On the temperature dependence of amide I frequencies of peptides in solution

The temperature dependence of the amide I vibrational frequencies of peptides in solution was investigated. In D2O, the amide I' bands of both an alpha-helical oligopeptide, the random-coil poly(L-lysine), and the simplest amide, N-methyl acetamide (NMA), exhibit linear frequency shifts of approximately 0.07 cm(-1)/degrees C with increasing temperature. Similar amide I frequency shifts are also observed for NMA in both polar (acetonitrile and DMSO) and nonpolar (1,4-dioxane) organic solvents, thus ruling out hydrogen-bonding strength as the cause of these effects. The experimental NMA amide I frequencies in the organic solvents can be accurately described by a simple theory based on the Onsager reaction field with temperature-dependent solvent dielectric properties and a solute molecular cavity. DFT-level calculations (BPW91/cc-pVDZ) for NMA with an Onsager reaction field confirm the significant contribution of the molecular cavity to the predicted amide I frequencies. Comparison of the computations to experimental data shows that the frequency-dependent response of the reaction field, taken into account by the index of refraction, is crucial for describing the amide I frequencies in polar solvents. The poor predictions of the model for the NMA amide I band in D2O might be due, in part, to the unknown temperature dependence of the refractive index of D2O in the mid-IR range, which was approximated by the available values in the visible region.     

Ab initio modeling of amide I coupling in antiparallel beta-sheets and the effect of 13C isotopic labeling on infrared spectra

Isotopic substitution with 13C on the amide C=O has become an important means of determining localized structural information about peptide conformations with vibrational spectroscopy. Various approaches to the modeling of the interactions between labeled amide sites, specifically for antiparallel two-stranded, beta-forming peptides, were investigated, including different force fields [dipole-dipole interaction vs density functional theory (DFT) treatments], basis sets, and sizes of model peptides used for ab initio calculations, as well as employing models of solvation. For these beta-sheet systems the effect of the relative positions of the 13C isotopic labels in each strand on their infrared spectra was investigated. The results suggest that the interaction between labeled amide groups in different strands can be used as an indicator of local beta-structure formation, because coupling between close-lying C=O groups on opposing chains leads to the largest frequency shifts, yet some alternate placements can lead to intensity enhancements. The basic character of the coupling interaction between labeled modes on opposing strands is independent of changes in peptide length, water solvent environment, twisting of the sheet structure, and basis set used in the calculations, although the absolute frequencies and detailed coupling magnitudes change under each of these perturbations. In particular, two strands of three amides each contain the basic interactions needed to simulate larger sheets, with the only exception that the C=O groups forming H-bonded rings at the termini can yield different coupling values than central ones of the same structure. Spectral frequencies and intensities were modeled ab initio by DFT primarily at the BPW91/6-31G** level for pairs of three, four, and six amide strands. Comparison to predictions of a classical coupled oscillator model show qualitative but not quantitative agreement with these DFT results.     

Studies of the characteristic frequencies of vapor-phase infrared spectra: II. The characteristic frequencies of ketones and aldehydes

Vapor-phase infrared characteristic frequencies of ketones and aldehydes have been studied. The CO stretching vibrations in vapor phase have higher frequencies than those in condensed phase. The shifts are about 20 cm⁻¹ for ketones and about 10 cm⁻¹ for aldehydes. Both ketone and aldehyde have an absorption band at the range 1300–1100 cm⁻¹, although their intensities are very different. This band was assigned to the CC stretching vibration of C(CO)unit.     

Characteristic frequencies in the infrared spectra of pyrazolines

Pyrazolines are characterized by valence vibrations at the following frequencies: C=N (1580–1627 cm^–1), H-C³=N (3040–3063 cm^–1), H-N (3270–3305 cm^–1) and CH₃-N (2780–2805 cm^–1). Lowering of the frequencies of the valence vibrations of C=N in pyrazolines, when compared with the magnitudes characteristic of alkyledene amines and oximes, is regarded as a consequence of coupling with the unshared electron pair of the neighboring nitrogen atom. By means of the IR spectra, it is possible to determine the position of the double bonds in the pyrazoline ring, to distinguish between pyrazolines substituted and nonsubstituted in positions 1 and 3, and to establish the presence of geminate (twin) methyl groups and methyl groups in position 1.     

Calculations of intermode coupling constants and simulations of amide I,II, and III vibrational spectra of dipeptides

Amide I, II, and III vibrations of polypeptides are important marker modes whose vibrational spectra can provide critical information on structure and dynamics of proteins in solution. The extent of delocalization and vibrational properties of amide normal mode can be described by the amide local mode frequencies and intermode coupling constants between a pair of amide local modes. To determine these fundamental quantities, the previous Hessian matrix reconstruction method has been generalized here and applied to the density functional theory results for various dipeptide conformers. The calculation results are then used to simulate IR absorption, vibrational circular dichroism, and 2D IR spectra of dipeptides. The relationships between dipeptide backbone conformations and these vibrational spectra are discussed. It is believed that the present computational method and results will be of use to quantitatively simulate vibrational spectra of complicated polypeptides beyond simple dipeptides     

Simulation of vibrational energy transfer in two-dimensional infrared spectroscopy of amide I and amide II modes in solution

Population transfer between vibrational eigenstates is important for many phenomena in chemistry. In solution, this transfer is induced by fluctuations in molecular conformation as well as in the surrounding solvent. We develop a joint electrostatic density functional theory map that allows us to connect the mixing of and thereby the relaxation between the amide I and amide II modes of the peptide building block N-methyl acetamide. This map enables us to extract a fluctuating vibrational Hamiltonian from molecular dynamics trajectories. The linear absorption spectrum, population transfer, and two-dimensional infrared spectra are then obtained from this Hamiltonian by numerical integration of the Schrodinger equation. We show that the amide I/amide II cross peaks in two-dimensional infrared spectra in principle allow one to follow the vibrational population transfer between these two modes. Our simulations of N-methyl acetamide in heavy water predict an efficient relaxation between the two modes with a time scale of 790 fs. This accounts for most of the relaxation of the amide I band in peptides, which has been observed to take place on a time scale of 450 fs in N-methyl acetamide. We therefore conclude that in polypeptides, energy transfer to the amide II mode offers the main relaxation channel for the amide I vibration.     

Single-conformation ultraviolet and infrared spectra of jet-cooled monolignols: p-coumaryl alcohol, coniferyl alcohol, and sinapyl alcohol

Single-conformation spectroscopy of the three lignin monomers (hereafter "monolignols") p-coumaryl alcohol (pCoumA), coniferyl alcohol (ConA), and sinapyl alcohol (SinA) has been carried out on the isolated molecules cooled in a supersonic expansion. Laser-induced fluorescence excitation, dispersed fluorescence, resonant two-photon ionization, UV-UV hole-burning, and resonant ion-dip infrared spectroscopy were carried out as needed to obtain firm assignments for the observed conformers of the three molecules. In each case, two conformers were observed, differing in the relative orientations of the vinyl and OH substituents para to one another on the phenyl ring. In pCoumA, the two conformers have S(0)-S(1) origins nearly identical in size, split from one another by only 7 cm(-1), in close analogy with previous results of Morgan et al. on p-vinylphenol ( Chem. Phys. 2008 , 347 , 340 ). ConA, with its methoxy group ortho to the OH group, also has two low-energy conformers forming a syn/anti pair, in this case with the OH group locked into an orientation in which it forms an intramolecular H-bond with the adjacent methoxy group. The electronic frequency shift between the two conformers is dramatically increased to 805 cm(-1), with the dominant conformer of ConA (with S(0)-S(1) origin at 32?640 cm(-1)) about 5 times the intensity of its minor counterpart (with S(0)-S(1) origin at 33?444 cm(-1)). The presence of an OH···OCH(3) intramolecular H-bond is established by the shift of the OH stretch fundamental of the OH group to 3599 cm(-1), as it is in o-methoxyphenol ( Fujimaki et al. J. Chem. Phys. 1999 , 110 , 4238 ). Analogous single-conformation UV and IR spectra of o-methoxy-p-vinylphenol show a close similarity to ConA and provide a basis for a firm assignment of the red-shifted (blue-shifted) conformer of both molecules to the syn (anti) conformer. The two observed conformers of SinA, with its two methoxy group straddling the OH group, have S(0)-S(1) origins split by 239 cm(-1) (33?055 and 33?294 cm(-1)), a value between those in pCoumA and ConA. A combination of experimental data and calculations on the three monolignols and simpler derivatives is used to establish that the conformational preferences of the monolignols reflect the preferences of each of the ring substituents separately, enhanced by the presence of the intramolecular OH···OCH(3) H-bond. Taken as a whole, the presence of multiple flexible substituents locks in certain preferred orientations of the groups relative to one another, even in the apparently flexible allyl alcohol side chain (-CH═CH-CH(2)OH), where the OH group orients itself so that the hydrogen is pointed back over the vinyl π cloud in order to minimize interactions between the oxygen lone pairs and the π electrons.     

Dynamic metal-ligand coupling in the infrared MCD spectra of the cobalt(II) tetrahalides

The axial single-crystal magnetic circular dichroism spectra of Cs₃ZnCl₅/Co²⁺ and Cs₃ZnBr₅/Co²⁺ have been measured over the 4000–7000 cm^?1 region of the ⁴A₂ → ⁴T₁ (F) transition at ambient and liquid-helium temperature. The B/D and C/D terms obtained give transition moment ratios, 〈t₂∥m∥t₂〉/〈e∥m∥t₂〉, in accord with the value required (?3^{$\text{1}\text{2}$}/2^{$\text{1}\text{2}$}) by a dynamic ligand-polarisation model for d-electron transition probabilities in tetrahedral metal complexes.     

Non-Gaussian statistics of amide I mode frequency fluctuation of N-methylacetamide in methanol solution: linear and nonlinear vibrational spectra

By carrying out molecular dynamics simulations of an N-methylacetamide (NMA) in methanol solution, the amide I mode frequency fluctuation and hydrogen bonding dynamics were theoretically investigated. Combining an extrapolation formula developed from systematic ab initio calculation studies of NMA-(CH3OH)n clusters with a classical molecular dynamics simulation method, we were able to quantitatively describe the solvatochromic vibrational frequency shift induced by the hydrogen-bonding interaction between NMA and solvent methanol. It was found that the fluctuating amide I mode frequency distribution is notably non-Gaussian and it can be decomposed into two Gaussian peaks that are associated with two distinctively different solvation structures. The ensemble-average-calculated linear response function associated with the IR absorption is found to be oscillating, which is in turn related to the doublet amide I band shape. Numerically calculated infrared absorption spectra are directly compared with experiment and the agreement was found to be excellent. By using the Onsager's regression hypothesis, the rate constants of the interconversion process between the two solvation structures were obtained. Then, the nonlinear response functions associated with two-dimensional infrared pump-probe spectroscopy were simulated. The physics behind the two-dimensional line shape and origin of the cross peaks in the time-resolved pump-probe spectra is explained and the result is compared with 2D spectra experimentally measured recently by Woutersen et al.     

Single-conformation ultraviolet and infrared spectroscopy of model synthetic foldamers: beta-peptides Ac-beta3-hPhe-NHMe and Ac-beta3-hTyr-NHMe

The conformational preferences and infrared and ultraviolet spectral signatures of two model beta-peptides, Ac-beta3-hPhe-NHMe (1) and Ac-beta3-hTyr-NHMe (2), have been explored under jet-cooled, isolated molecule conditions. The mass-resolved, resonant two-photon ionization spectra of the two molecules were recorded in the region of the S0-S1 origin of the phenyl or phenol ring substituents, respectively. UV-UV hole-burning spectroscopy was used to determine that two conformations of 1 are present, with the transitions due to conformer A, with S0-S1 origin at 34431 cm(-1), being almost 20 times larger than those due to conformer B, with S0-S1 origin at 34404 cm(-1). Only one conformation of 2 was observed. Resonant ion-dip infrared spectroscopy provided single-conformation infrared spectra in the 3300-3700 cm(-1) region. The spectra of conformer A of both molecules have H-bonded and free amide NH stretch infrared transitions at 3400 and 3488 cm(-1), respectively, while conformer B of 1 possesses bands at 3417 and 3454 cm(-1). For comparison with experiment, full optimizations of all low-lying minima of 1 were carried out at the DFT B3LYP/6-31+G* and RIMP2/aug-cc-pVDZ levels of theory, and single point MP2/6-31+G* calculations at the DFT geometries. On the basis of the comparison with previous studies in solution and the calculated results, conformer A of 1 and 2 were assigned to a C6 conformer, while conformer B of 1 was assigned to a unique C8 structure with a weak intramolecular H-bond. The reasons for the preference for C6 over C8 structures and the presence of only two conformations in the jet-cooled spectrum are discussed in light of the predictions from calculations.     

Vibrational-exciton couplings for the amide I, II, III, and A modes of peptides

The couplings between all amide fundamentals and their overtones and combination vibrational states are calculated. Combined with the level energies reported previously (Hayashi, T.; Zhuang, W.; Mukamel, S. J. Phys. Chem. A 2005, 109, 9747), we obtain a complete effective vibrational Hamiltonian for the entire amide system. Couplings between neighboring peptide units are obtained using the anharmonic vibrational Hamiltonian of glycine dipeptide (GLDP) at the BPW91/6-31G(d,p) level. Electrostatic couplings between non-neighboring units are calculated by the fourth rank transition multipole coupling (TMC) expansion, including 1/R3 (dipole-dipole), 1/R4 (quadrupole-dipole), and 1/R5 (quadrupole-quadrupole and octapole-dipole) interactions. Exciton delocalization length and its variation with frequency in the various amide bands are calculated. The simulated infrared amide I and II absorptions and CD spectra of 24 residue alpha-helical motifs (SPE3) are in good agreement with experiment.     

Calculation of the frequencies and intensities in the infrared and raman spectra of cyclopropenone

By using the values of the vibrational frequencies of normal and deuterated cyclopropenone (II-d₀ , II-d₂ ) and ¹⁶ O-and ¹⁸ O-substituted dimethylcyclopropenone (III) as -well as the infrared and Raman intensities of II a consistent set of force constants has been derived for the cyclopropenone skeleton. The derived values show that the zwitterionic form makes a substantial contribution to the electronic ground state of the molecule. The combined frequency and intensity calculation - simulation of the infrared and the Raman spectrum - is shown to be a good method for making a proper assignment of calculated and observed vibrations and deriving realistic sets of force constants.     

Photolytic control and infrared probing of amide I mode in the dipeptide backbone-caged with the 4,5-dimethoxy-2-nitrobenzyl group

Alanine dipeptide analog 1 backbone-caged with a photolabile linker, 4,5-dimethoxy-2-nitrobenzyl (DmNb), was synthesized. UV-pulse-induced photochemical reaction of 1 was monitored by Fourier transform IR absorption spectroscopy under a steady-state condition or in a fast-scan mode. Upon photolysis of 1, the amide I band is changed from a doublet to a singlet with concomitant line shape changes of several IR bands. The change of the amide I band is directly associated with the photocleavage of the covalent N-C bond connecting the backbone amide of 2 to DmNb. Therefore, IR spectroscopy is useful for directly probing the photocleavage of backbone-caged peptide 1 and the concurrent release of native peptide 2. In contrast, UV-vis spectroscopy probing the irradiation-induced structural change of the 2-nitrobenzyl moiety itself may not provide a clue directly relevant to the photocleavage of such N-C bond. Time-resolved IR spectra recorded in a fast-scan mode after pulsed UV irradiation of 1 reveal that such photocleavage occurs at least faster than a few seconds of our instrumental time resolution.     

The infrared spectra and theoretical calculations of frequencies of fac-tricarbonyl octahedral complexes of manganese(I)

The carbonyl stretching frequencies in the infrared spectra of 38 fac-tricarbonyl octahedral complexes of manganese(I) prepared in this laboratory were determined. These complexes may be grouped into three types: (a) neutral complexes of the structure (CO)(3)Mn(P-P)Z where P-P represents depe, dppe, or dppp, and Z represents various anionic functional groups bonded to the manganese; (b) ionic complexes of the structure [(CO)(3)Mn(P-P)Z](+)BF(4)(-) where Z represents various neutral molecules possessing one phosphorous, nitrogen, or oxygen atom coordinated to the manganese; (c) complexes of the structure (CO)(3)Mn(pn)Z where the chelating pn represents 1,1-diphenylphosphino-2,2-dimethylaminoethane, Ph(2)PCH(2)CH(2)NMe(2). All of these complexes show three carbonyl stretching modes (2A' + A"). The effects on the frequencies of these modes induced by both the various Z groups and the various ligands are discussed. Theoretical calculations (B3LYP/6-31G) with optimization of the full molecule make it possible to distinguish between the three stretching modes and to make unambiguous assignments of appropriate symmetry species to each.     

Vibrational relaxation pathways of amide I and amide II modes in N-methylacetamide

We studied the vibrational energy relaxation mechanisms of the amide I and amide II modes of N-methylacetamide (NMA) monomers dissolved in bromoform using polarization-resolved femtosecond two-color vibrational spectroscopy. The results show that the excited amide I vibration transfers its excitation energy to the amide II vibration with a time constant of 8.3 ± 1 ps. In addition to this energy exchange process, we observe that the excited amide I and amide II vibrations both relax to a final thermal state. For the amide I mode this latter process dominates the vibrational relaxation of this mode. We find that the vibrational relaxation of the amide I mode depends on frequency which can be well explained from the presence of two subbands with different vibrational lifetimes (~1.1 ps on the low frequency side and ~2.7 ps on the high frequency side) in the amide I absorption spectrum.     

Simulation of infrared spectra for beta-hairpin peptides stabilized by an Aib-Gly turn sequence: correlation between conformational fluctuation and vibrational coupling

Vibrational spectra of a 12-residue beta-hairpin peptide, RYVEVBGKKILQ (HBG), stabilized by an Aib-Gly turn sequence (B = Aib) were investigated theoretically using a combination of molecular dynamics (MD) and density functional theory (DFT) calculations. Selected conformations of HBG were extracted from a classical MD trajectory and used for spectral simulations. DFT calculations, based on the Cartesian coordinate spectral property transfer protocol, were carried out for peptide structures in which all residues are replaced with Ala, except for the Aib and Gly residues, but the backbone (phi, psi, omega) structure of the original configuration is retained. The simulations provide a basis for interpretation of the HBG amide I infrared spectra in terms of structural variables such as detailed secondary structure and thermal conformational fluctuation as well as vibrational coupling as indicated by spectra of 13C isotope-labeled variants. The characteristic amide I band shape of such small beta-hairpin peptides appears to arise from the structure of the short antiparallel beta-sheet strands. The role of structural parameter fluctuation in vibrational coupling is evaluated by comparison of DFT-derived amide coupling constants for selected configurations and from transition dipole coupling calculations of coupling parameters between (13)C isotopically labeled residues for a MD-derived ensemble of configurations. Calculated results were compared with the experimentally obtained spectra for several (13)C isotope-labeled peptides of this sequence.     

Nonadiabatic effects in the two-dimensional infrared spectra of peptides: application to alanine dipeptide

A method of simulating two-dimensional infrared spectra accounting for nonadiabatic effects is presented. The method is applied to the amide I modes of a dipeptide. The information necessary to construct the time-dependent Hamiltonian for the system is extracted from molecular dynamics simulations using a recently published ab initio-based model. It is shown that the linear absorption spectrum agrees with experiment only if the nonadiabatic effects are accounted for. The two-dimensional infrared spectrum is predicted for a range of mixing times. It is shown that population transfer between the amide I site vibrations affects the anisotropy at longer mixing times. It is also demonstrated that the population transfer can, to a good approximation, be extracted from the simulated spectra using a procedure that should also be applicable to experimental spectra.     

Visualization and characterization of the infrared active amide I vibrations of proteins

To facilitate the analysis of frequency-structure correlations in the amide I vibrational spectroscopy of proteins, we investigate visualization methods and spatial correlation functions that describe delocalized vibrations of proteins and protein secondary structures. To study those vibrational modes revealed in infrared spectroscopy, we characterize frequency-dependent bright states obtained from doorway mode analysis. Our visualization methods pictorially color code amplitude and phase of each oscillator within the structure to reveal spatially varying patterns characteristic of excitations within sheets and helices. Spatial correlation functions in the amplitude and phase of amide I oscillators quantitatively address the extent of delocalization and the alpha helical and beta sheet character of these modes. Specifically, we investigate the vibrations of idealized antiparallel beta sheets and alpha helices and perform case studies on three proteins: concanavalin A, myoglobin, and ubiquitin.