Density functional theory,restricted Hartree–Fock simulations and vibrational spectroscopic studies of nicorandil

Fourier transform infrared and Raman spectra of nicorandil have been recorded. The structure, conformational stability, geometry optimisation and vibrational frequencies have been investigated. Complete vibrational assignments were made for the stable conformer of the molecule using restricted Hartree–Fock (RHF) and density functional theory (DFT) calculations (B3LYP) with the 6-31G(d,p) basis set. Comparison of the observed fundamental vibrational frequencies of the molecule and calculated results by RHF and DFT methods indicates that B3LYP is superior for molecular vibrational problems. The thermodynamic functions of the title molecule were also performed using the RHF and DFT methods. Natural bond order analysis of the title molecule was also carried out. Comparison of the simulated spectra with the experimental spectra provides important information about the ability of the computational method to describe the vibration modes.     

Spectroscopic characterisation of n-octanohydroxamic acid and potassium hydrogen n-octanohydroxamate

The crystal structure and spectroscopic characteristics of n-octanohydroxamic acid and the potassium compound of that acid have been investigated by XRD, XPS, FTIR and Raman spectroscopy. XRD revealed that the acid is in the keto Z conformation with the alkyl chains oriented along the z-direction and hydrogen bonding between hydroxamate moieties. Vibrational spectra confirm this conclusion. Chemical analysis, XRD and XPS established that the potassium compound is the acid salt KH(C₇H₉CONO)₂. The crystal structure showed that the hydroxamate groups are also in the keto Z conformation and this is supported by vibrational spectra. In the acid salt, the two hydroxamate moieties are connected by a symmetrical O-H-O short hydrogen bonded linkage between the two hydroxamate oxygen atoms and this explains the absence of a discernible O-H stretch band in the vibrational spectra. Identification of the vibrational bands displayed is supported by deuteration and ¹⁵N substitution.     

Molecular structure,vibrational spectra and first-order hyperpolarisability analysis of 2-amino-6-nitrobenzothiazole by DFT method

Vibrational analysis of 2-amino-6-nitrobenzothiazole (2A6NBT) molecule has been carried out at room temperature using FT-IR and FT-Raman spectroscopic techniques. The equilibrium geometry, bonding features and harmonic vibrational frequencies have been investigated with the help of the density functional theory DFT method. The non-linear optical (NLO) behaviour of the examined molecule has been studied followed by the determination of the electric dipole moment μ, the polarisability α and hyperpolarisability β using HF/6-31G(d,p) method. Stability of the molecule arising from hyperconjugative interactions and charge delocalisation have been analysed using the natural bond orbital analysis. The results show that charge in electron density in the σ^* and π^* antibonding orbitals and second-order delocalisation energies (E²) confirms the occurrence of intramolecular charge transfer within the molecule. The assignments of the vibrational spectra have been carried out with the help of normal coordinate analysis following the scaled quantum mechanical force field methodology. The energy and oscillator strength calculated by time-dependent density functional theory complements with the experimental findings. The simulated spectra satisfactorily coincide with the experimental spectra.     

FT-IR,FT-Raman spectra and DFT vibrational analysis of 2-aminobiphenyl

In this work, the Fourier transform infrared (FT-IR) and Fourier transform Raman (FT-Raman) spectra of 2-aminobiphenyl (2ABP) were recorded in the solid phase. The optimised geometry, frequency and intensity of the vibrational bands of 2ABP were obtained by the density functional theory (BLYP and B3LYP) methods with complete relaxation in the potential energy surface using 6-31G(d) basis set. The harmonic vibrational frequencies were calculated and the scaled values have been compared with experimental FT-IR and FT-Raman spectra. The observed and the calculated frequencies are found to be in good agreement. The experimental spectra also coincide satisfactorily with those of theoretically constructed spectrograms.     

DFT study of structure and vibrational spectra of ceramide 3: comparison to experimental data

The Fourier transform Raman and infrared (IR) spectra of the Ceramide 3 (CER3) have been recorded in the regions 200–3500 cm^? 1 and 680–4000 cm^? 1, respectively. We have calculated the equilibrium geometry, harmonic vibrational wavenumbers, electrostatic potential surfaces, absolute Raman scattering activities and IR absorption intensities by the density functional theory with B3LYP functionals having extended basis set 6-311G. This work is undertaken to study the vibrational spectra of CER3 completely and to identify the various normal modes with better wavenumber accuracy. Good consistency is found between the calculated results and experimental data for the IR and Raman spectra.     

Spectroscopic characterisation of copper acetohydroxamate and copper n-octanohydroxamate

The nature of the bonding in acetohydroxamic acid, copper acetohydroxamate and copper n-octanohydroxamate has been investigated by chemical analysis, XPS, FTIR and Raman spectroscopy. Vibrational spectra show the acid to be in the keto Z conformation as was previously established for the n-octano homologue. Chemical analysis established that the copper compounds have a copper:hydroxamate stoichiometry of 1:1. XPS confirms that they are Cu^II compounds. The absence of vibrational spectral bands that were previously identified with N-H vibrations for n-octanohydroxamic acid and its potassium compound, together with the presence of a CN stretch band that shifts when the nitrogen is labelled with ¹⁵N, confirms that the hydroxamate moieties in the Cu^II compounds are in the enol configuration. Some interaction between Cu and N is indicated by the spectra and could explain the 1:1 stoichiometry of the Cu^II hydroxamates investigated.     

Vibrational spectral assignments of paraldehyde by ab initio and density functional methods

The FTIR and Laser-Raman spectra of paraldehyde have been recorded in the regions 4000–400 cm⁻¹ and 3500–250 cm⁻¹ respectively. Molecular electronic energy, geometrical structure, harmonic vibrational spectra, infrared intensities and Raman scattering activities have been computed at the HF/6-31G(d,p) and B3LYP/6-31G(d,p) levels of theory. The results were compared with experimental values with the help of scaling procedures. The observed wave numbers in FTIR and Laser-Raman spectra were analyzed and assigned to different normal modes of the molecule. Most of the modes have wave numbers in the expected range and are in good agreement with computed values.     

Molecular structure,spectroscopic (FT-IR,FT-Raman,UV–vis), NBO,thermochemistry analysis of bis(thiourea)zinc(II) chloride crystals

The experimental and theoretical studies on the molecular structure and vibrational spectra of bis(thiourea)zinc(II) chloride (BTZC) crystals were investigated. The Fourier transform infrared, Fourier transform Raman and UV–vis spectra of BTZC were recorded. The molecular geometry and vibrational frequencies of BTZC in the ground state were calculated by using B3LYP with LANL2DZ as basis set. Comparison of the observed structural parameters of BTZC with single-crystal X-ray studies yields a good agreement. Vibrational analysis of the simultaneous IR and Raman activation of the Zn–Cl stretching mode in the molecule provides the evidence for the charge transfer interaction taking place within the molecule. The energy and oscillator strength are calculated by time-dependent density functional theory. The simulated spectra satisfactorily coincide with the experimental spectra.     

Molecular structure and vibrational spectra of 4-nitrobenzylchloride by ab initio Hartree–Fock and density functional methods

The Fourier transform Raman and Fourier transform infrared spectra 4-nitrobenzylchloride of (NBC) were recorded in the solid phase. The Fourier transform gas phase infrared spectrum of NBC was also recorded. The equilibrium geometry, harmonic vibrational frequencies, infrared intensities and Raman scattering activities were calculated by HF/DFT (B3LYP and BLYP) and SVWN methods with the 6-31G(d,p) basis set. The scaled theoretical wave numbers by B3LYP showed very good agreement with the experimental ones. A detailed interpretation of the infrared and Raman spectra of NBC is reported on the basis of the calculated potential energy distribution. The theoretical spectrograms for the IR spectrum of the title molecule have been constructed.     

Sensing site‐specific structural characteristics and chirality using vibrational circular dichroism of isotope labeled peptides

Isotope labeling has a long history in chemistry as a tool for probing structure, offering enhanced sensitivity, or enabling site selection with a wide range of spectroscopic tools. Chirality sensitive methods such as electronic circular dichroism are global structural tools and have intrinsically low resolution. Consequently, they are generally insensitive to modifications to enhance site selectivity. The use of isotope labeling to modify vibrational spectra with unique resolvable frequency shifts can provide useful site‐specific sensitivity, and these methods have been recently more widely expanded in biopolymer studies. While the spectral shifts resulting from changes in isotopic mass can provide resolution of modes from specific parts of the molecule and can allow detection of local change in structure with perturbation, these shifts alone do not directly indicate structure or chirality. With vibrational circular dichroism (VCD), the shifted bands and their resultant sign patterns can be used to indicate local conformations in labeled biopolymers, particularly if multiple labels are used and if their coupling is theoretically modeled. This mini‐review discusses selected examples of the use of labeling specific amides in peptides to develop local structural insight with VCD spectra.     

Quantum chemical insight on vibration spectra of silica systems

A set of silicate ions and corresponding lithium salts have been quantum chemically (QC) simulated in a “free molecule” approach. The infrared (IR), inelastic neutron scattering (INS), and Raman spectra have been simulated and fitted to the experimentally registered ones. The complete assignment of the vibrational bands along with the intensities and potential energy distribution has been performed. The applicability of the traditionally used quasimolecule Si–O–Si model to the interpretation of bands near 440–480 cm^? 1 and so-called “Boson” peak near 50 cm^? 1 has been critically discussed.     

Elucidation of the absolute configuration of JNJ-27553292, a CCR2 receptor antagonist, by vibrational circular dichroism analysis of two precursors

The absolute configurations of two precursors, that is, 1-(3',4'-dichlorophenyl)-propanol and 1-(3',4'-dichlorophenyl)-propanamine, of a potent 2-mercapto-imidazole CCR-2 receptor antagonist, JNJ-27553292, were determined using vibrational circular dichroism. As a consequence, the absolute configuration of the antagonist itself was also determined. The two precursor compounds were subjected to a thorough conformational analysis and rotational strengths were calculated at the B3LYP/cc-pVTZ level of theory. Based on these data, vibrational circular dichroism spectra were simulated, which in turn were compared with experimental spectra. Agreement between the spectra allowed the assignment of the absolute configuration, which is in agreement with the proposed configuration based on stereospecific reactions on similar compounds.     

Experimental and Theoretical Studies of Calcium Fructoborate

Calcium fructoborate samples of composition Ca(C₆H₁₀O₆BO)₂·3.5H₂O were characterized by chemical analysis, infrared and Raman spectroscopy, and thermoanalytical (thermogravimetric and differential thermal analysis) data. Theoretical studies, using density functional theory, were made for seven different structural models of the fructoborate moiety, and the most stable structure could be derived from these calculations. The results of the theoretical study also allow improving the assignment of the vibrational spectra of the compound.     

FTIR,FT-Raman spectra and quantum chemical studies of nebivolol

Fourier transform infrared and Raman spectra of nebivolol have been recorded. The structure, conformational stability, geometry optimisation, and vibrational wave numbers have been investigated. Satisfactory vibrational assignments were made for the stable conformer of the molecule using Restricted Hartree–Fock (RHF) and density functional theory (DFT) calculation (B3LYP) with the 6-31G(d,p) basis set. Comparison of the observed fundamental vibrational wave numbers of the molecule and calculated results by RHF and DFT methods indicates that B3LYP is superior for molecular vibrational problems. Comparison of the simulated spectra with the experimental spectra provides important information about the ability of the computational method to describe the vibrational modes. The RHF and DFT-based NMR calculation procedure was also done. It was used to assign the ¹³C NMR chemical shift of nebivolol.     

Hydration of hyaluronan polysaccharide observed by IR spectrometry. II. Definition and quantitative analysis of elementary hydration spectra and water uptake

We recorded a series of spectra of sodium hyaluronan (HA) films that were in equilibrium with their surrounding humid atmosphere. The hygrometry of this atmosphere extended from 0 to 0.97% relative humidity. We performed a quantitative analysis of the corresponding series of hydration spectra that are the difference spectra of the film at a defined hygrometry minus the spectrum of the dried film (hygrometry = 0). The principle of this analysis is to use this series of hydration spectra to define a limited number (four) of "elementary hydration spectra" over which we can decompose all hydration spectra with good accuracy. This decomposition, combined with the measurements of the numbers of H(2)O molecules at the origin in these elementary hydration spectra of the three characteristic vibrational bands of H(2)O, allowed us to calculate the hydration number under different relative humidity conditions. This number compares well with that determined by thermogravimetry. Furthermore, the decomposition defines for each hygrometry value which chemical mechanisms represented by elementary hydration spectra are active. This analysis is pursued by determining for the elementary hydration spectra the number of hydrogen bonds established by each of the four alcohol groups found in each disaccharide repeat unit before performing the same analysis for amide and carboxylate groups. These results are later utilized to discuss the structure of HA at various stages of hydration.     

Pressure dependence of vibrational optical activity of model biomolecules. A computational study

Change of molecular properties with pressure is an attracting means to regulate molecular reactivity or biological activity. However, the effect is usually small and so far explored rather scarcely. To obtain a deeper insight and estimate the sensitivity of vibrational optical activity spectra to pressure-induced conformational changes, we investigate small model molecules. The Ala-Ala dipeptide, isomaltose disaccharide and adenine-uracil dinucleotide were chosen to represent three different biomolecular classes. The pressure effects were modeled by molecular dynamics and density functional theory simulations. The dinucleotide was found to be the most sensitive to the pressure, whereas for the disaccharide the smallest changes are predicted. Pressure-induced relative intensity changes in vibrational circular dichroism and Raman optical activity spectra are predicted to be 2–3-times larger than for non-polarized IR and Raman techniques.     

The conformational and vibrational behavior of the inhibitory neuropeptide derived from beta-endorphin

In this study, conformational behavior, structural, and vibrational characterization of the carboxy terminal dipeptide of β-endorphin (glycy-l-glutamine, glycyl-glutamine, beta-endorphin_30-31), which is an inhibitory neuropeptide synthesized from beta-endorphin_1-31 in brain stem regions, has been investigated. The theoretically possible stable conformers were searched by means of molecular mechanics method to determine their energetically preferred conformations. The 360 different conformations were calculated with the φ, Ψ, χ dihedral angles using the Ramachandran maps. The most stable conformation of the title molecule is characterized by the extended backbone shape (e) in the BR conformational range with ?.78 kcal/mol energy. The cis- and trans-dimeric forms of the dipeptide were also formed and energetically preferred conformations of dimers were investigated. The experimental methods (FT-IR, micro-Raman spectroscopies) coupled with quantum chemical calculations based on density functional theory (DFT) have been used to identify the geometrical, energetic, and vibrational characteristics of the dipeptide. The assignment of the vibrational spectra was performed based on the potential energy distribution of the vibrational modes. To investigate the electronic properties, such as nonlinear optical properties, the electric dipole moment, the mean polarizability, the mean first hyperpolarizability, and HOMO–LUMO energy gaps were computed using the DFT with the B3LYP/6-31++G(d,p) basis set combination. The second-order interaction energies were derived from natural bonding orbital analysis. The focus of this study is to determine possible stable conformation on inhibitory neuropeptide and to investigate molecular geometry, molecular vibrations of monomeric and dimeric forms, and hydrogen bonding interactions of glycy-l-glutamine dipeptide.     

Antineoplastic activity of new lanthanide (cerium, lanthanum and neodymium) complex compounds

Cerium (III), lanthanum (III) and neodymium (III) complexes with 3,3'-benzylidenebis[4-hydroxycoumarin] were synthesized in view of their application as cytotoxic agents. The complexes were characterized by different physicochemical methods: elemental analysis, mass spectrometry, 1H NMR, 13C NMR and IR spectroscopy. The spectra of the complexes were interpreted on the basis of comparison with the spectrum of the free ligand. The vibrational analysis showed that in the complexes the ligand coordinated to the metal ion through both deprotonated hydroxyl groups; however, participation of the carbonyl groups in the coordination to the metal ion was also suggested. The evaluation of the cytotoxic activity of the novel lanthanide complexes on HL-60 myeloid cells revealed that they are potent cytotoxic agents. The cerium complex was found to exhibit superior activity in comparison to the lanthanum and neodymium coordination compounds, the latter being the least active. Our data give us reason to conclude that the newly synthesized lanthanide complexes should be submitted to further more detailed pharmacological and toxicological evaluation.     

Frequency analysis of infrared absorption and vibrational circular dichroism of proteins in D2O solution.

The IR absorption frequencies as derived from second derivatives of the Fourier transform IR spectra of the amide I' bands of globular proteins in D2O are compared to those obtained from band fitting of the vibrational circular dichroism (VCD) spectra. The two sets of frequencies are in very good agreement, yielding consistent ranges where amide I' VCD and IR features occur. Use of VCD to complement the IR allows one to add sign information to the frequency information so that features occurring in the overlapping frequency ranges that might arise from different secondary structures can be better discriminated. From this comparison, it is clear that correlation just of the frequency of a given IR transition to secondary structure can lead to a nonunique solution. Different sign patterns were identified for correlated groups of globular proteins in restricted frequency ranges that have been previously assigned to defined secondary structural elements. Hence, different secondary structural elements must contribute band components to a given frequency range.