Struct. Biol.
2011, 173, 57-66.

 
Two GTPases in the signal recognition particle (SRP) and SRP receptor (SR) interact with one another to mediate the cotranslational protein targeting pathway. Previous studies have shown that a universally conserved SRP RNA facilitates an efficient SRP–SR interaction in the presence of a signal sequence bound to SRP. However, a remarkable exception has been found in chloroplast SRP (cpSRP) pathway, in which the SRP RNA is missing. Based on biochemical and structural analyses, it is proposed that free cpSRP receptor (cpFtsY) has already been preorganized into a closed state for efficient cpSRP–cpFtsY association. However, no direct evidence has been reported to support this postulation thus far. In this study, we characterized the structural dynamics of cpFtsY and its conformational rearrangements induced by GTP binding using molecular dynamics (MD) simulations. Our results showed that the GTP-binding event triggered substantial conformational changes in free cpFtsY, including the relative orientation of N–G domain and several conserved motifs that are critical in complex formation. These rearrangements enabled the cpFtsY to relax into a preorganized ‘closed’ state that favored the formation of a stable complex with cpSRP54. Interestingly, the intrinsic flexibility of αN1 helix facilitated these rearrangements. In addition, GTP binding in cpFtsY was mediated by conserved residues that have been shown in other SRP GTPases. These findings suggested that GTP-bound cpFtsY could fluctuate into conformations that are favorable to form the stable complex, providing explanation of why SRP–SR interaction bypasses the requirement of the SRP RNA at a molecular level.
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• 2nd June, 2010  

Ultra-low resistance at TTF–TCNQ organic interfaces


Shuhao Wen, Wei-Qiao Deng and Ke-Li Han.
Chem. Comm.
2010, 46, 5133-5135.

We have investigated the conduction mechanism at the TTF–TCNQ organic hetero-interface by means of quantum mechanical (QM) calculations. The calculated resistances at the TTF–TCNQ interface are 39–64 kΩ cm-2, which is in good agreement with the experimental values of 1–30 kΩ cm-2.
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• 28th Janarary, 2010  

TD-DFT Study on the Sensing Mechanism of a Fluorescent Chemosensor for Fluoride: Excited-State Proton Transfer

Guang-Yue Li, Guang-Jiu Zhao, Yu-Hui Liu, Ke-Li Han, Guo-Zhong He.
J. Comput. Chem.
DOI: 10.1002/jcc.21466.

An excited-state proton transfer (ESPT) process, induced by both intermolecular and intramolecular hydrogen-bonding interactions, is proposed to account for the fluorescence sensing mechanism of a fluoride chemosensor, phenyl-1H-anthra(1,2-d)imidazole-6,11-dione. The time-dependent density functional theory (TDDFT) method has been applied to investigate the different electronic states. The present  study of this chemosensor, as well as its anion and fluoride complex, has been conducted with a view to monitoring its structural and photophysical properties. The proton of the chemosensor can shift to fluoride in the ground state but transfers from the proton donor (NH group) to a proton acceptor (neighboring carbonyl group) in the first singlet excited state. This may explain the observed red shifts in the fluorescence spectra in the relevant fluorescent sensing mechanism.
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• 25th December, 2009  

Anion-Exchange-Triggered 1,3-Shift of NH Proton to Iridium in Protic N-Hetero-cyclic Carbenes: Hydrogen-Bonding and Ion-Pairing Effects

Guoyong Song, Yan Su, Roy A. Periana, Robert H. Crabtree, Keli Han, Hongjie Zhang and Xingwei Li.
Angew. Chem. Int. Ed. DOI: 10.1002/anie.200905691.

We have synthesized a series of 18-electron iridium(I) protic NHC complexes by the C–H activation of 1,9-phenanthroline. The protic NHC ligand is stabilized by NH···Cl hydrogen bonds, disruption of which by anion exchange leads to an equilibrium between iridium(I) protic NHC complexes and the corresponding cationic iridium(III) hydride aryl complexes, as a result of a reversible 1,3- hydrogen shift from the nitrogen to the iridium center. The effects of the solvent, counteranion, chelating ligand, and phosphine have been studied. A combination of DFT and experimental studies strongly supports a novel water-assisted proton-relay mechanism in this transformation. The tuning of the energies of protic NHC complexes and their hydride precursors by readily controllable parameters should make it possible for each species to perform its role to full capacity in catalytic systems. Further studies on the reactivity and catalytic properties of iridium protic NHC complexes are in progress.
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• 5th November, 2009  

Integral and differential cross sections for the S(1D)+HD reaction employing the ground adiabatic electronic state

H. Yang, K.-L. Han, G. C. Schatz, S.-H. Lee, K. Liu, S. C. Smith and M. Hankel
Phys. Chem. Chem. Phys. 2009, 11, 11587-11595.

We present converged quantum mechanical calculations for the title reaction employing a time-dependent wavepacket method. We obtained integral and differential cross sections over an energy range from 0.23 to 0.35 eV total energy as well as product state distributions for both product channels. The excitation functions decrease with energy and point to statistical dynamics as do the cold vibrational distributions and highly inverted rotational distributions. The differential cross sections oscillate strongly with energy for both product channels. Our differential cross sections for both product channels at 2.5 kcal/mol, one of the experimental energies, compare well to the experimental results. The quantum results obtained in this study are similar to what has been found employing QCT methods, implying that the differences between the experimental and theoretical results are due to the potential energy surface or non-adiabatic effects rather than due to quantum effects or the methods employed.
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• 5th November, 2009  

Theoretical study of single attosecond pulse generation with a three-colour laser field


Rui-Feng Lu, Hai-Xiang He, Ya-Hui Guo and Ke-Li Han.
J. Phys. B: At. Mol. Opt. Phys. 2009, 42, 225601 .

We present a method of producing single attosecond pulses by using a few-cycle (5 fs) driving pulse with two additional weak control pulses. We discuss how single attosecond pulses produced from high-order harmonic generation processes in a synthesized three-colour laser field are similar to those processes in a much shorter single-colour laser field. Based on the high-order harmonic spectrum, classical ionizing and returning energy maps, time–frequency maps and time profiles of the attosecond pulses, the actions of the synthesized three-colour laser field are analogous to a 3 fs field although some differences still exist, and our method is proved to be a potential way to reduce the attosecond pulse duration from high-order harmonic generation with a currently available ultrafast laser source instead of a shorter pulse.
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• 7th September, 2009 

First Principles Investigation of Anistropic Hole Mobilities in Organic Semiconductor

Shu-Hao Wen, An Li, Junling Song, Wei-Qiao Deng, Ke-Li Han, and William A. Goddard III
J. Phys. Chem. B 2009, 113, 8813-8819.

Based on Quantum Mechanics with Marcus-Hush theory we developed a mobility orientation function establishing the quantitative relationship between angular-resolution anisotropic mobilities and molecular packing architecture parameters (r, θ and γ) and underlying electronic properties (electronic coupling V and reorganization energies λ) of organic materials. We validate that this model correctly predicts the anisotropic hole mobilities of ruberene, pentacene, tetracene, 5,11-dichlorotetracene (DCT) and hexathiapentacene (HTP), leading to results in good agreement with experiment.
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• 7th May, 2009 

Dynamics of OH Formation in the Photodissociation of o-Nitrobenzoic Acid at 295 and 355 nm

Can-Hua Zhou, Shi-Bo Cheng, Ju-Long Sun, Hong-Ming Yin, Ke-Li Han and Guo-Zhong He.
J. Phys. Chem. A 2009, 113, 4923–4929.

Photodissociation dynamics of o-nitrobenzoic acid at 295 and 355 nm is studied by probing the nascent OH photoproduct employing the single-photon laser-induced fluorescence technique. At both of the photolysis wavelengths, the OH fragments are found to be vibrationally cold but have different rotational state distributions. Upon photolysis at 295 nm, the relative population of OH in different rotational states does not follow the Boltzmann equilibrium distribution, whereas upon photo-lysis at 355 nm, a Boltzmann distribution is observed with a rotational temperature of 1010 ± 100 K. Between the two spin−orbit states, 2Π3/2 and 2Π1/2, the former is found to be preferentially populated, and the distribution of the Π(A′) state for the Λ-doublet is dominant at both of the wavelengths studied. Several possible dissociation pathways of o-nitrobenzoic acid leading to formation of the OH fragment are investigated computationally. On the basis of the theoretical and experimental studies, a possible mechanism of OH formation from the photo-dissociation of o-nitrobenzoic acid at 295 and 355 nm is proposed.
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• 8th April, 2009 

Nonadiabatic effects in the H+H2 exchange reaction: Accurate quantum dynamics calculations at a state-to-state level

Tian-Shu Chu, Ke-Li Han, Marlies Hankel, Gabriel G. Balint-Kurti, Aron Kuppermann, and Ravinder Abrol
J. Chem. Phys. 2009, 130, 144301.

Real wave packet propagations were carried out on both a single ground electronic state and two-coupled-electronic states of the title reaction to investigate the extent of nonadiabatic effects on the distinguishable-atom reaction cross sections. The latest diabatic potential matrix of Abrol and Kuppermann [J. Chem. Phys. 116, 1035 (2002)] was employed in the present nonadiabatic quantum state-to-state scattering calculations over a total energy range-from threshold (the zero point of the reagent H2) to 3.0 eV. Based on the assumption that the hydrogen atoms are distinguishable in the collisions where the inelastic and elastic ones are excluded, no significant nonadiabatic effects have been found in the calculations of the full state-to-state integral and differential cross sections up to a total energy of 3.0 eV for product vibrational levels v=0, 1, 2, 3. Our results therefore confirm the recent and the previous studies of the geometric phase effects in H+H2 employing a different diabatic double many-body expansion potential matrix or a different BKMP2 potential energy surface.
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• 13th March, 2009 

Photodissociation Dynamics of Alkyl Nitrites at 266 and 355 nm: The OH Product Channel

Xian-Fang Yue, Ju-Long Sun, Hong-Ming Yin,
Qiang Wei and Ke-Li Han
J. Phys. Chem. A 2009, 113, 3303–3310.

Photodissociation of methyl nitrite and n-butyl nitrite at 266 and 355 nm has been investigated in the gas phase at room temperature. OH photoproducts were observed, and their internal state distributions were measured by the one-photon laser-induced fluorescence (LIF) technique. It was found that the nascent OH from the 266 nm photolysis of methyl nitrite was vibrationally cold, and its rotational state distribution conformed to a Boltzmann behavior with a rotational temperature of Trot = 2200 ± 150 K. In contrast, the nascent OH from the 266 nm photolysis
of n-butyl nitrite was found to be vibrationally excited, and the measured relative population of v′′ = 0:1 was 0.78:0.22. The rotational state distribution of the OH
v′′ = 1 state conformed to Boltzmann behavior, with a rotational temperature of Trot = 1462 ± 120 K. However, a simple Boltzmann distribution was not found for the OH v′′ = 0 state. In the photolysis of n-butyl nitrite at 355 nm, the OH fragment was found to be vibrationally cold and its rotational state distribution showed non-Boltzmann behavior. A photodissociation mechanism involving an intramolecular hydrogen atom transfer process is proposed for the OH product pathway for methyl nitrite, which has been compared with the potential energy surfaces obtained from density functional theory (DFT) calculations. A photodissociation mechanism of n-butyl nitrite is also proposed for the OH product pathway, which differs from that of methyl nitrite due to the effects of the different alkoxy substituents.
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