Peptide models. XXXIII. Extrapolation of low-level Hartree-Fock data of peptide conformation to large basis set SCF, MP2, DFT, and CCSD(T) results. The Ramachandran surface of alanine dipeptide computed at various levels of theory

A. Perczel, O. Farkas, Imre Jákli, Igor A. Topol, I. Csizmadia

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55 Citations (Scopus)

Abstract

At the dawn of the new millenium, new concepts are required for a more profound understanding of protein structures. Together with NMR and X-ray-based 3D-stucture determinations in silica methods are now widely accepted. Homology-based modeling studies, molecular dynamics methods, and quantum mechanical approaches are more commonly used. Despite the steady and exponential increase in computational power, high level ab initio methods will not be in common use for studying the structure and dynamics of large peptides and proteins in the near future. We are presenting here a novel approach, in which low- and medium-level ab initio energy results are scaled, thus extrapolating to a higher level of information. This scaling is of special significance, because we observed previously on molecular properties such as energy, chemical shielding data, etc., determined at a higher theoretical level, do correlate better with experimental data, than those originating from lower theoretical treatments. The Ramachandran surface of an alanine dipeptide now determined at six different levels of theory [RHF and B3LYP 3-21G, 6-31+G(d) and 6-311 + +G(d,p)] serves as a suitable test. Minima, first-order critical points and partially optimized structures, determined at different levels of theory (SCF, DFT), were completed with high level energy calculations such as MP2, MP4D, and CCSD(T). For the first time three different CCSD(T) sets of energies were determined for all stable B3LYP/6-311 + +G(d,p) minima of an alanine dipeptide. From the simplest ab initio data (e.g., RHF/3-21G) to more complex results [CCSD(T)/6-311 +G(d,p)//B3LYP/6-311 ++G(d,p)] all data sets were compared, analyzed in a comprehensive manner, and evaluated by means of statistics.

Original languageEnglish
Pages (from-to)1026-1042
Number of pages17
JournalJournal of Computational Chemistry
Volume24
Issue number9
DOIs
Publication statusPublished - Jul 15 2003

Fingerprint

Dipeptides
Conformation
Extrapolation
Discrete Fourier transforms
Peptides
Alanine
Conformations
Proteins
Energy
Silicon Dioxide
Shielding
Electron energy levels
Molecular dynamics
Silica
Nuclear magnetic resonance
Statistics
Protein Structure
Energy Levels
Molecular Dynamics
X rays

Keywords

  • Ab inito and DFT computation
  • MP and CCSD(T)
  • Peptides
  • Ramachandran surface
  • Structure and stability
  • X-ray structure

ASJC Scopus subject areas

  • Chemistry(all)
  • Safety, Risk, Reliability and Quality

Cite this

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title = "Peptide models. XXXIII. Extrapolation of low-level Hartree-Fock data of peptide conformation to large basis set SCF, MP2, DFT, and CCSD(T) results. The Ramachandran surface of alanine dipeptide computed at various levels of theory",
abstract = "At the dawn of the new millenium, new concepts are required for a more profound understanding of protein structures. Together with NMR and X-ray-based 3D-stucture determinations in silica methods are now widely accepted. Homology-based modeling studies, molecular dynamics methods, and quantum mechanical approaches are more commonly used. Despite the steady and exponential increase in computational power, high level ab initio methods will not be in common use for studying the structure and dynamics of large peptides and proteins in the near future. We are presenting here a novel approach, in which low- and medium-level ab initio energy results are scaled, thus extrapolating to a higher level of information. This scaling is of special significance, because we observed previously on molecular properties such as energy, chemical shielding data, etc., determined at a higher theoretical level, do correlate better with experimental data, than those originating from lower theoretical treatments. The Ramachandran surface of an alanine dipeptide now determined at six different levels of theory [RHF and B3LYP 3-21G, 6-31+G(d) and 6-311 + +G(d,p)] serves as a suitable test. Minima, first-order critical points and partially optimized structures, determined at different levels of theory (SCF, DFT), were completed with high level energy calculations such as MP2, MP4D, and CCSD(T). For the first time three different CCSD(T) sets of energies were determined for all stable B3LYP/6-311 + +G(d,p) minima of an alanine dipeptide. From the simplest ab initio data (e.g., RHF/3-21G) to more complex results [CCSD(T)/6-311 +G(d,p)//B3LYP/6-311 ++G(d,p)] all data sets were compared, analyzed in a comprehensive manner, and evaluated by means of statistics.",
keywords = "Ab inito and DFT computation, MP and CCSD(T), Peptides, Ramachandran surface, Structure and stability, X-ray structure",
author = "A. Perczel and O. Farkas and Imre J{\'a}kli and Topol, {Igor A.} and I. Csizmadia",
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T1 - Peptide models. XXXIII. Extrapolation of low-level Hartree-Fock data of peptide conformation to large basis set SCF, MP2, DFT, and CCSD(T) results. The Ramachandran surface of alanine dipeptide computed at various levels of theory

AU - Perczel, A.

AU - Farkas, O.

AU - Jákli, Imre

AU - Topol, Igor A.

AU - Csizmadia, I.

PY - 2003/7/15

Y1 - 2003/7/15

N2 - At the dawn of the new millenium, new concepts are required for a more profound understanding of protein structures. Together with NMR and X-ray-based 3D-stucture determinations in silica methods are now widely accepted. Homology-based modeling studies, molecular dynamics methods, and quantum mechanical approaches are more commonly used. Despite the steady and exponential increase in computational power, high level ab initio methods will not be in common use for studying the structure and dynamics of large peptides and proteins in the near future. We are presenting here a novel approach, in which low- and medium-level ab initio energy results are scaled, thus extrapolating to a higher level of information. This scaling is of special significance, because we observed previously on molecular properties such as energy, chemical shielding data, etc., determined at a higher theoretical level, do correlate better with experimental data, than those originating from lower theoretical treatments. The Ramachandran surface of an alanine dipeptide now determined at six different levels of theory [RHF and B3LYP 3-21G, 6-31+G(d) and 6-311 + +G(d,p)] serves as a suitable test. Minima, first-order critical points and partially optimized structures, determined at different levels of theory (SCF, DFT), were completed with high level energy calculations such as MP2, MP4D, and CCSD(T). For the first time three different CCSD(T) sets of energies were determined for all stable B3LYP/6-311 + +G(d,p) minima of an alanine dipeptide. From the simplest ab initio data (e.g., RHF/3-21G) to more complex results [CCSD(T)/6-311 +G(d,p)//B3LYP/6-311 ++G(d,p)] all data sets were compared, analyzed in a comprehensive manner, and evaluated by means of statistics.

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KW - Ramachandran surface

KW - Structure and stability

KW - X-ray structure

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