Molecular dynamics conformational search for the factors that determine conformation of modified cyclodextrins

Shinji Usui, Keita Hamasaki, Tetsuo Kuwabara, Asao Nakamura, Tsukasa Ikeda, Hiroshi Ikeda, Akihiko Ueno, Fujio Toda

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

Modified cyclodextrins (modified CDs), which have an appending moiety, form various conformations depending on its moiety. In this study we examined the factors that determine the conformation of modified CDs with p-dimethylaminobenzoyl and p-nitrobenzoyl moiety as a pendant (DMAB-β-CD and NB-β-CD, respectively) using computational chemistry. The structures and potential energies were calculated using molecular dynamics conformational search, and the relationship between conformation and energy calculated from force field was investigated. These calculations suggested that the conformation of the modified CDs is dominated by the opposing influences of the van der Waals energy, which favors locating the appending moiety inside the CD cavity, and the angle related to the bending energy, which favors the moiety outside the cavity.

Original languageEnglish
Pages (from-to)57-67
Number of pages11
JournalSupramolecular Chemistry
Volume9
Issue number1
Publication statusPublished - 1997
Externally publishedYes

Fingerprint

Cyclodextrins
Conformations
Molecular dynamics
Computational chemistry
Potential energy

Keywords

  • Conformation
  • Modified cyclodextrin
  • Molecular dynamics
  • Molecular mechanics

ASJC Scopus subject areas

  • Chemistry(all)

Cite this

Molecular dynamics conformational search for the factors that determine conformation of modified cyclodextrins. / Usui, Shinji; Hamasaki, Keita; Kuwabara, Tetsuo; Nakamura, Asao; Ikeda, Tsukasa; Ikeda, Hiroshi; Ueno, Akihiko; Toda, Fujio.

In: Supramolecular Chemistry, Vol. 9, No. 1, 1997, p. 57-67.

Research output: Contribution to journalArticle

Usui, Shinji ; Hamasaki, Keita ; Kuwabara, Tetsuo ; Nakamura, Asao ; Ikeda, Tsukasa ; Ikeda, Hiroshi ; Ueno, Akihiko ; Toda, Fujio. / Molecular dynamics conformational search for the factors that determine conformation of modified cyclodextrins. In: Supramolecular Chemistry. 1997 ; Vol. 9, No. 1. pp. 57-67.
@article{7954e151638e43bba3983e0c846763e7,
title = "Molecular dynamics conformational search for the factors that determine conformation of modified cyclodextrins",
abstract = "Modified cyclodextrins (modified CDs), which have an appending moiety, form various conformations depending on its moiety. In this study we examined the factors that determine the conformation of modified CDs with p-dimethylaminobenzoyl and p-nitrobenzoyl moiety as a pendant (DMAB-β-CD and NB-β-CD, respectively) using computational chemistry. The structures and potential energies were calculated using molecular dynamics conformational search, and the relationship between conformation and energy calculated from force field was investigated. These calculations suggested that the conformation of the modified CDs is dominated by the opposing influences of the van der Waals energy, which favors locating the appending moiety inside the CD cavity, and the angle related to the bending energy, which favors the moiety outside the cavity.",
keywords = "Conformation, Modified cyclodextrin, Molecular dynamics, Molecular mechanics",
author = "Shinji Usui and Keita Hamasaki and Tetsuo Kuwabara and Asao Nakamura and Tsukasa Ikeda and Hiroshi Ikeda and Akihiko Ueno and Fujio Toda",
year = "1997",
language = "English",
volume = "9",
pages = "57--67",
journal = "Supramolecular Chemistry",
issn = "1061-0278",
publisher = "Taylor and Francis Ltd.",
number = "1",

}

TY - JOUR

T1 - Molecular dynamics conformational search for the factors that determine conformation of modified cyclodextrins

AU - Usui, Shinji

AU - Hamasaki, Keita

AU - Kuwabara, Tetsuo

AU - Nakamura, Asao

AU - Ikeda, Tsukasa

AU - Ikeda, Hiroshi

AU - Ueno, Akihiko

AU - Toda, Fujio

PY - 1997

Y1 - 1997

N2 - Modified cyclodextrins (modified CDs), which have an appending moiety, form various conformations depending on its moiety. In this study we examined the factors that determine the conformation of modified CDs with p-dimethylaminobenzoyl and p-nitrobenzoyl moiety as a pendant (DMAB-β-CD and NB-β-CD, respectively) using computational chemistry. The structures and potential energies were calculated using molecular dynamics conformational search, and the relationship between conformation and energy calculated from force field was investigated. These calculations suggested that the conformation of the modified CDs is dominated by the opposing influences of the van der Waals energy, which favors locating the appending moiety inside the CD cavity, and the angle related to the bending energy, which favors the moiety outside the cavity.

AB - Modified cyclodextrins (modified CDs), which have an appending moiety, form various conformations depending on its moiety. In this study we examined the factors that determine the conformation of modified CDs with p-dimethylaminobenzoyl and p-nitrobenzoyl moiety as a pendant (DMAB-β-CD and NB-β-CD, respectively) using computational chemistry. The structures and potential energies were calculated using molecular dynamics conformational search, and the relationship between conformation and energy calculated from force field was investigated. These calculations suggested that the conformation of the modified CDs is dominated by the opposing influences of the van der Waals energy, which favors locating the appending moiety inside the CD cavity, and the angle related to the bending energy, which favors the moiety outside the cavity.

KW - Conformation

KW - Modified cyclodextrin

KW - Molecular dynamics

KW - Molecular mechanics

UR - http://www.scopus.com/inward/record.url?scp=0002394787&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0002394787&partnerID=8YFLogxK

M3 - Article

AN - SCOPUS:0002394787

VL - 9

SP - 57

EP - 67

JO - Supramolecular Chemistry

JF - Supramolecular Chemistry

SN - 1061-0278

IS - 1

ER -