Vibrational Raman Spectra Research Articles

Using Gaussian process regression to simulate the vibrational Raman spectra of molecular crystals

Vibrational properties of molecular crystals are constantly used as structural fingerprints, in order to identify both the chemical nature and the structural arrangement of molecules. The simulation of these properties is typically very costly, especially when dealing with response properties of materials to e.g. electric fields, which require a good description of the perturbed electronic density. In this work, we use Gaussian process regression (GPR) to predict the static polarizability and dielectric susceptibility of molecules and molecular crystals. We combine this framework with ab initio molecular dynamics to predict their anharmonic vibrational Raman spectra. We stress the importance of data representation, symmetry, and locality, by comparing the performance of different flavors of GPR. In particular, we show the advantages of using a recently developed symmetry-adapted version of GPR. As an examplary application, we choose Paracetamol as an isolated molecule and in different crystal forms. We obtain accurate vibrational Raman spectra in all cases with fewer than 1000 training points, and obtain improvements when using a GPR trained on the molecular monomer as a baseline for the crystal GPR models. Finally, we show that our methodology is transferable across polymorphic forms: we can train the model on data for one crystal structure, and still be able to accurately predict the spectrum for a second polymorph. This procedure provides an independent route to access electronic structure properties when performing force-evaluations on empirical force-fields or machine-learned potential energy surfaces.

Spectral and quantum chemical analysis of ethyl 4-[3-(adamantan-1-yl)-4-phenyl-5-sulfanylidene-4,5-dihydro-1H-1,2,4-triazole-1-yl]methylpiperazine-1-carboxylate

The Fourier transform infrared and Raman spectra of the adamantane-based compound ethyl 4-[3-(adamantan-1-yl)-4-phenyl-5-sulfanylidene-4,5-dihydro-1H-1,2,4-triazol-1-yl]methylpiperazine-1-carboxylate were recorded in the ranges of 3200–650[Formula: see text]cm[Formula: see text] and 3200–150[Formula: see text]cm[Formula: see text], respectively. The UV/Vis spectrum of solution of the title compound in ethanol was measured in the range of 450–200[Formula: see text]nm. The DFT calculations at the B3LYP/cc-pVDZ and B3LYP/cc-pVTZ levels of the theory were performed to obtain the equilibrium geometric structure and to predict vibrational IR and Raman spectra of the title molecule. The TDDFT calculations at the CAM-B3LYP/cc-pVTZ level of the theory, as well as MRPT calculations at the CASSCF(4,5)/XMCQDPT2 level of the theory were carried out to reproduce the electronic absorption spectrum. The experimental IR, Raman and UV/Vis spectra were interpreted on the basis of results of quantum chemical modeling. Based on Mulliken and Löwdin atomic population analysis, it was established that the compound under study exhibits features of an intramolecular charge transfer.

β-As Monolayer: Vibrational Properties and Raman Spectra.

Recently, semiconducting and other extraordinary properties of the monolayer of the V-group element have attracted a broad interest and attention. The success of experimentally growing antimonene and black phosphorus makes the arsenic monolayer a reasonable candidate for two-dimensional semiconductors. By using DFT calculation, we investigate the vibrational properties and Raman spectra of the buckled honeycomb monolayer of arsenic (β-As) for four commonly used laser lines. By calculating Raman tensor of each active modes of the β-As monolayer, we obtained polarization angle-dependent Raman intensities when the wave vector of incident light is parallel and perpendicular with the plane of the β-As monolayer. We found that the nonresonant Raman spectra have two peaks at 235 and 305 cm–1 that correspond to the in-plane vibrating mode Eg and out-of-plane vibrating mode A1g, which is similar to germanene, blue phosphorene, and β-Sb monolayer Raman spectra. There are two (four) minima and two (four) maxima when the polarization direction of scattered light is parallel (perpendicular) to that of the incident light and the wave vector of the incident light is parallel to the β-As monolayer. The Raman intensities of neither parallel polarization configuration nor perpendicular polarization configuration depend on the polarization direction when the wave vector of incident light is perpendicular to the β-As monolayer. The relation between shapes of the polar plots and relative values of Raman tensor elements is found. The Raman intensities decrease with increasing wavelength of incident laser lines in most cases. Our results will help experimentalists to identify the existence and the orientation of the β-As monolayer while they are growing the β-As monolayer.

Anharmonic effects in the low-frequency vibrational modes of aspirin and paracetamol crystals

The low-frequency range of vibrational spectra is sensitive to collective vibrations of the lattice. In molecular crystals, it can be decisive to identify the structure of different polymorphs, and in addition, it plays an important role on the magnitude of the temperature-dependent component of vibrational free energy differences between these crystals. In this work we study the vibrational Raman spectra and vibrational density of states of different polymorphs of the flexible Aspirin and Paracetamol crystals based on dispersion-corrected density-functional theory, density-functional perturbation theory, and $ab\,initio$ molecular dynamics. We examine the effect of quasi-harmonic lattice expansion and compare the results of harmonic theory and the time correlation formalism for vibrational spectra. Lattice expansion strongly affects the collective vibrations below 300 cm$^{-1}$, but it is significantly less important at higher frequencies, while thermal nuclear motion can be important in the full vibrational range. We also observe that the inclusion or neglect of many-body van der Waals dispersion interactions do not cause large differences in the low-frequency range of Raman spectra or vibrational density of states, provided the lattice constants are fixed. We obtain quantitative agreement with experimental room-temperature Raman spectra below 300 cm$^{-1}$ for all polymorphs studied. Examining the two-dimensional correlations between different vibrations, we find which modes show a larger degree of anharmonic coupling to others, providing a possible route to assess the accuracy of harmonic free energy evaluations in different cases.

On the Models for the Investigation of Charged Defects in Solids: The Case of the VN- Defect in Diamond.

Local charged defects in periodic systems are usually investigated by adopting the supercell charge compensated (CC) model, which consists of two main ingredients: (i) the periodic supercell, hopefully large enough to reduce to negligible values the interaction among defects belonging to different cells; (ii) a background of uniform compensating charge that restores the neutrality of the supercell and then avoids the "Coulomb catastrophe". Here, an alternative approach is proposed and compared to CC, the double defect (DD) model, in which another point defect is introduced in the supercell that provides (or accept) the electron to be transferred (subtracted) to the defect of interest. The DD model requires obviously a (much) larger supercell than CC, and the effect of the relative position of the two defects must be explored. A third possible option, the cluster approach, is not discussed here. The two models have been compared with reference to the VN- defect; for DD, the positive compensating charge is provided by a P atom. Three cubic supercells of increasing size (containing 216, 512, and 1000 atoms) and up to eight relative VN--P+ defect-defect positions have been considered. The comparison extends to the equilibrium geometry around the defect, band structure, charge and spin distribution, IR and Raman vibrational spectra, and electron paramagnetic resonance constants. It turns out that the CC and DD models provide very similar results for all of these properties, in particular when the P+ compensating defect is not too close to VN-.

Structure and spectroscopic characterization of pharmaceutical co-crystal formation between acetazolamide and 4-hydroxybenzoic acid.

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.

Structural, Vibrational and UV/Vis Studies of Adamantane-Containing Triazole Thiones by Spectral, DFT and Multi-reference ab initio Methods

Abstract The Fourier transform infrared and Raman spectra of two adamantane-containing triazole thiones, namely 3-(adamantan-1-yl)-1-[(4-benzylpiperazin-1-yl)methyl]-4-phenyl-1H-1,2,4-triazole-5(4H)-thione and 3-(adamantan-1-yl)-4-phenyl-1-[(4-phenylpiperazin-1-yl)methyl]-1H-1,2,4-triazole-5(4H)-thione, were examined in the ranges of 3200–650 cm−1 and 3200–150 cm−1, respectively. The density functional theory calculations were performed for the geometric structures and vibrational spectra for the title molecules. The accurate equilibrium geometry structures of the molecules were determined on the basis of full geometry optimization at the B3LYP/cc-pVDZ level of the theory. The IR and Raman vibrational spectra were calculated and compared with the experimental ones. The experimental vibrational FT-IR and Raman spectra were interpreted. Based on the structure of the molecules the biological activity indices were predicted. It is established that compounds under consideration are very likely to exhibit the analgesic activities. The UV/Vis spectra of solution of the compounds in ethanol were measured in the range of 450–200 nm. The UV/Vis spectra simulations at the Time-Dependent DFT and Multi-Reference Perturbation Theory levels of theory demonstrate unsuitability of the TDDFT for description of the experimental spectra of the title molecules. It is highly probable that this is a consequence of the intramolecular charge transfer. In contrast, the MRPT results are in a good agreement with the experimental spectra.

Co-Crystal Formation of Antibiotic Nitrofurantoin Drug and Melamine Co-Former Based on a Vibrational Spectroscopic Study.

The co-crystallization of active pharmaceutical ingredients (APIs) has received increasing attention due to the modulation of the relative physicochemical properties of APIs such as low solubility, weak permeability and relatively inferior oral bioavailability. Crystal engineering plays a decisive role in the systematic design and synthesis of co-crystals by means of exerting control on the inter-molecular interactions. The characterization and detection of such co-crystal formations plays an essential role in the field of pharmaceutical research and development. In this work, nitrofurantoin (NF), melamine (MELA) and their hydrated co-crystal form were characterized and analyzed by using terahertz time-domain spectroscopy (THz-TDS) and Raman vibrational spectroscopy. According to the experimental THz spectra, the hydrated co-crystal form has characteristic absorption peaks at 0.67, 1.05, 1.50 and 1.73 THz, while the THz spectra for the two raw parent materials (NF and MELA) are quite different within this spectral region. Similar observations were made from the experimental Raman vibrational spectra results. Density functional theory (DFT) calculation was performed to help determine the major vibrational modes of the hydrated co-crystal between nitrofurantoin and melamine, as well as identify the structural changes due to inter- and/or intra-molecular hydrogen bonding motifs between NF and MELA. The results of the theoretical frequency calculations corroborate the THz and Raman experimental spectra. The characteristic bands of the NF–MELA-hydrated co-crystal between nitrofurantoin and melamine were also determined based on the DFT simulated calculation. The reported results in this work provide us with a wealth of structural information and a unique vibrational spectroscopic method for characterizing the composition of specific co-crystals and inter-molecular hydrogen bonding interactions upon pharmaceutical co-crystallization.

Raman spectroscopy of glycolic acid complexes with N2

High overtone excitation induced conformational isomerization of glycolic acid – nitrogen complex in an argon matrix was investigated by Raman spectroscopy. The interaction between glycolic acid and nitrogen change the green light (532 nm) induced isomerization processes compared to non-complexed glycolic acid. The 180° rotation around of the CC bond and stabilization of carboxyl OCOH dihedral angle to trans position were the main conformational changes observed in the complex of the lowest energy conformer and nitrogen. Interestingly, only one stable light-induced conformational product was observed, which isomerises back to the lowest energy conformer upon prolonged irradiation at 532 nm. The vibrational Raman spectrum of glycolic acid – nitrogen complex and the analysis of the isomerization kinetics are presented.

Vibrational properties and Raman spectra of pristine and fluorinated blue phosphorene.

Using density functional theory, we investigated the vibrational properties and Raman spectra of pristine blue phosphorene and fluorinated blue phosphorene. The fluorinated blue phosphorene possesses a Dirac cone at the K point (about 310 cm-1). The shape of the Dirac cone remains unchanged under different tensile strains. The Raman tensor and thus angle-dependent Raman intensities of all Raman active modes are calculated for the polarizations of scattered light parallel and perpendicular to that of the incident light. The characteristics of angle-dependent Raman intensities are discussed. Moreover, the polarization direction averaged non-resonant Raman spectra of pristine blue phosphorene and fluorinated blue phosphorene are compared with that of germanene and black phosphorene.

Nitrogen substitutional defects in silicon. A quantum mechanical investigation of the structural, electronic and vibrational properties.

The vibrational infrared (IR) and Raman spectra of seven substitutional defects in bulk silicon are computed, by using the quantum mechanical CRYSTAL code, the supercell scheme, an all electron Gaussian type basis set and the B3LYP functional. The relative stability of various spin states has been evaluated, the geometry optimized, the electronic structure analyzed. The IR and Raman intensities have been evaluated analitically. In all cases the IR spectrum is dominated by a single N peak (or by two or three peaks with very close wavenumbers), whose intensity is at least 20 times larger than the one of any other peak. These peaks fall in the 645-712 cm-1 interval, and a shift of few cm-1 is observed from case to case. The Raman spectrum of all defects is dominated by an extremely intense peak at about 530 cm-1, resulting from the (weak) perturbation of the peak of pristine silicon.

A complete characterization of vibrational IR and Raman spectra of the highly-symmetrical octathia[8]circulene

The highly-symmetrical octathia[8]circulene molecule (8S) was synthesized and well studied 10 years ago in Moscow, including X-ray diffraction, IR and Raman spectra assignment on the ground of molecular DFT calculation. Nevertheless, this comprehensive study could not explain a big number of interesting deviations from the DFT predictions based on the molecular D8h symmetry restriction being specific for a free species in a gas phase. In present work we have performed DFT optimization of the 8S tetramer starting with the X-ray diffraction analysis of a similar crystal structure. DFT calculation of IR and Raman spectra of such a huge system provides a good assignment of the crystal-field splitting and new band occurrence. The force-field distortions, electric charges and polarizability dependence on the tetramer structure are well reproduced by the B3LYP functional with the dispersion correction. Thus, the small shifts of IR and Raman bands, their splitting and intensity redistribution upon weak intermolecular interactions in crystal packing are explained and full assignment of all observed bands is presented.

The theoretical study about the ESIPT mechanism for 2,4‐bis(benzooxazol‐2′‐yl)hydroquinone: Single or double?

AbstractOn the basis of the density functional theory (DFT) and time‐dependent DFT (TDDFT) methods, we theoretically study the excited‐state intramolecular proton transfer (ESIPT) mechanism of 2,4‐bis(benzooxazol‐2′‐yl)hydroquinone (2,4‐DHBO), which is reported in the previous literature (Ulrich et al. New J. Chem. 2016, 40, 5877). The calculated absorption and fluorescence spectra of 2,4‐DHBO are accordant with previous experiment, which indicates that the selective theoretical method is credible. The comparisons of the calculated bond lengths, angles, infrared, and Raman vibrational spectra of 2,4‐DHBO manifest that two intramolecular hydrogen bonds (HBs) strengthen in the excited state (S1), which should be triggered the ESIPT reaction. In addition, the calculated frontier molecular orbitals (MOs) and the map of the electron density difference between the ground (S0) and S1 states provide that the ESIPT reactions are facilitated by charge transfer after photoexcitation. Moreover, to explore the detailed ESIPT mechanism of 2,4‐DHBO, the potential energy surfaces (PESs) in the S0 and S1 states are constructed. Because of the low excited‐state potential barriers on the PESs of 2,4‐DHBO, the single and stepwise double ESIPT mechanisms are revealed in the S1 state, which is different from single ESIPT mechanism proposed by experiment. We hope the detailed ESIPT mechanism of this fluorophore based on my theoretical research will help researchers to design such kinds of fluorophores in the future.

When finite becomes infinite: convergence properties of vibrational spectra of oligomer chains.

We present a computational study of convergence properties of vibrational IR and Raman spectra for a series of increasingly long units of polyethylene, cis- and trans-polyacetylenes, and polyynes. Convergent behavior to the spectra of infinitely long polymers was observed in all cases when chains reached lengths of approximately 60 carbon atoms, both with respect to the positions of the bands and to their intensities. The vibrational spectra of longer chains are practically indistinguishable. The convergence rate depends on the degree of the π conjugation in a studied system: Vibrational spectra for oligoethylenes converge noticeably faster than the spectra for the conjugated systems. The slowest convergence is observed for skeletal motions of the oligomer chains, which may require more than a hundred carbon atoms in the chain to show deviations smaller than 1cm-1 to the corresponding solid-state calculations. The results suggest that the boundary between the properties of finite and infinite molecular systems fades away for a surprisingly small number of atoms.

Raman spectroscopic transcriptome

Cell Biology Raman spectroscopy records the vibrational Raman spectra of biomolecules, allowing the determination of chemical species in target samples. Although nondisruptive and label-free, its application in cell imaging is limited because of the complexity of cellular compositions. Kobayashi-Kirschvink et al. described computational approaches to extract key information from cellular Raman spectra in yeast and bacteria. Dimension-reduction methods enabled a direct prediction of transcriptomes from cellular Raman spectra. A better correlation between the Raman spectra and noncoding transcriptome revealed a more linear correspondence of noncoding RNAs with cellular constituent biomolecules. Although it remains unknown if the linkage can be demonstrated at the single-cell level, spectroscopic live-cell omics provides new possibilities to monitor different cellular states. Cell Syst. 7 , 104 (2018).

Sustainable Waste Tire Derived Carbon Material as a Potential Anode for Lithium-Ion Batteries

The rapidly growing automobile industry increases the accumulation of end-of-life tires each year throughout the world. Waste tires lead to increased environmental issues and lasting resource problems. Recycling hazardous wastes to produce value-added products is becoming essential for the sustainable progress of society. A patented sulfonation process followed by pyrolysis at 1100 °C in a nitrogen atmosphere was used to produce carbon material from these tires and utilized as an anode in lithium-ion batteries. The combustion of the volatiles released in waste tire pyrolysis produces lower fossil CO2 emissions per unit of energy (136.51 gCO2/kW·h) compared to other conventional fossil fuels such as coal or fuel–oil, usually used in power generation. The strategy used in this research may be applied to other rechargeable batteries, supercapacitors, catalysts, and other electrochemical devices. The Raman vibrational spectra observed on these carbons show a graphitic carbon with significant disorder structure. Further, structural studies reveal a unique disordered carbon nanostructure with a higher interlayer distance of 4.5 Å compared to 3.43 Å in the commercial graphite. The carbon material derived from tires was used as an anode in lithium-ion batteries exhibited a reversible capacity of 360 mAh/g at C/3. However, the reversible capacity increased to 432 mAh/g at C/10 when this carbon particle was coated with a thin layer of carbon. A novel strategy of prelithiation applied for improving the first cycle efficiency to 94% is also presented.

Structural and vibrational properties of SnxGe1-x: Modeling and experiments

The effects of the composition and macroscopic strain on the structural properties and lattice vibrations of SnxGe1-x solid solutions (SSs) are investigated numerically, employing Tersoff empirical inter-atomic potentials, and experimentally. The calculations provide statistical distributions of bond lengths, pair correlation function, and vibrational Raman spectra of the SSs. Using this approach, we are able to evaluate the tin-content-dependent shifts due to the local environment (i.e., changes in the atomic mass and bond stiffness) and strain effects in the calculated Raman spectra and compare them to experimental data. The relative importance of the composition dependent effects of the local environment and strain for epitaxial layers of GeSn solid solutions is analysed.

β‐[SbI2][AlI4] – A Second Polymorph of Diiodidoantimony‐Tetraiodido Aluminate with a Polymeric Structure

The reaction of antimony triiodide and aluminum triiodide at 160 °C yields orange crystals of β‐[SbI2][AlI4] (1) via gas phase deposition. This second polymorph of [SbI2][AlI4] crystallizes monoclinic in space group P21/n and is built of [SbI2]+ and [AlI4]– ions connected via long Sb–I bonds. Sb is coordinated in form of a distorted square pyramid. These SbI5 polyhedra are connected alternately by edges and corners by almost regular tetrahedral tetraiodido aluminate units to undulated [SbI2AlI4]n chains. This stands in contrast to the molecular structure of the α polymorph consisting of molecular, tetranuclear units ([SbI2][AlI4])2. The Raman vibrational spectra were calculated at density‐functional (DFT) level and compared to the experimental spectrum. Additionally, the normal modes were analysed.

Spectral Analysis of 3-(Adamantan-1-yl)-4-Ethyl-1-[(4-Phenylpiperazin-1-yl) Methyl]-1H-1,2,4-Triazole-5(4H)-Thione

Vibrational IR (3200–650 cm–1) and Raman spectra (3200–150 cm–1) of adamantane-containing 3-(adamantan-1-yl)-4-ethyl-1-[(4-phenylpiperazin-1-yl)methyl]-1H-1,2,4-triazole-5(4H)-thione, which is promising for drug design, were examined. The UV/Vis spectrum (450–200 nm) of the compound in EtOH was measured. Full geometry optimization using density functional theory (DFT) in the B3LYP/cc-pVDZ approximation allowed the equilibrium configuration of the molecule to be determined and IR and Raman spectra to be calculated. Based on these, the experimental vibrational IR and Raman spectra were interpreted and the biological activity indices were predicted. The UV/Vis spectrum of the title compound was simulated at the time-dependent DFT/CAM-B3LYP/cc-pVDZ level with and without solvent effects and at the ab initio multi-reference perturbation theory XMCQDPT2 level. The UV/Vis spectrum that was simulated using the multi-reference XMCQDPT2 approximation agreed very successfully with the experimental data, in contrast to the single-reference DFT method. This was probably a consequence of intramolecular charge transfer.

Vibrational and Thermal Properties of Oxyanionic Crystals

The vibrational and thermal properties of dolomite and alkali chlorates and perchlorates were studied in the gradient approximation of density functional theory using the method of a linear combination of atomic orbitals (LCAO). Long-wave vibration frequencies, IR and Raman spectra, and mode Gruneisen parameters were calculated. Equation-of-state parameters, thermodynamic potentials, entropy, heat capacity, and thermal expansion coefficient were also determined. The thermal expansion coefficient of dolomite was established to be much lower than for chlorates and perchlorates. The temperature dependence of the heat capacity at T > 200 K was shown to be generally governed by intramolecular vibrations.