Vibrations Of Molecules Research Articles

Explicitly correlated study of the torsional vibrations of HSOSH molecule. Comparison with MP2/CBS(T,Q) level of theory

Geometric parameters of equilibrium configurations of trans- and cis-conformers of HSOSH molecule, their dipole moments, rotational constants in the ground electronic and vibrational states, and kinetic parameters corresponding to two torsional coordinates and were calculated at CCSD(T)-F12/cc-pVDZ-F12 level of theory. In the latter case, at each node of the two-dimensional grid and all other geometric parameters of the molecule were optimized. The obtained configurations were used for calculation of 2D potential energy surface at CCSD(T)-F12/cc-pVTZ-F12 level without additional optimization. The energies of a number of excited torsional states were determined by numerically solving the vibrational Schrödinger equation of restricted dimensionality using two-dimensional complex Fourier series. The obtained data on the frequencies of torsional vibrations of S-H groups in the two conformers and the frequencies of tunneling in the ground and excited torsional states are compared with the results obtained earlier at MP2/CBS(T,Q) level of theory.

Theoretical insights into interaction energy, IR intensity and Raman activity enhancements of H2O adsorbed on Mg containing Zn3O3 nanoclusters: A computational study

Theoretical insights into H2O detection ability of Zn3O3 and Mg containing Zn3O3 nanoclusters are provided using density functional theory (DFT) based calculations. For this, the IR and Raman spectral properties of H2O adsorbed on Zn3O3, Zn2MgO3 (Mg as substituent) and Zn3O3Mg (Mg as interstitial atom) nanoclusters are investigated. All the species in study are optimized at B3LYP/6-31G(d,p) computational model. While Zn site of Zn3O3 is favorable for interaction of the water molecule, the site of Mg in both the Zn2MgO3 and Zn3O3Mg is preferential for interaction of H2O molecule. The complex geometry formed by H2O interacting with Mg site of Zn2MgO3 shows highest interaction energy and significant magnitudes of molecular orbital interactions. The IR intensity calculations on the stable geometries show that the symmetric mode of vibration of water molecule enhances significantly, and the predicted IR enhancement agrees with an experimental finding. The Raman activity enhancement for the symmetric vibrational mode of H2O is notable, when H2O interacts with Zn3O3Mg at Mg site. The observed IR and Raman enhancements are substantiated by the calculations on dipole moment and polarizability components of the complex geometries distorted along normal coordinates of H2O vibrational modes. The time dependent (TD) DFT calculations carried out at B3LYP/6-31G(d,p) computational model, envisages that Zn3O3Mg is a good SERS substrate for amplification of Raman spectral lines of H2O by surface plasmon resonance.

Analytical prediction of enthalpy and Gibbs free energy of gaseous molecules

By employing the improved deformed Pöschl-Teller oscillator to describe the internal vibration of a diatomic molecule, new equations for predicting the molar enthalpy and Gibbs free energy of diatomic molecules were obtained. The equations were applied to the ground states phosphorus, nitrogen, and iodine monochloride molecules. Average absolute deviations of 0.8178%, 3.1939%, and 0.5312% from experimental data were obtained using the molar enthalpy equation. The analytical expression of Gibbs free energy yields average deviations of 0.3865%, 0.4360%, and 0.0405% for the diatomic molecules. The results are in good agreement with available literature data on P2, N2, and ICl gaseous molecules.

Ultrafast control of vibrational states of polar molecules with subcycle unipolar pulses

We investigate theoretically the nonresonant excitation of vibrational levels in polar molecules by unipolar radiation pulses of duration much shorter than the characteristic period of the molecule's vibration. We consider several profiles of the potential of the interaction of atoms in a diatomic molecule and derive analytically the probabilities of the molecule's transition to excited vibrational states when driven by subcycle unipolar pulses. It is shown that the excitation efficiency is governed by the electric pulse area so that unipolar half-cycle pulses turn out to be the most efficient ones. We introduce the characteristic scale of the electric pulse area, which serves as a measure of the pulse action on the vibrational states of the molecule. The results are generalized to the interaction of excited vibrational and rotational states and it is shown that the behavior of the vibrational levels' populations versus the electric pulse area as well as the introduced characteristic scale stays valid.

Quantum information scrambling in molecules

Out-of-time-order correlators (OTOCs) can be used to probe how quickly a quantum system scrambles information when the initial conditions of the dynamics are changed. In sufficiently large quantum systems, one can extract from the OTOC the quantum analog of the Lyapunov coefficient that describes the time scale on which a classical chaotic system becomes scrambled. OTOCs have been applied only to a very limited number of toy models, such as the SYK model connected with black hole information scrambling, but they could find much wider applicability for information scrambling in quantum systems that allow comparison with experiments. The vibrations of polyatomic molecules are known to undergo a transition from regular dynamics at low energy to facile energy flow at sufficiently high energy. Molecules therefore represent ideal quantum systems to study scrambling in many-body systems of moderate size (here 6 to 36 degrees of freedom). By computing quantum OTOCs and their classical counterparts we quantify how information becomes 'scrambled' quantum mechanically in molecular systems. Between early 'ballistic' dynamics, and late 'saturation' of the OTOC when the full density of states is explored, there is indeed a regime where a quantum Lyapunov coefficient can be defined for all molecules in this study. Comparison with experimental rate data shows that slow scrambling as measured by the OTOC can reach the time scale of molecular reaction dynamics. Even for the smallest molecules we discuss, the Maldacena bound remains satisfied by regularized OTOCs, but not by unregularized OTOCs, highlighting that the former are more useful for discussing information scrambling in this type of moderate-size quantum system.

Neutron-γ discrimination with organic scintillator crystal: 9-Phenylcarbazole (9-PCz) grown by Bridgman – Stockbarger method

Organic scintillator crystal 9-Phenylcarbazole (9-PCz) has been grown using Bridgman -Stockbarger technique. The crystal structure, lattice parameter and bond angle values are measured from single-crystal X-ray diffraction (SXRD) analysis. C–H inplane bending and out of plane bending and skeletal vibrations of 9-PCz molecule were identified from vibrational spectral analysis. UV–visible NIR spectral study shows that the crystal exhibits around 50% of transmittance in the infrared region and the direct optical bandgap energy is calculated to be 3.36 eV. Thermal properties of grown 9-PCz material were measured using thermogravimetric and differential thermal analyses (TG-DTA). The photoluminescence (PL) measurements show two emission bands with a maximum peak at 365 nm and a shoulder peak at 381 nm. X-ray induced luminescence spectrum of 9-PCz crystal exhibits a maximum emission peak at 381 nm. Scintillation decay time measurement shows the major component of 18 ns decay time. The pulse shape discrimination (PSD) capability of the grown crystal sample was studied for the signals induced by α-particles and γ-rays from 241Am and 137Cs sources, respectively. The figure of merit (FOM) is found to be 2.69. The preliminary results showed that the present studied organic crystal (9-PCz) scintillator can be considered in the field of fast neutron detection application.

Toward a SERS Diagnostic Tool for Discrimination between Cancerous and Normal Bladder Tissues via Analysis of the Extracellular Fluid.

Vibrational spectroscopy provides the possibility for sensitive and precise detection of chemical changes in biomolecules due to development of cancers. In this work, label-free near-infrared surface enhanced Raman spectroscopy (SERS) was applied for the differentiation between cancerous and normal human bladder tissues via analysis of the extracellular fluid of the tissue. Specific cancer-related SERS marker bands were identified by using a 1064 nm excitation wavelength. The prominent spectral marker band was found to be located near 1052 cm–1 and was assigned to the C–C, C–O, and C–N stretching vibrations of lactic acid and/or cysteine molecules. The correct identification of 80% of samples is achieved with even limited data set and could be further improved. The further development of such a detection method could be implemented in clinical practice for the aid of surgeons in determining of boundaries of malignant tumors during the surgery.

Reparametrised Pöschl–Teller oscillator and analytical molar entropy equation for diatomic molecules

In this study, the reparametrised Pöschl–Teller (RPT) oscillator is constructed for applications to diatomic molecules. Equations for bound state eigen energies and molar entropy are derived for the oscillator. With the aid of the proposed model, seven diatomic molecules are analysed including 7Li2 (a 3Σu +), Na2 (c 1Πu), HCl (X 1Σ+), MgO (X 1Σ+), SO (X 3Σ-), SiO (X 2Σ+), and TiO (X 2Σ+). The average absolute deviation (AAD) and mean absolute percentage deviation (MAPD) are employed as the goodness of fit indicators. Computed AAD and MAPD reveal that the RPT oscillator is an excellent model for the diatomic molecules, the potential is approximately equivalent to the improved Tietz and improved Scarf potentials in the literature. An MAPD of 0.3609% from observed data of gaseous HCl molecule is obtained using the equation of molar entropy proposed in this work. This is an indication that the RPT oscillator is a good model for representing the internal vibration of the HCl molecule.

Study of IR Spectroscopy of Crystalline Materials Structure Used in Laser Shutters

The IR absorption spectra of hexagonal crystals of lithium iodate α-LiIO3, used in laser shutters for ship wiring, where the quality, transparency and power of laser radiation are of great importance, are studied. The transmission spectra allowed us to determine the width of the crystal band gap 4.37 eV along the Z-axis (C6 [0001]) and 4.46 eV along the axis perpendicular to the Z axis. The activation energies and the wavelength of the vibrational centers associated with the vibrations of the H3O+, OH-, H2O groups, heavy D2O and semi-heavy molecules HDO are determined. It is established that the band 1450-1650 cm-1 is a superposition of at least two broad absorption maxima centered at ~1550 and ~1600 cm-1. It was experimentally established that the ratio of the absorption coefficients of these bands was ~1:1 (75:74 cm-1) for crystals grown in H2O, and ~2:1 (161:84 cm-1) – for crystals grown in D2O. This allows us to assume that in a lithium iodate crystal grown in D2O, the bands 1550 cm-1 and 1600 cm-1 correspond to the vibrations of the bound HDO and H2O molecules, the band 1150 cm-1 corresponds to the vibrations of heavy water molecules. The results of the study allowed us to propose a mechanism of transport and translational diffusion of protons and to determine the presence of heavy water molecules in crystalline materials, as well as to diagnose the quality of laser crystals.

Translational vibrations in α-N2 from x-ray data

Using the x-ray diffraction method, the mean square displacement of solid nitrogen molecules from its lattice point in α phase was determined. The temperature dependences of the amplitude of translational vibrations of nitrogen molecules are obtained in the isotropic approximation. Our experimental values were compared with the theoretical data and a qualitative difference was found. This discrepancy can be explained by the fact that the geometry of the molecule is not considered in theoretical models.

Two-Colour Sum-Frequency Generation Spectroscopy Coupled to Plasmonics with the CLIO Free Electron Laser

Nonlinear plasmonics requires the use of high-intensity laser sources in the visible and near/mid-infrared spectral ranges to characterise the potential enhancement of the vibrational fingerprint of chemically functionalised nanostructured interfaces aimed at improving the molecular detection threshold in nanosensors. We used Two-Colour Sum-Frequency Generation (2C-SFG) nonlinear optical spectroscopy coupled to the European CLIO Free Electron Laser in order to highlight an energy transfer in organic and inorganic interfaces built on a silicon substrate. We evidence that a molecular pollutant, such as thiophenol molecules adsorbed on small gold metal nanospheres grafted on silicon, was detected at the monolayer scale in the 10 µm infrared spectral range, with increasing SFG intensity of three specific phenyl ring vibration modes reaching two magnitude orders from blue to green–yellow excitation wavelengths. This observation is related to a strong plasmonic coupling to the thiophenol molecules vibrations. The high level of gold nanospheres aggregation on the substrate allows us to dramatically increase the presence of hotspots, revealing collective plasmon modes based on strong local electric fields between the gold nanoparticles packed in close contact on the substrate. This configuration favors detection of Raman active vibration modes, for which 2C-SFG spectroscopy is particularly efficient in this unusual infrared spectral range.

Unavoidable failure of point charge descriptions of electronic density changes for out-of-plane distortions

Population analyses based on point charge approximations accurately estimating the equilibrium dipole moment will systematically fail when predicting infrared intensities of out-of-plane vibrations of planar molecules, whereas models based on both charges and dipoles will always succeed. It is not a matter of how the model is devised but rather how many degrees of freedom are available for the calculation. Population analyses based on point charges are very limited in terms of the amount of meaningful chemical information they provide, whereas models employing both atomic charges and atomic dipoles should be preferred for molecular distortions. A good model should be able to correctly describe not only static, equilibrium structures but also distorted geometries in order to correctly assess information from vibrating molecules. The limitations of point charge models also hold for distortions much larger than those encountered vibrationally.

Qualitative and Quantitative Study on DL-Glutamic Acid and Its Monohydrate using Terahertz Spectra

The rotation, translation, and vibration of many amino acid molecules fall in the terahertz (THz) region, thus qualitative and quantitative researches on amino acids can be carried out through their THz absorption characteristic fingerprint peaks. In this paper, the room temperature THz absorption spectra of DL-glutamic acid and its monohydrate at 0.5-3.0THz were measured by utilizing terahertz time-domain spectroscopy (THz-TDS). It is found that the THz characteristic peaks of these two amino acids are obviously different. Moreover, according to the change of the absorption amplitude of the characteristic absorption peak (1.24THz) of DL-glutamate monohydrate at different sample concentrations, a quantitative analysis was carried out on the mixed samples of DL-glutamate and its monohydrate, and then the quantitative analysis formula was also verified. In addition, the optical mode of DL-glutamic acid and its monohydrate in THz region was predicted by using density functional theory (DFT). Under the condition that the theoretical data matched with the experimental peaks, the origins of THz absorption peaks obtained in the experiment were discussed and summarized. The results show that the THz characteristic peaks (<2.80THz) of DL-glutamic acid and its monohydrate come from the intermolecular interaction modes, and the other absorption peaks are resulted from the combination of intermolecular and intramolecular interaction modes.

Bulk Response of Carboxylic Acid Solutions Observed with Surface Sum-Frequency Generation Spectroscopy.

We study the molecular properties of aqueous acetic acid and formic acid solutions with heterodyne-detected vibrational sum-frequency generation spectroscopy (HD-VSFG). For acid concentrations up to ∼5 M, we observe a strong increase of the responses of the acid hydroxyl and carbonyl stretch vibrations with increasing acid concentration due to an increase of the surface coverage by the acid molecules. At acid concentrations >5 M we observe first a saturation of these responses and then a decrease. For pure carboxylic acids we even observe a change of sign of the Im[χ(2)] response of the carbonyl vibration. The decrease of the response of the hydroxyl vibration and the decrease and sign change of the response of the carbonyl vibration indicate the formation of cyclic dimers, which only show a quadrupolar bulk response in the HD-VSFG spectrum because of their antiparallel conformation. We also find evidence for the presence of a quadrupolar response of the CH vibrations of the acid molecules.

Terahertz Spectral Properties of 5-Substituted Uracils

Applications of terahertz time-domain spectroscopy (THz-TDS) in the fields of chemistry and biomedicine have recently received increased attention. Specifically, THz-TDS is particularly effective for the identification of alkaloid molecules, because it can distinguish the vibration types of base molecules in the THz band and provide a direct characteristic spectrum for the configuration and conformation of biomolecules. However, when THz-TDS technology is used to identify alkaloid molecules, most of them are concentrated in the 0.1–3.0 THz band, limiting the amount of information that can be obtained. In this work, a wide-spectrum THz-TDS system was independently built to explore the absorption spectra of uracil and its 5-substituents in the range of 1.3–6.0 THz. We found that, in the THz band, uracil and its 5-substituents have similar absorption peaks near 4.9 and 3.3 THz, while the 5-substituents have an additional absorption peak in the range of 1.5–2.5 THz. This absorption peak is red-shifted as the relative atomic mass of the 5-substituted atoms increases. Gaussian software was adopted to calculate the absorption spectra of the samples. The simulation conclusions were in good agreement with the experimental results, revealing that the vibration of the base molecule at low frequencies can be attributed to the inter-molecular vibration. This work demonstrates that THz-TDS technology can be used to accurately identify biomolecules with similar molecular structures, reflecting the importance of molecular structure in biological activity.

An investigation on the structure and group vibrations of balenine molecule by matrix isolation IR spectroscopy, DFT and MP2 based calculations

Stable conformers of neutral balenine were scanned through molecular dynamics simulations and energy minimizations using Allinger’s MM2 force field. For each of the found minimum-energy conformers, geometry optimization and thermochemistry calculations were performed by using B3LYP, MP2, G3MP2B3 methods, 6-31G(d), 6–311++G(d,p) and aug-cc-pvTZ basis sets. The calculation results have indicated that balenine has about twenty stable conformers whose relative energies are in the range of 0–9.5 kcal/mol. Three of these are thought to provide the major contribution to matrix isolation IR spectra of the molecule. Our solvent calculations using the polarized continuum model revealed the stable zwitterion structures which are predicted to dominate IR spectra of balenine in water and heavy water (D2O) solvents. Pulay’s SQM-FF method was used in scaling of the harmonic force constants and vibrational spectral data calculated for the neutral and zwitterion structures. These refined calculation data together with those obtained from anharmonic frequency calculations enabled us to correctly interpret the matrix isolation IR spectrum of balenine and the tautomerism-based changes observed in its KBr IR and solution (D2O) IR spectra. The results revealed the crucial role of conformation and zwitterionic tautomerism on the structure and vibrational spectral data of the molecule.

Resolving sub-angstrom ambient motion through reconstruction from vibrational spectra

Metal/organic-molecule interactions underpin many key chemistries but occur on sub-nm scales where nanoscale visualisation techniques tend to average over heterogeneous distributions. Single molecule imaging techniques at the atomic scale have found it challenging to track chemical behaviour under ambient conditions. Surface-enhanced Raman spectroscopy can optically monitor the vibrations of single molecules but understanding is limited by the complexity of spectra and mismatch between theory and experiment. We demonstrate that spectra from an optically generated metallic adatom near a molecule of interest can be inverted into dynamic sub-Å metal-molecule interactions using a comprehensive model, revealing anomalous diffusion of a single atom. Transient metal-organic coordination bonds chemically perturb molecular functional groups > 10 bonds away. With continuous improvements in computational methods for modelling large and complex molecular systems, this technique will become increasingly applicable to accurately tracking more complex chemistries.

Equation of State for Solid Benzene Valid for Temperatures up to 470 K and Pressures up to 1800 MPa

The thermodynamic property data for solid phase I of benzene are reviewed and utilized to develop a new fundamental equation of state (EOS) based on Helmholtz energy, following the methodology used for solid phase I of CO2 by Trusler [J. Phys. Chem. Ref. Data 40, 043105 (2011)]. With temperature and molar volume as independent variables, the EOS is able to calculate all thermodynamic properties of solid benzene at temperatures up to 470 K and at pressures up to 1800 MPa. The model is constructed using the quasi-harmonic approximation, incorporating a Debye oscillator distribution for the vibrons, four discrete modes for the librons, and a further 30 distinct modes for the internal vibrations of the benzene molecule. An anharmonic term is used to account for inevitable deviations from the quasi-harmonic model, which are particularly important near the triple point. The new EOS is able to describe the available experimental data to a level comparable with the likely experimental uncertainties. The estimated relative standard uncertainties of the EOS are 0.2% and 1.5% for molar volume on the sublimation curve and in the compressed solid region, respectively; 8%–1% for isobaric heat capacity on the sublimation curve between 4 K and 278 K; 4% for thermal expansivity; 1% for isentropic bulk modulus; 1% for enthalpy of sublimation and melting; and 3% and 4% for the computed sublimation and melting pressures, respectively. The EOS behaves in a physically reasonable manner at temperatures approaching absolute zero and also at very high pressures.

Quadrilateral Nucleic Acid Frame-Accelerating DNAzyme Walker Kinetics for Biosensing Based on Host-Guest Recognition-Enhanced Electrochemiluminescence.

Depending on the reaction between walkers and tracks, DNA walker is able to output signals continuously, which has attracted great attention from the bioanalytical community. Therefore, how to improve its reaction kinetics for efficient signal readout is of great significance. Herein, a quadrilateral DNAzyme walker was fabricated by colocalizing one walker and three DNA tracks in the quadrilateral nucleic acid frame to form a reaction unit (abbreviated as qDNA walker). Impressively, in contrast to the common free DNAzyme walker, the reaction kinetics of the qDNA walker was 2.3 times faster, which could achieve microRNA detection within 30 min. Meanwhile, an electrochemiluminescence (ECL) emitter of anthracene-cucurbituril supramolecular nanocrystals (Ant-CB SNCs) was obtained based on the self-assembly of cucurbituril (CB, host molecule) and anthracene (Ant, guest molecule). Benefiting from the host-guest recognition effect, the prepared Ant-CB SNCs exhibited enhanced ECL efficiency due to the supramolecular interaction between CB and Ant, which could inhibit vibration and rotation of the Ant molecules. We defined this new enhanced ECL phenomenon as "host-guest recognition-enhanced ECL." As a proof of concept, an ECL biosensor for microRNA-21 (miRNA-21) was constructed by combining the high-efficiency DNAzyme walker and the advanced ECL emitter of Ant-CB SNCs, which showed a linear range from 50 aM to 50 pM with a low limit of detection (11 aM), highlighting the great potential in clinical diagnosis.

Metal-insulator phase transition in the δ−(BEDT−TTF)4 [2,6-anthracene- bis(sulfonate)] ·4H2O studied by infrared spectroscopy

Temperature dependence of polarized infrared (IR) reflectance spectra of two-dimensional weakly dimerized organic conductor $\ensuremath{\delta}\text{\ensuremath{-}}{(\mathrm{BEDT}\text{\ensuremath{-}}\mathrm{TTF})}_{4}$[2,6-anthracene-bis(sulfonate)]$\ifmmode\cdot\else\textperiodcentered\fi{}4{\mathrm{H}}_{2}\mathrm{O}$ with $\frac{1}{4}$-filled band has been measured to investigate the metal-insulator phase transition at ${T}_{\mathrm{MI}}=85\phantom{\rule{0.16em}{0ex}}\mathrm{K}$ linked to charge ordering (CO). Vibrational bands related to $\mathrm{C}=\mathrm{C}$ stretching vibrations of the BEDT-TTF donor molecule give evidence of the CO and charge fluctuations both in the metallic and insulating phases above and below 85 K, respectively. Considerable modifications of the vibrational features due to electron-molecular vibration coupling are also observed. The phase transition is associated with the reorganization of hydrogen $\mathrm{OH}\ensuremath{\cdots}\mathrm{O}$ bonds in anion layers between the sulfonate moieties of the anion and the trapped water molecules, which is transmitted to conducting BEDT-TTF layers through weaker C-$\mathrm{H}\ensuremath{\cdots}\mathrm{O}$ bonds. The analysis of electronic bands confirms the presence of strong electronic correlations in the material. Two electronic absorptions are observed in the mid-IR region, attributed to transitions between Hubbard bands and transitions inside BEDT-TTF dimers. A low-energy electronic absorption in the far-IR region is attributed to collective excitations of the short-range charge order. Below 85 K, the opening of a charge gap of \ensuremath{\sim}24 meV is observed both parallel and perpendicular to the BEDT-TTF stacking direction. The spectroscopic data indicate that the CO phase transition is a consequence of both Coulomb interactions between charge carriers and donor-acceptor interactions.