2004
DOI: 10.1002/jcc.20012
|View full text |Cite
|
Sign up to set email alerts
|

Intramolecular interaction energies in model alanine and glycine tetrapeptides. Evaluation of anisotropy, polarization, and correlation effects. A parallel ab initio HF/MP2, DFT, and polarizable molecular mechanics study

Abstract: An extension of the SIBFA polarizable molecular mechanics procedure to flexible oligopeptides is reported. The procedure is evaluated by computing the relative conformational energies, deltaE(conf), of the alanine tetrapeptide in 10 representative conformations, which were originally derived by Beachy et al. (J Am Chem Soc 1997, 119, 5908) to benchmark molecular mechanics procedures with respect to ab initio computations. In the present study, a particular emphasis is on the separable nature of the components … Show more

Help me understand this report

Search citation statements

Order By: Relevance

Paper Sections

Select...
2
1
1
1

Citation Types

0
39
0

Year Published

2005
2005
2021
2021

Publication Types

Select...
8
1

Relationship

7
2

Authors

Journals

citations
Cited by 37 publications
(39 citation statements)
references
References 89 publications
0
39
0
Order By: Relevance
“…The cation-π and π-π stacking interactions have been studied by many authors using several QM methods [35,36]. The DFT method B3LYP is a widely used method in organic chemistry and biochemistry because of its higher accuracy and less computational workload [37,38]. However, in past twenty years the DFT methods were found to fail in describing the molecular dispersion interactions [39-42].…”
Section: Methodsmentioning
confidence: 99%
“…The cation-π and π-π stacking interactions have been studied by many authors using several QM methods [35,36]. The DFT method B3LYP is a widely used method in organic chemistry and biochemistry because of its higher accuracy and less computational workload [37,38]. However, in past twenty years the DFT methods were found to fail in describing the molecular dispersion interactions [39-42].…”
Section: Methodsmentioning
confidence: 99%
“…We have resorted to a procedure that was developed and tested in recent studies of Zn(II) finger oligopeptides,56 pentahydrated Zn(II) and Mg(II) complexes of 5′‐guanosine monophosphate,55 organometallic complexes of Cu(II),66 conformational studies of eleven model alanine and glycine tetrapeptides,67 and the complexes of metallo‐β‐lactamase with captopril and thiomandelate 52. Earlier tests published on Zn(II)‐binding to neutral and zwitterionic glycine,68 α‐ and β‐mercaptoxamides,69 and pyrophosphate53 had shown such a procedure to provide interaction energy values having relative errors wih respect to their QC counterparts of < 3%, which are similar to those from the approach treating the integral Zn‐binding ligand with its conformation‐specific multipoles and polarizabilities.…”
Section: Methodsmentioning
confidence: 99%
“…The LMP2 computations bring δE reductions that are intermediate between the DFT and MP2 ones. The results of Table 4b were commented on in more detail in ref 78 . It is observed that the δE tot (SIBFA) values with a scaling of 0.8 for E disp (conform to the value adopted in ref 28d…”
Section: Conformational Studies Of Oligopeptides Test On the Alaninementioning
confidence: 99%