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General Perturb-Then-Diagonalize Model for the Vibrational Frequencies and Intensities of Molecules Belonging to Abelian and Non-Abelian Symmetry Groups.

ABSTRACT: In this paper, we show that the standard second-order vibrational perturbation theory (VPT2) for Abelian groups can be used also for non-Abelian groups without employing specific equations for two- or threefold degenerate vibrations but rather handling in the proper way all the degeneracy issues and deriving the peculiar spectroscopic signatures of non-Abelian groups (e.g., l-doubling) by a posteriori transformations of the eigenfunctions. Comparison with the results of previous conventional implementations shows a perfect agreement for the vibrational energies of linear and symmetric tops, thus paving the route to the transparent extension of the equations already available for asymmetric tops to the energies of spherical tops and the infrared and Raman intensities of molecules belonging to non-Abelian symmetry groups. The whole procedure has been implemented in our general engine for vibro-rotational computations beyond the rigid rotor/harmonic oscillator model and has been validated on a number of test cases.

SUBMITTER: Mendolicchio M

PROVIDER: S-EPMC8280743 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Anharmonic Vibrational Frequencies of Water Borane and Associated Molecules.

Project description:Water borane (BH3OH2) and borinic acid (BH2OH) have been proposed as intermediates along the pathway of hydrogen generation from simple reactants: water and borane. However, the vibrational spectra for neither water borane nor borinic acid has been investigaged experimentally due to the difficulty of isolating them in the gas phase, making accurate quantum chemical predictions for such properties the most viable means of their determination. This work presents theoretical predictions of the full rotational and fundamental vibrational spectra of these two potentially application-rich molecules using quartic force fields at the CCSD(T)-F12b/cc-pCVTZ-F12 level with additional corrections included for the effects of scalar relativity. This computational scheme is further benchmarked against the available gas-phase experimental data for the related borane and HBO molecules. The differences are found to be within 3 cm-1 for the fundamental vibrational frequencies and as close as 15 MHz in the B0 and C0 principal rotational constants. Both BH2OH and BH3OH2 have multiple vibrational modes with intensities greater than 100 km mol-1, namely ν2 and ν4 in BH2OH, and ν1, ν3, ν4, ν9, and ν13 in BH3OH2. Finally, BH3OH2 has a large dipole moment of 4.24 D, which should enable it to be observable by rotational spectroscopy, as well.

| S-EPMC8658819 | biostudies-literature

Relativistic Four-Component DFT Calculations of Vibrational Frequencies.

Project description:We investigate the effect of relativity on harmonic vibrational frequencies. Density functional theory (DFT) calculations using the four-component Dirac-Coulomb Hamiltonian have been performed for 15 hydrides (H2X, X = O, S, Se, Te, Po; XH3, X = N, P, As, Sb, Bi; and XH4, X = C, Si, Ge, Sn, Pb) as well as for HC≡CPbH3. The vibrational frequencies have been calculated using finite differences of the molecular energy with respect to geometrical distortions of the nuclei. The influences of the choice of basis set, exchange-correlation functional, and step length for the numerical differentiation on the calculated harmonic vibrational frequencies have been tested, and the method has been found to be numerically robust. Relativistic effects are noticeable for the heavier congeners H2Te and H2Po, SbH3 and BiH3, and SnH4 and PbH4 and are much more pronounced for the vibrational modes with higher frequencies. Spin-orbit effects constitute a very small fraction of the total relativistic effects, except for H2Te and H2Po. For HC≡CPbH3 we find that only the frequencies of the modes with large contributions from Pb displacements are significantly affected by relativity.

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Project description:Plasmon hybridization theory, inspired by molecular orbital theory, has been extremely successful in describing the near-field coupling in clusters of plasmonic nanoparticles, also known as plasmonic molecules. However, the vibrational modes of plasmonic molecules have been virtually unexplored. By designing precisely configured plasmonic molecules of varying complexity and probing them at the individual plasmonic molecule level, intramolecular coupling of acoustic modes, mediated by the underlying substrate, is observed. The strength of this coupling can be manipulated through the configuration of the plasmonic molecules. Surprisingly, classical continuum elastic theory fails to account for the experimental trends, which are well described by a simple coupled oscillator picture that assumes the vibrational coupling is mediated by coherent phonons with low energies. These findings provide a route to the systematic optical control of the gigahertz response of metallic nanostructures, opening the door to new optomechanical device strategies.

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Ultrafast dynamics of vibrational symmetry breaking in a charge-ordered nickelate.

Project description:The ability to probe symmetry-breaking transitions on their natural time scales is one of the key challenges in nonequilibrium physics. Stripe ordering represents an intriguing type of broken symmetry, where complex interactions result in atomic-scale lines of charge and spin density. Although phonon anomalies and periodic distortions attest the importance of electron-phonon coupling in the formation of stripe phases, a direct time-domain view of vibrational symmetry breaking is lacking. We report experiments that track the transient multi-terahertz response of the model stripe compound La1.75Sr0.25NiO4, yielding novel insight into its electronic and structural dynamics following an ultrafast optical quench. We find that although electronic carriers are immediately delocalized, the crystal symmetry remains initially frozen-as witnessed by time-delayed suppression of zone-folded Ni-O bending modes acting as a fingerprint of lattice symmetry. Longitudinal and transverse vibrations react with different speeds, indicating a strong directionality and an important role of polar interactions. The hidden complexity of electronic and structural coupling during stripe melting and formation, captured here within a single terahertz spectrum, opens new paths to understanding symmetry-breaking dynamics in solids.

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Variation in crossover frequencies perturb crossover assurance without affecting meiotic chromosome segregation in Saccharomyces cerevisiae.

Project description:The segregation of homologous chromosomes during the Meiosis I division requires an obligate crossover per homolog pair (crossover assurance). In Saccharomyces cerevisiae and mammals, Msh4 and Msh5 proteins stabilize Holliday junctions and its progenitors to facilitate crossing over. S. cerevisiae msh4/5 hypomorphs that reduce crossover levels up to twofold at specific loci on chromosomes VII, VIII, and XV without affecting homolog segregation were identified recently. We use the msh4-R676W hypomorph to ask if the obligate crossover is insulated from variation in crossover frequencies, using a S. cerevisiae S288c/YJM789 hybrid to map recombination genome-wide. The msh4-R676W hypomorph made on average 64 crossovers per meiosis compared to 94 made in wild type and 49 in the msh4? mutant confirming the defect seen at individual loci on a genome-wide scale. Crossover reductions in msh4-R676W and msh4? were significant across chromosomes regardless of size, unlike previous observations made at specific loci. The msh4-R676W hypomorph showed reduced crossover interference. Although crossover reduction in msh4-R676W is modest, 42% of the four viable spore tetrads showed nonexchange chromosomes. These results, along with modeling of crossover distribution, suggest the significant reduction in crossovers across chromosomes and the loss of interference compromises the obligate crossover in the msh4 hypomorph. The high spore viability of the msh4 hypomorph is maintained by efficient segregation of the natural nonexchange chromosomes. Our results suggest that variation in crossover frequencies can compromise the obligate crossover and also support a mechanistic role for interference in obligate crossover formation.

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Retracted Article: Effect of temperature and large guest molecules on the C-H symmetric stretching vibrational frequencies of methane in structure H and I clathrate hydrates.

Project description:Large molecules such as 2-methylbutane (C5H12) or 2,2-dimethylbutane (C6H14) form structure H (sH) hydrates with methane (CH4) as a help gas. In this study, the Raman spectra of the C-H symmetric stretch region of CH4 enclathrated within various sH hydrates and structure I CH4 hydrates were analyzed in the temperature range 83-183 K. Thermal expansions of these sH hydrate samples were also measured using powder X-ray diffraction. Symmetric stretch vibrational frequencies of CH4 in host water cages increased because of varying temperature, and the sizes of the host water cages also increased; variation of CH4 in small cages was less than in larger cages. Comparing the variations of the C-H symmetric stretching frequencies of CH4 in gas hydrates with varying pressure and temperature, we suggest that the observed trend is caused by thermal vibrations of the CH4 molecule in water cages.

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Semiclassical Vibrational Spectroscopy of Biological Molecules Using Force Fields.

Project description:Semiclassical spectroscopy is a practical way to get an accurately approximate quantum description of spectral features starting from ab initio molecular dynamics simulations. The computational bottleneck for the method is represented by the cost of ab initio potential, gradient, and Hessian matrix estimates. This drawback is particularly severe for biological systems due to their unique complexity and large dimensionality. The main goal of this manuscript is to demonstrate that quantum dynamics and spectroscopy, at the level of semiclassical approximation, are doable even for sizable biological systems. To this end, we investigate the possibility of performing semiclassical spectroscopy simulations when ab initio calculations are replaced by computationally cheaper force field evaluations. Both polarizable (AMOEBABIO18) and nonpolarizable (AMBER14SB) force fields are tested. Calculations of some particular vibrational frequencies of four nucleosides, i.e., uridine, thymidine, deoxyguanosine, and adenosine, show that ab initio simulations are accurate and widely applicable. Conversely, simulations based on AMBER14SB are limited to harmonic approximations, but those relying on AMOEBABIO18 yield acceptable semiclassical values if the investigated conformation has been included in the force field parametrization. The main conclusion is that AMOEBABIO18 may provide a viable route to assist semiclassical spectroscopy in the study of large biological molecules for which an ab initio approach is not computationally affordable.

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Project description:Adsorbate vibrational excitations are an important fingerprint of molecule/surface interactions, affecting temperature contributions to the free energy and impacting reaction rate and equilibrium constants. Furthermore, vibrational spectra aid in identifying species and adsorption sites present in experimental studies. Despite their importance, knowledge of how adsorbate frequencies scale across materials is lacking. Here, by combining previously reported experimental data and our own density-functional theory calculations, we reveal linear correlations between vibrational frequencies of adsorbates on transition metal surfaces. Through effective-medium theory, linear muffin-tin orbital theory, and the d-band model, we rationalize the squares of the frequencies to be fundamentally linear in their scaling across transition metal surfaces. We identify the adsorbate-binding energy as a descriptor for certain molecular vibrations and rigorously relate errors in frequencies to errors in adsorption energies. We also discuss the impact of scaling on surface thermochemistry and adsorbate coverage.

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Vibrational Tunneling Spectra of Molecules with Asymmetric Wells: A Combined Vibrational Configuration Interaction and Instanton Approach.

Project description:A combined approach that uses the vibrational configuration interaction (VCI) and semiclassical instanton theory was developed to study vibrational tunneling spectra of molecules with multiple wells in full dimensionality. The method can be applied to calculate low-lying vibrational states in the systems with an arbitrary number of minima, which are not necessarily equal in energy or shape. It was tested on a two-dimensional double-well model system and on malonaldehyde, and the calculations reproduced the exact quantum mechanical (QM) results with high accuracy. The method was subsequently applied to calculate the vibrational spectrum of the asymmetrically deuterated malonaldehyde with nondegenerate vibrational frequencies in the two wells. The spectrum is obtained at a cost of single-well VCI calculations used to calculate the local energies. The interactions between states of different wells are computed semiclassically using the instanton theory at a comparatively negligible computational cost. The method is particularly suited to systems in which the wells are separated by large potential barriers and tunneling splittings are small, for example, in some water clusters, when the exact QM methods come at a prohibitive computational cost.

| S-EPMC9097297 | biostudies-literature

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