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Sample records for molecular spectroscopic studies

  1. Nonlinear spectroscopic studies of interfacial molecular ordering

    SciTech Connect

    Superfine, R.

    1991-07-01

    The second order nonlinear optical processes of second harmonic generation and sum frequency generation are powerful new probes of surfaces. They possess unusual surface sensitivity due to the symmetry properties of the nonlinear susceptibility. In particular, infrared-visible sum frequency generation (SFG) can obtain the vibrational spectrum of sub-monolayer coverages of molecules. In this thesis, we explore the unique information that can be obtained from SFG. We take advantage of the sensitivity of SFG to the conformation of alkane chains to study the interaction between adsorbed liquid crystal molecules and surfactant treated surfaces. The sign of the SFG susceptibility depends on the sign of the molecular polarizability and the orientation, up or down, of the molecule. We experimentally determine the sign of the susceptibility and use it to determine the absolute orientation to obtain the sign of the molecular polarizability and show that this quantity contains important information about the dynamics of molecular charge distributions. Finally, we study the vibrational spectra and the molecular orientation at the pure liquid/vapor interface of methanol and water and present the most detailed evidence yet obtained for the structure of the pure water surface. 32 refs., 4 figs., 2 tabs.

  2. [Spectroscopic Study of Salbutamol Molecularly Imprinted Polymers].

    PubMed

    Ren, Hui-peng; Guan, Yu-yu; Dai, Rong-hua; Liu, Guo-yan; Chai, Chun-yan

    2016-02-01

    In order to solve the problem of on-site rapid detection of salbutamol residues in feed and animal products, and develop a new method of fast detection of salbutamol on the basis of the molecular imprinting technology, this article uses the salbutamol (SAL) working as template molecule, methacrylic acid (MAA) working as functional monomer. On this basis, a new type of core-shell type salbutamol molecularly imprinted polymers were prepared with colloidal gold particles as triggering core. Superficial characteristics of the MIPs and the related compounds were investigated by ultraviolet (UV) spectra and infrared (IR) spectra, Raman spectra, Scanning electron microscopy (SEM) respectively. The results indicated that a stable hydrogen bonding complex has been formed between the carboxyl groups of SAL and MA with a matching ratio of 1:1. The complex can be easily eluted by the reagent containing hydrogen bonding. The chemical binding constant K reaches -0.245 x 10⁶ L² · mol⁻². The possible binding sites of the hydrogen bonding was formed between the hydrogen atoms of -COOH in MA and the oxygen atoms of C==O in SAL. IR and Raman spectrum showed that, compared with MA, a significant red shift of -OH absorption peak was manifested in MIPs, which proved that SAL as template molecule occurred a specific bond between MA. Red shift of stretching vibration absorption peak of C==O was also detected in the un-eluted MIPs and obvious energy loss happened, which demonstrated a possible binding sites is SAL intramolecular of C==O atom of oxygen. If the hydrogen atoms of -COOH in MA wanted to generate hydrogen bond. However, the shapes of absorption peak of other functional groups including C==C, C==O, and -OH were very similar both in MIPs and NIPs. Specific cavities were formed after the template molecules in MIPs were removed. It was proved by the adsorption experiment that the specific sites in these cavities highly match with the chemical and space structure of SAL

  3. Molecular spectroscopic study for suggested mechanism of chrome tanned leather

    NASA Astrophysics Data System (ADS)

    Nashy, Elshahat H. A.; Osman, Osama; Mahmoud, Abdel Aziz; Ibrahim, Medhat

    2012-03-01

    Collagen represents the structural protein of the extracellular matrix, which gives strength of hides and/or skin under tanning process. Chrome tan is the most important tanning agent all over the world. The methods for production of leather evolved over several centuries as art and engineering with little understanding of the underlying science. The present work is devoted to suggest the most probable mechanistic action of chrome tan on hide proteins. First the affect of Cr upon hide protein is indicated by the studied mechanical properties. Then the spectroscopic characterization of the hide protein as well as chrome tanned leather was carried out with Horizontal Attenuated Total Reflection (HATR) FT-IR. The obtained results indicate how the chromium can attached with the active sites of collagen. Molecular modeling confirms that chromium can react with amino as well as carboxylate groups. Four schemes were obtained to describe the possible interactions of chrome tan with hide proteins.

  4. Molecular spectroscopic study for suggested mechanism of chrome tanned leather.

    PubMed

    Nashy, Elshahat H A; Osman, Osama; Mahmoud, Abdel Aziz; Ibrahim, Medhat

    2012-03-01

    Collagen represents the structural protein of the extracellular matrix, which gives strength of hides and/or skin under tanning process. Chrome tan is the most important tanning agent all over the world. The methods for production of leather evolved over several centuries as art and engineering with little understanding of the underlying science. The present work is devoted to suggest the most probable mechanistic action of chrome tan on hide proteins. First the affect of Cr upon hide protein is indicated by the studied mechanical properties. Then the spectroscopic characterization of the hide protein as well as chrome tanned leather was carried out with Horizontal Attenuated Total Reflection (HATR) FT-IR. The obtained results indicate how the chromium can attached with the active sites of collagen. Molecular modeling confirms that chromium can react with amino as well as carboxylate groups. Four schemes were obtained to describe the possible interactions of chrome tan with hide proteins. PMID:22225606

  5. Spectroscopic Studies of Molecular Systems relevant in Astrobiology

    NASA Astrophysics Data System (ADS)

    Fornaro, Teresa

    2016-01-01

    In the Astrobiology context, the study of the physico-chemical interactions involving "building blocks of life" in plausible prebiotic and space-like conditions is fundamental to shed light on the processes that led to emergence of life on Earth as well as to molecular chemical evolution in space. In this PhD Thesis, such issues have been addressed both experimentally and computationally by employing vibrational spectroscopy, which has shown to be an effective tool to investigate the variety of intermolecular interactions that play a key role in self-assembling mechanisms of nucleic acid components and their binding to mineral surfaces. In particular, in order to dissect the contributions of the different interactions to the overall spectroscopic signals and shed light on the intricate experimental data, feasible computational protocols have been developed for the characterization of the spectroscopic properties of such complex systems. This study has been carried out through a multi-step strategy, starting the investigation from the spectroscopic properties of the isolated nucleobases, then studying the perturbation induced by the interaction with another molecule (molecular dimers), towards condensed phases like the molecular solid, up to the case of nucleic acid components adsorbed on minerals. A proper modeling of these weakly bound molecular systems has required, firstly, a validation of dispersion-corrected Density Functional Theory methods for simulating anharmonic vibrational properties. The isolated nucleobases and some of their dimers have been used as benchmark set for identifying a general, reliable and effective computational procedure based on fully anharmonic quantum mechanical computations of the vibrational wavenumbers and infrared intensities within the generalized second order vibrational perturbation theory (GVPT2) approach, combined with the cost-effective dispersion-corrected density functional B3LYP-D3, in conjunction with basis sets of

  6. Spectroscopic Studies of Molecular Systems relevant in Astrobiology

    NASA Astrophysics Data System (ADS)

    Fornaro, Teresa

    2016-01-01

    In the Astrobiology context, the study of the physico-chemical interactions involving "building blocks of life" in plausible prebiotic and space-like conditions is fundamental to shed light on the processes that led to emergence of life on Earth as well as to molecular chemical evolution in space. In this PhD Thesis, such issues have been addressed both experimentally and computationally by employing vibrational spectroscopy, which has shown to be an effective tool to investigate the variety of intermolecular interactions that play a key role in self-assembling mechanisms of nucleic acid components and their binding to mineral surfaces. In particular, in order to dissect the contributions of the different interactions to the overall spectroscopic signals and shed light on the intricate experimental data, feasible computational protocols have been developed for the characterization of the spectroscopic properties of such complex systems. This study has been carried out through a multi-step strategy, starting the investigation from the spectroscopic properties of the isolated nucleobases, then studying the perturbation induced by the interaction with another molecule (molecular dimers), towards condensed phases like the molecular solid, up to the case of nucleic acid components adsorbed on minerals. A proper modeling of these weakly bound molecular systems has required, firstly, a validation of dispersion-corrected Density Functional Theory methods for simulating anharmonic vibrational properties. The isolated nucleobases and some of their dimers have been used as benchmark set for identifying a general, reliable and effective computational procedure based on fully anharmonic quantum mechanical computations of the vibrational wavenumbers and infrared intensities within the generalized second order vibrational perturbation theory (GVPT2) approach, combined with the cost-effective dispersion-corrected density functional B3LYP-D3, in conjunction with basis sets of

  7. Spectroscopic studies of gas-phase molecular clusters

    NASA Astrophysics Data System (ADS)

    Wong, Chi-Kin

    Spectroscopic investigations of hydrogen-bonding and van der Waals' interactions in molecular clusters were studied by the techniques of infrared predissociation and resonance-enhanced multiphoton ionization spectroscopies (REMPI). Ab initio calculations were applied in conjunction for data interpretation. The infrared predissociation spectroscopy of CN-·(H 2O)n (n = 2--6) clusters was reported in the region of 2950--3850 cm-1. The hydrogen bondings for the C-site and N-site binding, and among the water molecules were identified for n = 2 to 4. A spectral transition was observed for n = 5 and 6, implying that the anion was surface-bound onto the water aggregates in larger clusters. The infrared predissociation spectroscopy of Br-·(NH 3) and I-·(NH3) n (n = 1--3) clusters was reported in the region of 3050--3450 cm-1. For the Br -·(NH3) complex, a dominating ionic NH stretch appeared at 3175 cm-1, and the weaker free NH stretch appeared at 3348 cm-1. The observed spectrum was consistent to the structure in which there was one nearly linear hydrogen bond between Br- and the NH3 moiety. For the I- ·(NH3) complex, five distinct IR absorption bands were observed in the spectrum. The spectrum was not consistent with basic frequency patterns of three geometries considered in the ab initio calculations---complex with one, two and three hydrogen bondings between I- and the NH3 moiety. Substantial inhomogenous broadening were displayed in the spectra for I- ·(NH3)n (n = 2--3), suggesting the presence of multiple isomers. The REMPI spectroscopy of the bound 4p 2pi 1/2 and 2pi3/2 states, and the dissociative 3d 2Sigma+1/2 state in the Al·Ar complex was reported. The dissociative spectrum at Al+ channel suggested the coupling of the 4p 2pi 1/2,3/2 states to the repulsive 3d 2Sigma+1/2 state. The spin-electronic coupling was further manifested in the dissociative Al+ spectrum of the 3d 2Sigma+1/2 state. Using the potential energy curves obtained from ab initio

  8. Spectroscopic investigations, molecular interactions, and molecular docking studies on the potential inhibitor "thiophene-2-carboxylicacid"

    NASA Astrophysics Data System (ADS)

    Karthick, T.; Balachandran, V.; Perumal, S.

    2015-04-01

    Thiophene derivatives have been focused in the past decades due to their remarkable biological and pharmacological activities. In connection with that the conformational stability, spectroscopic characterization, molecular (inter- and intra-) interactions, and molecular docking studies on thiophene-2-carboxylicacid have been performed in this work by experimental FT-IR and theoretical quantum chemical computations. Experimentally recorded FT-IR spectrum in the region 4000-400 cm-1 has been compared with the scaled theoretical spectrum and the spectral peaks have been assigned on the basis of potential energy distribution results obtained from MOLVIB program package. The conformational stability of monomer and dimer conformers has been examined. The presence of inter- and intramolecular interactions in the monomer and dimer conformers have been explained by natural bond orbital analysis. The UV-Vis spectra of the sample in different solvents have been simulated and solvent effects were predicted by polarisable continuum model with TD-DFT/B3LYP/6-31+G(d,p) method. To test the biological activity of the sample, molecular docking (ligand-protein) simulations have been performed using SWISSDOCK web server. The full fitness (FF) score and binding affinity values revealed that thiophene-2-carboxylicacid can act as potential inhibitor against inflammation.

  9. Spectroscopic studies on chemical- and photo-responsive molecular machines and their bio-applications

    NASA Astrophysics Data System (ADS)

    Lau, Yuen Agnes

    2011-07-01

    The four chapters presented in this dissertation describe how various spectroscopic techniques are used: 1) to study the operation of molecular machines in solution, 2) to track the operation of molecular machines inside a single cell, and 3) to investigate the photo-decomposition pathway of a biological chromophore. Recent advances in nanotechnology have enriched the development of nano-scale molecular assemblies to be used as delivery platforms for biologically relevant molecules. Among all the molecular assemblies, molecular machines that are incorporated onto various domains of mesoporous silica nanoparticles (MSN) hold considerable potential as a reliable delivery system. Because the ease of functionalization enables chemical or photo-responsive molecular moieties to be covalently attached to the silica framework, these molecular assemblies, with defined mechanized properties, can perform specific functions under external stimuli (pH, redox, or light). While the primary function of these molecular machines is to deliver stored cargo molecules, the means of activation and the motif in which they operate are different. In the first and second chapters of this dissertation, two types of molecular machines, nanovalves and nanoimpellers, and their operations are studied. The ability to continuously monitor and image progression of molecular-based biological events in real-time can enhance our understanding of intracellular processes upon drug, protein and nucleic acid delivery. Using the photo-activated nanoimpeller described in the second chapter, the third chapter explores how it can be used to transport a nuclear staining agent, PI, inside a single cell. Nanoimpellers are made by functionalizing azobenzene molecules to the internal pore surface of MSN. The continuous cis/trans isomerizations are set in motion upon laser illumination at optimal wavelength(s), which facilitate cargo molecules to be expelled from the pores to the surrounding medium. By refining a

  10. Millimeter-Wave Spectroscopic and Collisional Studies of Molecules and Molecular Ions

    NASA Astrophysics Data System (ADS)

    Pearson, John Christoffersen

    1995-01-01

    Molecular spectroscopy in the millimeter- and submillimeter-wave regions is an important tool in molecular physics. Information on molecular motions and interactions is obtained from spectroscopic studies of energy levels and collisions. This information and the data from which it is derived are essential in remote sensing of the atmosphere and the interstellar medium. Remote sensing at submillimeter wavelengths is now possible, making higher frequency and quantum number measurements of known interstellar species like water, propionitrile and ethyl alcohol necessary. Remote sensing improvements have also facilitated the need for spectral data on suspected interstellar molecules like propylene. The desire to extract quantitative information from atmospheric remote sensing has resulted in the need for a better understanding of the molecular interactions that cause pressure broadening. The use of a cold molecular ion to magnify the effects of intermolecular interactions has serious implications for pressure broadening theory. The measurement and analysis of rotational spectra of the asymmetric rotors water and propionitrile and the internal rotors propylene and ethyl alcohol are presented. These investigations provide the data and analysis necessary for astronomical observation. The ethyl alcohol investigation is the first experimental millimeter-wave study of a molecule with an asymmetric internal rotor. This study provides the data necessary for detailed theoretical modeling of this type of problem. A novel new experimental technique for generating and studying molecular ions is presented. The first temperature dependent microwave pressure broadening study of a molecular ion colliding with a neutral molecule, HCO^{+} on H_2 , is presented.

  11. Lanthanide and transition metal complexes of bioactive coumarins: molecular modeling and spectroscopic studies.

    PubMed

    Georgieva, I; Mihaylov, Tz; Trendafilova, N

    2014-06-01

    The present paper summarizes theoretical and spectroscopic investigations on a series of active coumarins and their lanthanide and transition metal complexes with application in medicine and pharmacy. Molecular modeling as well as IR, Raman, NMR and electronic spectral simulations at different levels of theory were performed to obtain important molecular descriptors: total energy, formation energy, binding energy, stability, conformations, structural parameters, electron density distribution, molecular electrostatic potential, Fukui functions, atomic charges, and reactive indexes. The computations are performed both in gas phase and in solution with consideration of the solvent effect on the molecular structural and energetic parameters. The investigations have shown that the advanced computational methods are reliable for prediction of the metal-coumarin binding mode, electron density distribution, thermodynamic properties as well as the strength and nature of the metal-coumarin interaction (not experimentally accessible) and correctly interpret the experimental spectroscopic data. Known results from biological tests for cytotoxic, antimicrobial, anti-fungal, spasmolytic and anti-HIV activities on the studied metal complexes are reported and discussed. PMID:24680836

  12. Binding of copper to lysozyme: Spectroscopic, isothermal titration calorimetry and molecular docking studies

    NASA Astrophysics Data System (ADS)

    Jing, Mingyang; Song, Wei; Liu, Rutao

    2016-07-01

    Although copper is essential to all living organisms, its potential toxicity to human health have aroused wide concerns. Previous studies have reported copper could alter physical properties of lysozyme. The direct binding of copper with lysozyme might induce the conformational and functional changes of lysozyme and then influence the body's resistance to bacterial attack. To better understand the potential toxicity and toxic mechanisms of copper, the interaction of copper with lysozyme was investigated by biophysical methods including multi-spectroscopic measurements, isothermal titration calorimetry (ITC), molecular docking study and enzyme activity assay. Multi-spectroscopic measurements proved that copper quenched the intrinsic fluorescence of lysozyme in a static process accompanied by complex formation and conformational changes. The ITC results indicated that the binding interaction was a spontaneous process with approximately three thermodynamical binding sites at 298 K and the hydrophobic force is the predominant driven force. The enzyme activity was obviously inhibited by the addition of copper with catalytic residues Glu 35 and Asp 52 locating at the binding sites. This study helps to elucidate the molecular mechanism of the interaction between copper and lysozyme and provides reference for toxicological studies of copper.

  13. Binding of copper to lysozyme: Spectroscopic, isothermal titration calorimetry and molecular docking studies.

    PubMed

    Jing, Mingyang; Song, Wei; Liu, Rutao

    2016-07-01

    Although copper is essential to all living organisms, its potential toxicity to human health have aroused wide concerns. Previous studies have reported copper could alter physical properties of lysozyme. The direct binding of copper with lysozyme might induce the conformational and functional changes of lysozyme and then influence the body's resistance to bacterial attack. To better understand the potential toxicity and toxic mechanisms of copper, the interaction of copper with lysozyme was investigated by biophysical methods including multi-spectroscopic measurements, isothermal titration calorimetry (ITC), molecular docking study and enzyme activity assay. Multi-spectroscopic measurements proved that copper quenched the intrinsic fluorescence of lysozyme in a static process accompanied by complex formation and conformational changes. The ITC results indicated that the binding interaction was a spontaneous process with approximately three thermodynamical binding sites at 298K and the hydrophobic force is the predominant driven force. The enzyme activity was obviously inhibited by the addition of copper with catalytic residues Glu 35 and Asp 52 locating at the binding sites. This study helps to elucidate the molecular mechanism of the interaction between copper and lysozyme and provides reference for toxicological studies of copper. PMID:27089183

  14. Exploring binding properties of sertraline with human serum albumin: Combination of spectroscopic and molecular modeling studies.

    PubMed

    Shahlaei, Mohsen; Rahimi, Behnoosh; Nowroozi, Amin; Ashrafi-Kooshk, Mohammad Reza; Sadrjavadi, Komail; Khodarahmi, Reza

    2015-12-01

    Human serum albumin (HSA)-drug binding is an important factor to determine half life and bioavailability of drugs. In the present research, the interaction of sertraline (SER) to HSA was investigated using combination of spectroscopic and molecular modeling techniques. Changes in the UV-Vis, CD and FT-IR spectra as well as a significant degree of tryptophan fluorescence quenching were observed upon SER-HSA interaction. Data obtained by spectroscopic methods along with the computational studies suggest that SER binds to residues located in subdomain IIA of HSA. Analysis of spectroscopic data represented the formation of 1:1 complex, significant binding affinity, negative values of entropy and enthalpy changes and the essential role of hydrophobic interactions in binding of SER to HSA. The binding models were demonstrated in the aspects of SER's conformation, active site interactions, important amino acids and hydrogen bonding. Computational mapping of the possible binding site of SER confirmed that the ligand to be bound in a large hydrophobic cavity of HSA. In accordance with experimental data, computational analyses indicated that SER binding does not alter the secondary structure of the protein. The results not only lead to a better understanding of interaction between SER and HSA but also provide useful data about the influence of SER on the protein conformation. PMID:26471709

  15. Synthesis, molecular structure, spectroscopic analysis, thermodynamic parameters and molecular modeling studies of (2-methoxyphenyl)oxalate

    NASA Astrophysics Data System (ADS)

    Şahin, Zarife Sibel; Kantar, Günay Kaya; Şaşmaz, Selami; Büyükgüngör, Orhan

    2015-05-01

    The aim of this study is to find out the molecular characteristic and structural parameters that govern the chemical behavior of a new (2-methoxyphenyl)oxalate compound and to compare predictions made from theory with experimental observations. The title compound, (2-methoxyphenyl)oxalate, (I), (C16H14O6), has been synthesized. The compound has been characterized by elemental analysis, IR, 1H NMR, 13C NMR spectroscopies and single crystal X-ray diffraction techniques. Optimized molecular structure, harmonic vibrational frequencies, 1H and 13C NMR chemical shifts have been investigated by B3LYP/6-31G(d,p) method using density functional theory (DFT). The calculated results show that the predicted geometry can well reproduce structural parameters. In addition, global chemical reactivity descriptors, molecular electrostatic potential map (MEP), frontier molecular orbitals (FMOs), Mulliken population method and natural population analysis (NPA) and thermodynamic properties have also been studied. The energetic behavior of title compound has been examined in solvent media using polarizable continuum model (PCM).

  16. Manipulating the proton transfer process in molecular complexes: synthesis and spectroscopic studies.

    PubMed

    Panja, Sumit Kumar; Dwivedi, Nidhi; Saha, Satyen

    2016-08-01

    The proton transfer process in carefully designed molecular complexes has been investigated directly in the solid and solution phase. SCXRD studies have been employed to investigate the N-H-O bonding interaction sites of the molecular complexes, with additional experimental support from FTIR and Raman spectroscopic studies, to gain information on the relative position of hydrogen in between the N and O centers. Further, the proton transfer process in solution is studied using UV-Visible spectroscopy through monitoring the intramolecular charge transfer (ICT) process in these molecular complexes, which is primarily governed by the number of electron withdrawing groups (nitro groups) on proton donor moieties (NP, DNP and TNP). It is found that the magnitude of the ICT process depends on the extent of proton transfer, which on the other hand depends on the relative stabilities of the constituent species (phenolate species). A correlation is observed between an increase in the number of nitro groups and an increase in the melting point of the molecular complexes, indicating the enhancement of ionic character due to the proton transfer process. The aliphatic H-bonding is identified and monitored using (1)H-NMR spectroscopy, which reveals that the identity of molecular complexes in solution interestingly depends on the extent of proton transfer, in addition to the nature of the solvents. The aliphatic C-H-O H-bonding interaction between the oxygen atom of the nitro group and the alkyl hydrogen in piperidinium was also found to play a significant role in strengthening the primary interaction involving a hydrogen transfer process. The conductivity of the molecular complexes increases with an increase in the number of nitro groups, indicating the enhancement in ionic character of the molecular complexes. PMID:27424765

  17. Spectroscopic Studies of Atomic and Molecular Processes in the Edge Region of Magnetically Confined Fusion Plasmas

    SciTech Connect

    Hey, J. D.; Brezinsek, S.; Mertens, Ph.; Unterberg, B.

    2006-12-01

    Edge plasma studies are of vital importance for understanding plasma-wall interactions in magnetically confined fusion devices. These interactions determine the transport of neutrals into the plasma, and the properties of the plasma discharge. This presentation deals with optical spectroscopic studies of the plasma boundary, and their role in elucidating the prevailing physical conditions. Recorded spectra are of four types: emission spectra of ions and atoms, produced by electron impact excitation and by charge-exchange recombination, atomic spectra arising from electron impact-induced molecular dissociation and ionisation, visible spectra of molecular hydrogen and its isotopic combinations, and laser-induced fluorescence (LIF) spectra. The atomic spectra are strongly influenced by the confining magnetic field (Zeeman and Paschen-Back effects), which produces characteristic features useful for species identification, temperature determination by Doppler broadening, and studies of chemical and physical sputtering. Detailed analysis of the Zeeman components in both optical and LIF spectra shows that atomic hydrogen is produced in various velocity classes, some related to the relevant molecular Franck-Condon energies. The latter reflect the dominant electron collision processes responsible for production of atoms from molecules. This assignment has been verified by gas-puffing experiments through special test limiters. The higher-energy flanks of hydrogen line profiles probably also show the influence of charge-exchange reactions with molecular ions accelerated in the plasma sheath ('scrape-off layer') separating limiter surfaces from the edge plasma, in analogy to acceleration in the cathode-fall region of gas discharges. While electron collisions play a vital role in generating the spectra, ion collisions with excited atomic radiators act through re-distribution of population among the atomic fine-structure sublevels, and momentum transfer to the atomic nuclei via

  18. Novel aldehyde and thiosemicarbazone derivatives: Synthesis, spectroscopic characterization, structural studies and molecular docking studies

    NASA Astrophysics Data System (ADS)

    Karakurt, Tuncay; Tahtaci, Hakan; Subasi, Nuriye Tuna; Er, Mustafa; Ağar, Erbil

    2016-12-01

    In this study our purpose is that, synthesis and characterization of compounds containing the aldehyde and thiosemicarbazone groups and comparison of the theoretical results with the experimental results. The structures of all synthesized compounds were elucidated by IR, 1H NMR, 13C NMR, elemental analyses techniques. The structure of compound (4) (C9H8N4O2S) was also elucidated by X-ray diffraction analysis. In addition, the theoretical IR spectrum, 1H NMR and 13C NMR chemical shift values, frontier molecular orbital values (FMO) of these molecules were analyzed by using Becke-3- Lee-Yang-Parr (B3LYP) method with LanL2DZ basis set. Finally, molecular docking studies were performed on synthesized compounds using the 4DKI beta-lactam protein structure to determine the potential binding mode of inhibitors.

  19. Molecular interaction study of the diisopropyl ether-propionic acid mixture by spectroscopic and dielectric studies

    NASA Astrophysics Data System (ADS)

    Arivazhagan, G.; Shanmugam, R.; Elangovan, A.

    2011-10-01

    FTIR and 13C NMR spectral studies have been carried out on diisopropyl ether-propionic acid binary mixture to probe the molecular interactions and stoichiometry of complexation. Density functional theory (DFT) calculations of vibrational frequencies of pure acid and ether-acid binary mixtures have also been performed. In addition, Kirkwood-correlation factors, excess permittivity and excess free energy of mixing have been obtained at various concentrations and at four different temperatures from the dielectric measurements. Excess permittivity is found to have positive deviation and excess free energy deviates negatively from ideal behaviour.

  20. Inhibitory effects of daidzein and genistein on trypsin: Insights from spectroscopic and molecular docking studies.

    PubMed

    Zeng, Hua-Jin; Wang, Ya-Ping; Yang, Ran; You, Jing; Qu, Ling-Bo

    2016-08-01

    In this work, the inhibitory effect of two isoflavonoids including daidzein and genistein on trypsin and their binding mechanism were determined by spectroscopic and molecular docking approaches. The results indicated that both daidzein and genistein reversibly inhibited trypsin in a competitive manner with IC50 values of 68.01×10(-6)molL(-1) and 64.70×10(-6)molL(-1) and Ki values of 62.12×10(-6)molL(-1) and 59.83×10(-6)molL(-1), respectively. They could spontaneously bind with trypsin mainly through hydrophobic force and electrostatic interactions with a single binding site. Analysis of circular dichrosim spectra and molecular docking revealed that both isoflavonoids bound directly into the catalytic cavity and the microenvironment and secondary structure of trypsin were changed in this process, which caused the inhibition of trypsin activity. All these experimental results and theoretical data in this work would be help in understanding the mechanism of inhibitory effects of daidzein and genistein against trypsin and the potential of isoflavonoid to relieve symptoms of pancreatitis. PMID:27109756

  1. Theoretical DFT study on spectroscopic signature and molecular dynamics of neurotransmitter and effect of hydrogen removal

    NASA Astrophysics Data System (ADS)

    Mukherjee, V.; Singh, N. P.; Yadav, R. A.

    2013-04-01

    Vibrational spectroscopic study has been made for the serotonin molecule and its deprotonated form. The Infrared and Raman spectra in optimum geometry of these two molecules are calculated using density functional theorem and the normal modes are assigned using potential energy distributions (PEDs) which are calculated using normal coordinate analysis method. The vibrational frequencies of these two molecules are reported and a comparison has been made. The effect of removal of the hydrogen atom from the serotonin molecule upon its geometry and vibrational frequencies are studied. Electronic structures of these two molecules are also studied using natural bond orbital (NBO) analysis. Theoretical Raman spectrum of serotonin at different exciting laser frequencies and at different temperatures are obtained and the results are discussed. Present study reveals that some wrong assignments had been made for serotonin molecule in earlier study.

  2. InGaP grown on Ge (100) by molecular beam epitaxy: a spectroscopic ellipsometry study

    NASA Astrophysics Data System (ADS)

    D'Costa, Vijay Richard; Khai Loke, Wan; Zhou, Qian; Fatt Yoon, Soon; Yeo, Yee-Chia

    2016-03-01

    We investigated the optical properties of disordered In0.52Ga0.48P alloys by spectroscopic ellipsometry in the far-infrared to ultraviolet energy range (0.037-5.1 eV). The alloys were grown on Ge (100) substrate by solid-source molecular beam epitaxy. The far-infrared dielectric function reveals two absorption peaks that can be attributed to InP- and GaP-like vibrational modes. The visible-UV dielectric function of In0.52Ga0.48P alloys nearly lattice-matched to Ge shows the critical points E 0, E 1, and E 2, energies of which are determined using a derivative analysis. A weak transition that can be identified as the E 1 + Δ1 critical point is revealed. The vibrational frequencies and the transition energies in In0.52Ga0.48P are lower relative to In0.49Ga0.51P lattice-matched to GaAs. The downward shifts in E 0 and phonons can be estimated using the compositional dependence of E 0 and phonons of bulk alloys.

  3. Spectroscopic studies, potential energy surface and molecular orbital calculations of pramipexole.

    PubMed

    Muthu, S; Uma Maheswari, J; Srinivasan, S; Isac paulraj, E

    2013-11-01

    A systematic vibrational spectroscopic assignment and analysis of pramipexole [(S)-N(6)-propyl-4,5,6,7-tetrahydro-1,3-benzothiazole-2,6-diamine] has been carried out using FT-IR and FT-Raman spectral data. The vibrational analysis was aided by an electronic structure calculation based on the hybrid density functional method B3LYP using a 6-311G(d, p) and cc-pVTZ basis sets. Molecular equilibrium geometries, electronic energies, IR and Raman intensities, harmonic vibrational frequencies have been computed. The assignments are based on the experimental IR and Raman spectra, and a complete assignment of the observed spectra has been proposed. The UV-visible spectrum of the compound was recorded and the electronic properties, such as HOMO and LUMO energies and the maximum absorption λmax were determined by time-dependent DFT (TD-DFT) method. The geometrical parameters, vibrational frequencies and absorption wavelengths were compared with the experimental data. The complete vibrational assignments are performed on the basis of the potential energy distributions (PEDs) of the vibrational modes in terms of natural internal coordinates. The simulated FT-IR, FT-Raman, and UV spectra of the title compound have been constructed. In addition, the potential energy surface, HOMO and LUMO energies, the molecular electrostatic potential and the first-order hyperpolarizability have been computed. The magnitude of the first-order hyperpolarizability is 5 times larger than that of urea and the title compound may be a potential applicant for the development of NLO materials. PMID:23831980

  4. Spectroscopic, viscositic and molecular modeling studies on the interaction of 3'-azido-daunorubicin thiosemicarbazone with DNA.

    PubMed

    Cui, Fengling; Liu, Qingfeng; Luo, Hongxia; Zhang, Guisheng

    2014-01-01

    A new daunorubicin has been synthesized and structurally characterized. The interaction of native calf thymus DNA (ctDNA) with 3'-azido-daunorubicin thiosemicarbazone (ADNRT) was investigated under simulated physiological conditions by multi-spectroscopic techniques, viscometric measurements and molecular modeling study. It concluded that ADNRT could intercalate into the base pairs of ctDNA, and the fluorescence quenching by ctDNA was static quenching type. Thermodynamic parameters calculated suggested that the binding of ADNRT to ctDNA was mainly driven by hydrophobic interactions. The relative viscosity of ctDNA increased with the addition of ADNRT, which confirmed the intercalation mode. Furthermore, molecular modeling studies corroborate the above experimental results. PMID:23974700

  5. Specific binding and inhibition of 6-benzylaminopurine to catalase: multiple spectroscopic methods combined with molecular docking study.

    PubMed

    Xu, Qin; Lu, Yanni; Jing, Longyun; Cai, Lijuan; Zhu, Xinfeng; Xie, Ju; Hu, Xiaoya

    2014-04-01

    6-Benzylaminopurine (6-BA) is a kind of cytokinin which could regulate the activities of the antioxidant defense system of plants. In this work, its interaction with and inhibition of beef liver catalase have been systematically investigated using spectroscopic, isothermal titration calorimetric and molecular docking methods under physiological conditions. The fluorescence quenching of beef liver catalase (BLC) by 6-BA is due to the formation of 6-BA-BLC complex. Hydrogen bonds and van der Waals interactions play major roles in stabilizing the complex. The Stern-Volmer quenching constant, binding constant, the corresponding thermodynamic parameters and binding numbers were measured. The results of UV-vis absorption, three-dimensional fluorescence, synchronous fluorescence and circular dichroism spectroscopic results demonstrate that the binding of 6-BA results in the micro-environment change around tyrosine (Tyr) and tryptophan (Trp) residues of BLC. The BLC-mediated conversion of H2O2 to H2O and O2, in the presence and absence of 6-BA, was also studied. Lineweaver-Burk plot indicates a noncompetitive type of inhibition. Molecular docking study was used to find the binding sites. PMID:24412785

  6. Molecular spectroscopic analyses of gelatin

    NASA Astrophysics Data System (ADS)

    Ibrahim, Medhat; Mahmoud, Abdel Aziz; Osman, Osama; Abd El-Aal, Mohamed; Eid, May

    2011-10-01

    The molecular structure of gelatin was studied using Fourier transform infrared spectroscopy FTIR. The spectrum is subjected to deconvolution in order to elucidate the constituents of the molecular structure. B3LYP/6-31g** was used to study 13 amino acids then the scaled spectrum was compared to those of protein in order to describe the contribution of each amino acid into protein structure. A special interest was paid to the NH and C dbnd O region. The reactivity of each amino acid was studied in terms of some important physical parameters like total dipole moment and HOMO/LUMO which describe the interaction of amino acid with their surrounding molecules. Results indicated that B3LYP/6-31g** model is a suitable and precise method for studying molecular structure of protein.

  7. [Interaction between ambroxol hydrochloride and human serum albumin studied by spectroscopic and molecular modeling methods].

    PubMed

    Liang, Jing; Feng, Su-Ling

    2011-04-01

    In the present paper, the interaction between ambroxol hydrochloride (ABX) and human serum albumin (HSA) was studied under simulative physiological condition by spectroscopy and molecular modeling method. Stern-Volmer curvers at different temperatures and UV-Vis absorption spectroscopy showed that ABX quenched the fluorescence of HSA mainly through dynamic quenching mode. On the basis of the thermodynamic data, the main binding force between them is hydrophobic interaction. According to the theory of Forster non-radiation energy transfer, the binding distance between the donor and the acceptor was 3.01 nm. The effect of ABX on the conformation of HSA was analyzed by the synchronous and three-dimensional fluorescence spectroscopy. Furthermore, using the molecular modeling method, the interaction between them was predicted from molecular angle: ABX might locate in the subdomain III A of HSA. PMID:21714251

  8. Spectroscopic and molecular modeling studies on binding of dorzolamide to bovine and human carbonic anhydrase II.

    PubMed

    Bijari, Nooshin; Ghobadi, Sirous; Mahdiuni, Hamid; Khodarahmi, Reza; Ghadami, Seyyed Abolghasem

    2015-09-01

    This report is a comparative evaluation on the interaction of dorzolamide (DZA) with bovine and human carbonic anhydrase II (bCA II and hCA II, respectively) using fluorimetry, UV-vis and circular dichroism (CD) spectroscopy as well as molecular docking and molecular dynamics studies. Fluorescence data obtained at different temperatures indicated that DZA quenched the intrinsic fluorescence of both enzymes through a static mechanism. Thermodynamic analysis of the quenching data revealed that hydrogen bonding and van der Waals interactions play important roles in drug binding. Calculations of the protein surface hydrophobicity (PSH) index, using 1-anilinonaphtalene-8-sulfonate, also indicated a decrease in PSH of the hCA II and minor increase in PSH value of the bCA II upon drug binding. The results of far- and near-UV CD experiments showed some alterations in the secondary and tertiary structures of both enzymes upon ligation. The structural changes induced by drug binding caused more reduction in the catalytic activity of hCA II than bCA II. Based on the experimental data and the possible binding mode revealed by molecular docking and molecular dynamic studies, we concluded that DZA binds stronger to hCA II active site cavity compared to bCA II. PMID:26093313

  9. Multi-spectroscopic and molecular modeling studies on the interaction of antihypertensive drug; methyldopa with calf thymus DNA.

    PubMed

    Shahabadi, Nahid; Maghsudi, Maryam

    2014-02-01

    The interaction of methyldopa [(S)-2-amino-3-(3,4-dihydroxyphenyl)-2-methyl propanoic acid] (MDP), antihypertensive drug, with calf thymus DNA (ct-DNA) was investigated by spectroscopic and viscometric techniques. According to the results arising from the fluorescence spectra, viscosity measurements and molecular modeling studies; we concluded that MDP is a minor groove binder of ct-DNA and preferentially binds to AT rich regions. Ethidium bromide (EB) displacement studies revealed that MDP did not have any effect on EB bound DNA which is indicative of groove binding. This was substantiated by displacement studies with Hoechst 33258, a known minor groove binder. In addition, the thermodynamic and docking parameters showed that hydrophobic interaction via drug aromatic rings inside the DNA minor groove plays a major role in this binding. PMID:24322393

  10. Molecular modelling, spectroscopic characterization and biological studies of tetraazamacrocyclic metal complexes

    NASA Astrophysics Data System (ADS)

    Rathi, Parveen; Sharma, Kavita; Singh, Dharam Pal

    2014-09-01

    Macrocyclic complexes of the type [MLX]X2; where L is (C30H28N4), a macrocyclic ligand, M = Cr(III) and Fe(III) and X = Cl-, CH3COO- or NO3-, have been synthesized by template condensation reaction of 1,8-diaminonaphthalene and acetylacetone in the presence of trivalent metal salts in a methanolic medium. The complexes have been formulated as [MLX]X2 due to 1:2 electrolytic nature of these complexes. The complexes have been characterized with the help of elemental analyses, molar conductance measurements, magnetic susceptibility measurements, electronic, infrared, far infrared, Mass spectral studies and molecular modelling. Molecular weight of these complexes indicates their monomeric nature. On the basis of all these studies, a five coordinated square pyramidal geometry has been proposed for all these complexes. These metal complexes have also been screened for their in vitro antimicrobial activities.

  11. [Spectroscopic study of diazepam molecularly imprinted polymers and initiative application to conductimetric sensor based on molecularly imprinted films].

    PubMed

    Liu, Xiao-fang; Li, Feng; Yao, Bing; Wang, Li; Liu, Guo-yan; Chai, Chun-yan

    2010-08-01

    The molecularly imprinted polymers were synthesized using diazepam as the template and molecularly imprinted films (MIF) prepared on screen printed electrodes (SPE). The binding mechanism and recognition characteristics of the molecularly imprinted polymers were studied by ultraviolet (UV) spectra and infrared (IR) spectra. In addition, a conductimetric sensor for diazepam was established preliminarily based on diazepam MIF modified SPE. The results of UV spectra indicated that template molecules and functional monomers had formed 1:2 hydrogen bonding complexes; the results of IR spectra showed that there were some functional groups in the molecularly imprinted polymers which could interact with the template molecules. The molecularly imprinted polymers manifested highly recognition to diazepam. The response of the conductimetric sensor to the concentration of diazepam displayed a linear correlation over a range of 0.04 to 0.62 mg x L(-1) with a detection limit of 0.008 mg x L(-1). The sensor is suitable for on-the-spot detection of diazepam. PMID:20939345

  12. Spectroscopic and molecular docking studies on the interaction of the drug olanzapine with calf thymus DNA

    NASA Astrophysics Data System (ADS)

    Shahabadi, Nahid; Bagheri, Somayeh

    2015-02-01

    The present study investigated the binding interaction between olanzapine and calf thymus DNA (ct-DNA) using emission, absorption, circular dichroism, viscosity measurements and molecular modeling. Thermodynamic parameters (ΔH < 0 and ΔS < 0) indicated that hydrogen bond and van der Waals play main roles in the binding of the drug to ct-DNA. Spectrophotometric studies of the interaction of olanzapine with DNA have shown that it could bind to ct-DNA (Kb = 2 × 103 M-1). The binding constant is comparable to standard groove binding drugs. Competitive fluorimetric studies with Hoechst 33258 have shown that olanzapine exhibits the ability to displace the DNA-bound Hoechst 33258 indicating that binds strongly in minor groove of DNA helix. Furthermore, the drug induces detectable changes in the CD spectrum of ct-DNA as well as changes in its viscosity. All of the experimental results prove that the groove binding must be predominant. The results obtained from experimental data were in good agreement with molecular modeling studies.

  13. Ab initio molecular orbital and infrared spectroscopic study of the conformation of secondary amides: derivatives of formanilide, acetanilide and benzylamides

    NASA Astrophysics Data System (ADS)

    Ilieva, S.; Hadjieva, B.; Galabov, B.

    1999-09-01

    Ab initio molecular orbital calculations at HF/4-31G level and infrared spectroscopic data for the frequencies are applied to analyse the grouping in a series model aromatic secondary amides: formanilide; acetanilide; o-methylacetanilide; 2,6-dimethylformanilide, 2,6-dimethylacetanilide; N-benzylacetamide and N-benzylformamide. The theoretical and experimental data obtained show that the conformational state of the molecules studied is determined by the fine balance of several intramolecular factors: resonance effect between the amide group and the aromatic ring, steric interaction between various substituents around the -NH-CO- grouping in the aromatic ring, conjugation between the carbonyl bond and the nitrogen lone pair as well as direct field influences inside the amide group.

  14. Spectroscopic studies of the molecular parentage of radical species in cometary comae

    NASA Astrophysics Data System (ADS)

    Lewis, Benjamin; Pierce, Donna; Cochran, Anita

    2015-11-01

    We have observed several comets using an integral-field unit spectrograph (the George and Cynthia Mitchell Spectrograph) on the 2.7m Harlan J. Smith telescope at McDonald Observatory. Full-coma spectroscopic images were obtained for various radical species (C2, C3, CH, CN, NH2). By constructing azimuthal average profiles from the full-coma spectroscopic images we can test Haser model parameters with our observations. The Haser model was used to determine production rates and possible parent lifetimes that would be consistent with the model. By iterating through a large range of possible parents lifetimes, we can see what range of values in which the Haser model is consistent with observations. Also, this type of analysis gives us perspective on how sensitive the model's fit quality is to changes in parent lifetimes. Here, we present the work completed to date, and we compare our results to other comet taxonomic surveys.

  15. Nonlinear vibrational spectroscopic studies of molecular interaction and charging behavior at solid/liquid interfaces

    NASA Astrophysics Data System (ADS)

    Zhang, Luning

    Solid-liquid interfaces have been the focus of different communities of scientists due to its importance in industrial applications and chemical processes in nature. Molecular interactions and surface charges affect the physicochemical properties of these interfaces and a thorough understanding is still lacking now. This thesis describes our work in studying several model solid-liquid interfaces using sum-frequency vibrational spectroscopy. Through the studies of interfacial vibrational spectra, we hope to gain better understanding of molecular interactions in competitive adsorption process and also surface charging behavior at different pH and salt concentrations. We start by studying alcohol-water mixture and the adsorption behavior at both hydrophilic and hydrophobic surfaces. In both cases, alcohol adsorbs preferentially from water. The tendency for water to form strong hydrogen-bonding network is the driving force for preferential adsorption of alcohol. We proposed two different interfacial molecular structures on hydrophilic and hydrophobic surfaces. We move on to study the interaction of pure water with a solid surface. Single crystal alumina is used as a model system. At different pH, the surface can undergo protonation and deprotonation reactions and accumulates surface charge. Both the hydrogen-bonding with water and the surface field created by surface charge can affect interfacial water structure. Combining the information obtained with intensity and phase spectra, we find water molecules have two types of bonding within the interfacial layer: weakly hydrogen-bonded species near 3450 cm-1 that does not flip with switching surface charge, and strongly hydrogen-bonded species at 3200 cm-1 that readily flips with switching surface field. One other system we have studied is nanoporous silica-water interface. We found that signal from interfacial water is reduced due to the porous nature of the film. The water spectral features tell us about the interfacial

  16. Interaction of diuron to human serum albumin: Insights from spectroscopic and molecular docking studies.

    PubMed

    Chen, Huilun; Rao, Honghao; Yang, Jian; Qiao, Yongxiang; Wang, Fei; Yao, Jun

    2016-01-01

    This investigation was undertaken to determine the interaction of diuron with human serum albumin (HSA) was studied by monitoring the spectral behavior of diuron-HSA system. The fluorescence of HSA at 340 nm excited at 230 nm was obviously quenched by diuron due to dynamic collision and the quenching constant was of the order of 10(4) L mol(-1) at 310 K. However, no fluorescence quenching was observed when excited at 280 nm. Thermodynamic investigations revealed that the combination between diuron and HSA was entropy driven by predominantly hydrophobic interactions. The binding of diuron induced the drastic reduction in α-helix conformation and the significant enhancement in β-turn conformation of HSA. In addition, both sites marker competition study and molecular modeling simulation evidenced the binding of diuron to HSA primarily took place in subdomain IIIA (Sudlow's site II). PMID:26671830

  17. Spectroscopic and molecular modeling methods to study the interaction between naphthalimide-polyamine conjugates and DNA.

    PubMed

    Tian, Zhiyong; Huang, Yingying; Zhang, Yan; Song, Lina; Qiao, Yan; Xu, Xuejun; Wang, Chaojie

    2016-05-01

    The effect of polyamine side chains on the interaction between naphthalimide-polyamine conjugates (1-7) and herring sperm DNA was studied by UV/vis absorption and fluorescent spectra under physiological conditions (pH=7.4). The diverse spectral data and further molecular docking simulation in silico indicated that the aromatic moiety of these compounds could intercalate into the DNA base pairs while the polyamine motif might simultaneously locate in the minor groove. The triamine compound 7 can interact more potently with DNA than the corresponding diamine compounds (1-6). The presence of the bulky terminal group in the diamine side chain reduced the binding strength of compound 1 with DNA, compared to other diamine compounds (2-6). In addition, the increasing methylene number in the diamine backbone generally results in the elevated binding constant of compounds-DNA complex. The fluorescent tests at different temperature revealed that the quenching mechanism was a static type. The binding constant and thermodynamic parameter showed that the binding strength and the type of interaction force, associated with the side chains, were mainly hydrogen bonding and hydrophobic force. And the calculated free binding energies of molecular docking are generally consistent with the stability of polyamine-DNA complexes. The circular dichroism assay about the impact of compounds 1-7 on DNA conformation testified the B to A-like conformational change. PMID:26926663

  18. Spectroscopic and molecular modelling studies of binding mechanism of metformin with bovine serum albumin

    NASA Astrophysics Data System (ADS)

    Sharma, Deepti; Ojha, Himanshu; Pathak, Mallika; Singh, Bhawna; Sharma, Navneet; Singh, Anju; Kakkar, Rita; Sharma, Rakesh K.

    2016-08-01

    Metformin is a biguanide class of drug used for the treatment of diabetes mellitus. It is well known that serum protein-ligand binding interaction significantly influence the biodistribution of a drug. Current study was performed to characterize the binding mechanism of metformin with serum albumin. The binding interaction of the metformin with bovine serum albumin (BSA) was examined using UV-Vis absorption spectroscopy, fluorescence, circular dichroism, density functional theory and molecular docking studies. Absorption spectra and fluorescence emission spectra pointed out the weak binding of metformin with BSA as was apparent from the slight change in absorbance and fluorescence intensity of BSA in presence of metformin. Circular dichroism study implied the significant change in the conformation of BSA upon binding with metformin. Density functional theory calculations showed that metformin has non-planar geometry and has two energy states. The docking studies evidently signified that metformin could bind significantly to the three binding sites in BSA via hydrophobic, hydrogen bonding and electrostatic interactions. The data suggested the existence of non-covalent specific binding interaction in the complexation of metformin with BSA. The present study will certainly contribute to the development of metformin as a therapeutic molecule.

  19. Molecular modeling and spectroscopic studies on the interaction of the chiral drug venlafaxine hydrochloride with bovine serum albumin

    NASA Astrophysics Data System (ADS)

    Shahabadi, Nahid; Hadidi, Saba

    2014-03-01

    This study was designed to examine the interaction of racemic antidepressant drug "S,R-venlafaxine hydrochloride (VEN)" with bovine serum albumin (BSA) under physiological conditions. The mechanism of interaction was studied by spectroscopic techniques combination with molecular modeling. Stern-Volmer analysis of fluorescence quenching data shows the presence of the static quenching mechanism. The thermodynamic parameters indicated that the hydrogen bonding and weak van der Waals interactions are the predominant intermolecular forces stabilizing the complex. The number of binding sites (n) was calculated. Through the site marker competitive experiment, VEN was confirmed to be located in subdomain IIIA of BSA. The binding distance (r = 4.93 nm) between the donor BSA and acceptor VEN was obtained according to Förster's non-radiative energy transfer theory. According to UV-vis spectra and CD data binding of VEN leaded to conformational changes of BSA. Molecular docking simulations of S and R-VEN revealed that both isomers have similar interaction and the same binding sites, from this point of view S and R isomers are equal.

  20. Molecular modeling and multi-spectroscopic approaches to study the interaction between antibacterial drug and human immunoglobulin G.

    PubMed

    Wang, Qin; Min, Suotian; Liu, Zhifeng; Zhang, Shengrui

    2016-05-01

    Mechanistic and conformational studies on the interaction of sulfamethoxazole (SMX) with human immunoglobulin G (HIgG) were performed by molecular modeling and multi-spectroscopic methods. The interaction mechanism was firstly predicted through molecular modeling that confirmed the interaction between SMX and HIgG. The binding parameters and thermodynamic parameters at different temperatures had been calculated according to the Stern-Volmer, Scatchard, Sips and Van 't Hoff equations, respectively. Experimental results showed that the fluorescence intensity of HIgG was quenched by the gradual addition of SMX. The binding constants of SMX with HIgG decreased with the increase of temperature, which meant that the quenching mechanism was a static quenching. Meanwhile, the results also confirmed that there was one independent class of binding site on HIgG for SMX during their interaction. The thermodynamic parameters of the reaction, namely standard enthalpy ΔH(0) and entropy ΔS(0) , had been calculated to be -14.69 kJ·mol(-1) and 22.99 J·mol(-1) ·K(-1) , respectively, which suggested that the electrostatic and hydrophobic interactions were the predominant intermolecular forces in stabilizing the SMX-HIgG complex. Furthermore, experimental results obtained from three-dimensional fluorescence spectroscopy, UV-vis absorption spectroscopy and circular dichroism (CD) spectroscopy confirmed that the conformational structure of HIgG was altered in the presence of SMX. Copyright © 2015 John Wiley & Sons, Ltd. PMID:26359789

  1. The molecular structure of chloritoid: a mid-infrared and near-infrared spectroscopic study.

    PubMed

    Li, Kuo; Liu, Qinfu; Cheng, Hongfei; Deng, Yutao; Frost, Ray L

    2015-06-15

    The mineral chloritoid collected from the argillite in the bottom of Yaopo Formation of Western Beijing was characterized by mid-infrared (MIR) and near-infrared (NIR) spectroscopy. The MIR spectra showed all fundamental vibrations including the hydroxyl units, basic aluminosilicate framework and the influence of iron on the chloritoid structure. The NIR spectrum of the chloritoid showed combination (ν+δ)OH bands with the fundamental stretching (ν) and bending (δ) vibrations. Based on the chemical component data and the analysis result from the MIR and NIR spectra, the crystal structure of chloritoid from western hills of Beijing, China, can be illustrated. Therefore, the application of the technique across the entire infrared region is expected to become more routine and extend its usefulness, and the reproducibility of measurement and richness of qualitative information should be simultaneously considered for proper selection of a spectroscopic method for the unit cell structural analysis. PMID:25828887

  2. The molecular structure of chloritoid: A mid-infrared and near-infrared spectroscopic study

    NASA Astrophysics Data System (ADS)

    Li, Kuo; Liu, Qinfu; Cheng, Hongfei; Deng, Yutao; Frost, Ray L.

    2015-06-01

    The mineral chloritoid collected from the argillite in the bottom of Yaopo Formation of Western Beijing was characterized by mid-infrared (MIR) and near-infrared (NIR) spectroscopy. The MIR spectra showed all fundamental vibrations including the hydroxyl units, basic aluminosilicate framework and the influence of iron on the chloritoid structure. The NIR spectrum of the chloritoid showed combination (ν + δ)OH bands with the fundamental stretching (ν) and bending (δ) vibrations. Based on the chemical component data and the analysis result from the MIR and NIR spectra, the crystal structure of chloritoid from western hills of Beijing, China, can be illustrated. Therefore, the application of the technique across the entire infrared region is expected to become more routine and extend its usefulness, and the reproducibility of measurement and richness of qualitative information should be simultaneously considered for proper selection of a spectroscopic method for the unit cell structural analysis.

  3. Theoretical and spectroscopic studies on molecular structure and hydrogen bonding of 2-trifluoroacetylphenol.

    PubMed

    Moosavi-Tekyeh, Zainab; Tayyari, Sayyed Faramarz

    2015-01-25

    The molecular structure, intramolecular hydrogen bonding, and vibrational frequencies of 2-trifluoroacetylphenol (TFAP), were investigated by means of density functional theory (DFT) calculations and NMR, IR, and Raman spectroscopy techniques. The calculated theoretical and observed experimental results were compared with the corresponding data for salicylaldehyde (SA). Calculations were performed at the B3LYP level, using 6-311++G(**) basis set. The observed vibrational frequencies of TFAP were assigned with aid of theoretical calculations. The scaled frequencies at the B3LYP/6-311++G(**) level are in good agreement with the corresponding observed values by acceptable deviations. To investigate the effect of CF3 group on the hydrogen bond strength, the charge distributions, steric effects, and electron delocalization in TFAP and SA are studied using the natural bond orbital (NBO) analysis. The computations were further complemented with an atoms-in-molecules (AIM) topological analysis to characterize the nature of the intramolecular hydrogen bond, IHB, in the considered molecules. The contradiction between experimental and theoretical results was interpreted by considering the opposite effects of steric effect and electron withdrawing nature of CF3 group. PMID:25150433

  4. Spectroscopic study of molecular-hydrogen processes in a mirror-confined plasma

    SciTech Connect

    Moran, T.G. |

    1995-04-01

    Visible and near-ultraviolet molecular hydrogen emission from the Tara Tandem Mirror central cell plasma was investigated in order to determine molecular densities, ionization rates, and continuum dissociation rates. Measurements of H{sub 2} {ital G}{r_arrow}{ital B} band emission were used to infer spatial density and ionization profiles, maximum densities of 4{times}10{sup 12} cm{sup {minus}3} at the gas injection port, and a total molecular ionization rate of 254 A. Continuum emission in the near ultraviolet was identified as the H{sub 2} dissociative continuum through its wavelength distribution, time behavior, and intensity. Wavelength-integrated continuum emission measurements were used to obtain the dissociation rate associated with the continuum: 6 A. The power expended in molecular ionization, dissociation, and radiation is estimated to be 8.4 kW out of 300 kW of rf power injected.

  5. Molecular modeling and spectroscopic studies of semustine binding with DNA and its comparison with lomustine-DNA adduct formation.

    PubMed

    Agarwal, Shweta; Chadha, Deepti; Mehrotra, Ranjana

    2015-01-01

    Chloroethyl nitrosoureas constitute an important family of cancer chemotherapeutic agents, used in the treatment of various types of cancer. They exert antitumor activity by inducing DNA interstrand cross-links. Semustine, a chloroethyl nitrosourea, is a 4-methyl derivative of lomustine. There exist some interesting reports dealing with DNA-binding properties of chloroethyl nitrosoureas; however, underlying mechanism of cytotoxicity caused by semustine has not been precisely and completely delineated. The present work focuses on understanding semustine-DNA interaction to comprehend its anti-proliferative action at molecular level using various spectroscopic techniques. Attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy is used to determine the binding site of semustine on DNA. Conformational transition in DNA after semustine complexation is investigated using circular dichroism (CD) spectroscopy. Stability of semustine-DNA complexes is determined using absorption spectroscopy. Results of the present study demonstrate that semustine performs major-groove-directed DNA alkylation at guanine residues in an incubation-time-drug-concentration-dependent manner. CD spectral outcomes suggest partial transition of DNA from native B-conformation to C-form. Calculated binding constants (Ka) for semustine and lomustine interactions with DNA are 1.53 × 10(3) M(-1) and 8.12 × 10(3) M(-1), respectively. Moreover, molecular modeling simulation is performed to predict preferential binding orientation of semustine with DNA that corroborates well with spectral outcomes. Results based on comparative study of DNA-binding properties of semustine and lomustine, presented here, may establish a correlation between molecular structure and cytotoxicity of chloroethyl nitrosoureas that may be instrumental in the designing and synthesis of new nitrosourea therapeutics possessing better efficacy and fewer side effects. PMID:25350567

  6. "Vibrational spectroscopic analysis and molecular docking studies of (E)-4-methoxy-N‧-(4-methylbenzylidene) benzohydrazide by DFT"

    NASA Astrophysics Data System (ADS)

    Maheswari, R.; Manjula, J.

    2016-07-01

    (E)-4-methoxy-N‧-(4-methylbenzylidene)benzohydrazide (4MN'MBH) a novel, organic, hydrazone Schiff base compound was synthesized and its structure was characterized by Fourier Transform Infrared (4000-400 cm-1), Fourier Transform Raman (3500-50 cm-1), Ultraviolet-Visible (200-800 nm) and 1H and 13C NMR spectroscopic analysis. Optimized molecular structure, vibrational frequencies and corresponding vibrational assignments regarding 4MN'MBH has become screened tentatively as well as hypothetically utilizing Gaussian09Wprogram package. Potential energy distributions of the normal modes of vibrations connected with vibrations are generally accomplished by applying VEDA program. Natural Bonding Orbital (NBO) assessment was completed with a reason to clarify charge transfer or conjugative interaction, the intra-molecular-hybridization and delocalization of electron density within the molecule. Electronic transitions were studied employing UV-Visible spectrum and the observed values were compared with theoretical values. 1H and13C NMR spectral assessment had been made with choosing structure property relationship by chemical shifts along with magnetic shielding effects of title compound. The first order hyperpolarizability (β0) and related properties (β, α0 and Δα) of 4MN'MBH were calculated. The computed first order hyperpolarizability commensurate with the documented worth of very similar structure and could be an interesting thing for more experiments on non linear optics. Molecular docking study has been performed by in silico method to analysis their antituberculosis aspects against Enoyl acyl carrier protein reductase (Mycobacterium tuberculosis InhA) protein.

  7. Encapsulation of serotonin in β-cyclodextrin nano-cavities: Fluorescence spectroscopic and molecular modeling studies

    NASA Astrophysics Data System (ADS)

    Chaudhuri, Sudip; Chakraborty, Sandipan; Sengupta, Pradeep K.

    2010-06-01

    Serotonin is a physiologically important biogenic amine, deficiency of which leads to mental disorders such as Alzheimer's disease, schizophrenia, infantile autism, and depression. Both β-cyclodextrin (β-CD) and its chemically substituted synthetic varieties (often possessing enhanced aqueous solubility and improved drug complexing abilities) are finding wide applications as drug delivery vehicles. Here we have studied the encapsulation of serotonin in β-CD and succinyl-2-hydroxypropyl β-cyclodextrin (SHP-β-CD) by exploiting the intrinsic serotonin fluorescence. Enhanced fluorescence emission intensity (which increases by ˜18% and 34% in β-CD and SHPβ-CD respectively) and anisotropy ( r) ( r = 0.075 and 0.1 in β-CD and SHPβ-CD respectively) are observed in presence of the cyclodextrins. From the fluorescence data host-guest interaction with 1:1 stoichiometry is evident, the association constants ( K) being 126.06 M -1 and 461.62 M -1 for β-CD and SHPβ-CD respectively. Additionally, molecular docking and semiempirical calculations have been carried out which provide, for the first time, detailed insights regarding the encapsulation process. In particular, it is evident that the indole ring is inserted within the β-CD cavity with the aliphatic amine side chain protruding towards the primary rim of the β-CD cavity. Docking calculations reveal that hydrogen bonding interactions are involved in the formation of the inclusion complex. Semiempirical calculations indicate that formation of the 1:1 inclusion complex is energetically favorable which is consistent with the fluorescence data.

  8. The molecular structure of the phosphate mineral chalcosiderite - A vibrational spectroscopic study

    NASA Astrophysics Data System (ADS)

    Frost, Ray L.; Xi, Yunfei; Scholz, Ricardo; Ribeiro, Carlos Augusto de Brito

    2013-07-01

    The mineral chalcosiderite with formula CuFe6(PO4)4(OH)8ṡ4H2O has been studied by Raman spectroscopy and by infrared spectroscopy. A comparison of the chalcosiderite spectra is made with the spectra of turquoise. The spectra of the mineral samples are very similar in the 1200-900 cm-1 region but strong differences are observed in the 900-100 cm-1 region. The effect of substitution of Fe for Al in chalcosiderite shifts the bands to lower wavenumbers. Factor group analysis (FGA) implies four OH stretching vibrations for both the water and hydroxyl units. Two bands ascribed to water are observed at 3276 and 3072 cm-1. Three hydroxyl stretching vibrations are observed. Calculations using a Libowitzky type formula show that the hydrogen bond distances of the water molecules are 2.745 and 2.812 Å which are considerably shorter than the values for the hydroxyl units 2.896, 2.917 and 2.978 Å. Two phosphate stretching vibrations at 1042 and 1062 cm-1 in line with the two independent phosphate units in the structure of chalcosiderite. Three bands are observed at 1102, 1159 and 1194 cm-1 assigned to the phosphate antisymmetric stretching vibrations. FGA predicts six bands but only three are observed due to accidental degeneracy. Both the ν2 and ν4 bending regions are complex. Four Raman bands observed at 536, 580, 598 and 636 cm-1 are assigned to the ν4 bending modes. Raman bands at 415, 420, 475 and 484 cm-1are assigned to the phosphate ν2 bending modes. Vibrational spectroscopy enables aspects of the molecular structure of chalcosiderite to be assessed.

  9. The molecular structure of the phosphate mineral chalcosiderite--a vibrational spectroscopic study.

    PubMed

    Frost, Ray L; Xi, Yunfei; Scholz, Ricardo; Ribeiro, Carlos Augusto de Brito

    2013-07-01

    The mineral chalcosiderite with formula CuFe6(PO4)4(OH)8·4H2O has been studied by Raman spectroscopy and by infrared spectroscopy. A comparison of the chalcosiderite spectra is made with the spectra of turquoise. The spectra of the mineral samples are very similar in the 1200-900 cm(-1) region but strong differences are observed in the 900-100 cm(-1) region. The effect of substitution of Fe for Al in chalcosiderite shifts the bands to lower wavenumbers. Factor group analysis (FGA) implies four OH stretching vibrations for both the water and hydroxyl units. Two bands ascribed to water are observed at 3276 and 3072 cm(-1). Three hydroxyl stretching vibrations are observed. Calculations using a Libowitzky type formula show that the hydrogen bond distances of the water molecules are 2.745 and 2.812 Å which are considerably shorter than the values for the hydroxyl units 2.896, 2.917 and 2.978 Å. Two phosphate stretching vibrations at 1042 and 1062 cm(-1) in line with the two independent phosphate units in the structure of chalcosiderite. Three bands are observed at 1102, 1159 and 1194 cm(-1) assigned to the phosphate antisymmetric stretching vibrations. FGA predicts six bands but only three are observed due to accidental degeneracy. Both the ν2 and ν4 bending regions are complex. Four Raman bands observed at 536, 580, 598 and 636 cm(-1) are assigned to the ν4 bending modes. Raman bands at 415, 420, 475 and 484 cm(-1)are assigned to the phosphate ν2 bending modes. Vibrational spectroscopy enables aspects of the molecular structure of chalcosiderite to be assessed. PMID:23602955

  10. Vibrational spectroscopic and molecular docking study of 4-Methylphenylquinoline-2-carboxylate

    NASA Astrophysics Data System (ADS)

    Fazal, E.; Panicker, C. Yohannan; Varghese, Hema Tresa; Nagarajan, S.; Sudha, B. S.; War, Javeed Ahamad; Srivastava, S. K.; Harikumar, B.; Anto, P. L.

    2015-05-01

    FT-IR and FT-Raman spectra of 4-Methylphenylquinoline-2-carboxylate were recorded and analyzed. The structure of the molecule has been optimized and structural characteristics have been determined by density functional theory. The geometrical parameters (DFT) are in agreement with the XRD results. HOMO and LUMO and other chemical properties are reported. Nonlinear optical properties are also reported. A detailed molecular picture of the title compound and its interactions were obtained from NBO analysis. The negative (red and yellow) regions of the MEP are related to electrophilic reactivity and the positive (blue) regions to nucleophilic reactivity, as shown in the MEP plot and the carbonyl group and the phenyl rings are observed as electrophilic. PASS analysis predicts that the 4-Methylphenylquinoline-2-carboxylate might exhibit anti-diabetic activity. Molecular docking results suggest that the compound might exhibit inhibitory activity against GPb.

  11. Molecular structure, spectroscopic and DFT computational studies on 4,5-bis(tert-butylsulfanyl)phthalonitrile

    NASA Astrophysics Data System (ADS)

    Tanak, H.

    2015-06-01

    The molecular geometry, vibrational frequencies and gauge including atomic orbital (GIAO) 1H and 13C NMR chemical shift values of 4,5-bis(tert-butylsulfanyl)phthalonitrile in the ground state were calculated using the density functional method (B3LYP) with 6-311++G(d,p) basis set. The calculated results show that the optimized geometry can well reproduce the crystal structure, and the theoretical vibrational frequencies and chemical shift values show good agreement with experimental values. To investigate the NLO properties of the title compound, the electric dipole moment (μ), the polarizability (α) and the first hyperpolarizability (β) were calculated using the density functional B3LYP method with the 6-311++G(d,p) basis set. For the results, the title compound shows nonzero (β) value revealing second order NLO behavior. The molecular electrostatic potential (MEP) at the B3LYP/6-311++G(d,p) basis optimized geometry has also been calculated to predict reactive sites for electrophilic or nucleophilic attack for the title compound.

  12. Spectroscopic study on deuterated benzenes. I. Microwave spectra and molecular structure in the ground state

    SciTech Connect

    Kunishige, Sachi; Katori, Toshiharu; Baba, Masaaki; Nakajima, Masakazu; Endo, Yasuki

    2015-12-28

    We observed microwave absorption spectra of some deuterated benzenes and accurately determined the rotational constants of all H/D isotopomers in the ground vibrational state. Using synthetic analysis assuming that all bond angles are 120°, the mean bond lengths were obtained to be r{sub 0}(C–C) = 1.3971 Å and r{sub 0}(C–H) = r{sub 0}(C–D) = 1.0805 Å. It has been concluded that the effect of deuterium substitution on the molecular structure is negligibly small and that the mean bond lengths of C–H and C–D are identical unlike small aliphatic hydrocarbons, in which r{sub 0}(C–D) is about 5 mÅ shorter than r{sub 0}(C–H). It is considered that anharmonicity is very small in the C–H stretching vibration of aromatic hydrocarbons.

  13. Synthesis, molecular structure, spectroscopic and theoretical studies on E-2-ethoxy-4-[(4-ethoxyphenylimino)methyl]phenol

    NASA Astrophysics Data System (ADS)

    Zeyrek, Celal Tuğrul; Alpaslan, Gökhan; Alyar, Hamit; Yıldız, Mustafa; Dilek, Nefise; Ünver, Hüseyin

    2015-05-01

    Synthesis, crystallographic characterization, spectroscopic (FT-IR) and density functional modelling studies of a new Schiff base E-2-ethoxy-4-[(4-ethoxyphenylimino)methyl]phenol C17H19NO3 have been reported. The molecular structure obtained from X-ray single-crystal analysis of the investigated compound in the ground state has been compared using Hartree-Fock (HF) and density functional theory (DFT), B3LYP and B1B95 functional with the 6-311++G(d,p) basis set. In addition to the optimized geometrical structures, atomic charges, molecular electrostatic potential (MEP), natural bond orbital (NBO), nonlinear optical (NLO) effects and thermodynamic properties of the compound have been investigated by using DFT calculations. The electronic properties of the title compound in solvent media were also examined using the DFT calculations. The potential energy surface (PES) scans about important torsion angles are performed by using B3LYP/6-311++G (d,p) level of theoretical approximation for the compound. The experimental (FT-IR) and calculated vibrational frequencies (using DFT calculations) of the title compound have been compared. The predicted NLO properties of the compound which calculated by the B3LYP method with 6-31G(d), 6-31+G(d,p), 6-31++G(d,p), 6-311+G(d) and 6-311++G(d,p) basis sets are greater than ones urea. The standard thermodynamic functions were obtained for the title compound with the temperature ranging from 200 to 450 K.

  14. Synthesis and spectroscopic characterization of fluorescent 4-aminoantipyrine analogues: Molecular docking and in vitro cytotoxicity studies

    NASA Astrophysics Data System (ADS)

    Premnath, D.; Mosae Selvakumar, P.; Ravichandiran, P.; Tamil Selvan, G.; Indiraleka, M.; Jannet Vennila, J.

    2016-01-01

    Two substituted aromatic carbonyl compounds (compounds 1 and 2) of 4-aminoantipyrine were synthesized by condensation of fluorine substituted benzoyl chlorides and 4-aminoantipyrine. The structures of synthesized derivatives were established on the basis of UV-Vis, IR, and Mass, 1H, 13C NMR and Fluorescence spectroscopy. Both compounds showed significant fluorescence emission and two broad emission bands were observed in the region at 340 nm and 450 nm on excitation at 280 nm. Theoretically to prove that the molecule has anticancer activity against cervical cancer cells, the compounds were analyzed for molecular docking interactions with HPV16-E7 target protein by Glide protocol. Furthermore, 4-aminoantipyrine derivatives were evaluated for their in vitro cytotoxic activity against human cervical cancer cells (SiHa) by MTT assay. Compound 1 showed two fold higher activity (IC50 = 0.912 μM) over compound 2, and its activity was similar to that of Pazopanib, suggesting that although the two compounds were chemically very similar the difference in substituent on the phenyl moiety caused changes in properties.

  15. IR spectroscopic study of hydroxyl groups of molecular sieves in the fundamental and combination tone regions

    NASA Astrophysics Data System (ADS)

    Löffler, E.; Zscherpel, U.; Peuker, Ch.; Staudte, B.

    1993-03-01

    The fundamental and combination vibrations of hydroxyl groups in zeolites (Y, ZSM-5) and silicoaluminophosphates (SAPO-5, -17, -34) are investigated. The influence of adsorbed molecules (C 6F 6, n-hexane) on the combination vibrations is also studied. Finally, remarks on quantitative evaluation of DRIFT spectra of NaHZSM-5 containing different amounts of bridging OH groups are given.

  16. Infrared spectroscopic studies to understand the effect of drugs at molecular level

    NASA Astrophysics Data System (ADS)

    Singh, Bhawana; Gautam, Rekha; Chandrasekar, Bhagawat; Rakshit, Srabanti; Kumar B. N., Vinay; Boopathy, Sivaraman; Nandi, Dipankar; Somasundaram, Kumaravel; Umapathy, Siva

    2012-06-01

    In the recent past, there have been enormous efforts to understand effect of drugs on human body. Prior to understand the effect of drugs on human body most of the experiments are carried out on cells or model organisms. Here we present our study on the effect of chemotherapeutic drugs on cancer cells and the acetaminophen (APAP) induced hepatotoxicity in mouse model. Histone deacetylase inhibitors (HDIs) have attracted attention as potential drug molecules for the treatment of cancer. These are the chemotherapeutic drugs which have indirect mechanistic action against cancer cells via acting against histone deacetylases (HDAC). It has been known that different HDAC enzymes are over-expressed in various types of cancers for example; HDAC1 is over expressed in prostate, gastric and breast carcinomas. Therefore, in order to optimise chemotherapy, it is important to determine the efficacy of various classes of HDAC inhibitor drugs against variety of over-expressed HDAC enzymes. In the present study, FTIR microspectroscopy has been employed to predict the acetylation and propionylation brought in by HDIs. The liver plays an important role in cellular metabolism and is highly susceptible to drug toxicity. APAP which is an analgesic and antipyretic drug is extensively used for therapeutic purposes and has become the most common cause of acute liver failure (ALF). In the current study, we have focused to understand APAP induced hepatotoxicity using FTIR microspectroscopy. In the IR spectrum the bands corresponding to glycogen, ester group and were found to be suitable markers to predict liver injury at early time point (0.5hr) due to APAP both in tissue and serum in comparison to standard biochemical assays. Our studies show the potential of FTIR spectroscopy as a rapid, sensitive and non invasive detection technique for future clinical diagnosis.

  17. Molecular spectroscopic studies and ab initio calculations of four alcohols derived from 2,2-dimethylpropane

    NASA Astrophysics Data System (ADS)

    Granzow, B.; Klaeboe, P.; Sablinskas, V.

    1995-04-01

    Four alcohols with the formulas C(CH 2OH) x(CH 3) 4- x (x=1,2,3,4) have been investigated by IR and Raman spectroscopy at different temperatures from the crystalline phases to the plastic phases and the melts. Solution spectra in different solvents have also been obtained. The alcohols with the highest vapour pressures, 2,2-dimethyl-1-propanol and 2,2-dimethyl-1,3-propanediol were studied in argon and nitrogen matrices at 4.5 K using the hot nozzle technique. As observed for the corresponding halogenated compounds, the alcohols are expected to have conformational equilibria due to restricted rotations around the C-C bonds in the plastic phases, the melts and in solution. Additional conformers from rotations around the C-O bonds cannot be excluded. The energies and frequencies of the expected conformations were determined by ab initio calculations using a 3-21 G∗ basis set and compared with the experimental values. The data reveal that the {G}/{G} ( C2) conformer is the most stable in 2,2-dimethyl-1,3-propanediol, while in 2-hydroxymethyl-2-methyl-1,3-propanediol the C1 conformer is more stable than both C3 and Cs with enthalpy differences of 2.9 and 3.7 kJ mol -1, respectively.

  18. Molecular structure and vibrational spectroscopic studies of prothionamide by density functional theory

    NASA Astrophysics Data System (ADS)

    Yilmaz, A.; Bolukbasi, O.

    2016-01-01

    Prothionamide (PTH) is the secondary drug used against Mycobacterium tuberculosis bacteria and leprosy. The aim of this work was to investigate the potential energy surface map, anharmonic and harmonic vibrational spectra, NBO analysis and ELF (Electron Localization Function) of the title compound using DFT approach with the B3LYP (Becke, three-parameter, Lee-Yang-Parr) exchange-correlation functional with the 6-31G++(d, p) and the Z3POLX basis sets were employed. In the experimental part of this study, FT-Mid IR, FT-Far IR and FT-Raman spectra of the molecule were recorded in the regions 4000-450 cm-1, 700-30 cm-1 and 4000-100 cm-1 respectively in the solid phase. The comparison between calculated and experimental vibrational spectra (infrared and Raman spectra) and assignments of fundamental vibrational modes were characterized by total energy distribution (TED). Theoretical spectra were seen to be in good agreement with those of the experimental ones.

  19. Molecular structure and vibrational spectroscopic studies of prothionamide by density functional theory.

    PubMed

    Yilmaz, A; Bolukbasi, O

    2016-01-01

    Prothionamide (PTH) is the secondary drug used against Mycobacterium tuberculosis bacteria and leprosy. The aim of this work was to investigate the potential energy surface map, anharmonic and harmonic vibrational spectra, NBO analysis and ELF (Electron Localization Function) of the title compound using DFT approach with the B3LYP (Becke, three-parameter, Lee-Yang-Parr) exchange-correlation functional with the 6-31G++(d,p) and the Z3POLX basis sets were employed. In the experimental part of this study, FT-Mid IR, FT-Far IR and FT-Raman spectra of the molecule were recorded in the regions 4000-450cm(-1), 700-30cm(-1) and 4000-100cm(-1) respectively in the solid phase. The comparison between calculated and experimental vibrational spectra (infrared and Raman spectra) and assignments of fundamental vibrational modes were characterized by total energy distribution (TED). Theoretical spectra were seen to be in good agreement with those of the experimental ones. PMID:26219021

  20. The molecular structure of the phosphate mineral turquoise—a Raman spectroscopic study

    NASA Astrophysics Data System (ADS)

    Frost, Ray L.; Reddy, B. Jagannadha; Martens, Wayde N.; Weier, Matt

    2006-05-01

    Three turquoise minerals of different origins with formula CuAl 6(PO 4) 4(OH) 8·4H 2O have been studied by Raman spectroscopy at 298 and 77 K and by infrared spectroscopy. A comparison of the turquoise spectra is made with the spectra of chalcosiderite. The spectra of the three mineral samples are very similar in the 1200-900 cm -1 region but strong differences are observed in the 900-100 cm -1 region. The effect of substitution of Fe for Al in chalcosiderite shifts the bands to lower wavenumbers. Factor group analysis (FGA) implies four OH stretching vibrations for both the water and hydroxyl units. Two bands ascribed to water are observed at 3276 and 3072 cm -1 at 298 K which becomes four bands at 77 K. Three hydroxyl stretching vibrations are observed in the 298 K spectrum and four in the 77 K spectrum. Calculations using a Libowitzky type formula show that the hydrogen bond distances of the water molecules are 2.735 and 2.665 Å which are considerably shorter than the values for the hydroxyl units 2.909, 2.853 and 2.840 Å. Two phosphate stretching vibrations at 1066 and 1042 cm -1 in line with the two independent phosphate units in the structure of turquoise. Three bands are observed at 1184, 1161 and 1106 cm -1 assigned to the phosphate antisymmetric stretching vibrations. FGA predicts six bands but only three are observed due to accidental degeneracy. Both the ν2 and ν4 bending regions are complex with increased complexity observed in the 77 K spectra.

  1. MOLECULAR OPTICAL SPECTROSCOPIC TECHNIQUES FOR HAZARDOUS WASTE SITE SCREENING

    EPA Science Inventory

    The U.S. Environmental Protection Agency is interested in field screening hazardous waste sites for contaminants in the soil and surface and ground water. his study is an initial technical overview of the principal molecular spectroscopic techniques and instrumentation currently ...

  2. The HITRAN2012 molecular spectroscopic database

    NASA Astrophysics Data System (ADS)

    Rothman, L. S.; Gordon, I. E.; Babikov, Y.; Barbe, A.; Chris Benner, D.; Bernath, P. F.; Birk, M.; Bizzocchi, L.; Boudon, V.; Brown, L. R.; Campargue, A.; Chance, K.; Cohen, E. A.; Coudert, L. H.; Devi, V. M.; Drouin, B. J.; Fayt, A.; Flaud, J.-M.; Gamache, R. R.; Harrison, J. J.; Hartmann, J.-M.; Hill, C.; Hodges, J. T.; Jacquemart, D.; Jolly, A.; Lamouroux, J.; Le Roy, R. J.; Li, G.; Long, D. A.; Lyulin, O. M.; Mackie, C. J.; Massie, S. T.; Mikhailenko, S.; Müller, H. S. P.; Naumenko, O. V.; Nikitin, A. V.; Orphal, J.; Perevalov, V.; Perrin, A.; Polovtseva, E. R.; Richard, C.; Smith, M. A. H.; Starikova, E.; Sung, K.; Tashkun, S.; Tennyson, J.; Toon, G. C.; Tyuterev, Vl. G.; Wagner, G.

    2013-11-01

    This paper describes the status of the 2012 edition of the HITRAN molecular spectroscopic compilation. The new edition replaces the previous HITRAN edition of 2008 and its updates during the intervening years. The HITRAN molecular absorption compilation is comprised of six major components structured into folders that are freely accessible on the internet. These folders consist of the traditional line-by-line spectroscopic parameters required for high-resolution radiative-transfer codes, infrared absorption cross-sections for molecules not yet amenable to representation in a line-by-line form, ultraviolet spectroscopic parameters, aerosol indices of refraction, collision-induced absorption data, and general tables such as partition sums that apply globally to the data. The new HITRAN is greatly extended in terms of accuracy, spectral coverage, additional absorption phenomena, and validity. Molecules and isotopologues have been added that address the issues of atmospheres beyond the Earth. Also discussed is a new initiative that casts HITRAN into a relational database format that offers many advantages over the long-standing sequential text-based structure that has existed since the initial release of HITRAN in the early 1970s.

  3. The HITRAN 2008 Molecular Spectroscopic Database

    NASA Technical Reports Server (NTRS)

    Rothman, Laurence S.; Gordon, Iouli E.; Barbe, Alain; Benner, D. Chris; Bernath, Peter F.; Birk, Manfred; Boudon, V.; Brown, Linda R.; Campargue, Alain; Champion, J.-P.; Chance, Kelly V.; Coudert, L. H.; Sung, K.; Toth, R. A.

    2009-01-01

    This paper describes the status of the 2008 edition of the HITRAN molecular spectroscopic database. The new edition is the first official public release since the 2004 edition, although a number of crucial updates had been made available online since 2004. The HITRAN compilation consists of several components that serve as input for radiative-transfer calculation codes: individual line parameters for the microwave through visible spectra of molecules in the gas phase; absorption cross-sections for molecules having dense spectral features, i.e., spectra in which the individual lines are not resolved; individual line parameters and absorption cross sections for bands in the ultra-violet; refractive indices of aerosols, tables and files of general properties associated with the database; and database management software. The line-by-line portion of the database contains spectroscopic parameters for forty-two molecules including many of their isotopologues.

  4. Ultrasonic promoted synthesis of novel s-triazine-Schiff base derivatives; molecular structure, spectroscopic studies and their preliminary anti-proliferative activities

    NASA Astrophysics Data System (ADS)

    El-Faham, Ayman; Soliman, Saied M.; Ghabbour, Hazem A.; Elnakady, Yasser A.; Mohaya, Talal A.; Siddiqui, Mohammed R. H.; Albericio, Fernando

    2016-12-01

    Novel series of s-triazine-Schiff base derivatives were synthesized employing ultrasonic irradiation and characterized by NMR (1H and 13C), FT-IR, and elemental analysis. The use of ultrasonic irradiation has allowed the preparation of the target products with better yields in shorter reaction time and excellent purities compared to the conventional heating. X-ray single crystal diffraction experiments verified the molecular structure of four from the new prepared s-triaizne-Schiff base derivatives. The molecular structures of the studied compounds are computerized using DFT/B3LYP method. The effects of substituent at the triazine and phenyl ring on the electronic and spectroscopic properties of the studied compounds were also investigated. The natural atomic charges showed that pipridino-s-triazine derivatives are richer in electrons than those having morpholino derivatives. The anti-proliferative effects for the prepared compounds were tested against three different cancer cell lines.

  5. Ground and excited state proton transfer of the bioactive plant flavonol robinetin in a protein environment: spectroscopic and molecular modeling studies.

    PubMed

    Pahari, Biswa Pathik; Chaudhuri, Sudip; Chakraborty, Sandipan; Sengupta, Pradeep K

    2015-02-12

    We performed spectroscopic and molecular modeling studies to explore the interaction of the bioactive plant flavonol robinetin (3,7,3',4',5'-OH flavone), with the carrier protein human serum albumin (HSA). Multiparametric fluorescence sensing, exploiting the intrinsic "two color" fluorescence of robinetin (comprising excited state intramolecular proton transfer (ESIPT) and charge transfer (CT) emissions) reveals that binding to HSA significantly affects the emission and excitation profiles, with strongly blue-shifted (∼29 nm) normal fluorescence and remarkable increase in the ESIPT fluorescence anisotropy (r) and lifetime (τ). Flavonol-induced HSA (tryptophan) fluorescence quenching data yield the dynamic quenching constant (KD) as 5.42 × 10(3) M(-1) and the association constant (Ks) as 5.59 × 10(4) M(-1). Time-resolved fluorescence anisotropy decay studies show dramatic (∼170 times) increase in the rotational correlation time (τ(rot)), reflecting greatly enhanced restrictions in motion of robinetin in the protein matrix. Furthermore, prominent induced circular dichroism (ICD) bands appear, indicating that the chiral environment of HSA strongly perturbs the electronic transitions of the intrinsically achiral robinetin molecule. Molecular docking calculations suggest that robinetin binds in subdomain IIA of HSA, where specific interactions with basic residues promote ground state proton abstraction and stabilize an anionic species, which is consistent with spectroscopic observations. PMID:25313717

  6. Spectroscopic studies and molecular orbital calculations of charge transfer complexation between 3,5-dimethylpyrazole with DDQ in acetonitrile

    NASA Astrophysics Data System (ADS)

    Habeeb, Moustafa M.; Al-Attas, Amirah S.; Al-Raimi, Doaa S.

    2015-05-01

    Charge transfer (CT) interaction between 3,5-dimethylpyrazole (DMP) with the π-acceptor 2,3-dichloro-5,6-dicyano-p-benzoquinon (DDQ) has been investigated spectrophotometrically in acetonitrile (AN). Simultaneous reddish brown color has been observed upon mixing donor with acceptor solutions attributing to CT complex formation. The electronic spectra of the formed complex exhibited multi-charge transfer bands at 429, 447, 506, 542 and 589 nm, respectively. Job's method of continuous variations and spectrophotometric titration methods confirmed the formation of the studied complex in 1:2 ratio between DMP and DDQ. Benesi-Hildebrand equation has been applied to calculate the stability constant of the formed complex where it recorded high value supporting formation of stable complex. Molecular orbital calculations using MM2 method and GAMESS (General Atomic and Molecular Electronic Structure System) interface computations as a package of ChemBio3D Ultra12 software were carried out for more analysis of the formed complex in the gas phase. The computational analysis included energy minimisation, stabilisation energy, molecular geometry, Mullikan charges, molecular electrostatic potential (MEP) surfaces of reactants and complex as well as characterization of the higher occupied molecular orbitals (HOMO) and lower unoccupied molecular orbitals (LUMO) surfaces of the complex. A good consistency between experimental and theoretical results has been recorded.

  7. Spectroscopic and microcalorimetric studies on the molecular binding of food colorant acid red 27 with deoxyribonucleic acid.

    PubMed

    Basu, Anirban; Kumar, Gopinatha Suresh

    2016-08-01

    Interaction of the food colorant acid red 27 with double stranded DNA was investigated using spectroscopic and calorimetric methods. Absorbance and fluorescence studies suggested an intimate binding interaction between the dye and DNA. The quantum efficiency value testified an effective energy transfer from the DNA base pairs to the dye molecules. Minor groove displacement assay with Hoechst 33258 revealed that the binding occurs in the minor groove of DNA. Circular dichroism studies revealed that acid red 27 induces moderate conformational perturbations in DNA. Results of calorimetric studies suggested that the complexation process was driven largely by positive entropic contribution with a smaller favorable enthalpy contribution. The equilibrium constant of the binding was calculated to be (3.04 ± 0.09) × 10(4)  M(-1) at 298.15 K. Negative heat capacity value along with the enthalpy-entropy compensation phenomenon established the involvement of dominant hydrophobic forces in the binding process. Differential scanning calorimetry studies presented evidence for an increased thermal stability of DNA on binding of acid red 27. Copyright © 2016 John Wiley & Sons, Ltd. PMID:26846192

  8. Spectroscopic studies of the molecular interactions in n-ethylamines and 2-nitropropane/n-ethylamine mixtures.

    PubMed

    Gobin, Cédric; Marteau, Philippe; Petitet, Jean-Pierre

    2004-01-01

    New experimental results are reported on molecular interactions in the n-ethylamines and 2-nitropropane (2-NP)/n-ethylamine mixtures studied by Raman spectroscopy under pressure in a diamond anvil cell (0-50 GPa) and, at ambient pressure, by infrared spectroscopy. Modifications of the infrared spectra in 2-NP in presence of triethylamine (TEA) or diethylamine (DEA) have been observed at ambient pressure and interpreted as a specific molecular interaction. High-pressure fluorescence in the vicinity of the liquid-solid phase transition of the 2-NP/DEA and 2-NP/monoethylamine mixtures, is highlighted and discussed. PMID:14670495

  9. Spectroscopic studies of the molecular interactions in n-ethylamines and 2-nitropropane/ n-ethylamine mixtures

    NASA Astrophysics Data System (ADS)

    Gobin, Cédric; Marteau, Philippe; Petitet, Jean-Pierre

    2004-01-01

    New experimental results are reported on molecular interactions in the n-ethylamines and 2-nitropropane (2-NP)/ n-ethylamine mixtures studied by Raman spectroscopy under pressure in a diamond anvil cell (0-50 GPa) and, at ambient pressure, by infrared spectroscopy. Modifications of the infrared spectra in 2-NP in presence of triethylamine (TEA) or diethylamine (DEA) have been observed at ambient pressure and interpreted as a specific molecular interaction. High-pressure fluorescence in the vicinity of the liquid-solid phase transition of the 2-NP/DEA and 2-NP/monoethylamine mixtures, is highlighted and discussed.

  10. Surfactants induced release of a red emitting dye from the nanocavity of a molecular container: A spectroscopic and calorimetric study.

    PubMed

    Ahmed, Sayeed Ashique; Chatterjee, Aninda; Maity, Banibrata; Seth, Debabrata

    2016-08-01

    Supramolecular interaction of a red emitting dye Nile blue A (NBA) with Cucurbit[7]uril (CB7) in aqueous solution was studied and the release of the dye from the hydrophobic cavity of CB7 was reported. To investigate the supramolecular host-guest complex formation and release of dye, we have used the steady state absorption, fluorescence and time resolved fluorescence emission spectroscopy, (1)H NMR spectroscopy and isothermal titration calorimetry (ITC). The spectral properties of NBA were changed in the presence of CB7. The change in spectral features of NBA in presence of CB7 indicates the formation of supramolecular host-guest complexes. By using the SED equation the diameter of the complex was estimated. The complex formation further affirmed by the (1)H NMR study. Upfield and downfield shifts of the protons of NBA was observed in both the aliphatic and aromatic region. From the ITC measurement, we have drawn up the forces involved for the complexation of NBA with CB7. We have studied the release of NBA from the hydrophobic cavity of CB7 by using ionic, neutral surfactants and ionic liquid with the help of spectroscopic and calorimetric techniques. It is observed that on addition of SDS and ionic liquid (

  11. Spectroscopic study of sprites

    NASA Astrophysics Data System (ADS)

    Kanmae, Takeshi

    Optical emissions from sprites--large electric discharges in the mesosphere caused by intense lightning strokes--have been studied for decades. Studies have identified that sprite emissions are primarily composed of molecular band emissions of nitrogen and notably identified the near ultraviolet and blue emission from the N2+ First Negative system, which provided direct evidence of ionization in sprites. This implies that further evidence of the ionization may be provided by the visible and near infrared emission from the N2+ Meinel system, which is more accessible from ground-based platforms, though anticipated strong quenching in the mesosphere and below have made the presence of the emission somewhat controversial. To investigate the presence of the Meinel emission along the vertical extent of sprites, we made ground-based spectral observations in 2005. The observed spectra were mainly composed of the N2 First Positive system, and no or little indication of the Meinel bands were found. This study suggests that the quenching is indeed severe at sprite altitude, and it is difficult to study the ionization process in sprites via the Meinel emission. In addition, the data allowed us to investigate details of the First Positive emission from sprites. The observed First Positive spectra showed that the vibrational distribution of the upper state varies along the vertical extent of sprites, which is in agreement with previous reports, and furthermore this study indicates that the variation is associated with altitude, implying that collisional energy transfer processes play roles in exciting the First Positive emission, particularly at lower altitudes. Recent high-speed imaging observations have revealed the very dynamic nature of sprites: they develop within a few to 10 ms in forms of streamers and columnar glows. The underlying electron energies in these features have been inferred from their emissions in previous measurements, but they lacked either sufficient

  12. The relationship between molecular structure and biological activity of alkali metal salts of vanillic acid: Spectroscopic, theoretical and microbiological studies

    NASA Astrophysics Data System (ADS)

    Świsłocka, Renata; Piekut, Jolanta; Lewandowski, Włodzimierz

    In this paper we investigate the relationship between molecular structure of alkali metal vanillate molecules and their antimicrobial activity. To this end FT-IR, FT-Raman, UV absorption and 1H, 13C NMR spectra for lithium, sodium, potassium, rubidium and caesium vanillates in solid state were registered, assigned and analyzed. Microbial activity of studied compounds was tested against Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, Proteus vulgaris, Bacillus subtilis and Candida albicans. In order to evaluate the dependence between chemical structure and biological activity of alkali metal vanillates the statistical analysis was performed for selected wavenumbers from FT-IR spectra and parameters describing microbial activity of vanillates. The geometrical structures of the compounds studied were optimized and the structural characteristics were determined by density functional theory (DFT) using at B3LYP method with 6-311++G** as basis set. The obtained statistical equations show the existence of correlation between molecular structure of vanillates and their biological properties.

  13. A CRITICAL STUDY ON THE INTERACTIONS OF HESPERITIN WITH HUMAN HEMOGLOBIN: FLUORESCENCE SPECTROSCOPIC AND MOLECULAR MODELING APPROACH

    PubMed Central

    Chakraborty, Sandipan; Chaudhuri, Sudip; Pahari, Biswapathik; Taylor, Jasmine; Sengupta, Pradeep K.; Sengupta, Bidisha

    2012-01-01

    Hesperitin, a ubiquitous bioactive flavonoid abundant in citrus fruits is known to possess antioxidant, anti-carcinogenic, hypolipidemic, vasoprotective and other important therapeutic properties. Here we have explored the interactions of hesperitin with normal human hemoglobin (HbA), using steady state and time resolved fluorescence spectroscopy, far UV circular dicroism (CD) spectroscopy, combined with molecular modeling computations. Specific interaction of the flavonoid with HbA is confirmed from flavonoid-induced static quenching which is evident from steady state fluorescence as well as lifetime data. Both temperature dependent fluorescence measurements and molecular docking studies reveal that apart from hydrogen bonding and van der Waals interactions, electrostatic interactions also play crucial role in hesperitin-HbA interactions. Furthermore, electrostatic surface potential calculations indicate that the hesperitin binding site in HbA is intensely positive due to the presence of several lysine and histidine residues. PMID:22543928

  14. Spectroscopic and Theoretical Study on the Structures and Dynamics of Functional Molecules - Towards AN Understanding of the Molecular Recognition for Encapsulation Complexes

    NASA Astrophysics Data System (ADS)

    Ebata, Takayuki; Kusaka, Ryoji; Inokuchi, Yoshiya; Xantheas, Sotiris S.

    2011-06-01

    Functional molecules, such as crown ethers and calixarenes, can act as hosts for encapsulating guest species through non-covalent interactions. Applications of crown ethers and calixarenes as molecular receptors, metal cation extraction agents, fluoro-ionophores and phase transfer catalytic media have been previously reported in a number of studies in the literature. One of the important aspects of these host/guest molecular assemblies is their selectivity in the encapsulation of guest species. Two important factors that control this selectivity are: (1) the size and the flexibility of the host cavity and (2) the properties of solvent molecules. Molecular complexes formed in supersonic jets provide ideal systems for the selective study of the conformational preference and micro-solvated effects under solvent-controlled conditions. This talk will review our spectroscopic and theoretical studies of the structures of dibenzo-18-crown-6-ether (DB18C6), benzo-18-crown-6-ether (B18C6), calix[4]arene (C4A) and their complexes with guest molecules. We apply laser-induced fluorescence (LIF), resonance enhanced two-photon ionization (R2PI) and UV-UV hole-burning (HB) spectroscopy for obtaining electronic spectra and IR-UV doubleresonance and IR photodissociation (IRPD) spectroscopy for the IR spectra. The electronic and IR spectra are compared with the corresponding results obtained by DFT calculations and high-level first principles electronic structure calculations [MP2 and CCSD(T)]. Based on these joint studies we can elucidate the nature of interactions that control the encapsulation of a guest molecular species as well as how the host can adjust its conformation to accommodate a specific guest, leading to the molecular recognition.

  15. On the Influence of Crosslinker on Template Complexation in Molecularly Imprinted Polymers: A Computational Study of Prepolymerization Mixture Events with Correlations to Template-Polymer Recognition Behavior and NMR Spectroscopic Studies

    PubMed Central

    Shoravi, Siamak; Olsson, Gustaf D.; Karlsson, Björn C. G.; Nicholls, Ian A.

    2014-01-01

    Aspects of the molecular-level basis for the function of ethylene glycol dimethacrylate and trimethylolproprane trimethacrylate crosslinked methacrylic acid copolymers molecularly imprinted with (S)-propranolol have been studied using a series of all-component and all-atom molecular dynamics studies of the corresponding prepolymerization systems. The crosslinking agents were observed to contribute to template complexation, and the results were contrasted with previously reported template-recognition behavior of the corresponding polymers. Differences in the extent to which the two crosslinkers interacted with the functional monomer were identified, and correlations were made to polymer-ligand recognition behavior and the results of nuclear magnetic resonance spectroscopic studies studies. This study demonstrates the importance of considering the functional monomer–crosslinker interaction when designing molecularly imprinted polymers, and highlights the often neglected general contribution of crosslinker to determining the nature of molecularly imprinted polymer-template selectivity. PMID:24927149

  16. Study on the interaction of the epilepsy drug, zonisamide with human serum albumin (HSA) by spectroscopic and molecular docking techniques

    NASA Astrophysics Data System (ADS)

    Shahabadi, Nahid; Khorshidi, Aref; Moghadam, Neda Hossinpour

    2013-10-01

    In the present investigation, an attempt has been made to study the interaction of zonisamide (ZNS) with the transport protein, human serum albumin (HSA) employing UV-Vis, fluorometric, circular dichroism (CD) and molecular docking techniques. The results indicated that binding of ZNS to HSA caused strong fluorescence quenching of HSA through static quenching mechanism, hydrogen bonds and van der Waals contacts are the major forces in the stability of protein ZNS complex and the process of the binding of ZNS with HSA was driven by enthalpy (ΔH = -193.442 kJ mol-1). The results of CD and UV-Vis spectroscopy showed that the binding of this drug to HSA induced conformational changes in HSA. Furthermore, the study of molecular docking also indicated that zonisamide could strongly bind to the site I (subdomain IIA) of HSA mainly by hydrophobic interaction and there were hydrogen bond interactions between this drug and HSA, also known as the warfarin binding site.

  17. Spectroscopic and molecular simulation studies on the interaction of di-(2-ethylhexyl) phthalate and human serum albumin.

    PubMed

    Wang, Yaping; Zhang, Guowen

    2015-03-01

    Di-(2-ethylhexyl) phthalate (DEHP) is widely used as a plasticizer in industrial production, but may have a potential health risk. In this study, the binding characteristics of DEHP with human serum albumin (HSA) in aqueous solution at pH 7.4 were determined using UV/vis absorption, fluorescence, Fourier transform infrared (FTIR) spectroscopy and circular dichroism (CD), along with a molecular simulation technique. Analysis of the fluorescence titration data at different temperatures suggested that the fluorescence quenching mechanism of HSA by DEHP was static. The calculated thermodynamic parameters indicated that hydrophobic forces played a predominant role in formation of the DEHP-HSA complex, but hydrogen bonds could not be omitted. Site marker competitive experiments and denaturation studies showed that the binding of DEHP to HSA primarily took place in subdomain IIA of HSA, and molecular docking results further corroborated the binding sites. The synchronous fluorescence, UV/vis absorption, FTIR and CD spectra revealed that the addition of DEHP induced changes in the secondary structure of HSA. Protein surface hydrophobicity (PSH) tests indicated that DEHP binding to HSA caused an increase in the PSH. Moreover, the effects of some metal ions on the binding constant of DEHP - HSA interaction were also investigated. PMID:24913815

  18. Effect of guanidine hydrochloride and urea on the interaction of 6-thioguanine with human serum albumin: a spectroscopic and molecular dynamics based study.

    PubMed

    Ishtikhar, Mohd; Khan, Anam; Chang, Chih-Kai; Lin, Lilian Tsai-Wei; Wang, Steven S-S; Khan, Rizwan Hasan

    2016-07-01

    6-thioguanine (6-TG) is an antineoplastic, nucleobase guanine, purine analog drug belongs to thiopurine drug-family of antimetabolites. In the present study, we report an experimental approach towards interaction mechanism of 6-TG with human serum albumin (HSA) and examine the chemical stability of HSA in the presence of denaturants such as guanidine hydrochloride (GdnHCl) and urea. Interaction of 6-TG with HSA has been studied by various spectroscopic and spectropolarimeteric methods to investigate what short of binding occurs at physiological conditions. 6-TG binds in the hydrophobic cavity of subdomain IIA of HSA by static quenching mechanism which induces conformation alteration in the protein structure. That helpful for further study of denaturation process where change in secondary structures causes unfolding of protein that also responsible for severance of domain III from rest of the protein part. We have also performed molecular simulation and molecular docking study in the presence of denaturating agents to determine the binding property of 6-TG and the effect of denaturating agents on the structural activity of HSA. We had found that GdnHCl is more effective denaturating agent when compared to urea. Hence, this study provides straight evidence of the binding mechanism of 6-TG with HSA and the formation of intermediate or unfolding transition that causes unfolding of HSA. PMID:26208966

  19. Spectroscopic [FT-IR and FT-Raman] and molecular modeling (MM) study of benzene sulfonamide molecule using quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Vinod, K. S.; Periandy, S.; Govindarajan, M.

    2016-07-01

    The spectroscopic and molecular modeling (MM) study includes, FT-IR, FT-Raman and 13C NMR and 1H NMR spectra of the Benzene sulfonamide were recorded for the analysis. The observed experimental and theoretical frequencies (IR and Raman) were assigned according to their distinctive region. The present study of this title molecule have been carried out by hybrid computational calculations of HF and DFT (B3LYP) methods with 6-311+G(d,p) and 6-311++G(d,p) basis sets and the corresponding results are tabulated. The structural modifications of the compound due to the substitutions of NH2 and SO2 were investigated. The minimum energy conformers of the compound were studied using conformational analysis. The alternations of the vibrational pattern of the base structure related to the substitutions were analyzed. The thermodynamic parameters (such as zero-point vibrational energy, thermal energy, specific heat capacity, rotational constants, entropy, and dipole moment) of Benzene sulfonamide have been calculated. The donor acceptor interactions of the compound and the corresponding UV transitions are found out using NBO analysis. The NMR spectra were simulated by using the gauge independent atomic orbital (GIAO) method with B3LYP methods and the 6-311++G(d,p) basis set and their spectra were simulated and the chemical shifts related to TMS were compared. A quantum computational study on the electronic and optical properties absorption wavelengths, excitation energy, dipole moment and frontier molecular orbital energies, were performed by HF and DFT methods. The energy gap of the present compound was calculated related to HOMO and LUMO energies which confirm the occurring of charge transformation between the base and ligand group. Besides frontier molecular orbitals (FMO), molecular electrostatic potential (MEP) was performed. The thermodynamic properties (heat capacity, entropy, and enthalpy) of the title compound at different temperatures were calculated in gas phase and

  20. Interaction of meropenem with 'N' and 'B' isoforms of human serum albumin: a spectroscopic and molecular docking study.

    PubMed

    Rehman, Md Tabish; Ahmed, Sarfraz; Khan, Asad U

    2016-09-01

    Carbapenems are used to control the outbreak of β-lactamases expressing bacteria. The effectiveness of drugs is influenced by its interaction with human serum albumin (HSA). Strong binding of carbapenems to HSA may lead to decreased bioavailability of the drug. The non-optimal drug dosage will provide a positive selection pressure on bacteria to develop resistance. Here, we investigated the interaction between meropenem and HSA at physiological pH 7.5 (N-isoform HSA) and non-physiological pH 9.2 (B-isoform HSA). Results showed that meropenem quenches the fluorescence of both 'N' and 'B' isoforms of HSA (ΔG < 0 and binding constant ~10(4) M(-1)). Electrostatic interactions and van der Waal interactions along with H-bonds stabilized the complex of meropenem with 'N' and 'B' isoforms of HSA, respectively. Molecular docking results revealed that meropenem binds to HSA near Sudlow's site II (subdomain IIIA) close to Trp-214 with a contribution of a few residues of subdomain IIA. CD spectroscopy showed a change in the conformation of both the isoforms of HSA upon meropenem binding. The catalytic efficiency of HSA (only N-isoform) on p-nitrophenyl acetate was increased primarily due to a decrease in Km and an increase in kcat values. This study provides an insight into the molecular basis of interaction between meropenem and HSA. PMID:26372227

  1. Spectroscopic and molecular docking studies on the interaction between N-acetyl cysteine and bovine serum albumin.

    PubMed

    Jahanban-Esfahlan, Ali; Panahi-Azar, Vahid; Sajedi, Sanaz

    2015-11-01

    The interaction between N-acetyl cysteine (NAC) and bovine serum albumin (BSA) was investigated by UV-vis, fluorescence spectroscopy, and molecular docking methods. Fluorescence study at three different temperatures indicated that the fluorescence intensity of BSA was reduced upon the addition of NAC by the static quenching mechanism. Binding constant (K(b)) and the number of binding sites (n) were determined. The binding constant for the interaction of NAC and BSA was in the order of 10(3) M(-1), and the number of binding sites was obtained to be equal to 1. Enthalpy (ΔH), entropy (ΔS), and Gibb's free energy (ΔG) as thermodynamic values were also achieved by van't Hoff equation. Hydrogen bonding and van der Waals force were the major intermolecular forces in the interaction process and it was spontaneous. Finally, the binding mode and the binding sites were clarified using molecular docking which were in good agreement with the results of spectroscopy experiments. PMID:26139573

  2. Vibrational spectroscopic study of the phosphate mineral kryzhanovskite and in comparison with reddingite-implications for the molecular structure

    NASA Astrophysics Data System (ADS)

    Frost, Ray L.; Scholz, Ricardo; Wang, Lina

    2016-08-01

    We have studied the phosphate mineral kryzhanovskite (Fe3+,Mn2+)3(PO4)2(OH,H2O) which is a member of the phosphoferrite mineral group using a combination of scanning electron microscopy with energy dispersive spectroscopy and Raman and infrared spectroscopy. Chemical analysis shows the presence of P, Mn and Fe and confirms the formula given above. The presence of hydroxyl units in the structure is indicative of ferric iron in the formula that is an oxidised product. Raman spectroscopy coupled with infrared spectroscopy supports the concept of phosphate, hydrogen phosphate and dihydrogen phosphate units in the structure of kryzhanovskite -phosphoferrite. Infrared and Raman bands attributed to water and hydroxyl stretching modes are identified. Vibrational spectroscopy adds useful information to the molecular structure of kryzhanovskite -phosphoferrite.

  3. Spectroscopic and molecular docking studies of binding interaction of gefitinib, lapatinib and sunitinib with bovine serum albumin (BSA).

    PubMed

    Shen, Guo-Feng; Liu, Ting-Ting; Wang, Qi; Jiang, Min; Shi, Jie-Hua

    2015-12-01

    The binding interactions of three kinds of tyrosine kinase inhibitors (TKIs), such as gefitinib, lapatinib and sunitinib, with bovine serum albumin (BSA) were studied using ultraviolet spectrophotometry, fluorescence spectroscopy, circular dichroism (CD), Fourier transform infrared spectroscopy (FT-IR) and molecular docking methods. The experimental results showed that the intrinsic fluorescence quenching of BSA induced by the three TKIs resulted from the formation of stable TKIs-BSA complexes through the binding interaction of TKIs with BSA. The stoichiometry of three stable TKIs-BSA complexes was 1:1 and the binding constants (Kb) of the three TKIs-BSA complexes were in the order of 10(4)M(-1) at 310 K, indicating that there was a strong binding interaction of the three TKIs with BSA. Based on the analysis of the signs and magnitudes of the free energy change (ΔG(0)), enthalpic change (ΔH(0)) and entropic change (ΔS(0)) in the binding process, it can be deduced that the binding process of the three TKIs with BSA was spontaneous and enthalpy-driven process, and the main interaction forces between the three TKIs and BSA were van der Waals force and hydrogen bonding interaction. Moreover, from the results of CD, FT-IR and molecular docking, it can be concluded that there was a significant difference between the three TKIs in the binding site on BSA, lapatinib was located on site II (m) of BSA while gefitinib and sunitinib were bound on site I of BSA, and there were some changes in the BSA conformation when binding three TKIs to BSA but BSA still retains its secondary structure α-helicity. PMID:26555641

  4. Combined docking, molecular dynamics simulations and spectroscopic studies for the rational design of a dipeptide ligand for affinity chromatography separation of human serum albumin.

    PubMed

    Aghaee, Elham; Ghasemi, Jahan B; Manouchehri, Firouzeh; Balalaie, Saeed

    2014-10-01

    A computational approach to designing a peptide-based ligand for the purification of human serum albumin (HSA) was undertaken using molecular docking and molecular dynamics (MD) simulation. A three-step procedure was performed to design a specific ligand for HSA. Based on the candidate pocket structure of HSA (warfarin binding site), a peptide library was built. These peptides were then docked into the pocket of HSA using the GOLD program. The GOLDscore values were used to determine the affinity of peptides for HSA. Consequently, the dipeptide Trp-Trp, which shows a high GOLDscore value, was selected and linked to a spacer arm of Lys[CO(CH2)5NH] on the surface of ECH-lysine sepharose 4 gel. For further evaluation, the Autodock Vina program was used to dock the linked compound into the pocket of HSA. The docking simulation was performed to obtain a first guess of the binding structure of the spacer-Trp-Trp-HSA complex and subsequently analyzed by MD simulations to assess the reliability of the docking results. These MD simulations indicated that the ligand-HSA complex remains stable, and water molecules can bridge between the ligand and the protein by hydrogen bonds. Finally, absorption spectroscopic studies were performed to illustrate the appropriateness of the binding affinity of the designed ligand toward HSA. These studies demonstrate that the designed dipeptide can bind preferentially to the warfarin binding site. PMID:25220335

  5. Nuclear spectroscopic studies

    SciTech Connect

    Bingham, C.R.; Guidry, M.W.; Riedinger, L.L.; Sorensen, S.P.

    1993-02-08

    The Nuclear Physics group at the University of Tennessee, Knoxville is involved in several aspects of heavy-ion physics including both nuclear structure and reaction mechanisms. While our main emphasis is on experimental problems involving heavy-ion accelerators, we have maintained a strong collaboration with several theorists in order to best pursue the physics of our measurements. During the last year we have led several experiments at the Holifield Heavy Ion Research Facility and participated in others at Argonne National Laboratory. Also, we continue to be very active in the collaboration to study ultra-relativistic heavy ion physics utilizing the SPS accelerator at CERN in Geneva, Switzerland and in a RHIC detector R D project. Our experimental work is in four broad areas: (1) the structure of nuclei at high angular momentum, (2) heavy-ion induced transfer reactions, (3) the structure of nuclei far from stability, and (4) ultra-relativistic heavy-ion physics. The results of studies in these particular areas will be described in this document in sections IIA, IIB, IIC, and IID, respectively. Areas (1), (3), and (4) concentrate on the structure of nuclear matter in extreme conditions of rotational motion, imbalance of neutrons and protons, or very high temperature and density. Area (2) pursues the transfer of nucleons to states with high angular momentum, both to learn about their structure and to understand the transfer of particles, energy, and angular momentum in collisions between heavy ions. An important component of our program is the strong emphasis on the theoretical aspects of nuclear structure and reactions.

  6. [Study of interaction between levofloxacin and human serum albumin by multi-spectroscopic and molecular modeling methods].

    PubMed

    Huang, Fang; Dong, Cheng-Yu; Zhang, Li-Yang; Liu, Ying

    2014-04-01

    Levofloxacin (LVFX) is widely used in clinical treatment due to it has a broad spectrum of in vitro activity against Gram-positive and Gram-negative bacteria. Human serum albumin (HSA) is the most abundant protein in plasma and constitutes approximately half of the protein founds in human blood. And more than 90% of the drugs used in people are bound to HSA. So it is commonly used for the investigation of drug-serum albumin interaction because the binding will significantly influence the absorption, distribution, metabolism excretion, stability and toxicity of the drugs. Therefore, detailed investigating the interaction of LVFX with HSA is very important to understand the pharmacokinetic behavior of the LVFX. In this paper, the interaction of LVFX and HSA has been studied fluorescence, UV, Fourier transform infrared (FT-IR) and molecular modeling method. The results indicated that LVFX induced the intrinsic fluorescence quenching of HSA though a static quenching procedure, and the effective binding constants (K(a)) were calculated to be 9.44 x 10(4) L x mol(-1) (294 K) and 2.74 x 10(4) L x mol(-1) (310 K) by used of the Stern-Volmer equation. According to the Vant's Hoff equation, the reaction was characterized by negative enthalpy (deltaH = -59.00 kJ x mol(-1)) and negative entropy (delta S = - 105.38 J x mol(-1) x K(-1)), indicated that the predominant forces in the LVFX-HSA complex were hydrogen bonding and van der Waals forces. By displacement measurements, the specific binding of LVFX in the vicinity of Site I of HSA was clarified. The binding distance of 3.66 nm between Trp214 and HSA was obtained by the Förster theory on resonance energy transfer. Furthermore, the binding details between LVFX and HSA were further confirmed by molecular docking studies, which were consistent with the experimental results. The alternations of protein secondary structure were calculated from FT-IR spectra. Upon formation of LVFX-HSA complexes, the amount of alpha

  7. Molecular structural investigation of adenosine using spectroscopic and quantum computational calculations

    NASA Astrophysics Data System (ADS)

    Bakkiyaraj, D.; Periandy, S.; Xavier, S.

    2016-09-01

    In this study; spectroscopic investigation of adenosine having clinical importance was studied computationally and obtained results were compared with experimental ones. In this scope, geometric optimization and conformational analysis were studied and vibrational spectroscopic properties were studied on the most stable form. NMR and TD-DFT studies on the title compound were conducted with its experimental data. In addition atomic charge distribution, NBO, frontier molecular analysis, thermodynamic analysis and hyperpolarization features were studied.

  8. Molecular modeling and spectroscopic studies on binding of 2,6-bis[4-(4-amino-2-trifluoromethylphenoxy)benzoyl] pyridine to human serum albumin

    NASA Astrophysics Data System (ADS)

    He, Wen-ying; Chen, Hui-juan; Sheng, Fen-ling; Yao, Xiao-jun

    2009-10-01

    BAFP (2,6-bis[4-(4-amino-2-trifluoromethylphenoxy)benzoyl] pyridine), a synthesized polyimide compound, was exploited for the first time to analyze its interaction with human serum albumin (HSA) by molecular modeling, fluorescence and Fourier transform infrared attenuated total reflection spectroscopy (FTIR ATR) with drug concentrations of 3.3 × 10 -6 to 3.0 × 10 -5 mol L -1. Molecular docking was performed to reveal the possible binding mode. The results suggested that BAFP can strongly bind to human serum albumin (HSA) and the primary binding site of BAFP is located in site II of HSA, which is supported by the results from the competitive experiment. The binding constants for the interaction of BAFP with HSA have been evaluated from relevant fluorescence data at different temperatures (296, 303, 310 and 308 K). The alterations of the protein secondary structure in the presence of BAFP in aqueous solution were quantitatively calculated by the evidences from FTIR ATR spectroscopes. The binding process was exothermic and spontaneous, as indicated by the thermodynamic analyses, and the major part of the binding energy is hydrophobic interaction, which is also in good agreement with the results of molecule modeling study. The enthalpy change Δ H0, the free energy change Δ G0 and the entropy change Δ S0 of 296 K were calculated to be -7.75, -27.68 kJ mol -1 and 67.33 J mol -1 K -1, respectively.

  9. Molecular structure investigation and spectroscopic studies on 2,3-difluorophenylboronic acid: A combined experimental and theoretical analysis

    NASA Astrophysics Data System (ADS)

    Karabacak, Mehmet; Kose, Etem; Atac, Ahmet; Ali Cipiloglu, M.; Kurt, Mustafa

    2012-11-01

    This work presents the characterization of 2,3-difluorophenylboronic acid (abbreviated as 2,3-DFPBA, C6H3B(OH)2F2) by quantum chemical calculations and spectral techniques. The spectroscopic properties were investigated by FT-IR, FT-Raman UV-Vis, 1H and 13C nuclear magnetic resonance (NMR) techniques. The FT-IR spectrum (4000-400 cm-1) and the FT-Raman spectrum (3500-10 cm-1) in the solid phase were recorded for 2,3-DFPBA. The 1H and 13C NMR spectra were recorded in DMSO solution. The UV-Vis absorption spectra of the 2,3-DFPBA that dissolved in water and ethanol were recorded in the range of 200-400 nm. There are four possible conformers for this molecule. The computational results diagnose the most stable conformer of the 2,3-DFPBA as the trans-cis form. The structural and spectroscopic data of the molecule were obtained for all four conformers from DFT (B3LYP) with 6-311++G (d,p) basis set calculations. The theoretical wavenumbers were scaled and compared with experimental FT-IR and FT-Raman spectra. The complete assignments were performed on the basis of the experimental results and total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method, interpreted in terms of fundamental modes. We obtained good consistency between experimental and theoretical spectra. 13C and 1H NMR chemical shifts of the molecule were calculated by using the gauge-invariant atomic orbital (GIAO) method. The electronic properties, such as excitation energies, absorption wavelengths, HOMO and LUMO energies, were performed by time-dependent DFT (TD-DFT) approach. Finally the calculation results were analyzed to simulate infrared, Raman, NMR and UV spectra of the 2,3-DFPBA which show good agreement with observed spectra.

  10. Molecular structure investigation and spectroscopic studies on 2,3-difluorophenylboronic acid: a combined experimental and theoretical analysis.

    PubMed

    Karabacak, Mehmet; Kose, Etem; Atac, Ahmet; Ali Cipiloglu, M; Kurt, Mustafa

    2012-11-01

    This work presents the characterization of 2,3-difluorophenylboronic acid (abbreviated as 2,3-DFPBA, C(6)H(3)B(OH)(2)F(2)) by quantum chemical calculations and spectral techniques. The spectroscopic properties were investigated by FT-IR, FT-Raman UV-Vis, (1)H and (13)C nuclear magnetic resonance (NMR) techniques. The FT-IR spectrum (4000-400 cm(-1)) and the FT-Raman spectrum (3500-10 cm(-1)) in the solid phase were recorded for 2,3-DFPBA. The (1)H and (13)C NMR spectra were recorded in DMSO solution. The UV-Vis absorption spectra of the 2,3-DFPBA that dissolved in water and ethanol were recorded in the range of 200-400 nm. There are four possible conformers for this molecule. The computational results diagnose the most stable conformer of the 2,3-DFPBA as the trans-cis form. The structural and spectroscopic data of the molecule were obtained for all four conformers from DFT (B3LYP) with 6-311++G (d,p) basis set calculations. The theoretical wavenumbers were scaled and compared with experimental FT-IR and FT-Raman spectra. The complete assignments were performed on the basis of the experimental results and total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method, interpreted in terms of fundamental modes. We obtained good consistency between experimental and theoretical spectra. (13)C and (1)H NMR chemical shifts of the molecule were calculated by using the gauge-invariant atomic orbital (GIAO) method. The electronic properties, such as excitation energies, absorption wavelengths, HOMO and LUMO energies, were performed by time-dependent DFT (TD-DFT) approach. Finally the calculation results were analyzed to simulate infrared, Raman, NMR and UV spectra of the 2,3-DFPBA which show good agreement with observed spectra. PMID:22902933

  11. Synthesis, vibrational spectroscopic investigations, molecular docking, antibacterial and antimicrobial studies of 5-ethylsulphonyl-2-(p-aminophenyl)benzoxazole

    NASA Astrophysics Data System (ADS)

    Parveen S, Shana; Al-Alshaikh, Monirah A.; Panicker, C. Yohannan; El-Emam, Ali A.; Arisoy, Mustafa; Temiz-Arpaci, Ozlem; Van Alsenoy, C.

    2016-07-01

    The optimized molecular structure, vibrational wavenumbers, corresponding vibrational assignments of 5-ethylsulphonyl-2-(p-aminophenyl)benzoxazole have been investigated experimentally and theoretically based on density functional theory. Synthesis and antibacterial and antimicrobial activities of the title compound were reported. The FT-IR and FT-Raman spectra were recorded in solid phase and the experimental bands were assigned and characterized on the basis of potential energy distribution. The HOMO and LUMO energies show that the charge transfer occur within the molecule. Stability arising from hyperconjugative interactions and charge delocalization were analysed using natural bond orbital analysis. Binding free energy of -9.8 kcal/mol as predicted by docking studies suggests good binding affinity and the inhibitor forms a stable complex with FAK as is evident from the ligand-receptor interactions. The title compound possesses lower activity against Candida albicans with MIC value of 64 μg/ml than the compared reference drugs as fluconazole and amphotericin B and possesses the same activity with value of 64 μg/ml against Candida krusei as the reference drug, fluconazole.

  12. Synthesis, Spectroscopic, Molecular Structure, and Antibacterial Studies of Dibutyltin(IV) Schiff Base Complexes Derived from Phenylalanine, Isoleucine, and Glycine

    PubMed Central

    Singh, Har Lal; Singh, Jangbhadur

    2014-01-01

    New series of organotin(IV) complexes and Schiff bases derived from amino acids have been designed and synthesized from condensation of 1H-indole-2,3-dione, 5-chloro-1H-indole-2,3-dione, and α-amino acids (phenylalanine, isoleucine, and glycine). All compounds are characterized by elemental analyses, molar conductance measurements, and molecular weight determinations. Bonding of these complexes is discussed in terms of their UV-visible, infrared, and nuclear magnetic resonance (1H, 13C, and 119Sn NMR) spectral studies. The results suggest that Schiff bases behave as monobasic bidentate ligands and coordinate with dibutyltin(IV) in octahedral geometry according to the general formula [Bu2Sn(L)2]. Elemental analyses and NMR spectral data of the ligands with their dibutyltin(IV) complexes agree with their proposed distorted octahedral structures. Few representative compounds are tested for their in vitro antibacterial activity against Gram-positive (B. cereus, Staphylococcus spp.) and Gram-negative (E. coli, Klebsiella spp.) bacteria. The results show that the dibutyltin complexes are more reactive with respect to their corresponding Schiff base ligands. PMID:25525422

  13. The molecular structure of the borate mineral szaibelyite MgBO2(OH) - A vibrational spectroscopic study

    NASA Astrophysics Data System (ADS)

    Frost, Ray L.; Scholz, Ricardo; López, Andrés; Belotti, Fernanda Maria

    2015-06-01

    We have studied the borate mineral szaibelyite MgBO2(OH) using electron microscopy and vibrational spectroscopy. EDS spectra show a phase composed of Mg with minor amounts of Fe. Both tetrahedral and trigonal boron units are observed. The nominal resolution of the Raman spectrometer is of the order of 2 cm-1 and as such is sufficient enough to identify separate bands for the stretching bands of the two boron isotopes. The Raman band at 1099 cm-1 with a shoulder band at 1093 cm-1 is assigned to BO stretching vibration. Raman bands at 1144, 1157, 1229, 1318 cm-1 are attributed to the BOH in-plane bending modes. Raman bands at 836 and 988 cm-1 are attributed to the antisymmetric stretching modes of tetrahedral boron. The infrared bands at 3559 and 3547 cm-1 are assigned to hydroxyl stretching vibrations. Broad infrared bands at 3269 and 3398 cm-1 are assigned to water stretching vibrations. Infrared bands at 1306, 1352, 1391, 1437 cm-1 are assigned to the antisymmetric stretching vibrations of trigonal boron. Vibrational spectroscopy enables aspects of the molecular structure of the borate mineral szaibelyite to be assessed.

  14. Elucidating molecular iridium water oxidation catalysts using metal-organic frameworks: a comprehensive structural, catalytic, spectroscopic, and kinetic study.

    PubMed

    Wang, Cheng; Wang, Jin-Liang; Lin, Wenbin

    2012-12-01

    As a new class of porous, crystalline, molecular materials, metal-organic frameworks (MOFs) have shown great promise as recyclable and reusable single-site solid catalysts. Periodic order and site isolation of the catalytic struts in MOFs facilitate the studies of their activities and reaction mechanisms. Herein we report the construction of two highly stable MOFs (1 and 2) using elongated dicarboxylate bridging ligands derived from Cp*Ir(L)Cl complexes (L = dibenzoate-substituted 2,2'-bipyridine, bpy-dc, or dibenzoate-substituted 2-phenylpyridine, ppy-dc) and Zr(6)O(4)(OH)(4)(carboxylate)(12) cuboctahedral secondary building units (SBUs) and the elucidation of water oxidation pathways of the Cp*Ir(L)Cl catalysts using these MOFs. We carried out detailed kinetic studies of Ce(4+)-driven water oxidation reactions (WORs) catalyzed by the MOFs using UV-vis spectroscopy, phosphorescent oxygen detection, and gas chromatographic analysis. These results confirmed not only water oxidation activity of the MOFs but also indicated oxidative degradation of the Cp* rings during the WOR. The (bpy-dc)Ir(H(2)O)(2)XCl (X is likely a formate or acetate group) complex resulted from the oxidative degradation process was identified as a competent catalyst responsible for the water oxidation activity of 1. Further characterization of the MOFs recovered from WORs using X-ray photoelectron, diffuse-reflectance UV-vis absorption, luminescence, and infrared spectroscopies supported the identity of (bpy-dc)Ir(H(2)O)(2)XCl as an active water oxidation catalyst. Kinetics of MOF-catalyzed WORs were monitored by Ce(4+) consumptions and fitted with a reaction-diffusion model, revealing an intricate relationship between reaction and diffusion rates. Our work underscores the opportunity in using MOFs as well-defined single-site solid catalytic systems to reveal mechanistic details that are difficult to obtain for their homogeneous counterparts. PMID:23136923

  15. Spectroscopic and dynamic properties of arachidonoyl serotonin- β-lactoglobulin complex: A molecular modeling and chemometric study.

    PubMed

    Gholami, Samira; Bordbar, Abdol-Khalegh; Akvan, Nadia

    2016-09-01

    UV-Vis absorption data of β-lactoglobulin (BLG) and arachidonoyl serotonin (AA-5HT) in BLG complex were examined and analyzed using chemometrics method. Analysis of the spectral data matrices by using the multivariate curve resolution-alternating least squares (MCR-ALS) algorithm resulted to the pure concentration calculation and spectral profiles resolution of the chemical constituents and the values of (6.433±0.019)×10(4)M(-1), (4.532±0.007)×10(4)M(-1), (3.364±0.010)×10(4)M(-1) and (2.977±0.013)×10(4)M(-1) as estimated equilibrium constants at 288, 293, 298 and 303K, respectively. The number of chemical constituents involved in the interaction which was extracted by PCA method were free and bound BLG. The spontaneity of the binding process and critical role of hydrogen bonding and van der Waals interactions in stabilizing protein-ligand complex have been designated by negative values of Gibbs free energy, entropy and enthalpy changes. Molecular docking study showed that AA-5HT binds to Val(41), Leu(39), Leu(54), Ile(71), Phe(82), Asn(90), Val(92), Phe(105), Met(107), Glu(108) with the free binding energy of -37.478kJ/mol. Computational studies predicted that in spite of serotonin (5HT) which anchors to the outer surface of BLG by hydrogen bonds, AA-5HT is situated in the calyx pose and stayed there during the entire time of simulation. This binding is accompanying with no apparent influence on secondary structure and partially destabilization of tertiary structure of BLG which pointed the suitability of this protein as drug carrier for AA-5HT. PMID:27472903

  16. Vibrational spectroscopic study of fluticasone propionate

    NASA Astrophysics Data System (ADS)

    Ali, H. R. H.; Edwards, H. G. M.; Kendrick, J.; Scowen, I. J.

    2009-03-01

    Fluticasone propionate is a synthetic glucocorticoid with potent anti-inflammatory activity that has been used effectively in the treatment of chronic asthma. The present work reports a vibrational spectroscopic study of fluticasone propionate and gives proposed molecular assignments on the basis of ab initio calculations using BLYP density functional theory with a 6-31G* basis set and vibrational frequencies predicted within the quasi-harmonic approximation. Several spectral features and band intensities are explained. This study generated a library of information that can be employed to aid the process monitoring of fluticasone propionate.

  17. Structure and Dynamics of Antifreeze Protein--Model Membrane Interactions: A Combined Spectroscopic and Molecular Dynamics Study.

    PubMed

    Kar, Rajiv K; Mroue, Kamal H; Kumar, Dinesh; Tejo, Bimo A; Bhunia, Anirban

    2016-02-11

    Antifreeze proteins (AFPs) are the key biomolecules that enable species to survive under subzero temperature conditions. The physiologically relevant activities of AFPs are based on the adsorption to ice crystals, followed by the inhibition of subsequent crystal layer growth of ice, routed with depression in freezing point in a noncolligative manner. The functional attributes governing the mechanism by which AFPs inhibit freezing of body fluids in bacteria, fungi, plants, and fishes are mainly attributed to their adsorption onto the surface of ice within the physiological system. Importantly, AFPs are also known for their application in cryopreservation of biological samples that might be related to membrane interaction. To date, there is a paucity of information detailing the interaction of AFPs with membrane structures. Here, we focus on elucidating the biophysical properties of the interactions between AFPs and micelle models that mimic the membrane system. Micelle model systems of zwitterionic DPC and negatively charged SDS were utilized in this study, against which a significant interaction is experienced by two AFP molecules, namely, Peptide 1m and wfAFP (the popular AFP sourced from winter flounder). Using low- and high-resolution biophysical characterization techniques, such as circular dichroism (CD) and NMR spectroscopy, a strong evidence for the interactions of these AFPs with the membrane models is revealed in detail and is corroborated by in-depth residue-specific information derived from molecular dynamics simulation. Altogether, these results not only strengthen the fact that AFPs interact actively with membrane systems, but also demonstrate that membrane-associated AFPs are dynamic and capable of adopting a number of conformations rendering fluidity to the system. PMID:26785292

  18. Combined matrix isolation IR spectroscopic and ab initio quantum chemical study of the molecular structure of aminomethylphosphinic acid

    NASA Astrophysics Data System (ADS)

    Stepanian, S. G.; Reva, I. D.; Radchenko, E. D.; Latajka, Z.; Wierzejewska, M.; Ratajczak, H.

    1999-06-01

    The molecular structure of 1-methylaminophosphinic acid (AMPA) was investigated with the matrix isolation IR spectroscopy and ab initio calculations performed with RHF, MP2, MP3, MP4(DQ), MP4(SDQ) and MP4(SDTQ) methods. Three pseudopotential basis sets designed as CEP-31G were used in the calculations: Basis Set I-CEP-31G with the d-functions on phosphorus; Basis Set II-CEP-31G with the d-functions on all heavy atoms; Basis Set III-CEP-31G with the d-functions on all heavy atoms and p-functions on hydrogens. Four stable molecular and four stable zwitterion conformers of aminophosphinic acid were found via ab initio calculations. According to the calculations, molecular conformers are always more stable than the zwitterion conformers, irrespective of the basis set size and level of theory. This result is in good agreement with matrix IR spectrum of the AMPA. The presence of the bands of OH stretching and NH 2 bending vibrations and the absence of the bands of POO - and NH 3+ vibrations are the evidence of molecular structure of AMPA in the isolated state. An increased number of vibrational bands is found in the IR spectrum. It is explained by the high conformation lability of AMPA molecules which is related to very low barrier of rotation about C-P bond. The IR spectrum is actually determined by multiple sites of AMPA molecule packed in the Ar crystal, which considerably increases the number of bands in the IR spectrum.

  19. A microwave molecular solution based approach towards high-κ-tantalum(V)oxide nanoparticles: synthesis, dielectric properties and electron paramagnetic resonance spectroscopic studies of their defect chemistry.

    PubMed

    Hoffmann, R C; Kaloumenos, M; Spiehl, D; Erdem, E; Repp, S; Weber, S; Schneider, J J

    2015-12-21

    Stable dispersions of tantalum oxide nanoparticles are accessible from solutions of tantalum(V) complexes with a mixed malonato and alkanolato ligand sphere in ethoxyethanol by microwave processing. The malonato ligand is cleaved during decomposition and acetic acid or acetic acid esters are formed as derived from in situ spectroscopic studies. The solubility of the tantalum precursor and the obtained particle size therefrom depend strongly on the type of alkanolato ligand moiety. Dispersions of the molecular complexes possess good film forming properties. Films with low surface roughness can be obtained by spincoating. These exhibited a dielectric constant of about 15 and disruptive strengths above 1.5 MV cm(-1). The electrical measurements indicate that the presence of moisture is detrimental with respect to the dielectric performance of the films. After removal of the solvent from the suspensions of the nanoparticles, the residue can be redispersed in aprotic solvents. The particles can be isolated therefrom by precipitation with pentane. XRD and HRTEM indicate that the material remains amorphous up to temperatures of 750 °C. XPS proved that only Ta2O5 is formed as lower oxidation states of Ta cannot be detected. A detailed EPR study allows us to gain insight into the surface defect chemistry. Multiple types of oxygen vacancies exist at the surface of the Ta2O5 particles which are influenced by additional calcination and annealing in a vacuum. PMID:26566047

  20. Rich spectroscopic and molecular dynamic studies on the interaction of cytotoxic Pt(II) and Pd(II) complexes of glycine derivatives with calf thymus DNA.

    PubMed

    Eslami Moghadam, Mahboube; Saidifar, Maryam; Divsalar, Adeleh; Mansouri-Torshizi, Hassan; Saboury, Ali Akbar; Farhangian, Hossein; Ghadamgahi, Maryam

    2016-01-01

    Some amino acid derivatives, such as R-glycine, have been synthesized together with their full spectroscopic characterization. The sodium salts of these bidentate amino acid ligands have been interacted with [M(bpy)(H2O)2](NO3)2 giving the corresponding some new complexes with formula [M(bpy)(R-gly)]NO3 (where M is Pt(II) or Pd(II), bpy is 2,2'-bipyridine and R-gly is butyl-, hexyl- and octyl-glycine). Due to less solubility of octyl derivatives, the biological activities of butyl and hexyl derivatives have been tested against chronic myelogenous leukemia cell line, K562. The interaction of these complexes with highly polymerized calf thymus DNA has been extensively studied by means of electronic absorption, fluorescence and other measurements. The experimental results suggest that these complexes positive cooperatively bind to DNA presumably via groove binding. Molecular dynamic results show that the DNA structure is largely maintained its native structure in hexylglycine derivative-water mixtures and at lower temperatures. The simulation data indicates that the more destabilizing effect of butylglycine is induced by preferential accumulation of these molecules around the DNA and due to their more negative free energy of binding via groove binding. PMID:25734364

  1. Synthesis, molecular structure and spectroscopic studies of some new quinazolin-4(3H)-one derivatives; an account on the N- versus S-Alkylation

    NASA Astrophysics Data System (ADS)

    Hagar, Mohamed; Soliman, Saied M.; Ibid, Farahate; El Ashry, El Sayed H.

    2016-03-01

    A new series of N- and S-alkylated products of 3-aryl-1H,3H-quinazolin-2,4-dione and 3-aryl-2-mercapto-3H-quinazolin-4-one, respectively, were prepared in good yields via efficient nucleophilic substitution reaction of the SH and NH substrates with methyl iodide, ethyl bromoacetate, allyl bromide, propagyl bromide, 2-bromoethanol, 1,3-dibromopropane or phenacyl bromide in DMF as a solvent and anhydrous potassium carbonate. The quinazolin-2,4-dione favored the N-alkylation while the 2-mercapto-3H-quinazolin-4-one goes via the S-alkylation. DFT reactivity studies showed that the former have the N-site with higher nucleophilicity compared to the O-site. In contrast, the S-site is the more nucleophilic centre than the N-atom of the latter. The structures of the synthesized products have been established on the basis of their melting point (m.p), IR and 1HNMR data. The molecular structures of the products were calculated using the DFT B3LYP/6-311G(d,p) method. The electronic and spectroscopic properties (Uv-Vis and NMR spectra) were calculated using the same level of theory. The chemical reactivity descriptors that could help to understand the biological activity of the products are also predicted.

  2. The molecular structure of the borate mineral inderite Mg(H4B3O7)(OH)ṡ5H2O - A vibrational spectroscopic study

    NASA Astrophysics Data System (ADS)

    Frost, Ray L.; López, Andrés; Xi, Yunfei; Lima, Rosa Malena Fernandes; Scholz, Ricardo; Granja, Amanda

    2013-12-01

    We have undertaken a study of the mineral inderite Mg(H4B3O7)(OH)ṡ5H2O a hydrated hydroxy borate mineral of magnesium using scanning electron microscopy, thermogravimetry and vibrational spectroscopic techniques. The structure consists of [ soroborate groups and Mg(OH)2(H2O)4 octahedra interconnected into discrete molecules by the sharing of two OH groups. Thermogravimetry shows a mass loss of 47.2% at 137.5 °C, proving the mineral is thermally unstable. Raman bands at 954, 1047 and 1116 cm-1 are assigned to the trigonal symmetric stretching mode. The two bands at 880 and 916 cm-1 are attributed to the symmetric stretching mode of the tetrahedral boron. Both the Raman and infrared spectra of inderite show complexity. Raman bands are observed at 3052, 3233, 3330, 3392 attributed to water stretching vibrations and 3459 cm-1 with sharper bands at 3459, 3530 and 3562 cm-1 assigned to OH stretching vibrations. Vibrational spectroscopy is used to assess the molecular structure of inderite.

  3. Studies on the interaction between promethazine and human serum albumin in the presence of flavonoids by spectroscopic and molecular modeling techniques.

    PubMed

    He, Ling-Ling; Wang, Zhi-Xin; Wang, Yong-Xia; Liu, Xian-Ping; Yang, Yan-Jie; Gao, Yan-Ping; Wang, Xin; Liu, Bin; Wang, Xin

    2016-09-01

    Fluorescence, absorption, time-correlated single photon counting (TCSPC), and circular dichroism (CD) spectroscopic techniques as well as molecular modeling methods were used to study the binding characterization of promethazine (PMT) to human serum albumin (HSA) and the influence of flavonoids, rutin and baicalin, on their affinity. The results indicated that the fluorescence quenching mechanism of HSA by PMT is a static quenching due to the formation of complex. The reaction was spontaneous and mainly mediated by hydrogen bonds and hydrophobic interactions. The binding distance between the tryptophan residue of HSA and PMT is less than 8nm, which indicated that the energy transfer from the tryptophan residue of HSA to PMT occurred. The binding site of PMT on HSA was located in sites I and the presence of PMT can cause the conformational changes of HSA. There was the competitive binding to HSA between PMT and flavonoids because of the overlap of binding sites in HSA. The flavonoids could decrease the association constant and increase the binding distance. In addition, their synergistic effect can further change the conformation of HSA. The decrease in the affinities of PMT binding to HSA in the presence of flavonoids may lead to the increase of free drug in blood, which would affect the transportation or disposition of drug and evoke an adverse or toxic effect. Hence, rationalising dosage and diet regimens should be taken into account in clinical application of PMT. PMID:27315330

  4. Study on the interaction between pelargonidin-3-O-glucoside and bovine serum albumin using spectroscopic, transmission electron microscopy and molecular modeling techniques.

    PubMed

    Li, Shu; Tang, Lin; Bi, Hongna

    2016-03-01

    The aim of this study is to evaluate the binding behavior between pelargonidin-3-O-glucoside (P3G) and bovine serum albumin (BSA) using multi-spectroscopic, transmission electron microscopy (TEM) and molecular docking methods under physiological conditions. Fluorescence spectroscopy and time-resolved fluorescence showed that the fluorescence of BSA could be quenched remarkably by P3G via a static quenching mechanism, and there is a single class of binding site on BSA. In addition, the thermodynamic functions ΔH and ΔS were -21.69 kJ/mol and 24.46 J/mol/K, indicating that an electrostatic interaction was a main acting force. The distance between BSA and P3G was 2.74 nm according to Förster's theory, illustrating that energy transfer occurred. In addition, the secondary structure of BSA changed with a decrease in the α-helix content from 66.2% to 64.0% as seen using synchronous fluorescence, UV/vis, circular dichroism and Fourier transform infrared spectroscopies, whereas TEM images showed that P3G led to BSA aggregation and fibrillation. Furthermore, site marker competitive experiments and molecular docking indicated that P3G could bind with subdomain IIA of BSA. The calculated results of the equilibrium fraction showed that the concentration of free P3G in plasma was high enough to be stored and transported from the circulatory system to its target sites to provide therapeutic effects. PMID:26249529

  5. The molecular structure of the phosphate mineral kidwellite NaFe93+(PO4)6(OH)11ṡ3H2O - A vibrational spectroscopic study

    NASA Astrophysics Data System (ADS)

    Frost, Ray L.; López, Andrés; Theiss, Frederick L.; Scholz, Ricardo; Souza, Larissa

    2014-09-01

    The mineral kidwellite, a hydrated hydroxy phosphate of ferric iron and sodium of approximate formula NaFe93+(PO4)6(OH)11ṡ3H2O, has been studied using a combination of electron microscopy with EDX and vibrational spectroscopic techniques. Raman spectroscopy identifies an intense band at 978 cm-1 and 1014 cm-1. These bands are attributed to the PO43- ν1 symmetric stretching mode. The ν3 antisymmetric stretching modes are observed by a large number of Raman bands. The series of Raman bands at 1034, 1050, 1063, 1082, 1129, 1144 and 1188 cm-1 are attributed to the ν3 antisymmetric stretching bands of the PO43- and HOPO32- units. The observation of these multiple Raman bands in the symmetric and antisymmetric stretching region gives credence to the concept that both phosphate and hydrogen phosphate units exist in the structure of kidwellite. The series of Raman bands at 557, 570, 588, 602, 631, 644 and 653 cm-1are assigned to the PO43- ν2 bending modes. The series of Raman bands at 405, 444, 453, 467, 490 and 500 cm-1 are attributed to the PO43- and HOPO32- ν4 bending modes. The spectrum is quite broad but Raman bands may be resolved at 3122, 3231, 3356, 3466 and 3580 cm-1. These bands are assigned to water stretching vibrational modes. The number and position of these bands suggests that water is in different molecular environments with differing hydrogen bond distances. Infrared bands at 3511 and 3359 cm-1 are ascribed to the OH stretching vibration of the OH units. Very broad bands at 3022 and 3299 cm-1 are attributed to the OH stretching vibrations of water. Vibrational spectroscopy offers insights into the molecular structure of the phosphate mineral kidwellite.

  6. The molecular organization of prenylated flavonoid xanthohumol in DPPC multibilayers: X-ray diffraction and FTIR spectroscopic studies.

    PubMed

    Arczewska, Marta; Kamiński, Daniel M; Górecka, Ewa; Pociecha, Damian; Rój, Edward; Sławińska-Brych, Adrianna; Gagoś, Mariusz

    2013-02-01

    Xanthohumol (XN) is the major prenylated flavonoid found in hop resin. It has attracted considerable attention in recent years due to its wide spectrum of biological activities and the beneficial effect on human health. Since lipid membrane is first target for biologically active compounds, we decided to investigate the influence of XN on the dipalmitoylphosphatidylcholine (DPPC) multibilayers. Interactions of XN with DPPC were investigated as a function of temperature and its concentration by using X-ray diffraction and the ATR-FTIR spectroscopy techniques. The aim of understanding the mechanisms of molecular interactions between XN and DPPC was to indicate the localization of the XN with respect to the membrane and the type of interaction with phospholipids. The results revealed that XN changes the physical properties of the DPPC multibilayers in the form of dry film. A new complex formation between XN and DPPC is reported. The detailed analysis of refraction effect indicates the changes in electron density ratio between hydrophobic and hydrophilic zones of lipid at phase transition. This is in compliance with reported changes in FTIR spectra where at pretransition XN moves from interface region between polar heads to the neighborhood of phosphate groups. PMID:23085000

  7. Molecular structure and spectroscopic analysis of homovanillic acid and its sodium salt - NMR, FT-IR and DFT studies

    NASA Astrophysics Data System (ADS)

    Samsonowicz, M.; Kowczyk-Sadowy, M.; Regulska, E.; Lewandowski, W.

    2014-01-01

    The estimation of the electronic charge distribution in metal complex or salt allows to predict what kind of deformation of the electronic system of ligand would undergo during complexation. It also permits to make more precise interpretation of mechanism by which metals affect the biochemical properties of ligands. The influence of sodium cation on the electronic system of homovanillic acid was studied in this paper. Optimized geometrical structures of studied compounds were calculated by B3LYP/6-311++G** method. Mulliken, MK and ChelpG atomic charges were analyzed. The theoretical NMR and IR spectra were obtained. 1H and 13C NMR as well as FT-IR and FT-Raman spectra of studied compounds were also recorded and analyzed. The calculated parameters are compared with experimental characteristics of these molecules.

  8. From molecular fragments to crystals: a UV Raman spectroscopic study on the mechanism of Fe-ZSM-5 synthesis.

    PubMed

    Fan, Fengtao; Sun, Keju; Feng, Zhaochi; Xia, Haian; Han, Bo; Lian, Yuxiang; Ying, Pinliang; Li, Can

    2009-01-01

    The nucleation process of iron-exchanged zeolite Fe-ZSM-5, from the assembly of distorted tetrahedrally coordinated iron species and silicate rings in the precursor to the final Fe-ZSM-5 crystals, as well as variations in the coordination environment of iron, were studied by UV resonance Raman spectroscopy and complementary techniques.The entire sequence of crystallization events of Fe-ZSM-5 was monitored by UV Raman spectroscopy in combination with HRTEM, UV/Vis spectroscopy, X-ray diffraction patterns, and periodic DFT calculations. Fe-ZSM-5 was synthesized by an organic-free method to avoid signal interference from the organic template in Raman spectra. Framework iron atoms with resonance Raman bands at 516, 1115, and 1165 cm(-1), and a Raman band at 1016 cm(-1) are detected for Fe-ZSM-5. In the early stage of Fe-ZSM-5 synthesis, the precursor contains iron atoms in distorted tetrahedral coordination and five- and six-membered silicate rings. Nucleation by aggregation of the precursor species was monitored by UV Raman spectroscopy based on the resonance Raman effect, and confirmed by periodic DFT calculations. Evolution of iron species on the surface and in the bulk phase was monitored by UV Raman spectroscopy with excitation at 244 and 325 nm, as well as HRTEM. Nucleation takes place first in the core of the amorphous particles, and crystalline nuclei with Fe-ZSM-5 structure are formed in the core by consuming the amorphous shell. Finally the amorphous particles are completely transformed into Fe-ZSM-5 crystals. PMID:19197930

  9. The molecular structure of the phosphate mineral beraunite Fe2+Fe53+(PO4)4(OH)5ṡ4H2O - A vibrational spectroscopic study

    NASA Astrophysics Data System (ADS)

    Frost, Ray L.; López, Andrés; Scholz, Ricardo; Xi, Yunfei; Lana, Cristiano

    2014-07-01

    The mineral beraunite from Boca Rica pegmatite in Minas Gerais with theoretical formula Fe2+Fe53+(PO4)4(OH)5ṡ4H2O has been studied using a combination of electron microscopy with EDX and vibrational spectroscopic techniques. Raman spectroscopy identifies an intense band at 990 cm-1 and 1011 cm-1. These bands are attributed to the PO43- ν1 symmetric stretching mode. The ν3 antisymmetric stretching modes are observed by a large number of Raman bands. The Raman bands at 1034, 1051, 1058, 1069 and 1084 together with the Raman bands at 1098, 1116, 1133, 1155 and 1174 cm-1 are assigned to the ν3 antisymmetric stretching vibrations of PO43- and the HOPO32- units. The observation of these multiple Raman bands in the symmetric and antisymmetric stretching region gives credence to the concept that both phosphate and hydrogen phosphate units exist in the structure of beraunite. The series of Raman bands at 567, 582, 601, 644, 661, 673, and 687 cm-1 are assigned to the PO43- ν2 bending modes. The series of Raman bands at 437, 468, 478, 491, 503 cm-1 are attributed to the PO43- and HOPO32- ν4 bending modes. No Raman bands of beraunite which could be attributed to the hydroxyl stretching unit were observed. Infrared bands at 3511 and 3359 cm-1 are ascribed to the OH stretching vibration of the OH units. Very broad bands at 3022 and 3299 cm-1 are attributed to the OH stretching vibrations of water. Vibrational spectroscopy offers insights into the molecular structure of the phosphate mineral beraunite.

  10. Spectroscopic (FT-IR, FT-Raman, UV, NMR, NBO) investigation and molecular docking study of (R)-2-Amino-1-PhenylEthanol

    NASA Astrophysics Data System (ADS)

    Subashini, K.; Periandy, S.

    2016-08-01

    A systematic spectroscopic study of (R)-2-Amino-1-Phenylethanol was carried out using FT-IR, FT-Raman, NMR and UV analysis. FT-IR (4000-400 cm-1) and FT-Raman (4000-100 cm-1) spectrum of the title molecule were recorded in solid phase, the 1H and 13C NMR spectra were recorded in CDCl3 (deuterated chloroform) solution phase and the UV-Vis (200-800 nm) spectrum was recorded in gas phase and ethanol solution phase. Potential energy surface (PES) scan was performed using B3LYP functional with 6-311++G (d, p) basis set. The geometrical parameters (such as bond length, bond angle, dihedral angles) and theoretical frequencies of the title compound were studied from density functional theory (DFT) using B3LYP and B3PW91 functionals with 6-311++G (d, p) basis sets. The computed frequencies were scaled and compared with the experimental values and potential energy distribution (PED) has been tabulated. A comparative study of atomic charges was made by calculating Mulliken, Natural Population Analysis (NPA) and Electrostatic Potential (ESP) simultaneously, with B3LYP/6-311++G (d, p) basis set. 1H and 13C NMR spectra were recorded and chemical shifts were compared to TMS by Gauge-Independent Atomic Orbital (GIAO) method. Electronic properties such as excitation energy, energy gap between HOMO and LUMO was calculated using time dependent DFT technique. NBO analysis, which predicts the different possibilities of electronic transition in the molecule, was computed using B3PW91 functional with 6-311++G (d, p) basis set. The thermodynamic properties such as heat capacity, entropy and enthalpy at different temperatures were computed and analyzed. Molecular docking study shows that the secondary hydroxyl group and the primary amino group in the aliphatic chain attached to the benzene ring are crucial for binding and the title compound might exhibit inhibitory activity against Bacteroides fragilis (3P24) and may act as anti-bacterial agent.

  11. Quadrupole resonance spectroscopic study of narcotic materials

    NASA Astrophysics Data System (ADS)

    Rayner, Timothy J.; West, Rebecca; Garroway, Allen N.; Lyndquist, R.; Yesinowski, James P.

    1997-02-01

    Bulk narcotic detection systems based upon Quadrupole Resonance Analysis (QRA) technology have a major advantage over imaging technologies, in that QRA is chemical-specific and consequently has a lower rate of false alarms. QRA is a magnetic resonance technology which occurs as a result of the inherent molecular properties of the atomic nuclei in crystalline and amorphous solids. The QRA response is characterized by 1) the precessional frequency of the nucleus, and 2) the nature of the electric field gradient experienced by the nucleus,due to its molecular environment. Another important detection parameter is linewidth, resonant quality. All of these parameters depend on sample purity and manufacturing process. Quantum Magnetics recently carried out a study on the QRA signatures of various narcotic materials with the support of the US Army, US Customs, and the Office of National Drug Control Policy. The aim of the study was to fully characterize the variation in QRA spectroscopic parameters of different samples of cocaine base and cocaine hydrochloride. The results from this study ar discussed here.

  12. Molecular weight, polydispersity, and spectroscopic properties of aquatic humic substances

    USGS Publications Warehouse

    Chin, Y.-P.; Aiken, G.; O'Loughlin, E.

    1994-01-01

    The number- and weight-averaged molecular weights of a number of aquatic fulvic acids, a commercial humic acid, and unfractionated organic matter from four natural water samples were measured by high-pressure size exclusion chromatography (HPSEC). Molecular weights determined in this manner compared favorably with those values reported in the literature. Both recent literature values and our data indicate that these substances are smaller and less polydisperse than previously believed. Moreover, the molecular weights of the organic matter from three of the four natural water samples compared favorably to the fulvic acid samples extracted from similar environments. Bulk spectroscopic properties of the fulvic substances such as molar absorptivity at 280 nm and the E4/E6 ratio were also measured. A strong correlation was observed between molar absorptivity, total aromaticity, and the weight average molecular weights of all the humic substances. This observation suggests that bulk spectroscopic properties can be used to quickly estimate the size of humic substances and their aromatic contents. Both parameters are important with respect to understanding humic substance mobility and their propensity to react with both organic and inorganic pollutants. ?? 1994 American Chemical Society.

  13. Nickel(II) Complexation with Nitrate in Dry [C4mim][Tf2N] Ionic Liquid: A Spectroscopic, Microcalorimetric, and Molecular Dynamics Study.

    PubMed

    Melchior, Andrea; Gaillard, Clotilde; Gràcia Lanas, Sara; Tolazzi, Marilena; Billard, Isabelle; Georg, Sylvia; Sarrasin, Lola; Boltoeva, Maria

    2016-04-01

    The complex formation of nitrate ions with nickel(II) in dry [C4mim][Tf2N] ionic liquid (IL) was investigated by means of UV-visible spectrophotometry, isothermal titration calorimetry (ITC), extended X-ray absorption fine structure spectroscopy (EXAFS), and molecular dynamics (MD) simulations. EXAFS spectroscopy and MD simulations show that the solvated Ni(II) cation is initially coordinated by the oxygens of the [Tf2N](-) anion of IL, which can behave either as mono- or bidentate. Spectroscopic and thermodynamic data show that Ni(II) is able to form up to three stable mononuclear complexes with nitrate in this solvent. The stability constants for Ni(NO3)j complexes (j = 1-3) calculated from spectrophotometry and ITC experiments decrease in the order log K1 > log K2 > log K3. The formation of the first two species is enthalpy-driven, while the third species is entropy-stabilized. The UV-vis spectra of solutions containing different nitrate/Ni(II) ratios show that the metal ion retains the six-coordinate geometry. Furthermore, the EXAFS evidences that nitrate is always bidentate. Molecular dynamics simulations show that the [Tf2N](-) anions bind Ni(II) through the sulfonyl oxygen atoms and can coordinate either as monodentate or chelate. The analysis of the MD data shows that introduction of nitrates in the first coordination sphere of the metal ion results in remarkable structural rearrangement of the ionic liquid. PMID:26999457

  14. Spectroscopic detectability of the molecular Aharonov-Bohm effect

    NASA Astrophysics Data System (ADS)

    Englman, R.

    2016-01-01

    It is theoretically shown that the emission spectra from an excited Jahn-Teller state in which the ions undergo a forced periodic trajectory have an M-shaped form, directly due to the sign change by the Berry-phase factor. The presence of a weak spectral sideline is noted and the effects of a nonlinear vibronic coupling are calculated. Experimental verifications of the results, e.g., on R'-centers in LiF, are proposed. The dip in the M-shaped emission line is a novel, and perhaps unique, spectroscopic manifestation of the "molecular Aharonov-Bohm effect."

  15. Spectroscopic detectability of the molecular Aharonov-Bohm effect.

    PubMed

    Englman, R

    2016-01-14

    It is theoretically shown that the emission spectra from an excited Jahn-Teller state in which the ions undergo a forced periodic trajectory have an M-shaped form, directly due to the sign change by the Berry-phase factor. The presence of a weak spectral sideline is noted and the effects of a nonlinear vibronic coupling are calculated. Experimental verifications of the results, e.g., on R'-centers in LiF, are proposed. The dip in the M-shaped emission line is a novel, and perhaps unique, spectroscopic manifestation of the "molecular Aharonov-Bohm effect." PMID:26772550

  16. Measurement artifacts identified in the UV-vis spectroscopic study of adduct formation within the context of molecular imprinting of naproxen

    NASA Astrophysics Data System (ADS)

    Perez, Martin; Concu, Riccardo; Ornelas, Mariana; Cordeiro, M. Natália D. S.; Azenha, Manuel; Fernando Silva, A.

    2016-01-01

    The ultraviolet-visible spectroscopy has been assessed as a technique for the evaluation of the strength of template-precursor adduct in the development of molecular imprints of the non-steroidal anti-inflammatory drug naproxen (NAP). The commonly employed approach relies on the collection of UV spectra of drug + precursor mixtures at different proportions, the spectra being recorded against blanks containing the same concentration of the precursor. The observation of either blue or red band-shifts and abatement of a major band are routinely attributed to template-precursor adduct formation. Following the described methodology, the precursors 1-(triethoxysilylpropyl)-3-(trimethoxysilylpropyl)-4,5-dihydroimidazolium iodide (AO-DHI+) and 4-(2-(trimethoxysilyl)ethyl)pyridine (PETMOS) provoked a blue-shift and band abatement effect on the NAP spectrum. Molecular dynamics simulations indicated a reasonable affinity between NAP and these precursors (coordination numbers 0.33 for AO-DHI+ and 0.18 for PETMOS), hence showing that NAP-precursor complexation is in fact effective. However, time dependent density functional theory (TD-DFT) calculations of the spectra of both free and precursor-complexed NAP were identical, thus providing no theoretical basis for the complexation-induced effects observed. We realized that the intense spectral bands of AO-DHI+ and PETMOS (at around 265 nm) superimpose partially with the NAP bands, and the apparent "blue-shifting" in the NAP spectra when mixed with AO-DHI + and PETMOS was in this case a spurious effect of the intense background subtraction. Therefore, extreme care must be taken when interpreting other spectroscopic results obtained in a similar fashion.

  17. Measurement artifacts identified in the UV-vis spectroscopic study of adduct formation within the context of molecular imprinting of naproxen.

    PubMed

    Perez, Martin; Concu, Riccardo; Ornelas, Mariana; Cordeiro, M Natália D S; Azenha, Manuel; Silva, A Fernando

    2016-01-15

    The ultraviolet-visible spectroscopy has been assessed as a technique for the evaluation of the strength of template-precursor adduct in the development of molecular imprints of the non-steroidal anti-inflammatory drug naproxen (NAP). The commonly employed approach relies on the collection of UV spectra of drug+precursor mixtures at different proportions, the spectra being recorded against blanks containing the same concentration of the precursor. The observation of either blue or red band-shifts and abatement of a major band are routinely attributed to template-precursor adduct formation. Following the described methodology, the precursors 1-(triethoxysilylpropyl)-3-(trimethoxysilylpropyl)-4,5-dihydroimidazolium iodide (AO-DHI(+)) and 4-(2-(trimethoxysilyl)ethyl)pyridine (PETMOS) provoked a blue-shift and band abatement effect on the NAP spectrum. Molecular dynamics simulations indicated a reasonable affinity between NAP and these precursors (coordination numbers 0.33 for AO-DHI(+) and 0.18 for PETMOS), hence showing that NAP-precursor complexation is in fact effective. However, time dependent density functional theory (TD-DFT) calculations of the spectra of both free and precursor-complexed NAP were identical, thus providing no theoretical basis for the complexation-induced effects observed. We realized that the intense spectral bands of AO-DHI(+) and PETMOS (at around 265 nm) superimpose partially with the NAP bands, and the apparent "blue-shifting" in the NAP spectra when mixed with AO-DHI+ and PETMOS was in this case a spurious effect of the intense background subtraction. Therefore, extreme care must be taken when interpreting other spectroscopic results obtained in a similar fashion. PMID:26458249

  18. The molecular structure of the borate mineral rhodizite (K, Cs)Al4Be4(B, Be)12O28 - A vibrational spectroscopic study

    NASA Astrophysics Data System (ADS)

    Frost, Ray L.; López, Andrés; Xi, Yunfei; Scholz, Ricardo; Souza, Larissa; Lana, Cristiano

    2014-07-01

    We have studied the borate mineral rhodizite (K, Cs)Al4Be4(B, Be)12O28 using a combination of DEM with EDX and vibrational spectroscopic techniques. The mineral occurs as colorless, gray, yellow to white crystals in the triclinic crystal system. The studied sample is from the Antandrokomby Mine, Sahatany valley, Madagascar. The mineral is prized as a semi-precious jewel. Semi-quantitative chemical composition shows a Al, Ca, borate with minor amounts of K, Mg and Cs. The mineral has a characteristic borate Raman spectrum and bands are assigned to the stretching and bending modes of B, Be and Al. No Raman bands in the OH stretching region were observed.

  19. Spectroscopic Studies of Abell Clusters

    NASA Astrophysics Data System (ADS)

    Way, Michael Joseph

    The objectives of this work are to use spectroscopic techniques to accurately categorize galaxies as either HII region star forming galaxies or as Active Galactic Nuclei powered via a black hole, and to use radial velocities and projected positions of galaxies in clusters to obtain the total cluster mass and its distribution. The masses and distributions compare well to X-ray mass measurements. The commonly used Dressler, A., Thompson, I. & Shectman, S. 1985, ApJ, 288, 481 technique for discriminating between Active Galactic Nuclei and HII region galaxies uses the measurement of the equivalent width of the emission lines (OII) 3727 A, H/beta, and (OIII) 5007 A. High quality spectra from 42 galaxies were taken and it is shown that their method is not capable of distinguishing between Active Galactic Nuclei and HII region galaxies. The emission line flux from H/beta, (OIII) 5007 A, (OI) 6300 A, Hα, (NII) 6583 A, and (SII) 6716+6731 A in combination with the method of Veilleux, S. & Osterbrock, D. E. 1987, ApJS, 63, 295 must be used to accurately distinguish between Active Galactic Nuclei and HII region galaxies. Galaxy radial velocities from spectroscopic data and their projected 2-D positions in clusters are used to obtain robust estimates of the total mass and mass distribution in two clusters. The total mass is calculated using the Virial theorem after removing substructure. The mass distribution is estimated via several robust statistical tests for 1-D, 2-D and 3-D structure. It is shown that the derived mass estimates agree well with those found independently from hot X-ray gas emission in clusters.

  20. Synthesis, spectroscopic, molecular orbital calculation, cytotoxic, molecular docking of DNA binding and DNA cleavage studies of transition metal complexes with N-benzylidene-N'-salicylidene-1,1-diaminopropane

    NASA Astrophysics Data System (ADS)

    Al-Mogren, Muneerah M.; Alaghaz, Abdel-Nasser M. A.; Elbohy, Salwa A. H.

    2013-10-01

    Eight mononuclear chromium(III), manganese(II), iron(III), cobalt(II), nickel(II), copper(II), zinc(II) and cadmium(II) complexes of Schiff's base ligand were synthesized and determined by different physical techniques. The complexes are insoluble in common organic solvents but soluble in DMF and DMSO. The measured molar conductance values in DMSO indicate that the complexes are non-electrolytic in nature. All the eight metal complexes have been fully characterized with the help of elemental analyses, molecular weights, molar conductance values, magnetic moments and spectroscopic data. The analytical data helped to elucidate the structure of the metal complexes. The Schiff base is found to act as tridentate ligand using N2O donor set of atoms leading to an octahedral geometry for the complexes around all the metal ions. Quantum chemical calculations were performed with semi-empirical method to find the optimum geometry of the ligand and its complexes. Additionally in silico, the docking studies and the calculated pharmacokinetic parameters show promising futures for application of the ligand and complexes as high potency agents for DNA binding activity. The interaction of the complexes with calf thymus DNA (CT-DNA) has been investigated by UV absorption method, and the mode of CT-DNA binding to the complexes has been explored. Furthermore, the DNA cleavage activity by the complexes was performed. The Schiff base and their complexes have been screened for their antibacterial activity against bacterial strains [Staphylococcus aureus (RCMB010027), Staphylococcus epidermidis (RCMB010024), Bacillis subtilis (RCMB010063), Proteous vulgaris (RCMB 010085), Klebsiella pneumonia (RCMB 010093) and Shigella flexneri (RCMB 0100542)] and fungi [(Aspergillus fumigates (RCMB 02564), Aspergillus clavatus (RCMB 02593) and Candida albicans (RCMB05035)] by disk diffusion method. All the metal complexes have potent biocidal activity than the free ligand.

  1. Evaluation of the biointeraction of colorant flavazin with human serum albumin: insights from multiple spectroscopic studies, in silico docking and molecular dynamics simulation.

    PubMed

    Peng, Wei; Ding, Fei; Jiang, Yu-Ting; Sun, Ying; Peng, Yu-Kui

    2014-06-01

    Azo compounds are the largest chemical class of agents frequently used as colorants in a variety of consumer goods and farm produce; therefore, they may become a hazard to public health, because numerous azo compounds and their metabolites are proven to be carcinogens and mutagens. Herein several qualitative and quantitative analytical techniques, including steady state and time-resolved fluorescence, circular dichroism (CD), computer-aided molecular docking as well as molecular dynamics simulation, were employed to ascertain the molecular recognition between the principal vehicle of ligands in human plasma, albumin and a model azo compound, flavazin. The results show that the albumin spatial structure was changed in the presence of flavazin with a decrease of α-helix suggesting partial protein destabilization/self-regulation, as derived from steady state fluorescence, far-UV CD and detailed analyses of three-dimensional fluorescence spectra. Time-resolved fluorescence further evinced that the recognition mechanism is related to albumin-flavazin adduct formation with an association intensity of 10(4) M(-1), and the driving forces were found to be chiefly π-π interactions, hydrophobic interactions and hydrogen bonds. The specific binding domain of flavazin in protein was defined from molecular docking; subdomain IIA (Sudlow's site I) was found to retain high affinity for the ligand flavazin. This finding corroborates the results of competitive ligand displacement experiments, a hydrophobic 8-anilino-1-naphthalenesulfonic acid probe study and protein denaturation results, placing flavazin at the warfarin-azapropazone site. Based on molecular dynamics simulation, it can be said with certainty that the results of molecular docking are credible, and the key amino acid residues participating in the molecular recognition of flavazin by protein are clearly Trp-214, Arg-222 and Lys-436. The outcomes presented here will help to further comprehend the molecular recognition

  2. Synthesis, spectroscopic studies, molecular modeling and antimicrobial activity of binuclear Co(II) and Cu(II) complexes of 4,6-diacetylresorcinol.

    PubMed

    Shebl, Magdy; Khalil, Saied M E; Taha, A; Mahdi, M A N

    2013-09-01

    Reactions of 4,6-diacetylresorcinol with different cobalt(II) and copper(II) salts viz., OAc(-), Cl(-), NO3(-) and SO4(2-), yielded a new series of binuclear metal complexes. Reactions of the ligand with these metal ions in the presence of a secondary ligand (L') [O,O-donor; acetylacetone, N,O-donor; 8-hydroxyquinoline or N,N-donor; 1,10-phenanthroline and N,N,N',N'-tetramethylethylenediamine] in 1:2:2 (L:M:L') molar ratio yielded mixed-ligand complexes with different molar ratios. The metal complexes were characterized by elemental and thermal analyses, IR, electronic, ESR and mass spectra as well as conductivity and magnetic susceptibility measurements. The analytical and spectroscopic data suggested that the H2L ligand behaves as a neutral, monobasic or dibasic tetradentate ligand, depending on the type of the anion and secondary ligand used, through the two phenolic and two carbonyl groups. Electronic spectra, magnetic and conductivity measurements showed that all complexes are octahedral with non-electrolytic nature. The profile of ESR spectra of copper(II) complexes suggested the octahedral geometry and the spin Hamiltonian parameters of the complexes were calculated and discussed. Molecular orbital calculations were performed for metal complexes using Hyperchem 7.52 program on the bases of PM3 level and the results correlated with the experimental data. The free ligand and some of its metal complexes showed antimicrobial activity towards some of Gram-positive and Gram-negative bacteria, yeast (Candida albicans) and fungus (Aspergillus fumigatus). PMID:23743042

  3. Synthesis, spectroscopic studies, molecular modeling and antimicrobial activity of binuclear Co(II) and Cu(II) complexes of 4,6-diacetylresorcinol

    NASA Astrophysics Data System (ADS)

    Shebl, Magdy; Khalil, Saied M. E.; Taha, A.; Mahdi, M. A. N.

    2013-09-01

    Reactions of 4,6-diacetylresorcinol with different cobalt(II) and copper(II) salts viz., OAc-, Cl-, NO3- and SO42-, yielded a new series of binuclear metal complexes. Reactions of the ligand with these metal ions in the presence of a secondary ligand (L‧) [O,O-donor; acetylacetone, N,O-donor; 8-hydroxyquinoline or N,N-donor; 1,10-phenanthroline and N,N,N‧,N‧-tetramethylethylenediamine] in 1:2:2 (L:M:L‧) molar ratio yielded mixed-ligand complexes with different molar ratios. The metal complexes were characterized by elemental and thermal analyses, IR, electronic, ESR and mass spectra as well as conductivity and magnetic susceptibility measurements. The analytical and spectroscopic data suggested that the H2L ligand behaves as a neutral, monobasic or dibasic tetradentate ligand, depending on the type of the anion and secondary ligand used, through the two phenolic and two carbonyl groups. Electronic spectra, magnetic and conductivity measurements showed that all complexes are octahedral with non-electrolytic nature. The profile of ESR spectra of copper(II) complexes suggested the octahedral geometry and the spin Hamiltonian parameters of the complexes were calculated and discussed. Molecular orbital calculations were performed for metal complexes using Hyperchem 7.52 program on the bases of PM3 level and the results correlated with the experimental data. The free ligand and some of its metal complexes showed antimicrobial activity towards some of Gram-positive and Gram-negative bacteria, yeast (Candida albicans) and fungus (Aspergillus fumigatus).

  4. Spectroscopic studies of copper enzymes

    SciTech Connect

    Dooley, D.M.; Moog, R.; Zumft, W.; Koenig, S.H.; Scott, R.A.; Cote, C.E.; McGuirl, M.

    1986-05-01

    Several spectroscopic methods, including absorption, circular dichroism (CD), magnetic CD (MCD), X-ray absorption, resonance Raman, EPR, NMR, and quasi-elastic light-scattering spectroscopy, have been used to probe the structures of copper-containing amine oxidases, nitrite reductase, and nitrous oxide reductase. The basic goals are to determine the copper site structure, electronic properties, and to generate structure-reactivity correlations. Collectively, the results on the amine oxidases permit a detailed model for the Cu(II) sites in these enzymes to be constructed that, in turn, rationalizes the ligand-binding chemistry. Resonance Raman spectra of the phenylhydrazine and 2,4-dinitrophenyl-hydrazine derivatives of bovine plasma amine oxidase and models for its organic cofactor, e.g. pyridoxal, methoxatin, are most consistent with methoxatin being the intrinsic cofactor. The structure of the Cu(I) forms of the amine oxidases have been investigated by X-ray absorption spectroscopy (XAS); the copper coordination geometry is significantly different in the oxidized and reduced forms. Some anomalous properties of the amine oxidases in solution are explicable in terms of their reversible aggregation, which the authors have characterized via light scattering. Nitrite and nitrous oxide reductases display several novel spectral properties. The data suggest that new types of copper sites are present.

  5. Molecular spectroscopic analysis of nano-chitosan blend as biosensor

    NASA Astrophysics Data System (ADS)

    Ibrahim, Medhat; Mahmoud, Abdel Aziz; Osman, Osama; Refaat, Ahmed; El-Sayed, El-Sayed M.

    2010-11-01

    Chitosan/starch and chitosan/gelatin of different ratios were prepared following casting method. FTIR results indicate the formation of hydrogen bonding which dedicates the prepared blends for interaction with wide range of molecules specially those of NH 2 and COOH terminals. The results obtained with molecular modeling PM3 model are in agreement with spectroscopic data. As a result of increasing starch and gelatin in chitosan blends HOMO-LUMO energy slightly decreased while total dipole moment increased. UV-vis spectroscopy indicated the suitability of chitosan/starch blend as a glycine sensor. Further enhancement in the sensing performance of chitosan/starch blend was achieved by introducing 5 nm TiO 2 into the blend.

  6. The HITRAN molecular spectroscopic database and HAWKS (HITRAN atmospheric workstation)

    NASA Astrophysics Data System (ADS)

    Rothman, Laurence S.; Rinsland, Curtis P.; Goldman, Aaron; Massie, Steven T.; Edwards, David P.; Flaud, Jean-Marie; Perrin, Agnes; Camy-Peyret, Claude; Dana, Victor; Mandin, Y.-Y.; Schroeder, John W.; Gamache, Robert R.; Wattson, R. B.; Yoshino, Kouichi; Chance, Kelly V.; Jucks, Kenneth W.; Brown, L. R.; Nemtchinov, Vassilii; Varanasi, Prasad

    1998-07-01

    Nineteen ninety-eight marks the 25th anniversary of the release of the first HITRAN database. HITRAN is recognized as the international standard of the fundamental spectroscopic parameters for diverse atmospheric and laboratory transmission and radiance calculations. There have been periodic editions of HITRAN over the past decades as the database has been expanded and improved with respect to the molecular species and spectral range covered, the number of parameters included, and the accuracy of this information. The 1996 edition not only includes the customary line-by-line transition parameters familiar to HITRAN users, but also cross-section data, aerosol indices of refraction, software to filter and manipulate the data, and documentation. This paper describes the data and features that have been added or replaced since the previous edition of HITRAN. We also cite instances of critical data that is forthcoming. A new release is planned for 1998.

  7. GAS PHASE MOLECULAR DYNAMICS: HIGH-RESOLUTION SPECTROSCOPIC PROBES OF CHEMICAL DYNAMICS.

    SciTech Connect

    HALL, G.E.

    2006-05-30

    This research is carried out as part of the Gas Phase Molecular Dynamics group program in the Chemistry Department at Brookhaven National Laboratory. High-resolution spectroscopic tools are developed and applied to problems in chemical dynamics. Recent topics have included the state-resolved studies of collision-induced electronic energy transfer, dynamics of barrierless unimolecular reactions, and the kinetics and spectroscopy of transient species.

  8. Spectroscopic study in Z-pinch discharge

    SciTech Connect

    Garamoon, A.A.; Saudy, A.H.; Shark, W.

    1995-12-31

    The temporal variation of the emitted line intensity has been investigated, and thus an important information about the dynamic ionization stages in the Z-pinch discharge has been studied. Also the electron temperature Te, has been deduced by using a spectroscopic technique.

  9. Computational study of the vibrational spectroscopic studies, natural bond orbital, frontier molecular orbital and second-order non-linear optical properties of acetophenone thiosemicarbazone molecule

    NASA Astrophysics Data System (ADS)

    Li, Xiao-Hong; Mei, Zheng; Zhang, Xian-Zhou

    2014-01-01

    The vibrational frequencies of acetophenone thiosemicarbazone in the ground state have been calculated using density functional method (B3LYP) with 6-31G(d), 6-31G(d,p) and 6-311++G(d,p) basis sets. The analysis of natural bond orbital was also performed. The IR spectra were obtained and interpreted by means of potential energies distributions (PEDs) using MOLVIB program. In addition, the results show that there exist Nsbnd H…N and Nsbnd H…S hydrogen bonds in the title compound, which play a major role in stabilizing the molecule and are confirmed by the natural bond orbital analysis. The predicted NLO properties show that the title compound is a good candidate as second-order NLO material. In addition, the frontier molecular orbitals were analyzed and the crystal structure obtained by molecular mechanics belongs to the Pbca space group, with lattice parameters Z = 8, a = 16.0735 Å, b = 7.1719 Å, c = 7.8725 Å, ρ = 0.808 g/cm3.

  10. Computational study of the vibrational spectroscopic studies, natural bond orbital, frontier molecular orbital and second-order non-linear optical properties of acetophenone thiosemicarbazone molecule.

    PubMed

    Li, Xiao-Hong; Mei, Zheng; Zhang, Xian-Zhou

    2014-01-24

    The vibrational frequencies of acetophenone thiosemicarbazone in the ground state have been calculated using density functional method (B3LYP) with 6-31G(d), 6-31G(d,p) and 6-311++G(d,p) basis sets. The analysis of natural bond orbital was also performed. The IR spectra were obtained and interpreted by means of potential energies distributions (PEDs) using MOLVIB program. In addition, the results show that there exist N-H…N and N-H…S hydrogen bonds in the title compound, which play a major role in stabilizing the molecule and are confirmed by the natural bond orbital analysis. The predicted NLO properties show that the title compound is a good candidate as second-order NLO material. In addition, the frontier molecular orbitals were analyzed and the crystal structure obtained by molecular mechanics belongs to the Pbca space group, with lattice parameters Z=8, a=16.0735 Å, b=7.1719 Å, c=7.8725 Å, ρ=0.808 g/cm(3). PMID:24084483

  11. Comparative ab initio studies on the molecular structure and spectroscopic properties of FeF2: Single reference versus multireference methods.

    PubMed

    Solomonik, Victor G; Stanton, John F; Boggs, James E

    2008-06-28

    The electronic excitation energies, molecular geometry, quadratic force fields, and vibrational frequencies in the ground (5)Delta(g) and low-lying excited (5)Sigma(g) (+) and (5)Pi(g) electronic states of iron difluoride are studied at sophisticated levels of theory. Two families of basis sets, nonrelativistic and Douglas-Kroll-Hess relativistic, are used that range in quality from triple-zeta to quintuple-zeta. These are augmented by additional diffuse functions (on fluorine atoms) and tight functions (on all atoms) for the description of core-valence correlation and utilized to determine complete basis set molecular properties. The quality of electron correlation treatment using conventional single reference coupled cluster methods CCSD and CCSD(T) is compared to that attained at the multiconfigurational quasidegenerate second-order perturbation theory (CASSCF+MCQDPT2) and the electron attachment equation-of-motion coupled cluster (EOMEA-CCSD) levels. Spin-orbit coupling effects are studied by the SO-MCQDPT2 method using the full Breit-Pauli spin-orbit operator. Effects of spin contamination in the coupled cluster molecular calculations are carefully analyzed. Results of the single reference CCSD(T) and multireference calculations are found to be in a remarkable agreement. The calculations indicate that the EOMEA-CC approach provides a suitable tool for an accurate treatment of FeF(2) and other systems where delicate electron correlation effects have to be carefully dealt with. The inclusion of relativistic effects is shown to be necessary for an accurate description of the molecular geometry and excitation energies of FeF(2). The results of calculations are in good agreement with the experimental data available. The predicted FeF(2) molecular properties are compared to those of the related FeF(3). PMID:18601314

  12. Binding of DNA-binding alkaloids berberine and palmatine to tRNA and comparison to ethidium: Spectroscopic and molecular modeling studies

    NASA Astrophysics Data System (ADS)

    Islam, Md. Maidul; Pandya, Prateek; Chowdhury, Sebanti Roy; Kumar, Surat; Kumar, Gopinatha Suresh

    2008-11-01

    The interaction of two natural protoberberine plant alkaloids berberine and palmatine with tRNA phe was studied using various biophysical techniques and molecular modeling and the data were compared with the binding of the classical DNA intercalator, ethidium. Circular dichroic studies revealed that the tRNA conformation was moderately perturbed on binding of the alkaloids. The cooperative binding of both the alkaloids and ethidium to tRNA was revealed from absorbance and fluorescence studies. Fluorescence quenching studies advanced a conclusion that while berberine and palmatine are partially intercalated, ethidium is fully intercalated on the tRNA molecule. The binding of the alkaloids as well as ethidium stabilized the tRNA melting, and the binding constant evaluated from the averaged optical melting temperature data was in agreement with fluorescence spectral-binding data. Differential scanning calorimetry revealed that the tRNA melting showed three close transitions that were affected on binding of these small molecules. Molecular docking calculations performed showed the preferred regions of binding of these small molecules on the tRNA. Taken together, the results suggest that the binding of the alkaloids berberine and palmatine on the tRNA structure appears to be mostly by partial intercalation while ethidium intercalates fully on the tRNA. These results further advance our knowledge on the molecular aspects on the interaction of these alkaloids to tRNA.

  13. Studying Young Stars with Large Spectroscopic Surveys

    NASA Astrophysics Data System (ADS)

    Martell, Sarah L.

    2016-01-01

    Galactic archaeology is the study of the history of star formation and chemical evolution in the Milky Way, based on present-day stellar populations. Studies of young stars are a key anchor point for Galactic archaeology, since quantities like the initial mass function and the star formation rate can be studied directly in young clusters and star forming regions. Conversely, massive spectroscopic Galactic archaeology surveys can be used as a data source for young star studies.

  14. Interaction of methotrexate with trypsin analyzed by spectroscopic and molecular modeling methods

    NASA Astrophysics Data System (ADS)

    Wang, Yanqing; Zhang, Hongmei; Cao, Jian; Zhou, Qiuhua

    2013-11-01

    Trypsin is one of important digestive enzymes that have intimate correlation with human health and illness. In this work, the interaction of trypsin with methotrexate was investigated by spectroscopic and molecular modeling methods. The results revealed that methotrexate could interact with trypsin with about one binding site. Methotrexate molecule could enter into the primary substrate-binding pocket, resulting in inhibition of trypsin activity. Furthermore, the thermodynamic analysis implied that electrostatic force, hydrogen bonding, van der Waals and hydrophobic interactions were the main interactions for stabilizing the trypsin-methotrexate system, which agreed well with the results from the molecular modeling study.

  15. Molecular structure, spectroscopic and quantum chemical studies of 1‧,3‧,3‧-trimethylspiro[benzo[f]chromene-3,2‧-indoline

    NASA Astrophysics Data System (ADS)

    Asiri, Abdullah M.; Ersanlı, Cem Cüneyt; Şahin, Onur; Arshad, Muhammad Nadeem; Hameed, Salem A.

    2016-05-01

    In this work, synthesis, X-ray single crystal determination, nuclear magnetic resonance (1H NMR and 13C NMR), Ultraviolet-Visible (UV-vis), Fourier transform infrared spectroscopy (FT-IR) and quantum mechanical studies of the 1‧,3‧,3‧-trimethylspiro[benzo[f]chromene-3,2‧-indoline [(C23H21NO), TMSBCI] have been both experimentally and theoretically reported. The molecular structure obtained from X-ray single-crystal analysis of the investigated compound in the ground state has been compared using Hartree-Fock (HF) and density functional theory (DFT) with the functional B3LYP using the 6-31G(d,p) as basis set. In addition to the optimized geometrical structures, atomic charges, molecular electrostatic potential (MEP) and natural bond orbital (NBO) have been investigated by using B3LYP/6-31G(d,p) level of the theoretical approximation for the title compound. The energetic behavior of TMSBCI has been examined in solvent media using polarizable continuum model (PCM). The total dipole moment (μ), the average linear polarizability (α), and the first-order hyperpolarisability (β) values of the investigated molecule have been computed using the same method. The experimental measurements (1H NMR, 13C NMR and UV-vis) have been compared with its corresponding the calculated values (using DFT). Besides, frontier molecular orbitals (FMOs) and thermodynamic properties have also been studied.

  16. Spectroscopic, quantum chemical studies, Fukui functions, in vitro antiviral activity and molecular docking of 5-chloro-N-(3-nitrophenyl)pyrazine-2-carboxamide

    NASA Astrophysics Data System (ADS)

    Sebastian, S. H. Rosline; Al-Alshaikh, Monirah A.; El-Emam, Ali A.; Panicker, C. Yohannan; Zitko, Jan; Dolezal, Martin; VanAlsenoy, C.

    2016-09-01

    The molecular structural parameters and vibrational frequencies of 5-chloro-N-(3-nitrophenyl)pyrazine-2-carboxamide have been obtained using density functional theory technique in the B3LYP approximation and CC-pVDZ (5D, 7F) basis set. Detailed vibrational assignments of observed FT-IR and FT-Raman bands have been proposed on the basis of potential energy distribution and most of the modes have wavenumbers in the expected range. In the present case, the NH stretching mode is a doublet in the IR spectrum with a difference of 138 cm-1 and is red shifted by 76 cm-1 from the computed value, which indicates the weakening of NH bond resulting in proton transfer to the neighboring oxygen atom. The molecular electrostatic potential has been mapped for predicting sites and relative reactivities towards electrophilic and nucleophilic attack. The hyperpolarizability values are calculated in order to find its role in nonlinear optics. From the molecular docking study, amino acids Asn161, His162 forms H-bond with pyrazine ring and Trp184, Gln19 shows H-bond with Cdbnd O group and the docked ligand, title compound forms a stable complex with cathepsin K and the results suggest that the compound might exhibit inhibitory activity against cathepsin K. Moderate in vitro antiviral activity with EC50 at tens of μM was detected against feline herpes virus, coxsackie virus B4, and influenza A/H1N1 and A/H3N2.

  17. NGC 6067: A spectroscopic study

    NASA Astrophysics Data System (ADS)

    Alonso-Santiago, J.; Negueruela, I.; Marco, A.; Dorda, R.

    2015-05-01

    NGC 6067 is a young open cluster in the Norma Cloud. Its age is around 100 Ma. It hosts a large population of evolved stars: 14 luminous red stars (most of which K Ib supergiants and late-G/early-K giants), 6--8 B giants, two A/F supergiants and two Cepheids (F/G supergiants). All this would imply that NGC 6067 represent one of the best laboratories in the Galaxy to study the evolution of intermediate-mass stars. Thackeray et al. (1962, MNRAS 124, 445T) performed the first complete study of this cluster but it has been poorly studied since then. We obtained high resolution echelle spectra (R=48000) using FEROS (Fiber Extended Range Optical Spectrograph) mounted on the ESO 2.2 m telescope at La Silla Observatory (Chile) in May 2011. Here we present preliminary results based on this spectroscopy and the UBV photometry listed in Terndrup & Pinsonneault (2007, ApJ 671, 1640).

  18. Spectroscopic study of Mentha oils

    NASA Astrophysics Data System (ADS)

    Rai, A. K.; Singh, A. K.

    The visible fluorescence and excitation spectra of Mentha oils (Japanese mint oil, peppermint oil and spearmint oil) have been recorded. Different physical constants which are characteristic of the fluorescent molecules have been calculated for all three oils. Results reveal that the same group of organic compounds dominate in the oils of peppermint and spearmint, whereas some different compound is present in Japanese mint oil. It is also found that the fluorescence intensity of these oils is comparable to that of Rhodamine 6G dye in methanol solution. Our studies suggest that Mentha oils may be a useful lasing material in the 450-600 nm wavelength range.

  19. Nuclear spectroscopic studies. Progress report

    SciTech Connect

    Bingham, C.R.; Guidry, M.W.; Riedinger, L.L.; Sorensen, S.P.

    1994-02-18

    The Nuclear Physics group at UTK is involved in heavy-ion physics including both nuclear structure and reaction mechanisms. During the last year experimental work has been in 3 broad areas: structure of nuclei at high angular momentum, structure of nuclei far from stability, and ultra-relativistic heavy-ion physics. Results in these areas are described in this document under: properties of high-spin states, study of low-energy levels of nuclei far from stability, and high-energy heavy-ion physics (PHENIX, etc.). Another important component of the work is theoretical interpretation of experimental results (Joint Institute for Heavy Ion Research).

  20. Nuclear spectroscopic studies. Progress report

    SciTech Connect

    Bingham, C.R.; Guidry, M.W.; Riedinger, L.L.; Sorensen, S.P.

    1993-02-08

    The Nuclear Physics group at the University of Tennessee, Knoxville is involved in several aspects of heavy-ion physics including both nuclear structure and reaction mechanisms. While our main emphasis is on experimental problems involving heavy-ion accelerators, we have maintained a strong collaboration with several theorists in order to best pursue the physics of our measurements. During the last year we have led several experiments at the Holifield Heavy Ion Research Facility and participated in others at Argonne National Laboratory. Also, we continue to be very active in the collaboration to study ultra-relativistic heavy ion physics utilizing the SPS accelerator at CERN in Geneva, Switzerland and in a RHIC detector R&D project. Our experimental work is in four broad areas: (1) the structure of nuclei at high angular momentum, (2) heavy-ion induced transfer reactions, (3) the structure of nuclei far from stability, and (4) ultra-relativistic heavy-ion physics. The results of studies in these particular areas will be described in this document in sections IIA, IIB, IIC, and IID, respectively. Areas (1), (3), and (4) concentrate on the structure of nuclear matter in extreme conditions of rotational motion, imbalance of neutrons and protons, or very high temperature and density. Area (2) pursues the transfer of nucleons to states with high angular momentum, both to learn about their structure and to understand the transfer of particles, energy, and angular momentum in collisions between heavy ions. An important component of our program is the strong emphasis on the theoretical aspects of nuclear structure and reactions.

  1. Spectroscopic studies of the transplutonium elements

    SciTech Connect

    Carnall, W.T.; Conway, J.G.

    1983-01-01

    The challenging opportunity to develop insights into both atomic structure and the effects of bonding in compounds makes the study of actinide spectroscopy a particularly fruitful and exciting area of scientific endeavor. It is also the interpretation of f-element spectra that has stimulated the development of the most sophisticated theoretical modeling attempted for any elements in the periodic table. The unique nature of the spectra and the wealth of fine detail revealed make possible sensitive tests of both physical models and the results of Hartree-Fock type ab initio calculations. This paper focuses on the unique character of heavy actinide spectroscopy. It discusses how it differs from that of the lighter member of the series and what are the special properties that are manifested. Following the introduction, the paper covers the following: (1) the role of systematic studies and the relationships of heavy-actinide spectroscopy to ongoing spectroscopic investigations of the lighter members of the series; (2) atomic (free-ion) spectra which covers the present status of spectroscopic studies with transplutonium elements, and future needs and directions in atomic spectroscopy; (3) the spectra of actinide compounds which covers the present status and future directions of spectroscopic studies with compounds of the transplutonium elements; and other spectroscopies. 1 figure, 2 tables.

  2. Spectroscopic Studies of Classical Cepheids.

    NASA Astrophysics Data System (ADS)

    Gauthier, Robert Paul

    The extent and nature of the distortions of the emergent flux spectrum of cepheids due to the effects of the pulsation as a function of period and amplitude are not clearly understood. A multiphase classification study of a sample of 26 cepheids from the southern hemisphere at the relatively high dispersion of 67(ANGSTROM)/mm has been undertaken and complemented with the recent high quality photometric data for Pel (1976) in order to observe the results of increasing period and amplitude of pulsation on the line spectrum. The original framework of such investigations set up by Struve (1944) and Code (1947) has been enlarged upon principally through the use of modern MK standard supergiant sequences. It has been found that, while the spectrum of weak metal lines (in cepheids with periods less than forty days) can always be found to match that of a non-variable supergiant, anomalies in the strengths of the strong metal lines and Balmer H(delta) and H(gamma) lines increase both in number and intensity with increasing period and amplitude. The consequences of this on the line blanketing of the atmosphere are seen to be significant when comparing the color-spectrum relations of different period bins, indicating the inappropriateness of extending intrinsic color relations established with short period variables to the longer period ones. It has also been found that the effects of the amplitude of the pulsation are more directly felt by the atmosphere near the extrema of the physical displacement as evidenced by the sudden widening of the period-spectrum relation at the mid-descending and mid-rising branch phases. Following the suggestions by Sorvari (1974) that the luminosity sensitive OI 7773(ANGSTROM) triplet is responding to the dynamical effects of the pulsation on the atmosphere, a moderate dispersion (27(ANGSTROM)/mm) study of a small sample of cepheids (4) and supergiant standards has been undertaken. It has been found that the strength of this feature throughout

  3. Spectroscopic study of carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Curran, Seamus; Weldon, Declan N.; Blau, Werner J.; Zandbergen, Henny W.; Kastner, J.; Kuzmany, Hans

    1994-11-01

    We present a comprehensive experimental study of the vibrational spectra of nanotubes. There are two main lines observed in the Raman spectrum, one positioned at 1350 cm-1, the D line, and the other at 1580 cm-1, the G line. Both these lines are very similar to those seen with disordered graphite. The disorder induced D line is very weak compared to the G line which is indicative of high crystalline materials. The position and intensity of the D line strongly depends on the energy of the exciting laser. This dispersion effect was also observed for graphitic particles and may be explained by a photoselective resonance process of nanotubes with different sizes. There are two optically active modes in the Infrared spectrum for highly orientated polycrystalline graphite which are the E1u and A2u modes. The E1u mode is positioned at 1587 cm-1 while the A2u mode is positioned at 868 cm-1. The Infrared spectrum of the nanotubes shows both modes although the E1u mode is downshifted to 1575 cm-1.

  4. Spectroscopic studies, fluorescence quenching by molecular oxygen and amplified spontaneous emission of 1,4-bis [2-(2-pyridyl) vinyl] benzene (P2VB) diolefinic laser dye

    NASA Astrophysics Data System (ADS)

    El-Daly, Samy A.; Ebeid, E. M.

    2014-04-01

    The UV-visible electronic absorption spectra, molar absorptivity, fluorescence spectra, fluorescence quantum yield and excited state lifetime of 1,4-bis [2-(2-pyridyl) vinyl] benzene P2VB were measured in different solvents. The fluorescence quenching of P2VB by molecular oxygen was also studied using lifetime measurements. A 2 × 10-4 mol dm-3 solution of P2VB in dimethyl formamide (DMF) gave amplified spontaneous emission (ASE) in blue spectral region with emission maximum at 420 nm upon pumping by 337.1 nitrogen laser pulse. The photochemical quantum yields (ϕc) of trans-cis photoisomerization of P2VB were calculated in different organic solvents. The photoreactivity of P2VB are also studied PMMA matrix.

  5. Spectroscopic investigations and molecular docking study of 3-(1H-imidazol-1-yl)-1-phenylpropan-1-one, a potential precursor to bioactive agents

    NASA Astrophysics Data System (ADS)

    Al-Alshaikh, Monirah A.; Mary Y, Sheena; Panicker, C. Yohannan; Attia, Mohamed I.; El-Emam, Ali A.; Alsenoy, C. Van

    2016-04-01

    The optimized molecular structure, vibrational wavenumbers, corresponding vibrational assignments of 3-(1H-imidazol-1-yl)-1-phenylpropan-1-one have been investigated theoretically and experimentally. The calculated geometrical parameters of the title compound are in agreement with the reported XRD data. The HOMO and LUMO analysis is used to determine the charge transfer within the molecule. The stability of the molecule arising from hyper-conjugative interaction and charge delocalization has been analyzed using NBO analysis. Molecular electrostatic potential was performed by the DFT method and from the MEP plot, it is evident that the negative charge covers the carbonyl group and the nitrogen atom N3 of the imidazole ring and the positive region is over the remaining portions of the molecule. The first and second hyperpolarizabilities are calculated and the first hyperpolarizability of the title compound is 16.99 times that of standard NLO material urea and the title compound and its derivatives are good object for further studies in nonlinear optics. The docked ligand title compound forms a stable complex with plasmodium falciparum and gives a binding affinity value of -5.5 kcal/mol and the preliminary results suggest that the compound might exhibit antimalarial activity against plasmodium falciparum.

  6. Vibrational spectroscopic and molecular docking study of 2-Benzylsulfanyl-4-[(4-methylphenyl)-sulfanyl]-6-pentylpyrimidine-5-carbonitrile, a potential chemotherapeutic agent

    NASA Astrophysics Data System (ADS)

    Haress, Nadia G.; El-Emam, Ali A.; Al-Deeb, Omar A.; Panicker, C. Yohannan; Al-Saadi, Abdulaziz A.; Van Alsenoy, Christian; War, Javeed Ahmad; Srivastava, S. K.

    2015-02-01

    FT-IR and FT-Raman spectra of 2-Benzylsulfanyl-4-[(4-methylphenyl)-sulfanyl]-6-pentylpyrimidine-5-carbonitrile were recorded and analyzed. The structure of the molecule has been optimized and the structural characteristics have been determined by density functional theory. The geometrical parameters (DFT) are in agreement with the XRD results. HOMO and LUMO and other chemical properties are reported. Nonlinear optical properties are reported. A detailed molecular picture of the title compound and its interactions were obtained from NBO analysis. The negative (red and yellow) regions of the MEP are related to electrophilic reactivity and the positive (blue) regions to nucleophilic reactivity, as shown in the MEP plot and the title compound has several possible sites, Ctbnd N, N atom of pyrimidine ring and sulfur atoms for electrophilic attack. From the molecular docking studies it is clear that the title compound binds at the catalytic site of the substrate by weak non-covalent interactions most prominent of which are H-bonding, π-π, alkyl-π, and amide-π interactions.

  7. Relationship of carbohydrate molecular spectroscopic features in combined feeds to carbohydrate utilization and availability in ruminants

    NASA Astrophysics Data System (ADS)

    Zhang, Xuewei; Yu, Peiqiang

    To date, there is no study on the relationship between carbohydrate (CHO) molecular structures and nutrient availability of combined feeds in ruminants. The objective of this study was to use molecular spectroscopy to reveal the relationship between CHO molecular spectral profiles (in terms of functional groups (biomolecular, biopolymer) spectral peak area and height intensity) and CHO chemical profiles, CHO subfractions, energy values, and CHO rumen degradation kinetics of combined feeds of hulless barley with pure wheat dried distillers grains with solubles (DDGS) at five different combination ratios (hulless barley to pure wheat DDGS: 100:0, 75:25, 50:50, 25:75, 0:100). The molecular spectroscopic parameters assessed included: lignin biopolymer molecular spectra profile (peak area and height, region and baseline: ca. 1539-1504 cm-1); structural carbohydrate (STCHO, peaks area region and baseline: ca. 1485-1186 cm-1) mainly associated with hemi- and cellulosic compounds; cellulosic materials peak area (centered at ca. 1240 cm-1 with region and baseline: ca. 1272-1186 cm-1); total carbohydrate (CHO, peaks area region and baseline: ca. 1186-946 cm-1). The results showed that the functional groups (biomolecular, biopolymer) in the combined feeds are sensitive to the changes of carbohydrate chemical and nutrient profiles. The changes of the CHO molecular spectroscopic features in the combined feeds were highly correlated with CHO chemical profiles, CHO subfractions, in situ CHO rumen degradation kinetics and fermentable organic matter supply. Further study is needed to investigate possibility of using CHO molecular spectral features as a predictor to estimate nutrient availability in combined feeds for animals and quantify their relationship.

  8. A Spectroscopic-Based Laboratory Experiment for Protein Conformational Studies

    ERIC Educational Resources Information Center

    Ramos, Carlos Henrique I.

    2004-01-01

    This article describes a practical experiment for teaching basic spectroscopic techniques to introduce the topic of protein conformational change to students in the field of molecular biology, biochemistry, or structural biology. The spectroscopic methods employed in the experiment are absorbance, for protein concentration measurements, and…

  9. Host-guest interaction between 3,4-dihydroisoquinoline-2(1H)-sulfonamide and β-cyclodextrin: Spectroscopic and molecular modeling studies

    NASA Astrophysics Data System (ADS)

    Seridi, Saida; Seridi, Achour; Berredjem, Malika; Kadri, Mekki

    2013-11-01

    The inclusion complex of 3,4-dihydroisoquinoline-2(1H)-sulfonamide with β-cyclodextrin was investigated experimentally and by molecular modeling studies. The stoichiometric ratio of the complex was found to be 1:1 and the stability constant was evaluated using the Benesi-Hildebrand equation. Estimation of the thermodynamic parameters of the inclusion complex in vacuum showed that it is an enthalpy driven process phase and an enthalpy-entropy co-driven process in aqueous solution, which is in accord with the experimental results. Semi-empirical calculations using PM3, PM6 and ONIOM2 methods, in vacuum and in water, were performed. The energetically more favorable structure obtained with the ONIOM2 method leads to the formation of intermolecular hydrogen bonds between sulfonamide and β-cyclodextrin. These interactions were investigated using the Natural Bond Orbital (NBO).

  10. Microwave and millimeter wave astrochemistry: Laboratory studies of transition metal-containing free radicals and spectroscopic observations of molecular interstellar environments

    NASA Astrophysics Data System (ADS)

    Adande, Gilles Rapotchombo

    Progress in our understanding of the chemical composition of the interstellar medium leans both on laboratory analyses of high resolution rotational spectra from molecules that may be present in these regions, and on radio astronomical observations of molecular tracers to constrain astrochemical models. Due to the thermodynamic conditions in outer space, some molecules likely to be found in interstellar regions in relevant abundances are open shell radicals. In a series of laboratory studies, the pure rotational spectra of the transition metal containing radicals sulfur species ScS, YS, VS and ZnSH were obtained for the first time. In addition to accurate and precise rest frequencies for these species, bonding characteristics were determined from fine and hyperfine molecular parameters. It was found that these sulfides have a higher degree of covalent bonding than their mostly ionic oxide counterparts. Isomers and isotope ratios are excellent diagnostic tools for a variety of astrochemical models. From radio observations of isotopes of nitrile species, the galactic gradient of 14N/15N was accurately established. A further study of this ratio in carbon rich asymptotic giant branch stars provided observational evidence for an unknown process in J type carbon stars, and highlighted the need to update stellar nucleosynthesis models. Proper radiative transfer modeling of the emission spectra of interstellar molecules can yield a wealth of information about the abundance and distribution of these species within the observed sources. To model the asymmetric emission of SO and SO2 in oxygen-rich supergiants, an in-house code was developed, and successfully applied to gain insight into circumstellar sulfur chemistry of VY Canis Majoris. It was concluded that current astrochemistry kinetic models, based on spherical symmetry assumptions, need to be revisited.

  11. Conformational analysis, spectroscopic study (FT-IR, FT-Raman, UV, 1H and 13C NMR), molecular orbital energy and NLO properties of 5-iodosalicylic acid

    NASA Astrophysics Data System (ADS)

    Karaca, Caglar; Atac, Ahmet; Karabacak, Mehmet

    2015-02-01

    In this study, 5-iodosalicylic acid (5-ISA, C7H5IO3) is structurally characterized by FT-IR, FT-Raman, NMR and UV spectroscopies. There are eight conformers, Cn, n = 1-8 for this molecule therefore the molecular geometry for these eight conformers in the ground state are calculated by using the ab-initio density functional theory (DFT) B3LYP method approach with the aug-cc-pVDZ-PP basis set for iodine and the aug-cc-pVDZ basis set for the other elements. The computational results identified that the most stable conformer of 5-ISA is the C1 form. The vibrational spectra are calculated DFT method invoking the same basis sets and fundamental vibrations are assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method with PQS program. Total density of state (TDOS) and partial density of state (PDOS) and also overlap population density of state (COOP or OPDOS) diagrams analysis for C1 conformer were calculated using the same method. The energy and oscillator strength are calculated by time-dependent density functional theory (TD-DFT) results complement with the experimental findings. Besides, charge transfer occurring in the molecule between HOMO and LUMO energies, frontier energy gap, molecular electrostatic potential (MEP) are calculated and presented. The NMR chemical shifts (1H and 13C) spectra are recorded and calculated using the gauge independent atomic orbital (GIAO) method. Mulliken atomic charges of the title molecule are also calculated, interpreted and compared with salicylic acid. The optimized bond lengths, bond angles and calculated NMR and UV, vibrational wavenumbers showed the best agreement with the experimental results.

  12. Prediction of molecular properties and spectroscopic profile of Riluzole with different functionals (B3LYP, M06-2X, MPWLYP): A combined theoretical and experimental study

    NASA Astrophysics Data System (ADS)

    Shukla, Vikas K.; Sachan, Alok K.; Pathak, Shilendra K.; Srivastava, Ruchi; Prasad, Onkar; Sinha, Leena

    2016-02-01

    Comprehensive investigation of molecular geometry and electronic structure of Riluzole (6-(trifluoromethoxy)benzothiazol-2-amine) in ground as well as in the first excited state has been carried out. The stable conformers of the title compound have been determined from the 3D potential energy scan calculated at DFT/B3LYP, by varying selected dihedral angles, responsible for conformational flexibility. The most stable conformers were further optimized to obtain ground state structure using pure GGA (MPWLYP), hybrid GGA (B3LYP) and meta-hybrid GGA (M06-2X) functionals. Detailed vibrational analysis has been done for the structure obtained at B3LYP as it corresponds to the minimum energy structure. Experimental FT-IR and FT-Raman spectra were compared with theoretical spectral data. Dipole moment, polarizability, first static hyperpolarizability has been calculated at different functionals used in the study. Natural bond orbital (NBO) analysis has been done to study the stability of the compound arising from charge delocalization. UV-Vis spectrum of the title compound was also recorded and electronic properties such as frontier orbitals and band gap energies were calculated by TD-DFT approach.

  13. Complexation of tetrandrine with calcium ion probed by various spectroscopic methods and molecular modeling

    NASA Astrophysics Data System (ADS)

    Stanculescu, Ioana; Mandravel, Cristina; Landy, David; Woisel, Patrice; Surpateanu, Gheorghe

    2003-07-01

    The formation of the complex between tetrandrine and the calcium ion, in solution, was studied using FTIR, UV-Vis, 1H NMR, 13C NMR and electrospray mass spectroscopy spectroscopic methods and molecular modeling. The calcium salts used were: Ca(ClO 4) 2·4H 2O and Ca(Picrate) 2 in the solvents: acetonitrile (CH 3CN), deuterated acetonitrile (CD 3CN) and tetrahydrofurane (THF). The determined complex stability constant was: 20277±67 dm 3 mol -1 and corresponding free energy Δ G0=-5.820±0.002 kcal mol -1. The molecular simulation of the complex formation with the MM3 Augmented force field integrated in CAChe provided useful data about its energy. Combining the experimental results and molecular modeling we propose a model for the structure of tetrandrine-Ca complex with an eight coordinated geometry.

  14. One pot synthesis, molecular structure and spectroscopic studies (X-ray, IR, NMR, UV-Vis) of novel 2-(4,6-dimethoxy-1,3,5-triazin-2-yl) amino acid ester derivatives.

    PubMed

    El-Faham, Ayman; Soliman, Saied M; Osman, Sameh M; Ghabbour, Hazem A; Siddiqui, Mohammed R H; Fun, Hoong-Kun; Albericio, Fernando

    2016-04-15

    Novel series of 2-(4,6-dimethoxy,1,3,5-triazin-2-yl) amino acid ester derivatives were synthesized using simple one pot method in methanol. The products were obtained in high yields and purities as observed from their spectral data, elemental analyses, GC-MS and X-ray crystallographic analysis. The B3LYP/6-311G(d,p) calculated molecular structures are well correlated with the geometrical parameters obtained from the X-ray analyses. The spectroscopic properties such as IR vibrational modes, NMR chemical shifts and UV-Vis electronic transitions were discussed both experimentally and theoretically. The IR vibrational frequencies showed good correlations with the experimental data (R(2)=0.9961-0.9995). The electronic spectra were assigned based on the TD-DFT results. Intense electronic transition band is calculated at 198.1 nm (f=0.1389), 204.2 nm (f=0.2053), 205.0 (f=0.1704) and 205.7 (0.2971) for compounds 6a-i, respectively. The molecular orbital energy levels contributed in the longest wavelength transition band were explained. For all compounds, the experimental wavelengths showed red shifts compared to the calculations due to the solvent effect. The NMR chemical shifts were calculated using GIAO method. The NBO analyses were performed to predict the stabilization energies due to the electron delocalization processes occur in the studied systems. PMID:26845586

  15. One pot synthesis, molecular structure and spectroscopic studies (X-ray, IR, NMR, UV-Vis) of novel 2-(4,6-dimethoxy-1,3,5-triazin-2-yl) amino acid ester derivatives

    NASA Astrophysics Data System (ADS)

    El-Faham, Ayman; Soliman, Saied M.; Osman, Sameh M.; Ghabbour, Hazem A.; Siddiqui, Mohammed R. H.; Fun, Hoong-Kun; Albericio, Fernando

    2016-04-01

    Novel series of 2-(4,6-dimethoxy,1,3,5-triazin-2-yl) amino acid ester derivatives were synthesized using simple one pot method in methanol. The products were obtained in high yields and purities as observed from their spectral data, elemental analyses, GC-MS and X-ray crystallographic analysis. The B3LYP/6-311G(d,p) calculated molecular structures are well correlated with the geometrical parameters obtained from the X-ray analyses. The spectroscopic properties such as IR vibrational modes, NMR chemical shifts and UV-Vis electronic transitions were discussed both experimentally and theoretically. The IR vibrational frequencies showed good correlations with the experimental data (R2 = 0.9961-0.9995). The electronic spectra were assigned based on the TD-DFT results. Intense electronic transition band is calculated at 198.1 nm (f = 0.1389), 204.2 nm (f = 0.2053), 205.0 (f = 0.1704) and 205.7 (0.2971) for compounds 6a-i, respectively. The molecular orbital energy levels contributed in the longest wavelength transition band were explained. For all compounds, the experimental wavelengths showed red shifts compared to the calculations due to the solvent effect. The NMR chemical shifts were calculated using GIAO method. The NBO analyses were performed to predict the stabilization energies due to the electron delocalization processes occur in the studied systems.

  16. Synthesis and spectroscopic studies on charge-transfer molecular complexes formed in the reaction of imidazole and 1-benzylimidazole with σ- and π-acceptors

    NASA Astrophysics Data System (ADS)

    Mostafa, Adel; Bazzi, Hassan S.

    2011-09-01

    The spectrophotometric characteristics of the solid charge-transfer molecular complexes (CT) formed in the reaction of the electron donors imidazole (IML) and 1-benzylimidazole (BIML) with the σ-acceptor iodine and π-acceptors 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ), tetracyanoethylene (TCNE) and 2,3,5,6-tetrachloro-1,4-benzoquinone (CHL) have been studied in chloroform at 25 °C. These were investigated through electronic and infrared spectra as well as elemental analysis. The results show that the formed solid CT-complexes have the formulas [(IML) 2 I]I 3, [(IML)(DDQ)], [(IML) 2(TCNE) 5] and [(IML)(CHL)] for imidazole and [(BIML) I]I 3, [(BIML)(DDQ) 2], [(BIML)(TCNE) 2] and [(BIML)(CHL) 2] for 1-benzylimidazole in full agreement with the known reaction stoichiometries in solution as well as the elemental measurements. The formation constant KCT, molar extinction coefficient ɛCT, free energy change Δ G0, CT energy ECT and ionization potential Ip have been calculated for the CT-complexes [(IML) 2 I]I 3, [(IML)(DDQ)], [(IML)(CHL)], [(BIML) I]I 3, [(BIML)(DDQ) 2], [(BIML)(TCNE) 2] and [(BIML)(CHL) 2].

  17. Synthesis, spectroscopic and thermal studies of charge-transfer molecular complexes formed in the reaction of 1,4-bis (3-aminopropyl) piperazine with σ- and π acceptors

    NASA Astrophysics Data System (ADS)

    AlQaradawi, Siham Y.; Mostafa, Adel; Bazzi, Hassan S.

    2012-03-01

    In the present study, solid charge-transfer (CT) molecular complexes formed in the reaction of the electron donor 1,4-bis (3-aminopropyl) piperazine (APPIP) with the σ-electron acceptor iodine and π-acceptors 7,7,8,8-tetracyanoquinodimethane (TCNQ), tetracyanoethylene (TCNE), 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ), and 2,4,4,6-tetrabromo-2,5-cyclohexadienone (TBCHD) have been investigated spectrophotometrically in chloroform at 25 °C. These were characterized through electronic and infrared spectra as well as elemental and thermal analysis. The obtained results showed that the formed solid CT-complexes have the formulas [(APPIP) I]+I3-, [(APPIP)(TCNQ)], [(APPIP)2(TCNE)3], [(APPIP)(DDQ)] and [(APPIP)(TBCHD)] in full agreement with the known reaction stoichiometries in solution as well as the elemental measurements. The formation constant KCT, molar extinction coefficient ɛCT, free energy change ΔG0, CT energy ECT and the ionization potential Ip have been calculated for the CT complexes [(APPIP) I]+I3-, [(APPIP)(TCNQ)], [(APPIP)(DDQ)] and [(APPIP)(TBCHD)].

  18. In vitro binding of leukotriene B4 (LTB4) to human serum albumin: evidence from spectroscopic, molecular modeling, and competitive displacement studies.

    PubMed

    Zsila, Ferenc; Bikádi, Zsolt; Lockwood, Samuel F

    2005-08-15

    Circular dichroism (CD) and UV absorption spectroscopy were utilized for the first time to investigate the interaction between leukotriene B4 (LTB4) and human serum albumin (HSA) in vitro. The weak intrinsic CD signal of LTB4 was enhanced fivefold in the presence of HSA. The red-shifted, hypochromic, and reduced vibrational fine structure of the ligand/protein UV absorption spectrum indicated complexation of the two molecules in solution. Results obtained from CD titration experiments were subjected to non-linear regression analysis to estimate the binding parameters (Ka = 6.7 x 10(4) M(-1), n = 1). Palmitic acid strongly decreased the induced CD signal of the LTB4/HSA complex, suggesting the role of a high-affinity fatty acid HSA binding site in the leukotriene complexation. Molecular modeling calculations based on the crystal structure of HSA predicted that the long-chain fatty acid site that overlaps with drug binding site II in subdomain IIIA was the most likely binding location for LTB4. Using the drug site II-specific marker ligand rac-ibuprofen, this prediction was confirmed with induced-CD displacement measurements. To the authors' knowledge, the current study represents the first demonstration of binding of LTB4 to HSA in vitro and has implications for the biological transport of this important pro-inflammatory mediator in vivo. PMID:15993588

  19. Preferential binding of anti-cancer drug adriamycin to the Sp1 binding site in c-met promoter region: A spectroscopic and molecular modeling study

    NASA Astrophysics Data System (ADS)

    Singhal, Garima; Rajeswari, Moganty R.

    2009-02-01

    The c-met gene encodes a transmembrane glycoprotein receptor with tyrosine kinase activity and overexpression of MET receptor is found in a number of common human malignancies. Regulation of c-met oncogene expression in general can be controlled by several DNA binding anti-cancer drugs. Interaction of adriamycin with a short oligonucleotide (24RY), which is part of the positive regulatory element (-233 to -68) in c-met gene was studied using UV-Vis absorption and fluorescence spectroscopy, UV-thermal melting, and molecular modeling. Strong binding of adriamycin to 24RY (overall binding constant K, 1- 3 × 10 5 M -1) is thermodynamically favored and is accompanied by the following: a marked increase in the melting temperature of 24RY by +15 °C and ˜60% decrease in absorption at 480 nm, ˜80% quenching of fluorescence at 555 nm along with a blue shift of the λemimax to 522 nm of adriamycin. Present data reveals that adriamycin binds to ˜ 5 bp (GCGGG) of the Sp1 binding site in 24RY and thus competes with Sp1 binding to the promoter site which results in down-regulation of kinase. Therefore, targeting c-met is a promising approach as it is an attractive novel oncogene for cancer therapeutics.

  20. Spectroscopic properties with a combined approach of ab initio molecular dynamics and wavelet analysis

    NASA Astrophysics Data System (ADS)

    Pagliai, Marco; Muniz-Miranda, Francesco; Cardini, Gianni; Righini, Roberto; Schettino, Vincenzo

    2011-05-01

    In order to extract spectroscopic information from trajectories obtained by classical or ab initio molecular dynamics simulations, usually Fourier transforms are employed. In recent years wavelet transforms have been shown to be a valid alternative tool to analyze time-series, due to their capability of localizing a signal both in time and frequency. In this article wavelet transforms are applied for the analysis of Car-Parrinello molecular dynamics simulations to the purpose of time-correlating structural and spectroscopic properties of methyl acetate dissolved in water and methanol. The results demonstrate the possibility of obtaining information that may be of valuable help in the interpretation of time-resolved spectroscopic data.

  1. Molecular structure, spectroscopic assignments and other quantum chemical calculations of anticancer drugs - A review.

    PubMed

    Ghasemi, A S; Deilam, M; Sharifi-Rad, J; Ashrafi, F; Hoseini-Alfatemi, S M

    2015-01-01

    In many texts, both theoretical and experimental studies on molecular structure and spectroscopic assignments of anticancer medicines have been reported. Molecular geometry parameters have been experimentally obtained by x-ray structure determination method and optimized using computational chemistry method like density functional theory. In this review, we consider calculations based on density function theory at B3LYP/6-31G (d,p) and B3LYP/6-311++G (d,p) levels of theory. Based on optimized geometric parameters of the molecules, molecular structures (length of bonds, bond angles and torsion angles) and vibrational assignments have been obtained. Molecular stability and bond strength have been investigated by applying natural bond orbital (NBO) analysis. Other molecular properties such as mulliken population analysis, thermodynamic properties and polarizabitities of these drugs have been reported. Calculated energies of HOMO and LUMO show that charge transfer occurs in the molecular. Information about the size, shape, charge density distribution and site of molecular chemical reactivity has been obtained by mapping electron density isosurface of electrostatic and compared with experiment data. PMID:26638891

  2. Synthesis, spectroscopic properties, molecular docking, anti-colon cancer and anti-microbial studies of some novel metal complexes for 2-amino-4-phenylthiazole derivative

    NASA Astrophysics Data System (ADS)

    Al-Harbi, Sami A.; Bashandy, Mahmoud S.; Al-Saidi, Hammed M.; Emara, Adel A. A.; Mousa, Tarek A. A.

    2015-06-01

    This article describes the synthesis of novel bidentate Schiff base (H2L) from condensation of 2-amino-4-phenylthiazole (APT) with 4,6-diacetylresorcinol (DAR) in the molar ratio 2:1. We studied interaction of ligand (H2L) with transition metal ions such as Cr(III), Fe(III), Cu(II), Zn(II) and Cd(II). The ligand (H2L) has two bidentate sets of (N-O) units which can coordinate with two metal ions to afford novel binuclear metal complexes. The directions of coordinate bonds are from nitrogen atoms of azomethine groups and oxygen atoms of the phenolic groups. Structures of the newly synthesized complexes were confirmed by elemental analysis, IR, UV, 1H NMR, ESR, TGA and mass spectral data. All of the newly synthesized complexes were evaluated for their antibacterial and anti-fungal activities. They were also evaluated for their in vitro anticancer activity against human colon carcinoma cells (HCT-116) and mammalian cells of African green monkey kidney (VERO). The Cu(II) complex with selectivity index (S.I.) = 21.26 exhibited better activity than methotrexate (MTX) as a reference drug with S.I. value = 13.30, while Zn(II) complex with S.I. value = 10.24 was found to be nearly as active as MTX. Molecular docking studies further helped in understanding the mode of action of the compounds through their various interactions with active sites of dihydrofolate reductase (DHFR) enzyme. The observed activity of Fe(III) and Cu(II) complexes gave rise to the conclusion that they might exert their action through inhibition of the DHFR enzyme.

  3. Spectroscopic (FT-IR, FT-Raman, UV, NMR, NBO, NLO) investigation and molecular docking study of (R)-2-Methylamino-1-Phenylethanol (Halostachine)

    NASA Astrophysics Data System (ADS)

    Subashini, K.; Govindarajan, R.; Surendran, R.; Mukund, K.; Periandy, S.

    2016-12-01

    FT-IR (4000-400 cm-1) and FT-Raman (4000-100 cm-1) spectra of (R)-2-Methylamino-1-Phenylethanol have been recorded in solid phase, 1H and 13C NMR in deuterated chloroform (CDCl3) phase and UV spectrum (200-400 nm) in solid phase and in ethanol solution. The different conformers of the compound and their minimum energies were studied by potential energy surface scan, using semi-empirical method PM6. The computed wavenumbers obtained from B3LYP and B3PW91 functionals along with 6-311++G (d, p) basis sets were scaled so as to agree with the experimental values and the scaling factors have been reported. All the fundamental modes have been assigned based on the potential energy distribution (PED) values and the structure of the molecule was analyzed in parameters like bond length, bond angle and dihedral angles through B3LYP and B3PW91 functionals along with 6-311++G(d,p) basis set. The values of dipole moment (μ), polarizability (α) and hyper polarizability (β) of the molecule were calculated using which, the non-linear optical property of the molecule has been discussed. The observed HOMO-LUMO mappings reveals the different charge transfer possibilities within the molecule. Natural Bond Orbital analysis was computed and possible transitions were correlated with the electronic transitions. Mulliken charges, electrostatic potential charges and natural charges are also predicted. The theoretical 1H and 13C NMR chemical shifts were computed using B3LYP functionals using 6-311++G (2d, p) basis sets. The temperature dependence of the thermodynamic properties; heat capacity, entropy and enthalpy for the title compound were also determined by B3LYP functionals with 6-311++G (d, p) basis set. Molecular docking study shows that the title compound might exhibit inhibitory activity against Bacillus anthracis (3V5O).

  4. Molecular structure, spectroscopic (FT-IR and UV-Vis) and DFT quantum-chemical studies on 2-[(2,4-Dimethylphenyl)iminomethyl]-6-methylphenol

    NASA Astrophysics Data System (ADS)

    Tanak, Hasan

    2014-06-01

    Density functional calculations of the structure, vibrational spectra, molecular electrostatic potential and thermodynamic functions have been performed at the B3LYP/6-311++G(d,p) level of theory for the Schiff base compound 2-[(2,4-Dimethylphenyl)iminomethyl]-6-methylphenol. Experimental and theoretical Fourier transform infrared (FT-IR) studies of the title compound show the preference of enol form, as supported by X-ray analysis results. Using the time-dependent density functional theory (TD-DFT) method, electronic absorption spectra of the compound have been predicted and a good agreement is determined with the experimental ones. To investigate the tautomeric stability, optimisation calculations at B3LYP/6-311++G(d,p) level were performed for the enol and keto forms of the title compound. Calculated results show that its enol form is more stable than that of the keto form. The predicted non-linear optical properties of the title compound are much greater than those of urea. The changes in thermodynamic properties for the formation of the title compound with the temperature ranging from 200 K to 500 K have been obtained using the statistical thermodynamic method. At 298.15 K the change of Gibbs free energy for the formation reaction of the title compound is 37.03 kJ/mol. The title compound cannot be spontaneously produced from the isolated monomers at room temperature. The tautomeric equilibrium constant is also computed as 1.23×10-3 at 298.15 K for enol ↔ keto tautomerisation of the title compound.

  5. Microsolvation of 2-thiouracil: molecular structure and spectroscopic parameters of the thiouracil-water complex.

    PubMed

    Puzzarini, Cristina; Biczysko, Malgorzata

    2015-05-28

    State-of-the-art quantum-chemical computations have been employed to accurately determine the equilibrium structure and interaction energy of the 2-thiouracil-water complex, thus extending available reference data for biomolecule solvation patterns. The coupled-cluster level of theory in conjunction with a triple-ζ basis set has been considered together with extrapolation to the basis set limit, performed by employing second-order Møller-Plesset perturbation theory, and inclusion of core-correlation and diffuse-function corrections. On the basis of the comparison of experiment and theory for 2-thiouracil [ Puzzarini et al. Phys. Chem. Chem. Phys. 2013 , 15 , 16965 - 16975 ], structural changes due to water complexation have been pointed out. Molecular and spectroscopic properties of the 2-thiouracil-water complex have then been studied by means of the composite computational approach introduced for the molecular structure evaluation. Among the results achieved, we mention the accurate determination of the molecular dipole moment and of the spectroscopic parameters required for predicting the rotational spectrum. PMID:25474644

  6. Thiazole-based nitrogen mustards: Design, synthesis, spectroscopic studies, DFT calculation, molecular docking, and antiproliferative activity against selected human cancer cell lines

    NASA Astrophysics Data System (ADS)

    Łączkowski, Krzysztof Z.; Świtalska, Marta; Baranowska-Łączkowska, Angelika; Plech, Tomasz; Paneth, Agata; Misiura, Konrad; Wietrzyk, Joanna; Czaplińska, Barbara; Mrozek-Wilczkiewicz, Anna; Malarz, Katarzyna; Musioł, Robert; Grela, Izabela

    2016-09-01

    Synthesis, characterization and investigation of antiproliferative activity of ten thiazole-based nitrogen mustard against human cancer cells lines (MV4-11, A549, MCF-7 and HCT116) and normal mouse fibroblast (BALB/3T3) is presented. The structures of novel compounds were determined using 1H and 13C NMR, FAB(+)-MS, and elemental analyses. Among the derivatives, 5b, 5c, 5e, 5f and 5i were found to exhibit high activity against human leukaemia MV4-11 cells with IC50 values of 2.17-4.26 μg/ml. The cytotoxic activity of compound 5c and 5f against BALB/3T3 cells is up to 20 times lower than against cancer cell lines. Our results also show that compounds 5e and 5i have very strong activity against MCF-7 and HCT116 with IC50 values of 3.02-4.13 μg/ml. Moreover, spectroscopic characterization and cellular localization for selected compound were performed. In order to identify potential drug targets we perform computer simulations with DNA-binding site of hTopoI and hTopoII and quantum chemical calculation of interaction and binding energies in complexes of the five most active compounds with guanine.

  7. Combined spectroscopic and quantum chemical studies of ezetimibe

    NASA Astrophysics Data System (ADS)

    Prajapati, Preeti; Pandey, Jaya; Shimpi, Manishkumar R.; Srivastava, Anubha; Tandon, Poonam; Velaga, Sitaram P.; Sinha, Kirti

    2016-12-01

    Ezetimibe (EZT) is a hypocholesterolemic agent used for the treatment of elevated blood cholesterol levels as it lowers the blood cholesterol by blocking the absorption of cholesterol in intestine. Study aims to combine experimental and computational methods to provide insights into the structural and vibrational spectroscopic properties of EZT which is important for explaining drug substance physical and biological properties. Computational study on molecular properties of ezetimibe is presented using density functional theory (DFT) with B3LYP functional and 6-311++G(d,p) basis set. A detailed vibrational assignment has been done for the observed IR and Raman spectra of EZT. In addition to the conformational study, hydrogen bonding and molecular docking studies have been also performed. For conformational studies, the double well potential energy curves have been plotted for the rotation around the six flexible bonds of the molecule. UV absorption spectrum was examined in methanol solvent and compared with calculated one in solvent environment (IEF-PCM) using TD-DFT/6-31G basis set. HOMO-LUMO energy gap of both the conformers have also been calculated in order to predict its chemical reactivity and stability. The stability of the molecule was also examined by means of natural bond analysis (NBO) analysis. To account for the chemical reactivity and site selectivity of the molecules, molecular electrostatic potential (MEPS) map has been plotted. The combination of experimental and calculated results provide an insight into the structural and vibrational spectroscopic properties of EZT. In order to give an insight for the biological activity of EZT, molecular docking of EZT with protein NPC1L1 has been done.

  8. Indentation device for in situ Raman spectroscopic and optical studies

    NASA Astrophysics Data System (ADS)

    Gerbig, Y. B.; Michaels, C. A.; Forster, A. M.; Hettenhouser, J. W.; Byrd, W. E.; Morris, D. J.; Cook, R. F.

    2012-12-01

    Instrumented indentation is a widely used technique to study the mechanical behavior of materials at small length scales. Mechanical tests of bulk materials, microscopic, and spectroscopic studies may be conducted to complement indentation and enable the determination of the kinetics and physics involved in the mechanical deformation of materials at the crystallographic and molecular level, e.g., strain build-up in crystal lattices, phase transformations, and changes in crystallinity or orientation. However, many of these phenomena occurring during indentation can only be observed in their entirety and analyzed in depth under in situ conditions. This paper describes the design, calibration, and operation of an indentation device that is coupled with a Raman microscope to conduct in situ spectroscopic and optical analysis of mechanically deformed regions of Raman-active, transparent bulk material, thin films or fibers under contact loading. The capabilities of the presented device are demonstrated by in situ studies of the indentation-induced phase transformations of Si thin films and modifications of molecular conformations in high density polyethylene films.

  9. Interaction of Lysozyme with Rhodamine B: A combined analysis of spectroscopic & molecular docking.

    PubMed

    Millan, Sabera; Satish, Lakkoji; Kesh, Sandeep; Chaudhary, Yatendra S; Sahoo, Harekrushna

    2016-09-01

    The interaction of Rhodamine B (RB) with Lysozyme (Lys) was investigated by different optical spectroscopic techniques such as absorption, fluorescence, and circular-dichroism (CD), along with molecular docking studies. The fluorescence results (including steady-state and time-resolved mode) revealed that the addition of RB effectively causes strong quenching of intrinsic fluorescence in Lysozyme and mostly, by the static quenching mechanism. Different binding and thermodynamic parameters were calculated at different temperatures and the binding constant value was found to be 2963.54Lmol(-1) at 25°C. The average distance (r0) was found to be 3.31nm according to Förster's theory of non-radiative energy transfer between Lysozyme and RB. The conformational change in Lysozyme during interaction with RB was confirmed from absorbance, synchronous fluorescence, and circular dichroism measurements. Finally, molecular docking studies were done to confirm that the dye binds with Lysozyme. PMID:27390893

  10. Spectroscopic, quantum chemical calculation and molecular docking of dipfluzine

    NASA Astrophysics Data System (ADS)

    Srivastava, Karnica; Srivastava, Anubha; Tandon, Poonam; Sinha, Kirti; Wang, Jing

    2016-12-01

    Molecular structure and vibrational analysis of dipfluzine (C27H29FN2O) were presented using FT-IR and FT-Raman spectroscopy and quantum chemical calculations. The theoretical ground state geometry and electronic structure of dipfluzine are optimized by the DFT/B3LYP/6-311++G (d,p) method and compared with those of the crystal data. The 1D potential energy scan was performed by varying the dihedral angle using B3LYP functional at 6-31G(d,p) level of theory and thus the most stable conformer of the compound were determined. Molecular electrostatic potential surface (MEPS), frontier orbital analysis and electronic reactivity descriptor were used to predict the chemical reactivity of molecule. Energies of intra- and inter-molecular hydrogen bonds in molecule and their electronic aspects were investigated by natural bond orbital (NBO). To find out the anti-apoptotic activity of the title compound molecular docking studies have been performed against protein Fas.

  11. MRCI study on the spectroscopic parameters and molecular constants of the X1Σ+, a3Σ+, A1Π and C1Σ- electronic states of the SiO molecule.

    PubMed

    Shi, Deheng; Li, Wentao; Sun, Jinfeng; Zhu, Zunlue

    2012-02-15

    The potential energy curves (PECs) of the X(1)Σ(+), a(3)Σ(+), A(1)Π and C(1)Σ(-) electronic states of the SiO molecule are studied using an ab initio quantum chemical method. The calculations have been made employing the complete active space self-consistent field (CASSCF) method, which is followed by the valence internally contracted multireference configuration interaction (MRCI) approach in combination with several correlation-consistent basis sets. The effect on the PECs by the core-valence correlation and relativistic corrections is included. The way to consider the relativistic correction is to use the third-order Douglas-Kroll Hamiltonian approximation. The core-valence correlation correction is carried out with the cc-pCVQZ basis set, and the relativistic correction is performed at the level of the cc-pVQZ basis set. To obtain more reliable results, the PECs determined by the MRCI calculations are also corrected for size-extensivity errors by means of the Davidson modification (MRCI+Q). The PECs of these electronic states are extrapolated to the complete basis set limit by the total-energy extrapolation scheme. Employing these PECs, the spectroscopic parameters are calculated and compared with those reported in the literature. With these PECs determined by the MRCI+Q/CV+DK+56 calculations, by solving the radial Schrödinger equation of nuclear motion, 110 vibrational states for the X(1)Σ(+), 69 for the a(3)Σ(+), 54 for the A(1)Π and 67 for the C(1)Σ(-) electronic state are predicted when the rotational quantum number J equals zero. The vibrational manifolds of the first 20 vibrational states are reported and compared with the available RKR data for each electronic state. On the whole, as expected, the most accurate spectroscopic parameters and molecular constants of the SiO molecule are obtained by the MRCI+Q/CV+DK+56 calculations. And the present molecular constants of the a(3)Σ(+), C(1)Σ(-) and A(1)Π electronic states determined by the MRCI

  12. Effects of molecular conformation on the spectroscopic properties of 4,4‧-disubstituted benzylideneanilines

    NASA Astrophysics Data System (ADS)

    Fang, Zhengjun; Wu, Feng; Yi, Bing; Cao, Chenzhong; Xie, Xin

    2016-01-01

    The relationship between the molecular conformation and spectroscopic properties of unsymmetrical 4,4‧-disubstituted benzylideneanilines, was explored by the combination of experiment and reference data. Crystal structure information and spectroscopic behaviors of the seventeen samples p-X-C6H4CHdbnd NC6H4-p-Y (X = NMe2, OMe, Me, Cl, CN, or NO2, Ydbnd NMe2, OMe, Me, Cl, CN, or NO2) were provided for this study. Among these seventeen compounds, nine ones were synthesized firstly, and five crystal structures were determined and analyzed. It was observed that the twist angle of the aniline ring with respect to the rest of the molecule (τ) is systematically controlled by the substituent at the aromatic ring. The correlation results show that the UV maximum absorption in wavenumbers (υmax) is dependent on the substituent at the aromatic ring and the dihedral angle τ of the titled molecules, and a sine function of τ (sin(τ)) is suitable to modify the substituent effects on the υmax. However, the dihedral angle τ has a limited effect on the values of 13C NMR chemical shifts δC(Cdbnd N). The results indicate that the dihedral angle τ has an significant effect on UV spectra of Schiff bases with different parent structure although there is something different about the parameter metrics. While it has a relatively limited effect on the values of δC(Cdbnd N) in both unsymmetrical and unsymmetrical Schiff bases. This study provides an sufficient evidence of the molecular conformation on spectroscopic properties of Schiff bases.

  13. Vibrational spectroscopic (FT-IR and FT-Raman) studies, natural bond orbital analysis and molecular electrostatic potential surface of 3-hydroxy-6-methyl-2-nitropyridine

    NASA Astrophysics Data System (ADS)

    Karnan, M.; Balachandran, V.; Murugan, M.

    2012-10-01

    The optimized molecular structure and corresponding vibrational assignments of 3-hydroxy-6-methyl-2-nitropyridine have been investigated using density functional theory (DFT) B3LYP method with 6-311++G(d,p), 6-311++G(2d,2p) and 6-311++G(3d,3p) basis sets. Investigation of the relative orientation of the hydroxyl group with respect to the nitro group has shown that two conformers (O-cis) and (O-trans) exist. The vibrational analysis of the stable conformer of the title compound is performed by means of infrared absorption and Raman spectroscopy in combination with theoretical simulations. The molecular stability and bond strength were investigated by applying the natural bond orbital (NBO) analysis. Information about the size, shape, charge density distribution and site of chemical reactivity of the molecule has been obtained by mapping electron density isosurface with electrostatic potential (ESP). The isotropic chemical shift computed by 1H and 13C nuclear magnetic resonance (NMR) chemical shifts of the HMNP calculated using the gauge invariant atomic orbital (GIAO) method also shows good agreement with experimental observations.

  14. Spectroscopic study of solar twins and analogues

    NASA Astrophysics Data System (ADS)

    Datson, Juliet; Flynn, Chris; Portinari, Laura

    2015-02-01

    Context. Many large stellar surveys have been and are still being carried out, providing huge amounts of data, for which stellar physical parameters will be derived. Solar twins and analogues provide a means to test the calibration of these stellar catalogues because the Sun is the best-studied star and provides precise fundamental parameters. Solar twins should be centred on the solar values. Aims: This spectroscopic study of solar analogues selected from the Geneva-Copenhagen Survey (GCS) at a resolution of 48 000 provides effective temperatures and metallicities for these stars. We test whether our spectroscopic parameters, as well as the previous photometric calibrations, are properly centred on the Sun. In addition, we search for more solar twins in our sample. Methods: The methods used in this work are based on literature methods for solar twin searches and on methods we developed in previous work to distinguish the metallicity-temperature degeneracies in the differential comparison of spectra of solar analogues versus a reference solar reflection spectrum. Results: We derive spectroscopic parameters for 148 solar analogues (about 70 are new entries to the literature) and verify with a-posteriori differential tests that our values are well-centred on the solar values. We use our dataset to assess the two alternative calibrations of the GCS parameters; our methods favour the latest revision. We show that the choice of spectral line list or the choice of asteroid or time of observation does not affect the results. We also identify seven solar twins in our sample, three of which are published here for the first time. Conclusions: Our methods provide an independent means to differentially test the calibration of stellar catalogues around the values of a well-known benchmark star, which makes our work interesting for calibration tests of upcoming Galactic surveys. Based on observations made with ESO Telescopes at the La Silla Observatory under programme ID 077.D

  15. Synthesis, click reaction, molecular structure, spectroscopic and DFT computational studies on 3-(2,6-bis(trifluoromethyl)phenoxy)-6-(prop-2-yn-1-yloxy)phthalonitrile

    NASA Astrophysics Data System (ADS)

    Hasan, Muhammad; Shalaby, Mona

    2016-06-01

    The compound 3-(2,6-bis(trifluoromethyl)phenoxy)-6-(prop-2-yn-1-yloxy)phthalonitrile has been synthesized and confirmed by different characterization techniques such as elemental analysis, IR, UV-vis spectroscopy, and X-ray single-crystal determination. The molecular geometry from X-ray determination of this compound in the ground state has been compared using the Hartree-Fock (HF) and density functional theory (DFT) with the 6-31G(d) basis set. This compound reacted with sugar azide via click reaction to form triazol ring. The synergy between carbohydrate molecule and fluorinated organic compound achieved novel synthetic pathways, properties, and applications in chemistry science.

  16. Spectroscopic and molecular modeling study on the separate and simultaneous bindings of alprazolam and fluoxetine hydrochloride to human serum albumin (HSA): With the aim of the drug interactions probing

    NASA Astrophysics Data System (ADS)

    Dangkoob, Faeze; Housaindokht, Mohmmad Reza; Asoodeh, Ahmad; Rajabi, Omid; Rouhbakhsh Zaeri, Zeinab; Verdian Doghaei, Asma

    2015-02-01

    The objective of the present research is to study the interaction of separate and simultaneous of alprazolam (ALP) and fluoxetine hydrochloride (FLX) with human serum albumin (HSA) in phosphate buffer (pH 7.4) using different kinds of spectroscopic, cyclic voltammetry and molecular modeling techniques. The absorbance spectra of protein, drugs and protein-drug showed complex formation between the drugs and HSA. Fluorescence analysis demonstrated that ALP and FLX could quench the fluorescence spectrum of HSA and demonstrated the conformational change of HSA in the presence of both drugs. Also, fluorescence quenching mechanism of HSA-drug complexes both separately and simultaneously was suggested as static quenching. The analysis of UV absorption data and the fluorescence quenching of HSA in the binary and ternary systems showed that FLX decreased the binding affinity between ALP and HSA. On the contrary, ALP increased the binding affinity of FLX and HSA. The results of synchronous fluorescence and three-dimensional fluorescence spectra indicated that the binding of drugs to HSA would modify the microenvironment around the Trp and Tyr residues and the conformation of HSA. The distances between Trp residue and the binding sites of the drugs were estimated according to the Förster theory, and it was demonstrated that non-radiative energy transfer from HSA to the drugs occurred with a high probability. Moreover, according to CV measurements, the decrease of peak current in the cyclic voltammogram of the both drugs in the presence of HSA revealed that they interacted with albumin and binding constants were calculated for binary systems which were in agreement with the binding constants obtained from UV absorption and fluorescence spectroscopy. The prediction of the best binding sites of ALP and FLX in binary and ternary systems in molecular modeling approach was done using of Gibbs free energy.

  17. Spectroscopic and molecular modeling study on the separate and simultaneous bindings of alprazolam and fluoxetine hydrochloride to human serum albumin (HSA): with the aim of the drug interactions probing.

    PubMed

    Dangkoob, Faeze; Housaindokht, Mohmmad Reza; Asoodeh, Ahmad; Rajabi, Omid; Rouhbakhsh Zaeri, Zeinab; Verdian Doghaei, Asma

    2015-02-25

    The objective of the present research is to study the interaction of separate and simultaneous of alprazolam (ALP) and fluoxetine hydrochloride (FLX) with human serum albumin (HSA) in phosphate buffer (pH 7.4) using different kinds of spectroscopic, cyclic voltammetry and molecular modeling techniques. The absorbance spectra of protein, drugs and protein-drug showed complex formation between the drugs and HSA. Fluorescence analysis demonstrated that ALP and FLX could quench the fluorescence spectrum of HSA and demonstrated the conformational change of HSA in the presence of both drugs. Also, fluorescence quenching mechanism of HSA-drug complexes both separately and simultaneously was suggested as static quenching. The analysis of UV absorption data and the fluorescence quenching of HSA in the binary and ternary systems showed that FLX decreased the binding affinity between ALP and HSA. On the contrary, ALP increased the binding affinity of FLX and HSA. The results of synchronous fluorescence and three-dimensional fluorescence spectra indicated that the binding of drugs to HSA would modify the microenvironment around the Trp and Tyr residues and the conformation of HSA. The distances between Trp residue and the binding sites of the drugs were estimated according to the Förster theory, and it was demonstrated that non-radiative energy transfer from HSA to the drugs occurred with a high probability. Moreover, according to CV measurements, the decrease of peak current in the cyclic voltammogram of the both drugs in the presence of HSA revealed that they interacted with albumin and binding constants were calculated for binary systems which were in agreement with the binding constants obtained from UV absorption and fluorescence spectroscopy. The prediction of the best binding sites of ALP and FLX in binary and ternary systems in molecular modeling approach was done using of Gibbs free energy. PMID:25300043

  18. First principal studies of spectroscopic (IR and Raman, UV-visible), molecular structure, linear and nonlinear optical properties of L-arginine p-nitrobenzoate monohydrate (LANB): A new non-centrosymmetric material

    NASA Astrophysics Data System (ADS)

    Shkir, Mohd.; AlFaify, S.; Abbas, Haider; Muhammad, Shabbir

    2015-08-01

    In current work, the authors have been applied the density functional theory (DFT) using B3LYP and CAM-B3LYP exchange-correlation functional with 6-31G∗ basis set on L-arginine p-nitrobenzoate monohydrate (LANB) molecule for the first time to optimize its geometry and study the spectroscopic, electronic structure, nonlinear optical properties. Vibrational modes were found in good agreement with experimental reports. The calculated UV spectra by B3LYP/6-31G∗ and CAM-B3LYP/6-31G∗ level of theory shows an electronic transition at ∼268 nm (4.63 eV) and 264 nm (4.70 eV) respectively. To explain the charge interaction taking place within the molecule highest occupied molecular orbital and lowest unoccupied molecular orbital were analyzed and their calculated energy gap was found to be 4.3 eV with an oscillatory strength 0.3796 at B3LYP/6-31G∗ level of theory. The dipole moment (μtot), average and anisotropy of polarizability (αtot, Δα) and static and total first hyperpolarizability (β0, βtot) values were calculated. The value of μtot and βtot are found to be 4.124D and 1.630 × 10-30 esu and 4.127D and 1.133 × 10-30 esu using B3LYP/6-31G∗ and CAM-B3LYP/6-31G∗ functional respectively. The value of βtot is >4 and >3 times higher than prototype urea molecule calculated at both level of theory, respectively. The molecular electrostatic potential (MEP), frontier molecular orbital's (FMOs), global reactivity descriptors and thermodynamic properties are also calculated and discussed. The properties of LANB calculated at B3LYP are in good correlation with experimental than the CAM-B3LYP level of theory. The obtained results show that LANB molecule can be treated as a good candidate for nonlinear optical devices.

  19. Heavy-ion irradiation on crystallographically oriented cordierite and the conversion of molecular CO2 to CO: a Raman spectroscopic study

    NASA Astrophysics Data System (ADS)

    Weikusat, Christian; Miletich, Ronald; Glasmacher, Ulrich A.; Trautmann, Christina; Neumann, Reinhard

    2010-07-01

    Crystallographically oriented sections of natural gemstone quality cordierite single-crystals have been irradiated with swift heavy ions of GeV energy and various fluences. Irradiation effects on the crystal lattice were investigated by means of Raman spectroscopy. Raman line scans along the trajectory of the ions reveal a close correlation of beam parameters (such as fluence and energy loss d E/d x along the ion path) to strain due to associated changes in lattice dimensions and defect concentration. The luminescence background also scales with the ion fluence and suggests the formation of point defects, which could also account for the macroscopically observable colouration of the irradiated samples. In addition, changes in the amount and nature of volatile species inside the structural channels are observed. They also scale with d E/d x and confirm the previously postulated irradiation-induced conversion of CO2 to CO. Irradiations along the crystallographic a-, b- and c-axis reveal no significant anisotropy effect with respect to lattice alterations. The polarisation characteristics of the Raman-active modes confirm the preferred molecular alignment of CO and CO2 along the a-axis direction.

  20. Molecular level investigation of 2,2,6,6-tetramethyl-3,5-heptanedione on Si(1 0 0)-2 × 1: Spectroscopic and computational studies

    NASA Astrophysics Data System (ADS)

    Perrine, Kathryn A.; Skliar, Dimitri B.; Willis, Brian G.; Teplyakov, Andrew V.

    2008-07-01

    The molecular level chemistry of 2,2,6,6-tetramethyl-3,5-heptanedione (dpmH) has been investigated on a Si(1 0 0)-2 × 1 surface. The dpmH compound is a β-diketone, whose deprotonated form is used as a ligand in chemical precursors for metal-organic chemical vapor deposition (MOCVD). A combination of multiple internal reflection Fourier-transform infrared spectroscopy (MIR-FTIR), temperature programmed desorption (TPD), Auger electron spectroscopy (AES) and density functional theory (DFT) were employed to analytically detect and monitor surface species under different thermal conditions. Upon adsorption at cryogenic temperatures dpmH was shown to be present in the enolic form, while primarily OH dissociation and [2 + 2] carbonyl cycloaddition were revealed at room temperature. Upon heating from room temperature to 900 K, isobutene evolution into the gas phase was found to be a minor reaction pathway. The remainder of dpmH decomposes on the surface to release hydrogen into the gas phase.

  1. Vibrational spectroscopic (FT-IR and FT-Raman) studies, natural bond orbital analysis and molecular electrostatic potential surface of Isoxanthopterin

    NASA Astrophysics Data System (ADS)

    Prabavathi, N.; Nilufer, A.; Krishnakumar, V.

    2013-10-01

    The FTIR and FT-Raman spectra of Isoxanthopterin have been recorded in the region 4000-450 and 4000-100 cm-1, respectively. The optimized geometry, frequency and intensity of the vibrational bands of Isoxanthopterin were obtained by the density functional theory (DFT) using 6-311++G(d,p) basis set. The harmonic vibrational frequencies were scaled and compared with experimental values. The observed and the calculated frequencies are found to be in good agreement. The 1H and 13C nuclear magnetic resonance chemical shifts of the molecule were also calculated using the gauge independent atomic orbital (GIAO) method. The UV-visible spectrum was also recorded and compared with the theoretical values. The calculated HOMO and LUMO energies show that charge transfer occurs within molecule. The first order hyperpolarizability (β0), related properties (β, α0 and Δα) and the Mulliken charges of the molecule were also computed using DFT calculations. Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. The results show that charge in electron density (ED) in the σ* and π* antibonding orbitals and second order delocalization energies (E2) confirms the occurrence of intramolecular charge transfer (ICT) within the molecule. Information about the charge density distribution of the molecule and its chemical reactivity has been obtained by mapping molecular electrostatic potential surface. In addition, the non-linear optical properties were discussed from the dipole moment values and excitation wavelength in the UV-visible region.

  2. Vibrational spectroscopic (FT-IR and FT-Raman) studies, natural bond orbital analysis and molecular electrostatic potential surface of Isoxanthopterin.

    PubMed

    Prabavathi, N; Nilufer, A; Krishnakumar, V

    2013-10-01

    The FTIR and FT-Raman spectra of Isoxanthopterin have been recorded in the region 4000-450 and 4000-100 cm(-1), respectively. The optimized geometry, frequency and intensity of the vibrational bands of Isoxanthopterin were obtained by the density functional theory (DFT) using 6-311++G(d,p) basis set. The harmonic vibrational frequencies were scaled and compared with experimental values. The observed and the calculated frequencies are found to be in good agreement. The (1)H and (13)C nuclear magnetic resonance chemical shifts of the molecule were also calculated using the gauge independent atomic orbital (GIAO) method. The UV-visible spectrum was also recorded and compared with the theoretical values. The calculated HOMO and LUMO energies show that charge transfer occurs within molecule. The first order hyperpolarizability (β0), related properties (β, α0 and Δα) and the Mulliken charges of the molecule were also computed using DFT calculations. Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. The results show that charge in electron density (ED) in the σ* and π* antibonding orbitals and second order delocalization energies (E2) confirms the occurrence of intramolecular charge transfer (ICT) within the molecule. Information about the charge density distribution of the molecule and its chemical reactivity has been obtained by mapping molecular electrostatic potential surface. In addition, the non-linear optical properties were discussed from the dipole moment values and excitation wavelength in the UV-visible region. PMID:23751224

  3. Anion pairs in room temperature ionic liquids predicted by molecular dynamics simulation, verified by spectroscopic characterization

    SciTech Connect

    Schwenzer, Birgit; Kerisit, Sebastien N.; Vijayakumar, M.

    2014-01-01

    Molecular-level spectroscopic analyses of an aprotic and a protic room-temperature ionic liquid, BMIM OTf and BMIM HSO4, respectively, have been carried out with the aim of verifying molecular dynamics simulations that predict anion pair formation in these fluid structures. Fourier-transform infrared spectroscopy, Raman spectroscopy and nuclear magnetic resonance spectroscopy of various nuclei support the theoretically-determined average molecular arrangements.

  4. Terahertz spectroscopic study of benzodiazepine sedative hypnotics

    NASA Astrophysics Data System (ADS)

    Deng, Fusheng; Shen, Jingling; Wang, Xianfeng

    2011-08-01

    Terahertz time domain spectroscopy (THz-TDS) is used to the pure active ingredient of three benzodiazepine sedative hypnotics with similar molecular structure. The absorption spectra of them are studied in the range of 0.2~2.6THz. Based on the experiment, the theoretical simulation results of diazepam, nitrazepam and clonazepam are got by the Gaussian03 package of DFT/B3LYP/6-31G* method in single-molecule models. The experimental results show that even if the molecular structure and medicine property of them are similar, the accurate identification of them can still be done with their characteristic absorption spectra. Theoretical simulation results are well consistent with the experimental results. It demonstrates that absorption peaks of them in THz range mainly come from intra-molecular forces and are less affected by the intermolecular interaction and crystal effects.ô

  5. Molecular structure, spectroscopic properties and DFT calculations of 2-(methylthio)nicotinic acid

    NASA Astrophysics Data System (ADS)

    Gökce, Halil; Bahçeli, Semiha

    2013-10-01

    The analyses of possible conformations, molecular structures, vibrational and electronic properties of 2-(methylthio)nicotinic acid molecule, C7H7NO2S, with the synonym 2-(methylsulfanyl)nicotinic acid have been first presented theoretically. At the same time, FT-IR and micro-Raman spectra of 2-(methylthio)nicotinic acid were recorded in the regions 400-4000 cm-1 and 100-4000 cm-1, respectively. In our calculations, the DFTB3LYP method with 6-311G(d, p) basis set was used to have the structural and spectroscopic data about the mentioned molecule in the ground state and the results obtained were compared with experimental values. Furthermore, gauge invariant atomic orbital (GIAO) 1H and 13C NMR chemical shifts in different solvents, UV-vis TD-DFT calculations, the highest occupied molecular orbitals (HOMO-2, HOMO-1, HOMO), lowest unoccupied molecular orbital (LUMO), molecular electrostatic potantial (MEP) surface, atomic charges and thermodynamic properties of molecule have been theoretically verified and simulated at the mentioned level. The energetic behavior of title molecule in different solvent media was investigated by using DFT/B3LYP method with 6-311G(d, p) basis set in terms of integral equation formalism polarizable continuum model (IEFPCM). In addition, the calculated infrared intensities, Raman activities, reduce masses and force constants of the compound under study have been also reported.

  6. Spectroscopic (FT-IR, FT-Raman, NMR and UV-Visible) and quantum chemical studies of molecular geometry, Frontier molecular orbital, NLO, NBO and thermodynamic properties of salicylic acid

    NASA Astrophysics Data System (ADS)

    Suresh, S.; Gunasekaran, S.; Srinivasan, S.

    2014-11-01

    The solid phase FT-IR and FT-Raman spectra of 2-hydroxybenzoic acid (salicylic acid) have been recorded in the region 4000-400 and 4000-100 cm-1 respectively. The optimized molecular geometry and fundamental vibrational frequencies are interpreted with the aid of structure optimizations and normal coordinate force field calculations based on density functional theory (DFT) method and a comparative study between Hartree Fork (HF) method at 6-311++G(d,p) level basis set. The calculated harmonic vibrational frequencies are scaled and they are compared with experimentally obtained FT-IR and FT-Raman spectra. A detailed interpretation of the vibrational spectra of this compound has been made on the basis of the calculated potential energy distribution (PED). The time dependent DFT method is employed to predict its absorption energy and oscillator strength. The linear polarizability (α) and the first order hyper polarizability (β) values of the investigated molecule have been computed. The electronic properties, such as HOMO and LUMO energies, molecular electrostatic potential (MEP) are also performed. Stability of the molecule arising from hyper conjugative interaction, charge delocalization has been analyzed using natural bond orbital (NBO) analysis.

  7. 4-Hydroxy-benzoic acid (4-diethylamino-2-hydroxy-benzylidene)hydrazide: DFT, antioxidant, spectroscopic and molecular docking studies with BSA.

    PubMed

    Sharma, Vibha; Arora, Ekta Kundra; Cardoza, Savio

    2016-05-01

    The Schiff base 4-hydroxy-benzoic acid (4-diethylamino-2-hydroxy-benzylidene) hydrazide (SL) was synthesized and characterized. Its antioxidant activity was evaluated using 1,1-diphenyl-2-picrylhydrazyl (DPPH) free radical scavenging action. Being a potent antioxidant its binding ability to the transport protein bovine serum albumin (BSA) was studied using fluorescence quenching and circular dichroism (CD) studies. The binding distance has been calculated by fluorescence resonance energy transfer (FRET) to be 1.85 Å and the Stern-Volmer quenching constant has been calculated to be (3.23 ± 0.45) × 10(5)  M(-1) . Quantum chemical analysis was carried out for the Schiff base using DFT with B3LYP and 6-311G** and related to the experimentally obtained results. For a deeper understanding of the mechanism of the interaction, the experimental data were complemented by protein-Schiff base docking calculations using Argus Lab. Copyright © 2015 John Wiley & Sons, Ltd. PMID:26333657

  8. The molecular structure of the phosphate mineral senegalite Al2(PO4)(OH)3ṡ3H2O - A vibrational spectroscopic study

    NASA Astrophysics Data System (ADS)

    Frost, Ray L.; López, Andrés; Xi, Yunfei; Murta, Natália; Scholz, Ricardo

    2013-09-01

    We have studied the mineral senagalite, a hydrated hydroxy phosphate of aluminium with formula Al2(PO4)(OH)3ṡ3H2O using a combination of electron microscopy and vibrational spectroscopy. Senegalite crystal aggregates shows tabular to prismatic habitus and orthorhombic form. The Raman spectrum is dominated by an intense band at 1029 cm-1 assigned to the PO43- ν1 symmetric stretching mode. Intense Raman bands are found at 1071 and 1154 cm-1 with bands of lesser intensity at 1110, 1179 and 1206 cm-1 and are attributed to the PO43- ν3 antisymmetric stretching vibrations. The infrared spectrum shows complexity with a series overlapping bands. A comparison is made with spectra of other aluminium containing phosphate minerals such as augelite and turquoise. Multiple bands are observed for the phosphate bending modes giving support for the reduction of symmetry of the phosphate anion. Vibrational spectroscopy offers a means for the assessment of the structure of senagalite.

  9. Molecular and mass spectroscopic analysis of isotopically labeled organic residues

    NASA Technical Reports Server (NTRS)

    Mendoza-Gomez, Celia X.; Greenberg, J. Mayo; Mccain, P.; Ferris, J. P.; Briggs, R.; Degroot, M. S.; Schutte, Willem A.

    1989-01-01

    Experimental studies aimed at understanding the evolution of complex organic molecules on interstellar grains were performed. The photolysis of frozen gas mixtures of various compositions containing H2O, CO, NH3, and CH4 was studied. These species were chosen because of their astrophysical importance as deducted from observational as well as theoretical studies of ice mantles on interstellar grains. These ultraviolet photolyzed ices were warmed up in order to produce refractory organic molecules like the ones formed in molecular clouds when the icy mantles are being irradiated and warmed up either by a nearby stellar source or impulsive heating. The laboratory studies give estimates of the efficiency of production of such organic material under interstellar conditions. It is shown that the gradual carbonization of organic mantles in the diffuse cloud phase leads to higher and higher visual absorptivity - yellow residues become brown in the laboratory. The obtained results can be applied to explaining the organic components of comets and their relevance to the origin of life.

  10. The molecular structure of the vanadate mineral mottramite [PbCu(VO4)(OH)] from Tsumeb, Namibia--a vibrational spectroscopic study.

    PubMed

    Frost, Ray L; Xi, Yunfei; López, Andrés; Corrêa, Lívia; Scholz, Ricardo

    2014-03-25

    We have studied a mineral sample of mottramite PbCu(VO4)(OH) from Tsumeb, Namibia using a combination of scanning electron microscopy with EDX, Raman and infrared spectroscopy. Chemical analysis shows principally the elements V, Pb and Cu. Ca occurs as partial substitution of Pb as well as P and As in substitution to V. Minor amounts of Si and Cr were also observed. The Raman band of mottramite at 829 cm(-1), is assigned to the ν1 symmetric (VO4(-)) stretching mode. The complexity of the spectra is attributed to the chemical composition of the Tsumeb mottramite. The ν3 antisymmetric vibrational mode of mottramite is observed as very low intensity bands at 716 and 747 cm(-1). The series of Raman bands at 411, 439, 451 cm(-1) and probably also the band at 500 cm(-1) are assigned to the (VO4(-)) ν2 bending mode. The series of Raman bands at 293, 333 and 366 cm(-1) are attributed to the (VO4(-)) ν4 bending modes. The ν3, ν3 and ν4 regions are complex for both minerals and this is attributed to symmetry reduction of the vanadate unit from Td to Cs. PMID:24316538

  11. Spectroscopic Studies of the Salmonella enterica Adenosyltransferase Enzyme SeCobA: Molecular-Level Insight into the Mechanism of Substrate Cob(II)alamin Activation

    PubMed Central

    2015-01-01

    CobA from Salmonella enterica (SeCobA) is a member of the family of ATP:Co(I)rrinoid adenosyltransferase (ACAT) enzymes that participate in the biosynthesis of adenosylcobalamin by catalyzing the transfer of the adenosyl group from an ATP molecule to a reactive Co(I)rrinoid species transiently generated in the enzyme active site. This reaction is thermodynamically challenging, as the reduction potential of the Co(II)rrinoid precursor in solution is far more negative than that of available reducing agents in the cell (e.g., flavodoxin), precluding nonenzymic reduction to the Co(I) oxidation state. However, in the active sites of ACATs, the Co(II)/Co(I) redox potential is increased by >250 mV via the formation of a unique four-coordinate (4c) Co(II)rrinoid species. In the case of the SeCobA ACAT, crystallographic and kinetic studies have revealed that the phenylalanine 91 (F91) and tryptophan 93 (W93) residues are critical for in vivo activity, presumably by blocking access to the lower axial ligand site of the Co(II)rrinoid substrate. To further assess the importance of the F91 and W93 residues with respect to enzymatic function, we have characterized various SeCobA active-site variants using electronic absorption, magnetic circular dichroism, and electron paramagnetic resonance spectroscopies. Our data provide unprecedented insight into the mechanism by which SeCobA converts the Co(II)rrinoid substrate to 4c species, with the hydrophobicity, size, and ability to participate in offset π-stacking interactions of key active-site residues all being critical for activity. The structural changes that occur upon Co(II)rrinoid binding also appear to be crucial for properly orienting the transiently generated Co(I) “supernucleophile” for rapid reaction with cosubstrate ATP. PMID:25423616

  12. A vibrational spectroscopic study of the borate mineral ezcurrite Na4B10O17·7H2O - Implications for the molecular structure

    NASA Astrophysics Data System (ADS)

    Frost, Ray L.; López, Andrés; Theiss, Frederick L.; Scholz, Ricardo; Belotti, Fernanda M.

    2014-07-01

    We have studied the boron containing mineral ezcurrite Na4B10O17·7H2O using electron microscopy and vibrational spectroscopy. Both tetrahedral and trigonal boron units are observed. The nominal resolution of the Raman spectrometer is of the order of 2 cm-1 and as such is sufficient enough to identify separate bands for the stretching bands of the two boron isotopes. The Raman band at 1037 cm-1 is assigned to BO stretching vibration. Raman bands at 1129, 1163, 1193 cm-1 are attributed to BO stretching vibration of the tetrahedral units. The Raman band at 947 cm-1 is attributed to the antisymmetric stretching modes of tetrahedral boron. The sharp Raman peak at 1037 cm-1 is from the 11-B component such a mode, then it should have a smaller 10-B satellite near (1.03) × (1037) = 1048 cm-1, and indeed a small peak at 1048 is observed. The broad Raman bands at 3186, 3329, 3431, 3509, 3547 and 3576 cm-1 are assigned to water stretching vibrations. Broad infrared bands at 3170, 3322, 3419, 3450, 3493, 3542, 3577 and 3597 cm-1 are also assigned to water stretching vibrations. Infrared bands at 1330, 1352, 1389, 1407, 1421 and 1457 cm-1 are assigned to the antisymmetric stretching vibrations of trigonal boron. The observation of so many bands suggests that there is considerable variation in the structure of ezcurrite. Infrared bands at 1634, 1646 and 1681 cm-1 are assigned to water bending modes. The number of water bending modes is in harmony with the number of water stretching vibrations.

  13. Fundamental spectroscopic studies of carbenes and hydrocarbon radicals

    SciTech Connect

    Gottlieb, C.A.; Thaddeus, P.

    1993-12-01

    Highly reactive carbenes and carbon-chain radicals are studied at millimeter wavelengths by observing their rotational spectra. The purpose is to provide definitive spectroscopic identification, accurate spectroscopic constants in the lowest vibrational states, and reliable structures of the key intermediates in reactions leading to aromatic hydrocarbons and soot particles in combustion.

  14. The molecular structure of the phosphate mineral beraunite Fe(2+)Fe5(3+)(PO4)4(OH)5⋅4H2O--a vibrational spectroscopic study.

    PubMed

    Frost, Ray L; López, Andrés; Scholz, Ricardo; Xi, Yunfei; Lana, Cristiano

    2014-07-15

    The mineral beraunite from Boca Rica pegmatite in Minas Gerais with theoretical formula Fe(2+)Fe5(3+)(PO4)4(OH)5⋅4H2O has been studied using a combination of electron microscopy with EDX and vibrational spectroscopic techniques. Raman spectroscopy identifies an intense band at 990 cm(-1) and 1011 cm(-1). These bands are attributed to the PO4(3)(-) ν1 symmetric stretching mode. The ν3 antisymmetric stretching modes are observed by a large number of Raman bands. The Raman bands at 1034, 1051, 1058, 1069 and 1084 together with the Raman bands at 1098, 1116, 1133, 1155 and 1174 cm(-1) are assigned to the ν3 antisymmetric stretching vibrations of PO4(3-) and the HOPO3(2-) units. The observation of these multiple Raman bands in the symmetric and antisymmetric stretching region gives credence to the concept that both phosphate and hydrogen phosphate units exist in the structure of beraunite. The series of Raman bands at 567, 582, 601, 644, 661, 673, and 687 cm(-1) are assigned to the PO4(3-) ν2 bending modes. The series of Raman bands at 437, 468, 478, 491, 503 cm(-1) are attributed to the PO4(3-) and HOPO3(2-) ν4 bending modes. No Raman bands of beraunite which could be attributed to the hydroxyl stretching unit were observed. Infrared bands at 3511 and 3359 cm(-1) are ascribed to the OH stretching vibration of the OH units. Very broad bands at 3022 and 3299 cm(-1) are attributed to the OH stretching vibrations of water. Vibrational spectroscopy offers insights into the molecular structure of the phosphate mineral beraunite. PMID:24682056

  15. Infrared spectroscopic study of sputtered tungsten oxide films

    SciTech Connect

    Paul, J.L.; Lassegues, J.C. )

    1993-10-01

    Recent infrared and Raman spectroscopic studies of various tungsten oxide films concluded either the formation of W=O terminal bonds or the transformation of such bonds into W-OH groups upon proton insertion. The infrared transmission and reflection spectra of bleached and colored sputtered films were reinvestigated in order to resolve the previous contradictory interpretations and for better insight into the mechanism of electrochromism at the molecular level. The new results confirm the first interpretation and allow us to show that H[sup +] or Li[sup +] insertion creates shorter ([approximately]1.7[angstrom]) and longer ([approximately]2 [angstrom]) W-O bonds around the W[sup 5+] centers. These results are in agreement with the concepts of small polaron and of intervalence charge transfer mechanism. They illustrate the local lattice distortion around a W[sup 5+] site. Aging of the initial films has also been followed and characterized by H/D in situ isotopic exchange.

  16. Conformational stability, spectroscopic and computational studies, hikes' occupied molecular orbital, lowest unoccupied molecular orbital, natural bond orbital analysis and thermodynamic parameters of anticancer drug on nanotube-A review.

    PubMed

    Ghasemi, A S; Mashhadban, F; Hoseini-Alfatemi, S M; Sharifi-Rad, J

    2015-01-01

    Today the use of nanotubes (CNTs) is widely spread a versatile vector for drug delivery that can officiate as a platform for transporting a variety of bioactive molecules, such as drugs. In the present study, the interaction between the nanotube and anticancer drugs is investigated. Density functional theory (DFT) calculations were using the Gauss view and the complexes were optimized by B3LYP method using B3LYP/6-31G (d, p) and B3LYP/6-311++G (d, p) basis set in the gas phase and water solution at 298.15K. The calculated hikes' occupied molecular orbital (HOMO) and the lowest unoccupied (LUMO) energies Show that charge transfer occurs within the molecule. Furthermore, the effects of interactions on the natural bond orbital analysis (NBO) have been used to a deeper investigation into the studied compounds. These factors compete against each other to determine the adsorption behavior of the tube computer simulation is seen to be capable to optimize anticancer drug design. This review article mainly concentrates on the different protocols of loading anticancer drugs onto CNTs as well as how to control the anticancer drug release and cancer treatment. PMID:26718433

  17. Spectroscopic study of HNO3 dissociation on ice.

    PubMed

    Marchand, Patrick; Marcotte, Guillaume; Ayotte, Patrick

    2012-12-13

    A detailed spectroscopic study of HNO(3):H(2)O binary amorphous mixtures, and of the adsorption of HNO(3) onto ice, is reported. Using a classical optics model, the extent of intermixing and of ionic dissociation of adsorbed HNO(3), which forms a strong acid with liquid water, is determined as a function of HNO(3) coverage and temperature. Even at temperatures as low as 45 K, where intermixing is limited to at most a few molecular layers at the interface, ionic dissociation of adsorbed HNO(3) is observed to be extensive. While some amount of molecularly adsorbed HNO(3) is observed at the surface of ice at 45 K, its ionic dissociation occurs irreversibly upon heating the ice substrate to 120 K. The molecularly adsorbed state of HNO(3) is not restored upon cooling, suggesting HNO(3) is a metastable entity at the surface of ice. Therefore, despite ionic dissociation of HNO(3) being thermodynamically favored, it appears to be kinetically inhibited at the surface of amorphous solid water at temperatures below 120 K. PMID:23130955

  18. Spectroscopic and quantum chemical studies on bromopyrazone

    NASA Astrophysics Data System (ADS)

    Gökce, Halil; Bahçeli, Semiha

    2014-12-01

    In this study, the FT-IR, micro-Raman and UV-vis. spectra of bromopyrazone molecule, C10H8BrN3O, (with synonym,1-phenyl-4-amino-5-bromopyridazon-(6) or 5-amino-4-bromo-2-phenyl-3(2H)-pyridazinone) were recorded experimentally. The molecular structure, vibrational wavenumbers, electronic transition absorption wavelengths in ethanol solvent, HOMOs and LUMOs analyses, molecular electrostatic potential (MEP), natural bond orbitals (NBO), nonlinear optical (NLO) properties and atomic charges of bromopyrazone molecule have been calculated by using DFT/B3LYP method with 6-311++G(d,p) basis set in ground state. The obtained results show that the calculated vibrational frequencies and UV-vis. values are in a good agreement with experimental data.

  19. Dissection of the binding of hydrogen peroxide to trypsin using spectroscopic methods and molecular modeling

    NASA Astrophysics Data System (ADS)

    Song, Wei; Yu, Zehua; Hu, Xinxin; Liu, Rutao

    2015-02-01

    Studies on the effects of environmental pollutants to protein in vitro has become a global attention. Hydrogen peroxide (H2O2) is used as an effective food preservative and bleacher in industrial production. The toxicity of H2O2 to trypsin was investigated by multiple spectroscopic techniques and the molecular docking method at the molecular level. The intrinsic fluorescence of trypsin was proved to be quenched in a static process based on the results of fluorescence lifetime experiment. Hydrogen bonds interaction and van der Waals forces were the main force to generate the trypsin-H2O2 complex on account of the negative ΔH0 and ΔS0. The binding of H2O2 changed the conformational structures and internal microenvironment of trypsin illustrated by UV-vis absorption, fluorescence, synchronous fluorescence, three-dimensional (3D) fluorescence and circular dichroism (CD) results. However, the binding site was far away from the active site of trypsin and the trypsin activity was only slightly affected by H2O2, which was further explained by molecular docking investigations.

  20. Dissection of the binding of hydrogen peroxide to trypsin using spectroscopic methods and molecular modeling.

    PubMed

    Song, Wei; Yu, Zehua; Hu, Xinxin; Liu, Rutao

    2015-02-25

    Studies on the effects of environmental pollutants to protein in vitro has become a global attention. Hydrogen peroxide (H2O2) is used as an effective food preservative and bleacher in industrial production. The toxicity of H2O2 to trypsin was investigated by multiple spectroscopic techniques and the molecular docking method at the molecular level. The intrinsic fluorescence of trypsin was proved to be quenched in a static process based on the results of fluorescence lifetime experiment. Hydrogen bonds interaction and van der Waals forces were the main force to generate the trypsin-H2O2 complex on account of the negative ΔH(0) and ΔS(0). The binding of H2O2 changed the conformational structures and internal microenvironment of trypsin illustrated by UV-vis absorption, fluorescence, synchronous fluorescence, three-dimensional (3D) fluorescence and circular dichroism (CD) results. However, the binding site was far away from the active site of trypsin and the trypsin activity was only slightly affected by H2O2, which was further explained by molecular docking investigations. PMID:25228036

  1. Molecular spectroscopic identification of the water compartments in bone.

    PubMed

    Unal, Mustafa; Yang, Shan; Akkus, Ozan

    2014-10-01

    Matrix bound water is a correlate of bone's fracture resistance and assessment of bound water is emerging as a novel measure of bone's mechanical integrity. Raman spectroscopy is one of the few nondestructive modalities to assess the hydration status in bone; however, it has not been used to study the OH-band in bone. A sequential dehydration protocol was developed to replace unbound (heat drying) and bound (ethanol or deuterium) water in bone. Raman spectra were collected serially to track the OH-band during dehydration. Spectra of synthetic hydroxyapatite, demineralized bone and bulk water were collected to identify mineral and collagen contributions to the OH-band. Band assignments were supported by computational simulations of the molecular vibrations of Gly-Pro-Hyp amino acid sequence. Experimentally and theoretically obtained spectra were interpreted for band-assignments. Water loss was measured gravimetrically and correlated to Raman intensities. Four peaks were identified to be sensitive to dehydration: 3220cm(-1) (water), 3325cm(-1) (NH and water), 3453cm(-1) (hydroxyproline and water), and 3584cm(-1) (mineral and water). These peaks were differentially sensitive to deuterium treatment such that some water peaks were replaced with deuterium oxide faster than the rest. Specifically, the peaks at 3325 and 3584cm(-1) were more tightly bound to the matrix than the remaining bands. Comparison of dehydration in mineralized and demineralized bone revealed a volume of water that may be locked in the matrix by mineral crystals. The OH-range of bone was dominated by collagen and the water since the spectral profile of dehydrated demineralized bone was similar to that of the mineralized bone. Furthermore, water associates to bone mainly by collagen as findings of experimentally and theoretically spectra. The current work is among the first thorough analysis of the Raman OH stretch band in bone and such spectral information may be used to understand the involvement of

  2. Analysis of Molecular Contamination on Genesis Collectors Through Spectroscopic Ellipsometry

    NASA Technical Reports Server (NTRS)

    McNamara, K. M.; Stansbery, Eileen K.

    2005-01-01

    Before the spacecraft returned to Earth in September, the Genesis mission had a preliminary assessment plan in place for the purpose of providing information on the condition and availability of collector materials to the science community as a basis for allocation requests. One important component of that plan was the evaluation of collector surfaces for molecular contamination. Sources of molecular contamination might be the on-orbit outgassing of spacecraft and science canister components, the condensation of thruster by-products during spacecraft maneuvers, or the condensation of volatile species associated with reentry. Although the non-nominal return of the Genesis spacecraft introduced particulate contamination to the collectors, such as dust and heatshield carbon-carbon, it is unlikely to have caused any molecular deposition. The contingency team's quick action in returning the damaged payload the UTTR cleanroom by 6 PM the evening of recovery help to ensure that exposure to weather conditions and the environment were kept to a minimum.

  3. Raman spectroscopic study of the Chromobacterium violaceum pigment violacein using multiwavelength excitation and DFT calculations.

    PubMed

    Jehlička, Jan; Edwards, Howell G M; Němec, Ivan; Oren, Aharon

    2015-12-01

    Violacein is a bisindole pigment occurring as a biosynthetic product of Chromobacterium violaceum and Janthinobacterium lividum. It has some structural similarities to the cyanobacterial UV-protective pigment scytonemin, which has been the subject of comprehensive spectroscopic and structural studies. A detailed experimental Raman spectroscopic study with visible and near-infrared excitation of violacein produced by C. violaceum has been undertaken and supported using theoretical DFT calculations. Raman spectra with 514 and 785 nm excitation of cultivated cells as well as extracts and Gaussian (B3LYP/6-311++G(d,p)) calculations with proposed molecular vibrational assignments are reported here. PMID:26151435

  4. Label free molecular sexing of monomorphic birds using infrared spectroscopic imaging.

    PubMed

    Steiner, Gerald; Preusse, Grit; Zimmerer, Cordelia; Krautwald-Junghanns, Maria-Elisabeth; Sablinskas, Valdas; Fuhrmann, Herbert; Koch, Edmund; Bartels, Thomas

    2016-04-01

    The absence of sexual dimorphism in many birds often makes sex determination difficult. In particular immature birds and adults of monomorphic species show no external sex characteristics. Molecular techniques based on DNA hybridization or polymerase chain reaction (PCR) are standard methods for sex identification. However, these methods are expensive and time consuming procedures and require special sample preparation. Noninvasive methods for a rapid determination of bird's gender are of increasing importance for ornithologists, breeders as well as for successful captive-breeding programs. Fourier transform infrared (FT-IR) spectroscopy is one such technique that can provide gender specific information. In this study, using the example of domestic pigeons (Columba livia f. dom.) we demonstrate that only a small amount of the feather pulp is needed to determine the gender. FT-IR spectroscopic images of feather pulp suspensions were recorded in transmission mode. Principal component analysis (PCA) and linear discriminant analysis (LDA) were performed to identify the sex. The gender related information are described by 2nd and 4th principal component principle component (PC). The 2nd PC represents different amounts of proteins while the 4th PC shows variations within the amide I and amide II bands as well as in the region of phosphate vibrations of nucleic acids. Blood cells of male pigeons exhibit a significantly higher amount of proteins and nucleic acids than those of female pigeons. Feather pulp samples of male species were assigned with 100% accuracy. Seven from eight female samples were assigned correctly while one sample could not be classified. This study demonstrates that the sex of domestic pigeons can be accurately and and rapidly identified by infrared spectroscopic imaging. PMID:26838394

  5. Spectroscopic studies of lead halo borate glasses

    NASA Astrophysics Data System (ADS)

    Sekhar, K. Chandra; Hameed, Abdul; Chary, M. Narasimha; Shareefuddin, Md.

    2015-06-01

    Glasses in the system xPbF2-(30-x) PbO-69B2O3-1CuO (x=5, 10, 15, 20, & 25 mole %) were prepared by melt quenching method and they are characterized by XRD to confirm the glassy nature. Electron Paramagnetic Resonance (EPR) studies at room temperature in the X-band frequencies and FTIR studies on prepared glass systems were reported. The non-linear variation of spin-Hamiltonian parameters with PbF2 content indicated the change in the ligand field strength around Cu2+ ions in the host glass. The ground state of Cu2+ ions in the glass is designated as dx2-y2 orbital (2B1g) while the observed symmetry around it is tetragonally distorted octahedral. The molecular orbital coefficients α2, β2 and β12 are evaluated for Cu2+ doped samples. From the FTIR studies it was observed that the glass made up of BO3 and BO4 units.

  6. Spectroscope and molecular model identify the behavior of doxorubicin-SPION binding to bovine hemoglobin.

    PubMed

    Liu, Yihong; Liu, Rutao

    2015-08-01

    To provide reference for the bio-safety evaluation of doxorubicin-loaded SPION, the interaction of bovine hemoglobin (BHb) with the drug delivery was investigated by multi-spectroscopic techniques and molecular modeling calculation. Multi-spectroscopic results indicated that DOX-SPION unfolded the conformation of BHb, decreased the content of α-helix from 38.89% to 35.08%, which verified the changes of protein's secondary structure quantificationally. Stern-Volmer analysis and molecular model showed there were two static interaction modes corresponding to the two reaction steps: DOX first immobilized on the particle adhered to the external region of BHb, leading to the increasing exposure of chromophore group, rendering particles to bond to the original hemoglobin central cavity (Site 2) in sequence. They finally generated a stable bioconjugate via hydrogen bonds. This work indicated that the drug delivery has deleterious effects on the frame conformation of BHb, affecting its physiological function. PMID:26033525

  7. Spectroscopic Monitoring of Mechanical Forces during Protein Folding by using Molecular Force Probes.

    PubMed

    Stauch, Tim; Hoffmann, Marvin T; Dreuw, Andreas

    2016-05-18

    Detailed folding pathways of proteins are still largely unknown. Real-time monitoring of mechanical forces acting in proteins during structural transitions would provide deep insights into these highly complex processes. Here, we propose two molecular force probes that can be incorporated into the protein backbone to gain insight into the magnitude and direction of mechanical forces acting in proteins during natural folding and unfolding through their optical spectroscopic response. In fact, changes in the infrared and Raman spectra are proportional to the mechanical force deforming the force probes, and the relevant bands can be intensified and shifted to a transparent window in the protein spectrum by isotopic substitution. As a result, the proposed molecular force probes can act as "force rulers", allowing the spectroscopic observation and measurement of mechanical forces acting within the proteins under natural conditions without external perturbation. PMID:26928925

  8. Multiprobe Spectroscopic Inverstigation of Molecular-level Behavior within Aqueous 1-Butyl-3-methylimidazolium Tetrafluoroborate

    SciTech Connect

    Sarkar, Abhra; Ali, Maroof; Baker, Gary A; Tetin, Sergey Y.; Ruan, Qiaoqiao; Pandey, Siddharth

    2009-01-01

    In this work, an array of molecular-level solvent featuressincluding solute-solvent/solvent-solvent interactions, dipolarity, heterogeneity, dynamics, probe accessibility, and diffusionswere investigated across the entire composition of ambient mixtures containing the ionic liquid 1-butyl-3-methylimidazolium tetrafluoroborate, [bmim][BF4], and pH 7.0 phosphate buffer, based on results assembled for nine different molecular probes utilized in a range of spectroscopic modes. These studies uncovered interesting and unusual solvatochromic probe behavior within this benchmark mixture. Solvatochromic absorbance probessa watersoluble betaine dye (betaine dye 33), N,N-diethyl-4-nitroaniline, and 4-nitroanilineswere employed to determine ET (a blend of dipolarity/polarizability and hydrogen bond donor contributions) and the Kamlet-Taft indices * (dipolarity/polarizability), R (hydrogen bond donor acidity), and (hydrogen bond acceptor basicity) characterizing the [bmim][BF4] + phosphate buffer system. These parameters each showed a marked deviation from ideality, suggesting selective solvation of the individual probe solutes by [bmim][BF4]. Similar conclusions were derived from the responses of the fluorescent polarity-sensitive probes pyrene and pyrene-1-carboxaldehyde. Importantly, the fluorescent microfluidity probe 1,3-bis(1-pyrenyl)propane senses a microviscosity within the mixture that significantly exceeds expectations derived from simple interpolation of the behavior in the neat solvents. On the basis of results from this probe, a correlation between microviscosity and bulk viscosity was established; pronounced solvent-solvent hydrogen-bonding interactions were implicit in this behavior. The greatest deviation from ideal additive behavior for the probes studied herein was consistently observed to occur in the buffer-rich regime. Nitromethane-based fluorescence quenching of pyrene within the [bmim][BF4] + phosphate buffer system showed unusual compliance with a sphere

  9. Fourier transform infrared spectroscopic study of truffles

    NASA Astrophysics Data System (ADS)

    Zhao, Dezhang; Liu, Gang; Song, Dingshan; Liu, Jian-hong; Zhou, Yilan; Ou, Jiaming; Sun, Shizhong

    2006-01-01

    Truffles are rare wild growing edible mushrooms belonging to Ascomycetes. In this paper, Fourier transform infrared (FTIR) spectroscopy was used to obtain vibrational spectra of truffles. The results show that the mushrooms exhibit characteristic spectra. The two strongest absorption bands appear at about 1077cm -1 and 1040 cm -1, which were described as C-O stretching in carbohydrate. The vibrational spectra indicate that the main compositions of the truffles are polysaccharide and protein. According to the characteristics bands and absorption ratios of spectra, different species of truffles can be discriminated. It is also found the great changes between moldy and healthy truffles, which the major differences are observed in the bands of protein. In addition, FTIR spectral differences are observed between the same species of truffles from different producing areas. It is showed that the FTIR spectroscopic method is valuable tool for rapid and nondestructive analysis of truffles prior to any extraction method used.

  10. Spectroscopic study of sorption of nitrogen heterocyclic compounds on phyllosilicates

    SciTech Connect

    Chattopadhyay, S.; Traina, S.J.

    1999-03-02

    The present study focused on understanding the sorption characteristics of acridine (AcN) and acridine-9-carboxylic acid (AcNCOOH), two typical nitrogen heterocyclic compounds (NHCs), on well-characterized phyllosilicates (hectorite, saponite, and muscovite). Results presented in this article show that the degree of sorption of NHCs on phyllosilicates was dependent on the nature of the participating sorbates and sorbents. Sorption of the selected NHCs was pH-dependent, with maximum sorption occurring at low pH conditions, especially at pH < pK{sub a} of the NHC. Though sorption of the cationic forms of the NHCs on clays was preferred, neutral, zwitterionic, and anionic species of NHCs also sorbed on the clay surfaces. Spectroscopic studies have shown that sorbed NHC molecules formed clusters on clay surfaces, which acted as templates for molecular aggregation. Finally, the authors have also found that the clay surfaces promoted protonation of neutral AcN molecules at low sorbate concentrations.

  11. Spectroscopic study of acetylene and hydrogen cyanide

    NASA Astrophysics Data System (ADS)

    Rozario, Hoimonti Immaculata

    High-resolution molecular spectroscopy has been used to study acetylene line parameters and emission spectra of hydrogen cyanide. All acetylene spectra were recorded in our laboratory at the University of Lethbridge using a 3-channel tuneable diode laser spectrometer. N2-broadened line widths and N2-pressure induced line shifts have been measured for transitions in the v1+v3 band of acetylene at seven temperatures in the range 213-333K to obtain the temperature dependences of broadening and shift coefficients. The Voigt and hard-collision line profile models were used to retrieve the line parameters. The line-broadening and line-shift coefficients as well as their temperature-dependent parameters have been also evaluated theoretically, in the frame work of a semi-classical approach based on an exponential representation of the scattering operator, an intermolecular potential composed of electrostatic quadrupole--quadrupole and pairwise atom--atom interactions as well as on exact trajectories driven by an effective isotropic potential. The experimental results for both N2-broadening and shifting show good agreement with the theoretical results. We have studied the line intensities of the 1vl 20←0v120 band system from the HCN emission spectrum. The infrared emission spectrum of H12C 14N was measured at the Justus-Liebig University, Giessen, Germany. The emission spectrum was analyzed with the spectrum analysis software Symath running using Mathematica as a platform. This approach allowed us to retrieve information on band intensity parameters.

  12. Photoacoustic spectroscopic imaging of intra-tumor heterogeneity and molecular identification

    NASA Astrophysics Data System (ADS)

    Stantz, Keith M.; Liu, Bo; Cao, Minsong; Reinecke, Dan; Miller, Kathy; Kruger, Robert

    2006-02-01

    Purpose. To evaluate photoacoustic spectroscopy as a potential imaging modality capable of measuring intra-tumor heterogeneity and spectral features associated with hemoglobin and the molecular probe indocyanine green (ICG). Material and Methods. Immune deficient mice were injected with wildtype and VEGF enhanced MCF-7 breast cancer cells or SKOV3x ovarian cancer cells, which were allowed to grow to a size of 6-12 mm in diameter. Two mice were imaged alive and after euthanasia for (oxy/deoxy)-hemoglobin content. A 0.4 mL volume of 1 μg/mL concentration of ICG was injected into the tail veins of two mice prior to imaging using the photoacoustic computed tomography (PCT) spectrometer (Optosonics, Inc., Indianapolis, IN 46202) scanner. Mouse images were acquired for wavelengths spanning 700-920 nm, after which the major organs were excised, and similarly imaged. A histological study was performed by sectioning the organ and optically imaging the fluorescence distribution. Results. Calibration of PCT-spectroscopy with different samples of oxygenated blood reproduced a hemoglobin dissociation curve consistent with empirical formula with an average error of 5.6%. In vivo PCT determination of SaO II levels within the tumor vascular was measurably tracked, and spatially correlated to the periphery of the tumor. Statistical and systematic errors associated with hypoxia were estimated to be 10 and 13%, respectively. Measured ICG concentrations determined by contrast-differential PCT images in excised organs (tumor, liver) were approximately 0.8 μg/mL, consistent with fluorescent histological results. Also, the difference in the ratio of ICG concentration in the gall bladder-to-vasculature between the mice was consistent with excretion times between the two mice. Conclusion. PCT spectroscopic imaging has shown to be a noninvasive modality capable of imaging intra-tumor heterogeneity of (oxy/deoxy)-hemoglobin and ICG in vivo, with an estimated error in SaO II at 17% and in

  13. Nonplanar property study of antifungal agent tolnaftate-spectroscopic approach

    NASA Astrophysics Data System (ADS)

    Arul Dhas, D.; Hubert Joe, I.; Roy, S. D. D.; Balachandran, S.

    2011-09-01

    Vibrational analysis of the thionocarbamate fungicide tolnaftate which is antidermatophytic, antitrichophytic and antimycotic agent, primarily inhibits the ergosterol biosynthesis in the fungus, was carried out using NIR FT-Raman and FTIR spectroscopic techniques. The equilibrium geometry, various bonding features, harmonic vibrational wavenumbers and torsional potential energy surface (PES) scan studies have been computed using density functional theory method. The detailed interpretation of the vibrational spectra has been carried out with the aid of VEDA.4 program. Vibrational spectra, natural bonding orbital (NBO) analysis and optimized molecular structure show the clear evidence for electronic interaction of thionocarbamate group with aromatic ring. Predicted electronic absorption spectrum from TD-DFT calculation has been compared with the UV-vis spectrum. The Mulliken population analysis on atomic charges and the HOMO-LUMO energy were also calculated. Vibrational analysis reveals that the simultaneous IR and Raman activation of the C-C stretching mode in the phenyl and naphthalene ring provide evidence for the charge transfer interaction between the donor and acceptor groups and is responsible for its bioactivity as a fungicide.

  14. Spectroscopic study of low-lying {sup 16}N levels

    SciTech Connect

    Bardayan, D. W.; Nesaraja, C. D.; Pain, S. D.; Smith, M. S.; O'Malley, P. D.; Cizewski, J. A.; Hatarik, R.; Peters, W. A.; Blackmon, J. C.; Chae, K. Y.; Jones, K. L.; Moazen, B. H.; Paulauskas, S.; Pittman, S. T.; Schmitt, K. T.; Chipps, K. A.; Kozub, R. L.; Shriner, J. F. Jr.; Matei, C.

    2008-11-15

    The magnitude of the {sup 15}N(n,{gamma}){sup 16}N reaction rate in asymptotic giant branch stars depends directly on the neutron spectroscopic factors of low-lying {sup 16}N levels. A new study of the {sup 15}N(d,p){sup 16}N reaction is reported populating the ground and first three excited states in {sup 16}N. The measured spectroscopic factors are near unity as expected from shell model calculations, resolving a long-standing discrepancy with earlier measurements that had never been confirmed or understood. Updated {sup 15}N(n,{gamma}){sup 16}N reaction rates are presented.

  15. Spectroscopic Line Shapes of Vibrational Quanta in the Presence of Molecular Resonances.

    PubMed

    Meierott, Stefan; Néel, Nicolas; Kröger, Jörg

    2016-07-01

    Line shapes of molecular vibrational quanta in inelastic electron tunneling spectroscopy may indicate the strength of electron-vibration coupling, the hybridization of the molecule with its environment, and the degree of vibrational damping by electron-hole pair excitation. Bare as well as C60-terminated Pb tips of a scanning tunneling microscope and clean as well as C60-covered Pb(111) surfaces were used in low-temperature experiments. Depending on the overlap of orbital and vibrational spectral ranges different spectroscopic line shapes of molecular vibrational quanta were observed. The energy range covered by the molecular resonance was altered by modifying the adsorption configuration of the molecule terminating the tip apex. Concomitantly, the line shapes of different vibrational modes were affected. The reported observations represent an experimental proof to theoretical predictions on the contribution from resonant processes to inelastic electron tunneling. PMID:27280313

  16. Use of Mo/ller-Plesset perturbation theory in molecular calculations: Spectroscopic constants of first row diatomic molecules

    SciTech Connect

    Dunning, T.H. , Jr.; Peterson, K.A.

    1998-03-01

    The convergence of Mo/ller{endash}Plesset perturbation expansions (MP2{endash}MP4/MP5) for the spectroscopic constants of a selected set of diatomic molecules (BH, CH, HF, N{sub 2}, CO, and F{sub 2}) has been investigated. It was found that the second-order perturbation contributions to the spectroscopic constants are strongly dependent on basis set, more so for HF and CO than for BH. The MP5 contributions for HF were essentially zero for the cc-pVDZ basis set, but increased significantly with basis set illustrating the difficulty of using small basis sets as benchmarks for correlated calculations. The convergence behavior of the {ital exact} Mo/ller{endash}Plesset perturbation expansions were investigated using estimates of the {ital complete basis set limits} obtained using large correlation consistent basis sets. For BH and CH, the perturbation expansions of the spectroscopic constants converge monotonically toward the experimental values, while for HF, N{sub 2}, CO, and F{sub 2}, the expansions oscillate about the experimental values. The perturbation expansions are, in general, only slowly converging and, for HF, N{sub 2}, CO, and F{sub 2}, appear to be far from convergence at MP4. In fact, for HF, N{sub 2}, and CO, the errors in the calculated spectroscopic constants for the MP4 method are {ital larger} than those for the MP2 method (the only exception is D{sub e}). The current study, combined with other recent studies, raises serious doubts about the use of Mo/ller{endash}Plesset perturbation theory to describe electron correlation effects in atomic and molecular calculations. {copyright} {ital 1998 American Institute of Physics.}

  17. Vibrational spectroscopic study of sulphated silk proteins

    NASA Astrophysics Data System (ADS)

    Monti, P.; Freddi, G.; Arosio, C.; Tsukada, M.; Arai, T.; Taddei, P.

    2007-05-01

    Degummed Bombyx mori ( B. m.) silk fibroin fabric and mutant naked pupa cocoons (Nd-s) consisting of almost pure silk sericin were treated with chlorosulphonic acid in pyridine and investigated by FT-IR and FT-Raman spectroscopies. Untreated silk fibroin and sericin displayed typical spectral features due to characteristic amino acid composition and molecular conformation (prevailing β-sheet with a less ordered structure in sericin). Upon sulphation, the degree of molecular disorder increased in both proteins and new bands appeared. The IR bands at 1049 and 1014 cm -1 were attributed to vibrations of sulphate salts and that at 1385 cm -1 to the νasSO 2 mode of organic covalent sulphates. In the 1300-1180 cm -1 range various contributions of alkyl and aryl sulphate salts, sulphonamides, sulphoamines and organic covalent sulphates, fell. Fibroin covalently bound sulphate groups through the hydroxyl groups of tyrosine and serine, while sericin through the hydroxyl groups of serine, since the δOH vibrations at 1399 cm -1 in IR and at 1408 cm -1 in Raman disappeared almost completely. Finally, the increase of the I850/ I830 intensity ratio of Raman tyrosine doublet in fibroin suggested a change towards a more exposed state of tyrosine residues, in good agreement with the more disordered conformation taken upon sulphation.

  18. Spectroscopic analysis (FT-IR, FT-Raman and NMR) and molecular docking study of ethyl 2-(4-oxo-3-phenethyl-3,4-dihydroquinazolin-2-ylthio)-acetate

    NASA Astrophysics Data System (ADS)

    El-Azab, Adel S.; Jalaja, K.; Abdel-Aziz, Alaa A.-M.; Al-Obaid, Abdulrahman M.; Sheena Mary, Y.; Yohannan Panicker, C.; Van Alsenoy, C.

    2016-09-01

    The vibrational wavenumbers, molecular structure, MEP, NLO, NBO and HOMO, LUMO analysis of Ethyl 2-(4-oxo-3-phenethyl-3,4-dihydroquinazolin-2-ylthio)-acetate (EPDA) were reported. The change in electron density in the antibonding orbitals and stabilization energies have been calculated by NBO analysis to give clear evidence of stabilization in the hyperconjugation of hydrogen bonded interaction. The difference in HOMO and LUMO energy support the charge transfer interaction within the molecule. NMR studies and Fukui functions are also reported. From molecular electrostatic potential plot it is evident that the negative charge covers the carbonyl groups, phenyl rings and the positive region is over the CH2 groups with the acetate group. Molecular docking studies shows that the title compound forms a stable complex with pyrrole inhibitor and gives a binding affinity value of -8.3 kcal/mol and the results suggest that the compound might exhibit inhibitory activity against pyrrole inhibitor.

  19. Raman spectroscopic protocol for the molecular recognition of key biomarkers in astrobiological exploration.

    PubMed

    Edwards, Howell G M

    2004-02-01

    Raman spectroscopy is proposed as novel instrumentation for the remote, robotic exploration of planetary surfaces, especially Mars. In recent years, information about the chemicals produced by organisms at the terrestrial limits of life, such as those surviving in Antarctic habitats, has facilitated the assembly of a spectral database of key biomarkers. In addition biogeological modifications which are essential for the survival strategies of environmentally stressed organisms have been identified. In this paper, the requirements for Raman spectroscopic instrumental detection of key bio--and bio-geological markers are outlined and a preliminary protocol established for the molecular spectral recognition of biological signatures in remote astrobiological exploration. PMID:14979640

  20. Investigation of the Interaction of Naringin Palmitate with Bovine Serum Albumin: Spectroscopic Analysis and Molecular Docking

    PubMed Central

    Zhang, Xia; Li, Lin; Xu, Zhenbo; Liang, Zhili; Su, Jianyu; Huang, Jianrong; Li, Bing

    2013-01-01

    Background Bovine serum albumin (BSA) contains high affinity binding sites for several endogenous and exogenous compounds and has been used to replace human serum albumin (HSA), as these two compounds share a similar structure. Naringin palmitate is a modified product of naringin that is produced by an acylation reaction with palmitic acid, which is considered to be an effective substance for enhancing naringin lipophilicity. In this study, the interaction of naringin palmitate with BSA was characterised by spectroscopic and molecular docking techniques. Methodology/Principal Findings The goal of this study was to investigate the interactions between naringin palmitate and BSA under physiological conditions, and differences in naringin and naringin palmitate affinities for BSA were further compared and analysed. The formation of naringin palmitate-BSA was revealed by fluorescence quenching, and the Stern-Volmer quenching constant (KSV) was found to decrease with increasing temperature, suggesting that a static quenching mechanism was involved. The changes in enthalpy (ΔH) and entropy (ΔS) for the interaction were detected at −4.11±0.18 kJ·mol−1 and −76.59±0.32 J·mol−1·K−1, respectively, which indicated that the naringin palmitate-BSA interaction occurred mainly through van der Waals forces and hydrogen bond formation. The negative free energy change (ΔG) values of naringin palmitate at different temperatures suggested a spontaneous interaction. Circular dichroism studies revealed that the α-helical content of BSA decreased after interacting with naringin palmitate. Displacement studies suggested that naringin palmitate was partially bound to site I (subdomain IIA) of the BSA, which was also substantiated by the molecular docking studies. Conclusions/Significance In conclusion, naringin palmitate was transported by BSA and was easily removed afterwards. As a consequence, an extension of naringin applications for use in food, cosmetic and medicinal

  1. Halo Nucleus Be11: A Spectroscopic Study via Neutron Transfer

    NASA Astrophysics Data System (ADS)

    Schmitt, K. T.; Jones, K. L.; Bey, A.; Ahn, S. H.; Bardayan, D. W.; Blackmon, J. C.; Brown, S. M.; Chae, K. Y.; Chipps, K. A.; Cizewski, J. A.; Hahn, K. I.; Kolata, J. J.; Kozub, R. L.; Liang, J. F.; Matei, C.; Matoš, M.; Matyas, D.; Moazen, B.; Nesaraja, C.; Nunes, F. M.; O'Malley, P. D.; Pain, S. D.; Peters, W. A.; Pittman, S. T.; Roberts, A.; Shapira, D.; Shriner, J. F., Jr.; Smith, M. S.; Spassova, I.; Stracener, D. W.; Villano, A. N.; Wilson, G. L.

    2012-05-01

    The best examples of halo nuclei, exotic systems with a diffuse nuclear cloud surrounding a tightly bound core, are found in the light, neutron-rich region, where the halo neutrons experience only weak binding and a weak, or no, potential barrier. Modern direct-reaction measurement techniques provide powerful probes of the structure of exotic nuclei. Despite more than four decades of these studies on the benchmark one-neutron halo nucleus Be11, the spectroscopic factors for the two bound states remain poorly constrained. In the present work, the Be10(d,​p) reaction has been used in inverse kinematics at four beam energies to study the structure of Be11. The spectroscopic factors extracted using the adiabatic model were found to be consistent across the four measurements and were largely insensitive to the optical potential used. The extracted spectroscopic factor for a neutron in an nℓj=2s1/2 state coupled to the ground state of Be10 is 0.71(5). For the first excited state at 0.32 MeV, a spectroscopic factor of 0.62(4) is found for the halo neutron in a 1p1/2 state.

  2. Structural and spectroscopic studies of fluoroprotactinates.

    PubMed

    De Sio, Stéphanie M; Wilson, Richard E

    2014-02-01

    Seven protactinium(V) fluoride compounds have been synthesized, and their crystal structures and Raman spectra are reported. (NH4)2PaF7, K2PaF7, Rb2PaF7, and Cs2PaF7 were found to crystallize in the monoclinic space group P21/c for the ammonium compound and C2/c for the K(+)-, Rb(+)-, and Cs(+)-containing compounds, with nine-coordinate Pa forming infinite chains through fluorine bridges. Na3PaF8 crystallizes in the tetragonal space group I4/mmm with eight-coordinate Pa in tetragonal geometry, while tetramethylammonium fluoroprotactinate shows two different structures: (Me4N)2(H3O)PaF8, an eight-coordinate molecular compound crystallizing in the monoclinic space group C2/c, and (Me4N)PaF6, an eight-coordinate Pa compound forming infinite chains and crystallizing in the orthorhombic space group Pnnm. A comparison of solid- and solution-state Raman data indicates that the PaF8(-) anion could be the predominant Pa(V) complex in concentrated solutions of aqueous HF. PMID:24437929

  3. A Herschel Spectroscopic Survey of Warm Molecular Gas in Local Luminous Infrared Galaxies

    NASA Astrophysics Data System (ADS)

    Lu, Nanyao Y.; Zhao, Y.; Xu, C. K.; Gao, Y.; Armus, L.; Appleton, P. N.; Charmandaris, V.; Diaz Santos, T.; Evans, A. S.; Howell, J.; Issak, K.; Iwasawa, K.; Leech, J.; Lord, S. D.; Mazzarella, J. M.; Petric, A.; Sanders, D. B.; Schulz, B.; Surace, J. A.; Van der Werf, P.

    2013-01-01

    We describe an on-going Herschel 194-671 micron spectroscopic survey of a flux-limited sample of 125 local luminous infrared galaxies (LIRGs), targeting primarily at the spectral line energy distribution (SLED) of the CO rotational line emission (from J=4-3 up to J=13-12) from warm and dense molecular gas, the [NII] 205 micron line from ionized gas, and the [CI] 370 and 609 micron lines arising mainly from less dense and colder molecular gas where the CO (J=1-0) line is also strong. We present observational results for the first set of 65 sample galaxies that are more or less point sources with respect to the Herschel beams, and show statistical correlations among the shape of the CO SLED, CO line luminosities, IR dust luminosity, and whether a target is known to harbor AGN or not.

  4. Inhibition of urinary calculi -- a spectroscopic study

    NASA Astrophysics Data System (ADS)

    Manciu, Felicia; Govani, Jayesh; Durrer, William; Reza, Layra; Pinales, Luis

    2008-10-01

    Although a considerable number of investigations have already been undertaken and many causes such as life habits, metabolic disorders, and genetic factors have been noted as sources that accelerate calculi depositions and aggregations, there are still plenty of unanswered questions regarding efficient inhibition and treatment mechanisms. Thus, in an attempt to acquire more insights, we propose here a detailed scientific study of kidney stone formation and growth inhibition based on a traditional medicine approach with Rotula Aquatica Lour (RAL) herbal extracts. A simplified single diffusion gel growth technique was used for synthesizing the samples for the present study. The unexpected Zn presence in the sample with RAL inhibitor, as revealed by XPS measurements, explains the inhibition process and the dramatic reflectance of the incident light observed in the infrared transmission studies. Raman data demonstrate potential binding of the inhibitor with the oxygen of the kidney stone. Photoluminescence results corroborate to provide additional evidence of Zn-related inhibition.

  5. Spectroscopic study of bituminous oxidative stress.

    PubMed

    Masmoudi, H; Rebufa, C; Raffi, J; Permanyer, A; Kister, J

    2004-05-01

    Bitumen, as each organic substance, is a product which alters over time. Indeed, roads deteriorate under the effect of several phenomena. A number of studies have been undertaken to increase the quality of road's coating, mostly by adding polymer to bitumen. This work was based on the study, by electron paramagnetic resonance (EPR), FTIR and Synchronous UV fluorescence, of different base and modified bitumens after different treatments used to simulate the ageing (gamma irradiation, thermal treatment). Our purpose was to compare and correlate the results obtained by different techniques to improve the knowledge of bitumen's reactivity and evolution submitted to ageing phenomena. PMID:15134733

  6. Spectroscopic analysis of bones for forensic studies

    NASA Astrophysics Data System (ADS)

    Tofanelli, Mirko; Pardini, Lorenzo; Borrini, Matteo; Bartoli, Fulvio; Bacci, Alessandra; D'Ulivo, Alessandro; Pitzalis, Emanuela; Mascherpa, Marco Carlo; Legnaioli, Stefano; Lorenzetti, Giulia; Pagnotta, Stefano; de Holanda Cavalcanti, Gildo; Lezzerini, Marco; Palleschi, Vincenzo

    2014-09-01

    The elemental analysis of human bones can give information about the dietary habits of the deceased, especially in the last years of their lives, which can be useful for forensic studies. The most important requirement that must be satisfied for this kind of analysis is that the concentrations of analyzed elements are the same as ante mortem. In this work, a set of bones was analyzed using Laser-Induced Breakdown Spectroscopy (LIBS) and validated using Inductively Coupled Plasma-Optical Emission Spectroscopy (ICP-OES), in order to compare those two techniques and to investigate the effect of possible alterations in the elemental concentrations' proportion resulting from the treatment usually applied for preparing the bones for traditional forensic analysis. The possibility that elemental concentrations' changes would occur after accidental or intentional burning of the bones was also studied.

  7. Progress report on nuclear spectroscopic studies

    SciTech Connect

    Bingham, C.R.; Guidry, M.W.; Riedinger, L.L.; Sorensen, S.P.

    1994-02-18

    The Nuclear Physics group at the University of Tennessee, Knoxville (UTK) is involved in several aspects of heavy-ion physics including both nuclear structure and reaction mechanisms. While the main emphasis is on experimental problems, the authors have maintained a strong collaboration with several theorists in order to best pursue the physics of their measurements. During the last year they have had several experiments at the ATLAS at Argonne National Laboratory, the GAMMASPHERE at the LBL 88 Cyclotron, and with the NORDBALL at the Niels Bohr Institute Tandem. Also, they continue to be very active in the WA93/98 collaboration studying ultra-relativistic heavy ion physics utilizing the SPS accelerator at CERN in Geneva, Switzerland and in the PHENIX Collaboration at the RHIC accelerator under construction at Brookhaven National Laboratory. During the last year their experimental work has been in three broad areas: (1) the structure of nuclei at high angular momentum, (2) the structure of nuclei far from stability, and (3) ultra-relativistic heavy-ion physics. The results of studies in these particular areas are described in this document. These studies concentrate on the structure of nuclear matter in extreme conditions of rotational motion, imbalance of neutrons and protons, or very high temperature and density. Another area of research is heavy-ion-induced transfer reactions, which utilize the transfer of nucleons to states with high angular momentum to learn about their structure and to understand the transfer of particles, energy, and angular momentum in collisions between heavy ions.

  8. Spectroscopic and quantum chemical studies of isocytosine

    SciTech Connect

    Tulub, A.A.; Semenov, S.G.; Stetsenko, A.I.; Yudovich, E.E.

    1988-07-01

    The methods of electronic and vibrational (IR) spectroscopy were used to study the spectral properties of isocytosine in H/sub 2/O, D/sub 2/O, chloroform, and hexane in a wide concentration interval. Quantum chemical calculations of tautomeric forms and dimers of isocytosine were carried out. The bands of the calculated and experimental spectra were assigned. The results of the quantum calculations were compared with the experimental data. The spectral bands were classified according to the type of tautomer or dimer to which they belong.

  9. Progress report on nuclear spectroscopic studies

    SciTech Connect

    Bingham, C.R.; Riedinger, L.L.; Sorensen, S.P.

    1996-01-16

    The experimental program in nuclear physics at the University of Tennessee, Knoxville, is led by Professors Carrol Bingham, Lee Riedinger, and Soren Sorenseni who respectively lead the studies of the exotic decay modes of nuclei far from stability, the program of high-spin research, and our effort in relativistic heavy-ion physics. Over the years, this broad program of research has been successful partially because of the shared University resources applied to this group effort. The proximity of the Oak Ridge National Laboratory has allowed us to build extremely strong programs of joint research, and in addition to play an important leadership role in the Joint Institute for Heavy Ion Research (JIHIR). Our experimental program is also very closely linked with those at other national laboratories: Argonne (collaborations involving the Fragment Mass Analyzer (FMA) and {gamma}-ray arrays), Brookhaven (the RHIC and Phenix projects), and Berkeley (GAMMASPHERE). We have worked closely with a variety of university groups in the last three years, especially those in the UNISOR and now UNIRIB collaborations. And, in all aspects of our program, we have maintained close collaborations with theorists, both to inspire the most exciting experiments to perform and to extract the pertinent physics from the results. The specific areas discussed in this report are: properties of high-spin states; study of low-energy levels of nuclei far from stability; and high energy heavy-ion physics.

  10. Spectroscopic studies of solutes in aqueous solution.

    PubMed

    Chai, Bing-hua; Zheng, Jian-ming; Zhao, Qing; Pollack, Gerald H

    2008-03-20

    Absorption and fluorescence characteristics of aqueous solutions of salts, sugars, and amino acids were studied using UV-vis spectroscopy and spectrofluorometry. Motivation stemmed from unanticipated absorption spectral and fluorescence features of the "exclusion zone" seen adjacent to various hydrophilic surfaces. Those features implied a structure distinct from that of bulk water (Adv. Colloid Interface Sci. 2006, 127, 19). Absorption peaks at approximately 270 nm similar to those observed in the exclusion zone were seen in solutions of the following substances: salts, Nafion 117 solution/film, l-lysine, d-alanine, d-glucose and sucrose. To determine the fate of the absorbed energy, we studied the fluorescence properties of these solutions. The salts showed fluorescence emission around 480-490 nm under different excitation wavelengths. The fluorescence intensity of LiCl was higher than NaCl, which was in turn higher than KCl-the same ordering as the absorption intensities. Fluorescence of Nafion 117 solution/film, l-lysine, d-alanine, d-glucose and sucrose were observed as well, with multiple excitation wavelengths. Hence, at least some of the absorbed energy is released as fluorescence. The results show features closely similar to those observed in the exclusion zone, implying that the aqueous region around the solutes resembles the aqueous zone adjacent to hydrophilic surfaces. Both may be more extensively ordered than previously thought. PMID:18298105

  11. Spectroscopic studies of silver boro tellurite glasses

    SciTech Connect

    Kumar, E. Ramesh Kumari, K. Rajani Rao, B. Appa Bhikshamaiah, G.

    2014-04-24

    The FTIR absorption and Raman scattering studies were used to obtain the structural information of AgI−Ag{sub 2}O−[(1−x)B{sub 2}O{sub 3}−xTeO{sub 2}] (x=0 to 1 mol% in steps of 0.2) glasses. The glassy nature of the compounds has been confirmed by X-ray diffraction. FTIR and Raman spectra were recorded for all samples at room temperature. FTIR spectra which provides the information about the change in bond structure of the glasses. Raman spectra provide the effect of TeO{sub 2} on SBT glass system is that as increasing the concentration of TeO{sub 2} the band intensity at 707 cm{sup −1} increase.

  12. Ultrafast spectroscopic studies of metal nanoparticles

    NASA Astrophysics Data System (ADS)

    Hu, Min

    An important aim of nanoparticle research is to understand how the properties of materials depend on their size and shape. In this thesis, time-resolved spectroscopy has been used to measure the physical properties of nanometer sized objects, such as the characteristic time scale for heat dissipation and their elastic moduli. In our experiments, metal nanoparticles are excited with a sub-picosecond laser pulse, which causes a rapid increase in the lattice temperature. In the first project, the rate of heat dissipation from Au nanoparticles to their surroundings was examined for different size gold nanospheres in aqueous solution. Laser induced lattice heating can also impulsively excite the phonon modes of the particle that correlate with the expansion co-ordinates. For spherical Au particles the symmetric breathing mode is excited. Experimental results for ˜50 nm diameter Au particles were compared to a model calculation where the expansion coordinate is treated as a damped harmonic oscillator. This gives information about the excitation mechanism. In the second project, the extensional and breathing modes of cylindrical gold nanorods were studied by time-resolved spectroscopy. These experiments yield values for the elastic constants for the rods. Both the extensional mode and the breathing mode results show that gold nanorods produced by wet chemical techniques have a smaller elastic moduli than bulk gold. HR-TEM and SAED studies show that the rods have a 5-fold twinned structure with growth along the [110] crystal direction. However, neither the growth direction nor the twinning provide a simple explanation for the reduced elastic moduli measured in the experiments. In a final project, polydisperse silver nanoparticle samples were investigated. A signal due to coherently excited vibrational motion was observed. The analysis shows that the observed signal arises from the triangular-shaped particles, rather than the rods or spheres that are present in the sample

  13. Raman spectroscopic studies of disordered ferroelectric oxides

    NASA Astrophysics Data System (ADS)

    Savvinov, Alexey A.

    Relaxational properties of compositionally disordered AB03 perovskite oxides were studied. These oxides are the prototypical soft ferroelectric (FE) mode systems, and their interesting dipolar relaxational properties are determined by their long, strongly temperature-dependent correlation lengths for the dipolar interactions. The simple cases involve dilute chemical substitutions in the incipient ferroelectrics KTaO3 and SrTiO3, which exhibit relatively weak, low-temperature Debye-type relaxations. More complicated dipolar interactions are seen in B-site disordered Nb-doped KTaO3, which exhibits glass-like relaxor and relaxor-to-ferroelectric crossover behaviors at low temperatures. Finally, there is a class of more complex perovskites represented by PMN, PZN-PT and the PLT that exhibit strong, high-temperature relaxor and/or ferroelectric properties. The renewed interest in the KTa1-xNbxO (KTN) mixed perovskite materials, especially in high quality thin films, is connected with their remarkable dielectric properties in the dilute compositions. Off-center Nb ions in the highly polarizable KTaO3 lattice provide a drastic increase in the dielectric peak, up to 20 times in comparison with the pure KTaO3 and KNbO3. The effects of the substrate and the symmetry-breaking defects on their vibration spectra were studied by micro-Raman spectroscopy. An anomalous residual intensity of the forbidden first-order scattering modes in the cubic paraelectric phase of the KTN films was connected with the formation of polar microregions even far above the bulk Tc. On the whole, the KTN film behavior shows the existence of specific defects enhancing the perovskite unit cell in the film so that the activity of off-center Nb ions increases in producing larger electric dipoles and extending the precursor phase above Tc. In diluted compositions with low Nb concentrations KTN materials exhibit formation of polar nano regions and relaxor like behavior. This behavior is analogous with

  14. Integrated Spectroscopic Studies of Anhydrous Sulfate Minerals

    NASA Technical Reports Server (NTRS)

    Lane, M. D.; Bishop, J. L.; Dyar, M. D.; Cloutis, E.; Forray, F. L.; Hiroi, T.

    2005-01-01

    Sulfates have been identified in Martian soils and bedrock and are emerging as an important indicator for aqueous activity on Mars. Sulfate minerals can form in a variety of low-temperature (evaporitic; chemical-weathering) and high-temperature (volcanic/fumarolic; hydrothermal) environments and their formational environments can range from alkaline to acidic. Although sulfates generally form in the presence of water, not all sulfates are hydrous or contain water in their structures. Many of these anhydrous sulfates (Dana group 28; Strunz class 67A) are minerals that form as accompanying phases to the main minerals in ore deposits or as replacement deposits in sedimentary rocks. However, some form from thermal decomposition of OH or H2O-bearing sulfates, such as from the reaction [1]: jarosite = yavapaiite + Fe2O3 + H2O. Where known, the stability fields of these minerals all suggest that they would be stable under martian surface conditions [2]. Thus, anhydrous sulfate minerals may contribute to martian surface mineralogy, so they must be well-represented in spectral libraries used for interpretation of the Martian surface. We present here the preliminary results of an integrated study of emittance, reflectance, and Mossbauer spectroscopy of a suite of wel-lcharacterized anhydrous sulfates.

  15. Spectroscopic study of biologically active glasses

    NASA Astrophysics Data System (ADS)

    Szumera, M.; Wacławska, I.; Mozgawa, W.; Sitarz, M.

    2005-06-01

    It is known that the chemical activity phenomenon is characteristic for some inorganic glasses and they are able to participate in biological processes of living organisms (plants, animals and human bodies). An example here is the selective removal of silicate-phosphate glass components under the influence of biological solutions, which has been applied in designing glasses acting as ecological fertilizers of controlled release rate of the nutrients for plants. The structure of model silicate-phosphate glasses containing the different amounts of the glass network formers, i.e. Ca 2+ and Mg 2+, as a binding components were studied. These elements besides other are indispensable of the normal growth of plants. In order to establish the function and position occupied by the particular components in the glass structure, the glasses were examined by FTIR spectroscopy (with spectra decomposition) and XRD methods. It has been found that the increasing amount of MgO in the structure of silicate-phosphate glasses causes the formation of domains the structure of which changes systematically from a structure of the cristobalite type to a structure corresponding to forsterite type. Whilst the increasing content of CaO in the structure of silicate-phosphate glasses causes the formation of domains the structure of which changes from a structure typical for cristobalite through one similar to the structure of calcium orthophosphate, to a structure corresponding to calcium silicates. The changing character of domains structure is the reason of different chemical activity of glasses.

  16. Fluorescence spectroscopic studies of DNA dynamics

    SciTech Connect

    Scalettar, B.A.

    1987-04-01

    Random solvent induced motions of DNA are manifest as nanosecond torsional oscillations of the helix backbone, nanosecond through millisecond bending deformations and overall rotational and translational diffusion of the polymer. Fluorescence spectroscopy is used to study this spectrum of DNA motions while ethidium monoazide was covalently bounded. The steady state fluorescence depolarization data indicate that the covalent monoazide/DNA complex exhibits internal motions characterized by an average angular amplitude of 26 degrees confirming reports of fast torsional oscillations in noncovalent ethidium bromide/DNA systems. Data obtained by use of a new polarized photobleaching recovery technique (FPR) reflect both the rotational dynamics of the polymer and the reversible photochemistry of the dye. To isolate the reorientational motion of the DNA, the FPR experiments were ran in two modes that differ only in the polarization of the bleaching light. A quotient function constructed from the data obtained in these two modes monitors only the rotational component of the FPR recovery. In specific applications those bending deformations of long DNA molecules that have characteristic relaxation times on the order of 100 microseconds have been resolved. A fluorescence correlation technique that relates fluctuations in particle number to center-of-mass motion was used to measure translational diffusion on coefficients of the plasmid PBR322 and a short oligomeric DNA. A theory that describes angular correlation in systems exhibiting cyclic, biologically directed reorientation and random Brownian rotation is developed.

  17. DAO Spectroscopic Study of Nova Cygni 1992

    NASA Astrophysics Data System (ADS)

    Garnavich, Peter M.

    1992-12-01

    The spectral development of Nova Cygni 1992 is being monitored at the Dominion Astrophysical Observatory. The brightest nova in over 15 years provides a rare opportunity to study, in detail, nova evolution from maximum to the late nebular stages. Our spectra during the early phases of the outburst had a resolution of 0.6 Angstroms while in the nebular phase the resolution ranged from 2 Angstroms to 4 Angstroms . The nova was observed at DAO on more than 40 nights in 1992. Our first spectrum was obtained near maximum light on February 22, 1992. It showed weak Hβ and Fe II emission lines with P-Cygni absorption components at -910 and -1670 km/s (IAUC 5457). During the early decline, the P-Cygni absorption complex spread blueward, eventually reaching -2900 km/s by the ides of March. Observations by IUE showed absorption troughs of UV lines extending to -2800 km/s even before maximum (IAUC 5456). This suggests that the apparent increase in the velocity of the diffuse-enhanced absorption is due to opacity effects, not a physical acceleration of the gas or the changing geometry of the expanding shells. The transition to the nebular phase occurred in late April, 1992. The emission lines were broad (FWHM of 2200 km/s) and contained as many as 10 velocity components. The temperature and density evolution of the major velocity components are estimated from diagnostic line ratios during the nebular stage. The similarity between Nova Cygni 1992 and V1500 Cyg suggested that the coronal line, [Fe X] 6374 Angstroms , might be present in the early nebular phase. The unusual shape and strength of the [O I] line at 6363 Angstroms added to this suspicion. In spectra taken 90 days after outburst, the [O I] 6300 Angstroms line was used to deconvolve the emission, but the contamination was found to be due to the Si II doublet 6347/71 Angstroms . Infrared observations indicated the onset of a coronal phase 200 days after maximum (IAUC 5612), and our data from this period are analyzed

  18. Spectroscopic investigation (FT-IR and FT-Raman), vibrational assignments, HOMO-LUMO analysis and molecular docking study of 1-hydroxy-4,5,8-tris(4-methoxyphenyl) anthraquinone

    NASA Astrophysics Data System (ADS)

    Renjith, R.; Sheena Mary, Y.; Tresa Varghese, Hema; Yohannan Panicker, C.; Thiemann, Thies; Shereef, Anas; Al-Saadi, Abdulaziz A.

    2015-12-01

    FT-IR and FT-Raman spectra of 1-hydroxy-4,5,8-tris(4-methoxyphenyl)anthraquinone were recorded and analyzed. The vibrational wavenumbers were computed using DFT quantum chemical calculations. The data obtained from wavenumber calculations were used to assign the vibrational bands obtained experimentally. A detailed molecular picture of the title compound and its interactions were obtained from NBO analysis. From the MEP plot it is clear that the negative electrostatic potential regions are mainly localized over carbonyl group. There is some evidence of a region of negative electrostatic potential due to π-electron density of the benzo groups. Molecular docking study shows that methoxy groups attached to the phenyl rings and hydroxyl group are crucial for binding and the title compound might exhibit inhibitory activity against PI3K and may act as an anti-neoplastic agent.

  19. Synthesis, molecular structure, spectroscopic characterization, NBO, NLO and NPA analysis and in vitro cytotoxicity study of 3-chloro-N-(4-sulfamoylphenethyl)propanamide with experimental and computational study

    NASA Astrophysics Data System (ADS)

    Durgun, Mustafa; Ceylan, Ümit; Yalçın, Şerife Pınar; Türkmen, Hasan; Özdemir, Namık; Koyuncu, İsmail

    2016-06-01

    In present work, the sulfonamide compound, 3-chloro-N-(4-sulfamoylphenethyl)propanamide, has been synthesized and characterized by FT-IR, 1H-NMR, 13C-NMR, UV-vis and X-Ray single crystal determination. The compound crystallizes in the monoclinic space group P21/c with a = 8.4493(4) Å, b = 17.5875(7) Å, c = 9.2593(4) Å and β = 103.579(4)°, and Z = 4 in the unit cell. The molecular geometry from X-ray experiment in the ground state and vibrational frequencies, 1H and 13C-NMR chemical shifts, absorption wavelengths have been calculated by using the Density Functional Theory (DFT) method with 6-311++G(d,p) basis set and compared with the experimental values. In addition, Molecular Electrostatic Potential (MEP), Natural Bond Orbital (NBO), Frontier Molecular Orbital (FMO) analysis, thermodynamic properties, dipole moments, and HOMO-LUMO energy were also computed. The calculated results show that the optimized geometry can well reproduce the crystal structure parameters, and the vibrational frequencies, 1H and 13C-NMR chemical shifts, absorption wavelengths are in agreement with experimental values. Further, the synthesized compound was evaluated for in vitro cytotoxic activity against various tumour cells and normal cell line using MTT assay. The synthesized compound show the highest antiproliferative effect against ECC-1 tumour cells (IC50 = 0,167 mM), while the lowest cytotoxic activity against normal cell (HEK-293 and PNT1A) cell line (IC50 = 0.603 and 0.696 mM, respectively).

  20. Spectroscopic studies of protein folding: Linear and nonlinear methods

    PubMed Central

    Serrano, Arnaldo L; Waegele, Matthias M; Gai, Feng

    2012-01-01

    Although protein folding is a simple outcome of the underlying thermodynamics, arriving at a quantitative and predictive understanding of how proteins fold nevertheless poses huge challenges. Therefore, both advanced experimental and computational methods are continuously being developed and refined to probe and reveal the atomistic details of protein folding dynamics and mechanisms. Herein, we provide a concise review of recent developments in spectroscopic studies of protein folding, with a focus on new triggering and probing methods. In particular, we describe several laser-based techniques for triggering protein folding/unfolding on the picosecond and/or nanosecond timescales and various linear and nonlinear spectroscopic techniques for interrogating protein conformations, conformational transitions, and dynamics. PMID:22109973

  1. Spectroscopic investigation (FT-IR and FT-Raman), vibrational assignments, HOMO-LUMO analysis and molecular docking study of 2-(Adamantan-1-yl)-5-(4-nitrophenyl)-1,3,4-oxadiazole.

    PubMed

    Haress, Nadia G; Al-Omary, Fatmah; El-Emam, Ali A; Mary, Y Sheena; Panicker, C Yohannan; Al-Saadi, Abdulaziz A; War, Javeed Ahmad; Van Alsenoy, Christian

    2015-01-25

    FT-IR and FT-Raman spectra of 2-(Adamantan-1-yl)-5-(4-nitrophenyl)-1,3,4-oxadiazole were recorded and analyzed. The vibrational wavenumbers were computed using DFT quantum chemical calculations. The data obtained from wavenumber calculations are used to assign vibrational bands obtained experimentally. The energy barriers of the internal rotations about the C-C bonds connecting the oxadiazole to the adamantane and benzene rings are reported. The geometrical parameters (DFT) of the title compound are in agreement with the XRD results. The calculated HOMO and LUMO energies allow the calculations of atomic and molecular properties and they also showed that charge transfer occurs in the molecule. A detailed molecular picture of the title compound and its interactions were obtained from NBO analysis. As can be seen from the MEP map of the title compound, which regions having the negative potential are over the electro negative atoms, the region having the positive potential are over the phenyl and adamantine rings and the remaining species are surrounded by zero potential. The molecular docking studies reveal that the adamantyl derivative may exhibit C-South African HIV-proteas inhibitory activity. PMID:25168235

  2. Spectroscopic investigation (FT-IR and FT-Raman), vibrational assignments, HOMO-LUMO analysis and molecular docking study of 2-(Adamantan-1-yl)-5-(4-nitrophenyl)-1,3,4-oxadiazole

    NASA Astrophysics Data System (ADS)

    Haress, Nadia G.; Al-Omary, Fatmah; El-Emam, Ali A.; Mary, Y. Sheena; Panicker, C. Yohannan; Al-Saadi, Abdulaziz A.; War, Javeed Ahmad; Van Alsenoy, Christian

    2015-01-01

    FT-IR and FT-Raman spectra of 2-(Adamantan-1-yl)-5-(4-nitrophenyl)-1,3,4-oxadiazole were recorded and analyzed. The vibrational wavenumbers were computed using DFT quantum chemical calculations. The data obtained from wavenumber calculations are used to assign vibrational bands obtained experimentally. The energy barriers of the internal rotations about the Csbnd C bonds connecting the oxadiazole to the adamantane and benzene rings are reported. The geometrical parameters (DFT) of the title compound are in agreement with the XRD results. The calculated HOMO and LUMO energies allow the calculations of atomic and molecular properties and they also showed that charge transfer occurs in the molecule. A detailed molecular picture of the title compound and its interactions were obtained from NBO analysis. As can be seen from the MEP map of the title compound, which regions having the negative potential are over the electro negative atoms, the region having the positive potential are over the phenyl and adamantine rings and the remaining species are surrounded by zero potential. The molecular docking studies reveal that the adamantyl derivative may exhibit C-South African HIV-proteas inhibitory activity.

  3. Using non-invasive molecular spectroscopic techniques to detect unique aspects of protein Amide functional groups and chemical properties of modeled forage from different sourced-origins

    NASA Astrophysics Data System (ADS)

    Ji, Cuiying; Zhang, Xuewei; Yu, Peiqiang

    2016-03-01

    The non-invasive molecular spectroscopic technique-FT/IR is capable to detect the molecular structure spectral features that are associated with biological, nutritional and biodegradation functions. However, to date, few researches have been conducted to use these non-invasive molecular spectroscopic techniques to study forage internal protein structures associated with biodegradation and biological functions. The objectives of this study were to detect unique aspects and association of protein Amide functional groups in terms of protein Amide I and II spectral profiles and chemical properties in the alfalfa forage (Medicago sativa L.) from different sourced-origins. In this study, alfalfa hay with two different origins was used as modeled forage for molecular structure and chemical property study. In each forage origin, five to seven sources were analyzed. The molecular spectral profiles were determined using FT/IR non-invasive molecular spectroscopy. The parameters of protein spectral profiles included functional groups of Amide I, Amide II and Amide I to II ratio. The results show that the modeled forage Amide I and Amide II were centered at 1653 cm- 1 and 1545 cm- 1, respectively. The Amide I spectral height and area intensities were from 0.02 to 0.03 and 2.67 to 3.36 AI, respectively. The Amide II spectral height and area intensities were from 0.01 to 0.02 and 0.71 to 0.93 AI, respectively. The Amide I to II spectral peak height and area ratios were from 1.86 to 1.88 and 3.68 to 3.79, respectively. Our results show that the non-invasive molecular spectroscopic techniques are capable to detect forage internal protein structure features which are associated with forage chemical properties.

  4. A Herschel Spectroscopic Survey of Warm Molecular Gas in Local Infrared Luminous Galaxies

    NASA Astrophysics Data System (ADS)

    Lu, N.; Zhao, Y.; Xu, C. K.; Gao, Y.; GOALS FTS Team

    2013-03-01

    We describe an on-going 194-671 μm spectroscopic survey of a flux-limited sample of 125 local luminous infrared galaxies (LIRGs) with Herschel SPIRE Fourier Transform Spectrometer (FTS). The survey targets primarily the CO spectral line energy distribution (SLED), from J = 4-3 up to J = 13-12, to probe dense and warm molecular gas that should play an intimate role in star formation and/or active galactic nuclear activities in these galaxies. The program is about 75% finished. At S/N > 5, besides the CO lines, we also detected [N ii] 205 μm and [C i] 370 μm (3 P 2 - 3P1) lines in every target observed. In about half of the observed targets, we also detected [C i] 609 μm (3 P 1 - 3P0).

  5. Synthesis, molecular structure, spectroscopic characterization and quantum chemical calculation studies of (2E)-1-(5-chlorothiophen-2-yl)-3-(2,3,4-trimethoxyphenyl)prop-2-en-1-one

    NASA Astrophysics Data System (ADS)

    Chidan Kumar, C. S.; Govindarasu, K.; Fun, Hoong-Kun; Kavitha, E.; Chandraju, Siddegowda; Quah, Ching Kheng

    2015-04-01

    High quality single crystal of efficient novel nonlinear optical (NLO) chalcone derivative (2E)-1-(5-chlorothiophen-2-yl)-3-(2,3,4-trimethoxyphenyl)prop-2-en-1-one crystal has been grown and its structure has been characterized by Fourier Transform Infrared (4000-400 cm-1), Fourier Transform Raman (3500-50 cm-1) and single-crystal X-ray diffraction techniques. The vibrational wavenumbers were computed using Density Functional Theory (DFT) and are assigned with the help of potential energy distribution (PED) method. The geometrical parameters of the title compound obtained from X-ray diffraction (XRD) studies are compared with the calculated (DFT) values using 6-31G(d,p) basis set. Stability of the molecule, hyperconjugative interactions, charge delocalization and intramolecular hydrogen bond has been analyzed by using natural bond orbital (NBO) analysis. Electronic structures were discussed by Time Dependent Density Functional Theory (TD-DFT) and the relocation of the electron density was determined. Nonlinear optical (NLO) properties were also investigated. The Time Dependent Density Functional Theory (TD-DFT) method has been used to calculate energies, oscillator strengths of electronic singlet-singlet transitions and the absorption wavelengths. The Higher occupied molecular orbital (HOMO) and the Lower unoccupied molecular orbital (LUMO) analysis are used to determine the charge transfer within the molecule. Comprehensive theoretical and experimental structural studies on the molecule have been carried out by FT-IR, FT-Raman and Ultra Violet-visible spectrometry (UV-Vis).

  6. Coordination mode of pentadentate ligand derivative of 5-amino-1,3,4-thiadiazole-2-thiol with nickel(II) and copper(II) metal ions: Synthesis, spectroscopic characterization, molecular modeling and fungicidal study

    NASA Astrophysics Data System (ADS)

    Chandra, Sulekh; Gautam, Seema; Kumar, Amit; Madan, Molly

    2015-02-01

    Complexes of nickel(II), and copper(II) were synthesized with pantadentate ligand i.e. 3,3‧-thiodipropionicacid-bis(5-amino-1,3,4-thiadiazole-2-thiol) (L). The ligand was synthesized by the condensation of thiodipropionic acid and 5-amino-1,3,4-thiadiazole-2-thiol in 1:2 ratio, respectively. Synthesized ligand was characterized by elemental analysis, mass, 1H NMR, IR, and molecular modeling. All the complexes were characterized by elemental analysis, molar conductance, magnetic moment, IR, electronic spectra, ESR, and molecular modeling. The newly synthesized complexes possessed general composition [M(L)X2] where M = Ni(II), Cu(II), L = pantadentate ligand and X = Cl-, CH3COO-. The IR spectral data indicated that the ligand behaved as a pantadentate ligand and coordinated to the metal ion through N2S3 donor atoms. The molar conductance value of Ni(II), and Cu(II) complexes in DMSO corresponded to their electrolytic behavior. On the basis of spectral study, octahedral and tetragonal geometry was assigned for Ni(II) and Cu(II) complexes, respectively. In vitro fungicidal study of ligand and its complexes was investigated against fungi Candida albicans, Candida parapsilosis, Candidia krusei, and Candida tropicalis by means of well diffusion method.

  7. Spectroscopic studies and molecular docking on the interaction of organotin antitumor compound bis[2,4-difluoro-N-(hydroxy-⟨κ⟩O)benzamidato-⟨κ⟩O]diphenyltin(IV) with human cytochrome P450 3A4 protease

    NASA Astrophysics Data System (ADS)

    Wei, Ying; Niu, Lin; Liu, Xinxin; Zhou, Hongyan; Dong, Hongzhou; Kong, Depeng; Li, Yunlan; Li, Qingshan

    2016-06-01

    A novel organotin DFDPT was synthesized and characterized by elemental analysis, IR, 1H, 13C, 119Sn, NMR techniques,etc. In order to investigate profoundly the relationship between DFDPT with human CYP3A4 proteaset and anticancer molecular mechanism of DFDPT, the intercalative mode of binding of DFDPT with CYP3A4 under physiological conditions were comprehensively evaluated using steady state, synchronous, three-dimensional fluorescence spectroscopy,circular dichroism and molecular docking. Fluorescence emission data showed that CYP3A4 fluorescence affected by DFDPT was a static quenching procedure, which implied that DFDPT-CYP3A4 complex had been formed. Apparent binding constants Kb of CYP3A4 with compound at 298 and 310 K were 2.51 × 107 and 3.09 × 105, respectively. The binding sites number n was 1.64 and 1.22, respectively. The thermodynamic parameters ΔH and ΔS of the DFDPT-CYP3A4 complex were negative, which indicated that their interaction was driven mainly by hydrogen bonding and van der Waals force. The binding of DFDPT-CYP3A4 was spontaneous process in which ΔG was negative. The synchronous results showed DFDPT induced conformational changes of CYP3A4 protein. Three-dimensional fluorescence and circular dichroism spectra results also revealed conformation of CYP3A4 protein had been possible changed in the presence of DFDPT. Molecular docking was used to study the interaction orientation between DFDPT and CYP3A4 protease. The results indicated that DFDPT interacted with a panel of amino acids in the active sites of CYP3A4 protein mainly through formation of hydrogen bond. Furthermore, the predicted binding mode of DFDPT into CYP3A4 appeared to adopt an orientation with interactions among Arg105, Ser119 and Thr309.

  8. Spectroscopic studies and molecular docking on the interaction of organotin antitumor compound bis[2,4-difluoro-N-(hydroxy-⟨κ⟩O)benzamidato-⟨κ⟩O]diphenyltin(IV) with human cytochrome P450 3A4 protease.

    PubMed

    Wei, Ying; Niu, Lin; Liu, Xinxin; Zhou, Hongyan; Dong, Hongzhou; Kong, Depeng; Li, Yunlan; Li, Qingshan

    2016-06-15

    A novel organotin DFDPT was synthesized and characterized by elemental analysis, IR, (1)H, (13)C, (119)Sn, NMR techniques,etc. In order to investigate profoundly the relationship between DFDPT with human CYP3A4 proteaset and anticancer molecular mechanism of DFDPT, the intercalative mode of binding of DFDPT with CYP3A4 under physiological conditions were comprehensively evaluated using steady state, synchronous, three-dimensional fluorescence spectroscopy,circular dichroism and molecular docking. Fluorescence emission data showed that CYP3A4 fluorescence affected by DFDPT was a static quenching procedure, which implied that DFDPT-CYP3A4 complex had been formed. Apparent binding constants Kb of CYP3A4 with compound at 298 and 310K were 2.51×10(7) and 3.09×10(5), respectively. The binding sites number n was 1.64 and 1.22, respectively. The thermodynamic parameters ΔH and ΔS of the DFDPT-CYP3A4 complex were negative, which indicated that their interaction was driven mainly by hydrogen bonding and van der Waals force. The binding of DFDPT-CYP3A4 was spontaneous process in which ΔG was negative. The synchronous results showed DFDPT induced conformational changes of CYP3A4 protein. Three-dimensional fluorescence and circular dichroism spectra results also revealed conformation of CYP3A4 protein had been possible changed in the presence of DFDPT. Molecular docking was used to study the interaction orientation between DFDPT and CYP3A4 protease. The results indicated that DFDPT interacted with a panel of amino acids in the active sites of CYP3A4 protein mainly through formation of hydrogen bond. Furthermore, the predicted binding mode of DFDPT into CYP3A4 appeared to adopt an orientation with interactions among Arg105, Ser119 and Thr309. PMID:27049867

  9. Spectroscopic and dynamical studies of highly energized small polyatomic molecules

    SciTech Connect

    Field, R.W.; Silbey, R.J.

    1993-12-01

    The authors have initiated a program to perform spectroscopic and dynamic studies of small molecules. Large amplitude motions in excited acetylene were discussed along with plans to record the dispersed fluorescence (DF) and the stimulated emission pumping (SEP) spectra. SEP spectra were reported for the formyl radical. A Fourier transform spectrometer was discussed with respect to its ability to probe the structure of radicals. This instrument is capable of performing studies using various techniques such as magnetic rotation spectroscopy and sub-Doppler sideband-OODR Zeman (SOODRZ) spectroscopy.

  10. Spectroscopic study of some diatomic molecules via the proper quantization rule

    NASA Astrophysics Data System (ADS)

    Falaye, B.

    Spectroscopic techniques are very essential tools in studying electronic structures, spectroscopic constants and energetic properties of diatomic molecules. These techniques are also required for parametrization of new method based on theoretical analysis and computational calculations. In this research, we apply the proper quantization rule in spectroscopic study of some diatomic molecules by solving the Schrödinger equation with two solvable quantum molecular systems-Tietz-Wei and shifted Deng-Fan potential models for their approximate nonrelativistic energy states via an appropriate approximation to the centrifugal term. We show that the energy levels can be determined from its ground state energy. The beauty and simplicity of the method applied in this study is that, it can be applied to any exactly as well as approximately solvable models. The validity and accuracy of the method is tested with previous techniques via numerical computation for H2 and CO diatomic molecules. The result also include energy spectrum of 5 different electronic states of NO and 2 different electronic state of ICl.