Vibrational Spectra In Terms Research Articles

Some opinions on MD-based vibrational spectroscopy of gas phase molecules and their assembly: An overview of what has been achieved and where to go

We hereby review molecular dynamics simulations for anharmonic gas phase spectroscopy and provide some of our opinions of where the field is heading. With these new directions, the theoretical IR/Raman spectroscopy of large (bio)-molecular systems will be more easily achievable over longer time-scale MD trajectories for an increase in accuracy of the MD-IR and MD-Raman calculated spectra. With the new directions presented here, the high throughput ’decoding’ of experimental IR/Raman spectra into 3D-structures should thus be possible, hence advancing e.g. the field of MS-IR for structural characterization by spectroscopy. We also review the assignment of vibrational spectra in terms of anharmonic molecular modes from the MD trajectories, and especially introduce our recent developments based on Graph Theory algorithms. Graph Theory algorithmic is also introduced in this review for the identification of the molecular 3D-structures sampled over MD trajectories.

Infrared, Vibrational Circular Dichroism, and Raman Spectral Simulations for β-Sheet Structures with Various Isotopic Labels, Interstrand, and Stacking Arrangements Using Density Functional Theory

Infrared (IR), Raman, and vibrational circular dichroism (VCD) spectral variations for different β-sheet structures were studied using simulations based on density functional theory (DFT) force field and intensity computations. The DFT vibrational parameters were obtained for β-sheet fragments containing nine-amides and constrained to a variety of conformations and strand arrangements. These were subsequently transferred onto corresponding larger β-sheet models, normally consisting of five strands with ten amides each, for spectral simulations. Further extension to fibril models composed of multiple stacked β-sheets was achieved by combining the transfer of DFT parameters for each sheet with dipole coupling methods for interactions between sheets. IR spectra of the amide I show different splitting patterns for parallel and antiparallel β-sheets, and their VCD, in the absence of intersheet stacking, have distinct sign variations. Isotopic labeling by (13)C of selected residues yields spectral shifts and intensity changes uniquely sensitive to relative alignment of strands (registry) for antiparallel sheets. Stacking of multiple planar sheets maintains the qualitative spectral character of the single sheet but evidences some reduction in the exciton splitting of the amide I mode. Rotating sheets with respect to each other leads to a significant VCD enhancement, whose sign pattern and intensity is dependent on the handedness and degree of rotation. For twisted β-sheets, a significant VCD enhancement is computed even for sheets stacked with either the same or opposite alignments and the inter-sheet rotation, depending on the sense, can either further increase or weaken the enhanced VCD intensity. In twisted, stacked structures (without rotation), similar VCD amide I patterns (positive couplets) are predicted for both parallel and antiparallel sheets, but different IR intensity distributions still enable their differentiation. Our simulation results prove useful for interpreting experimental vibrational spectra in terms of β-sheet and fibril structure, as illustrated in the accompanying paper.

Raman and IR spectroscopic studies of fenamates – Conformational differences in polymorphs of flufenamic acid, mefenamic acid and tolfenamic acid

Solid-state Raman and IR spectra of two polymorphic forms of each of three fenamates (flufenamic acid, mefenamic acid and tolfenamic acid) display subtle but highly reproducible differences. Many of these spectral differences can be ascribed to different conformations of these molecules, involving two of four possible orientations of one substituted benzene ring with respect to the other. Interpretation of the vibrational spectra in terms of conformational differences has been facilitated by DFT calculations at the B3LYP/cc-pVDZ level for each conformer. The calculated spectra are compared with the experimental spectra in order to identify the conformers present in two polymorphic forms in each case, and detailed band assignments are obtained from the DFT calculations.

Atomic Velocity Projection Method: A New Analysis Method for Vibrational Spectra in Terms of Internal Coordinates for a Better Understanding of Zeolite Nanogrowth.

An efficient protocol is presented to identify signals in vibrational spectra of silica oligomers based on theoretical molecular dynamics (MD) simulations. The method is based on the projection of the atomic velocity vectors on the tangential directions of the trajectories belonging to a predefined set of internal coordinates. In this way only contributions of atomic motions along these internal coordinates are taken into consideration. The new methodology is applied to the spectra of oligomers and rings, which play an important role in zeolite synthesis. A suitable selection of the relevant internal coordinates makes the protocol very efficient but relies on intuition and theoretical insight. The simulation data necessary to compute vibrational spectra of relevant silica species are obtained through MD using proper force fields. The new methodology-the so-called velocity projection method-makes a detailed analysis of vibrational spectra possible by establishing a one-to-one correspondence between a spectral signal and a proper internal coordinate. It offers valuable perspectives in understanding the elementary steps in silica organization during zeolite nanogrowth. The so-called velocity projection method is generally applicable on data obtained from all types of MD and is a highly valuable alternative to normal-mode analysis which has its limitations due to the presence of many local minima on the potential energy surface. In this work the method is exclusively applied to inelastic neutron scattering, but extension to the infrared power spectrum is apparent.

Vibrational spectrum of reiditeZrSiO4from first principles

Structure, energetic characteristics, and the vibrational spectrum of reidite (${\text{ZrSiO}}_{4}$ polymorph isostructural with sheelite) were studied by periodic density-functional calculations and compared with those of zircon. The computed structural parameters are in a good agreement with known data. The calculations provide a nonempirical estimation of the elastic constants of this material. Making use of the results of the computations a complete assignment of the phonons at the $\ensuremath{\Gamma}$ point is proposed that accounts for features observed in the infrared and Raman spectra of reidite. The comparison of atomic displacements in the vibrational modes of the reidite and zircon structures permits to explain differences in their vibrational spectra in terms of structural peculiarities of the two lattices. Analysis of calculated effective charge tensors points to the validity of the two-body charge redistribution model and gives an estimation for the values of the corresponding charge transfer parameters.

Analysis of Secondary Structure Effects on the IR and Raman Spectra of Polypeptides in Terms of Localized Vibrations

We demonstrate how the recently developed methodology for the analysis of calculated vibrational spectra in terms of localized modes [J. Chem. Phys. 2009, 130, 084106] can be applied to investigate the influence of the secondary structure on infrared and Raman spectra of polypeptides. As a model system, a polypeptide consisting of 20 (S)-alanine residues in the conformation of an alpha-helix and of a 3(10)-helix is considered. Several features of the calculated spectra are analyzed in detail. First, we show for the amide II band how localized modes facilitate the decomposition of the total Raman intensities into contributions of certain groups of atoms, and how such an analysis can be used to identify the origin of differences in Raman intensity of the two helices. Second, we demonstrate how the shift of the position of the amide I band between the two considered structures can be rationalized and how the observed intensity distribution within the amide I band can be explained by considering the coupling constants between the localized modes. Third, we show how localized modes can be employed to analyze the positions of the bands found in the extended amide III region and how such an analysis makes it possible to gain a better understanding of how structural changes influence the coupling between the amide III and the C(alpha)-H bending modes in this region.

Rubbing-induced anisotropy of long alkyl side chains at polyimide surfaces

Molecular organization at polyimide surfaces used as alignment layers in liquid crystal displays was investigated using vibrational sum frequency generation (SFG) spectroscopy. We focus on the orientation of the long alkyl side groups at the polymer surface using polarization-selected SFG spectra of the CH(3)- and CH(2)-stretch modes of the side chain. Mechanical rubbing and baking, an accepted industrial procedure used to produce pretilt of the liquid crystal, was found to induce pronounced azimuthal anisotropy in the orientational distribution of the alkyl side chains. Orientational analysis of the SFG vibrational spectra in terms of the azimuthal and tilt angles (in and out of plane, respectively) of the alkyl side chains shows their preferential tilt along the rubbing direction, with the azimuthal distribution narrower for stronger rubbed polymer samples.

Vibrational Properties of the One-Dimensional, S = 1/2, Heisenberg Antiferromagnet Copper Pyrazine Dinitrate

We report the temperature-dependent infrared spectra of pure, deuterated, Zn-doped, and 2,6-dimethyl-substituted samples of the S = 1/2, one-dimensional Quantum Heisenberg Antiferromagnet (QHAF) copper pyrazine dinitrate (Cu(C4H4N2)(NO3)2). Of the more than 100 vibrational modes observed in the spectra, nearly one-third of them unexpectedly soften throughout the temperature range of investigation (300−5 K). We discuss the temperature dependence of the vibrational spectra in terms of several different models for mode softening. On the basis of detailed structural information and a comparison of the infrared spectra between pure copper pyrazine dinitrate and its chemically modified relatives, we conclude that the unusual softening observed in this low-dimensional molecular magnet is due to enhanced interchain hydrogen bonding with decreasing temperature.

A new way of analyzing vibrational spectra. I. Derivation of adiabatic internal modes

A new way of analyzing measured or calculated vibrational spectra in terms of internal vibrational modes associated with the internal parameters used to describe geometry and conformation of a molecule is described. The internal modes are determined by solving the Euler–Lagrange equations for molecular fragments ϕn described by internal parameters ζn. An internal mode is localized in a molecular fragment by describing the rest of the molecule as a collection of massless points that just define molecular geometry. Alternatively, one can consider the new fragment motions as motions that are obtained after relaxing all parts of the vibrating molecule but the fragment under consideration. Because of this property, the internal modes are called adiabatic internal modes, and the associated force constants ka, adiabatic force constants. Minimization of the kinetic energy of the vibrating fragment ϕn yields the adiabatic mass ma (corresponding to 1/Gnn of Wilson's G matrix) and, by this, adiabatic frequencies ωa. Adiabatic modes are perfectly suited to analyze and understand the vibrational spectra of a molecule in terms of internal parameter modes in the same way as one understands molecular geometry in terms of internal coordinates. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 67: 1–9, 1998

A new way of analyzing vibrational spectra. I. Derivation of adiabatic internal modes

A new way of analyzing measured or calculated vibrational spectra in terms of internal vibrational modes associated with the internal parameters used to describe geometry and conformation of a molecule is described. The internal modes are determined by solving the Euler–Lagrange equations for molecular fragments ϕn described by internal parameters ζn. An internal mode is localized in a molecular fragment by describing the rest of the molecule as a collection of massless points that just define molecular geometry. Alternatively, one can consider the new fragment motions as motions that are obtained after relaxing all parts of the vibrating molecule but the fragment under consideration. Because of this property, the internal modes are called adiabatic internal modes, and the associated force constants ka, adiabatic force constants. Minimization of the kinetic energy of the vibrating fragment ϕn yields the adiabatic mass ma (corresponding to 1/Gnn of Wilson's G matrix) and, by this, adiabatic frequencies ωa. Adiabatic modes are perfectly suited to analyze and understand the vibrational spectra of a molecule in terms of internal parameter modes in the same way as one understands molecular geometry in terms of internal coordinates. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 67: 1–9, 1998

Infrared and Raman spectra of alkylated guanine derivatives

The infrared and Raman spectra of 9-methylguanine, 9-ethylguanine and 1,9-dimethylguanine in the solid state are reported and discussed. Hydrogen bonds in the solid guanine derivatives bring about strong perturbations in the spectra from those of the isolated molecules. The results are discussed in terms of structural data from X-ray diffraction studies. The infrared spectra of guanine derivatives are compared with the spectra of these molecules isolated in low temperature argon matrices. This comparison allows the determination of the frequency changes due to hydrogen bonding and the interpretation of their vibrational spectra in terms of the normal modes calculated for the isolated guanine molecule.

Transition-metal carbonyl derivatives of the Germanes. Part III. Germyl(carbonyl)iron complexes

Reaction between chlorogermane and Na2Fe(CO)4 in n-nutane affords digermyltetracarbonyliron, (GeH3)2Fe(CO)4(I) and monogermylhydridotetracarbonyliron, GeH3(H)Fe(CO)4(II) together with H2Fe(CO)4(III). Germyl-(cyclopentadienyl)dicarbonyliron, GeH3Fe(C5H5)(CO)2(IV) can be obtained similarly from NaFe(C5H5)(CO)2. Physical properties, i.r., Raman, 1H n.m.r., and mass spectra of (I) and (II) are consistent with their fomulation as monomeric, cis-octahedral structures, allowing assignment of vibrational spectra in terms of C2v and C8 symmetry respectively. Gas-phase i.r. data for (III) in the range 4000–350 cm–1 are also reported and partially assigned. Reaction of (I) with HCl gives (II) in 46% yield; interaction of solid (I) with HgCl2 results in Ge–Fe bond cleavage with the formation of GeH3Cl, GeH4, and HCl.