Vibrational spectroscopy of protonated imidazole and its complexes with water molecules: ab initio anharmonic calculations and experiments

The results of anharmonic frequency calculations on neutral imidazole (C3N2H4, Im), protonated imidazole (ImH+), and its complexes with water (ImH+)(H2O)n, are presented and compared to gas phase infrared photodissociation spectroscopy (IRPD) data. Anharmonic frequencies are obtained via ab initio vibrational self-consistent field (VSCF) calculations taking into account pairwise interactions between the normal modes. The key results are: (1) Prediction of anharmonic vibrational frequencies on an MP2 ab initio potential energy surface show excellent agreement with experiment and outstanding improvement over the harmonic frequencies. For example, the ab initio calculated anharmonic frequency for (ImH+)(H2O)N2 exhibits an overall average percentage error of 0.6% from experiment. (2) Anharmonic vibrational frequencies calculated on a semiempirical potential energy surface fitted to ab initio harmonic data represents spectroscopy well, particularly for water complexes. As an example, anharmonic frequencies for (ImH+)H2O and (ImH+)(H2O)2 show an overall average deviation of 1.02% and 1.05% from experiment, respectively. This agreement between theory and experiment also supports the validity and use of the pairwise approximation used in the calculations. (3) Anharmonic coupling due to hydration effects is found to significantly reduce the vibrational frequencies for the NH stretch modes. The frequency of the NH stretch is observed to increase with the removal of a water molecule or replacement of water with N2. This result also indicates the ability of the VSCF method to predict accurate frequencies in a matrix environment. The calculation provides insights into the nature of anharmonic effects in the potential surface. Analysis of percentage anharmoncity in neutral Im and ImH+ shows a higher percentage anharmonicity in the NH and CH stretch modes of neutral Im. Also, we observe that anharmonicity in the NH stretch modes of ImH+ have some contribution from coupling effects, while that of neutral Im has no contribution whatsoever from mode-mode coupling. It is concluded that the incorporation of anharmonic effects in the calculation brings theory and experiment into much closer agreement for these systems.     

Vibrational spectroscopy of the G...C base pair: experiment, harmonic and anharmonic calculations, and the nature of the anharmonic couplings

The results of harmonic and anharmonic frequency calculations on a guanine-cytosine complex with an enolic structure (a tautomeric form with cytosine in the enol form and with a hydrogen at the 7-position on guanine) are presented and compared to gas-phase IR-UV double resonance spectral data. Harmonic frequencies were obtained at the RI-MP2/cc-pVDZ, RI-MP2/TZVPP, and semiempirical PM3 levels of electronic structure theory. Anharmonic frequencies were obtained by the CC-VSCF method with improved PM3 potential surfaces; the improved PM3 potential surfaces are obtained from standard PM3 theory by coordinate scaling such that the improved PM3 harmonic frequencies are the same as those computed at the RI-MP2/cc-pVDZ level. Comparison of the data with experimental results indicates that the average absolute percentage deviation for the methods is 2.6% for harmonic RI-MP2/cc-pVDZ (3.0% with the inclusion of a 0.956 scaling factor that compensates for anharmonicity), 2.5% for harmonic RI-MP2/TZVPP (2.9% with a 0.956 anharmonicity factor included), and 2.3% for adapted PM3 CC-VSCF; the empirical scaling factor for the ab initio harmonic calculations improves the stretching frequencies but decreases the accuracy of the other mode frequencies. The agreement with experiment supports the adequacy of the improved PM3 potentials for describing the anharmonic force field of the G...C base pair in the spectroscopically probed region. These results may be useful for the prediction of the pathways of vibrational energy flow upon excitation of this system. The anharmonic calculations indicate that anharmonicity along single mode coordinates can be significant for simple stretching modes. For several other cases, coupling between different vibrational modes provides the main contribution to anharmonicity. Examples of strongly anharmonically coupled modes are the symmetric stretch and group torsion of the hydrogen-bonded NH2 group on guanine, the OH stretch and torsion of the enol group on cytosine, and the NH stretch and NH out-of-plane bend of the non-hydrogen-bonded NH group on guanine.     

Vibrational assignment of the 4-hydroxycinnamyl chromophore in photoactive yellow protein

Photoactive yellow protein (PYP) is a bacterial photoreceptor containing a 4-hydroxycinnamyl chromophore. We report the Raman spectra for the dark state of PYP whose chromophore is isotopically labeled with 13C at the carbonyl carbon atom or at the ring carbon atoms. Spectra have been also measured with PYP in D2O where the exchangeable protons are deuterated. Most of the observed Raman bands are assigned on the basis of the observed isotope shifts and normal mode calculations using a density functional theory. We discuss the implication for the analysis of the infrared spectra of PYP. The comprehensive assignment provides a satisfactory framework for future investigations of the photocycle mechanism in PYP by vibrational spectroscopy.     

Photoinduced isomerization of the photoactive yellow protein (PYP) chromophore: interplay of two torsions, a HOOP mode and hydrogen bonding

We report on a detailed theoretical analysis, based on extensive ab initio calculations at the CC2 level, of the S(1) potential energy surface (PES) of the photoactive yellow protein (PYP) chromophore. The chromophore's photoisomerization pathway is shown to be fairly complex, involving an intimate coupling between single-bond and double-bond torsions. Furthermore, these torsional modes are shown to couple to a third coordinate of hydrogen out-of-plane (HOOP) type whose role in the isomerization is here identified for the first time. In addition, it is demonstrated that hydrogen bonding at the phenolate moiety of the chromophore can hinder the single-bond torsion and thus facilitates double-bond isomerization. These results suggest that the interplay between intramolecular factors and H-bonding determines the isomerization in native PYP.     

Structural evolution of the chromophore in the primary stages of trans/cis isomerization in photoactive yellow protein

We have studied the structural changes induced by optical excitation of the chromophore in wild-type photoactive yellow protein (PYP) in liquid solution with a combined approach of polarization-sensitive ultrafast infrared spectroscopy and density functional theory calculations. We identify the nuC8-C9 marker modes for solution phase PYP in the P and I0 states, from which we derive that the first intermediate state I0 that appears with a 3 ps time constant can be characterized to have a cis geometry. This is the first unequivocal demonstration that the formation of I0 correlates with the conversion from the trans to the cis state. For the P and I0 states we compare the experimentally measured vibrational band patterns and anisotropies with calculations and find that for both trans and cis configurations the planarity of the chromophore has a strong influence. The C7=C8-(C9=O)-S moiety of the chromophore in the dark P state has a trans geometry with the C=O group slightly tilted out-of-plane, in accordance with the earlier reported structure obtained in an X-ray diffraction study of PYP crystals. In the case of I0, experiment and theory are only in agreement when the C7=C8-(C9=O)-S moiety has a planar configuration. We find that the carboxylic side group of Glu46 that is hydrogen-bonded to the chromophore phenolate oxygen does not alter its orientation on going from the electronic ground P state, via the electronic excited P state to the intermediate I0 state, providing conclusive experimental evidence that the primary stages of PYP photoisomerization involve flipping of the enone thioester linkage without significant relocation of the phenolate moiety.     

Electronic structure of the PYP chromophore in its native protein environment

We report on supermolecular ab initio calculations which clarify the role of the local amino acid environment in determining the unique electronic structure properties of the photoactive yellow protein (PYP) chromophore. The extensive ab initio calculations, at the level of the CC2 and EOM-CCSD methods, allow us to explicitly address how the interactions between the deprotonated p-coumaric thio-methyl ester (pCTM-) chromophore and the surrounding amino acids act together to create a specifically stabilized pCTM- species. Particularly noteworthy is the role of the Arg52 amino acid in stabilizing the chromophore against autoionization, and the role of the Tyr42 and Glu46 amino acids in determining the hydrogen-bonding properties that carry the dominant energetic effects.     

Vibrational assignment of the normal modes of 2-phenyl-4-(4-methoxy benzylidene)-2-oxazolin-5-one via FTIR and Raman spectra, and ab inito calculations

Raman and FTIR spectra of 2-phenyl-4-(4-methoxy benzylidene)-2-oxazolin-5-one were recorded in the regions, 100-3300 and 400-4000 cm(-1), respectively. Vibrational frequencies and intensities of the fundamental modes of this hetrocyclic organic molecule were computed using ab initio as well as AM1 semiempirical molecular orbital methods. Ab initio calculations were carried out with basis set up to RHF/6-311G. Conformational studies regarding the effect of moving the methoxy group in the 2-phenyl-4-(4-methoxy benzylidene)-2-oxazolin-5-one molecule to a different position on the ring was also carried out. Observed vibrational wavenumbers were found to be mostly consistent with ab initio values. The most intense mode of vibration observed at 1250 cm(-1) in Raman spectra, also observed as a strong band in FTIR, was assigned as C-O stretching vibration in the methoxy group. Asymmetric stretching vibrations between CC and CN bonds was predicted as most intense mode by our ab initio calculation.     

Chain-length and mode-delocalization dependent amide-I anharmonicity in peptide oligomers

The diagonal anharmonicities of the amide-I mode in the alanine oligomers are examined in the normal-mode basis by ab initio calculations. The selected oligomers range from dimer to heptamer, in either the α-helical or β-sheet conformations. It is found that the anharmonicity varies from mode to mode within the same oligomer. For a given amide-I mode, the anharmonicity is closely related to the delocalization extent of the mode: the less it delocalizes, the larger the anharmonicity it has. Thus, the single-mode potential energy distribution (PED(max)) can be used as an indicator of the magnitude of the anharmonicity. It is found that as the peptide chain length increases, the averaged diagonal anharmonicity generally decreases; however, the sum of the averaged diagonal and off-diagonal anharmonicities within a peptide roughly remains a constant for all the oligomers examined, indicating the excitonic characteristics of the amide-I modes. Excitonic coupling tends to decrease the diagonal anharmonicities in a coupled system with multiple chromophores, which explains the observed behavior of the anharmonicities. The excitonic nature of the amide-I band in peptide oligomers is thus verified by the anharmonic computations. Isotopic substitution effect on the anharmonicities and mode localizations of the amide-I modes in peptides is also discussed.     

Kinetic isotope effects for Cl + CH4 ⇌ HCl + CH3 calculated using ab initio semiclassical transition state theory

Calculations were carried out for 25 isotopologues of the title reaction for various combinations of (35)Cl, (37)Cl, (12)C, (13)C, (14)C, H, and D. The computed rate constants are based on harmonic vibrational frequencies calculated at the CCSD(T)/aug-cc-pVTZ level of theory and X(ij) vibrational anharmonicity coefficients calculated at the CCSD(T) /aug-cc-pVDZ level of theory. For some reactions, anharmonicity coefficients were also computed at the CCSD(T)/aug-cc-pVTZ level of theory. The classical reaction barrier was taken from Eskola et al. [J. Phys. Chem. A 2008, 112, 7391-7401], who extrapolated CCSD(T) calculations to the complete basis set limit. Rate constants were calculated for temperatures from ～100 to ～2000 K. The computed ab initio rate constant for the normal isotopologue is in good agreement with experiments over the entire temperature range (～10% lower than the recommended experimental value at 298 K). The ab initio H/D kinetic isotope effects (KIEs) for CH(3)D, CH(2)D(2), CHD(3), and CD(4) are in very good agreement with literature experimental data. The ab initio (12)C/(13)C KIE is in error by ～2% at 298 K for calculations using X(ij) coefficients computed with the aug-cc-pVDZ basis set, but the error is reduced to ～1% when X(ij) coefficients computed with the larger aug-cc-pVTZ basis set are used. Systematic improvements appear to be possible. The present SCTST results are found to be more accurate than those from other theoretical calculations. Overall, this is a very promising method for computing ab initio kinetic isotope effects.     

The infrared spectrum of Au-.CO2

The Au-.CO2 ion-molecule complex has been studied by gas phase infrared photodissociation spectroscopy. Several sharp transitions can be identified as combination bands involving the asymmetric stretch vibrational mode of the CO2 ligand. Their frequencies are redshifted by several hundred cm(-1) from the frequencies of free CO2. We discuss our findings in the framework of ab initio and density-functional theory calculations, using anharmonic corrections to predict vibrational transition energies. The infrared spectrum is consistent with the formation of an aurylcarboxylate anion with a strongly bent CO2 subunit.     

Vibronic spectroscopy of the peroxyacetyl radical in the near IR

The A 2A'<--X 2A" electronic transition of the peroxyacetyl radical (PA) is observed employing NIR/VUV ion enhancement, supersonic jet spectroscopy. Rotational envelope simulations yield a rotational temperature for ground state PA of ca. 55 K. Ab initio calculations of transition energies and vibrational frequencies for the A<--X transition assist in the assignment of the observed spectrum. A number of the vibrational modes of the A state are assigned to observed transitions (the O-O stretch 2(1), the COO bend 5(1), and the CCOO backbone bend 6(1)). The calculations and mass spectra suggest that the ground state of the PA ion is repulsive. An increase in rotational linewidth of the overtone of the O-O stretch (2(1)) is observed and discussed in terms of A state dynamics. The O-O stretch anharmonicity is estimated to be 13.35 cm(-1).     

Theoretical investigation of the structure and vibrational spectra of carbamoyl azide

Molecular structure and vibrational frequencies of carbamoyl azide NH2CO-NNN have been investigated with ab initio and density functional theory (DFT) methods. The molecular geometries for all the possible conformers of the molecule were optimized using DFT-B3LYP, DFT-BLYP and MP2 applying the standard 6-311++G** basis set. From the calculations, the molecule was predicted to exist predominantly in cis conformation with the cis-trans rotational barrier of about 7.91-9.10 kcal/mol depending on the level of theory applied. The vibrational frequencies and the corresponding vibrational assignments of carbamoyl azide in Cs symmetry were examined theoretically and the calculated Infrared and Raman spectra of the molecule in the cis conformation were plotted. Observed frequencies for normal modes were compare with those calculated from normal mode coordinate analysis carried out on the basis of ab initio and DFT force fields using the standard 6-311++G** basis set of the theoretical optimized geometry. Theoretical IR intensities and Raman activities are reported.     

Ab initio prediction of the vibrational spectrum of the hydrogen bonded complex O2N...HONO2

The changes in the structural parameters and vibrational characteristics (vibrational frequencies, infrared intensities and Raman activities) arising from the hydrogen bonding between NO(2) and HONO(2) have been studied employing ab initio 6-31G(d, p)/UHF and 6-31+G(d, p)/UHF, and B3LYP/6-31G(d, p) calculations. The charge rearrangement upon hydrogen bonding have been, estimated using the Mulliken population analyses. It was established that the complexation between NO(2) and HONO(2) leads to changes in the structural parameters and the vibrational characteristics of the monomers. The most sensitive to the hydrogen bond formation are the vibrational characteristics of the normal modes of the monomer bonds participating in the hydrogen bonding. The predicted shifts in the vibrational frequencies by ab initio and B3LYP/6-31G(d, p) calculations are in very good agreement with the experimentally observed, which is an evidence for the reliance of the studied structure.     

Anharmonic vibrational probe for N-methylacetamide in different micro-environments

In the present study, anharmonic vibrational properties of the amide modes in N-methylacetamide (NMA), a model molecule for peptide vibrational spectroscopy, are examined by DFT calculations. The 3N-6 normal mode frequencies, diagonal and off-diagonal anharmonicities are evaluated by means of the second order vibrational perturbation theory (VPT2). Good performance of B3LYP/6-31+G** is found for predicting vibrational frequencies in comparison with gas phase experimental data. The amide vibrational modes are assigned through potential energy distribution analysis (PED). The solvation effect on the amide vibrational modes is modeled within the PCM method. From gas phase to polar solvents, red shifts are observed for both harmonic and anharmonic vibrational frequency of amide I mode while the CO bond length increases upon the solvent polarity. Cubic and quartic force constants are further calculated to evaluate the origin of the anharmonicity for the amide I mode of NMA in different micro-environments.     

Constrained dynamics and extraction of normal modes from ab initio molecular dynamics: application to ammonia

We present a methodology for extracting phonon data from ab initio Born-Oppenheimer molecular dynamics calculations of molecular crystals. Conventional ab initio phonon methods based on perturbations are difficult to apply to lattice modes because the perturbation energy is dominated by intramolecular modes. We use constrained molecular dynamics to eliminate the effect of bond bends and stretches and then show how trajectories can be used to isolate and define in particular, the eigenvalues and eigenvectors of modes irrespective of their symmetry or wave vector. This is done by k-point and frequency filtering and projection onto plane wave states. The method is applied to crystalline ammonia: the constrained molecular dynamics allows a significant speed-up without affecting structural or vibrational modes. All Gamma point lattice modes are isolated: the frequencies are in agreement with previous studies; however, the mode assignments are different.     

Role of hydrogen-bond network in energy storage of bacteriorhodopsin's light-driven proton pump revealed by ab initio normal-mode analysis

Vibrational modes of the hydrogen-bond network in the binding site of bacteriorhodopsin (bR), a protein in halobacteria functioning as a light-driven proton pump, were investigated by an ab initio quantum mechanical/molecular mechanical (QM/MM) method. Normal-mode analysis calculations for O-D and N-D stretching modes of internal water molecules and the Schiff base of the retinal chromophore in the early intermediate state, K, reproduced well experimentally observed vibrational spectra. Supported by agreement with observed spectra, the QM/MM calculation suggests that weakened hydrogen bonds upon photoisomerization of the chromophore are an important means of energy storage in bR.     

On assignment of fundamental vibrational modes of hypophosphite anion and its deuterated analogue

Results of ab initio and density functional theory calculations on the structure and vibrational frequencies of hypophosphite anion indicate earlier experimental assignments of the fundamental vibrational modes are correct while the recent reassignments of several modes proposed by Bickley et al. are inconsistent with the calculated results.     

Simulations of vibrational spectra from classical trajectories: calibration with ab initio force fields

An algorithm allowing simulating vibrational spectra from classical time-dependent trajectories was applied for infrared absorption, vibrational circular dichroism, Raman, and Raman optical activity of model harmonic systems. The implementation of the theory within the TINKER molecular dynamics (MD) program package was tested with ab initio harmonic force fields in order to determine the feasibility for more extended MD simulations. The results suggest that sufficiently accurate frequencies can be simulated with integration time steps shorter than about 0.5 fs. For a given integration time step, lower vibrational frequencies ( approximately 0-2000 cm(-1)) could be reproduced with a higher accuracy than higher-frequency vibrational modes (e.g., O-H and C-H stretching). In principle, the algorithm also provides correct intensities for ideal systems. In applied simulations, however, the intensity profiles are affected by an unrealistic energy distribution between normal modes and a slow energy relaxation. Additionally, the energy fluctuations may cause weakening of the intensities on average. For ab initio force fields, these obstacles could be overcome by an arbitrary normal mode energy correction. For general MD simulations, averaging of many shorter MD trajectories started with randomly distributed atomic velocities provided the best spectral shapes. alpha-pinene, D-gluconic acid, formaldehyde dimer, and the acetylprolineamide molecule were used in the tests.     

Vibrational spectroscopy of (SO4(2-)).(H2O)n clusters, n=1-5: harmonic and anharmonic calculations and experiment

The vibrational spectroscopy of (SO4(2-)).(H2O)n is studied by theoretical calculations for n=1-5, and the results are compared with experiments for n=3-5. The calculations use both ab initio MP2 and DFT/B3LYP potential energy surfaces. Both harmonic and anharmonic calculations are reported, the latter with the CC-VSCF method. The main findings are the following: (1) With one exception (H2O bending mode), the anharmonicity of the observed transitions, all in the experimental window of 540-1850 cm(-1), is negligible. The computed anharmonic coupling suggests that intramolecular vibrational redistribution does not play any role for the observed linewidths. (2) Comparison with experiment at the harmonic level of computed fundamental frequencies indicates that MP2 is significantly more accurate than DFT/B3LYP for these systems. (3) Strong anharmonic effects are, however, calculated for numerous transitions of these systems, which are outside the present observation window. These include fundamentals as well as combination modes. (4) Combination modes for the n=1 and n=2 clusters are computed. Several relatively strong combination transitions are predicted. These show strong anharmonic effects. (5) An interesting effect of the zero point energy (ZPE) on structure is found for (SO4(2-)).(H2O)(5): The global minimum of the potential energy corresponds to a C(s) structure, but with incorporation of ZPE the lowest energy structure is C2v, in accordance with experiment. (6) No stable structures were found for (OH-).(HSO4-).(H2O)n, for n相似文献   

Accurate equilibrium structures obtained from gas-phase electron diffraction data: sodium chloride

A novel method has been developed to allow the accurate determination of equilibrium gas-phase structures from experimental data, thus allowing direct comparison with theory. This new method is illustrated through the example of sodium chloride vapor at 943 K. Using this approach the equilibrium structures of the monomer (NaCl) and the dimer (Na(2)Cl(2)), together with the fraction of vapor existing as dimer, have been determined by gas-phase electron diffraction supplemented with data from microwave spectroscopy and ab initio calculations. Root-mean-square amplitudes of vibration (u) and distance corrections (r(a) - r(e)) have been calculated explicitly from the ab initio potential-energy surfaces corresponding to the vibrational modes of the monomer and dimer. These u and (r(a) - r(e)) values essentially include all of the effects associated with large-amplitude modes of vibration and anharmonicity; using them we have been able to relate the ra distances from a gas-phase electron diffraction experiment directly to the re distances from ab initio calculations. Vibrational amplitudes and distance corrections are compared with those obtained by previous methods using both purely harmonic force fields and those including cubic anharmonic contributions, and the differences are discussed. The gas-phase equilibrium structural parameters are r(e)(Na-Cl)(monomer) = 236.0794(4) pm; r(e)(Na-Cl)(dimer) = 253.4(9) pm; and <(e)ClNaCl = 102.7(11) degrees. These results are found to be in good agreement with high-level ab initio calculations and are substantially more precise than those obtained in previous structural studies.