Mixed quantum-classical molecular dynamics analysis of the molecular-level mechanisms of vibrational frequency shifts

A detailed analysis of the origins of vibrational frequency shifts of diatomic molecules (I2 and ICl) in a rare gas (Xe) liquid is presented. Specifically, vibrationally adiabatic mixed quantum-classical molecular dynamics simulations are used to obtain the instantaneous frequency shifts and correlate the shifts to solvent configurations. With this approach, important mechanistic questions are addressed, including the following: How many solvent atoms determine the frequency shift? What solvent atom configurations lead to blue shifts, and which lead to red shifts? What is the effect of solute asymmetry? The mechanistic analysis can be generally applied and should be useful in understanding what information is provided by infrared and Raman spectra about the environment of the probed vibrational mode.     

Interpreting protein structural dynamics from NMR chemical shifts

In this investigation, semiempirical NMR chemical shift prediction methods are used to evaluate the dynamically averaged values of backbone chemical shifts obtained from unbiased molecular dynamics (MD) simulations of proteins. MD-averaged chemical shift predictions generally improve agreement with experimental values when compared to predictions made from static X-ray structures. Improved chemical shift predictions result from population-weighted sampling of multiple conformational states and from sampling smaller fluctuations within conformational basins. Improved chemical shift predictions also result from discrete changes to conformations observed in X-ray structures, which may result from crystal contacts, and are not always reflective of conformational dynamics in solution. Chemical shifts are sensitive reporters of fluctuations in backbone and side chain torsional angles, and averaged (1)H chemical shifts are particularly sensitive reporters of fluctuations in aromatic ring positions and geometries of hydrogen bonds. In addition, poor predictions of MD-averaged chemical shifts can identify spurious conformations and motions observed in MD simulations that may result from force field deficiencies or insufficient sampling and can also suggest subsets of conformational space that are more consistent with experimental data. These results suggest that the analysis of dynamically averaged NMR chemical shifts from MD simulations can serve as a powerful approach for characterizing protein motions in atomistic detail.     

Vibrational recognition of adsorption sites for CO on platinum and platinum-ruthenium surfaces

We have studied the vibrational properties of CO adsorbed on platinum and platinum-ruthenium surfaces using density-functional perturbation theory within the Perdew-Burke-Ernzerhof generalized-gradient approximation. The calculated C-O stretching frequencies are found to be in excellent agreement with spectroscopic measurements. The frequency shifts that take place when the surface is covered with ruthenium monolayers are also correctly predicted. This agreement for both shifts and absolute vibrational frequencies is made more remarkable by the frequent failure of local and semilocal exchange-correlation functionals in predicting the stability of the different adsorption sites for CO on transition metal surfaces. We have investigated the chemical origin of the C-O frequency shifts introducing an orbital-resolved analysis of the force and frequency density of states, and assessed the effect of donation and backdonation on the CO vibrational frequency using a GGA+molecular U approach. These findings rationalize and establish the accuracy of density-functional calculations in predicting absolute vibrational frequencies, notwithstanding the failure in determining relative adsorption energies, in the strong chemisorption regime.     

Theory supplemented by experiment. Electronic effects on the rotational stability of the amide group in p-substituted acetanilides

The electronic effect of polar substituents on the barrier of internal rotation around the amide carbon-nitrogen bond in a series of 10 p-substituted acetanilides is studied by applying density functional theory at the B3LYP/6-31G(d,p) level. The theoretical results are supplemented by experimental data on the amide C=O and N-H stretching mode frequency shifts. It is shown that computations at the theoretical level employed provide a valuable approach in studying the factors determining the conformational stability of the studied series of compounds. It is found that an excellent linear dependence between the barriers of rotation and frequency shifts exists. It is concluded that the variations of the amide C=O stretching mode frequency can be used for quantitative characterization of the amide group conformational flexibility in the studied series of acetanilides.     

Obtaining more accurate Fourier transform ion cyclotron resonance mass measurements without internal standards using multiply charged ions

Space-charge effects produce frequency shifts in Fourier transform ion cyclotron resonance (FTICR) mass spectrometry and correction for these shifts is necessary for obtaining accurate mass measurements. We report a novel method for obtaining accurate mass calibration to correct for space-charge induced mass shifts without the requirement for internal calibrants. The new approach is particularly well suited for electrospray ionization-FTICR mass spectra that contain multiple charge states of the same molecular species. This method, deconvolution of Coulombic affected linearity (DeCAL), is described and presented with several examples demonstrating the increased mass measurement accuracy obtained. DeCAL provides the basis for more routinely obtaining higher mass accuracy measurements in conjunction with chromatographic separations for complex mixture analysis, and obviates the need for internal calibration in many applications.     

Determination of free energy profiles by repository based adaptive umbrella sampling: bridging nonequilibrium and quasiequilibrium simulations

We propose a new adaptive sampling approach to determine free energy profiles with molecular dynamics simulations, which is called as "repository based adaptive umbrella sampling" (RBAUS). Its main idea is that a sampling repository is continuously updated based on the latest simulation data, and the accumulated knowledge and sampling history are then employed to determine whether and how to update the biasing umbrella potential for subsequent simulations. In comparison with other adaptive methods, a unique and attractive feature of the RBAUS approach is that the frequency for updating the biasing potential depends on the sampling history and is adaptively determined on the fly, which makes it possible to smoothly bridge nonequilibrium and quasiequilibrium simulations. The RBAUS method is first tested by simulations on two simple systems: a double well model system with a variety of barriers and the dissociation of a NaCl molecule in water. Its efficiency and applicability are further illustrated in ab initio quantum mechanics/molecular mechanics molecular dynamics simulations of a methyl-transfer reaction in aqueous solution.     

Influence of molecular adsorption on the dielectric properties of a single wall nanotube: a model sensor

Recent measurements of the resonance frequency of a copper disk covered with carbon nanotube bundles have shown characteristic resonance shifts during exposure with various gas molecules. The shifts were interpreted as the change of the dielectric permittivity of the system forming the sensor due to the electric properties of the adsorbed molecules. Starting from a simplified sensor model formed by one single wall nanotube, we develop a self-consistent approach to describe the variation of the linear dielectric susceptibility of the tube at the atomic scale when molecules are adsorbed at its external surface. The sensitivity of this model sensor is tested as a function of the apolar or polar nature of the admolecules, their adsorption geometry, their concentration, and the characteristics of the tube (length, diameter,...). The comparison with data on dielectric constant changes vs adsorption, coming from measurements of the resonance frequency shifts, displays striking agreement for most of the molecular species considered.     

Temperature-Dependent Terahertz Spectra of Isonicotinamide in the Form I Studied Using the Quasi-Harmonic Approximation

Anharmonicity of molecular vibrational motions is closely associated with the thermal property of crystals. However, the origin of anharmonicity is still not fully understood. Low-frequency vibrations, which are usually defined in the terahertz (THz) range, show excellent sensitivity to anharmonicity. In this work, anharmonicity of isonicotinamide in the form I was investigated by using temperature-dependent terahertz time-domain spectroscopy and the quasi-harmonic approximation (QHA) approach at PBE-D3 and PBE-MBD levels. Both DFT calculations suggest the variation of π-π stacking conformation dominates in the thermal expansion of the unit cell. Frequency shifts of the modes in THz range obtained by QHA approach are found to be qualitatively consistent with experimental observations, demonstrating QHA approach is a useful tool for the interpretation of frequency shifts of modes induced by temperature.     

Measurements of infrared frequency shifts in stressed polymers

A difference-spectrum method is used to measure vibrational frequency shifts in mechanically stressed polymers. It is shown that the peak-to-peak height of the difference-spectrum intensity profile is a linear function of small frequency shifts with a slope inversely proportional to the band halfwidth for Lorentzian or Gaussian bands. The method is applied to measure frequency shifts in uniaxially stressed ultraoriented isotactic polypropylene films, using a double beam infrared grating dispersion spectrometer with a nonstressed sample in the reference beam. It is shown that frequency shifts can be measured with an accuracy of better than 0.01 cm^?1 using the difference-spectrum method.     

Correlation between solvent-induced vibrational frequency shifts of the CO moiety and solvent electron acceptor numbers: tetramethylurea

The CO stretching frequencies in the Raman spectra of 0.10 M solutions of tetramethylurea in seventeen solvents have been recorded. These frequencies exhibit a linear relationship with the solvent electron acceptor number. Comparison of the slopes of these lines and those obtained from analyzing literature data of ν(CO) reveals a correlation with the bond polarity. A linear correlation between (ν_hexane −ν_soln)/ν_hexane and the solvent acceptor number is also shown. The slopes of these latter plots can be related to ν_hexane and it is suggested that this approach be used to explain the specific solvent—solute interaction contributions to solvent-induced vibrational frequency shifts. This method is compared with the solvato-chromic method and it is shown that solvent acidity strongly influences the observed vibrational frequency shifts for the CO moiety of tetramethylurea.     

Quasiharmonic treatment of infrared and raman vibrational frequency shifts induced by tensile deformation of polymer chains. II. Application to the polyoxymethylene and isotactic polypropylene single chains and the three-dimensional orthorhombic polyethylene crystal

Quasiharmonic equations are derived for stress-induced vibrational frequency shifts in the infrared and Raman spectra of polymer chains subjected to a tensile stress. The expressions are applied to the helical chains of polyoxymethylene and isotactic polypropylene. Observed frequency shifts can be reproduced well by using reasonable anharmonic force constants. A semiquantitative interpretation is given for the close relationship between stress-induced vibrational frequency shifts and the deformation mechanism of the polymer chains. Stress-induced frequency shifts are also calculated for an orthorhombic polyethylene crystal subjected to uniaxial tension along the chain axis or to hydrostatic pressure. The results consistently and reasonably reproduce observed data, not only for the intramolecular vibrational modes but also for the external lattice modes. © 1992 John Wiley & Sons, Inc.     

Anharmonicity of weakly bound M(+)-H2 complexes

The anharmonicity of weakly bound complexes is studied using the vibrational self-consistent field (VSCF) approach for a series of metal cation dihydrogen (M(+)-H(2)) complexes. The H-H stretching frequency shifts of M(+)-H(2) (M(+) = Li(+), Na(+), B(+), and Al(+)) complexes are calculated with the coupled-cluster method including all single and double excitations with perturbative triples (CCSD(T)) level of theory with the cc-pVTZ basis set. The calculated H-H stretching frequency of Li(+)-H(2), B(+)-H(2), Na(+)-H(2), and Al(+)-H(2) is red-shifted by 121, 202, 74, and 62 cm(-1), respectively, relative to that of unbound H(2). The calculated red shifts and their trends are in good agreement with the available experimental and previously calculated data. Insight into the observed trends is provided by symmetry adapted perturbation theory (SAPT).     

Density functional theory calculations of pressure effects on the vibrational structure of alpha-RDX

Pressure effects on the vibrational structure of alpha-RDX were examined using density functional theory (DFT) up to 4 GPa. The calculated vibrational frequencies at ambient conditions are in better agreement with experimental data than are previous single molecule calculations. The calculations showed the following pressure-induced changes: (i) larger shifts for lattice modes and for internal modes associated with the CH(2) and NO(2) groups as compared to the pressure shifts for modes associated with the triazine ring, (ii) enhancement of mixing between different vibrations, for example, between NN stretching and CH(2) scissor, wagging, twisting vibrations, and (iii) increase in mixing between translational lattice vibrations and the NO(2) wagging vibrations, reducing the distinction between internal and lattice modes. The calculated volume and lattice constants at ambient pressure are larger than the experimental values, due to the inability of the present density functional approach to correctly account for van der Waals forces. Consequently, the pressure-induced frequency shifts of many modes deviate substantially from experimental data for pressures below 1 GPa. With increasing pressure, both the lattice constants and the frequency shifts agree more closely with experimental values.     

Sizable concentration-dependent frequency shifts in solution NMR using sensitive probes

With the growing use of high fields and ultrasensitive probes, radiation damping emerges as a significant feedback interaction in modern solution NMR. Motivated by recent observations of mysterious concentration-dependent frequency shifts, experiments carried out on a cryoprobe at 600 MHz have revealed a time-averaged frequency shift of up to +83/-81 Hz. The sizable frequency shifts arise from deviations in the phase of the radiation damping field from perfect orthogonality relative to the net transverse magnetization. The frequency shift is shown to depend on the longitudinal magnetization and probe tuning conditions through experiments and numerical simulations. Such unexpected shifts in the solvent precession frequency provide a physical explanation for the empirical practice of adjusting the irradiation frequency of the saturating B1 field in solvent presaturation to achieve optimal suppression. Additional applications of the radiation damping induced frequency shift to solvent suppression and NMR methodology are discussed.     

Hydrogen bonding in polymer mixtures

The enthalpy–infrared frequency shift correlation for simple acids and bases is extended to study hydrogen bonding in polymer systems. The acidity of a polymer is calibrated by comparing the shifts in hydroxyl absorption frequency of the acidic polymer when mixed with a series of bases with the corresponding spectral shifts of known acids with the same bases. The basicity of a polymer is calibrated by measuring the hydroxyl frequency shifts of known acids when mixed with the basic polymer. For polymers containing carbonyl groups, the shift in carbonyl absorption is also a measure of basicity. The acidity and basicity constants obtained for polymers are in good agreement with the values for small-molecule analogs. The enthalpies of hydrogen bond formation in polymer mixtures are calculated from the acidity or basicity constants.     

GFT NMR,a new approach to rapidly obtain precise high-dimensional NMR spectral information

Widely used higher-dimensional Fourier transform (FT) NMR spectroscopy suffers from two major drawbacks: (i) The minimal measurement time of an N-dimensional FT NMR experiment, which is constrained by the need to sample N - 1 indirect dimensions, may exceed by far the measurement time required to achieve sufficient signal-to-noise ratios. (ii) The low resolution in the indirect dimensions severely limits the precision of the indirect chemical shift measurements. To relax on constraints arising from these drawbacks, we present here an acquisition scheme which is based on the phase-sensitive joint sampling of the indirect dimensions spanning a subspace of a conventional NMR experiment. This allows one to very rapidly obtain high-dimensional NMR spectral information. Because the phase-sensitive joint sampling yields subspectra containing "chemical shift multiplets", alternative data processing is required for editing the components of the multiplets. The subspectra are linearly combined using a so-called "G-matrix" and subsequently Fourier-transformed. The chemical shifts are multiply encoded in the resonance lines constituting the shift multiplets. This corresponds to performing statistically independent multiple measurements, and the chemical shifts can thus be obtained with high precision. To indicate that a combined G-matrix and FT is employed, we named the new approach "GFT NMR spectroscopy". GFT NMR opens new avenues to establish high-throughput protein structure determination, to investigate systems with a higher degree of chemical shift degeneracy, and to study dynamic phenomena such as slow folding of biological macromolecules in greater detail.     

An electrostatic model for the frequency shifts in the carbonmonoxy stretching band of myoglobin: correlation of hydrogen bonding and the stark tuning rate

The effect of internal and applied external electric fields on the vibrational stretching frequency for bound CO (nu(CO)) in myoglobin mutants was studied using density functional theory. Geometry optimization and frequency calculations were carried out for an imidazole-iron-porphine-carbonmonoxy adduct with various small molecule hydrogen-bonding groups. Over 70 vibrational frequency calculations of different model geometries and hydrogen-bonding groups were compared to derive overall trends in the C-O stretching frequency (nu(CO)) in terms of the C-O bond length and Mulliken charge. Simple linear functions were derived to predict the Stark tuning rate using an approach analogous to the vibronic theory of activation.(1) Potential energy calculations show that the strongest interaction occurs for C-H or N-H hydrogen bonding nearly perpendicular to the Fe-C-O bond axis. The calculated frequencies are compared to the structural data available from 18 myoglobin crystal structures, supporting the hypothesis that the vast majority of hydrogen-bonding interactions with CO occur from the side, rather than the end, of the bound CO ligand. The nu(CO) frequency shifts agree well with experimental frequency shifts for multiple bands, known as A states, and site-directed mutations in the distal pocket of myoglobin. The model calculations quantitatively explain electrostatic effects in terms of specific hydrogen-bonding interactions with bound CO in heme proteins.     

Frequency shifts due to the interference of resolved peaks in magnitude-mode Fourier-transform ion cyclotron resonance mass spectra

We have obtained relationships for frequency shifts resulting from the interference of spectral components for the magnitude mode Fourier transform. The approximation of a weak perturbation of well resolved peaks has been used. Both the low- and high-pressure limits for Fourier-transform ion cyclotron resonance (FTICR) operation have been considered. We have found that the shifts can be either negative or positive, depending on the initial phase and/or the choice of the time-domain interval. The magnitude of shifts generally does not exceed the peak width. In the approximation of small perturbations the shifts produced by multiple peaks are additive. We have compared theoretical results with experimental shifts for isotopic clusters of multiply charged insulin. Up to 1 ppm frequency variations were experimentally observed for the insulin 5+ charge state, consistent with theoretical estimates. The peak interference is of particular significance in the case of bio-molecular mass spectra having a large number of peaks and covering a considerable dynamic range (i.e., relative abundance). We conclude that the common mass measurement procedure based on the location of the magnitude mode maxima of well resolved peaks can result in systematic mass measurement errors. The relationships obtained provide corrections for the frequency shifts and thus improve the mass measurement accuracy.     

Complete 1H and 13C signal assignment of prenol‐10 with 3D NMR spectroscopy

The complete assignment of ¹H and ¹³C chemical shifts of natural abundance prenol‐10 is reported for the first time. It was achieved using 3D NMR experiments, which were based on random sampling of the evolution time space followed by multidimensional Fourier transform. This approach makes it possible to acquire 3D NMR spectra in a reasonable time and preserves high resolution in indirectly detected dimensions. It is shown that the interpretation of 3D COSY–HMBC and 3D TOCSY–HSQC spectra is crucial in the structural analysis of prenol‐10. Copyright © 2009 John Wiley & Sons, Ltd.     

Flow-injection enzymatic assays

The advantages to be gained by conducting enzymatic assays in flow-injection systems are discussed. Selected examples based on the use of soluble and soluble and immobilized enzyme preparations are given. This approach not only offers high sampling frequency and convenient solution handling in assays for enzymes and substrates but is also valuable for testing sensor performance and monitoring bioreactors.