Internal Vibrational Frequencies Research Articles

Micromechanical and surface adhesive properties of single saccharomyces cerevisiae cells

The adhesion and mechanical properties of a biological cell (e.g. cell membrane elasticity and adhesiveness) are often strong indicators for the state of its health. Many existing techniques for determining mechanical properties of cells require direct physical contact with a single cell or a group of cells. Physical contact with the cell can trigger complex mechanotransduction mechanisms, leading to cellular responses, and consequently interfering with measurement accuracy. In the current work, based on ultrasonic excitation and interferometric (optical) motion detection, a non-contact method for characterizing the adhesion and mechanical properties of single cells is presented. It is experimentally demonstrated that the rocking (rigid body) motion and internal vibrational resonance frequencies of a single saccharomyces cerevisiae (SC) (baker’s yeast) cell can be acquired with the current approach, and the Young’s modulus and surface tension of the cell membrane as well as surface adhesion energy can be extracted from the values of these acquired resonance frequencies. The detected resonance frequency ranges for single SC cells include a rocking (rigid body) frequency of 330 ± 70 kHz and two breathing resonance frequencies of 1.53 ± 0.12 and 2.02 ± 0.31 MHz. Based on these values, the average work-of-adhesion of SC cells on a silicon substrate in aqueous medium is extracted, for the first time, as . Similarly, the surface tension and the Young’s modulus of the SC cell wall are predicted as and 9.20 ± 2.80 MPa, respectively. These results are compared to those reported in the literature by utilizing various methods, and good agreements are found. The current approach eliminates the measurement inaccuracies associated with the physical contact. Exciting and detecting cell dynamics at micro-second time-scales is significantly faster than the currently known metabolistic response times of cells (milliseconds to seconds), thus, it has the potential to decouple metabolistic and mechanotransduction effects from external stimuli and to operate at high throughput rates.

Synthesis and X-ray crystallographic and IR spectroscopic study of complex alkaline earth zirconium arsenates

Arsenates A0.5Zr2(AsO4)3 (A = Mg, Ca, Sr, Ba), synthesized through sol–gel route with subsequent heat treatment, have been studied by X-ray diffraction, electron probe microanalysis, and IR spectroscopy. Mg0.5Zr2(AsO4)3 crystallizes in the Sc2(WO4)3 structure type (space group P21/n). A0.5Zr2(AsO4)3 (A = Ca, Sr, Ba) crystallize in the NaZr2(PO4)3 structure type (space group \(R\bar 3\) ). The Ca0.5Zr2(AsO4)3 and Ba0.5Zr2(AsO4)3 structures have been refined by the full-profile analysis. The structure frameworks are composed of ZrO6 octahedra and AsO4 tetrahedra. The alkaline earth metal atoms occupy one of the two extraframework positions inside the structure columns. The internal vibrational frequencies of the AsO43- tetrahedron have been assigned. The number of the observed bands corresponds to the number predicted by the factor group analysis of vibrations for space groups \(R\bar 3\) and P21/n.

Molecular Modeling of Toxic Indole Derivatives from High Temperature Cooking

More than two decades ago, Japanese scientists discovered a new family of highly mutagenic compounds classified as heterocyclic aromatic amines from roasted meat and grilled Fish. This group of compounds will form the basis of this investigation from a theoretical perspective. In order to simulate high temperature cooking and explore the thermochemical properties of these compounds, high level quantum calculations were employed. Accordingly, the theoretical behaviour of indole derivatives; isoindazole, 1-methyl indole, 4,7-dimethyl isoindazole and carbazole were explored at a pressure of 1 atmosphere over a wide range of pyrolysis temperatures (323-923 K) typically at temperature increments of 50 K. Ab initio analytical gradients at MP2 level of theory with 3-21G and 6-31G(d,p) basis sets and Molecular Mechanics (MM) with universal force field (UFF) from Gaussian 03 computational platform were used for geometry optimization, internal energy calculations, molecular orbitals, and vibrational frequencies. It was observed that the internal energy for isoindazole at 323 K was 75.80 kcal/mol whereas that of carbazole was 123.78 kcal/mol under similar conditions of pressure and temperature. The stability of these molecular compounds decreased with increase in pyrolysis temperature. To make decent conclusions on the potency of these indole derivatives and their effect on human health, toxicity values were estimated using Quantitative Structural Activity Relationship (QSAR) method found in HypeChem computational software. Toxicity indices for isoindazole, 1-methyl indole, 4,7-dimethyl isoindazole and carbazole were -0.16, 0.01, 0.14 and -0.07 respectively, while those for their corresponding radicals were -0.12, -0.21, 0.19 and -0.17. These values point to highly hydrophilic species which indicate that they are very toxic. The thermochemical, and electronic properties of these compounds and their analog radicals will be presented. Additionally, theoretical NMR chemical shifts for the most toxic by-product of high temperature cooking are also reported in this work.

An exploration of the ozone dimer potential energy surface.

The (O3)2 dimer potential energy surface is thoroughly explored at the ab initio CCSD(T) computational level. Five minima are characterized with binding energies between 0.35 and 2.24 kcal/mol. The most stable may be characterized as slipped parallel, with the two O3 monomers situated in parallel planes. Partitioning of the interaction energy points to dispersion and exchange as the prime contributors to the stability, with varying contributions from electrostatic energy, which is repulsive in one case. Atoms in Molecules analysis of the wavefunction presents specific O⋯O bonding interactions, whose number is related to the overall stability of each dimer. All internal vibrational frequencies are shifted to the red by dimerization, particularly the antisymmetric stretching mode whose shift is as high as 111 cm(-1). In addition to the five minima, 11 higher-order stationary points are identified.

Dynamics and Thermodynamics of Crystalline Polymorphs. 2. β-Glycine, Analysis of Variable-Temperature Atomic Displacement Parameters

The molecular dynamics in the crystal and the thermodynamic functions of the β-polymorph of glycine have been determined from a combination of molecular translation-libration frequencies reflecting the temperature dependence of atomic displacement parameters (ADPs), with frequencies derived from ONIOM(DFT:PM3) calculations on a 15-molecule β-glycine cluster. ADPs have been obtained from variable-temperature diffraction data to 0.5 Å resolution collected with X-ray synchrotron (10-300 K) and sealed tube radiation (50-298 K). At the higher temperatures, the ADPs of β-glycine from synchrotron are larger than those from sealed tube probably due to different experimental conditions. The lattice vibration frequencies from normal-mode analysis of ADPs and the internal vibration frequencies from ONIOM(B3LYP/6-311+G(2d,p):PM3) calculations agree with those from spectroscopy. Estimation of thermodynamic functions using the vibrational frequencies, the Einstein and Debye models of heat capacity, and the room-temperature compressibility provides C(p), H(vib), and S(vib) that agree with those from calorimetry. The β-phase with higher H and G is found to be less stable than the α-phase in the temperature range of the experiment.

Polyamorphism in network structures

Reports of high-density amorphous forms of ice, quartz and Si have intensified the search for amorphous polymorphs in other systems. The network structures that exhibit pressure-induced amorphization are interesting from the point of view of polyamorphism. Recent in-situ high pressure Raman scattering and synchrotron x-ray diffraction studies on negative thermal expansion material zirconium tungstate have revealed an amorphous to amorphous transition at 19 GPa. The transition was identified for the discontinuities in the structural parameters such as position and height of the first peak of the structure factor and that in the tungstate internal vibrational mode frequency. Another compound, vanadium pentaoxide that forms a glass during melt-quenching, is also found to turn amorphous at 40 GPa, pointing to a possibility of polyamorphism.

Dynamics and Thermodynamics of Crystalline Polymorphs: α-Glycine, Analysis of Variable-Temperature Atomic Displacement Parameters

Multitemperature synchrotron diffraction data to 0.5 Å resolution in the temperature range 10-298 K and neutron data at 18 K of the α-glycine polymorph have been collected at the KEK photon factory (PF), SPring-8 and the Institut Laue Langevin (ILL) for the study of molecular motion in the crystal and of the associated thermodynamic functions. Atomic displacement parameters (ADPs) of non-H atoms are obtained from refinements based on nonspherical atomic scattering factors (invariom model) to minimize correlation between parameters describing thermal motion and valence electron density. The ADPs in the temperature range 50-298 K from SPring-8 connect smoothly with those from neutron diffraction at 18 K and 288-323 K. The combined ADPs from both sources covering the temperature range 18-323 K are used for a normal-mode analysis in the molecular mean field approximation. The lattice vibration frequencies from the ADP analysis and the internal vibration frequencies from an ONIOM (B3LYP/6-311+G(2d,p):PM3) calculation together with the Einstein, Debye, and Nernst-Lindemann models of heat capacity are used to calculate Cp, Hvib, and Svib values that are in good agreement with those from calorimetry.

Ensemble-Averaged QM/MM Kinetic Isotope Effects for the SN2 Reaction of Cyanide Anions with Chloroethane in DMSO Solution

The existence of solvent fluctuations leads to populations of reactant-state (RS) and transition-state (TS) configurations and implies that property calculations must include appropriate averaging over distributions of values for individual configurations. Average kinetic isotope effects 〈KIE〉 for NC(-) + EtCl → NCEt + Cl(-) in DMSO solution at 30 °C are best obtained as the ratio 〈f(RS)〉/〈f(TS)〉 of isotopic partition function ratios separately averaged over all RS and TS configurations. In this way the hybrid AM1/OPLS-AA potential yields 〈KIE〉 values for all six isotopic substitutions (2° α-(2)H(2), 2° β-(2)H(3), α-(11)C/(14)C, leaving group (37)Cl, and nucleophile (13)C and (15)N) for this reaction in the correct direction as measured experimentally. These thermally-averaged calculated KIEs may be compared meaningfully with experiment, and only one of them differs in magnitude from the experimental value by more than one standard deviation from the mean. This success contrasts with previous KIE calculations based upon traditional methods without averaging. The isotopic partition function ratios are best evaluated using all (internal) vibrational and (external) librational frequencies obtained from Hessians determined for subsets of atoms, relaxed to local minima or saddle points, within frozen solvent environments of structures sampled along molecular dynamics trajectories for RS and TS. The current method may perfectly well be implemented with other QM or QM/MM methods, and thus provides a useful tool for investigating KIEs in relation to studies of chemical reaction mechanisms in solution or catalyzed by enzymes.

Ab initio calculations of sulfur isotope fractionation factor for H2S in aqua–gas system

High level ab initio calculations have been performed for hydrogen sulfide in aqua–gas system. Based on B3LYP density functional and MP2 methods with two basis sets, 6-31G(d) and 6-311++G(d,p), we have obtained the minimum energy structures of H2S molecule and H2S·nH2O hydrogen bonded molecular clusters, where n=1–5. For these structures the internal and intermolecular harmonic vibrational frequencies were calculated. The calibration of vibrational frequencies by appropriate scaling factor has been made.Using statistical mechanics approach, we have calculated the reduced partition functions ratios (beta-factors) for these clusters and respective sulfur equilibrium isotope fractionation factors as a function of temperature. The calculated beta-factors for H2Ssolution drop nearly linearly from about 1.013 to 1.008 in a temperature range of 0–100°C. The obtained magnitude of isotope fractionation between H2Ssolution and H2Sgas (about +0.8‰ at 25°C and +0.5 at 100°C) is consistent with existing experimental data. This is the second theoretical determination of sulfur isotope fractionation between gaseous and hydrated hydrogen sulfide (dissolved H2S). The previous theoretical calculations by Otake et al. (2008) yielded significantly lower values, ranging from −0.17 to +0.38‰ at 25°C, in dependence on the used model.

Experimental and Theoretical Studies of the Vibrational and Electronic Spectra of a Lanthanide Ion at a Site of Th Symmetry: Pr3+ in Cs2NaPr(NO2)6

The Pr(3+) ion in Cs(2)NaPr(NO(2))(6) is situated at a site of T(h) symmetry with 12-coordination to O atoms of bidentate nitrito groups. First-principles calculations of the vibrational modes of the complex were carried out using the density functional theory with the generalized gradient approximation Perdew-Burke-Ernzerhof exchange-correlation functional. The calculations that treated the Pr(3+) 4f electrons as valence electrons showed better agreement with the experimental vibrational assignments compared with those treating the 4f electrons a part of the inner core. The (1)D(2) → (3)H(4) emission spectra of Cs(2)NaPr(NO(2))(6) at 7 K enabled assignments to be made for the crystal-field (CF) levels of the ground-state multiplet. The emission of the dilute system Cs(2)NaY(NO(2))(6):Pr(3+) was dominated by NO(2)(-) triplet emission, which was quenched at elevated temperatures by energy transfer to trace Eu(3+) impurity. From magnetic dipole calculations and the vibronic fingerprint, detailed assignments are given for the complex 10 K electronic absorption spectrum of Cs(2)NaPr(NO(2))(6) between 3940 and 18800 cm(-1), and the derived Pr(3+) 4f(2) energy-level data set has been fitted by calculation. By comparison with Cs(2)NaPrCl(6), the fourth-order CF parameter in Cs(2)NaPr(NO(2))(6) is relatively small so that interaction with a 4fnp configuration is not important. From the NO(2)(-) absorption bands above 20,000 cm(-1), the N-O bond length change upon excitation is small, whereas the angle O-N-O opens by more than 10° in the triplet state. By contrast to the NO(2)(-) internal vibration frequencies, which except for the wagging mode show only minor changes with the environment, the triplet-state energy shows a linear decrease with an increase of the lanthanide (Ln(3+)) ionic radius in Cs(2)NaLn(NO(2))(6). Using the eigenvectors from the energy-level fit, the variation of the inverse magnetic susceptibility with temperature has been calculated between 1 and 100 K and the values are somewhat lower than those from experiment.

Design of mechanical components for vibration reduction in an atomic force microscope

Vibration is a key factor to be considered when designing the mechanical components of a high precision and high speed atomic force microscope (AFM). It is required to design the mechanical components so that they have resonant frequencies higher than the external and internal vibration frequencies. In this work, the mechanical vibration in a conventional AFM system is analyzed by considering its mechanical components, and a vibration reduction is then achieved by reconfiguring the mechanical components. To analyze the mechanical vibration, a schematic of the lumped model of the AFM system is derived and the vibrational influences of the AFM components are experimentally examined. Based on this vibration analysis, a reconfigured AFM system is proposed and its effects are compared to a conventional system through a series of simulations and experiments.

A quantum-chemical study of the structure and conformational dynamics of the acrolein molecule in the ground electronic state

The geometric parameters (including vibrationally averaged parameters), energy differences (ΔE) between the s-cis and s-trans conformers, and barrier to internal rotation (Vt) were calculated for the acrolein molecule CH2=CHCHO by various quantum-chemical methods (MP2, DFT, CASSCF, QCISD, CCSD(T), and MR-AQCC). The MP2 and B3LYP methods were used to calculate internal rotation potential functions and vibrational frequencies; the calculations were performed in various anharmonic approximations. To refine the ΔE and Vt values, two-dimensional (using a basis set of atomic orbitals) VFPA extrapolation procedure was applied, which allowed the results to be estimated in the FCI/CBS approximation taking into account nonadiabaticity, core correlation effects, and changes in the difference between zero point energies.

Structural phase transitions and Raman spectra of pyridinium perrhenate at high pressures

The crystal structure and vibrational spectra of deuterated pyridinium perrhenate (d 5PyH)ReO 4 (C 5D 5NHReO 4) have been studied by means of X-ray diffraction and Raman spectroscopy at high pressures up to 15 and 9.5 GPa, respectively. Two phase transitions, from orthorhombic phase II with Cmc2 1 symmetry to phase I with Cmcm symmetry at P = 0.7 GPa and to new monoclinic phase IV with P2 1 symmetry at P = 5 GPa were observed. The internal vibrational modes frequencies, lattice parameters and unit cell volume as functions of pressure were obtained for different phases.

Dipole active vibrations and dipole moments of N2 and O2 physisorbed on a metal surface

We have, in infrared reflection absorption measurements, observed narrow dipole active absorption lines associated with the fundamental internal vibrational transitions of N(2) and O(2) physisorbed at 30 K on the chemically inert Pt(111)(1 x 1)H surface. Such transitions are forbidden for free homonuclear molecules and become dipole active at a metal surface due to polarization induced surface dipole moments. The measurements show that the internal stretch vibration frequencies are lowered by 7-8 cm(-1) relative to the gas phase values. The measured static and dynamic dipole moments are in the ranges of 0.06-0.07 and 0.001-0.002 D, respectively. We find that good estimates of the induced dynamic as well as the static dipole moments can in general be obtained from a van der Waals model but that the ratios of the measured static and dynamic moments indicates a need for a refinement of the dipole moment function.

An IR and Raman study of trigonal triple molybdates M 5 I M 0.5 II Hf1.5(MoO4)6 (MI = K, Tl; MII = Ca, Sr, Ba, Pb)

The vibration spectra of triple molybdates M 5 I M 0.5 II Hf1.5(MoO4)6 (MI = K, Tl; MII = Ca, Sr, Ba, Pb) were examined. The internal vibration frequencies of molybdate groups were assigned. The double-charged cations affect the symmetric stretching (v1), bending, and translation vibration frequencies in the Raman spectra. In the IR spectra, the triply degenerate stretching vibration of the MoO4 group (∼890–720 cm−1) is split, and the splitting increases with an increase in the radius of the double-charged cation.

Kinetic Isotope Effects and Variable Reaction Coordinates in Barrierless Recombination Reactions

The factors affecting kinetic isotope effects in barrierless recombination reactions are considered from the perspective of variational transition state theory (VTST). Despite the broad application of VTST methods, a general consideration of kinetic isotope effect predictions of the theory has not previously been undertaken, especially for cases where changes in the internal structure and vibrational frequencies of the fragments (i.e., the conserved modes) can be assumed to be negligible. Use of the center-of-mass separation as the reaction coordinate in such a case entails some restriction on the range of kinetic isotope effects which can be accommodated. Larger effects are possible within a variable reaction coordinate implementation of transition state theory, and the predicted kinetic isotope effects are shown to be strongly dependent on the location of the pivot point. Illustrative model calculations demonstrate the feasibility of reproducing the experimentally observed kinetic isotope effects for the CH + O2, HCC + O2, CH + C2H2, and CH + C2H4 reactions with realistic deviations of the pivot points from the center-of-mass. In contrast, calculations restricted to center-of-mass pivot points predict isotope effects that are even inverted. For the CH + CH4 reaction, the isotope effects appear too large to be explained by the reaction coordinate variations, and changes in the conserved modes play a key role in the observed isotope effects, as demonstrated with ab initio based TST simulations. Overall, the experimentally observed kinetic isotope effects in CH addition reactions are strongly suggestive of an optimum reaction coordinate corresponding to a pivot point located near the center of the radical orbital.

Oxygen interaction with disordered and nanostructured Ag(001) surfaces

We investigated O2 adsorption on Ag(001) in the presence of defects induced by Ne+ sputtering at different crystal temperatures, corresponding to different surface morphologies recently identified by scanning tunneling microscopy. The gas-phase molecules were dosed with a supersonic molecular beam. The total sticking coefficient and the total uptake were measured with the retarded reflector method, while the adsorption products were characterized by high resolution electron energy loss spectroscopy. We find that, for the sputtered surfaces, both sticking probability and total O2 uptake decrease. Molecular adsorption takes place also for heavily damaged surfaces but, contrary to the flat surface case, dissociation occurs already at a crystal temperature, T, of 105 K. The internal vibrational frequency of the O2 admolecules indicates that two out of the three O2− moieties present on the flat Ag(001) surface are destabilized by the presence of defects. The dissociation probability depends on surface morphology and drops for sputtering temperatures larger than 350 K, i.e., when surface mobility prevails healing the defects. The latter, previously identified with kink sites, are saturated at large O2 doses. The vibrational frequency of the oxygen adatoms, produced by low temperature dissociation, indicates the formation of at least two different adatom moieties, which we tentatively assign to oxygen atoms at kinks and vacancies.

Prediction of the Molecular Structure, Internal Rotational Barriers and Vibrational Frequencies of Formamide by Non-local Density Functional Theory

A state-of-the-art non-local density functional study of formamide is reported and compared with experimental molecular structure, internal rotational barriers and vibrational frequencies.

Energy distributions of neutrons scattered from solid C60 by the beryllium detector method

We measured the energy distribution of neutrons scattered from polycrystalline C60, using a high-resolution filter-analyzer spectrometer. In the energy range 30–90 meV (242–726 cm−1) we observed a rich spectrum that we fitted to a sum of 15 Gaussian functions, each of which is assigned to one or a set of several degenerate normal vibrational modes of the C60 molecule. We also observed two broad features in the energy range from 90–130 meV (726–1049 cm−1). Our results are generally in excellent agreement with published spectroscopic data. Detailed comparisons with the results of several first-principles calculations suggest that present-day theories can predict the internal vibrational frequencies of C60 rather well, at least in the 30–90 meV range of energies.

Theoretical studies of the RSOO, ROSO, RSO 2 and HOOS (R=H, CH 3) radicals

The geometries of the radicals HSOO, HOSO, HSO 2 and HOOS have been optimized at the MP2=FULL/6-31G * level, and energies obtained with Gaussian-2 theory. Internal rotations and vibrational frequencies are analyzed. The results yield values of Δ H f,298 for the four doublet radicals of 111.5, −241.4, −141.4 and 58.9 kJ mol −1, respectively. Implications for reactions of interest in combustion and atmospheric chemistry are discussed. The results are employed to derive Δ H f,0 for CH 3SOO, CH 3OSO and CH 3SO 2 of 91.8, −222.6 and −199.4 kJ mol −1, respectively. The calculated CH 3SOO bond strength is in excellent accord with a recent measurement.