Vibrational Spectral Properties Research Articles

Revisiting OD-stretching dynamics of methanol‑d4, ethanol-d6 and dilute HOD/H2O mixture with predefined potentials and wavelet transform spectra

• The stretching profiles of OD probes were obtained from classical trajectories. • The normalized frequency distribution and rotational anisotropy are reported. • An accurate and efficient method was reported for the spectral profiles. • The reported results are in an excellent agreement with that of the experiment. Classical molecular dynamics simulations were performed to explore the stretching profiles of hydrogen-bonded liquids using the wavelet transform of classical trajectories to calculate the time-resolved vibrational stretching frequencies of the probes. This method considers the instantaneous distance fluctuations of the unit vector and the momentum along the corresponding bond to calculate the instantaneous stretching frequencies and equilibrium distribution. In this work, we calculated the vibrational spectral properties of the O-D stretch modes in hydrogen-bonding liquids, water, methanol, and ethanol. The time-varying vibrational stretching frequencies of the probes were obtained from the simulated trajectory accurately as compared to other methods. The normalized frequency distribution, time-dependent decay of frequency fluctuations, rotational anisotropy calculations are reported, and relative comparison is made with the existing results. The results of the isotopically diluted HOD mixture and deuterated methanol molecules are in excellent agreement with the experiment, and the ethanol results are satisfactory. This computational method of determining the stretching frequency distribution comparable to the reported vibrational spectrum is one of the complementary accurate theoretical models for the ultrafast vibrational echo spectroscopy experiments. Further, the method can also be adapted to calculate the instantaneous stretching frequency of any probe of interest in a complicated molecular environment.

Synthesis, physicochemical and vibrational spectral properties of 2–pyridone and 2–aminopyridine derivatives: An experimental and theoretical study

A convenient and efficient one–pot three–component reaction of acetyl acetone, malononitrile and ammonium acetate was investigated for the synthesis of 3–cyano–4,6–dimethyl–2–pyridone (PI) and 2–amino–3–cyano–4,6–dimethylpyridine (PII). The products were achieved with high purity, high yields and short reaction time. The yields of the two products depend on the concentration of ammonium acetate, reaction time and the solvent used. The structures of the isolated products were confirmed by elemental analysis and spectral data, supported by quantum chemical (MP2) calculations, both in gas phase and solvents (water and ethanol), that were also employed to track the reaction mechanisms and model vibrational spectral properties for final characterization and interpretation of spectral data. A remarkable matching between theoretical predictions and experiments was attained both for the geometrical parameters, as compared to X-Ray data available in the literature, and for vibrational frequencies, leading to a correlation coefficient (R2) of 0.99. Molecular docking was further studied to predict the docking binding energy of the synthesized compounds with the target proteins.

Structural and Thermophysical Anomalies of Liquid Water: A Tale of Molecules in the Instantaneous Low- and High-Density Regions.

Water is believed to be a heterogeneous liquid comprising multiple density regions that arise because of the presence of interstitial molecules and can be differentiated by their structure as well as the existence of hydrogen-bonded pairs with varying strengths. First-principles molecular dynamics studies were performed at six different temperatures to investigate the effect of temperature on the thermophysical, structure, dynamics, and vibrational spectral properties of the water molecules using dispersion-corrected density functional theory. The variation of properties like density, cohesive energy, and compressibility with a change in temperature produces a trend that matches with the experiments and resembles the experimentally observed anomalous behavior. We explore the possibility of explaining the trends in calculated properties by analyzing the structure and dynamics of the water molecules in terms of instantaneous low- and instantaneous high-density regions that are found during the simulation time. The dynamics of these two types of water molecules were studied by calculating the lifetime from the proposed autocorrelation functions. The lifetime of formation of instantaneous low-density water is found to decrease with an increase in temperature, whereas the lifetime of instantaneous high-density water is found to be maximum at 298 K among all the considered temperatures. The presence of more interstitial water molecules is observed at this temperature. The signature of these water molecules is found in the radial distribution function, spatial distribution function, void distribution, configurational space, orientational dynamics, and spectral diffusion calculations. It is also found that around 298 K, these water molecules are present distinctively that mix up with the first and second solvation shells with the rise of the temperature. The outlook of the reported results can be extended to other thermodynamic conditions to explain some of the anomalous properties, which can be related to the presence of the interstitial molecules in water.

An equation of motion approach for the vibrational transition energies in the effective harmonic oscillator formalism: the Random phase approximation

A theory for calculating vibrational energy levels and infrared intensities is developed in the equation of motion framework at the random phase approximation level. The vibrational Hamiltonian is expanded in the harmonic oscillator ladder operators making a Hamiltonian a bosonic Hamiltonian. The excitation operator is expanded to include at most two creations and two annihilation operators making it equivalent to the random phase approximation. The method is applied for the calculation of vibrational spectral properties of two molecules. The results are found to be satisfactory, making this approach a viable option for large molecular systems. A theory for calculating vibrational energy levels and infrared intensities is developed in the equation of motion framework at the random phase approximation level. The vibrational Hamiltonian is expressed in bosonic representation. The excitation operator is expanded to include at most two creation and annihilation operators.

Solvent Effects on Nafion Dispersion Structure Probed By Infrared Spectroscopy

The structure of Nafion dispersed in water and ethanol solutions was investigated using infrared spectroscopy. Since the properties of dispersing fluids can affect the mechanical strength of solution-cast Nafion thin films,1 it was of interest to gain insights into the structure and the vibrational spectral properties of the ionomer in the dispersion phase. To minimize deleterious effects of optical dispersion,2 traditional transmission infrared spectra were recorded from both dispersions as well as solvent-free thin films. Subsequently, transitions from the dispersion, through the gel-phase and dried film were followed as a function of time during film formation using the attenuated total reflection (ATR) infrared sampling technique. The vibrational spectra of thin Nafion films prepared from dispersions in ethanol solvent and water solvent were similar, except the former had a pronounced shoulder near 1125 cm-1 and sharper 983 cm-1 peak, both of which can be ascribed to sidechain vibrations. The enrichment of trace water in the ethanol solvent during evaporative drying was quantified through analysis of the 2750 cm-1 – 3500 cm-1 spectral region using partial least square (PLS) modeling. In the gel-phase, water was detected above 50 mol%, indicating water enrichment should be considered in developing models for solvent effects on Nafion film formation. Kim, Y. S.; Welch, C. F.; Hjelm, R. P.; Mack, N. H.; Labouriau, A.; Orler, E. B. Origin of toughness in dispersion-cast Nafion membranes Macromolecules 2015, 48, 2161-2172.Kollath, V. O.; Liang, Y.; Mayer, F. D.; Ma, X.; Korzeniewski, C.; Karan, K. Model-based analyses of confined polymer electrolyte nanothin films experimentally probed by polarized ATR−FTIR spectroscopy J. Phys. Chem. C 2018, 122, 9578−9585. Figure 1

Heterogeneous Occupancy and Vibrational Dynamics of Spatially Patterned Water Molecules.

We performed first-principles molecular dynamics simulations of relatively dilute aqueous solutions of sulfate and thiosulfate dianions to analyze the structure, dynamics, and vibrational spectral properties of water molecules around the solute, especially the spatially patterned solvent molecules in the first solvation layer and the extended layers. This study also involves the investigation of dynamics of dangling OH groups in these layers and their role in patterning the water molecules around the dianions. Structural evaluation of the systems is carried out by radial distribution functions, number integrals, and spatial distribution functions. The lifetime of dangling OH groups inside the solvation shell is compared more to that of the bulk. By constructing the O-H groups in three ensembles (S1, S2, and S3) around the anion, we show that the frequency distribution of OH modes in the S1 ensemble show red-shifting for both sulfate and thiosulfate. The O-H groups in the S2 ensemble of the sulfate-water system show red-shifting by 10 cm-1, while in the case of thiosulfate-water, these O-H groups show blue-shifting by 8 cm-1. The water molecules in S1 and S2 subensembles have slower dynamics compared to those in the bulk (S3). The dynamics of various kinds of hydrogen bonds were characterized by hydrogen bond population correlation functions. The spectral diffusion of solvation shell O-H modes was performed through a frequency-time correlation function. We find a significant amount of orientational retardation of water molecules in the S1 layer and moderate retardation in the S2 layer as compared to that in the bulk, S3 layer. All these findings, the red shift of the OH stretching frequency in S1 and S2 layers, slowing down of the orientational dynamics of OH vectors in S1 and S2 layers, and less diffusivity of water in S1 and S2 layers, show the long-range kosmotropic effect of multivalent sulfate and thiosulfate oxyanions. Due to the long-range effect, heterogeneous occupancy of water molecules is observed, and the water molecules are found to arrange in a patterned manner in the vicinity of anions with varied local density.

Infrared Spectral and Dynamical Properties of Water Confined in Nanobubbles at Hybrid Interfaces of Diamond and Graphene: A Molecular Dynamics Study

In this work, we have studied the behavior of water molecules confined in nanobubbles at the hybrid interfaces of graphene and diamond surfaces at varying temperatures. We have performed molecular dynamics simulations to investigate different spectral and dynamical properties of the confined water. The confined water molecules are characterized through calculations of their vibrational spectral properties. The spectral features are found to change significantly with variation of temperature and density of the nanobubbles. The calculated vibrational spectral results are found to be in reasonably good agreement with available experiments. Furthermore, we have looked at the dynamical properties of water molecules in the graphene nanobubbles. The current results reveal the presence of strong heterogeneity in the dynamical properties in nanobubbles at supercritical temperature. Water molecules that are confined in small nanobubbles at high density are found to possess very slow relaxation time scales because of stronger hydrogen bonding and spatial constraints. These water molecules can be considered as essentially irrotational water molecules. In other cases, water molecules confined in nanobubbles at lower density at supercritical temperature are found to show very fast relaxation time scales as the thermal energy dominates the dynamics of water molecules in these cases.

Structure, isomerism, and vibrational assignment of aluminumtrifluoroacetylacetonate. An experimental and theoretical study

An interpretation of the experimental IR and Raman spectra of Aluminum (III) trifluoroacetylacetonate (Al(TFAA)3) complex, which were synthesized by us, is first reported here. The charge distribution, isomerism, strength of metal‑oxygen binding and vibrational spectral properties for this complex structure were theoretically investigated through population analysis, geometry optimization and harmonic frequency calculations, performed at B3LYP/6-311G* level of theory. In the population analysis, two different approaches reffered to as “Atoms in molecules (AIM)”, and “Natural Bond Orbital (NBO)” were used. According to the calculation resuls, the energy difference between the cis and trans isomers of Al(TFAA)3 is very small and indicates that both isomers coexist in the sample in comparable proportions. Comparison of the calculated frequency and intensity data with the observed IR and Raman spectra of the complex has supported this conclusion. On the other hand, comparison of the structural and vibrational spectral data of Al(TFAA)3, which were experimentally measured and calculated at B3LYP/6-311G* level, with the corresponding data of Aluminum acetylacetonate (Al(AA)3) has revealed the effects of CF3 substitution on the structural and vibrational spectral data associated with the CH3 groups in the complex structure.

Classical investigation of long-range coherence in biological systems.

Almost five decades ago, H. Fröhlich [H. Fröhlich, "Long-range coherence and energy storage in biological systems," Int. J. Quantum Chem. 2(5), 641-649 (1968)] reported, on a theoretical basis, that the excitation of quantum modes of vibration in contact with a thermal reservoir may lead to steady states, where under high enough rate of energy supply, only specific low-frequency modes of vibration are strongly excited. This nonlinear phenomenon was predicted to occur in biomolecular systems, which are known to exhibit complex vibrational spectral properties, especially in the terahertz frequency domain. However, since the effects of terahertz or lower-frequency modes are mainly classical at physiological temperatures, there are serious doubts that Fröhlich's quantum description can be applied to predict such a coherent behavior in a biological environment, as suggested by the author. In addition, a quantum formalism makes the phenomenon hard to investigate using realistic molecular dynamics simulations (MD) as they are usually based on the classical principles. In the current paper, we provide a general classical Hamiltonian description of a nonlinear open system composed of many degrees of freedom (biomolecular structure) excited by an external energy source. It is shown that a coherent behaviour similar to Fröhlich's effect is to be expected in the classical case for a given range of parameter values. Thus, the supplied energy is not completely thermalized but stored in a highly ordered fashion. The connection between our Hamiltonian description, carried out in the space of normal modes, and a more standard treatment in the physical space is emphasized in order to facilitate the prediction of the effect from MD simulations. It is shown how such a coherent phenomenon may induce long-range resonance effects that could be of critical importance at the biomolecular level. The present work is motivated by recent experimental evidences of long-lived excited low-frequency modes in protein structures, which were reported as a consequence of the Fröhlich's effect.

Theoretical studies on dimerization vs. microhydration of carboxylic acids

First principle based electronic structure calculations are carried out on two carboxylic acids (RCOOH: R=H, CH3); their dimers, (RCOOH)2; and hydrated clusters, RCOOH·nH2O It is predicted that carboxylic acid molecules form strong dimeric structures. In presence of sufficient number of water molecules, these dimeric structures break down and each monomeric acid molecule form hydrated clusters. Structures, energy parameters, rotational and vibrational spectral properties of these dimer as well as hydrated clusters of carboxylic acids are presented. Structures of acid dimers and hydrated clusters are calculated at DFT as well as MP2 level of theory and energy parameters of all these systems are further improved applying CCSD(T) level of theory. Minimum number of water molecules needed to break the dimeric structures of formic and acetic acids to form microhydrated structures is also examined by calculating free energy at low temperature (100K) and pressure (μTorr). Physical origin of molecular interactions between solvent water and solute acid molecules has been explored applying a scheme of energy decomposition analysis. Hydrogen bond strength of acid dimers and hydrated clusters of the acids is reported. Spectroscopic manifestation of formation of dimer and micro hydrated carboxylic acids in terms of IR bands is discussed.

L-Arginine trifluoroacetate salt bridges in its solid state compound: The low-temperature three dimensional structural determination of l-arginine bis(trifluoroacetate) crystal and its vibrational spectral analysis

Structural varieties of l-arginine trifluoroacetate (abbreviated as LATF) and l-arginine bis(trifluoroacetate), LABTF, in the solid state compounds were observed and analyzed by the nuclear magnetic resonance (NMR) spectroscopy. The guanidinium–carboxylate interaction plays an important role involving in the crystal structure construction. Conformational changes of l-Arg + and l-Arg 2+ cations result from the intrinsic structural difference by hydrogen bonding and electrostatic interactions. The low-temperature structure of its crystalline salt, l-arginine bis(trifluoroacetate), was determined to describe the hydrogen bonding interactions. In comparison with the crystal structure at room temperature, the low-temperature l-Arg 2+ cations present tiny conformational difference and the rotational disorder of CF 3 group disappears. FT-IR and Raman spectra were investigated and hydrogen bonding interactions were analyzed on the basis of its vibrational spectra. Results indicate that this type interaction is greatly contributive to the structural features and vibrational spectral properties.

Raman and mid-infrared spectroscopic study of geometrically frustrated hydroxyl cobalt halides at room temperature

Mid-infrared absorption and Raman spectra of the geometrically frustrated material series, hydroxyl cobalt halides ß-Co2(OH)3Cl and ß-Co2(OH)3Br, are first, to the best of our knowledge, measured at room temperature, to study the corresponding relationship between their vibrational spectral properties and crystal microstructures. Through the comparative analysis of the four spectra we have categorically assigned the OH-related vibration modes of hydroxyl groups in the trimeric hydrogen bond environment (Co3 ≡OH)3 … Cl/Br, and tentatively suggested vibration modes of O-Co-O, Co-O and Cl/Br-Co-Cl/Br units. These results can also become the basis for analysing their low-temperature spectral properties, which can help to understand the underlying physics of their exotic geometric frustration phenomena around phase transition temperatures.

Vibrational spectroscopic properties of botallackite-structure basic copper halides

Mid-infrared (4000–400 cm −1) absorption and Raman (4000–95 cm −1) spectra of the series of geometrically frustrated materials, botallackite-structure basic copper halides, α-Cu 2(OH) 3Cl and α-Cu 2(OH) 3Br polycrystalline samples were first, to the best of our knowledge, measured, respectively, to study the corresponding relationship between their vibrational spectral properties and crystal microstructures. Through the comparative analysis to the four spectra, the authors have definitely assigned or tentatively suggested the vibrational modes of hydroxyl groups in the trimeric hydrogen bond environment (OH) 3 Cl/Br, and atomic units O–Cu–O, Cu–O and Cl/Br–Cu–Cl/Br, etc. These results can be propitious to the low temperature spectral property of α-Cu 2(OH) 3Cl and α-Cu 2(OH) 3Br which must help to understand the underlying physics of their exotic geometric frustration phenomena at low temperatures.

Ab initio Calculations of Raman, IR‐Active Vibrational Modes in Isotopically Modified B12 Icosahedral Clusters.

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Ab-initio calculations of Raman, IR-active vibrational modes in isotopically modified B 12 icosahedral clusters

Computational calculations of Becke's three-parameter hybrid method using the LYP correlation functional (B3LYP) have been performed on (B 12H 12) 2− dodecaborane anions with different boron isotopic compositions. This was done in order to investigate isotopic dependence of vibrational spectral properties of B 12 icosahedra, and for comparison of the optical vibrational properties of the icosahedral molecule with the characteristics of inter- or intra-icosahedral optical phonon vibrational modes in boron-rich crystals.

Infrared spectroscopy of model electrochemical interfaces in ultrahigh vacuum: The archetypical case of carbon monoxide/water coadsorption on Pt(111)

Infrared reflection-absorption spectroscopic (IRAS) along with work-function measurements are presented for carbon monoxide and deuterated water co-dosed onto Pt(111) at 110 K in ultrahigh vacuum (uhv) in comparison with coverage- and potential-dependent infrared spectra for the analogous in situ Pt(111)-aqueous electrochemical interface. The twin objectives are to assess the manner and degree to which the former ‘‘uhv electrochemical modeling’’ tactic mimics the vibrational spectral properties of the latter interface, and to exploit the additional molecular structural information obtainable for the former surface configuration in elucidating solvation effects for the in situ electrochemical system. Postdosing water onto CO adlayers in uhv yields progressive attenuation of the C–O stretching (νCO) IRAS bands associated with atop and twofold bridging coordination on the clean Pt(111) surface, being replaced by bands at lower frequencies that are more characteristic of the CO coverage (θCO)-dependent νCO features observed for the electrochemical interface. This ‘‘titration-like’’ spectral response, indicating that the added water assembles into hydrogen-bound islands which are nonetheless microscopically intermixed with the contiguous CO adlayer regions, is typically complete by water coverages corresponding to about 2–3 ‘‘equivalent bilayers.’’ Water dosage-dependent spectra in the O–D stretching (νOD) region for zero or low predosed CO coverages display the hallmarks of markedly increased hydrogen bonding beyond the bilayer point, whereas such hydrogen bonding is prevalent even at submonolayer water dosages for intermediate or near-saturated θCO values. The work-function decreases, −ΔΦ, induced by water dosing also are indicative of synergistic water/CO interactions, larger −ΔΦ values being obtained in the presence of low or intermediate predosed CO coverages than in its absence. A distinction is drawn between ‘‘specific’’ and ‘‘nonspecific’’ water co-dosing effects upon the CO adlayer structure; the former involves adjacent CO/D2O coadsorbate interactions, while the latter is describable most simply by the changes in the surface potential. The θCO-dependent CO site occupancies and νCO frequencies for the hydrated uhv and electrochemical Pt(111) systems are found to be in close concordance, the latter when the interfaces are compared at equivalent values of the surface potential. The findings thereby support a close structural connection between analogous low-temperature hydrated uhv and ambient-temperature electrochemical interfaces.