Assesing the reliability of density functional methods in the conformational study of polypeptides: The treatment of intraresidue nonbonding interactions
CNR Ibb | back to homepage
CNR Ibb | back to homepage

Assesing the reliability of density functional methods in the conformational study of polypeptides: The treatment of intraresidue nonbonding interactions (410 views)

Improta R, Barone V

J Comput Chem (ISSN: 0192-8651, 1096-987xelectronic), 2004; 25(11): 1333-1341.

Export to BibTeX    Export to EndNote

Paper type: Journal Article,

Impact factor: 3.168, 5-year impact factor: 4.72

Url: http://www.scopus.com/inward/record.url?eid=2-s2.0-3142735758&partnerID=40&md5=456fedd2f2fa7196d8971380cc5f175c

Keywords: Density Functionals, Dipeptide Analog, Helical Conformers, Noncovalent Interactions, Atoms, Computational Methods, Conformations, Electrons, Electrostatics, Hydrogen Bonds, Mathematical Models, Molecular Dynamics, Molecular Structure, Probability Density Function, Alanine Dipeptide, Hartree-Fock Computations, Intraresidue Nonbonding Interactions, Repulsive Interactions, Polypeptides, Algorithm, Article, Chemical Structure, Chemistry, Protein Conformation, Thermodynamics,

Affiliations:
*** IBB - CNR ***

Dipartamento di Chimica, Università Federico II, Compleso Univ. Monte S. Angelo, Via Cintia, Napoli 1-80126, Italy
Ist di Biostrutture e Bioimmagini, CNR, 6 Via Mezzocannone, Napoli 1-80134, Italy


References:
Not available.
Assesing the reliability of density functional methods in the conformational study of polypeptides: The treatment of intraresidue nonbonding interactions

The role of intraresidue interactions in determining the conformational behavior of polypeptides is analyzed by means of density functional and post-Hartree-Fock computations on the alanine dipeptide analog and other model compounds. Our computations show that the accuracy of current density functionals is sufficient for H-bond, electrostatic, inductive, and short-range repulsive interactions, whereas medium-range attractions between electron-rich atoms and/or bonds are underestimated. This leads, in turn, to an underestimation of the stability of helical structures w.r.t. extended or folded conformers involving H-bonds. Those results could pave the route for devising local ad hoc corrections able to significantly improve structural and dynamic predictions for polypeptides issuing from DFT computations. © 2004 Wiley Periodicals, Inc.
Assesing the reliability of density functional methods in the conformational study of polypeptides: The treatment of intraresidue nonbonding interactions

▼    Study of the interaction between UV light and nucleic acids: elucidating the molecular mechanisms responsible of the genetic stability and of the oxidative damaging processes by using computational methods
Assesing the reliability of density functional methods in the conformational study of polypeptides: The treatment of intraresidue nonbonding interactions

Filter those results▼
Query:  [X]
Options:
   Extended  
   IBB affiliation
 
Authors:  [X]
Paper type:  [X]
Start date:  [X]
End date:  [X]
Site:
[Clear form]
Select the year: 
Other filter: ([btitle,keywords] "Density Functionals" ...

Sort by:   date ▼▲   title ▲ ▼   journal ▲ ▼   authors ▲ ▼   I.F. ▲ ▼
Di Stasi R, Diana D, Capasso D, Di Gaetano S, De Rosa L, Celentano V, Isernia C, Fattorusso R, D'Andrea LD
* VEGFR Recognition Interface of a Proangiogenic VEGF-Mimetic Peptide Determined In Vitro and in the Presence of Endothelial Cells by NMR Spectroscopy (358 views)
Chemistry (ISSN: 0947-6539, 1521-3765, 1521-3765electronic), 2018; 24(44): 11461-11466.
Impact Factor: 5.16
View    Export to BibTeX    Export to EndNote

Farina B, De Paola I, Russo L, Capasso D, Liguoro A, Gatto AD, Saviano M, Pedone PV, Di Gaetano S, Malgieri G, Zaccaro L, Fattorusso R
* A Combined NMR and Computational Approach to Determine the RGDechi-hCit-alphav beta3 Integrin Recognition Mode in Isolated Cell Membranes (706 views)
Chemistry (ISSN: 0947-6539, 1521-3765, 1521-3765electronic), 2016 Jan 11; 22(2): 681-693.
Impact Factor: 5.317
View    Export to BibTeX    Export to EndNote

Santoro F, Lami A, Improta R, Bloino J, Barone V
* Effective method for the computation of optical spectra of large molecules at finite temperature including the Duschinsky and Herzberg-Teller effect: The Qx band of porphyrin as a case study (476 views)
J Chem Phys (ISSN: 0021-9606, 0897-690online), 2008 Jun 14; 128(22): 17-17.
Impact Factor: 3.149
View    Export to BibTeX    Export to EndNote

Langella E, Improta R, Barone V
* Conformational and spectroscopic analysis of the tyrosyl radical dipeptide analogue in the gas phase and in aqueous solution by a density functional/continuum solvent model (757 views)
J Am Chem Soc (ISSN: 0002-7863, 0002-2786, 1520-5126), 2002 Sep 25; 124(38): 11531-11540.
Impact Factor: 6.201
View    Export to BibTeX    Export to EndNote

Improta R, Mele F, Crescenzi O, Benzi C, Barone V
* Understanding the role of stereoelectronic effects in determining collagen stability. 2. A quantum mechanical/molecular mechanical study of (Proline-Proline-Glycine)n polypeptides (340 views)
J Am Chem Soc (ISSN: 0002-7863, 0002-2786, 1520-5126), 2002 Jul 3; 124(26): 7857-7865.
Impact Factor: 6.201
View    Export to BibTeX    Export to EndNote

Langella E, Rega N, Improta R, Crescenzi O, Barone V
* Conformational analysis of the tyrosine dipeptide analogue in the gas phase and in aqueous solution by a density functional/continuum solvent model (292 views)
J Comput Chem (ISSN: 0192-8651, 1096-987xelectronic), 2002 Apr 30; 23(6): 650-661.
Impact Factor: 2.931
View    Export to BibTeX    Export to EndNote

Benzi C, Improta R, Scalmani G, Barone V
* Quantum mechanical study of the conformational behavior of proline and 4R-hydroxyproline dipeptide analogues in vacuum and in aqueous solution (304 views)
J Comput Chem (ISSN: 0192-8651, 1096-987xelectronic), 2002 Feb; 23(3): 341-350.
Impact Factor: 2.931
View    Export to BibTeX    Export to EndNote

Improta R, Kudin KN, Scuseria GE, Barone V
* Structure and magnetic properties of nitroxide molecular crystals by density functional calculations employing periodic boundary conditions (243 views)
J Am Chem Soc (ISSN: 0002-7863, 0002-2786, 1520-5126), 2002 Jan 9; 124(1): 113-120.
Impact Factor: 6.201
View    Export to BibTeX    Export to EndNote

Saracino GAA, Tedeschi A, D'Errico G, Improta R, Franco L, Ruzzi M, Corvaia C, Barone V
* Solvent polarity and pH effects on the magnetic properties of ionizable nitroxide radicals: A combined computational and experimental study of 2, 2, 5, 5-tetramethyl-3-carboxypyrrolidine and 2, 2, 6, 6-tetramethyl-4-carboxypiperidine nitroxides (312 views)
J Phys Chem A (ISSN: 1089-5639, 1520-5215electronic, 1089-5639linking), 2002; 106(44): 10700-10706.
Impact Factor: 2.765
View    Export to BibTeX    Export to EndNote

9 Records (8 excluding Abstracts).
Total impact factor: 40.856 (37.707 excluding Abstracts).
Total 5 year impact factor: 59.061 (55.94 excluding Abstracts).

Last modified by Marco Comerci on Sunday 12 July 2020, 13:15:10
410 views. Last view on Tuesday 11 July 2023, 12:10:03