Density functional theory peptides

Density functional theory (DFT),32 also a semi-empirical method, is capable of handling medium-sized systems of biological interest, and it is not limited to the second row of the periodic table. DFT has been used in the study of some small protein and peptide surfaces. Nevertheless, it is still limited by computer speed and memory. DFT offers a quantum mechanically based approach from a fundamentally different perspective, using electron density with an accuracy equivalent to post Hartree-Fock theory. The ideas have been around for many years,33 34 but only in the last ten years have numerous studies been published. DFT, compared to ab initio... 

Wieczorek R, Dannenberg JJ (2003b) Hydrogen bond cooperativity, vibrational coupling, and dependence of helix stability on changes in amino acid sequence in small 3io-helical peptides. A density functional theory study. J Am Chem Soc 125 14065-14071... 

Recently, a paper was published in which the acidities of aliphatic carboxylic acids were analysed in terms of a quantum mechanical model. The inductive effect of Taft was shown to be composed of one electrostatic and one polarization term [37]. We will discuss examples of similar approaches based on the hardness and electronegativity as strictly defined concepts of density functional theory in the chapter on amides and peptides, and also discuss the problem of ill-defined terms a bit further in the chapter on carbocations, coming next. 

Ji WF, Li ZL, Shen L, Kong DX, Zhang HY. (2007) Density Functional Theory methods as powerful tools to elucidate amino acid oxidation mechanisms A case study on methionine model peptide. /PByr Chem Bill 485 89. 

In a work towards the understanding of the optical properties of peptides, Sebek et studied those of an amide-group containing molecule (NMA), A-methyl-acetamide, CH3-NH-CO-CH3. Using time-dependent density-functional theory... 

N-methylformamide-benzene complex as a prototypical peptide N H- ji hydrogen-bonded system Density functional theory and MP2 studies76... 

Valdes H, Pluhackova K, Pitonak M, Rezac J, Hobza P (2008) Benchmark database on isolated small peptides containing an aromatic side chain comparison between wave function and density functional theory methods and empirical force field. Phys Chem Chem Phys 10 2747-2757... 

P. Bour and T. A. Keiderling, Structure, spectra and the effects of twisting of (3-sheet peptides. A density functional theory study, J. Mol. Struct. (Theochem) 675, 95-105 (2004). 

Xu, X.P, Case, D.A. Probing multiple effects on 15N, 13C alpha, 13C beta, and 13C chemical shifts in peptides using density functional theory. Biopolymers 2002, 65, 408-23. 

To study the vibrational energy relaxation of the amide I mode in N-methylacetamide, we employed the OPLS all-atom force field to model the solute and the flexible simple-point-charge (SPC) water modeF with doubled hydrogen masses to model the solvent D2O. To investigate the photoinduced heat transfer in photoswitchable peptides, we used the GROMOS96 united atom force field 43al. Additional force field parameters for the azobenzene unit were derived from density functional theory as described in Ref. [32]. We employed a united-atom modeP to describe the DMSO solvent, the SPC modeP to describe water, and the rigid all-atom model of Ref [57] to describe the chloroform solvent. 

P. Salvador, J.J. Dannenberg, Dependence upon basis sets of trans hydrogen-bond 13C-15N 3-bond and other scalar J-couphngs in amide dimers used as peptide models. A density functional theory study,. Phys. Chem. B 108 (2004) 15370. 

P. Salvador, I.-H. Tsai.J.J. Dannenberg,J-couphng constants for a trialanine peptide as a function of dihedral angles calculated by density functional theory over the fidl Ram-achandran space, Phys. Chem. Chem. Phys. 13 (2011) 17484—17493. 

Ahnora-barrios, N., and De Leeuw, N. H. 2010. A density functional theory study of the interaction of collagen peptides with hydroxyapatite surfaces. Langmuir. 26 14535. 

NMR spectroscopy is a well-suited technique to study the membrane interactions of antimicrobial peptides by taking advantage of the orientational dependence of nuclear spin interactions. This paper discusses several solid-state NMR experiments to extend information on the peptide structure and dynamics as well as on the effect of antimicrobial peptides on model membranes. More specifically, studies of peptide dynamics by and N CP/MAS and static experiments were reported. A set of orientational restraint potentials for solid-state NMR observables in-eluding N chemical shift and N- H dipolar coupling was developed. The N-H X (X = N,0,S) intramolecular hydrogen bond in the series of 2(2 -heteroaryl)pyrroles and their trifluoroacetyl derivatives was examined by the H, N spectroscopy and density functional theory (DFT)... 

El Aribi H, Rodriquez CF, Almeida DRP, Ling Y, Mak WWN, Hopkinson AC, Siu KWM (2003) Elucidation of fragmentation mechanisms of protonated peptide ions and their products a case study on glycylglycylglycine using density functional theory and threshold collision-induced dissociation. J Am Chem Soc 125 9229-9236... 

Pollet R, Brenner V (2008) Assessment of time-dependent density functional theory for predicting excitation energies of bichromophoric peptides case of tryptophan-phenylalanine. Theor Chem Acc 121 307... 

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