Cooperativity in Amide Hydrogen Bonding Chains. Relation between Energy, Position, and H-Bond Chain Length in Peptide and Protein Folding Models

Kobko, Nadya; Dannenberg, J. J.

doi:10.1021/jp0365209

Cited by 167 publications

(197 citation statements)

References 47 publications

(69 reference statements)

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“…Calculated cooperative effects in the urea chains can be compared with other H-bonded systems. All mentioned results for urea clusters are compatible to those obtained at the DFT levels for formamide [45,46], acetamide [13], N-methylformamide [47], polyalanine chains in a-helical and extended structure [48,49], and antiparallel b-sheet models [50]. B3LYP/6-311þþG** and MP2/6-311þþG** levels of theory, are presented in Table II.…”

Section: Equilibrium Geometriessupporting

confidence: 84%

Computational study on the characteristics of the interaction in linear urea clusters

Esrafili

Beheshtian

Hadipour

2010

Int J of Quantum Chemistry

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Quantum mechanics calculations were applied to investigate the NAHÁÁÁO hydrogen bonding properties in linear (urea) n¼1-10 clusters. We investigated geometries, binding energies, and 17O chemical shielding tensors of urea clusters, by means of MP2 and DFT methods. The charge-transfer character of the urea clusters was estimated using Natural Bonding Orbital characteristics. It was found that the cooperativity effects enhance significantly the NAHÁÁÁO hydrogen bond from À33.08 (dimer) to À47.67 kJ/mol (decamer). The n-dependent trend of 17 O shielding tensors was reasonably correlated with cooperative effects in r C¼ ¼O bond distance. To deepen the nature of the interaction in urea clusters, the scheme of decomposition of the interaction energies was applied using Morokuma analysis and a variant of symmetry-adapted perturbation theory (SAPT) based on DFT description of monomers, referred to as SAPT-DFT. The SAPT-DFT analysis of the interaction energy components indicates that the electrostatic and dispersive interactions are the most important attractive terms in the urea dimer.

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Section: Equilibrium Geometriessupporting

confidence: 84%

Computational study on the characteristics of the interaction in linear urea clusters

Esrafili

Beheshtian

Hadipour

2010

Int J of Quantum Chemistry

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“…(e) Behavior of this type is expected for the analogous case of peptides as has been discussed previously on the basis of theoretical calculations [40][41][42][43][44][45][46][47] and experiments. [48][49][50] This is an important consideration in understanding the stability of globular proteins.…”

Section: Discussionmentioning

confidence: 74%

The Crystalline Enol of 1,3-Cyclohexanedione and Its Complex with Benzene: Vibrational Spectra, Simulation of Structure and Dynamics and Evidence for Cooperative Hydrogen Bonding

et al. 2004

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The inelastic incoherent neutron scattering spectra of 1,3-cyclohexanedione (CHD) in its crystalline enol form and its cyclamer complexes with benzene and benzene-d 6 are compared with each other, with IR and Raman spectra and with the results of calculations using density functional theory (DFT). The crystal packing of the CHD enol is a linear hydrogen-bonded chain with conjugated donor and acceptor groups analogous to that found in peptide hydrogen bonding. The benzene complex is a closed hexameric hydrogen-bonded cycle. A DFT treatment is applied to the full hexamer of the benzene complex. The CHD chain is treated as a series of finite linear clusters by DFT, while the infinite one-dimensional chain and the three-dimensional crystal are treated by periodic DFT. Comparison is made with both the observed crystal structures and the vibrational spectra. The very good to excellent agreement of the computed vibrational spectra with experiment demonstrates that the models and computational treatments used are reliable. The theoretical treatment of the linear chain clusters exhibits a continuous change in structure with increasing chain length, converging to values near the observed structure. Emphasis is placed on the cooperative nature of hydrogen bonding in CHD as revealed by these systematic trends. The ability of DFT methods to treat hydrogen bonding in solids appears to be roughly as accurate as the crystal structure determinations.1,3-Cyclohexanedione (CHD) exists in its enol form in the solid state where it forms hydrogen-bonded chains with an antianti configuration having short (2.56 Å) O-O hydrogen bonding distances. 1 This structure is of interest for several reasons including the ordered hydrogen bonding arrangement, an orderdisorderphasetransitionthatinvolveshydrogenbondinterchange, 2-6 and indications derived from examination of crystal structures that CHD is an example of a resonance-assisted, cooperative hydrogen bonding network. [7][8][9][10][11][12][13] This cooperativity arises from the fact that when the enol of CHD forms a hydrogen bond, this polarizes the molecule such that the formation of an additional hydrogen bond with another CHD is more favorable. This may be thought of as due to an enhanced contribution of the ionic resonance form. When crystallized from benzene, this material forms a unique cyclamer structure (CHD 6 Bz) in which six CHD molecules form a syn-anti hydrogen bonded ring surrounding a central benzene molecule. 14 The related 1,3-cyclopentanedione (CPD) 15 forms an antianti linear chain structure very much like that of CHD. Methyl substitution of CPD or CHD can result in changes to the hydrogen-bonding pattern. 2-Methyl-CPD forms a linear chain with an anti-syn arrangement. 16 In this case the methyl-CHD molecules in a given linear chain all point in the same direction. This is in contrast to the anti-anti chain of CPD and CHD (Figure 1) where alternate molecules are oriented in opposite directions. The 2-methyl derivative of CHD has a structure similar to that of CHD 17 but t...

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“…On the other hand, the formation of an internal H-bond that occupies a NH group on one amide may not interfere with the ability of the C=O on the same peptide unit to act as proton acceptor to the NH of a neighboring molecule. And indeed, such an arrangement might be anticipated to strengthen the latter intermolecular H-bond, according to the principles of H-bond cooperativity, wherein proton donation from one part of a molecule tends to strengthen proton acceptance on a neighboring segment 28,64,65 . In fact, such positive cooperativity is a likely contributor to the stability of β-sheets containing three or more strands 23 or α-helices 66,67 .…”

Section: Conclusion and Discussionmentioning

confidence: 99%

Preferred Configurations of Peptide–Peptide Interactions

Adhikari

Scheiner

2013

J. Phys. Chem. A

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The natural and fundamental proclivities of interaction between a pair of peptide units is examined using high-level ab initio calculations. The NH···O H-bonded structure is found to be the most stable configuration of the N-methylacetamide (NMA) model dimer, but only slightly more so than a stacked arrangement. The H-bonded geometry is destabilized by only a small amount if the NH group is lifted out of the plane of the proton-accepting amide. This out-of-plane motion is facilitated by a stabilizing charge transfer from the CO π bond to the NH σ* antibonding orbital. The parallel and anti-parallel stacked dimers are nearly equal in energy, both only slightly less stable than the NH···O H-bonded structure. Both are stabilized by a combination of CH···O H-bonding and a π→π* transfer between the two CO bonds.There are no minima on the surface that are associated with O lp →π*(CO) transfers, due in large part to strong electrostatic repulsion between the two O atoms which resists an approach of a carbonyl O from above the C=O bond of the other amide.

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Cooperativity in Amide Hydrogen Bonding Chains. Relation between Energy, Position, and H-Bond Chain Length in Peptide and Protein Folding Models

Cited by 167 publications

References 47 publications

Computational study on the characteristics of the interaction in linear urea clusters

Computational study on the characteristics of the interaction in linear urea clusters

The Crystalline Enol of 1,3-Cyclohexanedione and Its Complex with Benzene: Vibrational Spectra, Simulation of Structure and Dynamics and Evidence for Cooperative Hydrogen Bonding

Preferred Configurations of Peptide–Peptide Interactions

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