DENPOL

A new program to determine electron densities of polypeptides using extremely localized molecular orbitals

Maurizio Sironi, Michela Ghitti, Alessandro Genoni, Giorgio Saladino, Stefano Pieraccini

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

A new method to compute high-quality electron densities of polypeptides is proposed. The method is based on the transferability properties of extremely localized molecular orbitals, which can be used to describe with great accuracy the different functional groups of a molecule. It is therefore possible to generate a database of such orbitals, each of them associated with specific amino acids or with the peptide bond. A new program, DENPOL, has been written in order to build up the electron density of a generic polypeptide using this database. Due to both the large number of orbitals required to describe a polypeptide and the non-orthogonal nature of these orbitals, a Divide & Conquer strategy has been used to assemble the final electron density. The application of this approach is particularly efficient thanks to the extreme localization of the orbitals. The comparison with the corresponding electron densities generated by the Hartree-Fock method, shows the accuracy of the proposed approach and indicates that the electron densities generated by DENPOL are very close to those generated by an ab initio approach.

Original languageEnglish
Pages (from-to)8-16
Number of pages9
JournalJournal of Molecular Structure: THEOCHEM
Volume898
Issue number1-3
DOIs
Publication statusPublished - Mar 30 2009

Fingerprint

polypeptides
Molecular orbitals
Carrier concentration
molecular orbitals
Electrons
Peptides
orbitals
Databases
Functional groups
peptides
amino acids
Amino Acids
Molecules
molecules

Keywords

  • Divide & Conquer
  • Electron densities of polypeptides
  • Extremely localized molecular orbitals

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Biochemistry
  • Condensed Matter Physics

Cite this

DENPOL : A new program to determine electron densities of polypeptides using extremely localized molecular orbitals. / Sironi, Maurizio; Ghitti, Michela; Genoni, Alessandro; Saladino, Giorgio; Pieraccini, Stefano.

In: Journal of Molecular Structure: THEOCHEM, Vol. 898, No. 1-3, 30.03.2009, p. 8-16.

Research output: Contribution to journalArticle

Sironi, Maurizio ; Ghitti, Michela ; Genoni, Alessandro ; Saladino, Giorgio ; Pieraccini, Stefano. / DENPOL : A new program to determine electron densities of polypeptides using extremely localized molecular orbitals. In: Journal of Molecular Structure: THEOCHEM. 2009 ; Vol. 898, No. 1-3. pp. 8-16.
@article{7005fee87a044aa39d3175664de4ea62,
title = "DENPOL: A new program to determine electron densities of polypeptides using extremely localized molecular orbitals",
abstract = "A new method to compute high-quality electron densities of polypeptides is proposed. The method is based on the transferability properties of extremely localized molecular orbitals, which can be used to describe with great accuracy the different functional groups of a molecule. It is therefore possible to generate a database of such orbitals, each of them associated with specific amino acids or with the peptide bond. A new program, DENPOL, has been written in order to build up the electron density of a generic polypeptide using this database. Due to both the large number of orbitals required to describe a polypeptide and the non-orthogonal nature of these orbitals, a Divide & Conquer strategy has been used to assemble the final electron density. The application of this approach is particularly efficient thanks to the extreme localization of the orbitals. The comparison with the corresponding electron densities generated by the Hartree-Fock method, shows the accuracy of the proposed approach and indicates that the electron densities generated by DENPOL are very close to those generated by an ab initio approach.",
keywords = "Divide & Conquer, Electron densities of polypeptides, Extremely localized molecular orbitals",
author = "Maurizio Sironi and Michela Ghitti and Alessandro Genoni and Giorgio Saladino and Stefano Pieraccini",
year = "2009",
month = "3",
day = "30",
doi = "10.1016/j.theochem.2008.07.013",
language = "English",
volume = "898",
pages = "8--16",
journal = "Journal of Molecular Structure: THEOCHEM",
issn = "0166-1280",
publisher = "Elsevier",
number = "1-3",

}

TY - JOUR

T1 - DENPOL

T2 - A new program to determine electron densities of polypeptides using extremely localized molecular orbitals

AU - Sironi, Maurizio

AU - Ghitti, Michela

AU - Genoni, Alessandro

AU - Saladino, Giorgio

AU - Pieraccini, Stefano

PY - 2009/3/30

Y1 - 2009/3/30

N2 - A new method to compute high-quality electron densities of polypeptides is proposed. The method is based on the transferability properties of extremely localized molecular orbitals, which can be used to describe with great accuracy the different functional groups of a molecule. It is therefore possible to generate a database of such orbitals, each of them associated with specific amino acids or with the peptide bond. A new program, DENPOL, has been written in order to build up the electron density of a generic polypeptide using this database. Due to both the large number of orbitals required to describe a polypeptide and the non-orthogonal nature of these orbitals, a Divide & Conquer strategy has been used to assemble the final electron density. The application of this approach is particularly efficient thanks to the extreme localization of the orbitals. The comparison with the corresponding electron densities generated by the Hartree-Fock method, shows the accuracy of the proposed approach and indicates that the electron densities generated by DENPOL are very close to those generated by an ab initio approach.

AB - A new method to compute high-quality electron densities of polypeptides is proposed. The method is based on the transferability properties of extremely localized molecular orbitals, which can be used to describe with great accuracy the different functional groups of a molecule. It is therefore possible to generate a database of such orbitals, each of them associated with specific amino acids or with the peptide bond. A new program, DENPOL, has been written in order to build up the electron density of a generic polypeptide using this database. Due to both the large number of orbitals required to describe a polypeptide and the non-orthogonal nature of these orbitals, a Divide & Conquer strategy has been used to assemble the final electron density. The application of this approach is particularly efficient thanks to the extreme localization of the orbitals. The comparison with the corresponding electron densities generated by the Hartree-Fock method, shows the accuracy of the proposed approach and indicates that the electron densities generated by DENPOL are very close to those generated by an ab initio approach.

KW - Divide & Conquer

KW - Electron densities of polypeptides

KW - Extremely localized molecular orbitals

UR - http://www.scopus.com/inward/record.url?scp=60749084755&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=60749084755&partnerID=8YFLogxK

U2 - 10.1016/j.theochem.2008.07.013

DO - 10.1016/j.theochem.2008.07.013

M3 - Article

VL - 898

SP - 8

EP - 16

JO - Journal of Molecular Structure: THEOCHEM

JF - Journal of Molecular Structure: THEOCHEM

SN - 0166-1280

IS - 1-3

ER -