A New Look at Proton Transfer Dynamics Along the Hydrogen Bonds in Amides and Peptides

Kearley, Gordon J.; Fillaux, F.; Baron, M. H.; Bennington, S. M.; Tomkinson, J.

doi:10.1126/science.264.5163.1285

Cited by 133 publications

(72 citation statements)

References 21 publications

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“…The discussion addresses the following issues: (i) the environmental effects on the structure and vibrational spectra of H 5 O 2 1 ; (ii) the relationship between the IR and INS spectra, specifically the broad IR bands compared to relatively narrow INS bands for the OÁ Á ÁH 1 Á Á ÁO vibrations. 20 …”

Section: Introductionmentioning

confidence: 99%

Environmental effects on vibrational proton dynamics in H₅O₂⁺: DFT study on crystalline H₅O₂⁺ClO₄⁻

Vener

Sauer

2005

Phys. Chem. Chem. Phys.

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The structure as well as IR and inelastic neutron scattering (INS) spectra of H 5 O 2 1 in crystalline H 5 O 2 1 ClO 4 À were simulated using Car-Parrinello molecular dynamics with the BLYP functional. The potential of the OÁ Á ÁH 1 Á Á ÁO fragment is very shallow. The Pnma structure, assumed in the X-ray study to be the most suitable choice, is a saddle point on the potential energy surface, while the P2 1 2 1 2 1 minimum structure is only 20 cm À1 lower in energy. The computed INS and IR spectra enable us to achieve a complete assignment of the observed spectra. The broad band between 1000 and 1400 cm À1 is due to the asymmetric stretch and one of the bending vibrations of the OÁ Á ÁH 1 Á Á ÁO fragment, while the band between 1600 and 1800 cm À1 is due to the bending vibration of the water molecules and the second bending of the OÁ Á ÁH 1 Á Á ÁO fragment. Comparison with the vibrational spectra of isolated H 5 O 2 1 , obtained using Born-Oppenheimer molecular dynamics simulation, reveals environmental effects on vibrational proton dynamics in strong H-bonded species. The most pronounced changes are found for the OÁ Á ÁH 1 Á Á ÁO bending modes because the two bending coordinates become distinctly different for the structure that the H 5 O 2 1 ion assumes in the crystal.

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Section: Introductionmentioning

confidence: 99%

Environmental effects on vibrational proton dynamics in H₅O₂⁺: DFT study on crystalline H₅O₂⁺ClO₄⁻

Vener

Sauer

2005

Phys. Chem. Chem. Phys.

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“…There have been reports (Kearley et al, 1994) suggesting that, in a-helices, the hydrogen bonding cooperativity is so effective in polarizing the N-H groups of the peptide bond that the protons are able to dissociate; if so, an ionic (N8-...H+ *-.O")), rather than a hydrogen bonded (N-H.*-O) representation would be appropriate for the main chain of the a-helix. This is an appealing concept, including the possibilities of proton tunneling and the idea that a proton might be transferred rapidly the complete length of a helix.…”

Section: Relevance To Aspects Of Proteinsmentioning

confidence: 99%

The partial charge of the nitrogen atom in peptide bonds

1997

Protein Science

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A majority of the standard texts dealing with proteins portray the peptide link as a mixture of two resonance forms, in one of which the nitrogen atom has a positive charge. As a consequence, it is often believed that the nitrogen atom has a net positive charge. This is in apparent contradiction with the partial negative charge on the nitrogen that is used in force fields for molecular modeling. However, charges on resonance forms are best regarded as formal rather than actual charges and current evidence clearly favors a net negative charge for the nitrogen atom. In the course of the discussion, new ideas about the electronic structure of amides and the peptide bond are presented.Keywords: a-helix; amides; electrostatics; hydrogen bonds; proteins; quantum mechanics This article begins with a listing of some estimates of the partial charges of the atoms of amides. The planarity of amides is typically explained by portraying them as two resonance forms, one of which has a nitrogen atom with a formal positive charge. However, it is chemically unsatisfactory for the nitrogen atom to have a net partial positive charge, and the reasons for this are given. The strongest evidence that the nitrogen is negative rather than positive comes from quantum mechanics. Some recent work on amides and its implications for the electronic structure of the and T orbitals of the CONH group are discussed in some detail. The effect of hydrogen bonding is then considered and, finally, the relevance of these insights for a-helices is addressed. Point charges on individual atoms:The resonance method used commonly to represent the peptide bond as in Figure 1 is often taken to imply that the nitrogen has a partial positive charge. This conflicts with the partial charges used widely in molecular mechanics force fields for modeling biological molecules. A set of calculated partial charges has been collected (Rogers, 1986), and a

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“…These values for the linear H…O hydrogen bonding system were also much larger than 0.0582 mdyn/Å observed from a hydrogen-bonded dimer 31 formed between trimethylamine and acetylene, (CH 3 ) 3 N… HC≡CH, in gas phase by Fourier-transform microwave spectroscopy. The hydrogen bonding proton stretching mode 33 in polyglycine I at 20 K studied by inelastic neutron scattering spectroscopy shows at 2960 cm −1 , with double minimum potential wells which is far below the normal N-H stretching vibrational frequency indicating strong hydrogen bonding.…”

Section: Resultsmentioning

confidence: 99%

Vibrational Analysis and Intermolecular Hydrogen Bonding of Azodicarbonamide in the Pentamer Cluster

2008

Bulletin of the Korean Chemical Society

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Pentamer cluster of azodicarbonamide (ADA) based on the crystalline structure was investigated for the equilibrium structure, the stabilization energies, and the vibrational properties at various levels of the density functional theory. Stretching force constants of N…H or O…H, and angle-bending force constants of N-H…N or N-H…O for intermolecular hydrogen bonds in the pentamer cluster were obtained in 0.2-0.5 mdyn/Å and 1.6-2.0 mdynÅ, respectively. The geometry of central ADA molecule fully hydrogen bonded with other four molecules shows good coincidence to the crystalline structure except the bond distances of N-H. Calculated Raman and infrared spectra of central ADA molecule in cluster represent well the experimental spectra of ADA obtained in the solid state compared to a single molecule. Detailed structural and vibrational properties of central ADA molecule in the pentamer cluster are presented.

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A New Look at Proton Transfer Dynamics Along the Hydrogen Bonds in Amides and Peptides

Cited by 133 publications

References 21 publications

Environmental effects on vibrational proton dynamics in H₅O₂⁺: DFT study on crystalline H₅O₂⁺ClO₄⁻

Environmental effects on vibrational proton dynamics in H₅O₂⁺: DFT study on crystalline H₅O₂⁺ClO₄⁻

The partial charge of the nitrogen atom in peptide bonds

Vibrational Analysis and Intermolecular Hydrogen Bonding of Azodicarbonamide in the Pentamer Cluster

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A New Look at Proton Transfer Dynamics Along the Hydrogen Bonds in Amides and Peptides

Cited by 133 publications

References 21 publications

Environmental effects on vibrational proton dynamics in H5O2+: DFT study on crystalline H5O2+ClO4−

Environmental effects on vibrational proton dynamics in H5O2+: DFT study on crystalline H5O2+ClO4−

The partial charge of the nitrogen atom in peptide bonds

Vibrational Analysis and Intermolecular Hydrogen Bonding of Azodicarbonamide in the Pentamer Cluster

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Product

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Environmental effects on vibrational proton dynamics in H₅O₂⁺: DFT study on crystalline H₅O₂⁺ClO₄⁻

Environmental effects on vibrational proton dynamics in H₅O₂⁺: DFT study on crystalline H₅O₂⁺ClO₄⁻