Ring Opening of Methylenecyclopropane over Lanthanocene Catalyst:  A Quantum-Chemical Molecular Dynamics Simulation Study

Luo, Yi; Selvam, Parasuraman; Ito, Yuki; Takami, Seiichi; Kubo, Momoji; Imamura, Ayano; Miyamoto, Akira

doi:10.1021/om030222g

Cited by 36 publications

(9 citation statements)

References 46 publications

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“…Quantum chemical calculations were carried out using the Colors program, which is based on our original tight-binding approximation (Kubo et al, 2004;Elanany et al, 2003;Luo et al, 2003;Jung et al, 2003). In the Colors program, high computational efficiency is realized by adopting parameters in the Hamiltonian.…”

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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“…Unfortunately, to the best of our knowledge, the influence of ligands on the periodic properties of organolanthanides is not noticed so far although ligand effect was found to affect the structure and activity of transition metal complexes [8,9]. It is also noteworthy here that density functional theory (DFT) calculations performed on certain lanthanide complexes [2,[10][11][12] show the significance of relativistic effects. Hence, the implementation of relativistic models in the DFT has been achieved at different precision levels, such as the zero-order regular approximation (ZORA) [13], which may further provide a sufficiently reliable description of the ligand effect in lanthanide complexes.…”

mentioning

confidence: 89%

Ligand effect on the periodic properties of trivalent organolanthanide complexes: a density functional study

Luo

Selvam

Koyama

et al. 2004

Inorganic Chemistry Communications

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“…Quantum chemical calculations were carried out using Colors program, which is based on our original tightbinding approximation (Kubo et al, 2004;Elanany et al, 2003;Luo et al, 2003;Jung et al, 2003). In the ''Colors'' program, high efficiency of computation is realized by adopting parameters in the Hamiltonian.…”

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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Ring Opening of Methylenecyclopropane over Lanthanocene Catalyst: A Quantum-Chemical Molecular Dynamics Simulation Study

Cited by 36 publications

References 46 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

Ligand effect on the periodic properties of trivalent organolanthanide complexes: a density functional study

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

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