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.     

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 (FTIR,FT-Raman,NMR and UV) and molecular structure investigations of 1,5-diphenylpenta-2,4-dien-1-one: a combined experimental and theoretical approach

The title molecule 1,5-diphenylpenta-2,4-dien-1-one (cinnamylideneacetophenone, CA) has been synthesised and characterised by FTIR, FT-Raman, NMR and UV–vis spectral analyses. The possible stable conformers of the CA molecule were searched by potential energy surface scan at B3LYP level of theory. The molecular geometry from X-ray determination of the CA molecule in the ground state has been compared using the density functional theory (DFT) with 6-31G(d,p) basis set. The harmonic vibrational modes, the corresponding wavenumbers and IR and Raman intensities of most stable conformer were calculated by the DFT method. The assignments of the fundamentals were proposed on the basis of total energy distribution calculations. The calculated ¹³C and ¹H NMR chemical shifts using gauge including atomic orbitals approach are in good agreement with the observed chemical shifts. The molecular stability and bond strength have been investigated by applying natural bond orbital analysis. Using the time-dependent DFT method, the electronic absorption spectrum of the title compound has been predicted and the electronic transitions within the molecule have been interpreted. The molecular electrostatic potential map was used for predicting possible hydrogen and oxygen bonding sites in the CA molecule.     

Laser Raman spectroscopy of lipid-protein systems. Differences in the effect of intrinsic and extrinsic proteins on the phosphatidylcholine Raman spectrum.

Laser Raman spectroscopy is used to examine the interactions of intrinsic and extrinsic proteins with the lipid layer structure. The interactions of cytochrome c and cytochrome c oxidase with lipids have been well established by others using a variety of techniques. Cytochrome c is thought to act as an extrinsic membrane protein while cytochrome c oxidase is thought to act as an intrinsic membrane protein. The lipid-cytochrome c and lipid cytochrome c oxidase systems are used to assist in interpreting the spectral changes due to extrinsic and intrinsic protein interactions. The two types of proteins examined produced differential changes in the lipid hydrocarbon C-H stretch Raman modes for both dimyristoyl and dipalmitoyl phosphatidylcholine. The plasma proteins albumin and fibrinogen were also found to differentially affect the lipid hydrocarbon C-H stretch Raman nodes. These proteins appear to interact with lipids in an extrinsic manner different from that of cytochrome c.     

Laser Raman spectroscopy of lipid-protein systems Differences in the effect of intrinsic and extrinsic proteins on the phosphatidylcholine Raman spectrum

Laser Raman spectroscopy is used to examine the interactions of intrinsic and extrinsic proteins with the lipid layer structure. The interactions of cytochrome c and cytochrome c oxidase with lipids have been well established by others using a variety of techniques. Cytochrome c is thought to act as an extrinsic membrane protein while cytochrome c oxidase is thought to act as an intrinsic membrane protein. The lipid-cytochrome c and lipid cytochrome c oxidase systems are used to assist in interpreting the spectral changes due to extrinsic and intrinsic protein interactions. The two types of proteins examined produced differential changes in the lipid hydrocarbon CH stretch Raman modes for both dimyristoyl and dipalmitoyl phosphatidylcholine. The plasma proteins albumin and fibrinogen were also found to differentially affect the lipid hydrocarbon CH stretch Raman modes. These proteins appear to interact with lipids in an extrinsic manner different from that of cytochrome c.     

Molecular structure,vibrational spectra and HOMO,LUMO analysis of 4-piperidone by density functional theory and ab initio Hartree–Fock calculations

Vibrational frequencies and geometrical parameters of 4-piperidone (4-PID) in the ground state have been calculated by using the Hartree–Fock (HF) and density functional methods (B3LYP) with 6-311++G(d,p) and 6-311+G(3df,2p) basis sets. These methods are proposed as a tool to be applied in the structural characterisation of 4-PID (C₅H₉NO). The title molecule has C _s point group symmetry, thus providing useful support in the interpretation of experimental IR and Raman data. The DFT-B3LYP/6-311+G(3df,2p) calculations have been found more reliable than the ab initio HF/6-311++G(d,p) calculations for the vibrational study of 4-PID. The calculated highest occupied molecular orbital and lowest unoccupied molecular orbital energies show that charge transfer occurs within the molecule. The theoretical spectrograms for FT-IR and FT-Raman spectra of the title molecule have been constructed.     

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 characterization,DFT studies,molecular docking and cytotoxic evaluation of 4‐nitro‐indole‐3‐carboxaldehyde: A potent lung cancer agent

The 4‐nitro‐1H‐indole‐carboxaldehyde (NICA) molecule was characterized experimentally using FT‐IR, FT‐Raman and UV‐Vis spectra, and it was studied theoretically using DFT calculations. The optimized structure of the NICA molecule was determined by DFT calculations using B3LYP functional with cc‐pVTZ basis set. The electron localization function (ELF) and local orbital localizer (LOL) studies were performed to visualize the electron delocalization in the molecule. The experimental and theoretical wavenumbers of the title molecule were assigned using VEDA 4.0 program. The charge delocalization and stability of the title molecule were investigated using natural bond orbital (NBO) analysis. Frontier molecular orbitals (FMOs) and related molecular properties were calculated. UV‐Vis spectrum was calculated theoretically and validated experimentally. The reactive sites of the molecule were studied from the MEP surface and Fukui function analysis. The molecular docking analysis reveals that the NICA ligand shows better inhibitory activity against RAS, which causes lung cancer. The in vitro cytotoxic activity of the molecule against human lung cancer cell lines (A549) was determined by MTT assay. Thus, the NICA molecule can be used as a potential candidate for the development of the drug against lung cancer.     

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.     

Cytochrome c oxidase: evidence for interaction of water molecules with cytochrome a

The resonance Raman spectra of cytochrome c oxidase in protonated buffer compared to that in deuterated buffer indicate that water molecules are near the heme of cytochrome a. Differences in widths of the heme line at 1610 cm-1, after short exposure to D2O, and, additionally, of the heme line at 1625 cm-1, after long exposure, can be accounted for by changes in resonance vibrational energy transfer between modes of cytochrome a2+ and the bending mode of water molecules in the heme pocket. On the basis of the assignment of these modes, we place one water molecule near the vinyl group and one water molecule near the formyl group of the cytochrome a heme. These water molecules may play several possible functional roles.     

Theoretical study of the infrared spectrum of 5-phenyl-1,3,4-oxadiazole-2-thiol by using DFT calculations

We have carried out a structural and vibrational study for 5-phenyl-1,3,4-oxadiazole-2-thiol by using the infrared (IR) spectrum and theoretical calculations. For a complete assignment of the compound IR spectrum, density functional theory calculations were combined with Pulay's scaled quantum mechanical force field methodology in order to fit the theoretical wavenumber values to the experimental ones. An agreement between theoretical and available experimental results was found. The theoretical vibrational calculations allowed us to obtain a set of scaled force constants fitting the observed wavenumbers. The results were then used to predict the Raman spectra, for which there are no experimental data. The nature of the benzyl and oxadiazole rings was studied by means of natural bond order and atoms in molecules theory calculations. In addition, the frontier molecular (highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO)) orbitals were analysed and compared with those calculated for the oxadiazole molecule.     

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.     

Direct Observation of Single DNA Structural Alterations at Low Forces with Surface-Enhanced Raman Scattering

DNA experiences numerous mechanical events, necessitating single-molecule force spectroscopy techniques to provide insight into DNA mechanics as a whole system. Inherent Brownian motion limits current force spectroscopy methods from observing possible bond level structural changes. We combine optical trapping and surface-enhanced Raman scattering to establish a direct relationship between DNA’s extension and structure in the low force, entropic regime. A DNA molecule is trapped close to a surface-enhanced Raman scattering substrate to facilitate a detectable Raman signal. DNA Raman modes shift in response to applied force, indicating phosphodiester mechanical alterations. Molecular dynamic simulations confirm the local structural alterations and the Raman sensitive band identified experimentally. The combined Raman and force spectroscopy technique, to our knowledge, is a novel methodology that can be generalized to all single-molecule studies.     

Vibrational analysis and spectra of orotic acid

The IR and Raman spectra of polycrystalline anhydrous orotic acid and its N1, N3, and O12 trideuterated isotopomer are recorded in the 4000-40 cm(-1) spectral interval as part of a series of vibrational analyses of nucleosides, nucleotides, and related compounds carried out in our laboratory. The frequencies of the fundamental transitions and the potential energy distributions of the 39 normal modes of orotic acid and its isotopomer are calculated by an ab initio density functional theory Becke3P86/6-311G** treatment. Assignments of the vibrational modes are proposed that consider the results of these calculations and the observed spectra. The results of the ab initio treatment are related to crystallographic and spectral data, and they are compared with previous assignments for similar molecules.     

Normal mode calculation of a netropsin–DNA complex: Effect of structural deformation on vibrational spectrum

Calculations of the normal mode spectrum of a netropsin-DNA complex, an isolated DNA helix of the same sequence, and a free netropsin molecule were carried out and compared with observations. We find that the frequency of modes of the complex that are primarily vibrations localized to the helix are relatively unchanged from the frequencies found for similar modes of the isolated helix. On the other hand, the frequencies of those modes of the complex that are found to be primarily in the netropsin are found to change significantly in the complex from that of the free netropsin. Further analysis indicates that the changes in the “netropsin modes” are primarily due to the conformational deformation induced in the netropsin by formation of the complex. All the frequencies and shifts in frequency are in good agreement with recent Raman measurements. © 1995 John Wiley & Sons, Inc.     

Molecular structure and spectroscopic (FT-IR,FT-Raman, 13C, 1H NMR and UV) studies of 3,4-dihydroxy-l-phenylalanine using density functional theory

Fourier transform infrared (FT-IR) and Fourier transform Raman (FT-Raman) spectra of 3,4-dihydroxy-l-phenylalanine (3,4-DPA) in solid phase were recorded and analysed in this research. Along with this, the IR spectra in CHCl₃ and the use of acetone as solvents of 3,4-DPA were also recorded. The equilibrium geometry, bonding features and harmonic vibrational frequencies were investigated with the help of density functional theory (DFT) method. The ¹H and ¹³C nuclear magnetic resonance chemical shifts of the molecule were calculated using the gauge including atomic orbital method and compared with experimental results. Stability of the molecule arising from hyperconjugative interactions and charge delocalisation was analysed using natural bond orbital analysis. The results show that charge in electron density (E _D) in the σ* and π* antibonding orbitals and second-order delocalisation energies E(2) confirms the occurrence of intramolecular charge transfer within the molecule. UV–vis spectrum of the compound was recorded and the electronic properties, such as HOMO and LUMO energies, were analysed using the time-dependent (TD)-DFT approach. Finally, the calculation results were applied to simulate infrared and Raman spectra of the title compound, which showed good agreement with the observed spectra.     

Conformational interconversion in protein crystals.

We present evidence that the structure of carbonmonoxy myoglobin crystals can be altered by lowering the pH. This structural change is monitored by the characteristic Fe-CO Raman modes at 508 and 491 cm-1 and is thought to involve a localized distal pocket transition from a "closed" conformation at pH 7 to a more "open" conformation at pH 4. These changes take place in the crystal without loss of intensity of a conformationally sensitive Raman mode at 252 cm-1 that signals a partial unfolding of the globin structure in solution. Quantitative studies, which monitor the open and closed populations as a function of laser photolysis, demonstrate that the interconversion rates (k+/-) in solution at 298 K are fast compared to the photolysis and CO entry rates (i.e. k+/- much greater than 10(3) s-1), while in frozen samples the interconversion is much slower than the experimental time scale (minutes). Since the open conformation is a minority species at pH 7, rapid exchange in aqueous solution is a necessary condition for this species to play a functional role. In the crystal, the interconversion rates are slowed compared to solution and begin to approach the photolysis rate (i.e. k+/- approximately 10(3) to 10(4) s-1). This indicates that the barriers for conformational exchange are increased in the crystal environment, compared to the solution, apparently due to the packing forces of the surrounding molecules. X-ray and neutron diffraction studies of MbCO crystals at high and low pH are needed to characterize the details of the structural changes and to test the hypothesis that closed and open distal pocket structures are associated with the 508 and 491 cm-1 Fe-CO modes.     

A Raman study of low frequency intrahelical modes in A-, B-, and C-DNA.

We have obtained low frequency (less than 200 cm-1) Raman spectra of calf-thymus DNA and poly(rI).poly(rC) as a function of water content and counterion species and of d(GGTATACC)2 and d(CGCGAATTCGCG)2 crystals. We have found that the Raman scattering from water in the first and second hydration shells does not contribute directly to the Raman spectra of DNA. We have determined the number of strong Raman active modes by comparing spectra for different sample orientations and polarizations and by obtaining fits to the spectra. We have found at least five Raman active modes in the spectra of A- and B-DNA. The frequencies of the modes above 40 cm-1 do not vary with counterion species, and there are only relatively small changes upon hydration. These modes are, therefore, almost completely internal. The mode near 34 cm-1 in A-DNA is mostly internal, whereas the mode near 25 cm-1 is dominated by interhelical interactions. The observed intensity changes upon dehydration were found to be due to the decrease in interhelical distance. Polymer length appears to play a role in the lowest frequency modes.     

The phospholipids of lamellar body material from fetal rabbit lung tissue in culture. Unusual phosphatidylcholine fatty acid profile

Tissue pieces of rabbit fetal lung, 23 days gestation, were cultured for 7 days in serum-free medium to obtain lamellar body material for phospholipid analysis. Cultures were maintained in culture medium without serum and (1) with no added hormones (control cultures), (2) with thyroxine (1 x 10(-7) M), (3) with cortisol (1 x 10(-7) M) and (4) with thyroxine plus cortisol (1 x 10(-7) M each). The hormonal response was evaluated by measuring the quantity of lamellar body material isolated from the tissue pieces after the 7-day culture period. Compared to control cultures, more lamellar body material was recovered from cultures treated with cortisol (180% of control) and with thyroxine plus cortisol (250% of control). Cultures treated with thyroxine alone yielded the same amount of lamellar body material as the controls. Hormone treatment produced only minor changes in the glycerophospholipid profile of the lamellar body material. A small but significant increase in the percentage of phosphatidylglycerol and a small but significant decrease in phosphatidylinositol were found in lamellar body material from cultures treated with thyroxine and thyroxine plus cortisol. The disaturated phosphatidylcholine content of the lamellar body material from culture was 28% of the total lamellar body phospholipid and was not affected by hormone treatment. This disaturated phosphatidylcholine content was low compared to the disaturated phosphatidylcholine of lamellar body material from adult lung (46%). The low proportion of disaturated phosphatidylcholine was due to the unusual presence of palmitoleic acid (16:1(cis-9)), which was more than one-fourth of the total fatty acid of the lamellar body phosphatidylcholine. It is possible that an abnormal delta 9 fatty acid desaturation activity was expressed in the lung tissue in vitro, which resulted in the high incorporation of the 16:1 fatty acid into lamellar body phosphatidylcholine.     

Potential scans and potential energy distributions of normal vibrational modes of trichloroacetyl isocyanate

The conformational stability and vibrational infrared and Raman spectra of trichloroacetyl isocyanate (CCl3CONCO) were investigated by ab initio MP2 and density functional B3LYP calculations using the 6-311++G** basis set. From the potential energy scans of the internal rotations in both the halomethyl and the isocyanate rotors, the molecule was predicted to exist predominantly in the cis-cis conformation. The steric hindrance between the halomethyl group and the nitrogen lone-pair was found to favor the staggered configuration for the chlorine atom, while conjugation effects favor the planar configuration for the C=O and the NCO groups. Vibrational wavenumbers were computed for the molecule at the DFT-B3LYP/6-311++G** level. Normal coordinate calculations were carried out to obtain the potential energy distributions (PED) among the symmetry coordinates of the normal modes for the molecule. The theoretical vibrational assignments were compared with experimental ones and ratios of observed to calculated wavenumbers of about 0.97-1.04 were obtained.