Assignment Of Vibrational Modes Research Articles

A vibrational study of inulin by means of experimental and theoretical methods

Inulin, a natural polymer formed by several units of fructose and just one unit of glucose, is found in different plants or directly in some fruits or vegetables. Due to its structure it has been used in many applications from medicine, pharmacology or food industry. In spite of this, a complete vibrational analysis of the molecule is missing in the literature. Moreover, there are contradictory results regarding the assignment of certain vibrational modes. Therefore, the aim of this study was to obtain a comprehensive vibrational investigation of inulin by means of experimental (FT-IR and Raman spectroscopy) and theoretical (density functional theory -DFT simulations) methods.

Temperature-dependent vibrational spectroscopic studies of pure and gold nanoparticles dispersed 4-n-Hexyloxy-4’-cyanobiphenyls

ABSTRACTRaman spectra of pure and 2 wt.% gold nanoparticles (GNPs) dispersed liquid crystalline compound 4-n-Hexyloxy-4ʹ- cyanobiphenyls (6OCB) has been recorded as a function of temperature from room temperature (solid crystal) to 80°C (isotropic liquid) in the spectral region of 500–2500 cm−1. The variation of Raman spectral parameters (peak positions and line width) with temperature is used to explain the changes in molecular alignment and its effect on inter-/intra-molecular interactions at crystal-Nematic (K-N) transition. To understand the change in molecular structure during phase transition and on account of dispersion of gold nanoparticles in pure liquid crystal more precisely, two spectral regions 1000–1500 cm−1 and 1500–2400 cm−1 have been selected separately. From the detailed study, it is concluded that increased orientational/vibrational freedom of the molecules as well as delocalisation of electron clouds results in the spectral anomalies at K-N transition. The geometrical structure of 6OCB was optimised using density functional theory (DFT) and theoretical Raman spectra have been obtained for comparison with experimental spectra. The tentative assignment of vibrational modes observed in our region of study was calculated based on potential energy distribution (PED) using vibrational energy distribution analysis (VEDA) calculation.

On some controversy regarding νOH assignments in CsH2PO4

Spectroscopic methods such as Raman scattering and IR absorption, as well as structural methods such as x-ray and n-diffraction, offer rather ambiguous interpretation of the high-frequency phonon spectrum of CsH2PO4 (CDP), especially regarding the proper assignment of proton vibrational modes. Empirical lattice dynamics (LD) simulations of the proton vibrational density of states ((H-VDOS)) in CDP also reveal a discrepancy in the frequency assignments of the OH stretching modes of its two non-equivalent hydrogen bonds. This may be resolved by accounting for the LD simulated directional (H-VDOS) along the three Cartesian axes of CDP, from which the corresponding anisotropy of the proton kinetic energy tensor can be deduced. The results may then be tested by a simple deep inelastic neutron scattering (DINS) measurement on a single crystal of para-electric CDP at room temperature.

Vibrational Properties of Bulk Boric Acid 2A and 3T Polymorphs and Their Two-Dimensional Layers: Measurements and Density Functional Theory Calculations.

Boric acid (H3BO3) is being used effectively nowadays in traps/baits for the management of Aedes aegypti L. and Aedes albopictus Skuse species of mosquitoes, which are the main spreading vectors worldwide for diseases such as malaria, dengue, and zika. Previously, we published results on the structural, electronic, and optical properties of its molecular triclinic H3BO3-2A and trigonal H3BO3-3T polymorphs within the framework of density functional theory (DFT). Because of the renewed importance of these materials, the focus of this work is on the vibrational properties of the bulk boric acid 2A and 3T polymorphs. We measured the infrared and Raman spectra of the former, which was accompanied and interpreted through state-of-the-art DFT calculations, supplemented by computations regarding the H3BO3 molecule and two-dimensional layers based on the bulk structures. We identify/assign their normal modes and find vibrational signatures for each polymorph as well as in- and out-of-plane motions and molecular vibrations, unveiling a nice agreement between the DFT level of theory employed and our improved spectroscopic measurements in the wavenumber ranges of 400-2000 cm-1 (infrared) and 0-1500 cm-1 (Raman). We show that a dispersion-corrected DFT functional within the generalized gradient approximation (GGA) can be very accurate in describing the vibrational properties of the boric acid polymorphs. Besides, several issues left open/not clearly resolved in previously published works on the vibrational mode assignments of the bulk and 2D sheets of boric acid are explained satisfactorily. Finally, phonon dispersions and associated densities of states were also evaluated for each polymorph along with their temperature-dependent DFT-calculated entropy, enthalpy, free energy, heat capacity, and Debye temperature. In particular, our DFT calculations suggest a possible way to differentiate the 2A and 3T boric acid polymorphs through Raman spectroscopy and heat capacity measurements.

The prediction of far-infrared spectra for planetary nitrile ices using periodic density functional theory with comparison to thin film experiments.

Future spacecraft missions to planetary systems, Trans-Neptunian objects, and cometary bodies could implement far-infrared surveys to confirm the presence of condensed-phase species via their unique lattice features. For composite molecular ices of astrophysical significance, laboratory reference spectra are required to provide absorption coefficients used to quantify solid-state abundances. However, due to strong intermolecular interactions in polar ice systems, laboratory data of mixed-phase ices are difficult to interpret. In this study we have applied periodic density functional theory code to model bulk molecular crystals. This method allows for more accurate simulation of thin-film spectra than approaches simulating small clusters. For this proof-of-principle study on a series of pure nitrile ices of planetary interest, our simulated far-infrared spectra show excellent agreement to data from thin film studies performed at the Australian Synchrotron (crystalline acetonitrile and propionitrile) and to previously published spectra (hydrogen cyanide, acrylonitrile, cyanoacetylene, and cyanogen). The combined theoretical and experimental approach has provided a new explanation for the asymmetric profile of the hydrogen cyanide lattice feature and a more systematic assignment of nitrile ice absorption bands to low-frequency lattice modes. We nominate prominent absorption features for the detection of crystalline nitrile carriers located on planetary surfaces.

Vibrational Study and Electronic Parameters of "2-Diphenylphosphanyl- 6-fluoro-pyridine"using First Principle

Vibrational investigations along with theoretical quantum chemical studies on “2-Diphenylphosphanyl-6-fluoro-pyridine (C17H14NFP)” have been carried out. The quantum chemical density functional method at B3LYP/3-21Glevel is used to obtain the equilibrium geometries of the title compound. We have also performed vibrational analysis of the title compound at their equilibrium geometries and established the complete assignments of the significant vibrational modes. Electronic parameters such as HOMO, LUMO and frontier orbital energy band gap, has been calculated. Besides it the thermodynamical parameters like internal thermal energy, entropy and constant volume specific heat capacity have been calculated.

Studies on structural, optical, thermal and vibrational properties of thienyl chalcone derivative: 1-(4-Nitrophenyl)-3-(2-thienyl)prop-2-en-1-one

The structural, optical, thermal and vibrational properties of thienyl chalcone derivative 1-(4-Nitrophenyl)-3-(2-thienyl)prop-2-en-1-one, C13H9NO3S were investigated combining nuclear magnetic resonance (1H and 13C NMR), X-ray diffraction (XRD), Fourier transform infrared (FTIR), UV–vis spectroscopy at room temperature assisted by density functional theory (DFT) calculations and Raman scattering at the temperature range 303–463 K. The electronic properties, including excitation energies, oscillator strengths, HOMO and LUMO energies were calculated by time-dependent DFT (TD-DFT) to complement the experimental findings. The B3LYP/6-311G (d,p) (B3LYP/cc-pVTZ) calculations led to the identification of ‘two minima on the molecules’ potential energy surfaces. From these calculations, it was predicted that the most stable conformer for C13H9NO3S in the gas phase is founded at 0 K relationship to dihedral angle C8C9C10S1, in agreement with XRD results. The molecular plot showed that the electrical charge mobility in the molecule occurs from thiophene to benzene ring. The optical band gap energy calculated from the difference between HOMO and LUMO orbitals was founded to be ∼3.87 (3.82) eV, in close agreement with the experimental value of 2.94 eV. The comparison between experimental and theoretical vibrational spectra gives a precise knowledge of the fundamental vibrational modes and leads to a better interpretation of the experimental Raman and infrared spectra. As temperature increases from room temperature to 443 K, it was observed the current phonon anharmonicity effects associated to changes in the Raman line intensities, line-widths and red-shift, in special in the external modes region, whereas the internal modes region remains almost unchanged due its strong chemical bonds. Furthermore, C13H9NO3S goes to phase transition in the temperature range 453–463 K. This thermal phenomenon was attributed to the disappearance of the lattice (∼10-200 cm−1) and molecular (∼300-4000 cm−1) modes in the Raman spectra. Finally, the vibrational mode assignment given in terms of potential energy distribution (PED) analysis leads to a more comprehensive interpretation of the vibrational spectra and origin of instability the investigated material.

Comprehensive spectroscopic (FT-IR, FT-Raman, 1H and 13C NMR) identification and computational studies on 1-acetyl-1H-indole-2,3-dione

AbstractFourier transform infrared (FT-IR) and FT-Raman spectra of 1-acetyl-1H-indole-2,3-dione (N-acetylisatin) were recorded in the solid phase and analyzed. The molecular geometry, vibrational frequencies, infrared intensities, Raman activities and atomic charges were calculated using density functional theory (DFT/B3LYP) calculations with a standard 6-311++G(d,p) basis set. The fundamental vibrational modes of N-acetylisatin were analyzed and fully assigned with the aid of the recorded FT-IR and FT-Raman spectra. The simulated FT-IR and FT-Raman spectra showed good agreement with the experimental spectra. The stability of the molecule, arising from hyper-conjugative interactions and charge delocalization, was analyzed using natural bond orbital (NBO) analysis. The dipole moment (µ), polarization (α) and hyperpolarization (β) values of N-acetylisatin were also computed. The potential energy distribution (PED) was computed for the assignment of unambiguous vibrational fundamental modes. The HOMO and LUMO energy gap illustrated the chemical activity of N-acetylisatin. The energy and oscillator strength were calculated by DFT. Gauge–including atomic orbital NMR (1H and 13C) chemical shift calculations were performed and compared with the experimental values. Thermodynamic properties (heat capacity, entropy and enthalpy) of the compound at different temperatures were also calculated.

Continuous gradient temperature Raman spectroscopy from −100 to 40 °C yields new molecular models of arachidonic acid and 2-Arachidonoyl-1-stearoyl-sn-glycero-3-phosphocholine

Despite its biochemical importance, a complete Raman analysis of arachidonic acid (AA, 20:4n-6) has never been reported. Gradient temperature Raman spectroscopy (GTRS) applies the temperature gradients utilized in differential scanning calorimetry (DSC) to Raman spectroscopy, providing a straightforward technique to identify molecular rearrangements that occur near and at phase transitions. Herein we utilize the GTRS technique for AA and 1-18:0, 2-20:4n-6 phosphatidyl choline (AAPC) from cryogenic to mammalian body temperatures. 20Mb three-dimensional data arrays with 0.2°C increments and first/second derivatives allowed complete assignment of solid, liquid and transition state vibrational modes. The AA DSC shows a large exothermic peak at −60°C indicating crystallization or a similar major structural change. No exothermic peak of this magnitude was observed in six other unsaturated lipids (DHA, n-3DPA, n-6DPA, LA, ALA, OA). Melting in AA occurs over a large range: (−60 to −35°C): very large frequency offsets and intensity changes correlate with premelting initiating circa −60°C, followed by melting (−37°C). Novel, unique 3D structures for both molecules reveal that AA is not symmetric as a free fatty acid, and it changes significantly when in the sn-2 phospholipid position. Further, different CH and CH2 sites are unequally elastic and nonequivalent.

Infrared properties of three plastic bonded explosive binders

ABSTRACTThree polymers are routinely used as binders for plastic bonded explosives by Lawrence Livermore National Laboratory, FK-800, Viton A 100, and Oxy 461. Attenuated total reflectance Fourier transform infrared measurements were performed on 10 different lots of FK-800, 5 different lots of Oxy 461, and 3 different lots of Viton A-100, one sample of Viton VTR 5883 and 2 Fluorel polymers of hexafluoropropene and vinylidene fluoride. The characteristic IR bands were measured. If possible, their vibrational modes were assigned based on literature data. Simple Mopac calculations were used to validate these vibrational mode assignments. Somewhat more sophisticated calculations were run using Gaussian on the same structures.

Vibrational Investigation of "2-Arsanyl-Pyridine" Using First Principle

Spectroscopic investigations along with theoretical quantum chemical studies on “2-Arsanyl-Pyridine (C5H7AsN)” have been carried out. The quantum chemical density functional method at B3LYP/6-31+g(d,p) level, is used to obtain the equilibrium geometries of the title compound. We have also performed vibrational analysis of the title compound at their equilibrium geometries and established the complete assignments of the significant vibrational modes. The calculated vibrational frequencies are shown to be in perfect agreement with the theoretically observed FTIR spectra of the molecule under study.

Polymorphism, structure and dynamics investigations of 4-cyano-3-fluorophenyl 4′-n-octylbenzoate (8CFPB) liquid crystal

Phase transition behavior of 4-cyano-3-fluorophenyl 4′-n-octylbenzoate (8CFPB) was studied by differential scanning calorimetry (DSC), polarizing microscopy, FT-IR spectroscopy and X-ray diffraction. Liquid-like and solid-like polymorphism with monotropic system of phases was identified. Assignment of the FT-IR vibrational modes in glass of the crystalline rotatory phase was done using the quantum mechanical calculation method and the relationship between molecular dynamics and crystalline structures is discussed.

Double and Triple Si-H-M Bridge Bonds: Matrix Infrared Spectra and Theoretical Calculations for Reaction Products of Silane with Ti, Zr, and Hf Atoms.

Infrared spectra of matrix isolated dibridged Si(μ-H)2MH2 and tribridged Si(μ-H)3MH molecules (M = Zr and Hf) were observed following the laser-ablated metal atom reactions with SiH4 during condensation in excess argon and neon, but only the latter species was observed with titanium. Assignments of the major vibrational modes, which included terminal MH, MH2 and hydrogen bridge Si-H-M stretching modes, were confirmed by the appropriate SiD4 isotopic shifts and density functional vibrational frequency calculations (B3LYP and BPW91). The Si-H-M hydrogen bridge bond is calculated as weak covalent interaction and compared with the C-H···M agostic interaction in terms of electron localization function (ELF) analysis and noncovalent interaction index (NCI) calculations. Furthermore, the different products of Ti, Zr, and Hf reactions with SiH4 are discussed in detail.

A terahertz study of taurine: Dispersion correction and mode couplings.

The low-frequency characteristics of polycrystalline taurine were studied experimentally by terahertz (THz) absorption spectroscopy and theoretically by ab initio density-functional simulations. Full optimizations with semi-empirical dispersion correction were performed in spectral computations and vibrational mode assignments. For comparison, partial optimizations with pure density functional theory were conducted in parallel. Results indicate that adding long-range dispersion correction to the standard DFT better reproduces the measured THz spectra than the popular partial optimizations. The main origins of the observed absorption features were also identified. Moreover, a coupled-oscillators model was proposed to explain the experimental observation of the unusual spectralblue-shift with the increase of temperature. Such coupled-oscillators model not only provides insights into the temperature dynamics of non-bonded interactions but also offers an opportunity to better understand the physical mechanisms behind the unusual THz spectral behaviors in taurine. Particularly, the simulation approach and novel coupled-oscillators model presented in this work are applicable to analyze the THz spectra of other molecular systems.

Template-Free Vapor-Phase Growth of Patrónite by Atomic Layer Deposition

Despite challenges to control stoichiometry in the vanadium–sulfur system, template-free growth of patronite, VS4, thin films is demonstrated for the first time. A novel atomic layer deposition (ALD) process enables the growth of phase pure films and the study of electrical and vibrational properties of the quasi-one-dimensional (1D) transition metal sulfide. Self-limiting surface chemistry during ALD of VS4 is established via in situ quartz crystal microbalance and quadrupole mass spectrometry between 150 and 200 °C. The V precursor, unconventionally, sheds all organic components in the first half-cycle, while the H2S half-cycle generates the disulfide dimer moiety, S2–2, and oxidizes V3+ to V4+. X-ray analysis establishes VS4 crystallinity and phase purity, as well as a self-limiting growth rate of 0.33 A/cy, modest roughness of 2.4 nm, and expected density of 2.7 g/cm3. Phase pure films enable a new assignment of vibrational modes and corresponding Raman activity of VS4 that is corroborated by density ...

Continuous gradient temperature Raman spectroscopy and differential scanning calorimetry of N-3DPA and DHA from −100 to 10 °C

Docosahexaenoic acid (DHA, 22:6n-3) is exclusively utilized in fast signal processing tissues such as retinal, neural and cardiac. N-3 docosapentaenoic acid (n-3DPA, 22:5n-3), with just one less double bond, is also found in the marine food chain yet cannot substitute for DHA. Gradient temperature Raman spectroscopy (GTRS) applies the temperature gradients utilized in differential scanning calorimetry (DSC) to Raman spectroscopy, providing a straightforward technique to identify molecular rearrangements that occur near and at phase transitions. Herein we apply GTRS and both conventional and modulated DSC to n-3DPA and DHA from −100 to 20°C. Three-dimensional data arrays with 0.2°C increments and first derivatives allowed complete assignment of solid, liquid and transition state vibrational modes. Melting temperatures n-3DPA (−45°C) and DHA (−46°C) are similar and show evidence for solid-state phase transitions not seen in n-6DPA (−27°C melt). The C6H2 site is an elastic marker for temperature perturbation of all three lipids, each of which has a distinct three dimensional structure. N-3 DPA shows the spectroscopic signature of saturated fatty acids from C1 to C6. DHA does not have three aliphatic carbons in sequence; n-6DPA does but they occur at the methyl end, and do not yield the characteristic signal. DHA appears to have uniform twisting from C6H2 to C12H2 to C18H2 whereas n-6DPA bends from C12 to C18, centered at C15H2. For n-3DPA, twisting is centered at C6H2 adjacent to the C2-C3-C4-C5 aliphatic moiety. These molecular sites are the most elastic in the solid phase and during premelting.

Structural, spectroscopic, electronic, nonlinear optical and thermodynamic properties of a synthesized Schiff base compound: A combined experimental and theoretical approach

A Schiff base compound, 2-[(1H-benzimidazol-2-ylimino)methyl]-4-bromophenol (BISB), was synthesized and its spectroscopic characterization was performed using experimental methods such as FT-IR, Raman, proton and carbon-13 NMR chemical shifts and UV–Vis. spectroscopies. Density functional theory (DFT/B3LYP/6-311G(d,p)) computations were used to investigate the optimized molecular geometry, conformational forms, harmonic vibrational wavenumbers, NMR chemical shifts, UV–Vis. spectroscopic parameters, natural bond orbital (NBO) analysis, HOMO-LUMO energies, nonlinear optical (NLO) properties, molecular electrostatic potential (MEP) map, atomic charges and thermodynamic properties of the BISB molecule. The assignments of vibrational modes were performed by means of potential energy distribution (PED) using VEDA4 program. The NBO analysis was used to investigate intramolecular hyrogen bonding (OH⋯N), bond species, hyperconjugation interactions and intramolecular charge transfers (ICTs). Considering the computed HOMO and LUMO energies, the quantum molecular descriptors such as ionization potential (I), electron affinity (A), chemical hardness (η), chemical softness (ζ), electronegativity (χ), chemical potential (μ) and electrophilicity index (ω) parameters were investigated for the BISB molecule. DFT computations were also performed to determine the dipole moment (μ), the mean polarizability (α), the anisotropy of the polarizability (Δα) and the first hyperpolarizability (β0) values. The recorded experimental spectroscopic results are in a good harmony with the computed data.

Quantum mechanical analysis, spectroscopic (FT-IR, FT-Raman, UV-Visible) study, and HOMO-LUMO analysis of (1 S ,2 R )-2-amino-1-phenylpropan-1-ol using Density Functional Theory

In this study, the Fourier Transform Infrared (FT-IR) and FT-Raman of (1S,2R)-2-amino-1-phenylpropan-1-ol (abbreviated as 2APPO) have been recorded in the regions 4000-100 cm− 1 and 4000–400 cm− 1, respectively. A complete assignment and analysis of the fundamental vibrational modes of the molecule were carried out. The observed fundamental modes have been compared with the harmonic vibrational frequencies computed using DFT (B3LYP) method by employing 6-31 ++G(d,p) basis set. The vibrational studies were interpreted in terms of potential energy distribution. This study is extended to the HOMO - LUMO analysis to calculate the HOMO and LUMO energy gap (Δ), Ionization potential (I), Electron Affinity (A), Global Hardness (η), Chemical Potential (μ), Global Electrophilicity (ω) and the calculated HOMO, LUMO energy reveals shows that the charge transfers occurring within the molecule. In the thermodynamic properties of the 2APPO compound have been calculated at different temperatures and the results reveal that the standard heat capacities (Cp,m), standard entropies (Sm) and standard enthalpy changes (Hm) increase with rise in temperature.

Synthesis, molecular structure, spectral analysis and cytotoxic activity of two new aroylhydrazones

Two new aroylhydrazones viz 4-nitro-N′-(1-(pyridin-2-yl)ethylidene)benzohydrazide, NPHY (4) and 4-nitro-N′-(1-(thiophen-2-yl)ethylidene)benzohydrazide, NPHT (5) have been prepared and characterized by 1H NMR, 13C NMR, FT-IR, UV–Visible spectroscopy and mass spectrometry. All quantum calculations were performed at DFT level of theory using B3LYP functional and 6-31G (d,p) as basis set. TD-DFT calculated electronic transitions are found to be in good agreement with experimental findings. The assignments for normal vibrational modes have been done by computing Potential Energy Distribution (PED) using Gar2ped. HOMO-LUMO analysis was performed and reactivity descriptors were also computed. Global electrophilicity index (ω) of 6.12–6.26 eV shows these aroylhydrazones to be strong electrophiles. Intramolecular interactions were analyzed by ‘Atoms in molecule’ (AIM) approach. Also, the computed first static hyperpolarizabilities (β0) of these hydrazones indicate their future application as an attractive non-linear optical (NLO) material. Cytotoxicity evaluated by MTT assay, suggested that the synthesized aroylhydrazones significantly reduce the cell viability of breast cancer cell lines (MCF7) and human prostate adenocarcinoma (DU145) in a dose dependent manner. Cytotoxic potencies (IC50) of these hydrazones against MCF7 and DU145 cell lines were found in range of 54.67–85.67 μM. The result of ROS activity provides supportive data for molecular mechanism of these hydrazones, which is related to apoptotic cellular death. Nuclear condensation assay performed by DAPI staining shows fragmented and condensed nuclei in MCF7 cells, suggesting cell death by apoptosis.

The Influence of Methoxy and Ethoxy Groups on Supramolecular Arrangement of Two Methoxy-chalcones

The structures of two methoxylated chalcones, namely (E)-1-(4-methoxyphenyl)-3-(3,4,5-trimethoxyphenyl)prop-2-en-1-one and (E)-3-(4-ethoxyphenyl)-1-(4-methoxyphenyl)prop-2-en-1-one, reveal the effect of the inclusion of the methoxyl and ethoxyl substituents of the conformation on methoxy-chalcone. Structural comparative study between two chalcones was done in this work and some effects on geometric parameters, such as planarity and dihedral angles, were described. In addition, intermolecular interactions responsible for crystalline packaging were investigated by Hirshfeld surfaces and the values of those interactions were analysed by comparing experimental and theoretical models. The molecular stability was expressed in terms of softness and hardness, both obtained from frontier molecular orbitals. Finally, there is a good agreement between calculated and experimental infrared spectrum, which allowed the assignment of the normal vibrational modes.