Anharmonic Analysis Research Articles

Study on vibrational relaxation dynamics of phenol–water complex by picosecond time-resolved IR-UV pump–probe spectroscopy in a supersonic molecular beam

A comparative study of vibrational energy relaxation (VER) between the monohydrated complexes of phenol-d0 and phenol-d1 is investigated in a supersonic molecular beam. The direct time-resolved measurement of energy redistribution from the phenolic OH/OD stretching mode of the phenol-d0-H2O/phenol-d1-D2O is performed by picosecond IR-UV pump–probe spectroscopy. Two complexes follow the same relaxation process that begins with the intramolecular vibrational energy redistribution (IVR) and the intermolecular vibrational energy redistribution (IVR), which is followed by the vibrational predissociation (VP). The difference in the relaxation lifetimes between them is discussed by anharmonic force field and RRKM calculations. Anharmonic analysis implies that intra- (IVR) and intermolecular (IVR) relaxations occur in parallel in the complexes. The RRKM-predicted dissociation (VP) lifetimes show qualitative agreement with the observed results, suggesting that VP takes place after the statistical energy distribution in the complexes.

Gas-phase spectroscopy and anharmonic vibrational analysis of the 3-residue peptide Z-Pro-Leu-Gly-NH2 by the laser desorption supersonic jet technique

The electronic excitation and infrared (IR) spectra of a capped tri-peptide, Z-PLG-NH2 (Z=benzyloxycarbonyl, P=Pro, L=Leu, G=Gly), were measured in the gas phase by using the laser desorption supersonic jet technique. By measuring an ultraviolet–ultraviolet hole burning spectrum, it was found that Z-PLG-NH2 has the maximum three conformers in the gas phase, but that the population is mainly distributed to a single conformation. Molecular dynamics simulations and density functional theory calculations well-reproduced the observed IR spectrum, except for splitting of the NH stretching bands by a β-turn structure that corresponds to a global minimum structure. Anharmonic vibrational analysis by vibrational quasi-degenerate perturbation theory (VQDPT) successfully reproduced the anharmonic splitting, and confirmed the assignments.

High resolution spectroscopy of several rovibronically excited bands of 5-cyanoindole – The effect of vibrational averaging

The rovibronic spectra of two bands of 5-cyanoindole at 348 and 884cm−1 have been measured and analyzed using a rigid rotor Hamiltonian. A vibrational assignment could be given on the basis of an anharmonic analysis of the vibrational spectrum of 5-cyanoindole making use of the information of the vibrationally averaged rotational constants. Strong vibronic mixing to a higher lying electronically excited state has been found.

High pressure studies on uranium and thorium silicide compounds: Experiment and theory

The actinide silicides ThSi, USi and USi2 have been studied under high pressure using both theory and experiment. High pressure synchrotron X-ray diffraction experiments were performed on polycrystalline samples in diamond anvil cells at room temperature and for pressures up to 54, 52 and 26GPa, for ThSi, USi and USi2, respectively. At ambient conditions, the uranium silicides crystallize in tetragonal structures (space groups: I4/mmm for USi and I41/amd for USi2), while ThSi adopts an orthorhombic structure (space group: Pbnm) (including an anharmonic analysis of the silicon). These structures are found to be stable with no structural transitions observed up to the highest pressures achieved. The zero-pressure bulk modulus B0 and its pressure derivative B0′ at ambient pressure are obtained from the measured P–V relations. The experiments are accompanied by first principles calculations using the full-potential linear muffin-tin orbital method within the generalized gradient approximation for exchange–correlation effects. Experimental results are well reproduced by the calculated equation of state and ground state properties.

Anharmonic vibrational studies of l-aspartic acid using HF and DFT calculations

The experimental and theoretical studies on the structure, molecular properties and vibrational spectra of l-aspartic acid are presented. The molecular structure, harmonic and anharmonic vibrational frequencies, molecular properties, MEP mapping, NBO analysis and electronic spectra of l-aspartic acid have been reported. Computed geometrical parameters and anharmonic frequencies of fundamental, combination and overtone transitions were found in satisfactory agreement with the experimental data. The UV–Vis spectrum of present molecule has been recorded and the electronic properties such as HOMO and LUMO energies and few low lying excited states were carried out by using time dependent density functional theory (TD-DFT) approach. Natural Bond Orbital (NBO) analysis has been performed for analyzing charge delocalization throughout the molecule. Molecular electrostatic potential map has also been used for quantitative measure of the chemical activities of various sites of the molecule.

Vibrational analysis of liquid n-butylmethylether

The complex refractive index spectrum in the NIR and MIR range of liquid n-butylmethylether (NBME) was determined. Thin film recording technique was required to obtain quantitative transmission spectra in the MIR range. The experimental part was supported by a conformer population analysis and anharmonic vibrational analysis based on the B2PLYP/N07D method. The resulting population of 11 NBME conformers was analyzed and their calculated anharmonic vibrational spectra and calculated abundances (at 298K) were used to obtain the resultant spectrum of n-butylmethylether. The band assignment procedure was based on the calculated potential energy distributions.

KOSMOS: a universal morph server for nucleic acids, proteins and their complexes

KOSMOS is the first online morph server to be able to address the structural dynamics of DNA/RNA, proteins and even their complexes, such as ribosomes. The key functions of KOSMOS are the harmonic and anharmonic analyses of macromolecules. In the harmonic analysis, normal mode analysis (NMA) based on an elastic network model (ENM) is performed, yielding vibrational modes and B-factor calculations, which provide insight into the potential biological functions of macromolecules based on their structural features. Anharmonic analysis involving elastic network interpolation (ENI) is used to generate plausible transition pathways between two given conformations by optimizing a topology-oriented cost function that guarantees a smooth transition without steric clashes. The quality of the computed pathways is evaluated based on their various facets, including topology, energy cost and compatibility with the NMA results. There are also two unique features of KOSMOS that distinguish it from other morph servers: (i) the versatility in the coarse-graining methods and (ii) the various connection rules in the ENM. The models enable us to analyze macromolecular dynamics with the maximum degrees of freedom by combining a variety of ENMs from full-atom to coarse-grained, backbone and hybrid models with one connection rule, such as distance-cutoff, number-cutoff or chemical-cutoff. KOSMOS is available at http://bioengineering.skku.ac.kr/kosmos.

Thin film IR and computational studies of liquid di-n-butylether

The complex refractive index spectrum in the NIR and MIR range of liquid di-n-butylether (DNBE) was determined. Thin film recording technique was required to obtain quantitative transmission spectra in the MIR range. Raman spectrum was also collected. The experiment was supported by a conformer population analysis and anharmonic vibrational analysis, with the use of B2PLYP/N07D method.

Optical constants of liquid pyrrole in the infrared

The spectrum of the complex refractive index in the 12,500–500cm−1 region was determined for liquid pyrrole from transmission studies. In the MIR region very thin layers with thicknesses of a few micrometers had to be used to obtain reliable data. FT-Raman spectra of the liquid are also reported. Identifications for numerous bands observed in the liquid phase were proposed basing on DFT and MP2 harmonic and anharmonic vibrational analyses. A short comparison of a few popular computational methods including B2PLYP functional with the aug-cc-pVTZ and N07D basis sets was performed.

Harmonic Debye-Waller analysis of anharmonic vibrations

We address the error resulting from application of the harmonic Debye-Waller factor to anharmonic vibrations. The mean-square atomic displacement $\ensuremath{\langle}{u}^{2}\ensuremath{\rangle}$ determined from the harmonic analysis is compared to values obtained from an exact anharmonic analysis. In the case of strong anharmonicity, we find that the harmonic approximation introduces at most a $\ensuremath{\sim}$25$%$ error. The temperature dependence determined from the harmonic analysis follows that found from the exact anharmonic analysis. Errors introduced by the harmonic approximation are comparable in magnitude to the usual systematic errors associated with diffraction experiments and Rietveld refinements.

Anharmonic vibrational analyses for the 1-silacyclopropenylidene molecule and its three isomers

The global minimum among possible structures of SiC2H2 has been experimentally and theoretically determined to be 1-silacyclopropenylidene (1S). In 1994 Maier and Reisenauer reported the generation of 1-silacyclopropenylidene and its three isomers (2S–4S) by pulsed-flash pyrolysis followed by matrix-spectroscopic identification. Reliable quartic force fields for 1-silacyclopropenylidene and its three isomers are determined employing ab initio coupled-cluster theory with single, double, and perturbative triple excitations [CCSD(T)] and the correlation-consistent core-valence quadruple zeta (cc-pCVQZ) basis set. Second-order vibrational perturbation theory (VPT2) has been utilized to determine equilibrium and zero-point vibration corrected rotational constants, centrifugal distortion constants, and harmonic and anharmonic vibrational frequencies. The distances between the average nuclear positions (r α ) are also determined. The predicted rotational constants, centrifugal distortion constants, and anharmonic frequencies for the four lowest-lying isomers (1S-4S) of SiC2H2, as well as their 13C and deuterated isotopologues, agree well with available experiments. Excluding the CH and CD stretching modes, the mean absolute deviation between theoretical anharmonic and experimental fundamental frequencies for isomer 1-silacyclopropenylidene (1S) is 4.1 cm−1 (5 isotopologues, 25 modes). The corresponding deviation for ethynylsilanediyl (2 S) is 4.9 cm−1 (7 isotopologues, 38 modes) without the SiH and SiD stretching modes, while it is 8.6 cm−1 (5 isotopologues, 22 modes) for silacyclopropyne (4S) without the SiC s-stretching, SiH2 a-stretching and SiD2 wagging modes. By comparing the theoretical harmonic and anharmonic with the experimental fundamental vibrational frequencies for the four isomers (1S-4S), it is demonstrated that the anharmonic effects greatly improve the harmonic results. This theoretically derived spectroscopic data should aid in the experimental detection of the transitions that have yet to be observed, particularly for the vinylidensilanediyl isomer. †Present address: Department of Chemistry, Tsinghua University, Beijing, P. R. China 100084

Hydrogen bonding characteristics of 2-pyrrolidinone: a joint experimental and theoretical study

The mid-IR spectrum of the hydrogen bonding lactam 2-pyrrolidinone in CCl(4) was studied using FT-IR spectroscopy accompanied by a quantum chemical anharmonic normal mode analysis combined with a Monte Carlo approach based on semi-empirical harmonic frequencies. We characterized and assigned the spectroscopic features in the range from 1500 cm(-1) to 3600 cm(-1) covering the respective amide bands related to hydrogen bonding CO and NH groups as well as the backbone CH vibrational band. By comparing theory and experiment we are able to assign all mid-IR features to a variety of distinct structures of 2-pyrrolidinone, ranging from monomers, singly and doubly hydrogen bonded dimers to longer hydrogen-bonded chains. These chains account for the most prominent features in the IR spectrum. Furthermore, two peaks in the CH band have been identified as highly localized axial and equatorial C-H stretch vibrations qualified for probes of conformational dynamics. The results provide a detailed microscopic picture of 2-pyrrolidinone in solution, helpful for further dynamical structure studies of this amide.

Integrating Theory, Simulations and Experiments to Reveal the Recognition-Specific Pathways in the Nuclear Co-Activator Binding Domain Ensemble

The nuclear receptor co-activator binding domain (NCBD) selectively recruits transcription co-activators (TCAs) during the formation of the transcription pre-initiation complex. However, the biophysical mechanisms of NCBD:TCA recognition remain unclear as both NCBD and several of its corresponding TCAs are intrinsically disordered. We therefore probed the conformational diversity of the apo- and holo-forms of NCBD using all-atom, explicit solvent molecular dynamics simulations (∼100 μ1/4s) and small-angle neutron scattering experiments. We integrated theory, simulations and experiments into a unified framework called anharmonic conformational analysis (ACA). ACA identifies a hierarchy of conformational sub-states, intermediates and pathways that play a key role in NCBD:TCA recognition. The transitions between sub-states can be modeled by a bent paperclip, whose arms correspond to helices, α1-α2-α3. The pathways reveal that α1 and α2 adopt conformations close to the holo-form and α3 undergoes extensive conformational changes in response to different TCAs (Fig. 1). The specificity binding loop in NCBD adopts intermediates that enables the bending and twisting of α1 and α2 into its final orientation with the target TCA. We hope this quantitative view of NCBD:TCA landscape can aid the design of novel cancer therapeutics.View Large Image | View Hi-Res Image | Download PowerPoint Slide

Conformational and vibrational studies of isomeric hydrogen cyanide tetramers by quantum chemical methods

The results of structural studies and detailed harmonic and anharmonic vibrational analysis on two hydrogen cyanide (HCN) tetramers diaminomaleonitrile (DAMN) and diaminofumaronitrile (DAFN), which are important molecules for understanding the chemistry of interstellar space and nitrile rich environments, are being reported on the basis of density functional theory using second-order perturbation theory. Both the molecules are found to have C1 symmetry. While all the heavy atoms of DAMN lie in the same plane (maximum deviation 6°), the two nitrogen atoms in DAFN are out of plane by about 15°. The two amino groups are tetrahedral and do not have significant bond angle anisotropy. Detailed conformational studies are reported on the two molecules and their possible rotational isomers are identified. Complete vibrational analysis based on harmonic and anharmonic frequencies, intensity of infrared and activity of Raman bands and potential energy distribution over the internal coordinates has been provided for the two molecules. Affect of hydrogen bonding on molecular geometry and frequencies of the NH stretch modes has been studied by calculations on the dimers of the two molecules. A close agreement has been observed between the experimental and calculated frequencies. Vibrational–rotational constants such as rotational constants in the ground vibrational state (A0, B0, C0) and the effective rotational constants (Ae, Be and Ce), including terms due to quartic centrifugal distortion constants, rotation–vibration coupling constants, Wilson and Nielsen's centrifugal distortion constants have been calculated using B3LYP and B97-1 functionals and 6-31G**, 6-311+G** and TZVP basis sets.

Anharmonic Vibrations of Nucleobases: III, Structural Basis of Oneand Two-Dimensional Infrared Spectra for DNA Stacking Dimers

In this work, DNA base monomers, 15 B-form stacking dimers and two G-quadruplex stacking dimers were studied by quantum chemical computations. Detailed anharmonic vibrational analysis was carried out to reveal vibrational signatures for structural aspect of the base monomers and dimers. It was found that from isolated base monomers to stacking dimers, particularly those containing guanine, the interaction between the C=O stretching is very strong, as depicted by the significant changes of their vibrational frequencies and anharmonicities. Such changes can be manifested well in simulated 113 IR and 2D IR spectra. Delocalization degree of the C=O vibrational modes in stacking dimers, represented by the potential energy distribution and the contribution to the diagonal anharmonicity composition from the vibrators, was found to have significant variations in comparison with isolated bases, which resulted from the influences of the C=O stretching and the nearby vibrations of stacking bases.

Silylidene (SiCH2) and its isomers: Anharmonic rovibrational analyses for silylidene, silaacetylene, and silavinylidene

Abstract Three equilibrium structures and two associated isomerization transition states for the SiCH 2 –HSiCH–CSiH 2 system have been theoretically investigated using highly correlated ab initio methods combined with the correlation-consistent polarized core-valence basis sets. Vibrational second-order perturbation theory (VPT2) has been employed to obtain the zero-point vibration corrected rotational constants, centrifugal distortion constants, and fundamental vibrational frequencies for each equilibrium structure. The comparison of the theoretically predicted rotational constants and fundamental frequencies for silylidene (SiCH 2 ) with existing experimental observations shows excellent agreement. The CH 2 (CD 2 ) rocking modes ( ν 6 ) are the most anharmonic among the six vibrational modes, consistent with limited experimental observations. The five stationary point structures and their relative energies on the ground state potential energy surface (PES) are accurately determined using the focal point extrapolation technique. Silylidene (SiCH 2 ) has been confirmed to be the global minimum. Silaacetylene (HSiCH) with a trans -bent structure is located 34.8 ± 0.3 kcal mol −1 (with zero-point vibrational energy, scalar relativistic effects, and DBOC corrections) above the global minimum. The barrier height for the critical reverse isomerization process [HSiCH → SiCH 2 ] is predicted to be 4.1 ± 0.3 kcal mol −1 . The third isomer silavinylidene (CSiH 2 ) is predicted to lie 84.6 ± 0.3 kcal mol −1 above the global minimum, with the barrier height for the reverse isomerization process [CSiH 2 → HSiCH] being only 2.6 ± 0.3 kcal mol −1 . The present research should assist the future experimental characterization of silylidene (SiCH 2 ) isomers.

OH stretching frequencies in systems with intramolecular hydrogen bonds: Harmonic and anharmonic analyses

OH stretching wavenumbers were investigated for 30 species with intramolecularly hydrogen-bonded hydroxyl groups, covering the range from 3600 to ca. 1900 cm −1. Theoretical wavenumbers were predicted with B3LYP/6-31G(d) density functional theory using the standard harmonic approximation, as well as the second-order perturbation theoretical (PT2) anharmonic approximations available with the Gaussian software package. The wavenumbers computed with the anharmonic procedures were found to be essentially linearly related to those obtained within the harmonic analysis. The theoretical wavenumbers were compared with experimental values taken from the literature, supplemented with values estimated from infrared (IR) absorption spectra recorded for the purpose of this study. An approximately linear relationship was established between the observed wavenumbers ν OH and the results of the harmonic analysis. This is significant in view of the fact that the full anharmonic PT2 analysis requires orders-of-magnitude more computing time than the harmonic analysis. ν OH also correlates with OH chemical shifts.

Anharmonic vibrations of nucleobases: Structural basis of one- and two-dimensional infrared spectra for canonical and mismatched base pairs

Canonical Watson-Crick base pairs and four representative mismatched base pairs have been studied by quantum chemical computations. Detailed anharmonic vibrational analysis was carried out to reveal some vibrational signatures characteristic of structural aspects of the base monomers and dimers, which were well manifested in simulated 1D IR and 2D IR spectra. The degree of delocalization of the selected normal modes, represented by the potential energy distribution, was found to vary significantly from isolated bases to H-bonded dimers, and was accompanied by changes in anharmonicities of these modes. Examples are given for the generally accepted carbonyl stretching mode of base pairs appearing in the 6-μm wavelength region of IR spectra.

Photoelectron spectra of dihalomethyl anions: Testing the limits of normal mode analysis

We report the 364-nm negative ion photoelectron spectra of CHX(2)(-) and CDX(2)(-), where X = Cl, Br, and I. The pyramidal dihalomethyl anions undergo a large geometry change upon electron photodetachment to become nearly planar, resulting in multiple extended vibrational progressions in the photoelectron spectra. The normal mode analysis that successfully models photoelectron spectra when geometry changes are modest is unable to reproduce qualitatively the experimental data using physically reasonable parameters. Specifically, the harmonic normal mode analysis using Cartesian displacement coordinates results in much more C-H stretch excitation than is observed, leading to a simulated photoelectron spectrum that is much broader than that which is seen experimentally. A (2 + 1)-dimensional anharmonic coupled-mode analysis much better reproduces the observed vibrational structure. We obtain an estimate of the adiabatic electron affinity of each dihalomethyl radical studied. The electron affinity of CHCl(2) and CDCl(2) is 1.3(2) eV, of CHBr(2) and CDBr(2) is 1.9(2) eV, and of CHI(2) and CDI(2) is 1.9(2) eV. Analysis of the experimental spectra illustrates the limits of the conventional normal mode approach and shows the type of analysis required for substantial geometry changes when multiple modes are active upon photodetachment.

Simulated Photoelectron Spectra of the Cyanide-Water Anion via Quasiclassical Molecular Dynamics

We present the simulated photoelectron spectrum (PES) for cyanide-water CN(H(2)O)(-) based on quasiclassical trajectory molecular dynamics (QCT-MD). Using density functional theory to generate trajectories and to calculate vertical detachment energies, we obtain simulated spectra that are in qualitative agreement with experiment. We obtain a theoretical 12 → 300 K temperature red shift of 0.1 eV as compared to an experimental redshift of 0.25 eV. The calculated linewidths of 0.3 eV are in excellent agreement with experiment. Our trajectories show that the temperature red shift as being dominated by dynamics within the basin of the N-bound minimum, however, at 300 K we predict conversion into the basin of the C-bound minimum, equilibrating at a 80:20 ratio of N- vs C-bound mixture. We discuss the potential advantages of QCT-MD over anharmonic Franck-Condon analysis such as natural incorporation of anharmonicity (as necessary for weakly bound systems), and reduced computational scaling, but also drawbacks such as neglect of final-state (e.g., Duschinsky) effects.