Transition Dipole Coupling Mechanism Research Articles

Amide I Infrared Spectral Features Characteristic of Some Untypical Conformations Appearing in the Structures Suggested for Amyloids

Amide I infrared (IR) spectral features are studied, by using the density functional theoretical method, for two untypical (but possibly rather prevalent) structures inspired from those recently suggested for amyloids: a structure consisting of loop regions in the (alpha L, alpha R) conformation stacked to form an alpha-sheet, and a structure involving some main-chain peptide groups (of any residues) and some side-chain amide groups of glutamine and asparagine residues closely located with each other. The amide I vibrational (off-diagonal) coupling constants are examined by extracting them from the calculated Cartesian-based force constants with the average partial vector method and by comparing them with those estimated on the basis of the transition dipole coupling mechanism. It is suggested that the amide I IR band characteristic of the alpha-sheet conformation in dry environment (without hydrogen bonding to solvent water molecules) is located in a high-frequency region (approximately >1670 cm(-1), somewhat higher than that of alpha-helix), because of the dependence of the diagonal (uncoupled) frequency and the off-diagonal coupling constant on the Phi and Psi dihedral angles. It is also shown that the amide I vibrations of the closely located peptide and amide groups are strongly coupled through-space with each other, and in the presence of this type of strong vibrational coupling, a noticeable change in the IR intensity upon (13)C=O substitution may occur even for a mode that arises mainly from an unsubstituted group and is not much shifted in frequency. The meaning of these results in the interpretation of observed amide I spectral profiles, especially the possible usefulness of IR spectroscopic measurements for detecting those untypical structures in the process of amyloid formation, is also discussed.

Influence of Ions on the Structural Organization of Dipolar Liquids Probed by the Noncoincidence Effect: Experimental and Quantum Chemical Results

The C=O stretching [nu(C=O)] Raman bands of the carbonyl solvents, S (acetone and acetophenone), in some electrolytic solutions of lithium and sodium salts (M(+)X(-)) are analyzed. The large and negative values of the noncoincidence effect (NCE=nu(ani)-nu(iso)) measured for the component of this band generated by the solvent-ion interactions are interpreted in the light of the results of ab initio quantum chemical calculations performed for clusters of type (S)nM(+) and also on the basis of the transition dipole coupling mechanism between pairs of nu(C=O) oscillators. The effects of the size of the ion M(+) and of the solvation number n on the NCE are analyzed. It is shown that the decrease of the NCE resulting from the change in the size of the ion M(+) from Li(+) to Na(+) is appreciably counterbalanced by the increase of the NCE arising form the change in the ion solvation number n from 4 for Li(+) to 6 for Na(+).

Simultaneous photon absorption as a probe of molecular interaction and hydrogen-bond cooperativity in liquids

We have investigated the simultaneous absorption of near-infrared photons by pairs of neighboring molecules in liquid methanol. Simultaneous absorption by two OH-stretching modes is found to occur at an energy higher than the sum of the two absorbing modes. This frequency shift arises from interaction between the modes, and its value has been used to determine the average coupling between neighboring methanol molecules. We find a rms coupling strength of 46+/-1 cm(-1), larger than can be explained from a transition-dipole coupling mechanism, suggesting that hydrogen-bond mediated interactions also contribute to the coupling. The most important aspect of simultaneous vibrational absorption is that it allows for a quantitative investigation of hydrogen-bond cooperativity. We derive the extent to which the hydrogen-bond strengths of neighboring molecules are correlated by comparing the line shape of the absorption band caused by simultaneous absorption with that of the fundamental transition. Surprisingly, neighboring hydrogen bonds in methanol are found to be strongly correlated, and from the data we obtain an estimate for the hydrogen-bond correlation coefficient of 0.69+/-0.12.

Time-Domain Calculations of the Polarized Raman Spectra, the Transient Infrared Absorption Anisotropy, and the Extent of Delocalization of the OH Stretching Mode of Liquid Water

The polarized Raman spectrum and the time dependence of the transient infrared (TRIR) absorption anisotropy are calculated for the OH stretching mode of liquid water (neat liquid H2O) by using time-domain formulations, which include the effects of both the diagonal frequency modulations (of individual oscillators) induced by the interactions between the dipole derivatives and the intermolecular electric field, and the off-diagonal (intermolecular) vibrational coupling described by the transition dipole coupling (TDC) mechanism. The IR spectrum of neat liquid H2O and the TRIR anisotropy of a liquid mixture of H2O/HDO/D2O are also calculated. It is shown that the calculated features of these optical signals, including the temperature dependence of the polarized Raman and IR spectra, are in reasonable agreement with the experimental results, indicating that the frequency separation between the isotropic and anisotropic components of the polarized Raman spectrum and the rapid decay (approximately 0.1 ps) of the TRIR anisotropy of the OH stretching mode of neat liquid H2O are mainly controlled by the resonant intermolecular vibrational coupling described by the TDC mechanism. Comparing with the time evolution of vibrational excitations, it is suggested that the TRIR anisotropy decays in the time needed for the initially localized vibrational excitations to delocalize over a few oscillators. It is also shown that the enhancement of the dipole derivatives by the interactions with surrounding molecules is an important factor in generating the spectral profiles of the OH stretching Raman band. The time-domain behavior of the molecular motions that affect the spectroscopic features is discussed.

Ultrafast anisotropy decay of coherent excitations and the non-coincidence effect for delocalized vibrational modes in liquids

The relation between the ultrafast anisotropy decay of coherent vibrational excitations and the non-coincidence effect of vibrational bands is examined theoretically. A Stockmayer fluid with a one-dimensional oscillator buried in each particle is used as a model liquid system. It is shown that delocalization of vibrational modes with a set of transition dipole coupling parameters typical of the OH stretching modes gives rise to an ultrafast decay of transient absorption anisotropy and a large magnitude of the non-coincidence effect. The relation with the widths of the vibrational bands due to the transition dipole coupling mechanism is also discussed.

Raman study of intramolecular frequency noncoincidence effect in dialkyl benzenedicarboxylates

Raman noncoincidence effects (NCE) of the C=O stretching band of dialkyl esters of benzenedicarboxylic (phthalic, isophthalic, and terephthalic) acids were measured as a function of concentration in acetonitrile and dioxane solutions. By quenching the intermolecular vibrational interactions between the C=O groups of neighboring molecules by dilution, the NCE arising from the coupling between two C=O stretching vibrations in a single molecule of the diesters was observed for the first time. The intramolecular NCE values for these molecules were negative and dependent on the relative orientation and distance between two C=O groups in a molecule. Similarly as for most intermolecular NCE, the intramolecular NCE is explained by the transition dipole coupling mechanism. The presence of a single dipolar coupling pair allows one to express the intramolecular NCE values by a simple analytical equation with a few molecular parameters including those for the arrangement of two C=O groups in a molecule. The observed intramolecular NCE values are well predicted, with a limitation of large dipolar distance, by the equation with the geometric parameters obtained from the ab initio optimized structures. In fact, the NCEs provided information about detailed conformational structure of the benzenedicarboxylates in dilute solutions. Since the intramolecular NCE value indeed corresponds to a frequency difference between the in-phase and out-of-phase C=O stretching normal modes of a molecule, the present result suggests that the vibrational coupling between the two C=O internal coordinates in these molecules is mainly due to the transition dipolar interaction.

Ab initio molecular orbital study of the amide I vibrational interactions between the peptide groups in di- and tripeptides and considerations on the conformation of the extended helix

Interrelationships among the coupling between the amide I vibrations of peptide groups, the A–E1 wavenumber difference of the amide I mode and the conformation of helical polypeptide chains were examined theoretically. Ab initio molecular orbital (MO) calculations were performed for a glycine dipeptide and a glycine tripeptide with various ϕ and ψ angles to obtain the coupling constants between the amide I vibrations of the nearest peptide groups and between those of the second nearest peptide groups. It was found that the coupling constants between the second nearest peptide groups were reasonably well explained by the transition dipole coupling mechanism, whereas the coupling constants between the nearest peptide groups contained other factors that mainly depended on ψ. The wavenumbers of the A and E1 components of the amide I mode were calculated for various helices on the basis of these coupling constants. The A component is strong in the infrared (IR) spectrum when the transition dipole of the amide I vibration is nearly parallel to the helix axis, whereas the E1 component has a strong IR intensity when they are nearly perpendicular to each other. The A component has a strong Raman intensity in both cases. Therefore, the Raman–infrared wavenumber difference of 10–20 cm-1 observed for the amide I bands of poly(L-glutamate) and poly(L-lysine) with charged side chains indicates that these polypeptides, in that so-called ‘extended helix’ state, have conformations giving rise to strong IR bands of the E1 component which are lower in wavenumber than the Raman bands of the A component by 10–20 cm-1. The ranges of the ϕ and ψ angles that are consistent with such spectral features are discussed on the basis of the calculated structures and amide I wavenumbers. © 1998 John Wiley & Sons, Ltd.

Ab initio molecular orbital study of the amide I vibrational interactions between the peptide groups in di- and tripeptides and considerations on the conformation of the extended helix

Interrelationships among the coupling between the amide I vibrations of peptide groups, the A–E1 wavenumber difference of the amide I mode and the conformation of helical polypeptide chains were examined theoretically. Ab initio molecular orbital (MO) calculations were performed for a glycine dipeptide and a glycine tripeptide with various ϕ and ψ angles to obtain the coupling constants between the amide I vibrations of the nearest peptide groups and between those of the second nearest peptide groups. It was found that the coupling constants between the second nearest peptide groups were reasonably well explained by the transition dipole coupling mechanism, whereas the coupling constants between the nearest peptide groups contained other factors that mainly depended on ψ. The wavenumbers of the A and E1 components of the amide I mode were calculated for various helices on the basis of these coupling constants. The A component is strong in the infrared (IR) spectrum when the transition dipole of the amide I vibration is nearly parallel to the helix axis, whereas the E1 component has a strong IR intensity when they are nearly perpendicular to each other. The A component has a strong Raman intensity in both cases. Therefore, the Raman–infrared wavenumber difference of 10–20 cm-1 observed for the amide I bands of poly(L-glutamate) and poly(L-lysine) with charged side chains indicates that these polypeptides, in that so-called ‘extended helix’ state, have conformations giving rise to strong IR bands of the E1 component which are lower in wavenumber than the Raman bands of the A component by 10–20 cm-1. The ranges of the ϕ and ψ angles that are consistent with such spectral features are discussed on the basis of the calculated structures and amide I wavenumbers. © 1998 John Wiley & Sons, Ltd.

Liquid Structure, Infrared and Isotropic/Anisotropic Raman Noncoincidence of the Amide I Band, and Low-Wavenumber Vibrational Spectra of Liquid Formamide: Molecular Dynamics and ab Initio Molecular Orbital Studies

The relationship between the liquid structure of formamide and wavenumber differences among its infrared (IR), isotropic Raman, and anisotropic Raman bands in the amide I region is analyzed theoretically. The following two methods are employed: (1) ab initio molecular orbital (MO) calculations on a few different cluster species of formamide molecules and (2) calculations of the IR and Raman spectra in the amide I region on the basis of the transition dipole coupling mechanism and the liquid structures derived from molecular dynamics simulations. It is shown that intermolecular interactions other than those involved in a one-dimensional hydrogen-bonded chain are required to reproduce the observed wavenumber difference between the amide I IR and isotropic Raman bands. This wavenumber difference originates from the difference in the vibrational patterns of the modes giving rise to these two bands. In the Raman noncoincidence, i.e., the wavenumber difference between the isotropic and anisotropic Raman bands,...

Collisional energy transfer of highly vibrationally excited NO2: The role of intramolecular vibronic coupling and the transition dipole coupling mechanism

The collisional relaxation of highly vibrationally excited NO2 has been studied for a variety of collision partners (He, Ar, CO, N2, O2, N2O, NO2, CO2, SF6, and toluene) by time-resolved Fourier transform infrared emission spectroscopy. The average energy 〈E〉 of the vibrationally excited NO2 molecules during collisional quenching was obtained from the IR spectra by modeling the ν3 and ν1+ν3 bands, using the known harmonic frequencies and anharmonicity constants. The average amount of energy lost per collision 〈ΔE〉 was determined from the 〈E〉 versus time data. The results show that there is a dramatic increase in the amount of energy transferred for all bath gases at NO2 energies above 10 000–12 000 cm−1, which is near the origin of the NO2 Ã2B2/B̃2B1 states. This threshold in the energy-transfer rate occurs because of strong vibronic coupling between the X̃2A1 and Ã2B2/B̃2B1 electronic states. The increase in vibration-to-vibration (V-V) energy transfer can be understood within the context of the transition dipole coupling model. Vibronic coupling in NO2 produces extensive broadband emission in the IR and near-IR, which enhances the V-V energy-transfer rate by relaxing the resonance conditions in dipole coupling. The V-V energy-transfer probability was calculated using the dipole coupling model, where the transition dipole moment of excited NO2 was directly extracted from the IR emission spectra. These calculations successfully reproduced the observed threshold in the V-V energy transfer probability. The transition dipole coupling model was also used to estimate the relative contribution of V-V versus vibration-to-translation, rotation (V-T,R) energy transfer for NO2 deactivation. The calculations showed that V-T,R energy transfer is the major relaxation channel for triatomic or smaller collision partners. For larger species like SF6, however, V-V energy transfer is the dominant channel. Vibronic coupling may cause an increase in the V-T,R energy-transfer rate by allowing electronic potential related terms, possibly the electronic transition dipole moment, to contribute to the matrix elements responsible for V-T,R energy transfer.

Raman Noncoincidence Effect and Intermolecular Interactions in Liquid Dimethyl Sulfoxide: Simulations Based on the Transition Dipole Coupling Mechanism and Liquid Structures Derived by Monte Carlo Method

Abstract Model calculations are performed on the Raman noncoincidence effect (frequency difference between the isotropic and anisotropic components) observed in the region of the S=O stretching band of liquid dimethyl sulfoxide (DMSO). Liquid structures are obtained by Monte Carlo simulations, by using potential functions without specific interactions involving the hydrogen atoms of the methyl groups. Intermolecular coupling between the S=O stretches is evaluated by the transition dipole coupling mechanism. The magnitude and the direction of the transition dipole are calculated by ab initio molecular orbital calculations at the second-order Møller–Plesset perturbation level with a basis set extended from 6-31G(2d,p). The calculated sign and magnitude of the Raman noncoincidence are in reasonable agreement with the observed, indicating that the observed large Raman noncoincidence can be mostly explained by the liquid structures obtained without specific interactions involving the hydrogen atoms of the methyl groups. The pair distribution function of liquid DMSO is also calculated to the second order in the orientation correlation of molecules. The origin of the Raman noncoincidence effect is discussed by comparing the cases of liquid DMSO, acetone, and methanol.

Density and temperature study of the noncoincidence effect in liquid carbon disulfide

The noncoincidence of the anisotropic and isotropic peak frequencies in the allowed Raman v 1 vibrational mode of liquid CS 2 is studied over an extended density range (1.18 to 1.58 g cm 3 ) by varying pressure (0.001 to 5.0 kbar) and temperature (−55 to 80°C). The noncoincidence value is negative and the absolute value increases as a function of both increasing density, at constant temperature, and increasing temperature, at constant density. The noncoincidence of the anisotropic and isotropic peak frequencies is attributed to a quadrupole induced transition dipole coupling mechanism because changes in the noncoincidence value can be correlated with changes in the intensity of the forbidden v 1 infrared mode.

Local order and transition dipole coupling in liquid methanol and acetone as the origin of the Raman noncoincidence effect

Model calculations are performed on the Raman noncoincidence effect (frequency difference between the isotropic and anisotropic components) observed for the C–O stretching band of liquid methanol and the C=O stretching band of liquid acetone. Microscopic liquid structures are obtained by Monte Carlo simulations, and coupling between molecular vibrations is introduced by the transition dipole coupling mechanism. Ab initio molecular orbital calculations are also performed to check the validity of the assumed direction of the transition dipole for the C–O stretching mode of methanol. The different signs of the Raman noncoincidence between the C–O stretching band of liquid methanol and the C=O stretching band of liquid acetone can be explained by the transition dipole coupling mechanism. The calculated magnitudes of the frequency separations between the isotropic and anisotropic components are in good agreement with the experimental results. Pressure dependence of the Raman noncoincidence is also calculated and compared with the experimental results. In the case of the C–O stretching band of liquid methanol, local anisotropy in the pressure-induced changes of the liquid structure is shown to be important for the pressure dependence of the Raman noncoincidence.

Model calculations on the amide-I infrared bands of globular proteins

Model calculations are performed on the amide-I infrared (ir) bands of globular proteins by assigning one oscillator with a transition dipole to each peptide group. Coupling between these oscillators is introduced through the transition dipole coupling mechanism. As examples of application of the model, the ir spectra in the amide-I region of eight representative proteins, viz., carbonmonoxy myoglobin, ribonuclease A, α-lactalbumin, lysozyme, flavodoxin, carboxypeptidase A, concanavalin A, and β-trypsin are calculated. Good agreement is obtained between the calculated and observed amide-I band envelopes. Some structure-spectrum correlations are discussed on the basis of the model calculations. The presence of bands with significant ir intensities for myoglobin in the region below 1640 cm−1 is consistent with its x-ray structure having no β sheet. Analysis of the contributions of β sheets to the amide-I band envelopes shows that parallel, antiparallel, and mixed parallel/antiparallel β sheets give rise to strong ir bands at a similar position in the wave number region below 1650 cm−1, and that no band in the region above 1650 cm−1 can be regarded as a reliable marker of antiparallel β sheets. The contributions of non-α-non-β parts spread over a wide wave number region. The differences in the amide-I band envelopes between α-lactalbumin and lysozyme originate most probably from the structural differences between the α-helical parts near the N termini of these proteins.

An infrared spectroscopic investigation of the phase behavior of a polydiacetylene. The case of polydiacetylene with side groups containing a urethane function

AbstractThe infrared spectrum of polydiacetylene with side chains containing urethane functions (1) was analyzed. Based on the polarization data and the changes observed as a function of temperature, the multiple bands in the Amide I region observed for the film sample were attributed to the transition dipole coupling mechanism. The consequences of this new assignment illustrate the difficulty in using vibrational spectroscopy as a definitive tool to characterize the relationship between structural reorganization of the side chain and the chromic transition at high temperature.