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[Display omitted] • Detailed conformational analysis of solvated l -DOPA in acidic conditions using MD and DFT. • Obtaining state-of-the-art VOA spectra of l -DOPA in an acidic aqueous solution. • Refined conformer ratios based on experimental data, thus improving simulation accuracy. • Paving the way for future research on deuterated l -DOPA analogs. l -DOPA plays a critical role as a precursor to dopamine and is a standard treatment for Parkinson's disease. Recent research has highlighted the potential therapeutic advantages of deuterated l -DOPA analogs having a longer biological half-life. For their spectroscopic characterization, the in-detail characterization of l -DOPA itself is necessary. This article presents a thorough examination of the vibrational spectra of l -DOPA, with a particular emphasis on chirally sensitive VOA techniques. We successfully obtained high-quality Raman and ROA spectra of l -DOPA in its cationic form, under low pH conditions, and at a high concentration of 100 mg/ml. These spectra cover a broad spectral range, allowing for precise comparisons with theoretical simulations. We also obtained IR and VCD spectra, but they faced limitations due to the narrow accessible spectral region. Exploration of l -DOPA's conformational landscape revealed its intrinsic flexibility, with multiple coexisting conformations. To characterize these conformations, we employed two methods: one involved potential energy surface scans with implicit solvation, and the other utilized molecular dynamics simulations with explicit solvation. Comparing ROA spectra from different conformer groups and applying spectral decomposition proved crucial in determining the correct conformer ratios. The use of explicit solvation significantly improved the quality of the final simulated spectral profiles. The accurate determination of conformer ratios, rather than solely relying on the number of averaged spectra, played a crucial role in simulation accuracy. In conclusion, our study offers valuable insights into the structure and conformational behavior of l -DOPA and represents a valuable resource for subsequent spectroscopic studies of its deuterated analogs. [ABSTRACT FROM AUTHOR]

[Display omitted] • Dual hydrogen bond strengthening resulting from photoexcitation facilitates ESIPT tendency for D3HF derivatives. • Charge redistribution and related variation of atomic charge promote ESIPT reaction for D3HF-O, D3HF-S and D3HF-Se fluorophores. • Variation of atomic electronegativity could play a regulatory effect on the single ESIPT behavior of D3HF and its derivatives. Inspired by the distinguished photochemical characteristics of new organic molecule containing the chalcogenide substitution that could be potentially applied across various disciplines, in this work, the effects of atomic electronegativity of chalcogen (O, S and Se) on hydrogen bond interactions and proton transfer (PT) reaction. We present the characteristic 2,8-diphenyl-3,7-dihydroxy-4H,6H-pyrano[3,2-g]-chromene-4,6-dione (D3HF), which is based on 3-hydroxyflavone (3HF) and contains intramolecular double hydrogen bonds that is the main objective of this study to explore in detail the influence of the change of atomic electronegativity on the dual hydrogen bond interaction and the excited state proton transfer (ESPT) behavior by photoexcitation. By comparing the structural changes and infrared (IR) vibrational spectra of the D3HF derivatives (D3HF-O, D3HF-S and D3HF-Se) fluorophores in S 0 and S 1 states, combined with the preliminary detection of hydrogen bond interaction by core-valence bifurcation (CVB) index, we can conclude that the hydrogen bond is strengthened in S 1 state, which is favorable for the occurrence of ESPT reactions. The charge recombination behavior of hydrogen bond induced by photoexcitation also further illustrates this point. Via constructing potential energy surfaces (PESs) based on restrictive optimization, we finally clarify the excited state single PT mechanism for D3HF derivatives. Specially, we confirm change of atomic electronegativity has a regulatory effect on the ESIPT behavior of D3HF and its derivatives, that is, the lower the atomic electronegativity is more conducive to the ESIPT reaction. [ABSTRACT FROM AUTHOR]

[Display omitted] • the molecules with stronger hydrogen bonds have higher IPs and EAs values. • The characteristics of molecular charge transfer are clarified and the contour map of electron cloud distribution is drawn. • The introduction of substituents promotes the ESIPT process. • The 2′-aminochalcone derivatives are promising materials for hole transport. This work investigates the different charge transfer characteristics and excited state intramolecular proton transfer process (ESIPT) of 2′-aminochalcones derivatives carrying different electron-withdrawing groups. Four new molecules are designed in the experiment and named as 2c, 3c, 4c and 5c, respectively. (Dyes and Pigments, 2022, 202.) Based on these four molecules, the effect of substituents on the ESIPT process and the charge transfer process are discussed in detail in our work. According to the study of the related parameters at the hydrogen bond site, infrared vibration spectrum, interaction region indicator isosurface (IRI) and scatter plots, it is concluded that the hydrogen bond interaction is enhanced under photoexcitation, and the descending order of the excited state hydrogen bond strength is 3c > 5c > 4c > 2c. The hydrogen bond energy is calculated by atoms in moleculs (AIM) topological analysis and core-valence bifurcation (CVB) index. The potential energy curve reveals the ESIPT mechanism. Frontier molecular orbital and electron-hole analyses explain the reasons for the changes in the ESIPT process at the electronic level. In addition, the ionization potentials (IPa and IPv), affinity energies (EAa and EAv) and reorganization energies are calculated to evaluate the potential application value of organic molecules in material transport field. [ABSTRACT FROM AUTHOR]

Vibrational circular dichroism (VCD) spectra of adenosine crystals exhibit few-orders-of-magnitude signal enhancement originating from long-range coupling of vibrations due to highly ordered supramolecular arrangement of the molecules in crystals. In contrast, infrared absorption (IR) spectra of adenosine crystals demonstrate unusually low intensity of the signal. An atypical negative feature in the IR spectrum denoted by an asterisk is connected with sample scattering and unique combination of sample and solvent refractive properties. [Display omitted] • The first VCD study of adenosine microcrystals is presented. • Regular packing of adenosine in crystals leads to enhanced supramolecular VCD signal. • VCD spectra with high signal-to-noise ratio can be recorded within minutes. • Unusually weak IR absorption of adenosine crystals is observed. • Adenosine microcrystals do not imbibe atmospheric water for at least two months. Adenosine is one of the building blocks of nucleic acids and other biologically important molecules. Spectroscopic methods have been among the most utilized techniques to study adenosine and its derivatives. However, most of them deal with adenosine in solution. Here, we present the first vibrational circular dichroism (VCD) spectroscopic study of adenosine crystals in solid state. Highly regular arrangement of adenosine molecules in a crystal resulted in a strongly enhanced supramolecular VCD signal originating from long-range coupling of vibrations. The data suggested that adenosine crystals, in contrast to guanosine ones, do not imbibe atmospheric water. Relatively large dimensions of the adenosine crystals resulted in scattering and substantial orientational artifacts affecting the spectra. Several strategies for tackling the artifacts have been proposed and tested. Atypical features in IR absorption spectra of crystalline adenosine (e.g., extremely low absorption in mid-IR spectral range) were observed and attributed to refractive properties of adenosine crystals. [ABSTRACT FROM AUTHOR]

On the basis of first-principles electronic structure calculations, crystallographic parameters have been refined for calcium hydroxozincate (Qatranaite mineral), and the vibration properties (frequencies and eigenvectors) calculated. A detailed analysis of vibration modes is done, in the context of comparison with infrared and Raman spectra previously available. Special attention is paid to a posteriori symmetry analysis of vibration modes, discussing the latters' attribution to four irreducible representations of the P 2 1 / c space group, and to identifying stretchings and bendings of particular chemical bonds, pronounced in different vibrations. It turns out that high-frequency (> 700 cm−1) vibrations of hydroxyl groups bridging the Ca or Zn cations differ quite considerably for crystallographically distinct hydroxyl positions. It is shown that the vibrations involving hydroxyl groups and crystalline water typically come about in quadruplets at very close frequencies, whereby different irreducible representations reflect different combinations of similar "molecular" vibrations of four identical entities (of each hydroxyl or water) present in the unit cell. However, some vibrations show exceptions from this rule. In addition to interpretation of earlier experimental investigations, our study indicates that the low-frequency (< 700 cm−1) vibrations within the cation–hydroxyl connected skeleton are of more "solid-state-like" character and cannot be reasonably interpreted in terms of "molecular" vibrations within ZnO 4 or CaO 6 units. [Display omitted] • Projection of vibration eigenvectors according to different criteria is suggested. • Contributions from different stretchings and bendings are naturally identified. • Molecular-type vibrations make almost degenerate symmetry-constrained combinations. • Vibrations throughout metal-oxygen cages make a dense quasi-continuous spectrum. [ABSTRACT FROM AUTHOR]

[Display omitted] • The strength of the asymmetric dual hydrogen bond (O1-H2 ... N3 and O4-H5 ... O6) is enhanced under photoexcitation. • Different strength of the dual hydrogen bond, indicating an excited stated stepwise double proton transfer. • The electrons are mainly deactivated by the ISC (S 1 ->T 1) resulting in only one fluorescence quenching. Recently, synthesized N-linked-disalicylaldehyde H 2 Q JI probes have been used to detect heavy metal ions in the experiment conveniently. Nevertheless, there needs to be a more in-depth examination of the excited state intramolecular proton transfer (ESIPT) mechanism and photophysical properties of the probe. This work remedied it based on quantum chemistry calculations. We contained due hydrogen bond (O1-H2 ⋯ N3 and O4-H5 ⋯ O6) and then analyzed bond parameters, IR vibration spectra, and non-covalent interaction. The bond strength is enhanced under photoexcitation, and the former is significantly stronger. The calculated electron spectra are in agreement with the experimental values. The results of the S 0 and S 1 potential energy curves and IRC calculations also confirm the unique ESIPT behavior, which is an excited stated stepwise double proton transfer. The fluorescence, internal conversion, and intersystem crossing rate of KD molecules (twisted-, double proton transfer) were calculated respectively to reveal the radiative and non-radiative pathways. It proved that the corresponding spectra are not obtained since the electrons are mainly deactivated by the ISC (S 1 ->T 1). Furthermore, the interfragment charge transfer (IFCT) approach indicates that the molecule possesses twisted intramolecular charge transfer (TICT) characteristics, which lead to the quenching of fluorescence introduction. [ABSTRACT FROM AUTHOR]

[Display omitted] • Isosbestic point was obviously observed in the Raman spectra of hydration shell. • New experimental evidence that continuum models can also generate the isosbestic point. • MD simulation was performed to further elucidate the mechanisms of isosbestic points in the Raman spectrum of the hydration shell. Isosbestic point is often observed in a series of spectra, but their interpretation is still controversial, such as whether the continuum model can produce an isosbestic point. In order to answer this question, the Raman spectra of hydration shell with continuous distribution structure in different ionic aqueous solutions were separated by Raman ratio spectra, and an isosbestic point was successfully observed. Our experimental results show that the continuum model can indeed produce the isosbestic point. In order to deepen the understanding of the isosbestic point, we calculate the first moment of the Raman spectra and conduct molecular dynamics (MD) simulations. Both experimental and theoretical findings indicate that elevated temperatures lead to increased disorder among water molecules within the hydration shell. [ABSTRACT FROM AUTHOR]

[Display omitted] • The strength of intramolecular hydrogen bonds in the excited state increases gradually as the electronegativity of the atom decreases. • The low atomic electronegativity can causes the red shift of absorption and fluorescence spectra. • As the atomic electronegativity decreases, the energy barrier of the excited state becomes lower, which helps to promote ESIPT. In this work, we theoretically explored the influence of atomic electronegativity on excited-state intramolecular proton transfer (ESIPT) behavior among novel fluorescent probes BTDI and its derivatives (BODI and BSeDI). A thorough examination of the optimized structural parameters and infrared vibrational spectra reveals an enhancement in intramolecular hydrogen bonding within BTDI and its derivatives upon light excitation. This finding is further reinforced by topological analysis and interaction region indicator scatter plots, which underscores the sensitivity of atomic electronegativity to variations in hydrogen bonding strength. With regards to absorption and fluorescence spectra, the decrease in atomic electronegativity leads to a pronounced redshift, primarily attributed to the narrowing of the energy gap. Additionally, an analysis of potential energy curves and the exploration of intrinsic reaction coordinate paths based on transition state structures afford a deeper understanding of the mechanism underlying ESIPT and being modulated through the manipulation of atomic electronegativity. We anticipate that this work on atomic electronegativity regulating ESIPT behavior will serve as a catalyst for novel fluorescent probes in the future, offering fresh perspectives and insights. [ABSTRACT FROM AUTHOR]

[Display omitted] • Raman spectra of IBA crystal from ambient to 30 GPa were measured. • Raman modes of IBA at ambient were assigned based on the CASTEP calculations. • Raman spectra of IBA under high pressure were analyzed in detail. • The phase transitions of IBA were observed at 1, 2 and 10 GPa, respectively. Isobutyramide (IBA) has attracted considerable attention due to its expansive prospects for practical applications in the synthesis of drugs, dyes and other organic compounds. Herein we perform the high-pressure studies of IBA crystal by Raman spectral measurements at room temperature from ambient pressure to 30 GPa by using diamond anvil cells (DACs) to gain comprehensive insights into its structure and stability. Raman vibrational modes of IBA crystal at ambient pressure are resolved based on the experimental results and the first-principles theoretical calculations. High-pressure Raman scattering results show the Raman bands splitting, emergence/disappearance of the Raman bands and discontinuous wavenumber shifts at 1, 2 and 10 GPa, which indicate that IBA crystal undergoes three structural phase transitions at corresponding pressure. In addition, softening of the C = O and N–H stretching vibrational modes of IBA with increasing pressure can be interpreted by the reorganization of the hydrogen bond network of IBA molecules due to phase transition. [ABSTRACT FROM AUTHOR]

Vibrational analysis plays a crucial role in the investigation of molecular systems. Though methodologies like second-order vibrational perturbation theory (VPT2) have paved the way to more accurate simulations, the computational cost remains a difficult barrier to overcome when the molecular size increases. Building upon recent advances in the identification of resonances, we propose an approach making anharmonic simulations possible for large-size systems, typically unreachable by standard means. This relies on the fact that, often, only portions of the whole spectra are of actual interest. Therefore, the anharmonic corrections can be included selectively on subsets of normal modes directly related to the regions of interest. Starting from the VPT2 equations, we evaluate rigorously and systematically the impact of the truncated anharmonic treatment onto simulations. The limit and feasibility of the reduced-dimensionality approach are detailed, starting on a smaller model system. The methodology is then challenged on the IR absorption and vibrational circular dichroism spectra of an organometallic complex in three different spectral ranges. [Display omitted] • Anharmonic VPT2 simulations of large systems. • Reduced-dimensionality scheme for anharmonic spectra of large systems with VTP2. • Simple indicators to evaluate a priori the impact of truncated anharmonicity terms. • New strategies to obtain converged spectra within selected spectral ranges. • First anharmonic IR and VCD spectra of large ruthenium carbonyl complexes. [ABSTRACT FROM AUTHOR]

[Display omitted] • Methods for diagnosing the cage of covariance. • Testing if covariance structure reduces robustness in spectroscopic models. • Spectroscopic model sensitivity to interfering analytes. When vibrational spectroscopy is used for quantification purposes, multivariate analysis is often used to extract information from covariances between the spectra and any given reference values. In complex samples, there is a high risk that the constituents covary with each other. In such scenarios many methods may confuse the analytes and use signal from several analytes, rather than just the analyte of interest. While this allows the method to use more signal, and thus have a better effective signal-to-noise ratio, it also makes them less robust to changes to the chemical composition in the samples. This effect has been termed the cage of covariance. In order to avoid cage of covariance to affect predictive performances, it is highly important to have simple diagnostic tools to analyze and review this effect. Therefore, in the present paper, a systematic overview of tools for diagnosing and quantifying the cage of covariance in spectroscopic calibration models is provided. A collection of previously published methods with some expansions is provided, as well as two completely new tools: covariance ratio and virtual spiking. Practical applications of the tools on three different datasets are also shown. [ABSTRACT FROM AUTHOR]

[Display omitted] • Traces of water in the sample can change the signs of ROA bands. • This was explained by supramolecular organization of studied acids around water and changed acidobasic equilibria. • Raman and ROA spectra of halogenated compounds were interpreted using MD/DFT. • Esterification of the halo acids caused significant changes in vibrational spectra. Chiral 2-halopropionic acids and their derivatives were synthesized and their properties studied computationally using Raman and Raman optical activity (ROA) spectroscopy. For neat acids present as liquids small amount of water led to significant changes in the spectra, resulting even to flipping of some ROA band signs. We find this interesting for the role water plays in interpretation of vibrational optical activity spectra of biomolecules. Analysis of the results shows that when the water is present, it can change ROA band signs due to the changes in acidobasic equilibrium. Corresponding esters without acidic hydrogens do not exhibit such effects. [ABSTRACT FROM AUTHOR]

[Display omitted] • A cluster model of a solute surrounded by 30 water molecules allows reproducing experimental Raman spectra of aqueous thymine. • B3LYP-D3/def2-TZVP or B3LYP-D3/aug-cc-pVDZ computations are sufficient for the above purpose. • The strong effect of water on vibrational spectra of thymine is mainly a result of hydrogen bonding with 6 nearest water molecules. As in the case of cytosine [Phys. Chem. Chem. Phys. 2023 , 25 , 24121–24128], Raman and infrared (IR) spectra of aqueous thymine and its N-deuterated derivative, thymine-d 2 have been computationally reproduced and interpreted with the use of the recently developed efficient protocol to explicit quantum mechanical modeling of structure and IR spectra of liquids and solutions [ J. Phys. Chem. B , 2020 , 124 , 6664–6670]. A cluster model of a solute surrounded by 30 water molecules is shown to be sufficient to reproduce experimental vibrational frequencies and relative Raman intensities with the use of B3LYP-D3/def2-TZVP or B3LYP-D3/aug-cc-pVDZ simulations. Analogous PBE-D3 computations provided a less good, but still reasonably accurate, modeling of Raman spectra. It is shown that strong changes of frequencies and relative intensities of the Raman bands of thymine, caused by its hydration, can be interpreted mainly as a result of hydrogen bonding with 6 nearest water molecules. Non-negligible improvement of the quality of simulations for larger clusters comprising water molecules that do not have direct contacts with the solute, suggests that spectroscopic effects of hydration should be ascribed to the joined action of solute–solvent and solvent–solvent interactions. Nevertheless, the moderate number of water molecules required for successful simulations of the Raman spectra of aqueous thymine, suggests that the vibrational modes and derivatives of the polarizability of the solute are mainly locally influenced, while the effect of bulk water is rather modest. [ABSTRACT FROM AUTHOR]

[Display omitted] • Techniques of vibrational spectroscopy allow the detection of fragrances on skin. • Multivariate statistical methods enable distinguishing fragrances from each other. • Fragrances induce structural changes in the skin. Nowadays, fragrances belong to the widely used cosmetics. Their composition is designed in a way that it evolves and changes over time. In this work, the effect of fragrances on the skin was studied – the interactions between pig skin samples and fragrances and the possibility of their detection and mutual differentiation. Non-invasive techniques of vibrational spectroscopy were used to obtain the data, namely FT-IR spectroscopy with attenuated total reflection accessory and Raman microspectroscopy. Vibrational spectra were measured within 8 h with different time intervals and after 22 h from the application of fragrance for FT-IR and Raman measurements, respectively. The obtained spectra were pre‑processed and subsequently evaluated by multivariate statistical methods. The study showed that skin treated by fragrances is well distinguishable from untreated skin, even after 22 h. In addition, it is possible to differentiate individual fragrances from each other; therefore, the use of spectroscopical techniques could be a potential tool for forensic analysis of fragrances. [ABSTRACT FROM AUTHOR]

[Display omitted] • Three kinds of absorbed stages are explored in structural evolutions. • Simulated photoelectron spectra agree with experiments. • Infrared and Raman spectra have deformation and breathing mode. • Neutral TiSn 16 cluster is the most stability motif. • TiSn 16 cluster has optoelectronic property from UV–Vis adsorption. The structural evolution, chemical stability, electronic and vibrational properties, as well as charge transfer and bonding character of TiSn n 0/−/2− (n = 4–17) clusters have been performed with density functional theory calculations using ABCluster search technique. Structurally, it is found that the growth patterns prefer three kinds of absorbed stages from polygonal bipyramidal configuration for n = 4–6, to absorbing additional Sn on the adjacent surfaces of pentagonal bipyramid unit from n = 7–12, and finally to the TiSn 13 0/−/2− cluster as the first foundational architectures, of which the encapsulated cage structure is formed when n = 11. The simulated PES spectra agree with available experiments. More interestingly, the neutral TiSn 16 cluster not only possesses the high thermodynamic and relative stability but also preferable photochemical reactivity, that can be further explained by superatom features and delocalized multi-center bonds (AdNDP), while the strong p-d hybridization between Ti atom and Sn unit plays an important role in the stabilities of clusters, making it as the most suitable building units. In addition, the UV–Vis absorption spectra of TiSn 16 are discussed, and the main transitions of crucial excited states are analyzed in detail. The Infrared and Raman vibrational characteristic peaks of all these neutral and charged species are properly assigned, of which the TiSn n 0/−/2− (n = 10–17) clusters possess degenerating deformation mode of Ti atom wagging in Sn cage framework (Infrared active) and breathing mode of Sn cage framework (Raman active). All these findings will provide a further understanding for the nanoalloy cluster as the most suitable building block with further development as a potential optoelectronic material. [ABSTRACT FROM AUTHOR]

[Display omitted] • Structures of cyclic dimers and tetramer of adenine were studied by DFT calculations. • The characteristics of N-H···N interactions were studied by NBO and AIM calculations. • Complete vibrational assignments of cyclic dimers are presented. • Vibronic bands are observed in the electronic spectra. • Different scaled force constants values show the cyclic dimers of adenine. In this work, three different cyclic dimers and a tetramer of adenine taken from the experimental structure determined by X-ray diffraction have been studied by combination of experimental FT-IR, FT-Raman and UV–Visible spectra with hybrid B3LYP/6–311++G** and scaled quantum mechanical force field (SQMFF) calculations in order to perform the complete assignments of bands observed in the vibrational spectra. The characteristics of different N-H···N interactions of those three cyclic structures together with the group of IR bands observed between 2865 and 2599 cm−1 have been elucidated considering the tetrameric structure. The cyclic dimers and the tetramer of adenine confirm that the bands observed between 2865 and 2599 cm−1 are not due to N-H···N interactions but to bands of combination, as was previously suggested. The experimental available deuterated IR and terahertz spectra have allowed the complete assignments of regions of higher and lower wavenumbers. Good correlations were acquired comparing the theoretical IR, Raman and UV spectra of three species and the tetramer with the analogous experimental ones, suggesting the presence of all species in both phases. Vibronic bands are observed in the electronic spectra when adenine concentration is increased in aqueous solution evidencing the presence of monomer, tautomers and dimers, as reported by different studies. Similar characteristics of H bonds interactions are predicted for dimers 1 and 2 but different from the dimer 3, as revealed by using NBO and AIM calculations. Different scaled force constants values were found for the cyclic dimers 1 and 2, as compared to the corresponding to dimer 3. [ABSTRACT FROM AUTHOR]

[Display omitted] • Yttrium nitride YN in different forms was investigated by using DFT/B3LYP level of theory. • A variety of properties of the YN (n,0) single-walled square nanotubes was studied, where the trend toward the square monolayer in the limit of large nanotube is attained. • Scanning mode procedure confirms that larger YN (n,0) single-walled hexagonal nanotubes are slightly distorted compared to their corresponding central point. Through this contribution, we aim to highlight the structural stability of low dimensional YN structures ranging from the 3D bulk to the 2D square and hexagonal monolayers and their corresponding 1D zigzag single walled nanotubes. For all arrangements, geometry optimization is achieved at the DFT/B3LYP level of theory using a Gaussian basis set. Then, the coupled perturbed Kohn-Sham and Hartree-Fock (CPKS/HF) computational approach is used to simulate Raman and IR spectrum. Rolling, cohesive and relaxation energies, electronic and vibrational contributions to the polarizability and equilibrium lattice parameters are also reported. Insights into their structural stability are provided by combining optimized parameters and vibrational phonon spectra. For the optimized 3D bulks, 2D monolayers and 1D square nanotubes, no imaginary frequency has been recorded in their vibrational spectra which reveals a dynamic stability. Likewise, imaginary frequencies appeared only for relatively large YN (n,0) single walled hexagonal nanotubes (n > 6) indicating that the optimized structures are not a real global minimum and implying a dynamic instability. A scaning mode procedure along the largest imaginary vibrational mode has been adopted to obtain the equilibrium geometry of (22,0) YN hexagonal nanotube. Therefore, it must be emphasized that the obtained potential energy surface presents two minima between a saddle point. These minima corresponds to a stable structures slightly distorted compared to the initial one. The absence of imaginary phonon frequencies in the Raman and IR spectra of the optimized (22,0) YN hexagonal nanotube confirms its structural stability. [ABSTRACT FROM AUTHOR]

[Display omitted] • Detailed theoretical study of structural, spectroscopic and electron scattering cross section study of glycolaldehyde. • Quantum chemical calculations for ground and excited states are performed using DFT and TD-DFT methods. • In the absence of sufficient experimental data on excited states of glycolaldehyde, we compare VES calculations with the available experimental data for an analogous molecule acetaldehyde. • Maiden theoretical attempt to provide Low-energy (0.1 to 20 eV) scattering cross-sectional data using R-matrix method. • We have detected one π* shape resonance in all the three models viz. SE, SEP and CC model. Detailed theoretical investigations on structural, spectroscopic and electron scattering cross sections of glycolaldehyde, the first ever detected sugar in space are reported in this work. Spectroscopic calculations are performed on the ground and excited states of glycolaldehyde using density functional theory (DFT) and time-dependent density functional theory (TDDFT), respectively. The optimized geometrical parameters and vibrational spectrum are in good agreement with the earlier reported work. Vertical excited state (VES) energies at the TDDFT/B3LYP/aug-cc-PVQZ level of theory along with detailed assignments are reported up to 30 transitions. The TDDFT predicted Rydberg series energies are compared with the Rydberg series of glycolaldehyde converging to its first IP, computed using the standard Rydberg formula and are found to be in good agreement. In the absence of sufficient experimental data on excited states of glycolaldehyde, the theoretical results are validated by comparison of VES calculations performed at the same level of theory with the available experimental data for an analogous molecule viz. acetaldehyde. Triplet excited-state energies for glycolaldehyde are reported here for the first time. Electron impact cross section calculations in the energy range 0.1 to 20 eV are carried out using ab-initio R-matrix method. We have detected one π* shape resonance in all the three models viz. SE, SEP and CC, which may also lead to a possible fragmentation channel wherein a hydrogen atom is removed from the molecule forming a glycolaldehyde dehydrogenated anionic radical (C 2 H 3 O 2 −). The π* shape resonance is correlated with the corresponding molecular orbital electronic structure calculations. Additionally, differential, electronic excitation, ionization and total cross sections are reported here for the first time. [ABSTRACT FROM AUTHOR]

[Display omitted] • The lowest iso -energetic conformers of DTT were identified as G′TG′1 and G′TT. • Its configurational isomers were observed to have higher energy than G′TG′1/G′TT. • Experimental Vibrational spectra were found in good agreement with the G′TG′1. • Both OH and SH groups engaged in intramolecular H-bonds. • These intramolecular interactions are responsible for the stability of DTT. A total of seven minimum energy geometries were obtained on exploring the conformational landscape of dithiothreitol (DTT) by varying the prominent dihedral angles in the molecule through a relaxed scan with a step size of 5° at B3LYP/cc-pVTZ with further geometry optimization at CCSD/cc-pVDZ level of theory. Single point energies were calculated for all the conformers at CCSD(T)/CBS limit with cc-pVNZ (N = T, Q) level of theory and revealed the similar energy pattern. The two conformers, namely G′TG′1 and G′TT, were found iso -energic even though they differed in their structure significantly and were of the lowest energy compared to others. Energies corresponding to the cyclic as well as other configurational counterpart of the global minimum were found much higher in energy compared to the global minimum structure. Intramolecular sulfur centered hydrogen bond was seen to stabilize the global minimum structure of DTT as revealed by AIM, NBO, FMO and ESP charge analysis. Computed NMR of DTT matched well with the experimental data gleaned from the literature. Vibrational spectra (Raman and IR) were measured and compared with computed normal modes of DTT, which were found in good agreement [ABSTRACT FROM AUTHOR]

[Display omitted] • An accurate potential energy curve (PEC) for the ground electronic state of phosphorus mononitride (PN) molecule has been determined from a variationally improved Hulburt-Hirschfelder (VIHH) oscillator model. • 61 vibrational energy levels for the ground electronic state of PN molecule were obtained. • The molar heat capacity, entropy, enthalpy, and Gibbs free energy are predicted by the VIHH model. In this work, an accurate potential energy curve (PEC) for the ground electronic state of phosphorus mononitride (PN) molecule has been determined from a variationally improved Hulburt-Hirschfelder (VIHH) oscillator model in conjunction with the experimental spectral constants (D e , ω e , ω e x e , B e , α e , r e). We have numerically solved the Schrödinger equation for the VIHH potential using the LEVEL program, obtaining the pure vibrational spectrum that converges to the dissociation limit. In addition, the partition functions of PN molecule are calculated using the full rovibrational energies. Ultimately, thermodynamic properties like molar heat capacity, entropy, enthalpy, and Gibbs free energy were calculated for the PN molecule and show good agreement with those data from the NIST (National Institute of Standards and Technology) database. [ABSTRACT FROM AUTHOR]

In this work, the structure–property relationship of push–pull chalcone derivative (3DPNP) has been studied through spectroscopic experiments and density functional theory calculations. The figure on the right side shows the non-linear absorption and non-linear refraction curves of 3DPNP. [Display omitted] • The structure–property relationship of a chalcone-based push–pull molecule (3DPNP) was explored using combined experimental and theoretical studies. • The vibrational and electronic contribution to NLO activity of 3DPNP was estimated. • Frequency-dependent NLO calculations shows abrupt changes when the incident frequency is doubled which confirms SHG efficiency of 3DPNP. • Z-scan studied indicated that the molecule 3DPNP is suitable for optical limiting application in CW laser regime. • The optical limiting threshold of 3DPNP is found to be 3.26 kJ/cm2. In this work, the optical limiting response of a highly π-conjugated push–pull chalcone derivative (2 E)-3-(2,3-dimethoxyphenyl)-1-(3-nitrophenyl)prop-2-en-1-one (abbreviated as 3DPNP) has been investigated. The structure–property relationship of 3DPNP was explored through spectroscopic investigation and quantum chemical computations. The existence of weak-non-covalent interactions and charge transfer species that responsible for the chemical stability of 3DPNP were studied by AIM and NBO analyses. The quantitative and qualitative analysis of vibrational and electronic contribution to non-linear optical (NLO) response of 3DPNP were discussed in detail. The normal vibrational modes associated with a change in the dipole moment, polarizability, first- and second-order hyperpolarizabilities of 3DPNP were identified using DFT calculations followed by potential energy distribution (PED) analysis using Gaussian 09 W software and Gar2ped program, respectively. The changes in the NLO parameters with respect to the varying frequencies and electric dipole fields were studied. The abrupt changes in the NLO properties were noticed when the frequency doubled, confirming the second harmonic generation (SHG) efficiency of 3DPNP. From the non-linear absorption and refraction studies through the z-scan experiment, the optical limiting threshold value of 3DPNP is determined to be 3.26 kJ/cm2, which shows the suitability of the material for optical limiting applications in the continuous wave (CW) laser regime. [ABSTRACT FROM AUTHOR]

[Display omitted] • Conformers of solute-DMSO complexes generated using Quantum cluster growth method. • The effects of incremental DMSO solvation and dynamicity of –OH group were explored. • Predicted and experimental vibrational circular dichroism spectra matched well. • The final populations of conformers are sensitive to the choice of functional used. Chiroptical spectroscopic measurements serve as routine methods to assign the absolute configuration of chiral compounds and interpret their conformational behavior in solution. One common challenge is the use of strongly hydrogen-bonding solvents, which can significantly bias the conformational ensemble and affect the vibrational circular dichroism (VCD) active bands in solution. One such solvent is dimethyl sulfoxide (DMSO)—an excellent solvent for stubborn compounds—that must be explicitly considered in VCD analysis. Explicit consideration of solvent remains a critical challenge in chiroptical spectroscopy due to the need to explore solute–solvent conformational space and the computational expense in modeling these clusters. Interested in the recent development of the Quantum Cluster Growth (QCG) program by the Grimme lab, we set out to model and interpret previously reported VCD spectra for several molecules using their efficient program. Our purposes are two-fold: (1) to investigate the applicability of the QCG program to the problem of reproducing VCD spectra in DMSO solvent and (2) to identify limitations in using this approach. We find that we can conveniently model and analyze the VCD spectra of investigated molecules in DMSO. However, the final set of conformers used for VCD calculations are functional dependent and different sets of conformers can provide satisfactory quantitative agreement between experimental and predicted VCD spectra. We hope that this study provides guidance for future chiroptical studies in the challenging DMSO solvent. [ABSTRACT FROM AUTHOR]

[Display omitted] • Vibrational spectral investigation has been carried out on 3-[(4-Nitrophenyl Azo)]-9H-Carbazole-9-Ethanol (NPACE) with the aid of B3LYP/6–311++G (d, p). • Vibrational contribution to the linear electro-optic effect has been examined. • Intramolecular charge transfer mechanism is discussed based on the simultaneous occurrence of a few vibrational modes from their vibrational spectra. • Second Harmonic Generation experiment is performed to validate the intramolecular charge transfer. • Terahertz spectral study is carried out to explore the low wavenumber vibrations. • Two-photon absorption coefficient and optical limiting threshold are estimated to be 0.9 × 10-11 mW−1 and 1.52 × 1013 Wm−2. Non-linear optical (NLO) features of 3-[(4-Nitrophenyl Azo)]-9H-Carbazole-9-Ethanol (NPACE) chromophore were investigated by FT-IR, FT-Raman, and UV–visible spectra aided by Density Functional Theory (DFT) using the B3LYP/6–311++G(d,p) basis set of Gaussian 16 W package. It is observed from the DFT calculation that the slight increase in the endocyclic angle of C 13 -C 14 -C 15 and the reduction in exocyclic angle of N 40 –N 39 -C 14 and C 15 -C 14 –N 39 ascertained by experimental XRD values indicating the intramolecular charge-transfer interaction between the carbazole and nitrophenyl group through the diazo bridge. The vibrational contribution to the linear electro-optic effect is 15% of the total hyperpolarizability being calculated at B3LYP/6–311++G (d, p) for the NPACE molecule. It is also observed that the 8a, 19a, and 19b modes of the carbazole ring and the 8a, 8b, and 19b modes of the phenyl ring are found to be simultaneously and intensely active in IR and Raman spectra explaining the charge transfer interactions throughout the molecule. The low value of the HOMO- LUMO energy gap (2.5843 eV) and the deviation between the measured absorption wavelength (3.36 eV) from the computed (3.87 eV), both these facts substantiate the intramolecular charge transfer. The polarizability and first-order hyperpolarizability were calculated as 6.48 × 10-24 and 3.8 × 10-29 esu, respectively. The second harmonic generation (SHG) measurement experiment of NPACE was carried out using the powder method. The SHG efficiency is measured in comparison with the urea standard. The calculated torsional mode at 20 cm−1 is in excellent quantitative agreement with the experimentally determined terahertz absorption peak. The two-photon absorption coefficient of NPACE was estimated to be 0.9 × 10-11 mW−1, which is mainly due to the D-π-A type of molecular structure, and the optical limiting threshold for NPACE was estimated to be 1.52 × 1013 Wm−2 enabling this material as a potential candidate for optical limiting applications. [ABSTRACT FROM AUTHOR]

[Display omitted] • Synchrotron-based FTIR analysis reveals subtle changes in DNA methylation status. • Changes in DNA conformation lead to changes in IR vibrational spectra. • The DNA-HALO resembles more native conformation in comparison to gDNA. • DNA-HALO structure captures more precisely the presence of unmethylated cytosine. • Peak ratio 1152/1070 cm−1 can be used to define methylation rate in DNA samples. Fourier transform infrared (FTIR) spectroscopy is a rapid, non-destructive and label-free technique for identifying subtle changes in all bio-macromolecules, and has been used as a method of choice for studying DNA conformation, secondary DNA structure transition and DNA damage. In addition, the specific level of chromatin complexity is introduced via epigenetic modifications forcing the technological upgrade in the analysis of such an intricacy. As the most studied epigenetic mechanism, DNA methylation is a major regulator of transcriptional activity, involved in the suppression of a broad spectrum of genes and its deregulation is involved in all non-communicable diseases. The present study was designed to explore the use of synchrotron-based FTIR analysis to monitor the subtle changes in molecule bases regarding the DNA methylation status of cytosine in the whole genome. In order to reveal the conformation-related best sample for FTIR-based DNA methylation analysis in situ , we used methodology for nuclear HALO preparations and slightly modified it to isolated DNA in HALO formations. Nuclear DNA-HALOs represent samples with preserved higher-order chromatin structure liberated of any protein residues that are closer to native DNA conformation than genomic DNA (gDNA) isolated by the standard batch procedure. Using FTIR spectroscopy we analyzed the DNA methylation profile of isolated gDNA and compared it with the DNA-HALOs. This study demonstrated the potential of FTIR microspectroscopy to detect DNA methylation marks in analyzed DNA-HALO specimens more precisely in comparison with classical DNA extraction procedures that yield unstructured whole genomic DNA. In addition, we used different cell types to assess their global DNA methylation profile, as well as defined specific infrared peaks that can be used for screening DNA methylation. [ABSTRACT FROM AUTHOR]

The (ro)vibrational spectra of thiirane, c -C 2 H 4 S, and its fully deuterated isotopologue, c -C 2 D 4 S, have been studied by means of vibrational configuration interaction theory, VCI, its incremental variant, iVCI, and subsequent variational rovibrational calculations, RVCI, which rely on multidimensional potential energy surfaces of coupled-cluster quality including up to four-mode coupling terms. Accurate geometrical parameters, fundamental vibrational transitions and first overtones, rovibrational spectra and rotational spectroscopic constants have been determined from these calculations and were compared with experimental results whenever available. A number of tentative misassignments in the vibrational spectra could be resolved and most results for the deuterated thiirane are high-level predictions, which may guide experiments to come. Besides this, a new implementation of infrared intensities within the iVCI framework has been tested for the transitions of the title compounds and are compared with results obtained from standard VCI calculations. [Display omitted] • Coupled cluster based PES with up to 4D terms for c -C 2 H 4 S and c -C 2 D 4 S. • VCI vibrational frequencies show excellent agreement with experiment. • A new implementation of IR intensities within iVCI is presented and validated. • Rovibrational spectra obtained from RVCI are compared to experimental results. • Spectroscopic constants are obtained through vibrational perturbation theory. [ABSTRACT FROM AUTHOR]

Co-crystals have great potential for drug research and development because the formation of co-crystal is accompanied by changes inter-molecular interactions between starting materials that enable to improve both physical and chemical properties of active pharmaceutical ingredients. In order to provide a more profound insight into the structural changes of specific drugs upon co-crystallization, spectroscopic characterization of solid-state acetazolamide (ACZ), 4-hydroxybenzoic acid (4HBA) and their co-crystal prepared by mechanical grinding approach has been performed with spectral techniques including terahertz time-domain spectroscopy (THz-TDS) and Raman spectroscopy. Experimental THz spectra show that the ACZ-4HBA co-crystal has a few significantly different absorption peaks in 0.82, 1.16, 1.28 and 1.64 THz respectively compared with parent materials in the frequency region from 0.2 to 1.8 THz. Likewise, such differences between the co-crystal and starting compounds could also be characterized by Raman vibrational spectra. Moreover, density functional theory (DFT) calculations were performed to simulate optimized structures and vibrational modes of three kind of possible co-crystal theoretical forms (form I, II and III) between ACZ and 4HBA. Theoretical results and THz/Raman vibrational spectra of ACZ-4HBA co-crystal show that the 4HBA links to the thiadiazole acetamide fragment of ACZ via the double-bridged heterodimeric synthon C(N)NH⋯HOOC inter-molecular hydrogen bonding interaction establishing the theoretical form I, which is more consistent with experimental observations than other two possible theoretical co-crystal forms. These results provide rich information and unique method for characterizing the composition of co-crystal structures and also inter-molecular interactions shown within pharmaceutical co-crystallization process at the molecular level. Unlabelled Image • THz and Raman spectra of acetazolamide and its co-crystal formed with 4-hydroxybenzoic acid are reported. • The major vibrational modes of the co-crystal are obtained and assigned. • THz and Raman spectroscopy techniques are potential to analysis structural changes upon co-crystallization. [ABSTRACT FROM AUTHOR]

Alumina nanopowders belonging to the γ and δ transition phases have been characterized by infrared and Raman spectroscopies. A quantitative interpretation of their vibrational spectra has been provided and related to their crystal structure, with particular emphasis on structural disorder and features not predicted by group-theoretical considerations. Both phases show very similar infrared dielectric functions, but with clear instances of mode-splitting in the δ phase, which are related to ordering in the tetrahedral Al positions. Raman spectroscopy was unable to resolve any modes in the sample identified as γ phase, but the full lattice vibrational region could be measured for the δ sample under UV and red excitation lines. Raman spectra are more complex than those obtained by infrared spectroscopy and cannot be completely explained by factor group analysis, in the absence of dedicated theoretical studies. Finally, the luminescent properties of these materials have been qualitatively explored and linked to disorder and substitutional impurities. In general, the results contained in this work prove that vibrational spectroscopies are powerful tools for quantitative analyses of these disordered nanomaterials and suggest the need for more theoretical work to understand their vibrational properties. [Display omitted] • Lattice vibrations of γ and δ alumina nanoparticles were studied by IR and Raman. • Particle size and structural disorder complicate analyses based on group theory. • IR modes observed only in δ are attributed to the ordering of tetrahedral Al cations. • Raman modes of δ can be observed at some excitation wavelengths, but not for γ. [ABSTRACT FROM AUTHOR]

We present the application of the recently implemented nuclear velocity perturbation theory, using the combined Gaussian and plane waves approach in CP2K, to the vibrational circular dichroism (VCD) spectra of a set of natural products. Even though the calculations were carried out for isolated molecules in the gas-phase limit, neglecting inter-molecular interactions and anharmonic effects, the match between simulated and experimental spectra is reasonable. We also study the influence of different density functionals on the conformational search and the resulting VCD spectra via group coupling matrices (GCMs). The GCM analysis reveals that the VCD signal can in some cases arise from moieties which are close to each other and in other cases from moieties far from each other. Differences in spectra obtained using different exchange–correlation density functionals can be attributed to interaction terms between different moieties in the molecules changing their sign. [Display omitted] • Vibrational circular dichroism spectra of natural products have been computed using the NVPT implemented in CP2K. • Group coupling matrices were calculated to analyze the spectra further. • Results obtained with different exchange–correlation density functionals were compared. [ABSTRACT FROM AUTHOR]

[Display omitted] • Thermal investigation on α-L-aspartyl-L-alanine through Raman and infrared spectroscopy and DSC. • The crystal undergone a phase transition at 387 K. • The phase transition involves changes in hydrogen bonds, possibly the rupture of at least one of them, and changes in the molecule's conformation. Crystals of dipeptide α-L-aspartyl-L-alanine (α-Asp-Ala), C 7 H 12 N 2 O 5 , were studied under high-temperature conditions through vibrational spectroscopy (IR and Raman) and thermal analysis (Differential Scanning Calorimetry – DSC). From the analysis of the results, it is possible to conclude that: (i) the studied material undergoes a reversible order-disorder phase transition at 373 K on heating, where several changes were observed in the vibrational spectra, especially with vibrational modes of the units that participate directly of the hydrogen bonds; (ii) the phase transition undergone by the α-Asp-Ala crystal (about 373 K) involves changes in hydrogen bonds, possibly the rupture of at least one of them, and change in the conformation of the molecules in the unit cell. [ABSTRACT FROM AUTHOR]

[Display omitted] • Vibrational properties of the Bi 2 (MoO 4) 3 at room temperature. • Lattice dynamic calculations based on the rigid ion model. • Effect of the pressure on the vibrational properties of the Bi 2 (MoO 4) 3. • Pressure-induced phase transformation in the Bi 2 (MoO 4) 3. This work reports a pressure-dependent Raman spectroscopic study and the theoretical lattice dynamics calculations of a Bi 2 (MoO 4) 3 crystal. The lattice dynamics calculations were performed, based on a rigid ion model, to understand the vibrational properties of the Bi 2 (MoO 4) 3 system and to assign the experimental Raman modes under ambient conditions. The calculated vibrational properties were helpful to support pressure-dependent Raman results, including eventual structural changes induced by pressure changes. Raman spectra were measured in the spectral region between 20 and 1000 cm−1 and the evolution of the pressures values was recorded in the range of 0.1–14.7 GPa. Pressure-dependent Raman spectra showed changes observed at 2.6, 4.9 and 9.2 GPa, these changes being associated with structural phase transformations. Finally, principal component analysis (PCA) and hierarchical cluster analysis (HCA) were performed to infer the critical pressure of phase transformations undergone by the Bi 2 (MoO 4) 3 crystal. [ABSTRACT FROM AUTHOR]

[Display omitted] • The vibrational bands of collagens are very promising to distinguish between normal colon tissue, benign and malignant colon polyps. • The screening of IR and Raman markers of human collagens I–V was carried out. • The IR/Raman spectral regions for colon tissues and colon polyps were investigated for the contribution of collagen vibrations. • Mentioned differences in collagen spectroscopic markers could be interest for early ex vivo diagnosis of colorectal carcinoma. Vibrational spectroscopic methods are widely used in the molecular diagnostics of carcinogenesis. Collagen, a component of connective tissue, plays a special role as a biochemical marker of pathological changes in tissues. The vibrational bands of collagens are very promising to distinguish between normal colon tissue, benign and malignant colon polyps. Differences in these bands indicate changes in the amount, structure, conformation and the ratio between the individual structural forms (subtypes) of this protein. The screening of specific collagen markers of colorectal carcinogenesis was carried out based on the FTIR and Raman (λ ex 785 nm) spectra of colon tissue samples and purified human collagens. It was found that individual types of human collagens showed significant differences in their vibrational spectra, and specific spectral markers were found for them. These collagen bands were assigned to specific vibrations in the polypeptide backbone, amino acid side chains and carbohydrate moieties. The corresponding spectral regions for colon tissues and colon polyps were investigated for the contribution of collagen vibrations. Mentioned spectral differences in collagen spectroscopic markers could be of interest for early ex vivo diagnosis of colorectal carcinoma if combine vibrational spectroscopy and colonoscopy. [ABSTRACT FROM AUTHOR]

The complex crystals of the family of the Tutton's salt have been investigated through the numerous experimental and theoretical studies to understand their physical properties and their potential technological applications. In spite of the more than 60 years of research, there are very few studies about the electronic properties of Tutton's salt. In our present work, we have calculated the stability, electronic properties and the first theoretical study of band structure of the three different crystals of the Tutton's salt, ammonium nickel sulfate hexahydrate ((NH 4) 2 Ni(SO 4) 2 ·6H 2 O), ammonium nickel‐copper sulfate hexahydrate ((NH 4) 2 Ni 0.5 Cu 0.5 (SO 4) 2 ·6H 2 O) and ammonium copper sulfate hexahydrate ((NH 4) 2 Ni(SO 4) 2 ·6H 2 O) with the help of periodic ab-initio calculations based on density functional theory (DFT). In addition to this, the internal Raman and FTIR modes of the ionic fragments [Ni(H 2 O) 6 ]2+, [Cu(H 2 O) 6 ]2+ NH 4 + and SO 4 2− of the sample crystals were obtained by employing the ab initio and the orientation of the molecular vibrations of the ionic fragments have been presented in picturized form. Furthermore, the Raman and FTIR spectroscopy of the sample crystals were measured in the range 100–4000 cm−1 and 400–4000 cm−1 respectively, and the internal vibrational modes obtained from experimental measurement have been compared with those obtained from DFT calculations. Unlabelled Image • Electronic properties and DFT band structure of Tutton's salt • Internal modes obtained from the ab initio and experimental study • Representations of the molecular vibrations of the ionic fragments [ABSTRACT FROM AUTHOR]

Abstract The study of the H 2 O dipole moment μ and polarisability α vibrational dependence is based on the comparison of experimental and calculated line shifts induced by argon, nitrogen, and air pressure in different H 2 O vibrational bands. Obtained dependence α on the stretching vibrations is in good agreement with the existing ab initio calculations in the literature, but the dependence α on the bending vibration is quite different. To clarify the dependence of μ and α on the bending vibration, the shifts of selected H 2 O lines of the 4ν 2 , 5ν 2 , and 6ν 2 bands induced by argon, hydrogen and helium pressure are measured with the help of a Bruker IFS HR 125 spectrometer at room temperature with a spectral resolution of 0.01 cm−1. The comparison of experimental and calculated results with different values of μ and α line shifts is given. Graphical Abstract Unlabelled Image Highlights • A new vibrational dependence of the H 2 O dipole moment was obtained. • The dipole moment and polarizability of H 2 O molecule from the line shift calculations. • The problem of the ambiguity for the highly excited bending states. [ABSTRACT FROM AUTHOR]

Abstract A novel fluorescence molecule (2‑hydroxy‑4‑methoxyphenyl)(phenyl)‑methanone azine (HMPM) has been explored theoretically in this present work. Based on density functional theory (DFT) and time-dependent density functional theory (TDDFT) methods, we investigate the excited state hydrogen bonding behaviors and excite state intramolecular proton transfer (ESIPT) process for HMPM molecule. Via simulating the reduced density gradient (RDG) versus sign(λ 2)ρ, we firstly verify the double intramolecular hydrogen bonds (O1 H2⋯N3 and O4 H5⋯N6) for HMPM system. Comparing with the changes about these two hydrogen bonds (i.e., bond distances, bond angles and infrared (IR) vibrational spectra), we find that they should be enhanced in the first excited state upon the photo-excitation. The shortened hydrogen bonding distance of H2⋯N3 and H5⋯N6 provide the possibility for ESIPT reaction. Given the photo-excitation process, we confirm the charge redistribution around the hydrogen bonding moieties plays an important role as a driving force for the ESIPT process. Further, via constructing S 0 -state and S 1 -state potential energy surfaces (PESs), we confirm the excited state double proton transfer (ESDPT) is excludable since the high optimized energy and high potential energy barrier. While the low potential barrier for excited state single proton transfer path results in the ultrafast ESIPT reaction, which explains why the initial HMPM fluorescence peak cannot be detected in previous experimental phenomenon. This work not only clarifies the excited state dynamical behavior for HMPM system, but also explains previous experimental phenomenon and attributions about steady state spectra. We hope this work can facilitate novel applications based on the novel HMPM system in future. Graphical Abstract Unlabelled Image Highlights • Hydrogen bond of HMPM should be strengthened in the first excited state. • Charge transfer facilitates the ESIPT process for HMPM molecule. • Only the excited state single proton transfer process occurs for HMPM molecule. [ABSTRACT FROM AUTHOR]

Abstract A detailed study on the vibrational spectra of monohalogenated acetylenes and their deuterated analogues has been reported in this work using the U(4) algebraic model. With detailed spectral analysis, it has been shown in this study that all the stable isotopes of monohalogenated acetylenes and their deuterated analogues can be approximated well using the U(4) algebraic model. Graphical Abstract Unlabelled Image Highlights • An economic set of parameters are needed to provide a good accuracy. • Complex potential energy surfaces and highly excited levels can be dealt well. • A general Hamiltonian can approximate all the molecules in a specific class. • Viable alternative to the traditional approaches [ABSTRACT FROM AUTHOR]

Abstract Fourier infrared spectrometer and X-ray diffractometer were used to detect the spectra of lab-made U:A (uracil and adenine hydrate dried at room temperature), lab-made C:G (cytosine and guanine hydrate dried at room temperature), U + A (mixture of uracil and adenine), and C + G (mixture of cytosine and guanine). The results of our testing showed that U:A did not form a eutectic, but C:G did. In order to further characterize the vibrational modes of RNA base pair crystals, the absorption spectra of 1‑methyl‑5‑bromouracil‑9‑methyladenine (abbreviated as 1M5BU:9MA) and 1‑methylcytosine‑9‑ethylguanine (abbreviated as 1MC:9EG) were calculated based on the PBC-GEBF (generalized energy-based fragmentation approach under periodic boundary conditions) method. To further study the effect of substituents on the vibrational mode of the crystal structure, the substituents of 1M5BU:9MA and 1MC:9EG were artificially removed. The results of calculation brought out that methyl and ethyl as substituents have little effect on the vibrational spectrum, but halogen atoms such as Br atom in 1M5BU:9MA has a certain influence on the spectrum. Furthermore, THz (terahertz) spectra of the RNA nucleotide sequence 5′-AUCG-3′ was analyzed. In the perspective of the spectra with DNA signatures, their spectra show a great deal of similarity regardless of RNA or DNA, or the base sequence difference. This study will provide a very important information for revealing the role of RNA in the formation of biological macromolecules and its mechanism. Graphical Abstract Terahertz spectra from RNA base pair crystal structures with and without substituents to RNA single strands. Unlabelled Image Highlights • PBC-GEBF method adopted by us is first time employed to calculate the THz spectra of the RNA base pair cocrystals. • U:A did not form a eutectic, but C:G did. • Normal modes are obtained to illustrate the vibrational modes. • Methyl and ethyl as substituents have little effect on the vibrational spectrum. • The vibration modes have undergone significant changes due to the addition of substituents. • THz spectra and corresponding vibrational modes of the short-chain DNA and RNA have nothing to do with their base sequence. [ABSTRACT FROM AUTHOR]

Abstract Temperature-dependent Raman spectroscopic study has been performed on scheelite-type sodium‑cerium molybdate - NaCe(MoO 4) 2 - in the temperature range 113–873 K. This study provides phonon properties of NaCe(MoO 4) 2 , which are very important to understand the mechanism governing eventual phase transitions undergone by the structure, since phonons are very sensitive to structural changes. The ambient scheelite phase remains stable in a low-temperature range (113–293 K), and no relevant modification is observed in the Raman spectra. However, the experiments reveal the existence of one reversible phase transition at high-temperature. The vibrational spectra of NaCe(MoO 4) 2 system showed anomalies above 748 K, where overlaps of some bands and the appearance of a band at 458 cm−1 are observed. These modifications were attributed to an isostructural phase transition and a discussion about the possible mechanism of this transformation is furnished. Graphical Abstract Unlabelled Image Highlights • Phonon properties of double scheelite-type NaCe(MoO 4) 2 system. • Temperature-dependent Raman scattering study has been performed on NaCe(MoO 4) 2. • Observation of a reversible isostructural phase transformation at around 748–773 K. [ABSTRACT FROM AUTHOR]

Abstract Ro-vibrational spectra of different electronic states of molecules are often used as absolute wavelength or frequency standards. These standards are also used to mitigate any slow drift of laser frequency during an experiment. In the precision experiment, the two most commonly used molecular standards are iodine and tellurium, both are homo-nuclear diatomic molecules. The former is mostly used as standard for the long wavelength (600–900 nm) region, while the tellurium spectrum is widely used in short wavelength (400–550 nm) including near ultraviolet. A comprehensive data on tellurium spectra can be obtained from the tellurium atlas [1]. However near the 455 nm range where a number of important atomic resonance line, the atlas provides no significant data. We have performed high resolution modulation transfer spectroscopy (MTS) on tellurium molecule in a hot cell in the region close to 455 nm wavelength thereby obtained more than 100 new spectral lines which were not observed before. The linewidth of each of these peaks is about a few tens of MHz, making them suitable for laser frequency locking. [ABSTRACT FROM AUTHOR]

Abstract Hydrogen bonding is a weak chemical interaction widely existed in the variety of organic and biological molecules. As an important structural motif of pyrimidine bases, the solvent effect of the hydrogen bonding of 2-cyclohexen-1-one (CHO) and 3-methyl- 2-cyclohexen-1-one (3MCHO) and its effect on the frequency shift of the C O stretching mode were investigated by using the FT-Raman and UV absorption spectra and density functional theory calculations. The electronic transitions associated with the UV absorptions in different solvents were calculated at B3LYP-TD/6-31++G(d,p) level of theory and employing SCIPCM solvent model. The vibrational spectra of CHO and 3MCHO were assigned on the basis of the FT-Raman spectra in neat liquid and different solvents, the calculated vibrational spectra of monomer and CHO dimers, and the concentration dependent experiments of the band pair intensities. Hydrogen bonding energies of CHO-(H 2 O) n (n = 1,2) clusters were predicted. The results reveal that the CHO-(H 2 O) 2 cluster and CHO monomer are respectively the major source of spectral observation in water and cyclohexane, while CHO dimmer and CHO monomer coexist in acetonitrile. The difference in the frequency of the ν C=O stretching mode between 3MCHO monomer and CHO monomer in cyclohexane were explored. Graphical Abstract Solvent effects on the UV absorption and FT-Raman spectra of CHO and 3MCHO in solution phases were evaluated by using the UV and FT-Raman spectroscopies and B3LYP-TD/6-31++G(d, p) calculations employing SCIPCM solvent model in cyclohexane, acetonitrile and water solutions. The Raman intensity profiles in the ν C O region of CHO and 3MCHO were affected strongly by solvents of different polarity and hydrogen bonding capability. The results indicated that nonpolar solvents favored CHO monomer, while protic solvents favored CHO-(H 2 O) n (n = 1,2) clusters. The new band at 1653 cm−1 for CHO and at 1643 cm−1 for 3MCHO in water were assigned respectively to CHO-(H 2 O) n clusters and 3MCHO-(H 2 O) n clusters. The hydrogen bonding of solvents and the π-σ superconjugation or π-p conjugation between C C C O and the neighbouring groups (such as CH 3 and NH 2) made the frequency of the ν C O mode down-shift. The Raman spectra of CHO and 3MCHO were assigned. Unlabelled Image Highlights • The Raman spectra of 2-cyclohexen-1-one (CHO) and 3-methyl- 2-cyclohexen-1-one (3MCHO) were assigned. • Effect of the UV and Raman spectra of CHO and 3MCHO by different polarity solvents and hydrogen bonding were clarified. • Effect of the electronic transitions of CHO by functionals were evaluated employing PCM and SCIPCM solvent models. • New band at 1653 cm−1 for CHO and at 1643 cm−1 for 3MCHO in water were assigned to their water clusters respectively. [ABSTRACT FROM AUTHOR]

Abstract A phase transition in new compound 2-nitroanilinium nitrate, (H2NA)NO 3 , was found. A symmetry lowering from orthorhombic, Pmn 2 1 , to monoclinic one, P 2 1 , at 249 K is observed. During the phase transition, the H2NA+ and nitrate ions displace from the mirror plane in high-temperature phase. As a result, hydrogen bonding network constructed by the ammonio group and NO 3 − anion is changed. Especially, a bifurcated hydrogen bond disappears. Mathematical operations using both elementary and hydrogen bond graph-set descriptors were used for the first time to describe a mechanism of phase transition. Changes in hydrogen bonding network were also studied by means of vibrational spectroscopy. Band shift associated with stretching and bending vibrations of the ammonio group indicates that the energy of intermolecular interactions rises along with temperature decrease. SHG response for the studied compound is higher than KDP, I (H2NA)NO3 = 1.1·I KDP , although a decay of the signal was observed due to instability of the sample. Graphical Abstract Unlabelled Image Highlights • The (H2NA)NO 3 crystallizes without a center of symmetry. • Crystal symmetry changes from Pmn 2 1 to P 2 1 at 249 K. • SHG intensity for (H2NA)NO 3 is 1.1I KDP. • Operations on the graph-set descriptors used to describe a mechanism of phase transition. [ABSTRACT FROM AUTHOR]

Abstract Rare-earth phosphates with the general formula REEPO 4 ·nH 2 O belong to four distinct structural types: monazite, rhabdophane, churchite, and xenotime. We report herein the first direct comparison between vibrational spectra of these compounds for the same metal cation i. e. gadolinium. The four GdPO 4 ·nH 2 O samples were prepared through wet chemistry methods and first characterized by X-ray diffraction. Three distinct spectral domains, associated to the deformation and stretching modes of phosphate tetrahedra (PO 4 ) and to water molecules vibrations were then analyzed from FTIR and Raman data, and discussed regarding the structural characteristics of each sample. The most obvious differences between the spectra were associated to δ(H 2 O) and δ s (PO 4 ) modes and led to propose a simple method to rapidly and unambiguously discriminate the four polymorphs. Graphical Abstract Unlabelled Image Highlights • Comparison between vibrational spectra of four GdPO 4 ·nH 2 O polymorphs was undertaken. • Vibration modes of PO 4 and H 2 O are discussed regarding the structural characteristics. • Differences between the spectra were mainly associated to δ(H 2 O) and δ s (PO 4 ) modes. • A simple method to rapidly and unambiguously discriminate the polymorphs is proposed. [ABSTRACT FROM AUTHOR]

Abstract Infrared spectra of small amounts of water on the “hydrophobic” polymers, polyethylene (PE), polypropylene (PP) and polytetrafluoroethylene (PTFE), include many negative infrared bands that become positive with increasing temperature. The new species that the bands represent must arise through absorption of the incident radiation to form short-lived femtosecond states that disappear by (a) induced (Einstein) emission, thus leading to negative IR bands, or (b) fragmentation with loss of vibrational energy or (c) are replaced by an infrared excited state. In addition, we must note that polyethylene, polypropylene and polytetrafluoroethylene carry water! and many water oligomers (chair, boat, and prism hexamer) are easily observed. Graphical Abstract Spectra of corner of Book 2. Unlabelled Image Highlights • IR of water on hydrophobic polymers displays negative bands. • Many water oligomers (chair, boat, and prism hexamer) are easily observed. • The negative bands arise from stimulated emission from femtosecond stable states. • Polyethylene, polypropylene and polytetrafluoroethylene carry water! [ABSTRACT FROM AUTHOR]

Abstract A new compound named 7-hydroxy-4-methyl-2-oxo- 2H -chromene-8-carbaldehyde oxime (7-Oxime) was synthesized and characterized by FT-IR, FT-Raman, 1H NMR and 13C NMR techniques. The conformer possibilities were studied to find the most stable conformer and its molecular geometry. Then, the dimer form of the most stable monomer was built and optimized. Density functional theory (DFT) B3LYP method with 6-311++G(d,p) basis set was applied to analyze the molecular electrostatic potential (MEP), HOMO and LUMO orbitals, the vibrational wavenumbers, the infrared intensities, the Raman scattering activities and several thermodynamic properties (at different temperatures). The stability of the molecule derived from hyperconjugative interactions and charge delocalization has been analyzed by using natural bond orbital (NBO) analysis. In order to find the possible inhibitory activity of 7-Oxime, an accurate molecular blind docking simulation was performed. The results indicated that the mentioned compound has a good binding affinity to interact with the active sites of human α-glucosidase and α-amylase. For the first time, our computational finding suggests that this compound has a potential to be used as a supplementary agent in the pre-management of diabetes mellitus. Graphical Abstract Unlabelled Image Highlights • 7-hydroxy-4-methyl-2-oxo-2 H -chromene-8-carbaldehyde oxime has been synthesized. • The complete vibrational assignments and spectroscopic analyses were performed. • The druglikeness of the title compound was investigated by following Lipinski's rule of five. • The electronic structures of ligand/receptors were investigated with the radius of 4 Å. [ABSTRACT FROM AUTHOR]

Abstract The drug action of ester type local anesthetic (LA) procaine hydrochloride (PRC HCl) is activated by blocking Na+ ion flow when it binds to the ion channel in the ligand gated sodium ion channel protein. Büchi's model, explains binding action of ester type LA drug with receptor in terms of charge transfer, dipole-dipole, hydrogen bonding and van der Waals interactions through lipophilic, ester and hydrophilic moieties. The present work investigates molecular structural and vibrational spectral features of para amino benzoate group, ester part and tertiary amino group respectively belonging to lipophilic, ester and hydrophilic moieties, accountable for the binding of drug to sodium channel. The electron transport mechanism through the ring responsible for structural deviation from benzenoid to quinonoid form and consequent dipolar nature of carbonyl group have been investigated, based on the analysis of XRD, DFT computed molecular structure, 8a ring mode and NBO charges. The characteristic UV absorption peaks and vibrational marker bands of LA drugs have been identified and the charge transfer interaction responsible for lipophilic binding has been investigated. The blocking of Na+ in the ion channel has been probed using attractive and repulsive energy profile. The molecular polarizability has been computed to substantiate the correlation between the structure activity relationship of LA drug molecule and molecular polarizability. The low toxicity of PRC HCl was evaluated using in vitro cytotoxicity study, confirming it as a potential short acting local anesthetic. Graphical Abstract Unlabelled Image Highlights • Vibrational spectral account of Büchi's model for local anesthetic drug action • Role of electron transport in benzenoid to quinonoid change and carbonyl activity • Blocking of Na+ ion in channel probed with attractive and repulsive energy profile • Charge transfer interaction responsible for lipophilic binding analyzed • IR and Raman spectral markers for ester type local anesthetics identified [ABSTRACT FROM AUTHOR]

A new chloranilate compound with 1-(2-fluorophenyl)piperazine has been synthesized and characterized using spectroscopic methods and X-ray diffraction. The atomic arrangement can be described by an H-bonded 3D network, formed by anionic entities, organic cations and H 2 O molecules linked together via N H…O, O H…Cl, C H…Cl and C H…O hydrogen bonds. The vibrational absorption bands of the various characteristic groups of this compound have been identified by infrared spectroscopy. Moreover, the thermal and dielectric analyses have shown that the title compound has a phase transition at 393 K. The surface mapped over the d norm property, highlights the A⋯H (A O, C, Cl and F) as the main intermolecular contacts. On the other hand, the geometry, intermolecular bonds and harmonic vibrational frequencies of the title molecule have been investigated using the B3LYP/6-31G (d, p) method. The stability of the structure obtained, as well as the charge transfer within the molecule, have been confirmed by determining the energies of the HOMO and LUMO levels and the theoretical gap energy. Molecular docking studies of the title compound have also been conducted as part of this study. [ABSTRACT FROM AUTHOR]

Vibrational infrared, Raman and surface-enhanced Raman scattering (SERS) spectra of clotrimazole (CTZ) were documented and evaluated. Density-functional theory, B3LYP/6-311++G(d,p), approach was implemented to identify the possible conformations, develop the electrostatic potential map, evaluate frontier molecular orbitals and calculate the vibrational spectra of the target compound. The silver-loaded graphene was shown to be an effective SERS substrate for CTZ trace detection. The SERS spectrum showed two enhanced bands at 670 cm −1 and 700 cm −1 which confirmed the absorption of the silver substrate through chlorine and nitrogen atoms. A detection limit as low as 5 nM could be reached with a determination coefficient of 0.9988 using the band at 670 cm −1 . The protein-ligand interaction with Secreted Aspartic Proteinase 2 (SAP2) of C. albicans showed that the four stable forms of CTZ maintain a free energy of binding of 6–7 kcal/mol, which could give insights into the mode of action in treating Candidiasis. [ABSTRACT FROM AUTHOR]

[Display omitted] • Purple bacterial reaction centers with phylloquinone incorporated into the Q A binding site were studied. • Vibrational properties of the phyllosemiquinone anion in the protein binding site were calculated. • Calculated and experimental spectra agree well. [Q A – – Q A ] Fourier transform infrared difference spectra have previously been obtained using purple bacterial reaction centers from Rhodobacter sphaeroides with unlabeled, 18O and 13C isotope labeled phylloquinone (PhQ, also known as vitamin K 1) incorporated into the Q A protein binding site (Breton, (1997), Proc. Natl. Acad. Sci. USA 94 11318–11323). The nature of the bands in these spectra and the isotope induced band shifts are poorly understood, especially for the phyllosemiquinone anion (PhQ–) state. To aid in the interpretation of the bands in these experimental spectra, ONIOM type QM/MM vibrational frequency calculations were undertaken. Calculations were also undertaken for PhQ– in solution. Surprisingly, both sets of calculated spectra are similar and agree well with the experimental spectra. This similarity suggests pigment-protein interactions do not perturb the electronic structure of the semiquinone in the Q A binding site. This is not found to be the case for the neutral PhQ species in the same protein binding site. PhQ also occupies the A 1 protein binding site in photosystem I, and the vibrational properties of PhQ– in the Q A and A 1 binding sites are compared and shown to exhibit considerable differences. These differences probably arise because of changes in the degree of asymmetry of hydrogen bonding of PhQ– in the A 1 and Q A binding sites. [ABSTRACT FROM AUTHOR]

[Display omitted] • We synthesized amorphous aluminosilicate gel in the presence of heavy metal ions. • The effect of heavy metal ions on structure of aluminosilicate gel has been investigated. • We used the vibrational spectra to describe the structure of C-(A)-S-H phase. • We have attempted to evaluate the mechanism of immobilization of individual ions. Calcium aluminosilicate hydrates (C-(A)-S-H) with two different C/S molar ratios of 1.0 and 1.7 were synthesized by precipitation with the use of the alkali-activation method. The samples were synthesized with solutions of heavy metals nitrates such as nickel (Ni), chromium (Cr), cobalt (Co), lead (Pb), and zinc (Zn). Metal cations were added in the amount of Ca:Me equal to 9:1, while Al/Si was 0.05. The influence of the addition of heavy metal cations on the structure of the C-(A-)S-H phase was investigated. For this purpose, XRD was used to examine the phase composition of the samples, FT-IR and Raman spectroscopy were used to determine the effect of heavy metal cations on the structure of the obtained C-(A)-S-H phase and their degree of polymerization. Using SEM and TEM, changes in the morphology of the obtained materials were determined. Possible mechanisms of immobilization of heavy metal cations have been determined. It was found that some heavy metals (Ni, Zn, and Cr) could be immobilized by precipitation of insoluble compounds. On the other hand, they could remove Ca2+ ions from the structure of aluminosilicate and take their place, as evidenced by the crystallization of Ca(OH) 2 in samples with the addition of Cd, but also Ni and Zn in small amounts. A third possibility is the incorporation of heavy metal cations at the silicon and/or aluminum tetrahedral sites, as is the case with Zn. [ABSTRACT FROM AUTHOR]

[Display omitted] • Raman spectra and vibrational properties of five FOX-7 polymorphs were calculated. • Phases α' and β are intermediate phases with transitional properties. • NH2 anti-symmetry-stretching softening under pressure corresponds to H-transfer. FOX-7 (1,1-diamino-2,2-dinitroethene) as one of the widely studied insensitive high explosives exists five polymorphs (α, β, γ, α', ε) whose crystal structures have been determined by XRD (X-rays Diffraction) and which are investigated by a density functional theory (DFT) approach in this work. The calculation results show that the GGA PBE-D2 method can reproduce the experimental crystal structure of FOX-7 polymorphs better. The calculated Raman spectra of FOX-7 polymorphs were compared in detail and fully with the experimental Raman spectra data and it was found that the calculated Raman spectra frequencies have an overall red-shift in middle band (800–1700 cm−1), and that the maximum deviation does not exceed 4 % (The maximum point is the mode of C C in plane bending). The high-temperature phase transform path (α → β → γ) and the high-pressure phase transform path (α → α'→ε) can be well represented in the computational Raman spectra. In addition, crystal structure of ε-FOX-7 was performed up to 70 GPa to probe Raman spectra and vibrational properties. The results showed that the NH 2 Raman shift is jittering with pressure (not smooth compared to other vibrational modes) and NH 2 anti-symmetry-stretching appears red-shifted. The vibration of hydrogen mixes in all of other vibrational modes. This work shows that the dispersion-corrected GGA PBE method can reproduce the experimental structure, vibrational properties and Raman spectra very well. [ABSTRACT FROM AUTHOR]