Vibrational Spectroscopic Study Research Articles

Ultrafast Charge-Transfer Dynamics in the Iron-Sulfur Complex of Rhodobacter capsulatus Ferredoxin VI.

Iron-sulfur proteins play essential roles in various biological processes. Their electronic structure and vibrational dynamics are key to their rich chemistry but nontrivial to unravel. Here, the first ultrafast transient absorption and impulsive coherent vibrational spectroscopic (ICVS) studies on 2Fe-2S clusters in Rhodobacter capsulatus ferreodoxin VI are characterized. Photoexcitation initiated populations on multiple excited electronic states that evolve into each other in a long-lived charge-transfer state. This suggests a potential light-induced electron-transfer pathway as well as the possibility of using iron-sulfur proteins as photosensitizers for light-dependent enzymes. A tyrosine chain near the active site suggests potential hole-transfer pathways and affirms this electron-transfer pathway. The ICVS data revealed vibrational bands at 417 and 484 cm-1, with the latter attributed to an excited-state mode. The temperature dependence of the ICVS modes suggests that the temperature effect on protein structure or conformational heterogeneities needs to be considered during cryogenic temperature studies.

Topological analysis (BCP) of vibrational spectroscopic studies, docking, RDG, DSSC, Fukui functions and chemical reactivity of 2-methylphenylacetic acid

Experimental FT-IR and FT-Raman spectra of 2-methylphenylacetic acid (MPA) were recorded and theoretical values are also analyzed. The non-linear optical (NLO) properties were evaluated by determination of first (5.5053×10−30 e.s.u.) and second hyper-polarizabilities (7.6833×10−36 e.s.u.) of the title compound. The Multiwfn package is used to find the weak non-covalent interaction (Van der Wall interaction) and strong repulsion (steric effect) of the molecule and examined by reduced density gradient. The molecular electrostatic potential (MEP) analysis used to find the most reactive sites for the electrophilic and nucleophilic attack. The chemical activity (electronegativity, hardness, chemical softness and chemical potential) of the title compound was predicted with the help of HOMO-LUMO energy values. The natural bond orbital (NBO) has been analyzed the stability of the molecule arising from the hyper-conjugative interaction. DSSCs were discussed in structural modifications that improve the electron injection efficiency of the title compound (MPA). The Fukui functions are calculated in order to get information associated with the local reactivity properties of the title compound. The binding sites of the two receptors were reported by molecular docking field and active site bond distance is same 1.9Å. The inhibitor of the title compound forms a stable complex with 1QYV and 2H1K proteins at the binding energies are −5.38 and −5.85 (∆G in kcal/mol).

Vibrational spectroscopy studies of structural changes in lignin under microwave irradiation

Structural changes that occur in lignin surface-modified with nickel nanoparticles during microwave- assisted dry reforming (DR) are studied via vibrational spectroscopy. IR spectroscopy reveals that the nickel deposition has a considerable effect on the structural characteristics of lignin. It is found that nickel deposition from an acetate salt substantially reduces the intensity of absorption bands at 1700 cm−1. This finding suggests that Ni(2+) interacts mostly with formate groups, which are subsequently oxidized to carboxylate groups. It is shown that with the deposition of metallic nickel particles from a colloidal nickel solution in toluene prepared via metal vapor synthesis, the nickel particles do not interact with the surface functional groups of the lignin. Deep conversion of an organic mass of lignin by DR to form synthesis gas reduces the intensity of the absorption bands of the identified functional groups and raises the intensity of the absorption bands of the aromatic rings. Raman spectroscopy shows that during lignin conversion, the aromatic rings condense partially to form amorphized graphite. In operando studies reveal that the DR of nickel-modified lignin heated to 200–400°C results in the isolation of vanillic oxygenates that are probably intermediate products of reforming.

Synthesis, molecular structure, vibrational spectroscopy, optical investigation and DFT study of a novel hybrid material: 3,3′-diammoniumdiphenylsulfone hexachloridostannate monohydrate

In his work we investigate a new halogenotin (IV) organic inorganic material. The structure, determined by single-crystal X-ray diffraction at 293 K of 3,3′-diammoniumdiphenylsulfone hexachloridostannate monohydrate abbreviated 3,3′(DDS)SnCl6, can be viewed as inorganic layers built from (SnCl6)2− octahedra and H2O molecules, between which, the organic entities [C12H14N2O2S]2+ are inserted. Experimental room-temperature X-ray studies were supported by theoretical methods using density functional theory (DFT). The detailed examination of the vibrational spectra of our material was correlated by DFT calculation using the unit cell parameters obtained from the experiment data.The optical properties in the UV–visible region have been explored by the UV–visible absorption. This material shows a single absorption band centred at 325 nm (318 eV). The energy difference between Occupied, HOMO and Lowest Unoccupied, LUMO orbital which is called energy gap can be used to predict the strength and stability of metal complexes, as well as in determining molecular electrical transport properties. For the calculation of excitation energies in the optical studies we used Time-Dependent Density Functional Theory (TD-DFT). In addition, Mulliken population method and molecular electrostatic potential (MEP) of the title material have been theoretically studied by GAUSSIAN 03 package.

Vibrational two-dimensional correlation spectroscopy (2DCOS) study of proteins

A tutorial is provided for the generalized two-dimensional correlation spectroscopy (2DCOS), which is applicable to the vibrational spectroscopic study of proteins and related systems. In 2DCOS, similarity or dissimilarity among variations of spectroscopic intensities, which are induced by applying an external perturbation to the sample, is examined by constructing correlation spectra defined by two independent spectral variable axes. By spreading congested or overlapped peaks along the second dimension, apparent spectral resolution is enhanced and interpretation of complex spectra becomes simplified. A set of simple rules for the intensities and signs of correlation peaks is used to extract insightful information. Simulated IR spectra for a model protein are used to demonstrate the specific utility of 2DCOS. Additional tools useful in the 2DCOS analysis of proteins, such as data segmentation assisted with moving-window analysis, 2D codistribution analysis, Pareto scaling, and null-space projection are also discussed.

Solid-state cocrystal formation between acyclovir and fumaric acid: Terahertz and Raman vibrational spectroscopic studies

The vibrational spectra of solid-state acyclovir, fumaric acid and their cocrystal have been investigated by using terahertz time-domain spectroscopy (THz-TDS) and Raman spectroscopy at room temperature. In experimental THz spectra, the cocrystal has absorption peaks in 0.65, 0.94 and 1.10THz respectively, while the raw materials are absolutely different in this region. Raman spectra also show similar results about differences between the cocrystal and raw materials. Density functional theory (DFT) was performed to simulate vibrational modes of different theoretical forms between acyclovir and fumaric acid. The calculation of theoretical THz spectra shows that O8C7N1H27 and the carboxyl group COOH establish a dimer theoretical cocrystal form by the hydrogen bonding effect, which makes contributions to the formation of absorption peaks in 0.70, 1.01 and 1.34THz, and agrees well with experimental observations. The theoretical Raman result also indicates that this dimer form matches with experimental results. The characteristic bands of the cocrystal between acyclovir and fumaric acid are also assigned based on the simulation results from the DFT calculation.

Probing the Conformation-Dependent Preferential Binding of Ethanol to Cationic Glycylalanylglycine in Water/Ethanol by Vibrational and NMR Spectroscopy.

The conformational propensity of amino acid residues is determined by an intricate balance of peptide-solvent and solvent-solvent interactions. To explore how the systematic replacement of water by a cosolvent affects the solvation of both the amino acid backbone and side chains, we performed a combined vibrational spectroscopy and NMR study of cationic glycylalanylglycine (GAG) in different ethanol/water mixtures of between 0 and 42 mol percent ethanol. Classical model peptide N'-methylacetamide was used as a reference system to probe solvent-induced spectroscopic changes. The alanine residue of GAG in water is known to exhibit a very high propensity for polyproline II (pPII). Adding up to 30 mol % ethanol at room temperature leads only to minor changes in the Ramachandran distribution of alanine, which mostly changes within the individual conformational subspaces. A further increase in the ethanol fractions leads to a destabilization of pPII and a stabilization of β-strand conformations. At higher temperatures, different degrees of enthalpy-entropy compensations lead to a much stronger influence of ethanol on the peptide's conformational distribution. Ethanol-induced changes in chemical shifts and amide I wavenumbers strongly suggest that ethanol replaces water preferentially in the solvation shell of the polar C-terminal peptide group and of the alanine side chain, whereas the N-terminal group remains mostly hydrated. Furthermore, we found that ethanol interacts more strongly with the peptide if the latter adopts β-strand conformations. This leads to an unusual positive temperature coefficient for the chemical shift of the C-terminal amide proton. Our data suggests a picture in which GAG eventually accumulates at water-ethanol interfaces if the ethanol fractions exceed 0.3, which explains why the further addition of ethanol eventually causes self-aggregation and the subsequent formation of a hydrogel.

Synthesis, experimental and theoretical vibrational studies of 1-methyl and 1,2-dimethyl, 3-propyl imidazolium bis(trifluoromethanesulfonyl) imide

In this study, two ionic liquids containing the bis(trifluoromethanesulfonyl)imide ( $$[(\hbox {CF}_{3}\hbox {SO}_{2})_{2}\hbox {N}^{-}]$$ ) anion are synthesized. The syntheses are based on an alkylation reaction of 1-methyl imidazole and 1,2-dimethyl imidazole followed by anion exchange. The obtained ILs are characterized by $$^{1}\hbox {H-NMR}$$ , $$^{13}\hbox {C-NMR}$$ , $$^{19}\hbox {F-NMR}$$ and FT-IR spectroscopy. Vibrational spectroscopy studies were conducted by infrared (FTIR/ATR), Raman spectroscopy and DFT calculations. The presence of methylation in the C2 position gives rise to specific marker bands in the Raman and IR spectra. In order to ascertain whether cation conformers are present in our ionic liquids, a computational study was performed using the density functional theory. The comparison of the experimental data and the computed spectra shows that three conformers of the imidazolium ions are present in both ionic liquids. Synopsis We synthesized and investigated the vibrational properties of two ionic liquids, namely, 1-methyl,3-propyl imidazolium bis(trifluoromethane-sulfonyl) imide ( $$[1\hbox {-MPrIM}^{+}][(\hbox {CF}_{3}\hbox {SO}_{2})_{2}\hbox {N}^{-}]$$ ) and 1,2-dimethyl,3-propyl imidazolium bis(trifluoromethane-sulfonyl) imide ( $$[1,2\hbox {-DMPrIM}^{+}][(\hbox {CF}_{3}\hbox {SO}_{2})_{2}\hbox {N}^{-}]$$ ). Methylation in the C2 position gives rise to specific marker bands in the Raman and IR spectra. The comparison of the experimental data and the computed spectra at DFT level shows that three conformers of the imidazolium ions are present in both ionic liquids.

Optical properties of AlGaN nanowires synthesized via ion beam techniques

AlGaN plays a vital role in hetero-structure high electron mobility transistors by employing a two-dimensional electron gas as an electron blocking layer in multi-quantum well light emitting diodes. Nevertheless, the incorporation of Al into GaN for the formation of the AlGaN alloy is limited by the diffusion barrier formed by instant nitridation of Al adatoms by reactive atomic N. The incorporation of Al above the miscibility limit, however, can be achieved by the ion beam technique. The well known ion beam mixing (IBM) technique was carried out with the help of Ar+ irradiation for different fluences. A novel approach was also adopted for the synthesis of AlGaN by the process of post-irradiation diffusion (PID) as a comparative study with the IBM technique. The optical investigations of AlGaN nanowires, synthesized via two different methods of ion beam processing, are reported. The effect of irradiation fluence and post-irradiation annealing temperature on the random alloy formation was studied by the vibrational and photoluminescence (PL) spectroscopic studies. Vibrational studies show one-mode phonon behavior corresponding to the longitudinal optical (LO) mode of A1 symmetry [A1(LO)] for the wurtzite phase of AlGaN nanowires in the random alloy model. A maximum Al atomic percentage of ∼6.3%–6.7% was calculated with the help of band bowing formalism from the Raman spectral analysis for samples synthesized in IBM and PID processes. PL studies show the extent of defects present in these samples.

Vibrational and UV spectroscopic studies of 2-coumaranone by experimental and density functional theory calculations

The vibrational and electronic properties of 2-coumaranone have been reported in the ground state using experimental techniques (FT-IR, FT-Raman, UV spectra and fluorescence microscopic imaging) and density functional theory (DFT) employing B3LYP correlation with the 6-31G(d, p) basis set. The theoretically reported optimized parameters, vibrational frequencies etc., were compared with the experimental values, which yielded good concurrence between the experimental and calculated values. The assignments of the vibrational spectra were done with the help of normal co-ordinate analysis (NCA) following the Scaled Quantum Mechanical Force Field(SQMFF) methodology. The whole assignments of fundamental modes were based on the potential energy distribution (PED) matrix. The electric dipole moment and the first order hyperpolarizability of the 2-coumaranone have been computed using quantum mechanical calculations. NBO and HOMO, LUMO analyses have been carried out. UV spectrum of 2-coumaranone was recorded in the region 100–300 nm and compared with the theoretical UV spectrum using TD-DFT and SAC-CI methods by which a good agreement is observed. Fluorescence microscopic imaging study reflects that the compound fluoresces in the green-yellow region.

Structure and vibrational spectroscopic study of alpha-tocopherol

We report here the vibrational and structural analysis of alpha-tocopherol. The vibrational analysis has been accomplished experimentally by infrared and Raman spectroscopic techniques and theoretically by density functional theory. Two conformers of alpha-tocopherol have been optimized with the help of density functional theory. Energy minimized structures have been further used for vibrational frequencies calculations. Calculated values of molecular parameters of both the conformers have been comparable with the available experimental values in literature. All the observed vibrational bands have been assigned with the help of potential energy distribution calculations and intensity patterns of the simulated spectra. The ultraviolet–visible spectrum has been reported in wavelength range of 200 nm–500 nm. Observed ultraviolet–visible bands have been assigned to various electronic transitions, which have also been calculated using time dependent density functional theory.

Crystal growth, crystal structure, vibrational spectroscopy, linear and nonlinear optical properties of guanidinium phosphates

Of the three guanidinium phosphates GuH2PO4 (space group P21/c), Gu2HPO4·H2O (space group P4¯21c) and Gu3PO4· 32 H2O (space group Cc) crystal structures and a vibrational spectroscopy study are presented. Large single crystals of GuH2PO4 and Gu2HPO4·H2O are grown. Refractive indices and their dispersion in the wavelength range 365 nm – 1083 nm are determined and used for the analysis of phase matching conditions for collinear SHG in the case of the non-centrosymmetric crystals of Gu2HPO4·H2O. The crystals are not phase-matchable within their transmission range. Both independent components of the SHG tensor of Gu2HPO4·H2O, determined by the Maker fringe method, are given, with d14 = 0.23 pm/V and d36 = 0.22 pm/V. In addition, the thermal stability and the anisotropy of thermal expansion of GuH2PO4 and Gu2HPO4·H2O is reported.

Vibrational and Raman Spectroscopic Study of Cubic Boron Nitride Under Pressure Using Density Functional Theory

Pressure-dependent mechanical, vibrational and Raman spectroscopic study of the cubic boron nitride in context of recent experimental Raman spectroscopic has been performed using theab initio calculations based on density functional theory. Detailed analysis of the pressure-dependent mechanical and phonon properties shows that the pressure significantly affects the elastic constants and phonon frequencies. There is a systematic variation of elastic properties with pressure while a polynomial expression is used to fit the pressure dependence of the Raman shift. The longitudinal optical–transverse optical (LO-TO) splitting reduces with pressure, and the intensity of both LO and TO peaks start diminishing after 750 GPa. The phonon dispersion curves up to 1000 GPa indicate its dynamical stability. The lower slope of frequency versus pressure for the LO and TO modes at higher pressures suggests its use for pressure calibration at higher pressures.

Quantum chemical studies on structural, vibrational, nonlinear optical properties and chemical reactivity of indigo carmine dye

Structural and vibrational spectroscopic studies were performed on indigo carmine (IC) isomers using FT-IR spectral analysis along with DFT/B3LYP method utilizing Gaussian 09 software. GaussView 5 program has been employed to perform a detailed interpretation of vibrational spectra. Simulation of infrared spectra has led to an excellent overall agreement with the observed spectral patterns. Mulliken population analyses on atomic charges, MEP, HOMO-LUMO, NLO, first order hyperpolarizability and thermodynamic properties have been examined by (DFT/B3LYP) method with the SDD basis set level. Density of state spectra (DOS) were calculated using GaussSum 3 at the same level of theory. Molecular modeling approved that DOS Spectra are the most significant tools for differentiating between two IC isomers so far. Moreover, The IC isomers (cis-isomer) have shown an extended applicability for manufacturing both NLO and photovoltaic devices such as solar cells.

Bis(diphenylphosphino)amines-containing ruthenium cymene complexes as potential anti-Mycobacterium tuberculosis agents

Several ruthenium complexes have been investigated regarding anti-Mycobacterium tuberculosis (anti-MTb) activity, with some diphosphine-containing ruthenium complexes comparable to first and second line drugs. However, to the best of our knowledge, there is no PNP-containing ruthenium complexes applied as metallodrugs. Thus, this study focused on the synthesis, characterization and anti-MTb activity of a new series of coordination compounds with general formula [RuCl(η6-p-cymene)(PNRP)]X (R=CH2Py (Py=pyridine)−[1a], CH2Ph (Ph=phenyl)−[1b], Ph−[1c] and p-tol (p-tol=p-tolyl)−[1d]; X=PF6− or BF4−). The complexes were fully characterized by NMR (1H, 31P{1H}), vibrational spectroscopy (FTIR), ESI-MS, molar conductance, elemental analysis and X-ray diffraction studies. The molecular structures of [1a]PF6, [1c]BF4 and [1d]PF6 were determined and confirm the spectroscopic and ESI-MS data. The complexes were used in anti-MTb trials, and the preliminary results are presented. The complexes are promising anti-MTb agents with MIC90 (Minimum Inhibitory Concentration of compounds required to inhibit the growth of 90% of MTb) values comparable with the Ethambutol, the reference drug used in this work, and complex [1a]BF4 presented the highest selectivity index.

Alcohol Oxidation at Platinum–Gas and Platinum–Liquid Interfaces: The Effect of Platinum Nanoparticle Size, Water Coadsorption, and Alcohol Concentration

Alcohol oxidation reaction over platinum nanoparticles with size ranging from 2 to 8 nm deposited on mesoporous silica MCF-17 was studied in the gas and liquid phases. Among methanol, ethanol, 2- propanol, and 2-butanol oxidations, the turnover frequency increased as the nanoparticle size became large in both reaction phases. The activation energy in the gas phase was higher than that in the liquid phase. Water coadsorption decreased the turnover rate of all the gas and liquid phase oxidations except for the gas-phase 2-butanol case, while a certain amount of water promoted 2-propanol oxidation in the liquid phase. Sum frequency generation vibrational spectroscopy study and DFT calculation revealed that the alcohol molecules pack horizontally on the metal surface in low concentration and stand up in high concentration, which affects the dissociation of β-hydrogen of the alcohol as the critical step in alcohol oxidation.

Copper(II) perchlorate complexes with N-arylalkyliminodiacetamide ligands: X-ray structural, vibrational spectroscopic, DFT and thermogravimetric studies

The reactions of N-arylalkyl derivatives of iminodiacetamide (Bnimda, Peimda, Ppimda; Bn=benzyl, Pe=2-phenylethyl; Pp=3-phenylprop-1-yl) with copper(II) sulfate and sodium perchlorate in aqueous solutions were investigated. Three new copper(II) complexes [Cu(Bnimda)2](ClO4)2 (1), [Cu(Peimda)2](ClO4)2 (2) and [Cu(Ppimda)2](ClO4)2·2H2O (3) were prepared and characterized by infrared spectroscopy and thermal analysis (TG/DTA). Complex 2 was found to be explosive upon heating. The octahedral coordination environments around the copper(II) ions in complexes 1 and 3 consist of two O,N,O′-tridentate N-arylalkyliminodiacetamide ligands, with imino N atoms in trans-position. Molecules are interconnected by extensive hydrogen bonding between the amide moieties and perchlorate ions or water molecules, forming 3D networks in both structures. However, the difference in the hydrophobic chain lengths leads to significant differences in the hydrogen bonding motifs in the two structures. The molecular geometry and infrared spectra of these complexes were also studied by DFT calculations using B3LYP/6-311G(d,p) computational model. The calculated spectra and molecular geometry agree very well with the experimental results despite the extensive hydrogen bonding frameworks which are present in the crystal structures of these compounds.

Vibrational spectroscopic studies combined with viscosity analysis and VTF calculation for hybrid polymer electrolytes

In order to gain further understanding of the ion transport mechanism in hybrid composite polymer electrolytes (HCPEs), infrared spectroscopy method was applied to characterize the polymer matrices of the HCPEs as well as the corresponding electrolytes. Systems based on poly(ethylene glycol) (PEG) and methylalumoxane – MAO with various types of lithium salts added were studied at various temperatures. This method was combined with viscosity experiments/conductivity and correlation between the results of these two methods is presented. Finally VTF calculations were applied to examine the structure-conductivity relations. The influence of hybrid inorganic filler (here methylalumoxane) in polymer electrolytes is described in terms of oligomer chain entanglements and salt dissociation. It has been demonstrated that changes of deformations modes of CH2 groups show significant differences depending on the polymer conformations. Moreover different dissociation rate of one of the lithium trifluoromethanesulfonate (LiTF) correlates with the inorganic phase content. In all types of hybrid polymer electrolytes macroscopic viscosity is increasing whereas microscopic viscosity is less affected after reaction with methylalumoxane.

Conformational analysis and vibrational spectroscopic studies of tetraethoxysilane and its hydrolysis products: A DFT prediction

The density functional theory was used to carry out a systematic investigation about the conformational and vibrational analyses of tetraethoxysilane (TEOS) and its hydrolysis products (Si(OCH2CH3)4−n(OH)n, n = 1–4). All possible potential energy curve (PEC) scans were performed in different symmetry point groups, D2d, S4, C2v and Cs, for the fully hydrolyzed product of TEOS, Si(OH)4. The main results indicate clear differences in the spectral profile of each molecular system, which can be used for monitoring the sol-gel processes at the hydrolysis stage. The most significative changes take place in 750–1000 cm−1, where mainly the νasSiO asymmetric stretching and δSiOH angular deformation modes are localized. A significant coupling between νasSiO and δSiOH is observed for the computed spectra of Si(OH)4 in gas-phase, with more pronounced effect for S4 ad D2d symmetries. For the partial hydrolysis products of TEOS (Si(OCH2CH3)4−n(OH)n, n = 1–3) this coupling is also present and it is evidenced by the fact that both vibrational bands in 750–900 cm−1 (δSiOH) and 900–1000 cm−1 (νSiO) show a great contribution of the SiO bond length displacements as much as of the SiOH bond angle changes.

Vibrational Spectroscopic and Molecular Docking Studies on N-Carbobenzoxy-L-2-phenylglycine by Density Functional Theory Method

Vibrational Spectroscopic and Molecular Docking Studies on N-Carbobenzoxy-L-2-phenylglycine by Density Functional Theory Method