Assesing the reliability of density functional methods in the conformational study of polypeptides: The treatment of intraresidue nonbonding interactions
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Assesing the reliability of density functional methods in the conformational study of polypeptides: The treatment of intraresidue nonbonding interactions (506 views)

Improta R, Barone V

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

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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

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Di Stasi R, Diana D, Capasso D, Di Gaetano S, De Rosa L, Celentano V, Isernia C, Fattorusso R, D'Andrea LD
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Impact Factor: 5.16
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Impact Factor: 5.317
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Santoro F, Lami A, Improta R, Bloino J, Barone V
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Impact Factor: 3.149
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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 (845 views)
J Am Chem Soc (ISSN: 0002-7863, 0002-2786, 1520-5126), 2002 Sep 25; 124(38): 11531-11540.
Impact Factor: 6.201
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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 (441 views)
J Am Chem Soc (ISSN: 0002-7863, 0002-2786, 1520-5126), 2002 Jul 3; 124(26): 7857-7865.
Impact Factor: 6.201
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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 (419 views)
J Comput Chem (ISSN: 0192-8651, 1096-987xelectronic), 2002 Apr 30; 23(6): 650-661.
Impact Factor: 2.931
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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 (437 views)
J Comput Chem (ISSN: 0192-8651, 1096-987xelectronic), 2002 Feb; 23(3): 341-350.
Impact Factor: 2.931
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Improta R, Kudin KN, Scuseria GE, Barone V
* Structure and magnetic properties of nitroxide molecular crystals by density functional calculations employing periodic boundary conditions (327 views)
J Am Chem Soc (ISSN: 0002-7863, 0002-2786, 1520-5126), 2002 Jan 9; 124(1): 113-120.
Impact Factor: 6.201
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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 (351 views)
J Phys Chem A (ISSN: 1089-5639, 1520-5215electronic, 1089-5639linking), 2002; 106(44): 10700-10706.
Impact Factor: 2.765
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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
506 views. Last view on Monday 07 October 2024, 17:56:24