Conformational structure, dynamics, and solvation energies of small alanine peptides in water and carbon tetrachloride

Xiang, Tian‐Xiang; Anderson, Bradley D.

doi:10.1002/jps.20453

Cited by 11 publications

(17 citation statements)

References 57 publications

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“…This scaling method gave better agreement between calculated and experimental chloroform/water partition coefficients of Nmethylated nucleic acid bases (52). Separately, we have shown that partial charges for alanine peptides obtained at the level of B3LYP/cc-pVTZ agree with those obtained at the level of HF/6-31G* when adjusted by a scaling factor of 1.2Y1.3 (53).…”

Section: Methodsmentioning

confidence: 51%

Distribution and Effect of Water Content on Molecular Mobility in Poly(vinylpyrrolidone) Glasses: A Molecular Dynamics Simulation

Xiang

Anderson

2005

Pharm Res

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Section: Methodsmentioning

confidence: 51%

Distribution and Effect of Water Content on Molecular Mobility in Poly(vinylpyrrolidone) Glasses: A Molecular Dynamics Simulation

Xiang

Anderson

2005

Pharm Res

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“…Moreover, since neither model PT is water-soluble and EHPT is only somewhat hydrocarbon-soluble, we would expect only small differences between the runs. Nevertheless, this dielectric-only technique has recently been successfully used to compare the differential behavior of small peptides [50] and collagen [51] in aqueous and organic solvent. We therefore feel that it provides an adequate ''sanity check'' on the new parameters before they are deployed in more realistic simulations.…”

Section: Replica Exchange MD In Implicit Solventsmentioning

confidence: 99%

Development and initial testing of an empirical forcefield for simulation of poly(alkylthiophenes)

Widge

Matsuoka

Kurnikova

2008

Journal of Molecular Graphics and Modelling

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Conductive polymers from the polythiophene (PT) family have attracted interest in numerous domains, including potential applications in biosensing. Despite this, atomistic simulations of PTs have tended to use general organic force fields without well-tuned PT parameters, and there exists no optimized and well-validated PT force field that is compatible and consistent with existing biomolecular simulation suites. We present here the development of a new PT forcefield following the AMBER approach, using the program ANTECHAMBER and ab initio calculations at the HF/6-31G* level of theory to assign partial charges and parameterize the critical backbone torsion potential. The optimized geometries and force field potentials match well with both empirical data and previous investigators' calculations. Initial testing of these parameters through a series of replica exchange simulations of two PT derivatives in aqueous and organic implicit solvents demonstrates that the parameters can match empirical expectations within the limits of an implicit solvent model. This new force field forms a framework for modeling of proposed PT-based devices and sensors, and is expected to accelerate device design and eventual deployment.

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“…Finally, the same solvents at the interface with water have also been used as a model for membrane/water interfaces to study membrane permeation by peptides or hydrophobic surface-induced peptide folding [168][169][170][171][172].…”

Section: Other Solventsmentioning

confidence: 99%

Computer Simulations Study of Biomolecules in Non-Aqueous or Cosolvent/Water Mixture Solutions

Roccatano

2008

CPPS

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Pure organic solvents or mixtures with water are very common environments for studying protein and peptide in solution. These milieu conditions are used either for improving the catalytic performance of enzymes or for studying the effect of solvent on the protein stability and hence gaining insight into the protein folding mechanism. The atomic details of these processes are mainly addressed using computer simulation approaches. In particular, Molecular Dynamics simulation represents the most powerful and versatile tool to investigate the details of solvation processes at atomic level. In the last few years, the number of publications peptide and protein simulations in non-natural environments has proliferated. These studies are providing important contributions to shed light on the nature of non-aqueous solvent effects. In this review, the achievements and the future prospects in this field of computational biochemistry are reviewed by summarizing the most important theoretical results published in the last 10 years.

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Conformational structure, dynamics, and solvation energies of small alanine peptides in water and carbon tetrachloride

Cited by 11 publications

References 57 publications

Distribution and Effect of Water Content on Molecular Mobility in Poly(vinylpyrrolidone) Glasses: A Molecular Dynamics Simulation

Distribution and Effect of Water Content on Molecular Mobility in Poly(vinylpyrrolidone) Glasses: A Molecular Dynamics Simulation

Development and initial testing of an empirical forcefield for simulation of poly(alkylthiophenes)

Computer Simulations Study of Biomolecules in Non-Aqueous or Cosolvent/Water Mixture Solutions

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