Theoretical calculations of infrared absorption, vibrational circular dichroism, and two-dimensional vibrational spectra of acetylproline in liquids water and chloroform

Infrared absorption, vibrational circular dichroism, and two-dimensional infrared pump-probe and photon echo spectra of acetylproline solutions are theoretically calculated and directly compared with experiments. In order to quantitatively determine interpeptide interaction-induced amide I mode frequency shifts, high-level quantum chemistry calculations were performed. The solvatochromic amide I mode frequency shift and fluctuation were taken into account by carrying out molecular dynamics simulations of acetylproline dissolved in liquids water and chloroform and by using the extrapolation method developed recently. We first studied correlation time scales of the two amide I vibrational frequency fluctuations, cross correlation between the two fluctuating local mode frequencies, ensemble averaged conformations of the acetylproline molecule in liquids water and chloroform. The corresponding conformations of the acetylproline in liquids water and chloroform are close to the ideal 3(10) helix and the C(7) structure, respectively. A few methods proposed to determine the angle between the two transition dipoles associated with the amide I vibrations were tested and their limitations are discussed.     

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.     

Computational spectroscopy of ubiquitin: comparison between theory and experiments

Using the constrained molecular dynamics simulation method in combination with quantum chemistry calculation, Hessian matrix reconstruction, and fragmentation approximation methods, the authors have established computational schemes for numerical simulations of amide I IR absorption, vibrational circular dichroism (VCD), and two-dimensional (2D) IR photon echo spectra of the protein ubiquitin in water. Vibrational characteristic features of these spectra in the amide I vibration region are discussed. From the semiempirical quantum chemistry calculation results on an isolated ubiquitin, amide I local mode frequencies and vibrational coupling constants were fully determined. It turns out that the amide I local mode frequencies of ubiquitin in both gas phase and aqueous solution are highly heterogeneous and site dependent. To directly test the quantitative validity of thus obtained spectroscopic properties, they compared the experimentally measured amide I IR, 2D IR, and electronic circular dichroism spectra with experiments, and found good agreements between theory and experiments. However, the simulated VCD spectrum is just qualitatively similar to the experimentally measured one. This indicates that, due to delicate cancellations between the positive and negative VCD contributions, the prediction of protein VCD spectrum is critically relied on quantitative accuracy of the theoretical model for predicting amide I local mode frequencies. On the basis of the present comparative investigations, they found that the site dependency of amide I local mode frequency, i.e., diagonal heterogeneity of the vibrational Hamiltonian matrix in the amide I local mode basis, is important. It is believed that the present computational methods for simulating various vibrational and electronic spectra of proteins will be of use in further refining classical force fields and in addressing the structure-spectra relationships of proteins in solution.     

Excitonic effects in two-dimensional vibrational spectra of liquid formamide

The linear and two-dimensional infrared (2DIR) responses of the amide I vibrational mode in liquid formamide are investigated experimentally and theoretically using molecular dynamics simulations. The recent method based on the numerical integration of the Schr?dinger equation is employed to calculate the 2DIR spectra. Special attention is devoted to the interplay of the structural dynamics and the excitonic nature of the amide I modes in determining the optical response of the studied system. In particular, combining experimental data, simulated spectra and analysis of the simulated atomic trajectory in terms of a transition dipole coupling model, we provide a convincing explanation of the peculiar features of the 2DIR spectra, which show a substantial increase of the antidiagonal bandwidth with increasing frequency. We point out that, at variance with liquid water, the 2DIR spectral profile of formamide is determined more by the excitonic nature of the vibrational states than by the fast structural dynamics responsible for the frequency fluctuations.     

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.     

Amide I vibrational dynamics of N-methylacetamide in polar solvents: the role of electrostatic interactions

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.     

Simulation of transient infrared spectra of a photoswitchable peptide

In transient infrared (IR) experiments, a molecular system may be photoexcited in a nonstationary conformational state, whose time evolution is monitored via IR spectroscopy with high temporal and structural resolution. As a theoretical formulation of these experiments, this work derives explicit expressions for transient one- and two-dimensional IR spectra and discusses various levels of approximation and sampling strategies. Adopting a photoswitchable octapeptide in water as a representative example, nonequilibrium molecular dynamics simulations are performed and the photoinduced conformational dynamics and associated IR spectra are discussed in detail. Interestingly, it is found that the time scales of dynamics and spectra may differ from residue to residue by up to an order of magnitude. Considering merely the cumulative spectrum of all residues, the contributions of the individual residues largely compensate each other, which may explain the surprisingly small frequency shifts and short photoproduct rise times found in experiment. Even when a localized amide I mode is probed (e.g., via isotope labeling), the vibrational frequency shift is shown to depend in a complicated way on the conformation of the entire peptide as well as on the interaction with the solvent. In this context, various issues concerning the interpretation of transient IR spectra and conformational dynamics in terms of a few exponential time scales are discussed.     

HCl solvation at the surface and within methanol clusters/nanoparticles II: Evidence for molecular wires

Condensed-phase solvation of HCl on and within methanol nanoparticles was investigated by Fourier transform infrared (FTIR) spectroscopy, on-the-fly molecular dynamics as implemented in the density functional code Quickstep (which is part of the CP2K package), and ab initio calculations. Adsorption and solvation stages are identified and assigned with the help of calculated infrared spectra obtained from the simulations. The results have been further checked with MP2-level ab initio calculations. The range of acid solvation states extends from the single-coordinated slightly stretched HCl to proton-sharing with Zundel-like methanol O...H+...X- states, and finally to MeOH2+...Cl- units with full proton transfer. Furthermore, once the proton moves to methanol, it is mobilized along methanol molecular chains. Since the proton dynamics reflects the evolving local structures, the "proton" spectra display broad bands usually with underlying continua.     

A transferable electrostatic map for solvation effects on amide I vibrations and its application to linear and two-dimensional spectroscopy

A method for modeling infrared solvent shifts using the electrostatic field generated by the solvent is presented. The method is applied to the amide I vibration of N-methyl acetamide. Using ab initio calculations the fundamental frequency, anharmonicity, and the transition dipoles between the three lowest vibrational states are parametrized in terms of the electrostatic field. The generated map, which takes into account the electric field and its gradients at four molecular positions, is tested in a number of common solvents. Agreement of solvent shift and linewidths with experimental Fourier transform infrared (FTIR) data is found to within seven and four wave numbers, respectively, for polar solvents. This shows that in these solvents electrostatic contributions dominate solvation effects and the map is transferable between these types of solvents. The effect of motional narrowing arising from the fast solvent fluctuations is found to be substantial for the FTIR spectra. Also the two-dimensional infrared (2DIR) spectra, simulated using the constructed map, reproduce experimental results very well. The effect of anharmonicity fluctuations on the 2DIR spectra was found to be negligible.     

Vibrational and Structural Dynamics of Mn(CO)5Br and Re(CO)5Br Examined Using Nonlinear Infrared Spectroscopy

Vibrational and structural dynamics of two transition metal carbonyl complexes, Mn(CO)₅Br and Re(CO)₅Br were examined in DMSO, using ultrafast infrared pump-probe spectroscopy, steady-state linear infrared spectroscopy and quantum chemistry computations. Two carbonyl stretching vibrational modes (a low-frequency A₁ mode and two high-frequency degenerate E modes) were used as vibrational probes. Central metal effect on the CO bond order and force constant was responsible for a larger E-A₁ frequency separation and a generally more red-shifted E and A₁ peaks in the Re complex than in the Mn complex. A generally broader spectral width for the A₁ mode than the E mode is believed to be partially due to vibrational lifetime effect. Vibrational mode-dependent diagonal anharmonicity was observed in transient infrared spectra, with a generally smaller anharmonicity found for the E mode in both the Mn and Re complexes.     

Dipeptide structure determination by vibrational circular dichroism combined with quantum chemistry calculations.

The solution structure and the local solvation environments of alanine dipeptide (AD, 1 a) and its isotopomer (AD*, 1 b, 13C on the acetyl end C==O) are studied by using infrared (IR) spectroscopy and vibrational circular dichroism (VCD). From the amide I IR spectra of AD* in various protic solvents, it is found that each of the two carbonyl groups is fully H-bonded to two water molecules. However, the number of alcohol molecules H-bonded to each C==O varies from one to two, and the local solvation environments are asymmetric around the two peptides of AD* in alcohol solutions. The amide I VCD spectra of AD and AD* in D2O are also measured, and a series of density functional theory (DFT, B3LYP/6-311++G**) calculations are performed to obtain the amide I normal-mode rotational strengths of AD and the intrinsic rotational strengths of its two peptide fragments. By combining the VCD-measurement and DFT-calculation results and employing a coupled oscillator theory, we show that the aqueous-solution structure of the dipeptide can be determined. We believe that the present method will be of use in building up a library of dipeptide solution structures in water.     

Infrared spectroscopic study of the interactions of nylon‐6 with water

We studied the interactions of nylon‐6 with water by following the Fourier transform infrared spectra of a hydrated thin film during dehydration. Very small changes in the spectra caused by the interactions were clearly revealed by the application of spectral subtraction. The water was found to interact with amide groups to form hydrogen bonds with non‐hydrogen‐bonded or free C?O and NH groups in the amorphous portion in the first hydration sphere. This was deduced from an analysis of minus and plus peaks appearing around the absorptions of the NH stretching, amide I band, and amide II bands in the difference spectra between the spectra during dehydration and the one at the most dehydration. The interactions of the amide groups with water were significantly stronger than the hydrogen bond between CO and NH in the crystalline portion, according to the magnitude of the frequency shift of relevant bands. Water, as the interacting counterpart, showed a distorted OH stretching absorption with two close peaks at about 3450 cm^?1. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 1722–1729, 2003     

Solvation dynamics of the electron produced by two-photon ionization of liquid polyols. 1. Ethylene glycol

Solvated electrons have been produced in ethylene glycol by two-photon ionization of the solvent with 263 nm femtosecond laser pulses. The two-photon absorption coefficient of ethylene glycol at 263 nm is determined to be beta = (2.1 +/- 0.2) x 10(-11) m W(-1). The dynamics of electron solvation in ethylene glycol has been studied by pump-probe transient absorption spectroscopy. So, time-resolved absorption spectra ranging from 430 to 710 nm have been measured. A blue shift of the spectra is observed for the first tens of picoseconds. Using the Bayesian data analysis method, the observed solvation dynamics are reconstructed with different models: stepwise mechanisms, continuous relaxation models, or combinations of stepwise and continuous relaxation. Comparison between models is in favor of continuous relaxation, which is mainly governed by solvent molecular motions.     

Self-trapping of the N-H vibrational mode in alpha-helical polypeptides

Recent calculations on the formation of self-trapped amide group vibrational states in alpha-helical polypeptides [J. Chem. Phys. 124, 134907 (2006)] are extended to the amide N-H normal mode vibrations. First, the adiabatic N-H vibrational single- and two-exciton states are examined by treating the longitudinal chain coordinates as parameters. Then, in using the multiconfiguration time-dependent Hartree method coupled exciton-chain vibrational quantum dynamics are accounted for. Based on the respective exciton-chain vibrational wave function propagation the infrared transient absorption related to a sequential pump-probe experiment is calculated. The modulation of local amide vibrational energies by the longitudinal chain coordinates is found to have a pronounced effect on the broadening of absorption lines. Moreover, the ultrafast exciton transfer in the system is studied in order to characterize the dynamics of the self-trapped single-exciton states on a time scale below 10 ps.     

Infrared spectroscopic study of molecular interaction of tacticity-controlled poly(N-isopropylacrylamide) in a cast film deposited on a solid substrate

Analytical results of a series of poly(N-isopropylacrylamide) (PNiPA) with different tacticities using infrared spectroscopy are presented for studying the influence of the solvation and molecular interactions between the polymeric chains. Infrared spectra of solid matter samples of the compounds exhibit a systematic band intensity change for three band components at 1,680, 1,659, and 1,628 cm⁻¹ involved in the amide I band. The three components correspond to the free, half, and full hydrogen bondings of the secondary amide group, which reflect the molecular configuration depending on the tacticity. When cast films of the compounds prepared on a solid surface are analyzed by infrared transmission spectrometry, another factor of the solvent used for the film preparation is found to be another factor which plays an important role in determining the molecular architecture in the films. This molecular imprint mechanism after the solvation is confirmed by measuring infrared multiple-angle incidence resolution spectra of annealed films. The molecular interactions in the polymeric samples have been revealed by the use of infrared spectroscopy and the tacticity-controlled samples.     

The Solvent‐Dependent Shift of the Amide I Band of a Fully Solvated Peptide as a Local Probe for the Solvent Composition in the Peptide/Solvent Interface

We determine the shift and line shape of the amide I band of a model AK peptide from molecular dynamics (MD) simulations of the peptide dissolved in methanol/water mixtures with varying composition. The IR spectra are determined from a transition dipole coupling exciton model. A simplified empirical model Hamiltonian is employed, which takes into account both the effect of hydrogen bonding and the intramolecular vibrational coupling. We consider a single isolated AK peptide in a mostly helical conformation, while the solvent is represented by 2600 methanol or water molecules, simulated for a pressure of 1 bar and a temperature of 300 K. Over the course of the simulations, minor reversible conformational changes at the termini are observed, which are found to only slightly affect the calculated spectral properties. Over the entire composition range, which varies from pure water to the pure methanol solvent, a monotonous shift towards higher frequency of the IR amide I band of about 8 wavenumbers is observed. This shift towards higher frequency is comparable to the shift found in preliminary experimental data also presented here on the amide I′ band. The shift is found to be caused by two counter‐compensating effects. An intramolecular red shift of about 1.2 wavenumbers occurs, due to stronger intramolecular hydrogen bonding in a methanol‐rich environment. Dominating, however, is the intermolecular solvent‐dependent shift towards higher frequency of about 10 wavenumbers, which is attributed to the less effective hydrogen‐bond‐donor capabilities of methanol compared to water. The importance of the solvent contribution to the IR shift, as well as the significantly different hydrogen formation capabilities of water and methanol, makes the amide I band sensitive to composition changes in the local environment close to the peptide/solvent interface. This allows, in principle, an experimental determination of the composition of the solvent in close proximity to the peptide surface. For the AK peptide case, we observe at low methanol concentrations a significantly enhanced methanol concentration at the peptide/solvent interface, supposedly promoted by the partially hydrophobic character of the AK peptide’s solvent‐accessible surface.     

Coherent two-dimensional infrared spectroscopy: quantitative analysis of protein secondary structure in solution

We present a method to quantitatively determine the secondary structure composition of globular proteins using coherent two-dimensional infrared (2DIR) spectroscopy of backbone amide I vibrations (1550-1720 cm(-1)). Sixteen proteins with known crystal structures were used to construct a library of 2DIR spectra, and the fraction of residues in α-helix, β-sheet, and unassigned conformations was determined by singular value decomposition (SVD) of the measured two-dimensional spectra. The method was benchmarked by removing each individual protein from the set and comparing the composition extracted from 2DIR against the composition determined from the crystal structures. To highlight the increased structural content extracted from 2DIR spectra a similar analysis was also carried out using conventional infrared absorption of the proteins in the library.     

FTIR studies of collagen model peptides: complementary experimental and simulation approaches to conformation and unfolding

X-ray crystallography of collagen model peptides has provided high-resolution structures of the basic triple-helical conformation and its water-mediated hydration network. Vibrational spectroscopy provides a useful bridge for transferring the structural information from X-ray diffraction to collagen in its native environment. The vibrational mode most useful for this purpose is the amide I mode (mostly peptide bond C=O stretch) near 1650 cm-1. The current study refines and extends the range of utility of a novel simulation method that accurately predicts the infrared (IR) amide I spectral contour from the three-dimensional structure of a protein or peptide. The approach is demonstrated through accurate simulation of the experimental amide I contour in solution for both a standard triple helix, (Pro-Pro-Gly)10, and a second peptide with a Gly --> Ala substitution in the middle of the chain that models the effect of a mutation in the native collagen sequence. Monitoring the major amide I peak as a function of temperature gives sharp thermal transitions for both peptides, similar to those obtained by circular dichroism spectroscopy, and the Fourier transform infrared (FTIR) spectra of the unfolded states were compared with polyproline II. The simulation studies were extended to model early stages of thermal denaturation of (Pro-Pro-Gly)10. Dihedral angle changes suggested by molecular dynamics simulations were made in a stepwise fashion to generate peptide unwinding from each end, which emulates the effect of increasing temperature. Simulated bands from these new structures were then compared to the experimental bands obtained as temperature was increased. The similarity between the simulated and experimental IR spectra lends credence to the simulation method and paves the way for a variety of applications.     

氯化钙甲醇溶液中离子溶剂化作用的理论研究

利用红外光谱研究不同温度下CaCl2/甲醇溶液体系的溶剂化作用,结果表明在溶液中CaCl2以离子形式与甲醇发生溶剂化作用,且溶剂化数随温度升高而降低.通过密度泛函理论（DFT）在B3LYP/6-31G＊＊水平下对CaCl2/甲醇溶液中可能存在的配位构型进行结构优化及热力学性质的计算,说明了在CaCl2/甲醇溶液中各种配位构型存在的可能性,得出温度升高热力学数据的变化规律,解释了溶剂化数随温度升高而降低的趋势.进一步对各种可能配位构型的红外吸收频率进行计算并与实验结果进行比较,推断在CaCl2/甲醇溶液中主要存在的配位构型为[CaCl（CH3OH）n]＋和[Cl（CH3OH）n]-.