Quantum Chemical Molecular Dynamics Simulation of the Plasma Etching Processes

Sasata, Katsumi; Yokosuka, Toshiyuki; Kurokawa, Hitoshi; Takami, Seiichi; Kubo, Momoji; Imamura, Akira; Shinmura, Tadashi; Kanoh, Masaaki; Selvam, Parasuraman; Miyamoto, Akira

doi:10.1143/jjap.42.1859

Cited by 39 publications

(38 citation statements)

References 5 publications

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“…In our program, the parameters are determined on the basis of DFT calculation results. This can realize both high calculation speed and high accuracy (Elanany et al, 2002(Elanany et al, , 2003Sasata et al, 2003;Jung et al, 2003). The crystal lattice size used for Colors calculations on truncated MTX-Asp27 complex and MTX-Thr113 complex was 20 Å 9 20 Å 9 20 Å and that on binding site containing MTX, Thr113, and Asp27 was 30 Å 9 30 Å 9 30 Å .…”

Section: Tight-binding Quantum Chemical Molecular Dynamics Methodsmentioning

confidence: 99%

Applying ultra-accelerated quantum chemical molecular dynamics technique for the evaluation of ligand protein interactions

et al. 2009

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Ligand-protein interactions have been studied using several chemical information techniques including quantum chemical methods that are applied to truncated systems composed of the ligand molecule and the surrounding amino acids of the receptor. Fragmented quantum molecular chemical studies are also a choice to study the enzyme-ligand system holistically, however there are still restrictions on the number of water molecules that can be included in a study of this nature. In this work we adopt a completely different approach to study ligandprotein interactions accounting explicitly for as many solvent molecules as possible and without the need for a fragmented calculation. Furthermore, we embed our quantum chemical calculations within a molecular dynamics framework that enables a fundamentally fast system for quantum chemical molecular dynamic simulations (QCMD). Central to this new system for QCMD is the tight binding QC system, newly developed in our laboratories, which combined with the MD paradigm results in an ultra-accelerated QCMD method for protein-ligand interaction evaluations. We have applied our newly developed system to the dihydrofolate MEDICINAL CHEMISTRY RESEARCH reductase (DHFR)-methotrexate (MTX) system. We show how the proposed method leads us to new insights into the main interactions that bind MTX to the enzyme, mainly the interaction between the amino group of MTX and Asp27 of DHFR, as well as MTX amino group with Thr113 of DHFR, which have been only elucidated experimentally to date.

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Section: Tight-binding Quantum Chemical Molecular Dynamics Methodsmentioning

confidence: 99%

Applying ultra-accelerated quantum chemical molecular dynamics technique for the evaluation of ligand protein interactions

et al. 2009

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Section: Methodsmentioning

confidence: 99%

Restoration of p53–DNA interaction loss upon R273H mutation by CP-31398: an ultra accelerated quantum chemical molecular dynamics approach

et al. 2010

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The mutation of Arginine273 to Histidine in the DNA binding domain of p53 is one of the most common mutations found in human cancer. Though R273H mutation retains wild-type conformation, the sequence-specific DNA binding is impaired and subsequently lack of transactivation function and the ability to suppress cell growth. CP-31398 can restore DNA binding activity to mutant p53 has shown by a chromatin immunoprecipitation assay but the underlying mechanism at atomistic level is not well understood. Our aim is to investigate theoretically the effect of R273H mutation on DNA binding and the mechanism of restoration of DNA binding by CP-31398, using docking and newly developed ultra accelerated quantum chemical molecular dynamics. Our results show that due to R273H mutation, p53 lost two hydrogen bonds with DNA at the binding site during interaction. CP-31398 helps to reestablish the lost hydrogen bond interactions at p53-DNA binding site, thus restore DNA binding activity and transcriptional activity. This will provide a deeper insight to structure-based drug designing.

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“…Tight-binding quantum chemical molecular dynamics calculations were performed using our original 'Colors' program [13][14][15][16]. In this program, the total energy is expressed by Eq.…”

Section: Tight-binding Quantum Chemical Molecular Dynamics Methodsmentioning

confidence: 99%

“…In our program, the parameters are determined on the basis of DFT calculation results. This can realize both high calculation speed and high accuracy [13][14][15][16].…”

Section: Tight-binding Quantum Chemical Molecular Dynamics Methodsmentioning

confidence: 99%

“…For the realization of quantum chemical molecular dynamics simulation using a large-scale model, we have developed a novel quantum chemical molecular dynamics program 'Colors' on the basis of our original tight-binding approximations. The program is over 5000 times faster than the conventional first-principles molecular dynamics programs, and has been successfully applied to various systems [13][14][15][16].…”

Section: Introductionmentioning

confidence: 99%

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Periodic density functional and tight-binding quantum chemical molecular dynamics study of catalytic properties on γ-Al2O3 supported Pt catalysts

Ishimoto

Jung

Tsuboi

et al. 2006

Applied Catalysis A: General

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Quantum Chemical Molecular Dynamics Simulation of the Plasma Etching Processes

Cited by 39 publications

References 5 publications

Applying ultra-accelerated quantum chemical molecular dynamics technique for the evaluation of ligand protein interactions

Applying ultra-accelerated quantum chemical molecular dynamics technique for the evaluation of ligand protein interactions

Restoration of p53–DNA interaction loss upon R273H mutation by CP-31398: an ultra accelerated quantum chemical molecular dynamics approach

Periodic density functional and tight-binding quantum chemical molecular dynamics study of catalytic properties on γ-Al2O3 supported Pt catalysts

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