Interplay of the Intramolecular Water Vibrations and Hydrogen Bond in N-Methylacetamide-Water Complexes: Ab Initio Calculation Studies

doi:10.5012/bkcs.2003.24.8.1061

Cited by 16 publications

(7 citation statements)

References 53 publications

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“…To check the validity of this approach, we calculated δω CO and δω NH as a function of r OH at a fixed angle of ∠CO···H = 120° (Figure a). In this calculation, the frequency of the isolated amide I mode was set to 1707 cm -1 for a direct comparison to recent ab initio calculations of NMA−water clusters and the NMA dimer. , By adjusting κ CO to 0.42 and κ NH to 0.96 cm kJ mol -1 , the distance dependence of the direct and indirect hydrogen-bond shifts agree quite well with those from the calculations. , The coefficient 0.42 for κ CO is also a reasonable value compared with 0.38 reported for N , N -dimethylacetamide 80 and 0.51−2.2 reported for other carbonyl modes. , For the frequency shift due to solvent exposure, we considered that δω solvent = 0 for the inner residues that are forming two hydrogen bonds to other residues. These residues are relatively shielded from solvent because of the protection provided by bulky side chains of Aib and (αMe)Val residues.…”

Section: Theoretical Calculationssupporting

confidence: 60%

“…First, hydrogen-bond strength depends on both distance and angle (there is an angle criterion for hydrogen-bond formation), but this formula does not consider angle dependence. Second, it has been experimentally and theoretically shown that hydrogen bonding on the CO and N−H group of the NMA molecule shifts the amide I frequency by approximately 15−25 and 10−15 cm -1 , respectively, and the frequency shifts are additive. − Thus, it is necessary to modify the formula to account for the frequency shift due to the N−H group being hydrogen-bonded. Another potential approach to estimate the amide I local mode frequencies is to utilize the linear relationship between the CO bond length and the amide I local mode frequency obtained in recent theoretical studies. , This approach requires an accuracy of at least 10 -3 Å for the calculated bond lengths.…”

Section: Theoretical Calculationsmentioning

confidence: 99%

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Two-Dimensional Infrared Spectral Signatures of 3₁₀- and α-Helical Peptides

Maekawa¹,

Toniolo²,

Broxterman³

et al. 2007

J. Phys. Chem. B

137

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Two-dimensional infrared (2D IR) spectra of Calpha-alkylated model octapeptides Z-(Aib)8-OtBu, Z-(Aib)5-L-Leu-(Aib)2-OMe, and Z-[L-(alphaMeVal)]8-OtBu have been measured in the amide I region to acquire 2D spectral signatures characteristic of 3(10)- and alpha-helical conformations. Phase-adjusted 2D absorptive spectra recorded with parallel polarizations are dominated by intense diagonal peaks, whereas 2D rephasing spectra obtained at the double-crossed polarization configuration reveal cross-peak patterns that are essential for structure determination. In CDCl3, all three peptides are of the 3(10)-helix conformation and exhibit a doublet cross-peak pattern. In 1,1,1,3,3,3-hexafluoroisopropanol, Z-[L-(alphaMeVal)]8-OtBu undergoes slow acidolysis and 3(10)-to-alpha-helix transition. In the course of this conformational change, its 2D rephasing spectrum evolves from an elongated doublet, characteristic of a distorted 3(10)-helix, to a multiple-peak pattern, after becoming an alpha-helix. The linear IR and 2D absorptive spectra are much less informative in discerning the structural changes. The experimental spectra are compared to simulations based on a vibrational exciton Hamiltonian model. The through-bond and through-space vibrational couplings are modeled by ab initio coupling maps and transition dipole interactions. The local amide I frequency is evaluated by a new approach that takes into account the effects of hydrogen-bond geometry and sites. The static diagonal and off-diagonal disorders are introduced into the Hamiltonian through statistical models to account for conformational fluctuations and inhomogeneous broadening. The sensitivity of cross-peak patterns to different helical conformations and the chain length dependence of the spectral features for short 3(10)- and alpha-helices are discussed.

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Section: Theoretical Calculationssupporting

confidence: 60%

Section: Theoretical Calculationsmentioning

confidence: 99%

Two-Dimensional Infrared Spectral Signatures of 3₁₀- and α-Helical Peptides

Maekawa¹,

Toniolo²,

Broxterman³

et al. 2007

J. Phys. Chem. B

137

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“…The frequency shifts were found to be in good correlation with the electrostatic energy of the intramolecularly hydrogen-bonded CO•••H−N groups, denoted as E KS . 279 By matching the model frequency shift to the results obtained from quantum mechanical calculations of NMA−water clusters, 334 the correlation coefficients in the above equations were obtained. 78,278 In addition to the intramolecular H-bonding effects, if the CO or N−H group is exposed to solvent, it is necessary to consider an additional decrease (increase) of the amide I (II) mode frequency due to the effect of solvation (δω solvent ).…”

Section: Amide II and Iii Vibrationsmentioning

confidence: 99%

Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction

et al. 2020

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Vibrational spectroscopy is an essential tool in chemical analyses, biological assays, and studies of functional materials. Over the past decade, various coherent nonlinear vibrational spectroscopic techniques have been developed and enabled researchers to study time-correlations of the fluctuating frequencies that are directly related to solute-solvent dynamics, dynamical changes in molecular conformations and local electrostatic environments, chemical and biochemical reactions, protein structural dynamics and functions, characteristic processes of functional materials, and so on. In order to gain incisive and quantitative information on the local electrostatic environment, molecular conformation, protein structure and inter-protein contacts, ligand binding kinetics, and electric and optical properties of functional materials, a variety of vibrational probes have been developed and site-specifically incorporated into molecular, biological, and material systems for time-resolved vibrational spectroscopic investigation. However, still, an allencompassing theory that describes the vibrational solvatochromism, electrochromism, and dynamic fluctuation of vibrational frequencies has not been completely established mainly due to the intrinsic complexity of intermolecular interactions in condensed phases. In particular, the amount of data obtained from the linear and nonlinear vibrational spectroscopic experiments has been rapidly increasing, but the lack of a quantitative method to interpret these measurements has been one major obstacle in broadening the applications of these methods. Among various theoretical models, one of the most successful approaches is a semi-empirical model generally referred to as the vibrational spectroscopic map that is based on a rigorous theory of intermolecular interactions. Recently, genetic algorithm, neural network, and machine learning approaches have been applied to the development of vibrational solvatochromism theory. In this review, we provide comprehensive descriptions of the theoretical foundation and various examples showing its extraordinary successes in the interpretations of experimental observations. In addition, a brief introduction to a newly created repository website (http://frequencymap.org) for vibrational spectroscopic maps is presented. We anticipate that a combination of the vibrational frequency map approach and state-of-theart multidimensional vibrational spectroscopy will be one of the most fruitful ways to study the structure and dynamics of chemical, biological, and functional molecular systems in the future.

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“…Nonlinear-IR spectroscopy of the amide I band can be modeled to obtain C ( t ) and other dynamical quantities. As NMA involves a single amide group, there has been considerable interest in measuring the frequency response of the amide I band of NMA and other peptides in various solvent environments. − ,,− …”

Section: Introductionmentioning

confidence: 99%

Amide I Vibrational Dynamics of N-Methylacetamide in Polar Solvents: The Role of Electrostatic Interactions

DeCamp¹,

DeFlores²,

McCracken³

et al. 2005

J. Phys. Chem. B

235

329

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The vibrational frequency of the amide I transition of peptides is known to be sensitive to the strength of its hydrogen bonding interactions. In an effort to account for interactions with hydrogen bonding solvents in terms of electrostatics, we study the vibrational dynamics of the amide I coordinate of N-methylacetamide in prototypical polar solvents: D2O, CDCl3, and DMSO-d6. These three solvents have varying hydrogen bonding strengths, and provide three distinct solvent environments for the amide group. The frequency-frequency correlation function, the orientational correlation function, and the vibrational relaxation rate of the amide I vibration in each solvent are retrieved by using three-pulse vibrational photon echoes, two-dimensional infrared spectroscopy, and pump-probe spectroscopy. Direct comparisons are made to molecular dynamics simulations. We find good quantitative agreement between the experimentally retrieved and simulated correlation functions over all time scales when the solute-solvent interactions are determined from the electrostatic potential between the solvent and the atomic sites of the amide group.

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Interplay of the Intramolecular Water Vibrations and Hydrogen Bond in N-Methylacetamide-Water Complexes: Ab Initio Calculation Studies

Cited by 16 publications

References 53 publications

Two-Dimensional Infrared Spectral Signatures of 3₁₀- and α-Helical Peptides

Two-Dimensional Infrared Spectral Signatures of 3₁₀- and α-Helical Peptides

Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction

Amide I Vibrational Dynamics of N-Methylacetamide in Polar Solvents: The Role of Electrostatic Interactions

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Interplay of the Intramolecular Water Vibrations and Hydrogen Bond in N-Methylacetamide-Water Complexes: Ab Initio Calculation Studies

Cited by 16 publications

References 53 publications

Two-Dimensional Infrared Spectral Signatures of 310- and α-Helical Peptides

Two-Dimensional Infrared Spectral Signatures of 310- and α-Helical Peptides

Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction

Amide I Vibrational Dynamics of N-Methylacetamide in Polar Solvents: The Role of Electrostatic Interactions

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Two-Dimensional Infrared Spectral Signatures of 3₁₀- and α-Helical Peptides

Two-Dimensional Infrared Spectral Signatures of 3₁₀- and α-Helical Peptides