Differences in hydration between cis- and trans-platin: Quantum insights by ab initio fragment molecular orbital-based molecular dynamics (FMO-MD)

Mori, Hirotoshi; Hirayama, Natsumi; Komeiji, Yuto; Mochizuki, Yuji

doi:10.1016/j.comptc.2012.02.008

Cited by 23 publications

(24 citation statements)

References 56 publications

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“…The droplet was confined within a sphere (radius = 9.0 Å ) by a harmonic restraint as described in Refs. [13,14,39,40]. The time step and temperature for the FMO-MD runs was set to 1 fs and 300 K, respectively.…”

Section: Computational Detailsmentioning

confidence: 99%

Theoretical Study on the Hydration Structure of Divalent Radium Ion Using Fragment Molecular Orbital–Molecular Dynamics (FMO–MD) Simulation

Matsuda

Mori

2014

J Solution Chem

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Using fragment molecular orbital-molecular dynamics (FMO-MD) simulation at the FMO3-HF/6-31G(d,p) level, the hydration of a Ra 2? ion was theoretically investigated. The first peaks of the radial distribution function (RDF) for Ra-O and Ra-H lengths were predicted to be 2.85 and 3.45 Å with broad envelopes in the ranges of 2.5-3.5 and 2.8-4.3 Å , respectively. The broad peaks shows that the first hydration shell of Ra 2? is much more flexible than those in the other hydrated divalent alkaline earth metal ions, i.e., Ra 2? is a structure-breaking ion. The hydration number of Ra 2? was predicted to be 8.1. From the angular distribution function (ADF), it was clarified that the octa hydrated Ra 2? ion has a flexible square antiprism structure at room temperature.

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Section: Computational Detailsmentioning

confidence: 99%

Theoretical Study on the Hydration Structure of Divalent Radium Ion Using Fragment Molecular Orbital–Molecular Dynamics (FMO–MD) Simulation

Matsuda

Mori

2014

J Solution Chem

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“…Figure 4 is RDF between chloride and solvent oxygen computed by RISM-SCF-SEDD, which looks very similar to that obtained by FMO(3)-MP2-MD method. 154 The energy profile computed with RISM-SCF-SEDD in aqueous solution is drastically changed from that in the gas phase (Please refer Figure 3 of the reference 153 ). The stabilization due to solvation is enhanced as the total charge of the Pt complex is increased through the reaction.…”

Section: Chemical Reactionsmentioning

confidence: 99%

A modern solvation theory: quantum chemistry and statistical chemistry

Sato

2013

Phys. Chem. Chem. Phys.

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This perspective highlights recent developments in the field of statistical mechanics for molecular liquids, i.e. the integral equation (IE) theory, especially focusing on hybrid approaches incorporating quantum chemistry and IE theory. The electronic structure of solvated molecules is characterized, followed by recent developments and applications. The latter includes for some specific systems: evaluation of acidity, basicity, pH and pKa, chemical equilibrium and molecular structure, chemical reactions, ionization and electron transfer reactions, as well as excited states and their free energy.

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“…Taking into account the platinum-platinum distances of 9.1–9.7 Å in the [Pt 2 (DTBPA)Cl 2 ](II) and [Pt 2 (TPXA)Cl 2 ](II) agents, and the distance of about 3.4 Å between two neighboring base pairs in B-DNA [ 24 , 25 , 33 , 34 ], it would be predicted that in the platinum-DNA adducts, the two platinum centers of [Pt 2 (DTBPA)Cl 2 ](II) or [Pt 2 (TPXA)Cl 2 ](II) would be capable of spanning 3–5 base pairs. Theoretically, Mori et al ., using ab initio fragment molecular orbital-based molecular dynamics (FMO-MD) simulations, presented that the Pt–Cl bond fluctuation and charge distribution for cis - and trans -platinum are important for activating their anticancer functions [ 35 , 36 ]. However, few theoretical studies devoted to the properties of the [Pt 2 (DTBPA)Cl 2 ](II) and [Pt 2 (TPXA)Cl 2 ](II) agents binding to DNA molecules.…”

Section: Introductionmentioning

confidence: 99%

Investigations of the Binding of [Pt2(DTBPA)Cl2](II) and [Pt2(TPXA)Cl2](II) to DNA via Various Cross-Linking Modes

Yue¹,

Yang²,

Wang³

et al. 2013

IJMS

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We have constructed models for a series of platinum-DNA adducts that represent the binding of two agents, [Pt2(DTBPA)Cl2](II) and [Pt2(TPXA)Cl2](II), to DNA via inter- and intra-strand cross-linking, and carried out molecular dynamics simulations and DNA conformational dynamics calculations. The effects of trans- and cis-configurations of the centers of these di-nuclear platinum agents, and of different bridging linkers, have been investigated on the conformational distortions of platinum-DNA adducts formed via inter- and intra-strand cross-links. The results demonstrate that the DNA conformational distortions for the various platinum-DNA adducts with differing cross-linking modes are greatly influenced by the difference between the platinum-platinum distance for the platinum agent and the platinum-bound N7–N7 distance for the DNA molecule, and by the flexibility of the bridging linkers in the platinum agent. However, the effects of trans/cis-configurations of the platinum-centers on the DNA conformational distortions in the platinum-DNA adducts depend on the inter- and intra-strand cross-linking modes. In addition, we discuss the relevance of DNA base motions, including opening, shift and roll, to the changes in the parameters of the DNA major and minor grooves caused by binding of the platinum agent.

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Differences in hydration between cis- and trans-platin: Quantum insights by ab initio fragment molecular orbital-based molecular dynamics (FMO-MD)

Cited by 23 publications

References 56 publications

Theoretical Study on the Hydration Structure of Divalent Radium Ion Using Fragment Molecular Orbital–Molecular Dynamics (FMO–MD) Simulation

Theoretical Study on the Hydration Structure of Divalent Radium Ion Using Fragment Molecular Orbital–Molecular Dynamics (FMO–MD) Simulation

A modern solvation theory: quantum chemistry and statistical chemistry

Investigations of the Binding of [Pt2(DTBPA)Cl2](II) and [Pt2(TPXA)Cl2](II) to DNA via Various Cross-Linking Modes

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