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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. Nonlinear spectroscopic studies of interfacial molecular ordering

    NASA Astrophysics Data System (ADS)

    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.

  3. [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

  4. 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.

  5. Spectroscopic and molecular docking studies on chlorambucil interaction with DNA.

    PubMed

    Charak, Sonika; Shandilya, Manish; Tyagi, Gunjan; Mehrotra, Ranjana

    2012-11-01

    Chlorambucil (CMB) is an anticancer drug used for the treatment of variety of cancers. Structural and conformational changes associated with DNA after binding with CMB were explored using spectroscopic techniques to get insight into the mechanism of action of CMB at molecular level. Different molar ratios of CMB-DNA complex were prepared with constant DNA concentration under physiological conditions. FTIR spectroscopy, UV-visible spectroscopy, CD spectroscopy and molecular docking studies were employed to determine the binding site and binding constant of CMB with DNA. The results show CMB binds DNA through nitrogenous bases (thymine, guanine and cytosine). The binding constant was calculated to be 1.3 × 10³ M⁻¹, which suggests weak binding of CMB with DNA double helix. FTIR and CD results show that CMB do not disturb native B-conformation of DNA and it continues to remain in its B conformation even at higher concentrations of CMB. The molecular docking results are in corroboration with our experimental results and provides structural insight into the interaction site. Copyright © 2012 Elsevier B.V. All rights reserved.

  6. Molecular docking, spectroscopic studies and quantum calculations on nootropic drug.

    PubMed

    Uma Maheswari, J; Muthu, S; Sundius, Tom

    2014-04-05

    A systematic vibrational spectroscopic assignment and analysis of piracetam [(2-oxo-1-pyrrolidineacetamide)] have 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) basis set. Molecular equilibrium geometries, electronic energies, IR and Raman intensities, and 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 wavelengths λmax were determined by the 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 (PED) 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. Molecular docking studies have been carried out in the active site of piracetam by using Argus Lab. In addition, the potential energy surface, HOMO and LUMO energies, first-order hyperpolarizability and the molecular electrostatic potential have been computed.

  7. 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

  8. Molecular interactions of flavonoids to pepsin: Insights from spectroscopic and molecular docking studies.

    PubMed

    Zeng, Hua-Jin; Yang, Ran; Liang, Huili; Qu, Ling-Bo

    2015-01-01

    In the work described on this paper, the inhibitory effect of 10 flavonoids on pepsin and the interactions between them were investigated by a combination of spectroscopic and molecular docking methods. The results indicated that all flavonoids could bind with pepsin to form flavonoid-pepsin complexes. The binding parameters obtained from the data at different temperatures revealed that flavonoids could spontaneously interact with pepsin mainly through electrostatic forces and hydrophobic interactions with one binding site. According to synchronous and three-dimensional fluorescence spectra and molecular docking results, all flavonoids bound directly into the enzyme cavity site and the binding influenced the microenvironment and conformation of the pepsin activity site which resulted in the reduced enzyme activity. The present study provides direct evidence at a molecular level to understand the mechanism of digestion caused by flavonoids.

  9. Spectroscopic studies of the molecular imprinting self-assembly process.

    PubMed

    Svenson, J; Andersson, H S; Piletsky, S A; Nicholls, I A

    1998-01-01

    A method for the rapid estimation of the extent of complex formation in molecular imprinting prepolymerization mixtures is described. By the use of a UV spectroscopy titration procedure, apparent binding constants for such self-assembly processes have been obtained. This method was used for comparison of the interactions between a dipeptide template (N-acetyl-L-phenylalaninyl-L-tryptophanyl methyl ester) and the functional monomer methacrylic acid, and the monomer analogues acetic acid and trifluoroacetic acid. The importance of template-monomer association during the molecular imprinting prepolymerization phase is discussed with respect to the systems studied.

  10. 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.

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

    PubMed

    Karthick, T; Balachandran, V; Perumal, S

    2015-04-15

    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. Copyright © 2015 Elsevier B.V. All rights reserved.

  12. Spectroscopic study of molecular structure, antioxidant activity and biological effects of metal hydroxyflavonol complexes

    NASA Astrophysics Data System (ADS)

    Samsonowicz, Mariola; Regulska, Ewa

    2017-02-01

    Flavonols with varied hydroxyl substitution can act as strong antioxidants. Thanks to their ability to chelate metals as well as to donate hydrogen atoms they have capacity to scavenge free radicals. Their metal complexes are often more active in comparison with free ligands. They exhibit interesting biological properties, e.g. anticancer, antiphlogistic and antibacterial. The relationship between molecular structure and their biological properties was intensively studied using spectroscopic methods (UV-Vis, IR, Raman, NMR, ESI-MS). The aim of this paper is review on spectroscopic analyses of molecular structure and biological activity of hydroxyflavonol metal complexes.

  13. Laser Raman and infrared spectroscopic studies of molecular systems: Structural analysis of some clathrate compounds

    NASA Astrophysics Data System (ADS)

    Akyuz, S.

    1990-09-01

    The structural analyses of some molecular systems, namely clathrates, depending on the laser Raman and infrared spectroscopic studies are reported. The following subject areas are covered: Raman effect; Raman spectroscopy; IR spectroscopy; mutual exclusion principle; vibrational spectra of the polymeric layers; and fundamental vibrations of pyrazine molecules.

  14. Spectroscopic Studies on the Molecular Ageing of Serum Albumin.

    PubMed

    Chudzik, Mariola; Maciążek-Jurczyk, Małgorzata; Pawełczak, Bartosz; Sułkowska, Anna

    2016-12-27

    Pathological states in the organism, e.g., renal or hepatic diseases, cataract, dysfunction of coronary artery, diabetes mellitus, and also intensive workout, induce the structural modification of proteins called molecular ageing or N-A isomerization. The aim of this study was to analyze the structural changes of serum albumin caused by alkaline ageing using absorption, spectrofluorescence, and circular dichroism spectroscopy. The N-A isomerization generates significant changes in bovine (BSA) and human (HSA) serum albumin subdomains-the greatest changes were observed close to the tryptophanyl (Trp) and tyrosyl (Tyr) residue regions while a smaller change was observed in phenyloalanine (Phe) environment. Moreover, the changes in the polarity of the Trp neighborhood as well as the impact of the ageing process on α-helix, β-sheet content, and albumin molecule rotation degree have been analyzed. Based on the spectrofluorescence study, the alterations in metoprolol binding affinity to the specific sites that increase the toxicity of the drug were investigated.

  15. Vibrational spectroscopic studies of 3-hydroxyphenylboronic acid: molecular structure

    NASA Astrophysics Data System (ADS)

    Sert, Y.; Ucun, F.; Böyükata, M.

    2013-02-01

    In this work, optimized molecular structure, vibrational frequencies and corresponding vibrational assignments, HOMO-LUMO energy values and electron density clouds of 3-hydroxyphenylboronic acid have been calculated by ab initio Hatree-Fock (HF) and density functional theory methods. The compound has eight conformers depending on the directions of hydrogen atoms bonded to oxygen. The computational results have diagnosed the most stable conformer of the compound as cis-trans (ctt) form. The calculated frequencies and optimized geometry parameters (bond lengths and bond angles) for the most stable conformer are in a good agreement with the corresponding experimental data.

  16. Molecular spectroscopic study of acid treated fenugreek seeds

    NASA Astrophysics Data System (ADS)

    Ibrahim, Medhat

    2010-12-01

    Fenugreek seeds were subjected to acid treatment in order to activate its surface. XRF indicated that there was no change in the level of metals and metal oxides as a result of the treatment. FTIR of the treated fenugreek showed no change in the characteristic bands and/or structure of the fenugreek. A shift in both OH and metal oxide bands suggest a role for metal, hydrated metal and metal oxide in fenugreek seed. Molecular modeling suggests that metal oxides such as Al 16O 24 offer its surface for the adsorption of gases. The interaction of gases with metal oxide is depending on the type of gas rather than the type of coordination. Finally results indicate that fenugreek could be used safely to control the level of gases in stomach.

  17. 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.

  18. Study of spectroscopic and thermal characteristics of nonlinear optical molecular crystals based on 4-nitrophenol

    NASA Astrophysics Data System (ADS)

    Pavlovetc, I. M.; Fokina, M. I.

    2016-08-01

    The paper presents the results of study of spectroscopic and thermal characteristics of molecular co-crystals: 2-aminopyridine-4-nitrophenol-4-mtrophenolate (2AP4N) and 2,6- diaminopyridine-4-nitrophenol-4nitrophenolate (26DAP4N). Crystals were successfully grown by slow evaporation technique. Optical transparency in the region of 190-1100 was found to be suitable for applications with cut off wavelengths 420 and 430 nm respectively. Thermogravimetric and differential thermal analysis show good quality and thermal stability for studied crystals. Kurtz and Perry powder technique proves that the crystals are acentric and have significant nonlinear optical response.

  19. 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

    2015-12-05

    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. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

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

    PubMed

    Jing, Mingyang; Song, Wei; Liu, Rutao

    2016-07-05

    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. Copyright © 2016 Elsevier B.V. All rights reserved.

  1. 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.

  2. Molecular hydraulic properties of montmorillonite: a polarized fourier transform infrared spectroscopic study.

    PubMed

    Amarasinghe, Priyanthi M; Katti, Kalpana S; Katti, Dinesh R

    2008-12-01

    Understanding the rates at which fluid flows into clay interlayers at the molecular level is fundamental to designing an effective clay barrier system. In this work, molecular interactions at the Na-montmorillonite (MMT)-water interface, emphasizing the flow properties of the clay interlayer, have been studied at the molecular and nanoscale level using polarized Fourier transform infrared (FT-IR) spectroscopic and X-ray diffraction (XRD) techniques. Clay-water slurries were smeared on inert gold-coated metal substrates for FT-IR experiments and slurries were smeared on quartz plates for XRD experiments. By analyzing the O-H stretching and H-O-H bending vibrations in clay slurries, it was concluded that the molecular behavior of interlayer water is significantly different from the molecular behavior of bulk water. With increasing clay-water interaction time, it was also seen that the Si-O stretching bands of clay are being significantly altered by the water molecules in the interlayer. Using these spectroscopic techniques we have estimated the time required for water to flow into the clay interlayer. Further, by analyzing the particle size of the clay using atomic force microscopy (AFM) imaging, we were able to estimate the flow velocity of the water in the clay interlayer. This velocity is found to be 3.23 x 10(-9) cm/s. This flow velocity was found to be of the same order of magnitude as the hydraulic conductivity of smectite-type clay reported elsewhere. Also described in this work is the correct positioning of the Si-O out-of-plane vibration band of MMT at the two-layer saturation level in the interlayer. This band was only observed in p-polarized spectra at 1211 cm(-1). Thus, we attribute this band to the Si-O out-of-plane vibration band.

  3. Inhibitory effect of morin on tyrosinase: insights from spectroscopic and molecular docking studies.

    PubMed

    Wang, Yajie; Zhang, Guowen; Yan, Jiakai; Gong, Deming

    2014-11-15

    Tyrosinase is a key enzyme in the production of melanin in the human body, excessive accumulation of melanin can lead to skin disorders. Morin is an important bioactive flavonoid compound widely distributed in plants and foods of plant origin. In this study, the inhibitory kinetics of morin on tyrosinase and their binding mechanism were determined using spectroscopic and molecular docking techniques. The results indicate that morin reversibly inhibited tyrosinase in a competitive manner through a multi-phase kinetic process. Morin was found to bind to tyrosinase at a single binding site mainly by hydrogen bonds and van der Waals forces. Analysis of circular dichroism spectra revealed that the binding of morin to tyrosinase induced rearrangement and conformational changes of the enzyme. Moreover, molecular docking results suggested that morin competitively bound to the active site of tyrosinase with the substrate levodopa. Copyright © 2014 Elsevier Ltd. All rights reserved.

  4. DNA-binding study of anticancer drug cytarabine by spectroscopic and molecular docking techniques.

    PubMed

    Shahabadi, Nahid; Falsafi, Monireh; Maghsudi, Maryam

    2017-01-02

    The interaction of anticancer drug cytarabine with calf thymus DNA (CT-DNA) was investigated in vitro under simulated physiological conditions by multispectroscopic techniques and molecular modeling study. The fluorescence spectroscopy and UV absorption spectroscopy indicated drug interacted with CT-DNA in a groove-binding mode, while the binding constant of UV-vis and the number of binding sites were 4.0 ± 0.2 × 10(4) L mol(-1) and 1.39, respectively. The fluorimetric studies showed that the reaction between the drugs with CT-DNA is exothermic. Circular dichroism spectroscopy was employed to measure the conformational change of DNA in the presence of cytarabine. Furthermore, the drug induces detectable changes in its viscosity for DNA interaction. The molecular modeling results illustrated that cytarabine strongly binds to groove of DNA by relative binding energy of docked structure -20.61 KJ mol(-1). This combination of multiple spectroscopic techniques and molecular modeling methods can be widely used in the investigation on the interaction of small molecular pollutants and drugs with biomacromolecules for clarifying the molecular mechanism of toxicity or side effect in vivo.

  5. Biochemical activity of a fluorescent dye rhodamine 6G: Molecular modeling, electrochemical, spectroscopic and thermodynamic studies.

    PubMed

    Al Masum, Abdulla; Chakraborty, Maharudra; Ghosh, Soumen; Laha, Dipranjan; Karmakar, Parimal; Islam, Md Maidul; Mukhopadhyay, Subrata

    2016-11-01

    Interaction of CT DNA with Rhodamine 6G (R6G) has been studied using molecular docking, electrochemical, spectroscopic and thermodynamic methods. From the study, it was illustrated that Rhodamine 6G binds to the minor groove of CT DNA. The binding was cooperative in nature. Circular voltametric study showed significant change in peak current and peak potential due to complexation. All the studies showed that the binding constant was in the order of 10(6)M(-1). Circular dichroic spectra showed significant conformational change on binding and DNA unwind during binding. Thermodynamic study showed that binding was favored by negative enthalpy and positive entropy change. From thermodynamic study it was also observed that several positive and negative free energies played significant role during binding and the unfavorable conformational free energy change was overcame by highly negative hydrophobic and salt dependent free energy changes. The experimental results were further validated using molecular docking study and the effect of structure on binding has been studied theoretically. From docking study it was found that the hydrophobic interaction and hydrogen bonds played a significant role during binding. The dye was absorbed by cell and this phenomenon was studied using fluorescent microscope. Cell survivability test showed that the dye active against Human Breast Cancer cells MDA-MB 468. ROS study showed that the activity is due to the production of reactive oxygen.

  6. Spectroscopic and molecular modeling studies on the interactions of N-Methylformamide with superoxide dismutase.

    PubMed

    Kalyani, Durai; Jyothi, Kanagaraj; Sivaprakasam, Chinnarasu; Nachiappan, Vasanthi

    2014-04-24

    N-Methylformamide, a polar solvent has a wide industrial applications and it is well-known for hepatotoxicity. The interaction between NMF with superoxide dismutase, an antioxidant defense enzyme has been studied for the first time using spectroscopic methods including Fourier transform infrared (FT-IR) spectroscopy, Circular dichroism (CD) spectroscopy and UV-visible spectroscopy under simulative physiological conditions and also by molecular modelling. Fourier Transform Infra Red analysis showed that the change in peak positions and shapes revealed that the secondary structure of SOD had been changed by the interaction with NMF. The data of CD spectra also confirmed that NMF decreased the degree of secondary structure of SOD, which directly resulted in destabilization of enzyme. We studied the inhibitory effect of NMF on enzyme kinetics by pyrogallol autoxidation revealed that protein-ligand complex caused structural unfolding which resulted in enzymatic inhibition. Thus the spectral behaviour of superoxide dismutase provides data concerning its conformational changes in the presence of NMF. Furthermore, molecular docking was applied to explore the binding mode between the protein-ligand complex. This suggested that Asn54 and Val302 residues of dimeric protein were predicted to interact with NMF. The present study provides direct evidence at a molecular level to show that exposure to NMF cause perturbation in its structure and function.

  7. Molecular spectroscopic study on the interaction of tetracyclines with serum albumins.

    PubMed

    Bi, Shuyun; Song, Daqian; Tian, Yuan; Zhou, Xin; Liu, Zhongying; Zhang, Hanqi

    2005-02-01

    A molecular spectroscopic investigation of the interaction between tetracyclines antibiotics and human serum albumin or bovine serum albumin was reported. The influences of some metal ions on the interaction were also studied. When tetracyclines drugs were added into the solution containing serum albumins, the fluorescence intensity of serum albumins decreased with the increasing of the drugs concentrations, which is due to the formation of new non-fluorescence complexes of drug-serum albumin. The tetracyclines acted as quenchers and quenched the fluorescence of the serum albumins. The binding constants and the number of the binding sites of the reaction of tetracyclines and serum albumins were obtained. The main sorts of acting force between the drugs and serum albumins were found and the action distances and the energy transfer efficiencies between donor-acceptor were calculated based on the Foster energy transference.

  8. Molecular spectroscopic study on the interaction of tetracyclines with serum albumins

    NASA Astrophysics Data System (ADS)

    Bi, Shuyun; Song, Daqian; Tian, Yuan; Zhou, Xin; Liu, Zhongying; Zhang, Hanqi

    2005-02-01

    A molecular spectroscopic investigation of the interaction between tetracyclines antibiotics and human serum albumin or bovine serum albumin was reported. The influences of some metal ions on the interaction were also studied. When tetracyclines drugs were added into the solution containing serum albumins, the fluorescence intensity of serum albumins decreased with the increasing of the drugs concentrations, which is due to the formation of new non-fluorescence complexes of drug-serum albumin. The tetracyclines acted as quenchers and quenched the fluorescence of the serum albumins. The binding constants and the number of the binding sites of the reaction of tetracyclines and serum albumins were obtained. The main sorts of acting force between the drugs and serum albumins were found and the action distances and the energy transfer efficiencies between donor-acceptor were calculated based on the Föster energy transference.

  9. 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

  10. Spectroscopic and molecular docking studies on the interaction of troxerutin with DNA.

    PubMed

    Subastri, A; Ramamurthy, C H; Suyavaran, A; Mareeswaran, R; Lokeswara Rao, P; Harikrishna, M; Suresh Kumar, M; Sujatha, V; Thirunavukkarasu, C

    2015-01-01

    Troxerutin (TXER) is a derivative of naturally occurring bioflavonoid rutin. It possesses different biological activities in rising clinical world. The biological activity possessed by most of the drugs mainly targets on macromolecules. Hence, in the current study we have examined the interaction mechanism of TXER with calf thymus DNA (CT-DNA) by using various spectroscopic methods, isothermal titration calorimetry (ITC) and molecular docking studies. Further, DNA cleavage study was carried out to find the DNA protection activity of TXER. UV-absorption and emission spectroscopy showed low binding constant values via groove binding. Circular dichroism study indicates that TXER does not modify native B-form of DNA, and it retains the native B-conformation. Furthermore, no effective positive potential peak shift was observed in TXER-DNA complex during electrochemical analysis by which it represents an interaction of TXER with DNA through groove binding. Molecular docking study showed thymine guanine based interaction with docking score -7.09 kcal/mol. This result was compared to experimental ITC value. The DNA cleavage study illustrates that TXER does not cause any DNA damage as well as TXER showed DNA protection against hydroxyl radical induced DNA damage. From this study, we conclude that TXER interacts with DNA by fashion of groove binding.

  11. Vibrational spectroscopic analysis, molecular dynamics simulations and molecular docking study of 5-nitro-2-phenoxymethyl benzimidazole

    NASA Astrophysics Data System (ADS)

    Menon, Vidya V.; Foto, Egemen; Mary, Y. Sheena; Karatas, Esin; Panicker, C. Yohannan; Yalcin, Gözde; Armaković, Stevan; Armaković, Sanja J.; Van Alsenoy, C.; Yildiz, Ilkay

    2017-02-01

    FT-IR and FT-Raman spectra of 5-nitro-2-phenoxymethylbenzimidazole were recorded and analyzed theoretically and experimentally. The splitting of Nsbnd H stretching mode in the IR spectrum with a red shift from the calculated value indicates the weakening of the NH bond. The theoretical calculations give the phenyl ring breathing modes at 999 cm-1 for mono substituted benzene ring and at 1040 cm-1 for tri-substituted benzene ring. The theoretical NMR chemical shifts are in agreement with the experimental chemical shifts. The most reactive sites for electrophilic and nucleophilic attack are predicted from the MEP analysis. HOMO of π nature is delocalized over the entire molecule whereas the LUMO is located over the complete molecule except mono-substituted phenyl ring and oxygen atom. Reactive sites of the title molecule have been located with the help of ALIE surfaces and Fukui functions. In order to determine locations prone to autoxidation and locations interesting for starting of degradation, bond dissociation energies have been calculated for all single acyclic bonds. For the determination of atoms with pronounced interactions with water we have calculated radial distribution functions obtained after molecular dynamics simulations. The calculated first hyperpolarizability of the title compound is 58.03 times that of standard nonlinear optical material urea. The substrate binding site interactions of the title compound with Topo II enzyme is reported by using molecular docking study. Biological activity studies show that the title compound can be leaded for developing new anticancer agents.

  12. Binding characteristics of psoralen with trypsin: Insights from spectroscopic and molecular modeling studies.

    PubMed

    Liu, Yingying; Zhang, Guowen; Liao, Yijing; Wang, Yaping

    2015-01-01

    Psoralen (PSO) is a naturally occurring furanocoumarin with a variety of pharmacological activities, however very limited information on the interaction of PSO with trypsin is available. In this study, the binding characteristics between PSO and trypsin at physiological pH were investigated using a combination of fluorescence, UV-vis absorption, circular dichroism (CD), Fourier transform infrared (FT-IR) spectroscopic, chemometric and molecular modeling approaches. It was found that the fluorescence quenching of trypsin by PSO was a static quenching procedure, ascribing the formation of a PSO-trypsin complex. The binding of PSO to trypsin was driven mainly by hydrophobic forces as the positive enthalpy change and entropy change values. The molecular docking showed that PSO inserted into the active site pocket of trypsin to interact with the catalytic residues His57, Asp102 and Ser195 and may cause a decrease in trypsin activity. The results of CD and FT-IR spectra along with the temperature-induced denaturation studies indicated that the addition of PSO to trypsin led to the changes in the secondary structure of the enzyme. The concentration profiles and spectra of the three components (PSO, trypsin, and PSO-trypsin complex) obtained by multivariate curve resolution-alternating least squares analysis exhibited the kinetic processes of PSO-trypsin interaction. This study will be helpful to understand the mechanism of PSO that affects the conformation and activity of trypsin in biological processes.

  13. Spectroscopic and dielectric properties of liquid water: A molecular dynamics simulation study

    NASA Astrophysics Data System (ADS)

    Bursulaya, Badry D.; Kim, Hyung J.

    1998-09-01

    The spectroscopic and dielectric properties of liquid water under an ambient condition are studied via a molecular dynamics (MD) computer simulation method. By employing the recent TAB/10D potential model [B. D. Bursulaya, J. Jeon, D. A. Zichi, and H. J. Kim, J. Chem. Phys. 108, 3286 (1997)], the evolving solvent electronic structure is incorporated into the simulation. Thus both the induced dipole and polarizability variations of individual water molecules with the fluctuating nuclear configuration are accounted for. The MD results on far-IR absorption, depolarized Raman scattering (DRS) and optical Kerr effect (OKE) spectroscopy are in reasonable agreement with experiments. It is found that the nonlinear electronic response of water to its fluctuating environment plays an important role in the DRS and OKE; it significantly enhances the contribution of the water librational motions to the spectra, compared with that of hindered translations. This indicates that not only molecular dynamics but also accompanying electronic structure modulations are essential to quantitative understanding of various electronic spectroscopy. The effects of H/D isotope substitution are briefly discussed.

  14. Accurate molecular structure and spectroscopic properties for nucleobases: A combined computational - microwave investigation of 2-thiouracil as a case study

    PubMed Central

    Puzzarini, Cristina; Biczysko, Malgorzata; Barone, Vincenzo; Peña, Isabel; Cabezas, Carlos; Alonso, José L.

    2015-01-01

    The computational composite scheme purposely set up for accurately describing the electronic structure and spectroscopic properties of small biomolecules has been applied to the first study of the rotational spectrum of 2-thiouracil. The experimental investigation was made possible thanks to the combination of the laser ablation technique with Fourier Transform Microwave spectrometers. The joint experimental – computational study allowed us to determine accurate molecular structure and spectroscopic properties for the title molecule, but more important, it demonstrates a reliable approach for the accurate investigation of isolated small biomolecules. PMID:24002739

  15. Chiral alkylated-aniline as a noninvasive fluorescence sensor: Spectroscopic and molecular modeling studies.

    PubMed

    Sengupta, Bidisha; Mukherjee, Chirantan Sen; Chakraborty, Sandipan; Muhammad, Maria Jones; Gladney, William; Armstrong, George

    2017-12-05

    Aniline, heterocyclic aromatic amines, and arylamines are known carcinogens. Recently aniline mustard has come into prominence as a novel anticancer agent. In this project, microwave irradiation has been used to synthesize an optically active alkylated aniline namely 2,6-dimethyl-4-(1-(p-tolyl)ethyl)aniline (abbreviated DMPA). The presence of quartet and doublet peaks in NMR and a single chromatogram in HPLC verified that the final product DMPA, prepared from the synthesis reactions, had no major impurities. By using a Lux chiral column in HPLC, two peaks have been detected in the chromatogram, which correspond to two enantiomers of the chiral aniline derivative. Fluorescence spectroscopic measurements on DMPA indicated conspicuous dependence of its emission behavior on the polarity (in terms of the empirical polarity parameter ET(30)) of the homogeneous solvents used, a property important for an optical sensor. The nature of the emission profiles, along with the relevant parameter namely wavelength at emission maximum (λem(max)) is used to infer the distribution, binding and microenvironment of the DMPA molecules in human serum albumin protein (HSA). DMPA is weakly fluorescent in aqueous buffer medium, with a dramatic enhancement in the fluorescence emission in the presence of HSA. Molecular modeling studies have been carried out on the two enantiomers (R and S) of DMPA with HSA. The implications of these findings are examined in relation to the potentialities of DMPA as a novel fluorescence sensor for biological systems. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. Chiral alkylated-aniline as a noninvasive fluorescence sensor: Spectroscopic and molecular modeling studies

    NASA Astrophysics Data System (ADS)

    Sengupta, Bidisha; Mukherjee, Chirantan Sen; Chakraborty, Sandipan; Muhammad, Maria Jones; Gladney, William; Armstrong, George

    2017-12-01

    Aniline, heterocyclic aromatic amines, and arylamines are known carcinogens. Recently aniline mustard has come into prominence as a novel anticancer agent. In this project, microwave irradiation has been used to synthesize an optically active alkylated aniline namely 2,6-dimethyl-4-(1-(p-tolyl)ethyl)aniline (abbreviated DMPA). The presence of quartet and doublet peaks in NMR and a single chromatogram in HPLC verified that the final product DMPA, prepared from the synthesis reactions, had no major impurities. By using a Lux chiral column in HPLC, two peaks have been detected in the chromatogram, which correspond to two enantiomers of the chiral aniline derivative. Fluorescence spectroscopic measurements on DMPA indicated conspicuous dependence of its emission behavior on the polarity (in terms of the empirical polarity parameter ET(30)) of the homogeneous solvents used, a property important for an optical sensor. The nature of the emission profiles, along with the relevant parameter namely wavelength at emission maximum (λemmax) is used to infer the distribution, binding and microenvironment of the DMPA molecules in human serum albumin protein (HSA). DMPA is weakly fluorescent in aqueous buffer medium, with a dramatic enhancement in the fluorescence emission in the presence of HSA. Molecular modeling studies have been carried out on the two enantiomers (R and S) of DMPA with HSA. The implications of these findings are examined in relation to the potentialities of DMPA as a novel fluorescence sensor for biological systems.

  17. Chiral lactic hydrazone derivatives as potential bioactive antibacterial agents: Synthesis, spectroscopic, structural and molecular docking studies

    NASA Astrophysics Data System (ADS)

    Noshiranzadeh, Nader; Heidari, Azam; Haghi, Fakhri; Bikas, Rahman; Lis, Tadeusz

    2017-01-01

    A series of novel chiral lactic-hydrazone derivatives were synthesized by condensation of (S)-lactic acid hydrazide with salicylaldehyde derivatives and characterized by elemental analysis and spectroscopic studies (FT-IR, 1H NMR and 13C NMR spectroscopy). The structure of one compound was determined by single crystal X-ray analysis. Antibacterial activity of the synthesized compounds was studied against Staphylococcus aureus, Streptococcus pneumonia, Escherichia coli and Pseudomonas aeruginosa as bacterial cultures by broth microdilution method. All of the synthesized compounds showed good antibacterial activity with MIC range of 64-512 μg/mL. Compounds (S,E)-2-hydroxy-N-(2-hydroxy-5-nitrobenzylidene)propanehydrazide (5) and (S,E)-2-hydroxy-N-((3-hydroxy-5-(hydroxymethyl)-2-methylpyridin-4-yl)propanehydrazide (7) were the most effective antibacterial derivatives against S. aureus and E. coli respectively with a MIC value of 64 μg/mL. Bacterial biofilm formation assay showed that these compounds significantly inhibited biofilm formation of P. aeruginosa. Also, in silico molecular docking studies were performed to show lipoteichoic acid synthase (LtaS) inhibitory effect of lactic hydrazone derivatives. The association between electronic and structural effects of some substituents on the benzylidene moiety and the biological activity of these chiral compounds were studied. Structural studies show that compound with higher hydrogen bonding interactions show higher antibacterial activity. The results show chiral hydrazone derivatives based on lactic acid hydrazide could be used as potential lead compounds for developing novel antibacterial agents.

  18. Spectroscopic studies of molecular iodine emitted into the gas phase by seaweed

    NASA Astrophysics Data System (ADS)

    Ball, S. M.; Hollingsworth, A. M.; Humbles, J.; Leblanc, C.; Potin, P.; McFiggans, G.

    2009-12-01

    Time profiles of molecular iodine emissions from seven species of seaweed have been measured at high time resolution (7.5 s) by direct spectroscopic quantification of the gas phase I2 using broadband cavity enhanced absorption spectroscopy. Substantial differences were found between species, both in the amounts of I2 emitted when the plants were exposed to air and in the shapes of their emission time profiles. Two species of kelp, Laminaria digitata and Laminaria hyperborea, were found to be the most potent emitters, producing an intense burst of I2 when first exposed to air. I2 was also observed from Saccharina latissima and Ascophyllum nodosum but in lower amounts and with broader time profiles. I2 mixing ratios from two Fucus species and Dictyopteris membranacea were at or below the detection limit of the present instrument (25 pptv). A further set of experiments investigated the time dependence of I2 emissions and aerosol particle formation when fragments of L. digitata were exposed to desiccation in air, to ozone and to oligoguluronate stress factors. Particle formation occurred in all L. digitata stress experiments where ozone and light were present, subject to the I2 mixing ratios being above certain threshold amounts. Moreover, the particle number concentrations closely tracked variations in the I2 mixing ratios, confirming the results of previous studies that the condensable particle-forming gases derive from the photochemical oxidation of the plant's I2 emissions. This work also supports the theory that particle nucleation in the coastal atmosphere occurs in "hot-spot" regions of locally elevated concentrations of condensable gases: the greatest atmospheric concentrations of I2 and hence of condensable iodine oxides are likely to be above plants of the most efficiently emitting kelp species and localised in time to shortly after these seaweeds are uncovered by a receding tide.

  19. Spectroscopic studies of molecular iodine emitted into the gas phase by seaweed

    NASA Astrophysics Data System (ADS)

    Ball, S. M.; Hollingsworth, A. M.; Humbles, J.; Leblanc, C.; Potin, P.; McFiggans, G.

    2010-07-01

    Time profiles of molecular iodine emissions from seven species of seaweed have been measured at high time resolution (7.5 s) by direct spectroscopic quantification of the gas phase I2 using broadband cavity enhanced absorption spectroscopy. Substantial differences were found between species, both in the amounts of I2 emitted when the plants were exposed to air and in the shapes of their emission time profiles. Two species of kelp, Laminaria digitata and Laminaria hyperborea, were found to be the most potent emitters, producing an intense burst of I2 when first exposed to air. I2 was also observed from Saccharina latissima and Ascophyllum nodosum but in lower amounts and with broader time profiles. I2 mixing ratios from two Fucus species and Dictyopteris membranacea were at or below the detection limit of the present instrument (25 pptv). A further set of experiments investigated the time dependence of I2 emissions and aerosol particle formation when fragments of L. digitata were exposed to desiccation in air, to ozone and to oligoguluronate stress factors. Particle formation occurred in all L. digitata stress experiments where ozone and light were present, subject to the I2 mixing ratios being above certain threshold amounts. Moreover, the particle number concentrations closely tracked variations in the I2 mixing ratios, confirming the results of previous studies that the condensable particle-forming gases derive from the photochemical oxidation of the plant's I2 emissions. This work also supports the theory that particle nucleation in the coastal atmosphere occurs in "hot-spot" regions of locally elevated concentrations of condensable gases: the greatest atmospheric concentrations of I2 and hence of condensable iodine oxides are likely to be above plants of the most efficiently emitting kelp species and localised in time to shortly after these seaweeds are uncovered by a receding tide.

  20. 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.

  1. Molecular interactions in ethyl acetate-chlorobenzene binary solution: Dielectric, spectroscopic studies and quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Karthick, N. K.; Kumbharkhane, A. C.; Joshi, Y. S.; Mahendraprabu, A.; Shanmugam, R.; Elangovan, A.; Arivazhagan, G.

    2017-05-01

    Dielectric studies using Time Domain Reflectometry method has been carried out on the binary solution of Ethyl acetate (EA) with Chlorobenzene (CBZ) over the entire composition range. Spectroscopic (FTIR and 13C NMR) signatures of neat EA, CBZ and their equimolar binary solution have also been recorded. The results of the spectroscopic studies favour the presence of (CBZ) Csbnd H ⋯ Odbnd C (EA), (EA) methylene Csbnd H ⋯ π electrons (CBZ) and (EA) methyl Csbnd H ⋯ Cl (CBZ) contacts which have been validated using quantum chemical calculations. Dimerization of CBZ has been identified. Presence of β-clusters has been identified in all the solutions. Although EA and CBZ molecules have nearly equal molar volumes, CBZ molecules experience larger hindrance for the rotation than EA molecules. Very small excess dielectric constant (εE) values may be correlated with weak heteromolecular forces and/or closed heteromolecular association.

  2. Spectroscopic and molecular modeling studies of the interaction between morin and polyamidoamine dendrimer.

    PubMed

    Zhang, Hongmei; Cao, Jian; Wang, Yanqing

    2014-09-01

    Interactions between the polyamidoamine (PAMAM) dendrimer and drug molecules are of interest for their potential biomedical applications. The goal of this work is to examine the interaction of PAMAM-C12 25% dendrimer with morin. The ultraviolet-visible, fluorescence spectroscopic methods as well as molecular modeling were used to analyze drug-binding mode, binding constants and binding sites, etc. The experimental data showed that the binding constant of morin-PAMAM-C12 25% is about 10(5) L/mol. The interaction of morin with PAMAM-C12 25% is mainly driven by the hydrophobic, electrostatic, hydrogen bonds and van der Waals forces. There are mainly three classes of binding site of morin at the interface of PAMAM-C12 25%. These results provided some useful information for self-assembling and disassembling the PAMAM dendrimer as well as efficient drug delivery and therapeutic applications. Copyright © 2013 John Wiley & Sons, Ltd.

  3. 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.

  4. Dynamics-function correlation in Cu, Zn superoxide dismutase: a spectroscopic and molecular dynamics simulation study.

    PubMed Central

    Falconi, M; Stroppolo, M E; Cioni, P; Strambini, G; Sergi, A; Ferrario, M; Desideri, A

    2001-01-01

    A single mutation (Val29-->Gly) at the subunit interface of a Cu, Zn superoxide dismutase dimer leads to a twofold increase in the second order catalytic rate, when compared to the native enzyme, without causing any modification of the structure or the electric field distribution. To check the role of dynamic processes in this catalytic enhancement, the flexibility of the dimeric protein at the subunit interface region has been probed by the phosphorescence and fluorescence properties of the unique tryptophan residue. Multiple spectroscopic data indicate that Trp83 experiences a very similar, and relatively hydrophobic, environment in both wild-type and mutant protein, whereas its mobility is distinctly more restrained in the latter. Molecular dynamics simulation confirms this result, and provides, at the molecular level, details of the dynamic change felt by tryptophan. Moreover, the simulation shows that the loops surrounding the active site are more flexible in the mutant than in the native enzyme, making the copper more accessible to the incoming substrate, and being thus responsible for the catalytic rate enhancement. Evidence for increased, dynamic copper accessibility also comes from faster copper removal in the mutant by a metal chelator. These results indicate that differences in dynamic, rather than structural, features of the two enzymes are responsible for the observed functional change. PMID:11371434

  5. Molecular structure, vibrational spectroscopic, first hyperpolarizability, NBO and HOMO, LUMO studies of P-Iodobenzene sulfonyl chloride.

    PubMed

    Arivazhagan, M; Prabhakaran, S; Gayathri, R

    2011-11-01

    In this work, the experimental and theoretical vibrational spectra of P-Iodobenzene sulfonyl chloride (P-IBSC) were studied. P-IBSC and its derivatives present in many biologically active compounds. Because of their spectroscopic properties and chemical significance in particular, sulfonyl chloride and its derivatives have been studied extensively by spectroscopic (FTIR and FT-Raman spectra) and theoretical methods. The infrared spectra of these compounds were recorded in condensed states, while the Raman spectra were measured without polarization using both parallel and perpendicular polarizations of scattered light. The molecular geometry, highest occupied molecular orbital (HOMO), lowest unoccupied molecular orbital (LUMO), first order hyperpolarizability and thermodynamic properties of P-IBSC have been computed with the help of density functional theory (B3LYP) and ab initio (HF) methods with the LanL2DZ basis set. The HOMO and LUMO energy gap explains the charge transfer interactions taking place within the molecule. NBO study explains charge delocalization of the molecule. The contributions of the different modes to each wave number were determined using potential energy distributions (PEDs). The experimental and calculated results were consistent with each other.

  6. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-11-01

    A systematic vibrational spectroscopic assignment and analysis of pramipexole [(S)-N6-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.

  8. Vibrational spectroscopic, molecular docking and density functional theory studies on 2-acetylamino-5-bromo-6-methylpyridine.

    PubMed

    Premkumar, S; Rekha, T N; Mohamed Asath, R; Mathavan, T; Milton Franklin Benial, A

    2016-01-20

    Conformational and molecular docking analysis of 2-acetylamino-5-bromo-6-methylpyridine molecule was carried out and the vibrational spectral analysis was also carried out using experimental and theoretical methods. The calculated and experimentally observed vibrational frequencies of the molecule were assigned and compared. The pyridine ring CH stretching and CH3 stretching vibrational modes were shifted towards higher wavenumber (blue shift). The C=O stretching vibrational frequency was shifted towards lower wavenumber (red shift). Ultraviolet-visible spectrum of the molecule simulated theoretically was further validated experimentally. Molecular reactivity and stability were investigated using the frontier molecular orbital analysis and the related quantum chemical molecular properties. Natural bond orbital analysis and the structure activity relations were also studied to confirm the bioactivity of the molecule. Anticancer activity was examined based on molecular docking analysis and it has been identified that the AABMP molecule can act as a good inhibitor against lung cancer.

  9. Synthesis, spectroscopic and molecular docking studies of imidazolium and pyridinium based ionic liquids with HSA as potential antimicrobial agents

    NASA Astrophysics Data System (ADS)

    Trush, Maria M.; Semenyuta, Ivan V.; Vdovenko, Sergey I.; Rogalsky, Sergiy P.; Lobko, Evgeniya O.; Metelytsia, Larisa O.

    2017-06-01

    The interaction between human serum albumin (HSA) and synthesized imidazolium and pyridinium based ionic liquids (ILs), as good potential microbial growth inhibitors, was investigated by spectroscopic techniques combined with molecular docking analysis. All compounds were significant active against the tested bacterial and fungal strains. FT-IR spectroscopy indicated that the interaction of HSA with ILs generates considerable changes in protein secondary structure. The results of the molecular docking study showed that the studied ILs are able to firmly bind in the subdomain IIA of HSA with almost equal binding affinity (about -6.23 kcal/mol). Investigated HSA-ILs complex binds through hydrogen bonding or/and cation-π interactions. This study provides a better understanding of the binding of imidazolium and pyridinium based ILs to HSA and opens the way for their further biological and pharmaceutical investigations as candidates with antimicrobial properties.

  10. Deciphering the interactions between chlorambucil and calf thymus DNA: a multi-spectroscopic and molecular docking study.

    PubMed

    Rehman, Sayeed Ur; Sarwar, Tarique; Ishqi, Hassan Mubarak; Husain, Mohammed Amir; Hasan, Ziaul; Tabish, Mohammad

    2015-01-15

    Non-covalent interactions of chlorambucil with calf thymus DNA was investigated using multi-spectroscopic techniques and molecular docking study. Binding constant calculated was found to be 1.54×10(4)M(-1) at 290K, significantly lower than various known intercalators. Quenching process was found to be static as evident by biomolecular quenching constant. Thermodynamic parameters revealed the involvement of hydrophobic interactions and hydrogen bonds in the binding. Chlorambucil was found to interact via external binding mode and follow groove binding as it replaces Hoechst (a typical groove binder) from the groove of DNA but does not replace intercalating dyes including ethidium bromide and acridine orange from the DNA helix. These results were further supported by KI quenching experiments, DNA melting studies, CD spectroscopy and molecular docking. Copyright © 2014 Elsevier Inc. All rights reserved.

  11. Spectroscopic, quantum mechanical and molecular docking studies of a new benzoxazole compound with an oxidoreductase enzyme and DNA

    NASA Astrophysics Data System (ADS)

    Zeyrek, Celal Tuğrul; Boyacioglu, Bahadir; Temiz-Arpaci, Özlem; Ünver, Hüseyin; Elmali, Ayhan

    2017-05-01

    The spectroscopic, theoretical molecular structure, full vibrational band assignments, MEP, NBO, frontier molecular orbitals, and NLO effects, and molecular docking studies of 5-ethylsulphonyl-2-(p-ethylphenyl)-benzoxazole, C17H17SO3N, (L) have been presented in this work. The quantum mechanical calculations have been performed by using the Hartree-Fock (HF)/6-311++G(d,p) and density functional theory (DFT) with the B3LYP/6-311++G(d,p) levels. Calculated vibrational frequencies have been compared with the experimental FT-IR spectra. The natural bond orbital (NBO) analysis has been performed to determine the hyper conjugative interactions. Frontier molecular orbitals have been defined to predict the chemical parameters of the L. The first order hyperpolarizability of L was calculated to find its role in nonlinear optics. Molecular docking of L with the oxidoreductase enzyme nicotinamide adenine dinucleotide phosphate (NADPH) exhibited the good binding affinity with energy of -8.8 kcal/mol. The molecular docking was also done to identify the interaction of L with the DNA.

  12. Molecular spectroscopic analyses of gelatin.

    PubMed

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

    2011-10-15

    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=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. Copyright © 2011 Elsevier B.V. All rights reserved.

  13. 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

    2014-04-05

    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. Copyright © 2013 Elsevier B.V. All rights reserved.

  14. Binding studies of lophirone B with bovine serum albumin (BSA): Combination of spectroscopic and molecular docking techniques

    NASA Astrophysics Data System (ADS)

    Chaves, Otávio Augusto; da Silva, Veridiana A.; Sant'Anna, Carlos Maurício R.; Ferreira, Aurélio B. B.; Ribeiro, Tereza Auxiliadora N.; de Carvalho, Mário G.; Cesarin-Sobrinho, Dari; Netto-Ferreira, José Carlos

    2017-01-01

    The interaction between the transport protein bovine serum albumin (BSA) and the natural product lophirone B, was investigated by spectroscopic techniques combined with a computational method (molecular docking). From the KSV and kq values it was concluded that lophirone B quenches the fluorescence of BSA by dynamic and static mechanisms. The Ka values, of the order of 104 M-1, and the number of binding sites (n ≈ 1), indicate that the binding is moderate and there is just one main binding site in BSA for lophirone B. The negative ΔG° values are in accordance with the spontaneity of the process and the positive ΔH° and ΔS° values indicate that the binding is entropically driven; the main binding forces for the association BSA:lophirone B are probably lipophilic interactions. Circular dichroism (CD) studies show there is not a significant perturbation on the secondary structure of the albumin upon the binding process. In order to better understand the spectroscopic results, a computational method was applied: molecular docking suggests Trp-213 site, as the main binding site for the ligand. Lophirone B seems to be exposed to the aqueous media as well as accommodated inside the protein cavity, resulting in a moderate affinity for the albumin. The Arg-198, His-287, Lys-294 and Lys-439 residues are interacting via hydrogen bonding with lophirone B, whereas the interaction with Trp-213 residue occurs through a lipophilic interaction.

  15. Binding of Bisphenol-F, a bisphenol analogue, to calf thymus DNA by multi-spectroscopic and molecular docking studies.

    PubMed

    Usman, Afia; Ahmad, Masood

    2017-08-01

    BPF (Bisphenol-F), a member of the bisphenol family, having a wide range of industrial applications is gradually replacing Bisphenol-A. It is a recognized endocrine disrupting chemical (EDC). EDCs have been implicated in increased incidences of breast, prostate and testis cancers besides diabetes, obesity and decreased fertility. Due to the adverse effects of EDCs on human health, attempts have been directed towards their mechanism of toxicity especially at the molecular level. Hence, to understand the mechanism at the DNA level, interaction of BPF with calf thymus DNA was studied employing multi-spectroscopic, voltammetric and molecular docking techniques. Fluorescence spectra, cyclic voltammetry (CV), circular dichroism (CD) and molecular docking studies of BPF with DNA were suggestive of minor groove binding of BPF. UV-visible absorption and fluorescence spectra suggested static quenching due to complex formation between BPF and ctDNA. Hoechst 33258 (HO) and ethidium bromide (EB) displacement studies further confirmed such mode of BPF interaction. Thermodynamic and molecular docking parameters revealed the mechanism of binding of BPF with ctDNA to be favorable and spontaneous due to negative ΔG and occurring through hydrogen bonds and van der waals interactions. BPF induced DNA cleavage under in vitro conditions by plasmid nicking assay suggested it to be genotoxic. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. Hydrogen bonding-assisted interaction between amitriptyline hydrochloride and hemoglobin: spectroscopic and molecular dynamics studies.

    PubMed

    Maurya, Neha; Maurya, Jitendra Kumar; Kumari, Meena; Khan, Abbul Bashar; Dohare, Ravins; Patel, Rajan

    2017-05-01

    Herein, we have explored the interaction between amitriptyline hydrochloride (AMT) and hemoglobin (Hb), using steady-state and time-resolved fluorescence spectroscopy, UV-visible spectroscopy, and circular dichroism spectroscopy, in combination with molecular docking and molecular dynamic (MD) simulation methods. The steady-state fluorescence reveals the static quenching mechanism in the interaction system, which was further confirmed by UV-visible and time-resolved fluorescence spectroscopy. The binding constant, number of binding sites, and thermodynamic parameters viz. ΔG, ΔH, ΔS are also considered; result confirms that the binding of the AMT with Hb is a spontaneous process, involving hydrogen bonding and van der Waals interactions with a single binding site, as also confirmed by molecular docking study. Synchronous fluorescence, CD data, and MD simulation results contribute toward understanding the effect of AMT on Hb to interpret the conformational change in Hb upon binding in aqueous solution.

  17. Hybrid materials chemistry: Spectroscopic studies of molecular materials, nanoscale materials and their combinations

    NASA Astrophysics Data System (ADS)

    Marlatt, Craig W.

    Materials chemistry is a widely-used label within the overall field of chemistry, with a diverse range of possible applications. In this report, two classes of materials are discussed. Host-guest molecular systems that operate under supramolecular principles are examined via Raman spectroscopy and electrochemistry, and a sensing application for such systems is offered in the proof-of-principle detection of nitroaromatic explosives via host-guest binding. Next, metallic nanostructures that have tunable optical properties are synthesized and characterized to demonstrate that tunable nature, and the way such structures might be used for surface-enhanced Raman studies of the previously described host-guest systems is discussed by examining the current literature. Lastly, strategies to couple molecular systems and nanostructure systems are discussed and developed, and speculation on possible applications utilizing these coupled systems is made based on recent literature and the established themes of the research in this report.

  18. Spectroscopic and molecular docking studies on the interaction of human serum albumin with copper(II) complexes

    NASA Astrophysics Data System (ADS)

    Guhathakurta, Bhargab; Pradhan, Ankur Bikash; Das, Suman; Bandyopadhyay, Nirmalya; Lu, Liping; Zhu, Miaoli; Naskar, Jnan Prakash

    2017-02-01

    Two osazone based ligands, butane-2,3-dione bis(2‧-pyridylhydrazone) (BDBPH) and hexane-3,4-dione bis(2‧-pyridylhydrazone) (HDBPH), were synthesized out of the 2:1 M Schiff base condensation of 2-hydrazino pyridine respectively with 2,3-butanedione and 3,4-hexanedione. The X-ray crystal structures of both the ligands have been determined. The copper(II) complex of HDBPH has also been synthesized and structurally characterized. HDBPH and its copper(II) complex have thoroughly been characterized through various spectroscopic and analytical techniques. The X-ray crystal structure of the copper complex of HDBPH shows that it is a monomeric Cu(II) complex having 'N4O2' co-ordination chromophore. Interaction of human serum albumin (HSA) with these ligands and their monomeric copper(II) complexes have been studied by various spectroscopic means. The experimental findings show that the ligands as well as their copper complexes are good HSA binders. Molecular docking investigations have also been done to unravel the mode of binding of the species with HSA.

  19. Spectroscopic and molecular docking studies on the interaction of human serum albumin with copper(II) complexes.

    PubMed

    Guhathakurta, Bhargab; Pradhan, Ankur Bikash; Das, Suman; Bandyopadhyay, Nirmalya; Lu, Liping; Zhu, Miaoli; Naskar, Jnan Prakash

    2017-02-15

    Two osazone based ligands, butane-2,3-dione bis(2'-pyridylhydrazone) (BDBPH) and hexane-3,4-dione bis(2'-pyridylhydrazone) (HDBPH), were synthesized out of the 2:1M Schiff base condensation of 2-hydrazino pyridine respectively with 2,3-butanedione and 3,4-hexanedione. The X-ray crystal structures of both the ligands have been determined. The copper(II) complex of HDBPH has also been synthesized and structurally characterized. HDBPH and its copper(II) complex have thoroughly been characterized through various spectroscopic and analytical techniques. The X-ray crystal structure of the copper complex of HDBPH shows that it is a monomeric Cu(II) complex having 'N4O2' co-ordination chromophore. Interaction of human serum albumin (HSA) with these ligands and their monomeric copper(II) complexes have been studied by various spectroscopic means. The experimental findings show that the ligands as well as their copper complexes are good HSA binders. Molecular docking investigations have also been done to unravel the mode of binding of the species with HSA.

  20. 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.

  1. Insights into the binding of 2-aminobenzothiazole with human serum albumin (HSA): spectroscopic investigation and molecular modeling studies.

    PubMed

    Sun, Yajing; Su, Baoling; Xu, Qifei; Liu, Rutao

    2012-07-01

    As one of the important thiazole derivatives, 2-aminobenzothiazole (2-ABT) has been widely used as a structural unit in the synthesis of anti-oxidants, anti-inflammatories, herbicides, antibiotics, and thermoplastic polymers. In this study, the interaction of 2-ABT with human serum albumin (HSA) was investigated in vitro under simulated physiological conditions, using multi-spectroscopic techniques and a molecular modeling study. The binding constant and binding sites were determined through fluorescence quenching spectra. The site-competitive replacement experiments revealed that the precise binding site of 2-ABT on HSA was site II (subdomain IIIA). Moreover, molecular docking results illustrated the electrostatic interaction between Glu 450 and 2-ABT, in accordance with the conclusions from the calculated thermodynamic parameters and the effect of ionic strength. The effect of 2-ABT on the conformational changes of HSA were evaluated by ultraviolet-visible (UV-Vis) absorption, three-dimensional (3D) fluorescence, synchronous fluorescence, and circular dichroism (CD) spectroscopy. This work facilitates comprehensive understanding of the binding of 2-ABT with HSA, contributing to evaluate the molecular transportation mechanism and biotoxicity of 2-aminobenzothiazole derivatives in vivo.

  2. 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.

  3. 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.

  4. Interaction of capsaicin with calf thymus DNA: A multi-spectroscopic and molecular modelling study.

    PubMed

    Qais, Faizan Abul; Abdullah, K M; Alam, Md Maroof; Naseem, Imrana; Ahmad, Iqbal

    2017-04-01

    Studying the mode of interaction between small molecules and DNA has received much attention in recent years, as many drugs have been reported to directly interact with DNA thereby regulating the expression of many genes. Capsaicin is a capsaiciniods family phytocompound having many therapeutic applications including diabetic neuropathy, rheumatoid arthritis, prevention of DNA strand breaks and chromosomal aberrations. In this study, we have investigated the interaction of capsaicin with calf thymus DNA using a number of biophysical techniques to get an insight and better understanding of the interaction mechanism. Analysis of UV-vis absorbance spectra and fluorescence spectra indicates the formation of complex between capsaicin and Ct-DNA. Thermodynamic parameters ΔG, ΔH, and ΔS measurements were taken at different temperatures indicated that hydrogen bonding and van der Waal's forces played major role in the binding process. Additional experiments such as iodide quenching, CD spectroscopy suggested that capsaicin possibly binds to the minor groove of the Ct-DNA. These observations were further confirmed by DNA melting studies, viscosity measurements. Molecular docking provided detailed computational interaction of capsaicin with Ct-DNA which proved that capsaicin binds to Ct-DNA at minor groove. Computational molecular docking also revealed the exact sites and groups to which capsaicin interacted. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. Spectroscopic and molecular modeling studies of caffeine complexes with DNA intercalators.

    PubMed Central

    Larsen, R W; Jasuja, R; Hetzler, R K; Muraoka, P T; Andrada, V G; Jameson, D M

    1996-01-01

    Recent studies have demonstrated that caffeine can act as an antimutagen and inhibit the cytoxic and/or cytostatic effects of some DNA intercalating agents. It has been suggested that this inhibitory effect may be due to complexation of the DNA intercalator with caffeine. In this study we employ optical absorption, fluorescence, and molecular modeling techniques to probe specific interactions between caffeine and various DNA intercalators. Optical absorption and steady-state fluorescence data demonstrate complexation between caffeine and the planar DNA intercalator acridine orange. The association constant of this complex is determined to be 258.4 +/- 5.1 M-1. In contrast, solutions containing caffeine and the nonplanar DNA intercalator ethidium bromide show optical shifts and steady-state fluorescence spectra indicative of a weaker complex with an association constant of 84.5 +/- 3.5 M-1. Time-resolved fluorescence data indicate that complex formation between caffeine and acridine orange or ethidium bromide results in singlet-state lifetime increases consistent with the observed increase in the steady-state fluorescence yield. In addition, dynamic polarization data indicate that these complexes form with a 1:1 stoichiometry. Molecular modeling studies are also included to examine structural factors that may influence complexation. PMID:8770220

  6. The vibrational spectroscopic studies and molecular property analysis of L-Phenylalanine using quantum chemical method

    NASA Astrophysics Data System (ADS)

    Borah, Mukunda Madhab; Devi, Th. Gomti

    2017-05-01

    In the present work, L-phenylalanine is studied using the experimental and theoretical methods. The spectral characterization of the molecule has been done using Raman, FTIR, Hartee-Fock(HF), density functional theory (DFT) and vibrational energy distribution analysis (VEDA) calculation. The optimization of the molecule has been studied using basis set HF/6-31G(d,p) and B3LYP/6-31G(d,p) for Hartree Fock and density functional theory calculation. The complete vibrational assignment of the molecule in monomer and dimer states have been attempted. The potential energy distribution and normal mode analysis are also carried out to determine the contributions of bond oscillators in each normal mode. The molecular geometry, HOMO-LUMO energy gap, molecular hardness (η), ionization energy (IE), electron affinity (EA), total energy and dipole moment were determined from the calculated data. The observed experimental and the scaled theoretical results are compared and found to be in good agreement. The vibrational assignment of molecule in different dimer states has also been done using SERS data and better correlated Raman peaks are observed as compare to normal Raman technique.

  7. Molecular characterization of myoglobin from Sciurus vulgaris meridionalis: Primary structure, kinetics and spectroscopic studies.

    PubMed

    Di Giuseppe, Antonella M A; Russo, Luigi; Russo, Rosita; Ragucci, Sara; Caso, J Valentina; Isernia, Carla; Chambery, Angela; Di Maro, Antimo

    2017-05-01

    Myoglobins (Mbs) are heme-proteins involved in dioxygen storage necessary for metabolic respiration. Mbs are intensely investigated as archetype to investigate structure/function relationship in globular proteins. In this work, the myoglobin from Sciurus vulgaris meridionalis has been for the first time isolated and purified with a high yield and homogeneity. The primary structure characterization has been performed by applying a strategy based on high resolution tandem mass spectrometry. Proximal (position 93, α-helix F8) and distal (position 64, α-helix E7) histidinyl residues as well as most of the amino acid residues (i.e., Leu29, Lys45, Thr67, Val68) involved in the autoxidation mechanism are conserved in the squirrel Mb. The structural and dynamical properties of the squirrel Mb have been also deeply investigated by CD, NMR. Furthermore, molecular dynamics studies of Mbs from different species have been performed. In addition, the functional properties of squirrel Mb have been characterized by determining its autoxidation kinetic and thermal stability in comparison with crested porcupine and reindeer Mbs. Interestingly, a higher autoxidation rate was revealed for squirrel Mb with respect to reindeer and crested porcupine Mbs. Even considering the very similar structural fold, molecular dynamics data show a higher conformational mobility of squirrel Mb with respect to reindeer and crested porcupine. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. 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. Copyright © 2016 Elsevier B.V. All rights reserved.

  9. Interaction of prometryn to human serum albumin: insights from spectroscopic and molecular docking studies.

    PubMed

    Wang, Yaping; Zhang, Guowen; Wang, Langhong

    2014-01-01

    Prometryn possesses much potential hazard to environment because of its chemical stability and biological toxicity. Here, the binding properties of prometryn with human serum albumin (HSA) and the protein structural changes were determined under simulative physiological conditions (pH 7.4) by multispectroscopic methods including fluorescence, UV-vis absorption, Fourier transform infrared (FT-IR) and circular dichroism (CD) spectroscopy, coupled with molecular modeling technique. The result of fluorescence titration suggested that the fluorescence quenching of HSA by prometryn was considered as a static quenching procedure. The negative enthalpy change (ΔH(○)) and positive entropy change (ΔS(○)) values indicated that the binding process was governed mainly by hydrophobic interactions and hydrogen bonds. The site marker displacement experiments suggested the location of prometryn binding to HSA was Sudlow's site I in subdomain IIA. Furthermore, molecular docking studies revealed prometryn can bind in the large hydrophobic activity of subdomain IIA. Analysis of UV-vis absorption, synchronous fluorescence, CD and FT-IR spectra demonstrated that the addition of prometryn resulted in rearrangement and conformational alteration of HSA with reduction in α-helix and increases in β-sheet, β-turn and random coil structures. This work provided reasonable model helping us further understand the transportation, distribution and toxicity effect of prometryn when it spreads into human blood serum.

  10. 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.

  11. 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.

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

    PubMed

    Shahabadi, Nahid; Hadidi, Saba

    2014-03-25

    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. Copyright © 2013 Elsevier B.V. All rights reserved.

  13. Functional stability and structural transitions of Kallikrein: spectroscopic and molecular dynamics studies.

    PubMed

    Dalal, Sayli; Mhashal, Anil; Kadoo, Narendra; Gaikwad, Sushama M

    2017-02-01

    Kallikrein, a physiologically vital serine protease, was investigated for its functional and conformational transitions during chemical (organic solvents, Gdn-HCl), thermal, and pH induced denaturation using biochemical and biophysical techniques and molecular dynamics (MD) simulations approach. The enzyme was exceptionally stable in isopropanol and ethanol showing 110% and 75% activity, respectively, after 96 h, showed moderate tolerance in acetonitrile (45% activity after 72 h) and much lower stability in methanol (40% activity after 24 h) (all the solvents [90% v/v]). Far UV CD and fluorescence spectra indicated apparent reduction in compactness of KLKp structure in isopropanol system. MD simulation studies of the enzyme in isopropanol revealed (1) minimal deviation of the structure from native state (2) marginal increase in radius of gyration and solvent accessible surface area (SASA) of the protein and the active site, and (3) loss of density barrier at the active site possibly leading to increased accessibility of substrate to catalytic triad as compared to methanol and acetonitrile. Although kallikrein was structurally stable up to 90 °C as indicated by secondary structure monitoring, it was functionally stable only up to 45 °C, implicating thermolabile active site geometry. In GdnHCl [1.0 M], 75% of the activity of KLKp was retained after incubation for 4 h, indicating its denaturant tolerance. A molten globule-like structure of KLKp formed at pH 1.0 was more thermostable and exhibited interesting structural transitions in organic solvents. The above results provide deeper understanding of functional and structural stability of the serine proteases at molecular level.

  14. A combined spectroscopic, molecular docking and molecular dynamic simulation study on the interaction of quercetin with β-casein nanoparticles.

    PubMed

    Mehranfar, Fahimeh; Bordbar, Abdol-Khalegh; Parastar, Hadi

    2013-10-05

    The interaction of quercetin with β-casein nanoparticle micelle was studied at various temperatures in order to do a complete thermodynamic and molecular analysis on the binding process. The results of fluorescence studies showed the possibility of fluorescence energy transfer between excited tryptophan and quercetin. The determined values of critical transfers distance and the mean distance of ligand from Trp-143 residues in β-casein micelle represents a non-radiative energy transfer mechanism for quenching and the existence of a significant interaction between this flavonoid and β-casein nanoparticle. The equilibrium binding of quercetin with β-casein micelle at different temperatures was studied by using UV-Vis absorption spectroscopy. The chemometric analysis (principal component analysis (PCA) and multivariate curve resolution-alternating least squares (MCR-ALS) methods) on spectrophotometric data revealed the existence of two components in solution (quercetin and β-casein-quercetin complex) and resolved their pure concentration and spectral profiles. This information let us to calculate the equilibrium binding constant at various temperatures and the relevant thermodynamic parameters of interaction (enthalpy, entropy and Gibbs free energy) with low uncertainty. The negative values of entropy and enthalpy changes represent the predominate role of hydrogen binding and van der Waals interactions in the binding process. Docking calculations showed the probable binding site of quercetin is located in the hydrophobic core of β-casein where the quercetin molecule is lined by hydrophobic residues and make five hydrogen bonds and several van der Waals contacts with them. Moreover, molecular dynamic (MD) simulation results suggested that this flavonoid can interact with β-casein, without affecting the secondary structure of β-casein. Simulations, molecular docking and experimental data reciprocally supported each other. Copyright © 2013 Elsevier B.V. All

  15. 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.

  16. Methyl-triclosan binding to human serum albumin: multi-spectroscopic study and visualized molecular simulation.

    PubMed

    Lv, Wenjuan; Chen, Yonglei; Li, Dayong; Chen, Xingguo; Leszczynski, Jerzy

    2013-10-01

    Methyl-triclosan (MTCS), a transformation product and metabolite of triclosan, has been widely spread in environment through the daily use of triclosan which is a commonly used anti-bacterial and anti-fungal substance in consumer products. Once entering human body, MTCS could affect the conformation of human serum albumin (HSA) by forming MTCS-HSA complex and alter function of protein and endocrine in human body. To evaluate the potential toxicity of MTCS, the binding mechanism of HSA with MTCS was investigated by UV-vis absorption, circular dichroism and Fourier transform infrared spectroscopy. Binding constants, thermodynamic parameters, the binding forces and the specific binding site were studied in detail. Binding constant at room tempreture (T = 298K) is 6.32 × 10(3)L mol(-1); ΔH(0), ΔS(0) and ΔG(0) were 22.48 kJ mol(-1), 148.16 J mol(-1)K(-1) and -21.68 kJ mol(-1), respectively. The results showed that the interactions between MTCS and HSA are mainly hydrophobic forces. The effects of MTCS on HSA conformation were also discussed. The binding distance (r = 1.2 nm) for MTCS-HSA system was calculated by the efficiency of fluorescence resonance energy transfer. The visualized binding details were also exhibited by molecular modeling method and the results could agree well with that from the experimental study.

  17. Multi-spectroscopic and molecular modeling studies of bovine serum albumin interaction with sodium acetate food additive.

    PubMed

    Mohammadzadeh-Aghdash, Hossein; Ezzati Nazhad Dolatabadi, Jafar; Dehghan, Parvin; Panahi-Azar, Vahid; Barzegar, Abolfazl

    2017-08-01

    Sodium acetate (SA) has been used as a highly effective protectant in food industry and the possible effect of this additive on the binding to albumin should be taken into consideration. Therefore, for the first time, the mechanism of SA interaction with bovine serum albumin (BSA) has been investigated by multi-spectroscopic and molecular modeling methods under physiological conditions. Stern-Volmer fluorescence quenching analysis showed an increase in the fluorescence intensity of BSA upon increasing the amounts of SA. The high affinity of SA to BSA was demonstrated by a binding constant value (1.09×10(3) at 310°K). The thermodynamic parameters indicated that hydrophobic binding plays a main role in the binding of SA to Albumin. Furthermore, the results of UV-vis spectra confirmed the interaction of this additive to BSA. In addition, molecular modeling study demonstrated that A binding sites of BSA play the main role in the interaction with acetate. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. 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.

  19. In Situ Infrared Spectroscopic Studies of Molecular Layer Deposition and Atomic Layer Etching Processes

    NASA Astrophysics Data System (ADS)

    DuMont, Jaime Willadean

    In this thesis, in situ Fourier transform infrared (FTIR) spectroscopy was used to study: i) the growth and pyrolysis of molecular layer deposition (MLD) films. ii) the surface chemistry of atomic layer etching (ALE) processes. Atomic layer processes such as molecular layer deposition (MLD) and atomic layer etching (ALE) are techniques that can add or remove material with atomic level precision using sequential, self-limiting surface reactions. Deposition and removal processes at the atomic scale are powerful tools for many industrial and research applications such as energy storage and semiconductor nanofabrication. The first section of this thesis describes the chemistry of reactions leading to the MLD of aluminum and tin alkoxide polymer films known as "alucone" and "tincone", respectively. The subsequent pyrolysis of these films to produce metal oxide/carbon composites was also investigated. In situ FTIR spectroscopy was conducted to monitor surface species during MLD film growth and to monitor the films background infrared absorbance versus pyrolysis temperature. Ex situ techniques such as transmission electron microscopy (TEM), four-point probe and X-ray diffraction (XRD) were utilized to study the properties of the films post-pyrolysis. TEM confirmed that the pyrolyzed films maintained conformality during post-processing. Four-point probe monitored film resistivity versus pyrolysis temperature and XRD determined the film crystallinity. The second section of this thesis focuses on the surface chemistry of Al2O3 and SiO2 ALE processes, respectively. Thermal ALE processes have been recently developed which utilize sequential fluorination and ligand exchange reactions. An intimate knowledge of the surface chemistry is important in understanding the ALE process. In this section, the competition between the Al2O3 etching and AlF 3 growth that occur during sequential HF (fluorinating agent) and TMA (ligand exchange) exposures is investigated using in situ FTIR

  20. Raman spectroscopic study of surfactant-mediated molecular beam epitaxially grown germanium/silicon

    NASA Astrophysics Data System (ADS)

    Brill, Gregory Nelson

    The epitaxial growth of Ge on Si substrates was carried out using surfactant-mediated epitaxy and standard growth procedures to study the effects of Si surface passivation prior to Ge nucleation. The growth experiments were conducted in a molecular beam epitaxy (MBE) chamber equipped with reflection high-energy electron diffraction (RHEED) to monitor the nucleation process. Arsenic was chosen as the surfactant material and Ge nucleation was conducted on both Si(001) and Si(211) orientated substrates. Post-growth experiments were conducted primarily utilizing Raman Spectroscopy, however scanning electron microscopy (SEM), transmission electron microscopy (TEM), and X-ray diffraction were also employed to gather information about the grown material. From these experiments, it was determined that passivating the Si surface prior to Ge deposition with a monolayer of As yields higher quality 2-dimensional material. Additionally, As acts as a suppressant to Ge - Si intermixing resulting in a highly ordered epilayer/substrate interface. If Ge is deposited directly on a clean Si substrate without As passivation, the resultant growth follows the theoretically predicted Stranski-Krastanov growth mode. A growth model is suggested that successfully describes the differences between surfactant-mediated and non-surfactant-mediated nucleation through a site-exchange mechanism between Ge and As atoms. Additionally, surfactant-mediated nucleation results as a function of substrate orientation are highlighted and a model for surface reconstruction of the As passivated Si(211) surface is proposed.

  1. "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.

  2. 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.

  3. Molecular spectroscopic and thermodynamic studies on the interaction of anti-platelet drug ticlopidine with calf thymus DNA.

    PubMed

    Afrin, Shumaila; Rahman, Yusra; Sarwar, Tarique; Husain, Mohammed Amir; Ali, Abad; Shamsuzzaman; Tabish, Mohammad

    2017-11-05

    Ticlopidine is an anti-platelet drug which belongs to the thienopyridine structural family and exerts its effect by functioning as an ADP receptor inhibitor. Ticlopidine inhibits the expression of TarO gene in S. aureus and may provide protection against MRSA. Groove binding agents are known to disrupt the transcription factor DNA complex and consequently inhibit gene expression. Understanding the mechanism of interaction of ticlopidine with DNA can prove useful in the development of a rational drug designing system. At present, there is no such study on the interaction of anti-platelet drugs with nucleic acids. A series of biophysical experiments were performed to ascertain the binding mode between ticlopidine and calf thymus DNA. UV-visible and fluorescence spectroscopic experiments confirmed the formation of a complex between ticlopidine and calf thymus DNA. Moreover, the values of binding constant were found to be in the range of 10(3)M(-1), which is indicative of groove binding between ticlopidine and calf thymus DNA. These results were further confirmed by studying the effect of denaturation on double stranded DNA, iodide quenching, viscometric studies, thermal melting profile as well as CD spectral analysis. The thermodynamic profile of the interaction was also determined using isothermal titration calorimetric studies. The reaction was found to be endothermic and the parameters obtained were found to be consistent with those of known groove binders. In silico molecular docking studies further corroborated well with the experimental results. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. Vibrational spectroscopic, molecular docking and quantum chemical studies on 6-aminonicotinamide

    NASA Astrophysics Data System (ADS)

    Mohamed Asath, R.; Premkumar, S.; Mathavan, T.; Milton Franklin Benial, A.

    2017-04-01

    The most stable molecular structure of 6-aminonicotinamide (ANA) molecule was predicted by conformational analysis and vibrational spectral analysis was carried out by experimental and theoretical methods. The calculated and experimentally observed vibrational frequencies were assigned and compared. The π→π* electronic transition of the molecule was predicted by theoretically calculated ultraviolet-visible spectra in gas and liquid phase and further validated experimentally using ethanol as a solvent. Frontier molecular orbitals analysis was carried out to probe the reactive nature of the ANA molecule and further the site selectivity to specific chemical reactions were effectively analyzed by Fukui function calculation. The molecular electrostatic potential surface was simulated to confirm the reactive sites of the molecule. The natural bond orbital analysis was also performed to understand the intra molecular interactions, which confirms the bioactivity of the ANA molecule. Neuroprotective nature of the ANA molecule was analyzed by molecular docking analysis and the ANA molecule was identified as a good inhibitor against Alzheimer's disease.

  5. Study on molecular structure, spectroscopic behavior, NBO, and NLO analysis of 3-methylbezothiazole-2-thione.

    PubMed

    Chand, Satish; Al-Omary, Fatmah A M; El-Emam, Ali A; Shukla, Vikas K; Prasad, Onkar; Sinha, Leena

    2015-07-05

    Experimentally observed spectral data (FT-TR and FT-Raman) of 3-methylbezothiazole-2-thione (3MBT2T) were compared with the spectral data obtained by DFT/B3LYP method using 6-311++G(d,p) basis set. UV-Vis spectrum of the title compound was recorded and the electronic properties, such as frontier molecular orbitals and band gap energies were calculated by TD-DFT approach. The molecular properties like dipole moment, polarizability, first static hyperpolarizability, molecular electrostatic potential surface (MEPs), and contour map were calculated to get a better comprehension of the properties of the title molecule. Natural bond orbital (NBO) analysis was applied to investigate the stability of the molecule arising from charge delocalization. Global and local reactivity descriptors were also computed to predict reactivity and reactive sites on the molecule. Copyright © 2015 Elsevier B.V. All rights reserved.

  6. 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.

  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. Studies of the interaction between FNC and human hemoglobin: a spectroscopic analysis and molecular docking.

    PubMed

    Li, Huiyi; Dou, Huanjing; Zhang, Yuhai; Li, Zhigang; Wang, Ruiyong; Chang, Junbiao

    2015-02-05

    FNC (2'-deoxy-2'-bfluoro-4'-azidocytidine) is a novel nucleoside analogue with pharmacologic effects on several human diseases. In this work, the binding of FNC to human hemoglobin (HHb) have been investigated by absorption spectroscopy, fluorescence quenching technique, synchronous fluorescence, three-dimensional fluorescence and molecular modeling methods. Analysis of fluorescence data showed that the binding of FNC to HHb occurred via a static quenching mechanism. Thermodynamic analysis and molecular modeling suggest that hydrogen bond and van der Waals force are the mainly binding force in the binding of FNC to HHb.

  9. A spectroscopic and molecular modeling study of sinomenine binding to transferrin.

    PubMed

    Du, Hongyan; Xiang, Junfeng; Zhang, Yazhou; Tang, Yalin

    2007-03-15

    Sinomenine, an herbal ingredient isolated from Sinomenium acutum, is used for the amelioration of arthritis. It has been found that this molecule could bind to human serum transferrin (Tf), the iron (III) transport protein in the blood, by using fluorescence, circular dichroism (CD) spectroscopy, and molecular modeling methods. The results provide possible usage of transferrin to transport sinomenine.

  10. Spectroscopic study of molecular hydrogen concentration at the vicinity of metal surfaces

    NASA Astrophysics Data System (ADS)

    Doi, Kenta; Sasao, Mamiko; Wada, Motoi

    2017-08-01

    Hydrogen atomic emission lines and molecular Fulcher-α bands were observed at the vicinity of metal surfaces bombarded with a magnetized hydrogen plasma. The target bias dependence as well as spatial dependence of emission intensities were obtained. The spatial distribution of Fulcher-α spectral intensities taken by varying the distance from the bombarded tantalum surface suggests that hydrogen molecules concentrate in region near the surface. Obtained Fulcher-α intensity and Hα/Hβ intensity ratio are higher for tantalum wall compared to tungsten wall. On the other hand, lower Hβ/Hγ intensity ratio was obtained for tantalum wall. The measured results are discussed in terms of tantalum wall effectiveness in increasing the local H- density and decreasing the electron density. The target bias dependences of atomic and molecular species indicate that the balance of particles incident onto the surface is a key factor determining the production rate of vibrationally excited molecules.

  11. Optical Control and Spectroscopic Studies of Collisional Population Transfer in Molecular Electronic States

    NASA Astrophysics Data System (ADS)

    Pan, Xinhua

    The quantum interference effects, such as the Autler-Townes (AT) effect and electromagnetically induced transparency (EIT) applied to molecular systems are the focus of this Dissertation in the context of high resolution molecular spectroscopy. We demonstrate that the AT effect can be used to manipulate the spin character of a spin-orbit coupled pair of molecular energy levels serving as a gateway between the singlet and triplet electronic states. We demonstrate that the singlet-triplet mixing characters of the gateway levels can be controlled by manipulating the coupling laser E field amplitude. We observe experimentally the collisional population transfer between electronic states G1pig (v = 12, J = 21, f) and 13Sigmag-( v = 1, N = 21, f) of 7Li 2. We obtain the Stern-Vollmer plot according to the vapor pressure dependence of collisional transfer rate. The triplet fluorescence from the mixed gateway levels to the triplet b 3piu(v' = 1, J' = 20, 21, 22) levels as a function of the probe laser detuning as well as the control laser detuning are observed and compared. The control laser power dependence of the triplet fluorescence signal intensity is recorded to demonstrate that the collisional transfer rate can be enhanced by increasing the control laser power level (Rabi frequency). The conservation of the molecular population transfer is confirmed by comparing the singlet and triplet fluorescence with the control laser detuning over the resonance. A large number of ro-vibrational levels of the 61Sigma g+ and 31pig electronic states of 85Rb2 are observed experimentally by optical-optical double resonance (OODR) spectroscopy technique. The rotational and vibrational Dunham coefficients are extracted from the experimental ro-vibrational energies, and the preliminary Rydberg-Klein-Rees (RKR) potential energy curves are constructed for both states. The ro-vibrational eigenvalues are calculated from the preliminary RKR potential energy curves by using the LEVEL program

  12. Study on the interaction of Co (III) DiAmsar with serum albumins: Spectroscopic and molecular docking methods

    NASA Astrophysics Data System (ADS)

    Farahani, Bahman Vasheghani; Bardajee, Ghasem Rezanejade; Rajabi, Farzaneh Hosseinpour; Hooshyar, Zari

    2015-01-01

    This study was designed to examine the interaction of cobalt-3,6,10,13,16,19-hexaazabicyclo[6.6.6]eicosane-1,8-diamine (Co(III) DiAmsar) as a hexadentate ligand with human serum albumin (HSA) and bovine serum albumin (BSA) under physiological conditions in Tris-HCl buffer solution at pH 7.4. To this aim, at first, Co (III) DiAmsar was synthesized and characterized by nuclear magnetic resonance (NMR), and mass spectroscopy and then its interaction with HSA and BSA was investigated by means of various spectroscopic methods (Fourier transform infrared (FT-IR), UV-visible (UV-vis), fluorescence, and cyclic voltammetry (CV)) and molecular docking technique. The results of fluorescence titration revealed that the Co (III) DiAmsar strongly quench the intrinsic fluorescence of HSA and BSA through a static quenching procedure. Binding constants (Ka) and the number of binding sites (n ∼ 1) were calculated using Stern-Volmer equations. The ΔG parameters at different temperatures were calculated. Subsequently, the values of ΔH and ΔS were also calculated, which revealed that the van der Waals and hydrogen bonding interaction splay a major role in Co (III) DiAmsar-HSA and Co (III) DiAmsar-BSA associations. The distance r between donor (HSA and BSA) and acceptor (Co (III) DiAmsar) was obtained according to fluorescence resonance energy transfer. The data obtained by the molecular modeling study revealed the surrounding residues of HSA and BSA around Co (III) DiAmsar.

  13. Study on the interaction of Co (III) DiAmsar with serum albumins: spectroscopic and molecular docking methods.

    PubMed

    Farahani, Bahman Vasheghani; Bardajee, Ghasem Rezanejade; Rajabi, Farzaneh Hosseinpour; Hooshyar, Zari

    2015-01-25

    This study was designed to examine the interaction of cobalt-3,6,10,13,16,19-hexaazabicyclo[6.6.6]eicosane-1,8-diamine (Co(III) DiAmsar) as a hexadentate ligand with human serum albumin (HSA) and bovine serum albumin (BSA) under physiological conditions in Tris-HCl buffer solution at pH 7.4. To this aim, at first, Co (III) DiAmsar was synthesized and characterized by nuclear magnetic resonance (NMR), and mass spectroscopy and then its interaction with HSA and BSA was investigated by means of various spectroscopic methods (Fourier transform infrared (FT-IR), UV-visible (UV-vis), fluorescence, and cyclic voltammetry (CV)) and molecular docking technique. The results of fluorescence titration revealed that the Co (III) DiAmsar strongly quench the intrinsic fluorescence of HSA and BSA through a static quenching procedure. Binding constants (Ka) and the number of binding sites (n∼1) were calculated using Stern-Volmer equations. The ΔG parameters at different temperatures were calculated. Subsequently, the values of ΔH and ΔS were also calculated, which revealed that the van der Waals and hydrogen bonding interaction splay a major role in Co (III) DiAmsar-HSA and Co (III) DiAmsar-BSA associations. The distance r between donor (HSA and BSA) and acceptor (Co (III) DiAmsar) was obtained according to fluorescence resonance energy transfer. The data obtained by the molecular modeling study revealed the surrounding residues of HSA and BSA around Co (III) DiAmsar.

  14. Studies of the interaction between demeclocycline and human serum albumin by multi-spectroscopic and molecular docking methods

    NASA Astrophysics Data System (ADS)

    Dong, Chengyu; Ma, Shuying; Liu, Ying

    2013-02-01

    This study was designed to examine the interaction of demeclocycline (DMCTC) with human serum albumin (HSA) by multi-spectroscopic and molecular docking methods. The inner filter effect was corrected before we calculated the binding parameters. Fluorescence and UV-vis spectroscopy revealed that DMCTC induced the fluorescence quenching of HSA though a static quenching procedure. Thermodynamic analysis by Van Hoff equation found enthalpy change (ΔH) and entropy change (ΔS) were -53.01 kJ mol-1 and -65.13 J mol-1 K-1, respectively, which indicated hydrogen bond and van der Waals force were the predominant force in the binding process. According to fluorescence resonance energy transfer (FRET), the specific binding distances between Trp-214 (donor) and DMCTC (acceptor) were 3.18 nm. Through site marker competitive experiments, subdomain IIA of HSA has been assigned to possess the high-affinity binding site of DMCTC. The three dimensional fluorescence showed that the conformation of HSA was changed after its complexation with DMCTC, and the alternations of protein secondary structure were quantitatively calculated from FT-IR with reduction of α-helices content about 4.8%, β-sheet from 30.3% to 21.6% and with increases of β-turn from 15.6% to 22.2%. Furthermore, the binding details between DMCTC and HSA were further confirmed by molecular docking studies, which revealed that DMCTC was bound at subdomain IIA through multiple interactions, such as hydrophobic effect, polar forces and π-π interactions. Moreover, the coexist metal ions such as Al3+, Fe3+, Cu2+, Cr3+ and Cd2+ can decrease the binding constants of DMCTC-HSA.

  15. Vibrational spectroscopic studies and molecular docking of 10,10-Dimethylanthrone

    NASA Astrophysics Data System (ADS)

    Sheena Mary, Y.; Yamuna, T. S.; Yohannan Panicker, C.; Yathirajan, H. S.; Siddegowda, M. S.; Al-Saadi, Abdulaziz A.; Van Alsenoy, Christian; War, Javeed Ahmad

    2015-01-01

    FT-IR and FT-Raman spectra of 10,10-Dimethylanthrone 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. In its most stable form, the title compound maintains C2v symmetry as determined by XRD results, where both methyl groups are staggered with respect to the corresponding C23sbnd C24 and C23sbnd C28 bonds. The geometrical parameters (B3LYP/6-311++G(d,p)(5D,7F)) 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 seen from the MEP map, negative potential regions are localized over the carbonyl group and are possible sites for electrophilic attack. The title compound, 10,10-Dimethylanthrone forms a stable complex with human topoisomerase-II as is evident from the ligand-receptor interactions and show appreciable antineoplastic activity.

  16. 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.

  17. Quantitative analysis of molecular orientation in chlorophyll a Langmuir monolayer: a polarized visible reflection spectroscopic study.

    PubMed Central

    Okamura, E; Hasegawa, T; Umemura, J

    1995-01-01

    Polarized visible reflection spectra of a chlorophyll a (Chl.a) Langmuir monolayer have been measured in situ at various surface pressures. By applying Hansen's optics to the three-phase plane-bounded system (air/Chl.a monolayer/water), the negative reflection absorbances observed were reproduced satisfactorily by the theoretical calculation. Molecular orientation of Chl.a in the monolayer was evaluated quantitatively as a function of surface pressure, from the reflection absorbance of p- and s-polarized spectra of the red (Qy) band. It has been proven that Chl.a molecules in the monolayer form aggregates (islands) even in the low surface pressure region and that during the monolayer compression the molecules are gradually reorganized from inhomogeneous islands to ordered structures, with the chromophores oriented on the average vertically to the water surface. Images FIGURE 1 PMID:8519968

  18. 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.

  19. 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.

  20. Adding Spectroscopic Dimension To The Study Of The Young Embedded Clusters: Serpens Molecular Cloud.

    NASA Astrophysics Data System (ADS)

    Gorlova, Nadya; Lada, E.; Steinhauer, A.

    2009-01-01

    We present the results of an investigation of the embedded cluster near the main core of the Serpens molecular cloud. Near-IR imaging and low resolution JH spectra were obtained for objects in this region using the multi-object near-IR imager and spectrograph FLAMINGOS at the Kitt Peak 4m telescope. We constructed Hertzsprpung-Russell diagram and determined ages and masses for 15 previously identified members and one new candidate. We show that 1-4 objects are young brown dwarfs with disks. We used our individually determined estimates of the photospheric parameters and extinction to separate the stellar flux from the spectral energy distribution (SED) and to verify the SED types determined by ISO and the Spitzer. We demonstrate that after correcting for extinction a number of the flat-type objects appear to have SEDs consistent with that of the classical T Tau stars, while some objects even indicate the presence of the inner disk holes. We show that the distance to the cluster is not well established yet. We obtain a medium age for the Serpens cluster of 1 Myr for distance of 380 pc and of 3 Myr for 260 pc, and an age spread of 5-10 Myr. The core of the cluster appears on average younger than the rest of the cluster. We draw attention to at least three diskless objects younger than 1 Myr, whose nature requires further investigation. Finally, we find an association of the young objects with the two dusty filaments in the cloud, indicating that star formation is not entirely confined to the cluster center.

  1. 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.

  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. Molecular spectroscopic studies on the interaction of glycosaminoglycans with brilliant cresol blue and its analytical application

    NASA Astrophysics Data System (ADS)

    Zhang, Shuzhen; Li, Na; Zhao, Fenglin; Li, Ke'an; Tong, Shenyang

    2002-01-01

    The interaction of brilliant cresol blue (BCB) with glycosaminoglycans (GAGs), such as heparin (Hep) and chondroitin 4-sulfate (CS), in aqueous solution has been studied by spectrophotometry and light scattering spectroscopy. Absorbance of BCB at 632 and 594 nm decreased on addition of Hep or CS with the appearance of a new blue-shifted absorption band at 550 nm, which indicated that new metachromatic complex formed. The linear decrease in absorbance of BCB at 632 nm was observed. In addition, Hep was more effective than CS (1.7 times) in decreasing absorbance of BCB. The stoichiometry of Hep or CS with BCB was determined by spectrophotometric titration and the MacIntosh extraction method. The result showed that the stoichiometry of BCB/Hep was 1.8 times that of BCB/CS. These results suggested that the interaction between GAGs and BCB was the result of electrostatic forces, and the differences between Hep and CS were attributed to the different negative charge numbers on repetitive disaccharides unit. Studies on the effects of alcohol and urea indicated that GAGs only interacted with the aggregates of BCB. Moreover, a strong light scattering signal was observed after mixing BCB with GAGs. Furthermore, the light scattering intensity at light scattering bands was proportional to the concentration of Hep or CS added when the concentration of BCB was constant.

  4. Vibrational spectroscopic, molecular structure, first hyperpolarizability and NBO studies of 4'-methylbiphenyl-2-carbonitrile

    NASA Astrophysics Data System (ADS)

    Kaur, Manpreet; Sheena Mary, Y.; Varghese, Hema Tresa; Yohannan Panicker, C.; Yathirajan, H. S.; Siddegowda, M. S.; Alsenoy, Christian Van

    2012-12-01

    The FT-IR, FT-Raman spectra and XRD of 4'-methylbiphenyl-2-carbonitrile were recorded and analyzed. The frequencies were computed at various density functional theoretical levels using Gaussian09 software package. The data obtained from theoretical calculations were used to assign vibrational bands obtained in infrared and Raman spectra of the studied molecule. Potential energy distribution of the normal modes of vibrations were done using GAR2PED program. The geometrical parameters of the title compound are in agreement with XRD crystal structure data. The first hyperpolarizability is comparable with the reported values of similar derivatives and is an attractive object for future studies of non linear optics. The stability of the molecule arising from hyper-conjugative interaction and charge delocalization has been analyzed using NBO analysis. According to XRD data, the dihedral angles between the mean planes of the two benzene rings is 44.7° and the crystal packing is stabilized by weak intermolecular π-π stacking interactions.

  5. 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.

  6. 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.; hide

    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.

  7. 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.

  8. Molecular structure and spectroscopic investigations combined with hypoglycemic/anticancer and docking studies of a new barbituric acid derivative

    NASA Astrophysics Data System (ADS)

    Barakat, Assem; Soliman, Saied M.; Elshaier, Yaseen A. M. M.; Ali, M.; Al-Majid, Abdullah Mohammed; Ghabbour, Hazem A.

    2017-04-01

    The one-pot synthesis reaction of barbituric acid derivative, 1,3-cyclohexandione, and 4-fluorobenzaldehyde in water mediated by NHEt2 as base afforded 4 with excellent yield. The synthesized compound was characterized by spectrophotometric tools as well as X-ray single crystal diffraction technique. The stability of the nine possible isomers of the synthesized compound was studied using the B3LYP method and 6-31G(d,p) basis set. The electronic and spectroscopic properties of the most stable isomer were predicted. The UV-Vis absorption spectrum displayed two bands at 203 and 257 nm in the solvent chloroform. The latter was calculated at 235.6 nm (f = 0.1995) in the gas phase due to H-2→L (42%) and H-1→L+2 (14%) excitations. In solution, using chloroform as a solvent, a slight bathochromic shift to 237.6 nm with an increase in the absorption intensity (f = 0.2898) was predicted. The molecular orbital energy level diagram of this transition band was characterized mainly by π-π* transitions. The 13C and 1H NMR chemical shifts correlated well with the experimental data. The correlations had higher correlation coefficients (R2) when solvent effects were considered. The atomic charges were calculated using natural population analysis and the charged regions were presented using a molecular electrostatic potential (MEP) map. The synthesized compound was examined as a hypoglycemic agent via inhibition of α-glucosidase and β-glucuronidase enzymes. Its inhibitory activity against α-glucosidase was 10 times greater than the inhibitory activity of the standard drug acarbose (IC50 77.9 ± 0.3 μM and 840 ± 1.73 μM, respectively). Moreover, the target compound was evaluated for anticancer activity against MCF-7, H460, 3T3, and Hela cell lines. It demonstrated inhibitory activity against the MCF-7 and H460 cell lines with IC50 5.80 ± 0.12 and 19.6 ± 0.5 μM, respectively, in comparison to doxorubicin. The docking study was performed using the OpenEye program.

  9. The HITRAN2016 Molecular Spectroscopic Database

    DOE PAGES

    Gordon, I. E.; Rothman, L. S.; Hill, C.; ...

    2017-07-05

    This article describes the contents of the 2016 edition of the HITRAN molecular spectroscopic compilation. The new edition replaces the previous HITRAN edition of 2012 and its updates during the intervening years. The HITRAN molecular absorption compilation is composed of five major components: 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, collision-induced absorption data, aerosol indices of refraction, 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, additionalmore » absorption phenomena, added line-shape formalisms, and validity. Moreover, molecules, isotopologues, and perturbing gases have been added that address the issues of atmospheres beyond the Earth. Of considerable note, experimental IR cross-sections for almost 300 additional molecules important in different areas of atmospheric science have been added to the database. The compilation can be accessed through www.hitran.org. Most of the HITRAN data have now been cast into an underlying relational database structure that offers many advantages over the long-standing sequential text-based structure. The new structure empowers the user in many ways. It enables the incorporation of an extended set of fundamental parameters per transition, sophisticated line-shape formalisms, easy user-defined output formats, and very convenient searching, filtering, and plotting of data. Finally, a powerful application programming interface making use of structured query language (SQL) features for higher-level applications of HITRAN is also provided.« less

  10. Studies on the interactions of SAP-1 (an N-terminal truncated form of cystatin S) with its binding partners by CD-spectroscopic and molecular docking methods.

    PubMed

    Yadav, Vikash Kumar; Mandal, Rahul Shubhra; Puniya, Bhanwar Lal; Singh, Sarman; Yadav, Savita

    2015-01-01

    SAP-1 is a 113 amino acid long single-chain protein which belongs to the type 2 cystatin gene family. In our previous study, we have purified SAP-1 from human seminal plasma and observed its cross-class inhibitory property. At this time, we report the interaction of SAP-1 with diverse proteases and its binding partners by CD-spectroscopic and molecular docking methods. The circular dichroism (CD) spectroscopic studies demonstrate that the conformation of SAP-1 is changed after its complexation with proteases, and the alterations in protein secondary structure are quantitatively calculated with increase of α-helices and reduction of β-strand content. To get insight into the interactions between SAP-1 and proteases, we make an effort to model the three-dimensional structure of SAP-1 by molecular modeling and verify its stability and viability through molecular dynamics simulations and finally complexed with different proteases using ClusPro 2.0 Server. A high degree of shape complementarity is examined within the complexes, stabilized by a number of hydrogen bonds (HBs) and hydrophobic interactions. Using HB analyses in different protein complexes, we have identified a series of key residues that may be involved in the interactions between SAP-1 and proteases. These findings will assist to understand the mechanism of inhibition of SAP-1 for different proteases and provide intimation for further research.

  11. Vibrational, spectroscopic, molecular docking and density functional theory studies on N-(5-aminopyridin-2-yl)acetamide

    NASA Astrophysics Data System (ADS)

    Asath, R. Mohamed; Rekha, T. N.; Premkumar, S.; Mathavan, T.; Benial, A. Milton Franklin

    2016-12-01

    Conformational analysis was carried out for N-(5-aminopyridin-2-yl)acetamide (APA) molecule. The most stable, optimized structure was predicted by the density functional theory calculations using the B3LYP functional with cc-pVQZ basis set. The optimized structural parameters and vibrational frequencies were calculated. The experimental and theoretical vibrational frequencies were assigned and compared. Ultraviolet-visible spectrum was simulated and validated experimentally. The molecular electrostatic potential surface was simulated. Frontier molecular orbitals and related molecular properties were computed, which reveals that the higher molecular reactivity and stability of the APA molecule and further density of states spectrum was simulated. The natural bond orbital analysis was also performed to confirm the bioactivity of the APA molecule. Antidiabetic activity was studied based on the molecular docking analysis and the APA molecule was identified that it can act as a good inhibitor against diabetic nephropathy.

  12. 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.

  13. Inclusion of Ethyl Acetoacetate Bearing 7-Hydroxycoumarin Dye by β-Cyclodextrin and its Cooperative Assembly with Mercury(II) Ions: Spectroscopic and Molecular Modeling Studies.

    PubMed

    Aliaga, Margarita E; Fierro, Angélica; Uribe, Iván; García-Río, Luis; Cañete, Álvaro

    2016-10-18

    The inclusion of the fluorescent organic dye, ethyl 3-(7-hydroxy-2-oxo-2H-chromen-3-yl)-3-oxopropanoate (1) by the host β-cyclodextrin (β-CD), and its response toward mercuric ions (Hg(2+) ), was studied by UV/Vis, fluorescence, and (1) H NMR spectroscopic analyses, mass spectrometry and molecular modeling studies. (1) H NMR measurements together with molecular modeling studies for dye 1 demonstrate that it exhibits two tautomeric forms (keto and enol); however, when the dye is included into the β-CD cavity, the enol form predominates. Moreover, by using spectroscopic and spectrometry techniques, a 1:1 stoichiometry was determined for the complexes formed between dye 1 (enol form) and β-CD, with a binding constant (Kb1 =1.8×10(4)  m(-1) ) and for the dye 1 (keto form)-Hg(2+) (Kb2 =2.3×10(3)  m(-1) ). Interestingly, in the presence of 1-β-CD complex and mercuric ions, a ternary supramolecular system (Hg-1-β-CD complex) was established, with a 1:1:1 stoichiometry and a Kb3 value of 4.3×10(3)  m(-1) , with the keto form of the dye being the only one present in this assembly. The three-component system provides a starting point for the development of novel and directed supramolecular assemblies.

  14. Significance of weak interactions in imidazolium picrate ionic liquids: spectroscopic and theoretical studies for molecular level understanding.

    PubMed

    Panja, Sumit Kumar; Dwivedi, Nidhi; Noothalapati, Hemanth; Shigeto, Shinsuke; Sikder, A K; Saha, Abhijit; Sunkari, Sailaja S; Saha, Satyen

    2015-07-21

    The effects of interionic hydrogen bonding and π-π stacking interactions on the physical properties of a new series of picrate anion based ionic liquids (ILs) have been investigated experimentally and theoretically. The existence of aromatic (C2-HO) and aliphatic (C7-HO-N22 and C6-HO-N20) hydrogen bonding and π-π stacking interactions in these ILs has been observed using various spectroscopic techniques. The aromatic and aliphatic C-HO hydrogen bonding interactions are found to have a crucial role in binding the imidazolium cation and picrate anion together. However, the π-π stacking interactions between two successive layers are found to play a decisive role in tight packing in ILs leading to differences in physical properties. The drastic difference in the melting points of the methyl and propyl derivatives (mmimPic and pmimPic respectively) have been found to be primarily due to the difference in the strength and varieties of π-π stacking interactions. While in mmimPic, several different types of π-π stacking interactions between the aromatic rings (such as picrate-picrate, picrate-imidazole and imidazolium-imidazolium cation rings) are observed, only one type of π-π stacking interaction (picrate-picrate rings) is found to exist in the pmimPic IL. NMR spectroscopic studies reveal that the interaction of these ILs with solvent molecules is different and depends on the dielectric constant of the solvent. While an ion solvation model explains the solvation in high dielectric solvents, an ion-pair solvation model is found to be more appropriate for low dielectric constant solvents. The enhanced stability of these investigated picrate ILs compared with that of inorganic picrate salts under high doses of γ radiation clearly indicates the importance of weak interionic interactions in ILs, and also opens up the possibility of the application of picrate ILs as prospective diluents in nuclear separation for advanced fuel cycling process.

  15. 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.

  16. Studies on the synthesis, spectroscopic analysis, molecular docking and DFT calculations on 1-hydroxy-2-(4-hydroxyphenyl)-4,5-dimethyl-imidazol 3-oxide

    NASA Astrophysics Data System (ADS)

    Benzon, K. B.; Sheena, Mary Y.; Panicker, C. Yohannan; Armaković, Stevan; Armaković, Sanja J.; Pradhan, Kiran; Nanda, Ashis Kumar; Van Alsenoy, C.

    2017-02-01

    In this work we have investigated in details the spectroscopic and reactive properties of newly synthesized imidazole derivative, namely the 1-hydroxy-2-(4-hydroxyphenyl)-4,5-dimethyl-imidazole 3-oxide (HHPDI). FT-IR and NMR spectra were measured and compared with theoretically obtained data provided by calculations of potential energy distribution and chemical shifts, respectively. Insight into the global reactivity properties has been obtained by analysis of frontier molecular orbitals, while local reactivity properties have been investigated by analysis of charge distribution, ionization energies and Fukui functions. NBO analysis was also employed to understand the stability of molecule, while hyperpolarizability has been calculated in order to assess the nonlinear optical properties of title molecule. Sensitivity towards autoxidation and hydrolysis mechanisms has been investigated by calculations of bond dissociation energies and radial distribution functions, respectively. Molecular docking study was also performed, in order to determine the pharmaceutical potential of the investigated molecule.

  17. Investigation into the interaction of losartan with human serum albumin and glycated human serum albumin by spectroscopic and molecular dynamics simulation techniques: A comparison study.

    PubMed

    Moeinpour, Farid; Mohseni-Shahri, Fatemeh S; Malaekeh-Nikouei, Bizhan; Nassirli, Hooriyeh

    2016-09-25

    The interaction between losartan and human serum albumin (HSA), as well as its glycated form (gHSA) was studied by multiple spectroscopic techniques and molecular dynamics simulation under physiological conditions. The binding information, including the binding constants, effective quenching constant and number of binding sites showed that the binding partiality of losartan to HSA was higher than to gHSA. The findings of three-dimensional fluorescence spectra demonstrated that the binding of losartan to HSA and gHSA would alter the protein conformation. The distances between Trp residue and the binding sites of the drug were evaluated on the basis of the Förster theory, and it was indicated that non-radiative energy transfer from HSA and gHSA to the losartan happened with a high possibility. According to molecular dynamics simulation, the protein secondary and tertiary structure changes were compared in HSA and gHSA for clarifying the obtained results.

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

    PubMed

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

    2015-05-05

    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 589nm, 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.

  19. 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 (

  20. Spectroscopic and reactive properties of a newly synthesized quinazoline derivative: Combined experimental, DFT, molecular dynamics and docking study

    NASA Astrophysics Data System (ADS)

    El-Azab, Adel S.; Mary, Y. Shyma; Mary, Y. Sheena; Panicker, C. Yohannan; Abdel-Aziz, Alaa A.-M.; Mohamed, Menshawy A.; Armaković, Stevan; Armaković, Sanja J.; Van Alsenoy, Christian

    2017-04-01

    The molecular geometry, the normal mode wavenumbers and corresponding vibrational assignments, natural bond orbital analysis and the HOMO-LUMO analysis of 3-(4-oxo-phenethyl-3,4-dihydroquinazolin-2-ylthio)-N-(3,4,5-trimethoxyphenyl)propanamide were performed by B3LYP level of theory using the 6-311++G(d,p)(5D,7F) basis set. The experimentally obtained wavenumbers are in agreement with the theoretically predicted wavenumbrs. From the MEP plot it is evident that the negative charge covers carbonyl group, mono substituted phenyl ring, O59 atom and the positive region is over the nitrogen atoms and hydrogen atoms. NLO behavior of the title molecule was investigated by the determination of the first and second order hyperpolarizabilities. The molecular orbitals and molecular electrostatic potential map are also reported. The NMR spectra and Fukui indices are also analyzed. Molecule sites important from the aspect of reactivity have been determined by calculations of average local ionization energy (ALIE), Fukui functions and bond dissociation energies (BDE). BDE for hydrogen abstraction served us to investigate the possibility for autoxidation mechanism of the investigated molecule. Molecular dynamics (MD) simulations were used in order to investigate which atoms of the title molecule have the most pronounced interactions with water molecules. Molecular docking studies reveal that the inhibitor forms a stable complex with HNE as is evident from the binding affinity -10.9 kcal/mol and the results suggest that the compound exhibit inhibitory activity against HNE.

  1. Fluorescence spectroscopic and molecular docking studies of the binding interaction between the new anaplastic lymphoma kinase inhibitor crizotinib and bovine serum albumin.

    PubMed

    Abdelhameed, Ali S; Alanazi, Amer M; Bakheit, Ahmed H; Darwish, Hany W; Ghabbour, Hazem A; Darwish, Ibrahim A

    2017-01-15

    Binding of the recently introduced anti-cancer drug, crizotinib (CRB) with the bovine serum albumin (BSA) was comprehensively studied with the aid of fluorescence and UV-Vis spectroscopic as well as molecular docking techniques. The collective results of the study under the simulated physiological conditions proposed a static type of binding occurring between the CRB and BSA with binding constants of 10(4)Lmol(-1). BSA conformational changes were investigated using three dimensional (3D) and synchronous fluorescence measurements. Moreover, the results of site marker competitive experiments and molecular docking, it could be deduced that CRB was inserted into the subdomain IIA (site I) of BSA yielding a more stabilized system. This was further confirmed with the molecular docking results which revealed that CRB is located in the active site residues Try149, Glu152, Ser191, Arg194, Arg198, Trp213, Arg217, Arg256, His287, Ala290, Glu291, Ser343, Asp450 within a radius of 6Å. Combining the molecular docking studies and the computed thermodynamic parameters, it can be inferred that hydrophobic and electrostatic interactions are the major binding forces involved in formation of the CRB-BSA complex.

  2. Fluorescence spectroscopic and molecular docking studies of the binding interaction between the new anaplastic lymphoma kinase inhibitor crizotinib and bovine serum albumin

    NASA Astrophysics Data System (ADS)

    Abdelhameed, Ali S.; Alanazi, Amer M.; Bakheit, Ahmed H.; Darwish, Hany W.; Ghabbour, Hazem A.; Darwish, Ibrahim A.

    2017-01-01

    Binding of the recently introduced anti-cancer drug, crizotinib (CRB) with the bovine serum albumin (BSA) was comprehensively studied with the aid of fluorescence and UV-Vis spectroscopic as well as molecular docking techniques. The collective results of the study under the simulated physiological conditions proposed a static type of binding occurring between the CRB and BSA with binding constants of 104 L mol- 1. BSA conformational changes were investigated using three dimensional (3D) and synchronous fluorescence measurements. Moreover, the results of site marker competitive experiments and molecular docking, it could be deduced that CRB was inserted into the subdomain IIA (site I) of BSA yielding a more stabilized system. This was further confirmed with the molecular docking results which revealed that CRB is located in the active site residues Try149, Glu152, Ser191, Arg194, Arg198, Trp213, Arg217, Arg256, His287, Ala290, Glu291, Ser343, Asp450 within a radius of 6 Å. Combining the molecular docking studies and the computed thermodynamic parameters, it can be inferred that hydrophobic and electrostatic interactions are the major binding forces involved in formation of the CRB-BSA complex.

  3. Synthesis, vibrational spectroscopic investigations, molecular docking, antibacterial studies and molecular dynamics study of 5-[(4-nitrophenyl)acetamido]-2-(4-tert-butylphenyl)benzoxazole

    NASA Astrophysics Data System (ADS)

    Sheena Mary, Y.; Al-Shehri, Mona M.; Jalaja, K.; Al-Omary, Fatmah A. M.; El-Emam, Ali A.; Yohannan Panicker, C.; Armaković, Stevan; Armaković, Sanja J.; Temiz-Arpaci, Ozlem; Van Alsenoy, C.

    2017-04-01

    Antimicrobial active 5-[(4-nitrophenyl)acetamido]-2-(4-tert-butylphenyl)benzoxazole (NATPB) was synthesized and observed IR, Raman bands are compared with the theoretically predicted wave numbers. In the IR spectrum the NH stretching wave number splits into a doublet with a noted difference and is red shifted from the computed value, which indicates the weakening of NH bond resulting in proton transfer to the neighbouring oxygen atom. The HOMO-LUMO plots reveal the charge transfer in the molecular system through the conjugated paths. The electrophilic and nucleophilic reactive sites are identified from the MEP plot. Mapping of average local ionization energy (ALIE) values to the electron density surface served us as a tool for prediction of molecule sites possibly prone to electrophilic attacks. Other important reactive centres of the title molecule were detected by calculations of Fukui functions. Calculations of bond dissociation energies (BDE) for hydrogen abstraction were used in order to assess whether the NATPB molecules is prone to autoxidation mechanism or not, while BDE of the remaining single acyclic bonds were used in order to determine the weakest bond. Interaction properties with water were investigated by molecular dynamics (MD) simulations and calculations of radial distribution functions (RDFs). The compound possessed broad spectrum activity against all of the tested Gram-positive and Gram-negative bacteria and yeasts, their minimum inhibitory concentrations (MICs) ranging between 32 and 128 μg/ml. The compound exhibited significant antibacterial activity (32 μg/ml) against an antibiotic resistant E. faecalis isolate, at same potency with the compared standard drugs vancomycin and gentamycin sulfate. The molecular docking studies show that the compound might exhibit inhibitory activity against CDK inhibitors.

  4. 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.

  5. Spectroscopic investigation, vibrational assignments, HOMO-LUMO, NBO, MEP analysis and molecular docking studies of oxoaporphine alkaloid liriodenine

    NASA Astrophysics Data System (ADS)

    Costa, Renyer A.; Pitt, Priscilla Olliveira; Pinheiro, Maria Lucia B.; Oliveira, Kelson M. T.; Salomé, Kahlil Schwanka; Barison, Andersson; Costa, Emmanoel Vilaça

    2017-03-01

    A combined experimental and theoretical DFT study of the structural, vibrational and electronic properties of liriodenine is presented using B3LYP function with 6-311G (2d, p) basis set. The theoretical geometry optimization data were compared with the X-ray data for a similar structure in the associated literature, showing similar values. In addition, natural bond orbitals (NBOs), HOMO-LUMO energy gap, mapped molecular Electrostatic Potential (MEP) surface calculation, first and second order hyperpolarizabilities were also performed with the same calculation level. Theoretical UV spectrum agreed well with the measured experimental data, with transitions assigned. The molecular electrostatic potential map shows opposite potentials regions that forms hydrogen bonds that stabilize the dimeric form, which were confirmed by the close values related to the C dbnd O bond stretching between the dimeric form and the experimental IR spectra (1654 cm- 1 for the experimental, 1700 cm- 1 for the dimer form). Calculated HOMO/LUMO gaps shows the excitation energy for Liriodenine, justifying its stability and kinetics reaction. Molecular docking studies with Candida albicans dihydrofolate reductase (DHFR) and Candida albicans secreted aspartic protease (SAP) showed binding free energies values of - 8.5 and - 8.3 kcal/mol, suggesting good affinity between the liriodenine and the target macromolecules.

  6. Exploring the binding of two potent anticancer drugs bosutinib and imatinib mesylate with bovine serum albumin: spectroscopic and molecular dynamic simulation studies.

    PubMed

    Pawar, Suma K; Naik, Roopa S; Seetharamappa, J

    2017-08-29

    Bosutinib (BST) and imatinib mesylate (IMT) are tyrosine kinase inhibitors (TKIs). In view of the importance of these inhibitors in cancer treatment, we investigated the mechanism of interaction between BST/IMT and bovine serum albumin (BSA) using various spectroscopic and molecular docking methods. Fluorescence studies indicated that BST/IMT interacted with BSA without affecting the microenvironment around the residue Trp213 of BSA. The quenching mechanism associated with the BST-BSA and IMT-BSA interactions was determined by performing fluorescence measurements at different temperatures. These results suggested that BST and IMT quenched the fluorescence intensity of BSA through static and dynamic processes, respectively, which was confirmed by time-resolved fluorescence measurements. Evaluation of the thermodynamic parameters ∆H°, ∆S°, and ∆G° suggested that hydrophobic and electrostatic interactions played significant roles in the BST-BSA interaction, while IMT-BSA was stabilized by hydrophobic forces. Competitive experimental results revealed that the primary binding sites for BST and IMT on BSA were sites II and I, respectively. This was supported by the results of molecular docking and dynamic simulation studies. The change in the secondary structure of BSA upon binding with BST/IMT was investigated by 3D fluorescence, absorption, and CD spectroscopic studies. In addition, the influences of β-cyclodextrin and metal ions (Cu(2+) and Zn(2+)) on the binding affinities of BST and IMT to BSA were examined. Graphical abstract Binding of BST and IMT in BSA at site II and site I respectively.

  7. X-ray photoelectron spectroscopic study of the oxide removal mechanism of GaAs /100/ molecular beam epitaxial substrates in in situ heating

    NASA Technical Reports Server (NTRS)

    Vasquez, R. P.; Lewis, B. F.; Grunthaner, F. J.

    1983-01-01

    A standard cleaning procedure for GaAs (100) molecular beam epitaxial (MBE) substrates is a chemical treatment with a solution of H2SO4/H2O2/H2O, followed by in situ heating prior to MBE growth. X-ray photoelectron spectroscopic (XPS) studies of the surface following the chemical treatment show that the oxidized As is primarily As(+ 5). Upon heating to low temperatures (less than (350 C) the As(+ 5) oxidizes the substrate to form Ga2O3 and elemental As, and the As(+ 5) is reduced to As(+ 3) in the process. At higher temperatures (500 C), the As(+ 3) and elemental As desorb, while the Ga(+ 3) begins desorbing at about 600 C.

  8. Caffeic acid binds to the minor groove of calf thymus DNA: A multi-spectroscopic, thermodynamics and molecular modelling study.

    PubMed

    Sarwar, Tarique; Ishqi, Hassan Mubarak; Rehman, Sayeed Ur; Husain, Mohammed Amir; Rahman, Yusra; Tabish, Mohammad

    2017-05-01

    Caffeic acid (CA) is a plant polyphenol which acts as an antioxidant and has various pharmacological effects. DNA is one of the major cellular targets of therapeutic molecules. Thus, studying the interaction of small molecules with DNA is of great importance. In the current article, we have studied the mode of binding of CA with calf thymus DNA (Ct-DNA) using a series of biophysical techniques. Formation of complex between CA and Ct-DNA is ascertained by analyzing the UV-vis absorbance and fluorescence emission spectra of CA upon successive addition of Ct-DNA. Binding constants of CA with Ct-DNA obtained using multiple experiments was in the order of 103 M-1 which is consistent with known groove binders. Analysis of thermodynamic parameters suggest that hydrogen bonding and van der Waal's forces played major role in the binding process. Competitive displacement studies confirmed that CA binds to the minor groove of Ct-DNA. These observations were further validated by KI quenching experiment, DNA melting studies, CD and viscosity measurements. In silico molecular docking further provided insight into the mode of binding of CA with Ct-DNA. Through in vitro experiments and in silico molecular docking studies, it was concluded that CA binds to the minor groove of Ct-DNA. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. Spectroscopic Studies of Melanin.

    DTIC Science & Technology

    1986-01-01

    il), and leading to the production of oxygen radicals (12). Gallas (13) and Kozikowski et al. (14) have studied melanin fluorescence. As part of a...Raman scattering unobservable in aqueous solution by continuous wave techniques. As was also observed by Kozikowski et al. (14), the intrinsic...168B. 14. Kozikowski SD, Wolfram LJ, Alfano RR. Fluorescence spectroscopy of eumelanins. IEEE J Quant Electron 1984;OE20:1379-1382. 15. Slawinski J

  10. Urea induced unfolding dynamics of flavin adenine dinucleotide (FAD): spectroscopic and molecular dynamics simulation studies from femto-second to nanosecond regime.

    PubMed

    Sengupta, Abhigyan; Singh, Reman K; Gavvala, Krishna; Koninti, Raj Kumar; Mukherjee, Arnab; Hazra, Partha

    2014-02-20

    Here, we investigate the effect of urea in the unfolding dynamics of flavin adenine dinucleotide (FAD), an important enzymatic cofactor, through steady state, time-resolved fluorescence spectroscopic and molecular dynamics (MD) simulation studies. Steady state results indicate the possibility of urea induced unfolding of FAD, inferred from increasing emission intensity of FAD with urea. The TCSPC and up-conversion results suggest that the stack-unstack dynamics of FAD severely gets affected in the presence of urea and leads to an increase in the unstack conformation population from 15% in pure water to 40% in 12 M urea. Molecular dynamics simulation was employed to understand the nature of the interaction between FAD and urea at the molecular level. Results depict that urea molecules replace many of the water molecules around adenine and isoalloxazine rings of FAD. However, the major driving force for the stability of this unstack conformations arises from the favorable stacking interaction of a significant fraction of the urea molecules with adenine and isoalloxazine rings of FAD, which overcomes the intramolecular stacking interaction between themselves observed in pure water.

  11. 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.

  12. Molecular encapsulation of 5-nitroindazole derivatives in 2,6-dimethyl-beta-cyclodextrin: electrochemical and spectroscopic studies.

    PubMed

    Pérez-Cruz, Fernanda; Jullian, Carolina; Rodriguez, Jorge; Arán, Vicente J; Olea-Azar, Claudio

    2009-07-01

    Four different 5-nitroindazole derivatives (1-4) and its inclusion with Heptakis(2,6-di-O-methyl)-beta-cyclodextrin (DMbetaCD) were investigated. The stoichiometric ratios and stability constants describing the extent of formation of the complexes were determined by phase-solubility measurements obtaining in all cases a type-A(L) diagram. Also electrochemical studies were carried out, where the observed change in the E(PC) value indicated a lower feasibility of the nitro group reduction. The same behavior was observed in the ESR studies. The detailed spatial configuration is proposed based on 2D NMR methods. These results are further interpreted using molecular modeling studies. The latter results are in good agreement with the experimental data.

  13. A Study of the Interaction of Bovine Hemoglobin with Synthetic Dyes Using Spectroscopic Techniques and Molecular Docking

    PubMed Central

    Kamaljeet; Bansal, Saurabh; SenGupta, Uttara

    2017-01-01

    Synthetic dyes are a very efficient class of dyes that are ingested or come into contact with the skin from numerous sources (cosmetics, textiles, leather, paper, and drugs). An important component of their safety profile is the interactions that they form after they enter the body. Hemoglobin is a functionally important protein that can form multiple interactions with soluble compounds present in the blood, and hence forms an important aspect of the toxicological or safety profile of the dyes. Here we study the interaction between bovine hemoglobin and organic dyes using UV-Vis absorbance and fluorescence spectroscopy. Molecular modeling was used to visualize the binding site and partners of the dye molecules, within the hemoglobin molecule. We find that all four dyes studied form sufficiently strong interactions with hemoglobin to allow for the formation of potentially toxic interactions. Molecular modeling showed that all four dyes bind within the central cavity of the hemoglobin molecule. However, binding partners could not be identified as multiple binding conformations with very similar energies were possible for each dye. PMID:28119912

  14. A study of the Interaction of bovine Hemoglobin with Synthetic dyes using Spectroscopic techniques and Molecular docking

    NASA Astrophysics Data System (ADS)

    Kamaljeet; Bansal, Saurabh; SenGupta, Uttara

    2016-12-01

    Synthetic dyes are a very efficient class of dyes that are ingested or come into contact with the skin from numerous sources (cosmetics, textiles, leather, paper, drugs). An important component of their safety profile is the interactions that they form after they enter the body. Hemoglobin is a functionally important protein that can form multiple interactions with soluble compounds present in the blood, and hence forms an important aspect of the toxicological or safety profile of the dyes. Here we study the interaction between bovine haemoglobin and organic dyes using UV-Vis absorbance and fluorescence spectroscopy. Molecular modelling was used to visualise the binding site and partners of the dye molecules, within the hemoglobin molecule. We find that all four dyes studied form sufficiently strong interactions with haemoglobin to allow for the formation of potentially toxic interactions. Molecular modelling showed that all 4 dyes bound within the central cavity of the haemoglobin molecule. However, binding partners could not be identified as multiple binding conformations with very similar energies were possible for each dye.

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

    PubMed

    Świsłocka, Renata; Piekut, Jolanta; Lewandowski, Włodzimierz

    2013-01-01

    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 (1)H, (13)C 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. Copyright © 2012 Elsevier B.V. All rights reserved.

  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. 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

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

    2014-06-12

    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.

  18. 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

  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. Multi-spectroscopic and molecular modeling studies of interaction between two different angiotensin I converting enzyme inhibitory peptides from gluten hydrolysate and human serum albumin.

    PubMed

    Assaran Darban, Reza; Shareghi, Behzad; Asoodeh, Ahmad; Chamani, Jamshidkhan

    2016-12-26

    The present study was carried out to characterize Angiotensin-converting enzyme (ACE) inhibitory peptides which are released from the trypsin hydrolysate of wheat gluten protein. The binding of two inhibitory peptide (P4 and P6) to human serum albumin (HSA) under physiological conditions has been investigated by multi-spectroscopic in combination with molecular modeling techniques. Time-resolved and quenching fluorescence spectroscopies results revealed that the quenching of HSA fluorescence by P4 and P6 in the binary and ternary systems caused HSA-peptides complexes formation. The results indicated that both peptides quenched the fluorescence intensity of HSA through a static mechanism. The binding affinities and number of binding sites were obtained for the HSA-peptides complexes. The circular dichroism (CD) data revealed that the presence of both peptides increased the α-helix content of HSA and induced the remarkable folding of the polypeptide of the protein. Therefore, the CD data determined that the protein structure has been stabilized in the percent of ACE inhibitory peptides in binary and ternary systems. The binding distances between HSA and both peptides were estimated by the Forster theory, and it was revealed that nonradiative energy transfer from HSA to peptides occurred with a high probability. ITC experiments reveal that, in the absence and presence of P6, the dominant forces are electrostatic in binary and ternary systems. Furthermore, molecular modeling studies confirmed the experimental results. Molecular modeling investigation suggested that P4 bound to the site IA and IIA of HSA in binary and ternary systems, respectively. This study on the interaction of peptides with HSA should prove helpful for realizing the distribution and transportation of food compliments and drugs in vivo, elucidating the action mechanism and dynamics of food compliments and drugs at the molecular level. It should moreover be of great use for understanding the

  1. 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.

  2. Potential charge transfer probe induced conformational changes of model plasma protein human serum albumin: Spectroscopic, molecular docking, and molecular dynamics simulation study.

    PubMed

    Jana, Sankar; Dalapati, Sasanka; Ghosh, Shalini; Guchhait, Nikhil

    2012-10-01

    The nature of binding of specially designed charge transfer (CT) fluorophore at the hydrophobic protein interior of human serum albumin (HSA) has been explored by massive blue-shift (82 nm) of the polarity sensitive probe emission accompanying increase in emission intensity, fluorescence anisotropy, red edge excitation shift, and average fluorescence lifetimes. Thermal unfolding of the intramolecular CT probe bound HSA produces almost opposite spectral changes. The spectral responses of the molecule reveal that it can be used as an extrinsic fluorescent reporter for similar biological systems. Circular dichrosim spectra, molecular docking, and molecular dynamics simulation studies scrutinize this binding process and stability of the protein probe complex more closely.

  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.

  4. Molecular binding of toxic phenothiazinium derivatives, azures to bovine serum albumin: A comparative spectroscopic, calorimetric, and in silico study.

    PubMed

    Das, Somnath; Islam, Md Maidul; Jana, Gopal Chandra; Patra, Anirudha; Jha, Pradeep K; Hossain, Maidul

    2017-07-01

    In this paper, the comparative binding behavior of antimalarial drug azure A, azure B and azure C with bovine serum albumin (BSA) has been studied. The interaction has been confirmed by multispectroscopic (UV, fluorescence, Fourier transform infrared (FT-IR), and circular dichroism) and molecular docking techniques. The experimental results show that azure B has the highest BSA binding affinity followed by azure A and azure C. The experimental evidence of binding showed a static quenching mechanism in the interaction azures with BSA. The isothermal titration calorimetry result reveals that the binding was exothermic with positive entropy contribution in each case. The thermodynamic parameters ΔH, ΔG, and ΔS at 25°C were calculated, which indicates that the weak van der Waals forces and hydrogen bonding rather than the hydrophobic effect played an important role in the interaction. According to the theory of Förster nonradiative energy transfer, the distance (r) between the donor (BSA) and acceptor azures found to be <7 nm in all the case. The circular dichroism and FT-IR studies show that the content of α-helix structure has increased for the azures-BSA system. Overall, experimental studies characterize the interaction dynamics and energetics of the binding of three toxic analogs towards the physiologically relevant serum albumins. We hope, the outcome of this work will be most helpful for synthesizing a new type of phenothiazinium derivatives of the better therapeutic application. Copyright © 2017 John Wiley & Sons, Ltd.

  5. 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.

  6. 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.

  7. Spectroscopic, molecular docking and structural activity studies of (E)-N‧-(substituted benzylidene/methylene) isonicotinohydrazide derivatives for DNA binding and their biological screening

    NASA Astrophysics Data System (ADS)

    Arshad, Nasima; Perveen, Fouzia; Saeed, Aamer; Channar, Pervaiz Ali; Farooqi, Shahid Iqbal; Larik, Fayaz Ali; Ismail, Hammad; Mirza, Bushra

    2017-07-01

    Acid catalyzed condensation of isoniazid with a number of suitably substituted aromatic and heterocyclic aldehydes was carried out in dry ethanol to afford the title (E)-N‧-(substituted benzylidene/methylene) isonicotinohydrazides (SF 1 - SF 4) in good yields. These compounds were characterized and further investigated for their binding with ds.DNA using UV- spectroscopy and molecular docking and for antitumor and antimicrobial potentials. A good correlation was found among spectroscopic, theoretical and biological results. UV- spectra in the presence of DNA concentrations and their data interpretation in terms binding constant ;Kb; and free energy change (ΔG) provided evidences for the significant and spontaneous binding of the compounds with DNA. Molecular docking studies and structural analysis further supported the UV-findings and indicated that the modes of interactions between bromo- (SF 1) and flouro- (SF 4) substituted isonicotinohydrazides is intercalation while methoxy- (SF 2) and hydroxy- (SF 3) substituted isonicotinohydrazides interact with DNA helix via groove binding. SF 1 exhibited comparatively higher Kb value (UV-; 8.07 × 103 M-1, docking; 8.11 × 103 M-1) which inferred that the respective compound muddles to DNA most powerfully. SF 1 has shown the lowest IC50 (345.3 μg/mL) value among all the compounds indicating its comparatively highest activity towards tumor inhibition. None of the compound has shown perceptible antibacterial and antifungal activities.

  8. 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.

  9. Binding modes of environmental endocrine disruptors to human serum albumin: insights from STD-NMR, ITC, spectroscopic and molecular docking studies.

    PubMed

    Yang, Hongqin; Huang, Yanmei; Liu, Jiuyang; Tang, Peixiao; Sun, Qiaomei; Xiong, Xinnuo; Tang, Bin; He, Jiawei; Li, Hui

    2017-09-11

    Given that bisphenols have an endocrine-disrupting effect on human bodies, thoroughly exposing their potential effects at the molecular level is important. Saturation transfer difference (STD) NMR-based binding studies were performed to investigate the binding potential of two bisphenol representatives, namely, bisphenol B (BPB) and bisphenol E (BPE), toward human serum albumin (HSA). The relative STD (%) suggested that BPB and BPE show similar binding modes and orientations, in which the phenolic rings were spatially close to HSA binding site. ITC analysis results showed that BPB and BPE were bound to HSA with moderately strong binding affinity through electrostatic interactions and hydrogen bonds. The order of binding affinity of HSA for two test bisphenols is as follows: BPE > BPB. The results of fluorescence competitive experiments using 5-dimethylaminonaphthalene-1-sulfonamide and dansylsarcosine as competitors, combined with molecular docking indicated that both bisphenols are prone to attach to the binding site II in HSA. Spectroscopic results (FT-IR, CD, synchronous and 3D fluorescence spectra) showed that BPB/BPE induces different degrees of microenvironmental and conformational changes to HSA.

  10. 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.

  11. 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.

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

    PubMed

    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 ((1)H, (13)C, and (119)Sn 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.

  13. 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

  14. Biophysical study on the interaction between eperisone hydrochloride and human serum albumin using spectroscopic, calorimetric, and molecular docking analysis.

    PubMed

    Rabbani, Gulam; Baig, Mohammad Hassan; Lee, Eun Ju; Cho, Won Kyung; Ma, Jin Yeul; Choi, Inho

    2017-04-05

    Eperisone hydrochloride (EH) is a widely used as a muscle relaxant for patients with muscular contracture, low back pain, or spasticity. Human serum albumin (HSA), a highly soluble negatively charged, endogenous and abundant plasma protein ascribed with the ligand binding and transport properties. The current study was undertaken to explore the interaction between EH and the serum transport protein, HSA. Study of the interaction between HSA and EH was carried by UV-vis, fluorescence quenching, circular dichroism (CD) spectroscopy, FRET, and ITC. Tryptophan fluorescence intensity of HSA was strongly quenched by EH. The binding constants (Kb) were obtained by fluorescence quenching and results shows that the EH-HSA interaction revealed a static mode of quenching, with binding constant Kb ~104 reflecting high affinity of EH for HSA. The negative ΔGº value for binding indicated that HSA-EH interaction is a spontaneous process. Thermodynamic analysis shows HSA-EH complex formation occurs primarily due to hydrophobic interactions and hydrogen bonds were facilitate the binding of EH. EH binding induces α-helix of HSA as obtained by far-UV CD and FTIR spectroscopy. In addition, the distance between EH (acceptor) and Trp residue of HSA (donor) was calculated 2.18 nm using Förster's resonance energy transfer theory. Furthermore, molecular docking results revealed EH binds with HSA, and binding site is positioned in Sudlow Site I of HSA (subdomain IIA). This work provides a useful experimental strategy for studying the interaction of myorelaxant with HSA, helping to understand the activity and mechanism of drug binding.

  15. Structural, spectroscopic and molecular docking studies on 2-amino-3-chloro-5-trifluoromethyl pyridine: A potential bioactive agent.

    PubMed

    Mohamed Asath, R; Premkumar, R; Mathavan, T; Milton Franklin Benial, A

    2017-03-15

    The most stable, optimized structure of the 2-amino-3-chloro-5-trifluoromethyl pyridine (ACTP) molecule was predicted by the density functional theory calculations using the B3LYP method with cc-pVQZ basis set. Antitumor activity of the ACTP molecule was evaluated by molecular docking analysis. The structural parameters and vibrational wavenumbers were calculated for the optimized molecular structure. The experimental and theoretical vibrational wavenumbers were assigned and compared. Ultraviolet-visible spectrum was simulated and validated experimentally. The molecular electrostatic potential surface was simulated. Frontier molecular orbitals and related molecular properties were computed and further density of states spectrum was simulated. The natural bond orbital analysis was also performed to confirm the bioactivity of the ACTP molecule. The molecular docking analysis reveals the better inhibitory nature of the ACTP molecule against the colony-stimulating factor 1 (CSF1) gene which causes tenosynovial giant-cell tumor. Hence, the ACTP molecule can act as a potential inhibitor against tenosynovial giant-cell tumor.

  16. Structural, spectroscopic and molecular docking studies on 2-amino-3-chloro-5-trifluoromethyl pyridine: A potential bioactive agent

    NASA Astrophysics Data System (ADS)

    Mohamed Asath, R.; Premkumar, R.; Mathavan, T.; Milton Franklin Benial, A.

    2017-03-01

    The most stable, optimized structure of the 2-amino-3-chloro-5-trifluoromethyl pyridine (ACTP) molecule was predicted by the density functional theory calculations using the B3LYP method with cc-pVQZ basis set. Antitumor activity of the ACTP molecule was evaluated by molecular docking analysis. The structural parameters and vibrational wavenumbers were calculated for the optimized molecular structure. The experimental and theoretical vibrational wavenumbers were assigned and compared. Ultraviolet-visible spectrum was simulated and validated experimentally. The molecular electrostatic potential surface was simulated. Frontier molecular orbitals and related molecular properties were computed and further density of states spectrum was simulated. The natural bond orbital analysis was also performed to confirm the bioactivity of the ACTP molecule. The molecular docking analysis reveals the better inhibitory nature of the ACTP molecule against the colony-stimulating factor 1 (CSF1) gene which causes tenosynovial giant-cell tumor. Hence, the ACTP molecule can act as a potential inhibitor against tenosynovial giant-cell tumor.

  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.

  18. Synthesis, spectroscopic, structural and optical studies of Ru2S3 nanoparticles prepared from single-source molecular precursors

    NASA Astrophysics Data System (ADS)

    Mbese, Johannes Z.; Ajibade, Peter A.

    2017-09-01

    Homonuclear tris-dithiocarbamato ruthenium(III) complexes, [Ru(S2CNR2)3] were prepared and characterized by spectroscopic techniques and thermogravimetric analyses. The thermogravimetric analyses (TGA) of the ruthenium complexes showed that the complexes decompose to ruthenium(III) sulfide nanoparticles. The ruthenium(III) complexes were dispersed in oleic acid and thermolysed in hexadecylamine to prepared oleic acid/hexadecylamine capped Ru2S3 nanoparticles. FTIR revealed that Ru2S3 nanoparticles are capped through the interaction of the -NH2 group of hexadecylamine HDA adsorbed on the surfaces of nanoparticles and it also showed that oleic acid (OA) is acting as both coordinating stabilizing surfactant and capping agent. EDS spectra revealed that the prepared nanoparticles are mainly composed of Ru and S, confirming the formation of Ru2S3 nanoparticles. Powder XRD confirms that the nanoparticles are in cubic phase. The inner morphology of nanoparticles obtained from transmission electron microscopy (TEM) showed nanoparticles with narrow particle size distributions characterized by an average diameter of 8.45 nm with a standard deviation of 1.6 nm. The optical band gap (Eg) determined from Tauc plot are in the range 3.44-4.18 eV.

  19. In vitro study on binding interaction of quinapril with bovine serum albumin (BSA) using multi-spectroscopic and molecular docking methods.

    PubMed

    Shi, Jie-Hua; Pan, Dong-Qi; Jiang, Min; Liu, Ting-Ting; Wang, Qi

    2016-08-07

    The binding interaction between quinapril (QNPL) and bovine serum albumin (BSA) in vitro has been investigated using UV absorption spectroscopy, steady-state fluorescence spectroscopic, synchronous fluorescence spectroscopy, 3D fluorescence spectroscopy, Fourier transform infrared spectroscopy, circular dichroism, and molecular docking methods for obtaining the binding information of QNPL with BSA. The experimental results confirm that the quenching mechanism of the intrinsic fluorescence of BSA induced by QNPL is static quenching based on the decrease in the quenching constants of BSA in the presence of QNPL with the increase in temperature and the quenching rates of BSA larger than 10(10) L mol(-1) s(-1), indicating forming QNPL-BSA complex through the intermolecular binding interaction. The binding constant for the QNPL-BSA complex is in the order of 10(5) M(-1), indicating there is stronger binding interaction of QNPL with BSA. The analysis of thermodynamic parameters together with molecular docking study reveal that the main binding forces in the binding process of QNPL with BSA are van der Waal's forces and hydrogen bonding interaction. And, the binding interaction of BSA with QNPL is an enthalpy-driven process. Based on Förster resonance energy transfer, the binding distance between QNPL and BSA is calculated to be 2.76 nm. The results of the competitive binding experiments and molecular docking confirm that QNPL binds to sub-domain IIA (site I) of BSA. It is confirmed there is a slight change in the conformation of BSA after binding QNPL, but BSA still retains its secondary structure α-helicity.

  20. Molecular, spectroscopic and thermal studies on catechol, 4,5-dibromocatechol, resorcinol, hydroquinone and 4-4‧-dihydroxybiphenyl derivatives armed with benzothiazole moieties

    NASA Astrophysics Data System (ADS)

    Alshargabi, Arwa; Yeap, Guan-Yeow; Mahmood, Wan Ahmad Kamil; Samikannu, Rakesh

    2013-05-01

    A new series of catechol, 4,5-dibromocatechol, resorcinol, hydroquinone and 4-4'-dihydroxybiphenyl derivatives possessing two benzothiazole moieties at respective positions of 1,2, 1,3, 1,4 and/or 4,4' has successfully been synthesized. The molecular structures were fully elucidated by spectroscopic techniques (1H NMR, 13C NMR and two dimensional COSY, HMBC, HMQC, DEPT-135 and DEPT-90). The connectivity study between the cause of using different core systems in the target compounds and the anisotropic behavior as inferred from phase transition temperature and relevant morphology studies has led to some unique features arising from this series. Compounds with ortho substituent exhibit enantiotropic N and SmA phases. The analogues containing resorcinol and 4,4'-disubstituentbiphenyl show enanotiotropic nematic behavior while the hydroquinone derivative induces the formation of monotropic nematogen. An extensive study to further substantiate the relationship between the stability of the nematic phase and associated transition temperatures due to different core systems is also reported.

  1. Molecular structure, experimental and theoretical spectroscopic characterization and non-linear optical properties studies of a new non-centrosymmetric hybrid material

    NASA Astrophysics Data System (ADS)

    Chihaoui, Nejla; Hamdi, Besma; Dammak, Thameur; Zouari, Ridha

    2016-11-01

    This paper gathers the synthesis and study of a novel nonlinear organic-inorganic (1,2-diammoniumcyclohexane tetrabromozincate (II) monohydrate; [C6H10(NH3)2]ZnBr4·H2O) hybrid. The newly developed hybrid was characterized by XRD and spectroscopic (FT-IR, Raman, UV-Visible and CP/MAS-NMR) studies. All theoretical calculations and structural optimization parameters were conducted by using DFT approach with B3LYP/6-31G(d) basis set and the vibrational wavenumbers were evaluated for the affectation of [C6H10(NH3)2]ZnBr4·H2O compound by using transferable scale factor. The inspection of intermolecular links in the studied framework has been executed by the Hirshfeld surface analysis. The nonlinear optical characteristics of this compound were theoretically explored also the molecular orbitals (HOMO) and (LUMO) properties are performed to describe the charge transfer within the crystal.

  2. Study on spectroscopic parameters and molecular constants of HC1(X1Σ+) molecule by using multireference configuration interaction approach

    NASA Astrophysics Data System (ADS)

    Zhang, Xiao-Niu; Shi, De-Heng; Zhang, Jin-Ping; Zhu, Zun-Lüe; Sun, Jin-Feng

    2010-05-01

    Equilibrium internuclear separations, harmonic frequencies and potential energy curves (PECs) of HC1(X1Σ+) molecule are investigated by using the highly accurate valence internally contracted multireference configuration interaction (MRCI) approach in combination with a series of correlation-consistent basis sets in the valence range. The PECs are all fitted to the Murrell-Sorbie function, and they are used to accurately derive the spectroscopic parameters (De, D0, ωeχe, αe and Be). Compared with the available measurements, the PEC obtained at the basis set, aug-cc-pV5Z, is selected to investigate the vibrational manifolds. The constants D0, De, Re, ωe, ωeχe, αe and Be at this basis set are 4.4006 eV, 4.5845 eV, 0.12757 nm, 2993.33 cm-1, 52.6273 cm-1, 0.2981 cm-1 and 10.5841 cm-1, respectively, which almost perfectly conform to the available experimental results. With the potential determined at the MRCI/aug-cc-pV5Z level of theory, by numerically solving the radial Schrödinger equation of nuclear motion in the adiabatic approximation, a total of 21 vibrational levels are predicted. Complete vibrational levels, classical turning points, inertial rotation and centrifugal distortion constants are reproduced, which are in excellent agreement with the available Rydberg-Klein-Rees data. Most of these theoretical vibrational manifolds are reported for the first time to the best of our knowledge.

  3. Synthesis, spectroscopic studies, DFT calculations, electrochemical evaluation, BSA binding and molecular docking of an aroylhydrazone -based cis-dioxido Mo(VI) complex

    NASA Astrophysics Data System (ADS)

    Mohamadi, Maryam; Faghih-Mirzaei, Ehsan; Ebrahimipour, S. Yousef; Sheikhshoaie, Iran; Haase, Wolfgang; Foro, Sabine

    2017-07-01

    A cis-dioxido Mo(VI) complex, [MoO2(L)(MeOH)], [L2-: (3-methoxy-2-oxidobenzylidene) benzohydrazonate], has been synthesized and characterized using physicochemical and spectroscopic techniques including elemental analysis, FT-IR, 1HNMR, UV-Vis spectroscopy, molar conductivity and single crystal X-ray diffraction. DFT calculations in the ground state of the complex were carried out using hybrid functional B3LYP with DGDZVP as basis set. Non-linear optical properties including electric dipole moment (μ), polarizability (α) and molecular first hyperpolarizability (β) of the compound were also computed. The values of linear polarizability and first hyperpolarizability obtained for the studied molecule indicated that the compound could be a good candidate of nonlinear optical materials. TD-DFT calculation and molecular electrostatic potential (MEP) were also performed. The thermodynamic properties (heat capacity, entropy, and enthalpy) of the complex at different temperatures have been calculated. The interaction of a synthesized complex, with bovine serum albumin was also thoroughly investigated using experimental and theoretical studies. UV-Vis absorption and fluorescence quenching techniques were used to determine the binding parameters as well as the mechanism of the interaction. The values of binding constants were in the range of 104-105 M-1 demonstrating a moderate interaction between the synthesized complex and BSA making the protein suitable for transportation and delivery of the compound. Thermodynamic parameters were also indicating a binding through van der Waals force or hydrogen bond of [MoO2(L)(MeOH)] to BSA. The results obtained from docking studies were consistent to those obtained from experimental studies.

  4. Spectroscopic, DFT, molecular dynamics and molecular docking study of 1-butyl-2-(4-hydroxyphenyl)-4,5-dimethyl-imidazole 3-oxide

    NASA Astrophysics Data System (ADS)

    Benzon, K. B.; Mary, Y. Sheena; Varghese, Hema Tresa; Panicker, C. Yohannan; Armaković, Stevan; Armaković, Sanja J.; Pradhan, Kiran; Nanda, Ashis Kumar; Van Alsenoy, C.

    2017-04-01

    FT-IR and FT-Raman spectrum of 1-butyl-2-(4-hydroxyphenyl)-4,5-dimethyl-imidazole 3-oxide were recorded and theoretical study has been made using Gaussian09 software package. DFT/B3LYP calculations have been done using 6-311++G (d, p) (5D, 7F) basis sets to investigate the vibrational frequencies and geometrical parameters. The assignments of the normal modes are done by potential energy distribution (PED) calculations. First and second hyperpolarizabilities are calculated in order to find its role in non-linear optics. The stability of the molecule arising from hyper-conjugative interaction and charge delocalization has been analyzed using NBO analysis. Molecular Electrostatic Potential was calculated by the DFT method and predicts the most reactive part in the molecule. The calculated NMR values are in good agreement with experimental data. Reactive sites of the title molecule have been determined by calculations of average local ionization surfaces and Fukui functions. Analyzing electron density between atoms, intra-molecular non-covalent interactions have been determined. Possible locations prone to autoxidation and locations where degradation could start have been determined by calculation of bond dissociation energies for all single acyclic bonds. Atoms with pronounced interactions with water molecules have been located by calculations of radial distribution functions, obtained after molecular dynamics simulations. The docked title compound forms a stable complex with CDK inhibitor and gives a binding affinity value of -6.3 kcal/mol and the results suggest that the compound might exhibit inhibitory activity against CDK inhibitor.

  5. 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.

  6. 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.

  7. Computational and spectroscopic studies of a new Schiff base 3-hydroxy-4-methoxybenzylidene(2-hydroxyphenyl)amine and molecular structure of its corresponding zwitterionic form.

    PubMed

    Habibi, Mohammad Hossein; Shojaee, Elahe; Ranjbar, Mahnaz; Memarian, Hamid Reza; Kanayama, Akihiko; Suzuki, Takayoshi

    2013-03-15

    Computational and spectroscopic properties of a novel Schiff base compound, 3-hydroxy-4-methoxybenzylidene(2-hydroxyphenyl)amine were studied. The crystal structures of the title compound and its corresponding zwitterionic form were analyzed by X-ray diffraction. The presence of N-H, C-O and C=N stretching vibrations in IR spectrum strongly suggest that the title compound has zwitterionic form in the solid state. Molecular geometry of the title compound in the ground state has been calculated using the density functional method (DFT) at B3LYP 6-31++G(d,p) basis set and was compared with the experimental data. The calculated results of the title compound show that the optimized geometry can well reproduce the crystal structure. The molecule shows absorption bands at 345 and 363 nm in EtOH. The shoulder-shaped bands at 415 nm can be assigned to n→π(*) transitions. The absorption band is observed at 285 nm in EtOH corresponds to the π→π(*) transitions.

  8. 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.

  9. 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.

  10. Matrix isolation spectroscopic and theoretical study of water adsorption and hydrolysis on molecular tantalum and niobium oxides.

    PubMed

    Zhou, Mingfei; Zhuang, Jia; Wang, Guanjun; Chen, Mohua

    2011-03-24

    The reactions of molecular tantalum and niobium monoxides and dioxides with water were investigated by matrix isolation infrared spectroscopy. In solid neon, the metal monoxide and dioxide molecules reacted with water to form the MO(H(2)O) and MO(2)(H(2)O) (M = Ta, Nb) complexes spontaneously on annealing. The MO(H(2)O) complexes photochemically rearranged to the more stable HMO(OH) isomers via one hydrogen atom transfer from water to the metal center under visible light excitation. In contrast, the MO(2)(H(2)O) complexes isomerized to the more stable MO(OH)(2) molecules via a hydrogen atom transfer from water to one of the oxygen atoms of metal dioxide upon visible light irradiation. The aforementioned species were identified by isotopic-substituted experiments as well as density functional calculations.

  11. 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.

  12. Use of spectroscopic, zeta potential and molecular dynamic techniques to study the interaction between human holo-transferrin and two antagonist drugs: comparison of binary and ternary systems.

    PubMed

    Kabiri, Mona; Amiri-Tehranizadeh, Zeinab; Baratian, Ali; Saberi, Mohammad Reza; Chamani, Jamshidkhan

    2012-03-12

    For the first time, the binding of ropinirole hydrochloride (ROP) and aspirin (ASA) to human holo-transferrin (hTf) has been investigated by spectroscopic approaches (fluorescence quenching, synchronous fluorescence, time-resolved fluorescence, three-dimensional fluorescence, UV-vis absorption, circular dichroism, resonance light scattering), as well as zeta potential and molecular modeling techniques, under simulated physiological conditions. Fluorescence analysis was used to estimate the effect of the ROP and ASA drugs on the fluorescence of hTf as well as to define the binding and quenching properties of binary and ternary complexes. The synchronized fluorescence and three-dimensional fluorescence spectra demonstrated some micro-environmental and conformational changes around the Trp and Tyr residues with a faint red shift. Thermodynamic analysis displayed the van der Waals forces and hydrogen bonds interactions are the major acting forces in stabilizing the complexes. Steady-state and time-resolved fluorescence data revealed that the fluorescence quenching of complexes are static mechanism. The effect of the drugs aggregating on the hTf resulted in an enhancement of the resonance light scattering (RLS) intensity. The average binding distance between were computed according to the forster non-radiation energy transfer theory. The circular dichroism (CD) spectral examinations indicated that the binding of the drugs induced a conformational change of hTf. Measurements of the zeta potential indicated that the combination of electrostatic and hydrophobic interactions between ROP, ASA and hTf formed micelle-like clusters. The molecular modeling confirmed the experimental results. This study is expected to provide important insight into the interaction of hTf with ROP and ASA to use in various toxicological and therapeutic processes.

  13. 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.

  14. 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.

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

    PubMed

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

    2014-01-24

    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. Theinfluence ofsodium 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. (1)H and (13)C 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.

  16. Synthesis of two new silver(I) complexes with 3-bromoquinoline: Molecular structure, spectroscopic characterizations and DFT studies.

    PubMed

    Soliman, Saied M; Abu-Youssef, Morsy A M; Kassem, Taher S; Assem, Rania

    2015-01-01

    Two new Ag(+) complexes with 3-bromoquinoline (3BrQ) have been synthesized and characterized using elemental analysis, FTIR, NMR and mass spectra. The studied complexes have the formula [Ag(3BrQ)(OAC)]; 1 and [Ag(3BrQ)3(TCA)]; 2 where OAC and TCA are acetate and trichloroacetate, respectively. Based on the DFT calculations, 1 and 2 showed distorted trigonal planar and distorted tetrahedral coordination geometry. The electronic properties such as dipole moment (μ), polarizability (α0), HOMO and LUMO energies are calculated using the same level of theory. These electronic parameters were used to predict the nonlinear optical properties of the studied compounds. The studied silver complexes were predicted to be better nonlinear optical materials than urea. The electronic spectra of these complexes are calculated using the TD-DFT calculations. The infrared vibrational spectra were assigned based on the potential energy distribution (PED) analysis. The calculated (1)H NMR chemical shift values using GIAO approach showed good agreement with the experimental data. The intramolecular charge transfer interactions of the title molecules were studied by natural bond orbital (NBO) analysis. Copyright © 2015 Elsevier B.V. All rights reserved.

  17. 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.

  18. Molecular imaging true-colour spectroscopic optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Robles, Francisco E.; Wilson, Christy; Grant, Gerald; Wax, Adam

    2011-12-01

    Molecular imaging holds a pivotal role in medicine due to its ability to provide invaluable insight into disease mechanisms at molecular and cellular levels. To this end, various techniques have been developed for molecular imaging, each with its own advantages and disadvantages. For example, fluorescence imaging achieves micrometre-scale resolution, but has low penetration depths and is mostly limited to exogenous agents. Here, we demonstrate molecular imaging of endogenous and exogenous chromophores using a novel form of spectroscopic optical coherence tomography. Our approach consists of using a wide spectral bandwidth laser source centred in the visible spectrum, thereby allowing facile assessment of haemoglobin oxygen levels, providing contrast from readily available absorbers, and enabling true-colour representation of samples. This approach provides high spectral fidelity while imaging at the micrometre scale in three dimensions. Molecular imaging true-colour spectroscopic optical coherence tomography (METRiCS OCT) has significant implications for many biomedical applications including ophthalmology, early cancer detection, and understanding fundamental disease mechanisms such as hypoxia and angiogenesis.

  19. 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.

  20. High temperature furnace system for vacuum ultraviolet spectroscopic studies.

    PubMed

    Brown, C M; Naber, R H; Tilford, S G; Ginter, M L

    1973-08-01

    An improved furnace system for use in vacuum ultraviolet spectroscopic studies of atomic and molecular species stable at high temperatures (800-2500 degrees C) is described in detail. A new and improved high resolution spectrum of Mg I and several impurity spectra produced in the furnace are presented.

  1. 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.

  2. Synthesis, crystal structure, Hirshfeld surface analysis, spectroscopic characterization, reactivity study by DFT and MD approaches and molecular docking study of a novel chalcone derivative

    NASA Astrophysics Data System (ADS)

    Arshad, Suhana; Pillai, Renjith Raveendran; Zainuri, Dian Alwani; Khalib, Nuridayanti Che; Razak, Ibrahim Abdul; Armaković, Stevan; Armaković, Sanja J.; Panicker, C. Yohannan; Van Alsenoy, C.

    2017-05-01

    In the present study, the title compound named as (E)-1-(4-bromophenyl)-3-(4-(trifluoromethyl)phenyl)prop-2-en-1-one was synthesized and structurally characterized by single-crystal X-ray diffraction. The compound crystallizes in monoclinic crystal system in P21/c space group, unit cell parameters a = 16.7629 (12) Å, b = 13.9681 (10) Å, c = 5.8740 (4) Å, β = 96.3860 (12)° and Z = 4. Hirshfeld surface analysis revealed that the molecular structure is dominated by H⋯H, C⋯H/H⋯C, Br⋯F/F⋯Br and F⋯F contacts. The FT-IR spectrum was recorded and interpreted in details with the aid of Density Functional Theory (DFT) calculations and Potential Energy Distribution (PED) analysis. Average local ionization energies (ALIE) and Fukui functions have been used as quantum-molecular descriptors to locate the molecule sites that could be of importance from the aspect of reactivity. Degradation properties have been assessed by calculations of bond dissociation energies (BDE) for hydrogen abstraction and the rest of the single acyclic bonds, while molecular dynamics (MD) simulations were used in order to calculate radial distribution functions and determine the atoms with significant interactions with water. In order to understand how the title molecule inhibits and hence increases the catalytic efficiency of MOA-B enzyme, molecular docking study was performed.

  3. 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.

  4. Binding site identification of metformin to human serum albumin and glycated human serum albumin by spectroscopic and molecular modeling techniques: a comparison study.

    PubMed

    Rahnama, Elaheh; Mahmoodian-Moghaddam, Maryam; Khorsand-Ahmadi, Sabra; Saberi, Mohammad Reza; Chamani, Jamshidkhan

    2015-01-01

    The interaction between metformin and human serum albumin (HSA), as well as its glycated form (gHSA) was investigated by multiple spectroscopic techniques, zeta potential, and molecular modeling under physiological conditions. The steady state and time-resolved fluorescence data displayed the quenching mechanism of HSA-metformin and gHSA-metformin was static. The binding information, including the binding constants, number of binding sites, effective quenching constant showed that the binding affinity of metformin to HSA was greater than to gHSA which also confirmed by anisotropy measurements. It was determined that metformin had two and one set of binding sites on HSA and gHSA, respectively. Far-UV CD spectra of proteins demonstrated that the α-helical content decreased with increasing metformin concentration. The zeta potential and resonance light scattering (RLS) diagrams provided that lower drug concentration induced metformin aggregation on gHSA surface as compare to HSA. The increase in polarizability was one of the important factors for the enhancement of RLS and the formation of drug/protein complexes. The zeta potential results suggested that both hydrophobic and electrostatic interactions played important roles in the protein-metformin complex formation. Site marker experiments and molecular modeling showed that the metformin bound to subdomain IIIA (Sudlow's site II) on HSA and gHSA.

  5. Vibrational spectroscopic investigations, molecular dynamic simulations and molecular docking studies of N‧-diphenylmethylidene-5-methyl-1H-pyrazole-3-carbohydrazide

    NASA Astrophysics Data System (ADS)

    Pillai, Renjith Raveendran; Menon, Vidya V.; Mary, Y. Shyma; Armaković, Stevan; Armaković, Sanja J.; Panicker, C. Yohannan

    2017-02-01

    FT-IR and FT-Raman spectra of N‧-diphenylmethylidene-5-methyl-1H-pyrazole-3-carbohydrazide were recorded and analyzed. Due to the industrial and biological importance of pyrazole derivatives, we have carried out an extensive quantum chemical study on N‧-diphenylmethylidene-5-methyl-1H-pyrazole-3-carbohydrazide. The theoretical ground state geometry and electronic structure of the title molecule were optimized by DFT/B3LYP/6-311G++(d,p) method and compared with those of the crystal data. The wave numbers obtained are assigned by potential energy distribution. The ring breathing modes of the benzene rings are assigned theoretically at 1009 cm-1 for the mono substituted phenyl rings. The first order hyperpolarizability is comparable with that of similar derivatives and 16 times that of the standard NLO material urea. Conformational analysis was conducted in order to locate all possible conformations of the title compound, followed by investigation of local reactivity properties by MEP and ALIE surfaces. Natural bond orbital analysis has been carried out to analyse the stability of the molecule arising from hyper-conjugative interactions and charge delocalization. Further, reactive properties via autoxidation and hydrolysis mechanisms have been assessed through calculations of bond dissociation energies and radial distribution functions. Docking results confirmed that the compound was a potential inhibitor of CDK2s and were in agreement with the previous reported studies.

  6. 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."

  7. 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.

  8. Study on molecular structure, spectroscopic properties (FTIR and UV-Vis), NBO, QTAIM, HOMO-LUMO energies and docking studies of 5-fluorouracil, a substance used to treat cancer.

    PubMed

    Almeida, Michell O; Barros, Daiane A S; Araujo, Sheila C; Faria, Sergio H D M; Maltarollo, Vinicius G; Honorio, Kathia M

    2017-09-05

    Cancer cells can expand to other parts of body through blood system and nodes from a mechanism known as metastasis. Due to the large annual growth of cancer cases, various biological targets have been studied and related to this disorder. A very interesting target related to cancer is human epidermal growth factor receptor 2 (HER2). In this study, we analyzed the main intermolecular interactions between a drug used in the cancer treatment (5-fluorouracil) and HER2. Molecular modeling methods were also employed to assess the molecular structure, spectroscopic properties (FTIR and UV-Vis), NBO, QTAIM and HOMO-LUMO energies of 5-FU. From the docking simulations it was possible to analyze the interactions that occur between some residues in the binding site of HER2 and 5-FU. To validate the choice of basis set that was used in the NBO and QTAIM analyses, theoretical calculations were performed to obtain FT-IR and UV/Vis spectra, and the theoretical results are consistent with the experimental data, showing that the basis set chosen is suitable. For the maximum λ from the theoretical calculation (254.89nm) of UV/Vis, the electronic transition from HOMO to LUMO occurs at 4.89eV. From NBO analyses, we observed interactions between Asp863 and 5-FU, i.e. the orbitals with high transfer of electrons are LP O15 (donor NBO) and BD* (π) N1-H10 (acceptor NBO), being that the value of this interaction is 7.72kcal/mol. Results from QTAIM indicate one main intermolecular H bond, which is necessary to stabilize the complex formed between the ligands and the biological target. Therefore, this study allowed a careful evaluation on the main structural, spectroscopic and electronic properties involved in the interaction between 5-FU and HER2, an important biological complex related to the cancer treatment. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. Study on molecular structure, spectroscopic properties (FTIR and UV-Vis), NBO, QTAIM, HOMO-LUMO energies and docking studies of 5-fluorouracil, a substance used to treat cancer

    NASA Astrophysics Data System (ADS)

    Almeida, Michell O.; Barros, Daiane A. S.; Araujo, Sheila C.; Faria, Sergio H. D. M.; Maltarollo, Vinicius G.; Honorio, Kathia M.

    2017-09-01

    Cancer cells can expand to other parts of body through blood system and nodes from a mechanism known as metastasis. Due to the large annual growth of cancer cases, various biological targets have been studied and related to this disorder. A very interesting target related to cancer is human epidermal growth factor receptor 2 (HER2). In this study, we analyzed the main intermolecular interactions between a drug used in the cancer treatment (5-fluorouracil) and HER2. Molecular modeling methods were also employed to assess the molecular structure, spectroscopic properties (FTIR and UV-Vis), NBO, QTAIM and HOMO-LUMO energies of 5-FU. From the docking simulations it was possible to analyze the interactions that occur between some residues in the binding site of HER2 and 5-FU. To validate the choice of basis set that was used in the NBO and QTAIM analyses, theoretical calculations were performed to obtain FT-IR and UV/Vis spectra, and the theoretical results are consistent with the experimental data, showing that the basis set chosen is suitable. For the maximum λ from the theoretical calculation (254.89 nm) of UV/Vis, the electronic transition from HOMO to LUMO occurs at 4.89 eV. From NBO analyses, we observed interactions between Asp863 and 5-FU, i.e. the orbitals with high transfer of electrons are LP O15 (donor NBO) and BD* (π) N1-H10 (acceptor NBO), being that the value of this interaction is 7.72 kcal/mol. Results from QTAIM indicate one main intermolecular H bond, which is necessary to stabilize the complex formed between the ligands and the biological target. Therefore, this study allowed a careful evaluation on the main structural, spectroscopic and electronic properties involved in the interaction between 5-FU and HER2, an important biological complex related to the cancer treatment.

  10. 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.

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

    PubMed

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

    2014-07-15

    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. Copyright © 2014 Elsevier B.V. All rights reserved.

  12. 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.

  13. 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).

  14. 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).

  15. Comparative study of an osazone based ligand and its palladium(II) complex with human serum albumin: A spectroscopic, thermodynamic and molecular docking approach.

    PubMed

    Bandyopadhyay, Nirmalya; Pradhan, Ankur Bikash; Das, Suman; Naskar, Jnan Prakash

    2017-08-01

    An osazone based ligand, hexane-3,4-dione-bis(2'-phenylhydrazone) (LH2), was synthesized by 1:2M Schiff base condensation of 3,4-hexanedione and phenylhydrazine in dehydrated methanol. Its palladium(II) complex (1) has also been synthesized. LH2 and 1 have thoroughly been characterized by several spectroscopic and analytical means. DFT optimized structure of 1 shows that it is a monomeric Pd(II) complex having 'N2Cl2' coordination chromophore. Our BVS analysis also satisfactorily reproduces the oxidation number of the palladium center. 1 shows irreversible Pd(II)/Pd(I) reduction in its CV in methanol. 1 is three-fold more emissive than LH2. This enhanced emission has also been supported by time correlated single photon counting (TCSPC) measurements at room temperature. Human serum albumin (HSA) binding aspects of both LH2 and 1 have been investigated through various biophysical techniques. The binding constants as determined from Benesi-Hilderbrand plot using the absorbance spectral analyses were found respectively to be 1.18×10(5) and 4.38×10(4)M(-1) for LH2 and 1. The experimental findings confirm that both are good HSA binders. The thermodynamic parameters (∆G°, ∆H° and ∆S°) have also been evaluated by isothermal titration calorimetric (ITC) experiments. These parameters indicate that the binding processes are spontaneous both for LH2 and 1. Molecular docking analyses reveal that both LH2 and 1 reside in domain-I of HSA. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. 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.

  17. 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.

  18. Spectroscopic and molecular docking studies on N,N-di-tert-butoxycarbonyl (Boc)-2-amino pyridine: A potential bioactive agent for lung cancer treatment

    NASA Astrophysics Data System (ADS)

    Mohamed Asath, R.; Premkumar, R.; Mathavan, T.; Milton Franklin Benial, A.

    2017-09-01

    Potential energy surface scan was performed and the most stable molecular structure of the N,N-di-tert-butoxycarbonyl (Boc)-2-amino pyridine (DBAP) molecule was predicted. The most stable molecular structure of the molecule was optimized using B3LYP method with cc-pVTZ basis set. Anticancer activity of the DBAP molecule was evaluated by molecular docking analysis. The structural parameters and vibrational wavenumbers were calculated for the optimized molecular structure. The experimental and theoretical wavenumbers were assigned and compared. Ultraviolet-Visible spectrum was simulated and validated experimentally. The molecular electrostatic potential surface was simulated and Fukui function calculations were also carried out to investigate the reactive nature of the DBAP molecule. The natural bond orbital analysis was also performed to probe the intramolecular interactions and confirm the bioactivity of the DBAP molecule. The molecular docking analysis reveals the better inhibitory nature of the DBAP molecule against the epidermal growth factor receptor (EGFR) protein which causes lung cancer. Hence, the present study unveils the structural and bioactive nature of the title molecule. The DBAP molecule was identified as a potential inhibitor against the lung cancer which may be useful in further development of drug designing in the treatment of lung cancer.

  19. 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

  20. Risk of drug-induced photosensitivity: focus on spectroscopic and molecular characteristics.

    PubMed

    Verdel, B M; Souverein, P C; Meyboom, R H B; Kardaun, S H; Leufkens, H G M; Egberts, A C G

    2009-07-01

    Drug-induced photosensitivity is difficult to predict and remains a challenge for both the dermatological clinical practice and pharmacovigilance. To assess the association between spectroscopic and molecular characteristics and the occurrence of photosensitivity reactions. For 143 well-known photosensitisers (e.g. tetracyclines, diuretics), we retrieved information on spectroscopic and molecular parameters, including: absorption maximum lambda(max), molar absorption coefficient epsilon, area under the absorption curve (AUC), molecular weight and configuration, hetero and aromatic halogen atoms, lipophilicity (log P) and acid/base status (pKa). In the WHO-ADR database, all reports with suspected adverse drug reactions of the study drugs were selected. We identified all reports on photosensitivity reactions and defined them as cases. All other reports were selected as non-cases. A case-non-case approach was performed to assess the spectroscopic and molecular exposure variables as a factor for photosensitivity reactions. Logistic regression was used to calculate odds ratios (OR) with 95% confidence intervals (CI). A lambda(max) between 290 and 320 nm (OR 3.74, 95% CI 3.45-4.06), and an epsilon > 20,000 M(-1) cm(-1) (OR 5.49, 95% CI 5.10-5.92) were highly associated with the reporting of photosensitivity reactions. Risk of the photosensitivity reactions was significantly increased among intermediate or high AUCs compared to low AUC. Low molecular weight and aromatic halogen atoms were associated with photosensitivity reactions (OR 2.37, 95% CI 2.07-2.71 resp. OR 3.37, 95% CI 3.15-3.61) as were log p < 1 and pKa < 7. The reporting of photosensitivity reactions to established phototoxic drug classes is strongly influenced by spectroscopic and physicochemical characteristics of individual drugs. (c) 2009 John Wiley & Sons, Ltd.

  1. 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.

  2. Molecular structure, spectroscopic (FT-IR, FT Raman, UV, NMR and THz) investigation and hyperpolarizability studies of 3-(2-Chloro-6-fluorophenyl)-1-(2-thienyl) prop-2-en-1-one

    NASA Astrophysics Data System (ADS)

    Kumar, Rajesh; Kumar, Amit; Deval, Vipin; Gupta, Archana; Tandon, Poonam; Patil, P. S.; Deshmukh, Prathmesh; Chaturvedi, Deepika; Watve, J. G.

    2017-02-01

    In the present work, a combined experimental and theoretical study on ground state molecular structure, spectroscopic and nonlinear optical properties of the chalcone derivative 3-(2-Chloro-6-fluorophenyl)-1-(2-thienyl) prop-2-en-1-one (2C6F2SC) is reported. Initial geometry generated from single crystal X-ray diffraction parameters was minimized at DFT level employing B3LYP/6-311++G (d,p) without any constraint to the potential energy surface. The molecule has been characterized using various experimental techniques FT-IR, FT-Raman, UV-Vis, 1H NMR, TD-THz and the spectroscopic data have been analyzed theoretically by Density Functional Theory (DFT) method. Harmonic vibrational frequencies were calculated theoretically using the optimized ground state geometry and the spectra were interpreted by means of potential energy distribution. Time Dependent Density Functional Theory (TD-DFT) has been used to calculate energies, absorption wavelengths, oscillator strengths of electronic singlet-singlet transitions. The calculated energy and oscillator strength complement with the experimental findings. The HOMO-LUMO energy gap explains the charge interaction taking place within the molecule. Good correlations between the experimental 1H NMR chemical shifts and calculated GIAO shielding tensors were found. Stability of the molecule, hyperconjugative interactions and charge delocalization has been analyzed by natural bond orbital (NBO) analysis. The first order hyperpolarizability (β) of this molecular system and related properties (μ, <α> and Δα) have been calculated using the finite-field approach.

  3. 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.

  4. Spectroscopic studies of microwave plasmas containing hexamethyldisiloxane

    NASA Astrophysics Data System (ADS)

    Nave, A. S. C.; Mitschker, F.; Awakowicz, P.; Röpcke, J.

    2016-10-01

    Low-pressure microwave discharges containing hexamethyldisiloxane (HMDSO) with admixtures of oxygen and nitrogen, used for the deposition of silicon containing films, have been studied spectroscopically. Optical emission spectroscopy (OES) in the visible spectral range has been combined with infrared laser absorption spectroscopy (IRLAS). The experiments were carried out in order to analyze the dependence of plasma chemical phenomena on power and gas mixture at relatively low pressures, up to 50 Pa, and power values, up to 2 kW. The evolution of the concentration of the methyl radical, CH3, and of seven stable molecules, HMDSO, CH4, C2H2, C2H4, C2H6, CO and CO2, was monitored in the plasma processes by in situ IRLAS using tunable lead salt diode lasers (TDL) and external-cavity quantum cascade lasers (EC-QCL) as radiation sources. To achieve reliable values for the gas temperature inside and outside the plasma bulk as well as for the temperature in the plasma hot and colder zones, which are of great importance for calculation of species concentrations, three different methods based on emission and absorption spectroscopy data of N2, CH3 and CO have been used. In this approach line profile analysis has been combined with spectral simulation methods. The concentrations of the various species, which were found to be in the range between 1011 to 1015 cm-3, are in the focus of interest. The influence of the discharge parameters power, pressure and gas mixture on the molecular concentrations has been studied. To achieve further insight into general plasma chemical aspects the dissociation of the HMDSO precursor gas including its fragmentation and conversion to the reaction products was analyzed in detail.

  5. 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.

  6. 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).

  7. 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.

  8. Spectroscopic, electrochemical and molecular docking study of the binding interaction of a small molecule 5H-naptho[2,1-f][1,2] oxathieaphine 2,2-dioxide with calf thymus DNA.

    PubMed

    Mukherjee, Abhijit; Mondal, Shovan; Singh, Bula

    2017-03-14

    The interaction of 5H-naptho[2,1-f][1,2]oxathieaphine2,2-dioxide (NOTD) with calf thymus DNA in Tris-HCl buffer at physiological pH was investigated with the help of various spectroscopic and electrochemical methods along with molecular docking study. Studying the non-covalent binding interaction of a neutral fluorophore with ctDNA has become an active field of research at the interface between medicinal chemistry and biological science. NOTD is known for its various toxicological, skin sensitization, and antiviral properties. Still, to date, its interaction style with ctDNA is not well elucidated. UV-vis absorption, fluorescence emission and circular dichroism spectroscopy (CD) suggest the complex formation between NOTD and ctDNA with binding constant value in the order of 3.12-4.1(×10(4))M(-1). Binding nature of NOTD with ctDNA is affirmed from the DNA helix melting experiment, comparative displacement assay using known DNA intercalator, cyclic voltammetry and finally molecular docking study. It was evident from experimental result that the probe NOTD binds with ctDNA in groove binding mode as manifested by a decrease in iodide quenching effect, spectral change in CD, a substantial increase in denaturing temperature in DNA and change in potential value. Furthermore, the molecular docking study insisted the above mentioned experimental result in a very affectionate way.

  9. 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.

  10. 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).

  11. 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.

  12. Spectroscopic studies of carbon impurities in PISCES-A

    SciTech Connect

    Ra, Y.; Hirooka, Y.; Leung, W.K.; Conn, R.W. . Inst. of Plasma and Fusion Research); Pospieszczyk, A. . Inst. fuer Plasmaphysik)

    1989-08-01

    The graphite used for the limiter of the tokamak reactor produces carbon-containing molecular impurities as a result of the interactions with the edge plasma. The behavior of these molecular impurities has been studied using emission spectroscopy. The present study includes: finding molecular bands and atomic lines in the visible spectral range which can be used for the study of the molecular impurities, studying the breakup processes of the molecular impurities on their way from the source into the plasma, developing a spectroscopic diagnostic method for the absolute measurement of the molecular impurity flux resulting from graphite erosion. For these studies, carbon-containing molecules such as CH{sub 4}, C{sub 2}H{sub 2}, C{sub 2}H{sub 4}, and CO{sub 2} were injected into the tokamak-boundary,like plasma generated by PISCES-A. The spectrograms of these gases were taken. Many useful bands and lines were determined from the spectrograms. The breakup processes of these gases were studied by observing the spatial profiles of the emission of the molecules and their radicals for different plasma conditions. For the absolute measurement of the eroded molecular impurity flux, the photon efficiency of the lines and bands were found by measuring the absolute number of the emitted photons and injected gas molecules. The chemical sputtering yield of graphite by hydrogen plasma was spectroscopically measured using the previously obtained photon efficiencies. It showed good agreement with results obtained by weight loss measurements. 16 refs., 7 figs., 1 tab.

  13. 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.

  14. 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.

  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 and molecular docking study on the interaction between salicylic acid and the induced disease-resistant protein OsAAA1 of rice.

    PubMed

    Chen, Ya H; Dai, Kang; Zhang, Hua; Wu, Yun H; Wang, Chun T; Liu, Xue Q; Liu, Xin Q

    2017-02-15

    The interaction between salicylic acid (SA) and the induced disease-resistant protein OsAAA1 in rice was studied using spectroscopy and molecular docking. Ultraviolet (UV) absorption spectroscopy demonstrated an interaction between OsAAA1 protein and SA. Spectroscopy showed that this interaction was a dynamic quenching process. Synchronous fluorescence spectroscopy (SFS) further revealed that this interaction caused changes in the microenvironment of tyrosine and tryptophan and that the interaction site was closer to the tryptophan residue. The structural model of protein OsAAA1 was determined by homology modeling method, and the molecular docking simulation diagram of OsAAA1 with SA was obtained. These models, in combination with a Ramachandran plot analysis, showed amino acid residues ranging from position 240 to position 420 as the possible site interacting with SA. Among them, Gly389, Lys257 and Glu425 might be three key amino acids that can form hydrogen bonds with SA.

  17. Spectroscopic investigation (FT-IR, FT-Raman), HOMO-LUMO, NBO analysis and molecular docking study of 4-chlorophenyl quinoline-2-carboxylate.

    PubMed

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

    2015-06-15

    FT-IR and FT-Raman spectra of 4-chlorophenyl quinoline-2-carboxylate 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. Potential energy distribution was done using GAR2PED program. The geometrical parameters obtained theoretically are in agreement with the XRD data. NBO analysis, HOMO-LUMO, first hyperpolarizability and molecular electrostatic potential results are also reported. The calculated hyperpolarizability of the title compound is 77.53 times that of the standard NLO material urea and the title compound and its derivatives are attractive object for future studies of nonlinear optical properties. Molecular docking results suggest that the compound might exhibit inhibitory activity against GPb. Copyright © 2015. Published by Elsevier B.V.

  18. Spectroscopic and molecular docking study on the interaction between salicylic acid and the induced disease-resistant protein OsAAA1 of rice

    NASA Astrophysics Data System (ADS)

    Chen, Ya H.; Dai, Kang; Zhang, Hua; Wu, Yun H.; Wang, Chun T.; Liu, Xue Q.; Liu, Xin Q.

    2017-02-01

    The interaction between salicylic acid (SA) and the induced disease-resistant protein OsAAA1 in rice was studied using spectroscopy and molecular docking. Ultraviolet (UV) absorption spectroscopy demonstrated an interaction between OsAAA1 protein and SA. Spectroscopy showed that this interaction was a dynamic quenching process. Synchronous fluorescence spectroscopy (SFS) further revealed that this interaction caused changes in the microenvironment of tyrosine and tryptophan and that the interaction site was closer to the tryptophan residue. The structural model of protein OsAAA1 was determined by homology modeling method, and the molecular docking simulation diagram of OsAAA1 with SA was obtained. These models, in combination with a Ramachandran plot analysis, showed amino acid residues ranging from position 240 to position 420 as the possible site interacting with SA. Among them, Gly389, Lys257 and Glu425 might be three key amino acids that can form hydrogen bonds with SA.

  19. Spectroscopic studies of individual plasmon resonant nanoparticles

    NASA Astrophysics Data System (ADS)

    Mock, Jack J.; Smith, David R.; Barbic, Mladen; Oldenburg, Steven J.; Schultz, David A.; Schultz, Sheldon

    2003-11-01

    We present a detailed description of the apparatus and techniques that we have utilized in our experimental study of individual plas on resonant nanoparticles,along with a brief description of some major results. The apparatus consists of a spectroscopic system combined with a modified darkfield microscope, which enables the user to sequentially select individual resonant nanostructures in the microscopic field of view for spectroscopic study. Plasmon resonant nanostructures scatter light elastically,and typically have very large scattering cross-sections at their resonant optical wavelengths. In general, spectra can be obtained with acquisition times between .1 to 30 seconds,and color images can be captured using consumer digital color cameras. Spheres,tetrahedrons,and pentagonal platelets were fabricated using colloidal chemistry techniques. To produce highly anisotropic structures such as nanorods and "barbells", templates were used. Many of these nanostructures have been individually spectroscopically characterized,and their spectra correlated with their shape and size as determined by transmission electron icroscope (TEM). The unique shape,size, composition,and dielectric surroundings of the individual plasmon resonant nanostructures determine their plasmon resonant behavior. We will show how the composition of the substrate on which the particles are immobilized and the dielectric of the surrounding medium have a significant effect on the plasmon resonance of the individual particles.

  20. 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…

  1. 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…

  2. 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.

  3. Spectroscopic (FT-IR, FT-Raman, UV, NMR, NLO) investigation and molecular docking study of 1-(4-Methylbenzyl) piperazine

    NASA Astrophysics Data System (ADS)

    Subashini, K.; Periandy, S.

    2017-04-01

    The title compound, 1-(4-Methylbenzyl) piperazine, was analyzed by recording FT-IR (4000-400 cm-1) and FT-Raman (4000-100 cm-1) spectra in solid phase, 1H and 13C NMR in CDCl3 (deuterated chloroform) 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. Density functional theory (DFT) calculation with 6-311++G (d, p) basis set along with B3LYP and B3PW91 functionals have been used to compute ground state molecular geometries and vibrational frequencies. The assignments of the vibrational spectra have carried out with the help of Potential Energy distribution (PED) analysis. Factor group analysis has also been tabulated. Charge distribution, Frontier Molecular Orbitals, UV-Vis spectra, Molecular Electrostatic Potential (MEP) maps, Non-linear optical (NLO) property and thermodynamic properties of the title compound at different temperatures, were determined using B3LYP functional along with 6-311++G (d, p) basis set. The theoretical 1H and 13C NMR chemical shifts were computed using B3LYP functional with 6-311++G (2d, p) basis sets. Natural Bond orbital analysis were computed and possible transitions were correlated with the electronic transitions. The title compound not only exhibits appreciable dipole moment and hyper polarizability (indicating good NLO properties) but also forms a stable complex with Bacillus cereus, (2HUC), with binding affinity -6.7 kcal/mol through molecular docking, suggesting that, it might exhibit inhibitory activity against Bacillus cereus.

  4. Structural, spectroscopic (FT-IR, NMR, UV-visible), nonlinear optical (NLO), cytotoxic and molecular docking studies of 4-nitro-isonitrosoacetophenone (ninapH) by DFT method

    NASA Astrophysics Data System (ADS)

    Kucuk, Ilhan; Kaya, Yunus; Kaya, A. Asli

    2017-07-01

    (4-Nitro-phenyl)-oxo-acetaldehyde oxime (ninapH) is a type of oxime, which has a oxime and α-carbonyl groups. This molecule has been synthesized from literature procedure. The structural properties and conformational behaviors were examined using the density functional theory (DFT) with the B3LYP method combined with the 6-311++G(d,p) basis set. As a result of the conformational studies, the most stable conformer was determined, and then this molecule was optimized with the same basis set. Comprehensive theoretical and experimental structural studies on the molecule have been carried out by FT-IR, NMR and UV-vis spectrometry. The calculated HOMO and LUMO energies show that charge transfer within the molecule. The first order hyperpolarizability and molecular electrostatic potential (MEP) were also performed. The thermodynamic properties (heat capacity, entropy, and enthalpy) of the ninapH have been calculated at different temperatures, 100-1000 K. In addition, the molecular docking studies have been performed with DNA and protein structures (downloaded from Protein Data Bank).

  5. 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.

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

    PubMed

    Zhang, Xuewei; Yu, Peiqiang

    2012-06-15

    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. Copyright © 2012 Elsevier B.V. All rights reserved.

  7. Quantum chemical studies on molecular structure, spectroscopic (IR, Raman, UV-Vis), NBO and HOMO-LUMO analysis of 1-benzyl-3-(2-furoyl) thiourea.

    PubMed

    Gil, Diego M; Defonsi Lestard, M E; Estévez-Hernández, O; Duque, J; Reguera, E

    2015-06-15

    Vibrational and electronic spectra for 1-benzyl-3-(2-furoyl) thiourea were calculated by using density functional method (B3LYP) with different basis sets. The complete assignment of all vibrational modes was performed on basis of the calculated frequencies and comparing with the reported IR and Raman spectra for that thiourea derivative. UV-visible absorption spectra of the compound dissolved in methanol were recorded and analyzed using time dependent density functional theory (TD-DFT). The calculated values for the geometrical parameters of the title compound are consistent with the ones reported from XRD studies. The stability of the molecule, related to hyper-conjugative interactions, and electron delocalization were evaluated using natural bond orbital (NBO) analysis. Intra-molecular interactions were studied by AIM approach. The HOMO and LUMO analysis are used to determine the charge transfer within the molecule. Molecular electrostatic potential map was performed by the DFT method. Copyright © 2015 Elsevier B.V. All rights reserved.

  8. Synthesis, spectroscopic (FT-IR, FT-Raman, NMR, UV-Visible), first order hyperpolarizability, NBO and molecular docking study of (E)-1-(4-bromobenzylidene)semicarbazide

    NASA Astrophysics Data System (ADS)

    Raja, M.; Muhamed, R. Raj; Muthu, S.; Suresh, M.

    2017-01-01

    The compound (E)-1-(4-bromobenzylidene)semicarbazide(4BSC) was synthesized and characterized by FT-IR, FT-Raman, UV-Visible, 1HNMR and 13CNMR spectra. The optimized molecular geometry(bond length, bond angle), the complete vibrational frequency, the infrared intensities and the Raman scattering activities were calculated by using density functional theory(DFT) B3LYP method with the help of 6-311++G(d,p) basis set. From the recorded UV-Visible spectrum, the electronic properties such as excitation energies, wavelength, band gap and oscillator strength are evaluated by TD-DFT in DMSO solution and gas phase methods using 6-311++G(d,p) basis set. The calculated HOMO - LUMO band gap energies confirm that charge transfer occurs within the molecule. The 1H and 13C nuclear magnetic resonance (NMR) chemical shifts of the molecule are calculated by the gauge-independent atomic orbital (GIAO) method and compared with experimental results. The hyperconjugative interaction energy E(2) and electron densities of donor (i) and acceptor (j) bonds were calculated using NBO analysis. Besides NLO and MEP were also calculated and interpreted. To study the biological activity of the investigation molecule, molecular docking was done to identify the hydrogen bond lengths and binding energy with different antimicrobial protein. Thermodynamic properties of the title compound at different temperatures have been calculated, revealing the correlations the heat capacity (C), entropy (S) and enthalpy changes (H) and temperatures.

  9. Spectroscopic studies of molecular interactions involving 2,6-diethylaniline and N-ethylaniline donors and iodine as an electron acceptor in different solvents

    NASA Astrophysics Data System (ADS)

    El-Gogary, Tarek M.; Diab, Mostafa A.; El-Tantawy, Shreen F.

    2007-01-01

    The charge-transfer complexes of 2,6-diethylaniline (DEA) and N-ethylaniline (NEA) with iodine, as a typical σ-acceptor were studied spectrophotometrically in chloroform, dichloromethane and carbontetrachloride solutions. Spectral data, formation constants and effect of solvent have been determined. Spectral characteristics and formation constants are discussed in the terms of donor molecular structure and solvent polarity. The stoichiometry of the complexes was established to be 1:1. For this purpose, optical data were subjected to the form of the Rose-Drago equation for 1:1 equilibria. The formation constant ( KAD) and molar absorptivities ( ɛλ) of complexes were determined by least square method. Electronic absorption spectra of the anilines were measured in different solvents. Spectral data were reported and band maxima were assigned to the appropriate molecular orbital transitions. Quantum chemical calculations were performed with the aid of the Gaussian 98 set of programs. The structure were fully optimized at MP2 level using 6-31 + G** basis set. The computations show that DEA is not planner with the amino group having a somewhat sp 3 hybridization-like character.

  10. 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.

  11. The Spectroscopic study of 33Ar

    NASA Astrophysics Data System (ADS)

    Adimi, N.; Dominguez-Reyes, R.; Alcorta, M.; Bey, A.; Blank, B.; Borge, M. J. G.; de Oliveira Santos, F.; Dossat, C.; Fynbo, H. O. U.; Giovinazzo, J.; Knudsen, H. H.; Madurga, M.; Matea, I.; Perea, A.; Sümmerer, K.; Tengblad, O.; Thomas, J. C.

    2011-10-01

    The proton-rich nucleus 33Ar has been produced at the low-energy facility SPIRAL at GANIL. Spectroscopic studies of gamma and p emission of this nucleus were performed with the "Silicon Cube" detection system. The analysis of proton and gamma singles and coincidence spectra allowed us to establish a complete decay scheme of this nucleus. The comparison of the Gamow-Teller strength distribution deduced from our experiment and the theoretical one obtained with the Shell Model permitted the determination of a quenching factor for the Gamow-Teller strength.

  12. The Spectroscopic study of {sup 33}Ar

    SciTech Connect

    Adimi, N.; Dominguez-Reyes, R.; Alcorta, M.; Borge, M. J. G.; Perea, A.; Tengblad, O.; Bey, A.; Blank, B.; Dossat, C.; Giovinazzo, J.; Matea, I.; Fynbo, H. O. U.; Knudsen, H. H.; Suemmerer, K.

    2011-10-28

    The proton-rich nucleus {sup 33}Ar has been produced at the low-energy facility SPIRAL at GANIL. Spectroscopic studies of gamma and p emission of this nucleus were performed with the 'Silicon Cube' detection system. The analysis of proton and gamma singles and coincidence spectra allowed us to establish a complete decay scheme of this nucleus. The comparison of the Gamow-Teller strength distribution deduced from our experiment and the theoretical one obtained with the Shell Model permitted the determination of a quenching factor for the Gamow-Teller strength.

  13. 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.

  14. A comparison study of the interaction between β-lactoglobulin and retinol at two different conditions: spectroscopic and molecular modeling approaches.

    PubMed

    Khorsand Ahmadi, Sabra; Mahmoodian Moghadam, Maryam; Mokaberi, Parisa; Reza Saberi, Mohammad; Chamani, Jamshidkhan

    2015-09-01

    The interaction between bovin β-Lactoglobulin (β-LG) and retinol at two different pH values was investigated by multispectroscopic, zeta potential, molecular modeling, and conductometry measurements. The steady state and polarization fluorescence spectroscopy revealed that complex formation at two different pH values could occur through a remarkable static quenching. According to fluorescence quenching, one set of binding site at pH 2 and two sets of binding sites at pH 7 were introduced for binding of retinol to β-LG that show the enhancement of saturation score of β-LG to retinol in dimmer condition. The polarization fluorescence analysis represented that there is more affinity between β-LG and retinol at pH 7 rather than at pH 2. The effect of retinol on β-LG was studied by UV-visible, circular dichroism (CD), and synchronous fluorescence, which indicated that retinol induced more structural changes on β-LG at pH 7. β-LG-retinol complex formation at two different pH values was recorded via applying resonance light scattering (RLS) and zeta potential. Conductometry and RLS showed two different behaviors of interaction between β-LG and retinol at two different pH values; therefore, dimmer formation played important roles in different behaviors of interaction between β-LG and retinol. The zeta potential was the implied combination of electrostatic and hydrophobic forces which are involved in β-LG-retinol complex at two different pH values, and the hydrophobic interactions play a dominant role in complex formation. Molecular modeling was approved by all experimental results. The acquired results suggested that monomer and dimmer states of β-LG can be induced by retinol with different behaviors.

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

    PubMed

    Karaca, Caglar; Atac, Ahmet; Karabacak, Mehmet

    2015-02-05

    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 ((1)H and (13)C) 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.

  16. Inhibitory effects of the dietary flavonoid quercetin on the enzyme activity of zinc(II)-dependent yeast alcohol dehydrogenase: Spectroscopic and molecular docking studies.

    PubMed

    Bhuiya, Sutanwi; Haque, Lucy; Pradhan, Ankur Bikash; Das, Suman

    2017-02-01

    A multispectroscopic exploration was employed to investigate the interaction between the metallo-enzyme alcohol dehydrogenase (ADH) from yeast with bioflavonoid quercetin (QTN). Here, we have characterized the complex formation between QTN and Zn(2+) in aqueous solution and then examined the effect of such complex formation on the enzymatic activity of a zinc(II)-dependent enzyme alcohol dehydrogenase from yeast. We have observed an inhibition of enzymatic activity of ADH in presence of QTN. Enzyme inhibition kinetic experiments revealed QTN as a non-competitive inhibitor of yeast ADH. Perturbation of Circular dichroic (CD) spectrum of ADH in presence of QTN is observed due to the structural changes of ADH on complexation with the above flavonoid. Our results indicate a conformational change of ADH due to removal of Zn(2+) present in the enzyme by QTN. This was further established by molecular modeling study which shows that the flavonoid binds to the Zn(2+) ion which maintains the tertiary structure of the metallo-enzyme. So, QTN abstracts only half of the Zn(2+) ions present in the enzyme i.e. one Zn(2+) ion per monomer. From the present study, the structural alteration and loss of enzymatic activity of ADH are attributed to the complex formation between QTN and Zn(2+).

  17. Study on effect of lomefloxacin on human holo-transferrin in the presence of essential and nonessential amino acids: Spectroscopic and molecular modeling approaches.

    PubMed

    Marouzi, Somaye; Sharifi Rad, Atena; Beigoli, Sima; Teimoori Baghaee, Parisa; Assaran Darban, Reza; Chamani, Jamshidkhan

    2017-04-01

    The purpose of this study was to determine how lomefloxacin (LMF) interacts with human holo-transferrin (HTF) in the presence of two kinds of essential and nonessential amino acids. The investigations were carried out by fluorescence spectroscopy, zeta potential and molecular modeling techniques under imitated physiological conditions. We were able to determine the number of binding sites, the drug binding affinity to HTF in the presence of essential and nonessential amino acids and the quenching source of HTF. The interaction between HTF with LMF suggested that the microenvironment of the Trp residues was altered causing a strong static fluorescence quenching in the binary and ternary systems. The results pointed at the formation of a complex in the binary and ternary systems which caused an enhancement of the RLS intensity that was analyzed using synchronous fluorescence spectroscopy. The density functional theory (DFT) was employed to determine the amino acid residues on HTF that interacted with LMF. Also, Steric and van der Waals forces as well as the contribution of small amounts of hydrogen bonds were stronger or Tyr 71 in chain (b) than for 128 Trp in chain (a) of HTF.

  18. Spectroscopic investigation (FT-IR, FT-Raman and SERS), vibrational assignments, HOMO-LUMO analysis and molecular docking study of Opipramol.

    PubMed

    Mary, Y Sheena; Panicker, C Yohannan; Kavitha, C N; Yathirajan, H S; Siddegowda, M S; Cruz, Sandra M A; Nogueira, Helena I S; Al-Saadi, Abdulaziz A; Van Alsenoy, Christian; War, Javeed Ahmad

    2015-02-25

    FT-IR and FT-Raman spectra of Opipramol were recorded and analyzed. SERS spectrum was recorded in silver colloid. The vibrational wave numbers were computed using DFT quantum chemical calculations. The data obtained from wave number calculations are used to assign vibrational bands obtained in infrared and Raman spectra as well as in SERS of the studied molecule. Potential energy distribution was done using GAR2PED program. The geometrical parameters (DFT) of the title compound are in agreement with the XRD results. The presence of CH2 stretching modes in the SERS spectrum indicates the close of piperazine ring with the metal surface and the interaction of the silver surface with this moiety. NBO analysis, HOMO-LUMO, first hyperpolarizability and molecular electrostatic potential results are also reported. The inhibitor Opipramol forms a stable complex with P4502C9 as is evident from the ligand-receptor interactions and a -9.0 kcal/mol docking score and may be an effective P4502C9 inhibitor if further biological explorations are carried out.

  19. Conformation, structure and molecular solvation: a spectroscopic and computational study of 2-phenoxy ethanol and its singly and multiply hydrated clusters

    NASA Astrophysics Data System (ADS)

    Macleod, Neil A.; Simons, John P.

    2002-10-01

    The conformational landscapes of 2-phenoxy ethanol (POX) and its hydrated clusters have been studied in the gas-phase, providing a model for pharmaceutical β-blockers. A combination of experimental techniques, including resonant two-photon ionisation (R2PI), laser-induced-fluorescence (LIF) and resonant ion-dip infra-red spectroscopy (RIDIRS), coupled with high-level ab initio calculations has allowed the assignment of the individually resolved spectral features to discrete conformational and supra-molecular structures. Assignments were made by comparison of experimental vibrational spectra and partially resolved ultra-violet rotational band contours with those predicted from quantum chemical calculations. The isolated molecule displays a solitary structure with an extended geometry of the side-chain which is stabilised by an intramolecular hydrogen-bond between the alcohol (proton donor) and the ether (proton acceptor) groups of the side-chain. In singly hydrated clusters the water molecule is accommodated by insertion into the intramolecular hydrogen-bond. In the doubly hydrated and higher clusters cyclic structures are generated which incorporate both the water molecules and the terminal OH group of the side-chain; additional (weak) hydrogen bonded interactions with the phenoxy group provide a degree of selectivity but essentially, the water 'droplet' forms on the end of the alcohol side-chain.

  20. Synthesis of a novel hydrazone derivative and biophysical studies of its interactions with bovine serum albumin by spectroscopic, electrochemical, and molecular docking methods.

    PubMed

    Tian, Fang-Fang; Jiang, Feng-Lei; Han, Xiao-Le; Xiang, Chen; Ge, Yu-Shu; Li, Jia-Han; Zhang, Yue; Li, Ran; Ding, Xin-Liang; Liu, Yi

    2010-11-25

    Hydrazone derivatives possess potential antitumor activities based on modulation of the iron metabolism in cancer cell. A novel hydrazone, N'-(2,4-dimethoxybenzylidene)-2-hydroxybenzohydrazide (DBH), has been synthesized and characterized, which is an analogue of 311 possessing potent anticancer activity. The interactions between DBH and bovine serum albumin (BSA) have been investigated systematically by fluorescence, molecular docking, circular dichroism (CD), UV-vis absorption, and electrochemical impedance spectroscopy (EIS) methods under physiological conditions. The fluorescence quenching observed is attributed to the formation of a complex between BSA and DBH, and the reverse temperature effect of the fluorescence quenching has been found and discussed. The primary binding pattern is determined by hydrophobic interaction occurring in Sudlow's site I of BSA. DBH could slightly change the secondary structure and induce unfolding of the polypeptides of protein. An average binding distance of ~4.0 nm has been determined on the basis of the Förster resonance energy theory (FRET). The effects of iron on the system of DBH-BSA have also been investigated. It is found that iron could compete against BSA to bind DBH. All of these results are supported by a docking study using a BSA crystal model. It is shown that DBH can efficiently bind with BSA and be transported to the focuses needed. Subsequent antitumor test and detailed anticancer mechanism are undergoing in our lab.

  1. 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.

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

    PubMed

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

    2015-06-15

    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, (1)H 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.

  4. 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).

  5. Interaction of vasicine with calf thymus DNA: Molecular docking, spectroscopic and differential scanning calorimetric insights

    NASA Astrophysics Data System (ADS)

    R. S., Sai Murali; R. S., Sai Siddhardha; Rajesh Babu, D.; Venketesh, S.; Basavaraju, R.; Nageswara Rao, G.

    2017-06-01

    The present study brings out the interaction between vasicine, an alkaloid and Adhatoda vasica Nees with double stranded DNA. The physico-chemical interaction between small molecules and nucleic acids is a major area of focus in screening drugs against various cancers. Molecular probing in our study using Molecular Operating Environment (MOE) has revealed interaction of vasicine with DNA double helix. Here we report the interaction of vasicine with Calf thymus DNA. We present for the first time the results obtained from UV-visible, fluorescence spectroscopic and differential scanning calorimetric techniques that suggest a moderate to strong electrostatic, hydrophobic and van der Waals interactions mediating the DNA binding properties of vasicine, leading to disruption of DNA secondary structure.

  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. 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.

  8. FT-Raman, FT-IR, UV spectroscopic, NBO and DFT quantum chemical study on the molecular structure, vibrational and electronic transitions of clopidogrel hydrogen sulfate form 1: A comparison to form 2

    NASA Astrophysics Data System (ADS)

    Srivastava, Anubha; Mishra, Rashmi; Tandon, Poonam; Bansal, A. K.

    2013-03-01

    Clopidogrel hydrogen sulfate (+)-(S)-(2-chlorophenyl)-6,7-dihydrothieno[3,2-c]pyridine-5(4H)-acetate sulfate (1:1), is a selective adenosine diphosphate (ADP) receptor antagonist often used in the treatment of coronary artery, peripheral vascular and cerebrovascular diseases. In the present communication, a comparative study of two polymorphic forms (forms 1 and 2) of clopidogrel hydrogen sulfate (CLP) has been reported. There is difference in conformation and intermolecular hydrogen bonding pattern of two forms. These differences are nicely reflected in the vibrational spectra. The molecular structure, fundamental vibrational frequencies and intensity of the vibrational bands of CLP form 1 are interpreted with the aid of structure optimizations and normal mode analysis based on ab initio HF and DFT method employing 6-311++G(d,p) basis. Polymorphism in CLP have been studied using various characterization tools like FT-Raman, FT-IR spectroscopy and DSC in combination with the quantum chemical calculations. UV-vis spectroscopic studies along with HOMO-LUMO analysis of both polymorphs were performed. The solvent effect calculated by TD-DFT/IEF-PCM/6-31G model results complements with the experimental findings. Stability of the molecule arising from hyper conjugative interactions and charge delocalization has been analyzed using natural bond orbital (NBO) analysis.

  9. Qualitative spectroscopic study of magnetic nozzle flow

    NASA Technical Reports Server (NTRS)

    Umeki, T.; Turchi, P. J.

    1992-01-01

    The physics of the magnetic nozzle flow for a 100-kW-level quasi-steady MPD thruster was studied by photographic spectroscopy focusing on the plasma model in the flow and the acceleration mechanism. Spectroscopic visualization for the flow-species analysis indicates that the plasma-exhaust flow dominated by NII species were confined by the magnetic nozzle effect to collimate the flow for the better thruster performance. Inside the nozzle, the plasma flow was found to be in nonhomogeneous collisional-radiative condition. There appears to be a substantial flow acceleration from the magnetic nozzle inlet to the outlet with slight expansion. This suggests that the flow resembles that of constant area supersonic duct flow with cooling.

  10. Binding properties of palmatine to DNA: spectroscopic and molecular modeling investigations.

    PubMed

    Mi, Ran; Tu, Bao; Bai, Xiao-Ting; Chen, Jun; Ouyang, Yu; Hu, Yan-Jun

    2015-12-01

    Palmatine, an isoquinoline alkaloid, is an important medicinal herbal extract with diverse pharmacological and biological properties. In this work, spectroscopic and molecular modeling approaches were employed to reveal the interaction between palmatine and DNA isolated from herring sperm. The absorption spectra and iodide quenching results indicated that groove binding was the main binding mode of palmatine to DNA. Fluorescence studies indicated that the binding constant (K) of palmatine and DNA was ~ 10(4)L·mol(-1). The associated thermodynamic parameters, ΔG, ΔH, and ΔS, indicated that hydrogen bonds and van der Waals forces played major roles in the interaction. The effects of chemical denaturant, thermal denaturation and pH on the interaction were investigated and provided further support for the groove binding mode. In addition to experimental approaches, molecular modeling was conducted to verify binding pattern of palmatine-DNA.

  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. 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.

  13. Synthesis, spectroscopic characterization, molecular modeling and potentiometric studies of Co(II), Ni(II), Cu(II) and Zn(II) complexes with 1,1-diaminobutane-Schiff base

    NASA Astrophysics Data System (ADS)

    Alaghaz, Abdel-Nasser M. A.

    2014-08-01

    Complexes of cobalt(II), nickel(II), copper(II) and zinc(II) of general composition [M(L)(H2O)2]·2H2O have been synthesized [L = N,N";-bis(2-hydroxybenzylidene)-1,1-diaminobutane]. The elemental analysis, molar conductance measurements, magnetic susceptibility measurements, mass, IR, UV, NMR, SEM, EDX, thermal and EPR spectral studies of the compounds led to the conclusion that the ligand acts as a tetradentate manner. The molar conductance of the complexes in fresh solution of DMSO lies in the range of 7.46-9.13 Ω-1 cm2 mol-1 indicating their non-electrolytic behavior. On the basis of analytical and spectroscopic techniques, octahedral geometry of the complexes was proposed. The Schiff base acts as tetradentate ligand, coordinated through deprotonated phenolic oxygen and azomethine nitrogen atoms. The ligand field parameters were calculated for Co(II), Ni(II) and Cu(II) complexes and their values were found in the range reported for a octahedral structure. The molecular parameters of the ligand and its Co(II), Ni(II), Cu(II) and Zn(II) complexes have been calculated. Protonation constants of Schiff base and stability constants of their binary metal complexes have been determined potentiometrically in 50% DMSO-water media at 25 °C and ionic strength 0.10 M sodium perchlorate.

  14. 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.

  15. Spectroscopic and molecular docking study on the structure-affinity relationship and mechanism in the interaction of genistein and its derivatives with bovine serum albumin.

    PubMed

    Guo, Yu; Shen, Lixian; Yao, Xu; Liu, Yang; Liu, Yunmei; Chen, Hongfei; Min, Ke; Zheng, Xing

    2017-06-14

    In this paper, the interaction of genistein (GEN) and its four derivatives (GEN1-4) with bovine serum albumin (BSA) were investigated by ultraviolet-visible absorption spectra, fluorescence, synchronous fluorescence, three-dimensional fluorescence spectroscopy, circular dichroism and molecular docking techniques. The experimental results showed that the intrinsic fluorescence of BSA was quenched by genisteins and was due to the formation of a genisteins-BSA complex. The quenching constant, binding constants, binding sites, intermolecular distances and thermodynamic properties were calculated at 298 K, 306 K and 310 K. Site marker competitive experiments indicated that the binding site of genisteins to BSA was mainly located in subdomain IIA. The conformational investigation showed that the presence of 0020 genisteins led to changes in the secondary structure of BSA and induced the slight unfolding of protein polypeptides, which confirmed some micro-environmental and conformational changes of BSA molecules. Furthermore, the binding affinity decreased in the order GEN1 > GEN > GEN4 > GEN3 > GEN2, which revealed that different type and position of substituents of genistein significantly influenced the affinity of compounds to BSA. The number of hydroxyl groups on the ring A was the most important factor because increasing the hydroxyl groups on ring A clearly enhanced the binding affinity. However, trifluoromethylation did not much affect the affinity, alkylation, esterification and difluoromethylation slightly enhanced the binding affinity. The results obtained herein will provide valuable information about the pharmacokinetics at a molecular level and be a useful guideline for the further design of much more suitable genistein derivatives. Copyright © 2017 John Wiley & Sons, Ltd.

  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.

  18. 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.

  19. 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.

    PubMed

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

    2015-08-05

    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 4.3eV 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.

  20. Fundamental spectroscopic studies of some atmospheric pollutants

    SciTech Connect

    Findley, G.L.; McGlynn, S.P.

    1980-01-01

    Molecular electronic transitions that lie in the vuv (vacuum ultraviolet) spectral region initiate many harmful photochemical modifications in the upper atmosphere. Consequently, investigations have focused on molecules that are primary atmospheric pollutants, but which are simple enough structurally to yield detailed photophysical information. Terminal electronic states for vuv transitions can be either valence or Rydberg and, at low enough energies, the distinction between the two becomes fuzzy. A major thrust of this program has been the classification and characterization of Rydberg transitions in an attempt to gain insight into Rydberg/valence state mixing Rydberg studies. It is concluded that in order to understand the nature of photochemical reactions of molecules in the upper atmosphere, it is necessary to understand the structure and function of high-energy molecular electronic states. It is also necessary to understand the ways in which these states interact and, thereby, facilitate energy transfer. The study of molecular Rydberg states provides information crucial to such an understanding.

  1. Molecular structure of Mg-Al, Mn-Al and Zn-Al halotrichites-type double sulfates--an infrared spectroscopic study.

    PubMed

    Palmer, Sara J; Frost, Ray L

    2011-05-01

    Near infrared (NIR), X-ray diffraction (XRD) and infrared (IR) spectroscopy have been applied to halotrichites of the formula MgAl(2)(SO(4))(4)·22H(2)O, MnAl(2)(SO(4))(4)·22H(2)O and ZnAl(2)(SO(4))(4)·22H(2)O. Comparison of the halotrichites in different spectral regions has shown that the incorporation of a divalent transition metal into the halotrichite structure causes a shift in OH stretching band positions to lower wavenumbers. Therefore, an increase of the hydrogen bond strength of the bonded water is observed for divalent cations with a larger molecular mass. XRD has confirmed the formation of halotrichite for all three samples and characteristic peaks of halotrichite have been identified for each halotrichite-type compound. It has been observed that Mg-Al and Mn-Al halotrichite are very similar in structure, while Zn-Al showed several differences particularly in the NIR spectra. This work has shown that compounds with halotrichite structures can be synthesised and characterised by infrared and NIR spectroscopy. Copyright © 2011 Elsevier B.V. All rights reserved.

  2. Synthesis, XRD crystal structure, spectroscopic characterization, local reactive properties using DFT and molecular dynamics simulations and molecular docking study of (E)-1-(4-bromophenyl)-3-(4-(trifluoromethoxy)phenyl)prop-2-en-1-one

    NASA Astrophysics Data System (ADS)

    Arshad, Suhana; Raveendran Pillai, Renjith; Zainuri, Dian Alwani; Khalib, Nuridayanti Che; Razak, Ibrahim Abdul; Armaković, Stevan; Armaković, Sanja J.; Renjith, Rishikesh; Panicker, C. Yohannan; Van Alsenoy, C.

    2017-06-01

    In the present study, the title compound named as (E)-1-(4-bromophenyl)-3-(4-(trifluoromethoxy)phenyl)prop-2-en-1-one was synthesized and structurally characterized by single-crystal X-ray diffraction. The FT-IR spectrum was recorded and interpreted in details with the aid of Density Functional Theory (DFT) calculations and Potential Energy Distribution (PED) analysis. Average local ionization energies (ALIE) and Fukui functions have been used as quantum-molecular descriptors to locate the molecule sites that could be of importance from the aspect of reactivity. Degradation properties have been assessed by calculations of bond dissociation energies (BDE) for hydrogen abstraction and the rest of the single acyclic bonds, while molecular dynamics (MD) simulations were used in order to calculate radial distribution functions and determine the atoms with significant interactions with water. In order to understand how the title molecule inhibits and hence increases the catalytic efficiency of MOA-B enzyme, molecular docking study was performed to fit the title compound into the binding site of MOA-B enzyme.

  3. Preparation of cesium targets for gamma-spectroscopic studies

    NASA Astrophysics Data System (ADS)

    Bhattacharyya, S.; Basu, S. K.; Chanda, S.; Deb, P.; Eqbal, Md; Kundu, S.; Joseph, D.

    2000-11-01

    A procedure to prepare monoisotopic cesium compound targets for gamma-spectroscopic experiments is described. Using this procedure, uniform targets up to thicknesses of 0.6-1.2 mg/cm 2 were prepared and used for in-beam spectroscopic studies. The purity of the target was tested by energy dispersive X-ray fluorescence (EDXRF) measurements.

  4. 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.

  5. Spectroscopic studies of nanoscale metal clusters

    NASA Astrophysics Data System (ADS)

    Gangopadhyay, P.

    2013-06-01

    The present article is intended to elucidate a range of novel spectroscopic studies of nanoscale metal clusters. Various bottom-up and top-down techniques have been utilized to synthesize the metal nanoclusters. Materials like metal nanoclusters of cobalt, silver or gold in various dielectric matrices facilitate to explore interesting phenomena through optical, photoluminescence and vibrational spectroscopy. Interaction of uv-visible light with free electrons of metal nanoclusters, for example, leads to fascinating colors of dielectric matrices through an optical effect known as surface-plasmon resonance. This effect of quantum-confinement of the electrons leads to large enhancements of local electric field in metal nanoclusters. Enhancements of Raman scattering from metal nanoclusters are attributed to the increase of local fields. Optical absorption and Raman scattering spectroscopy particularly have been highlighted here as powerful non-destructive experimental methods to study evolution of metal nanoclusters in different dielectric matrices. In relatively large metal nanoclusters, besides dipolar, quadrupolar surface-plasmon resonances have been observed.

  6. 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

  7. Spectroscopic studies of detonating heterogeneous explosives. [HNS

    SciTech Connect

    Renlund, A.M.; Trott, W.M.

    1985-01-01

    The experimental objectives of this work are to use real-time spectroscopic techniques, emission spectroscopy and Raman spectra to monitor chemical and physical changes in shock-loaded or detonating high explosive (HE) samples. The investigators hope to identify chemical species including any transient intermediates. Also, they wish to determine the physical state of the material when the reactions are taking place; measure the temperature and the pressure; and study the effect of different initiation parameters and bulk properties of the explosive material. This work is just part of the effort undertaken to gain information on the detailed chemistry involved in initiation and detonation. In summary, the investigators have obtained vibrational temperatures of some small radical products of detonation, which may correlate with the detonation temperature. They have also observed that NO/sub 2/ is an early product from detonating HNS and RDX, and that other electronically excited radical species such as CN(B) are formed in HNS detonations. In the Raman work, the single-pulse spectra could be obtained even in the severe environment of a detonation, and that the rate of removal of the parent molecule could be monitored. 2 refs., 6 figs.

  8. 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.

  9. Spectroscopic Study of Low Mass Members of NGC 2244

    NASA Astrophysics Data System (ADS)

    Alty, Michelle; Ybarra, Jason E.; Román-Zúñiga, Carlos G.; Lada, Elizabeth A.

    2017-01-01

    The results of a near-infrared spectroscopic study of low-mass stars in open cluster NGC 2244 are presented. JH spectra of the stars were obtained using the FLAMINGOS instrument at KPNO. To determine cluster membership, we used Spitzer Space Telescope mid-infrared photometry along with X-ray detections from the Chandra X-ray Observatory. The stars were spectral typed using absorption line ratios and spectral shapes. The stars were then plotted on an H-R diagram along with theoretical isochrones. We discuss these results in context of cluster evolution in the Rosette Molecular Complex. Work supported, in part, by the Dr. John W. Martin Summer Science Research Institute at Bridgewater College.

  10. Molecular structure identification and position of a dopant ion in diaqua(2,2‧-bipyridine)malonatozinc(II) by spectroscopic studies - II: VO(II)

    NASA Astrophysics Data System (ADS)

    Parthipan, Krishnan; Ramesh, Hema; Sambasiva Rao, P.

    2011-04-01

    Single crystal EPR, optical, FT-IR and powder XRD studies of VO(II) ion doped diaqua(2,2'-bipyridine) malonato zinc complex were carried out at room temperature to ascertain the structural properties. In EPR, the angular variation of vanadium hyperfine lines indicated a single site, with spin Hamiltonian parameters as: g xx = 1.968, g yy = 1.964, g zz = 1.928, A xx = 7.54 mT, A yy = 6.36 mT and A zz = 18.81 mT. In addition, the dopant had entered the lattice in an interstitial position and the position had been identified with the help of atom positions of the host lattice. The EPR and optical data was corroborated to obtain various bonding parameters, from which the nature of the bonding in the complex was discussed. FT-IR and powder XRD studies were used to observe the effect of dopant on structural parameters of the host lattice.

  11. 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.

  12. 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.

  13. 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. Copyright © 2013 Elsevier B.V. All rights reserved.

  14. 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.

  15. 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.

  16. Spectroscopic characterization of the interaction of molecular hydrogen with germanosilicate materials

    NASA Astrophysics Data System (ADS)

    Metroke, Tammy Lauren

    1997-12-01

    Scope and method of study. The purpose of this study was to (a) develop a complete structural model for germanosilicate materials as a function of catalyst, germania concentration, and temperature and (b) spectroscopically study the interaction of molecular hydrogen with sol-gel derived germanosilicate materials. Diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) and multinuclear (1H, 29Si CP/MAS, 29Si MAS, variable temperature 1H, and 73Ge) nuclear magnetic resonance spectroscopies were used. Findings and conclusions. The surface and bulk structures of acid- and base-catalyzed germanosilicate materials were found to be phase separated. Base-catalyzed germanosilicate materials were composed of small germania crystallites dispersed in an amorphous silica matrix, whereas acid-catalyzed materials were found to be composed of larger blocks of hexagonal crystalline germania dispersed in an amorphous silica matrix. After heating to 600oC, the surface of base-catalyzed germanosilicate materials contained primarily isolated Si-OH and Ge-OH groups. Acid-catalyzed germanosilicate materials contained higher concentrations of water and less isolated Si-OH and Ge-OH groups on the surface after heating to 600oC. A surface model illustrating the structure of acid- and base-catalyzed gels after heating to 600oC was presented. Acid-catalyzed materials reacted with molecular hydrogen to form molecular water. Base-catalyzed materials reacted with molecular hydrogen to form hydrogen-bonded water. Stable hydrides were not produced in the reaction with molecular hydrogen. A mechanism for the formation of water was proposed, based on the interaction of hydrogen with defect peroxy linkages, to explain the changes.

  17. 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.

    PubMed

    Suresh, S; Gunasekaran, S; Srinivasan, S

    2014-11-11

    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.

  18. 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.

  19. 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. Copyright © 2014 Elsevier B.V. All rights reserved.

  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. Copyright © 2014 Elsevier B.V. All rights reserved.

  1. Rapid Flow Analysis Studies with Spectroscopic Detectors.

    NASA Astrophysics Data System (ADS)

    Thalib, Amlius

    A rapid flow analysis study based on segmented flow and flow injection principles is described in this thesis. The main objective of this study was to establish the response characteristics in continuous flow analysis systems in order to improve sampling rates with several types of spectroscopic detectors. It was found from flame photometric studies that non-segmented flowing streams are applicable to rapid flow analysis with automatic sample aspiration. Calcium was used as a typical example and determined at sampling rates up to 360 h('-1) with a detection limit of 0.05 mg L(' -1). A rapid flow system is reported using direct aspiration for AAS analysis with both manual injection and automatic aspiration techniques, and found to give sampling rates of up to 600-720 samples h('-1). Speed of analysis was reduced by about 50% when using an external peristaltic pump in the flow system design, due to increased sample dispersion. A novel aspect of a rapid flow injection approach reported with ICPAES detection includes the method of injecting samples via a peristaltic pump with simultaneous computer data processing. Determination of serum cations (Na, K, Ca, Mg and Fe) was demonstrated as an example of an application of the technique at sampling rates of 240 h('-1). Precision and detection limits for 13 elements in a single standard solution are reported. The use of automated aspiration sampling is also reported in this method for comparison. Further studies on flow characteristics were carried out by a combination of the rapid flow system with very short sampling times as low as 2 seconds using UV-visible spectrophotometric detection. Analysis of human blood serum samples was used as an example where total protein and inorganic phosphate were determined at sampling rates of 240 h('-1) and 360 h('-1) respectively. The novel aspects of the results from these studies include the very rapid sample throughput developed with simple and inexpensive experimental approaches in

  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. 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

  4. Spectroscopic study of intermolecular complexes between FAD and some β-carboline derivatives

    NASA Astrophysics Data System (ADS)

    Codoñer, Armando; Monzó, Isidro S.; Tomás, Francisco; Valero, Rosa

    The formation of molecular complexes between flavine adenine dinucleotide (FAD) and some β-carboline derivatives [antidepressant drugs that have a pronounced inhibition of monoamine oxidase (MAO)] has been studied by using electronic absorption and fluorescence spectroscopic methods. Thermodynamic parameters have been determined from the values of association constants for the molecular complexes at various temperatures. The influence of substituents in the β-carboline molecule on the stability of the complexes formed was also investigated.

  5. Spectroscopic, biological, and molecular modeling studies on the interactions of [Fe(III)-meloxicam] with G-quadruplex DNA and investigation of its release from bovine serum albumin (BSA) nanoparticles.

    PubMed

    Ebrahimi, Malihe; Khayamian, Taghi; Hadadzadeh, Hassan; Sayed Tabatabaei, Badraldin Ebrahim; Jannesari, Zahra; Khaksar, Ghazale

    2015-01-01

    The guanine-rich sequence, specifically in DNA, telomeric DNA, is a potential target of anticancer drugs. In this work, a mononuclear Fe(III) complex containing two meloxicam ligands was synthesized as a G-quadruplex stabilizer. The interaction between the Fe(III) complex and G-quadruplex with sequence of 5'-G3(T2AG3)3-3' (HTG21) was investigated using spectroscopic methods, molecular modeling, and polymerase chain reaction (PCR) assays. The spectroscopic methods of UV-vis, fluorescence, and circular dichroism showed that the metal complex can effectively induce and stabilize G-quadruplex structure in the G-rich 21-mer sequence. Also, the binding constant between the Fe(III) complex and G-quadruplex was measured by these methods and it was found to be 4.53(±0.30) × 10(5) M(-1)). The PCR stop assay indicated that the Fe(III) complex inhibits DNA amplification. The cell viability assay showed that the complex has significant antitumor activities against Hela cells. According to the UV-vis results, the interaction of the Fe(III) complex with duplex DNA is an order of magnitude lower than G-quadruplex. Furthermore, the release of the complex incorporated in bovine serum albumin nanoparticles was also investigated in physiological conditions. The release of the complex followed a bi-phasic release pattern with high and low releasing rates at the first and second phases, respectively. Also, in order to obtain the binding mode of the Fe(III) complex with G-quadruplex, molecular modeling was performed. The molecular docking results showed that the Fe(III) complex was docked to the end-stacked of the G-quadruplex with a π-π interaction, created between the meloxicam ligand and the guanine bases of the G-quadruplex.

  6. 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

    2015-12-24

    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.

  7. Toxic interaction between acid yellow 23 and trypsin: spectroscopic methods coupled with molecular docking.

    PubMed

    Wang, Jing; Liu, Rutao; Qin, Pengfei

    2012-09-01

    Acid yellow 23 (AY23) is a pervasive azo dye used in many fields which is potentially harmful to the environment and human health. This paper studied the toxic effects of AY23 on trypsin by spectroscopic and molecular docking methods. The addition of AY23 effectively quenched the intrinsic fluorescence of trypsin via static quenching with association constants of K(290 K) = 3.67 × 10(5) L mol(-1) and K(310 K) = 1.83 × 10(5) L mol(-1). The calculated thermodynamic parameters conformed that AY23 binds to trypsin predominantly via electrostatic forces with one binding site. Conformational investigations indicated the skeletal structure of trypsin unfolded and the microenvironment of tryptophan changed with the addition of AY23. Molecular docking study showed that AY23 interacted with the His 57 and Lys 224 residue of trypsin and led to the inhibition of enzyme activity. This study offers a more comprehensive picture of AY23-trypsin interaction and indicates their interaction may perform toxic effects within the organism.

  8. Spectroscopic and DFT-based computational studies on the molecular electronic structural characteristics and the third-order nonlinear property of an organic NLO crystal: (E)-N‧-(4-chlorobenzylidene)-4-methylbenzenesulfonohydrazide

    NASA Astrophysics Data System (ADS)

    Sasikala, V.; Sajan, D.; Joseph, Lynnette; Balaji, J.; Prabu, S.; Srinivasan, P.

    2017-04-01

    Single crystals of (E)-N‧-(4-chlorobenzylidene)-4-methylbenzenesulfonohydrazide (CBMBSH) have been grown by slow evaporation crystal growth method. The structure stabilizing intramolecular donor-acceptor interactions and the presence of the Nsbnd H⋯O, Csbnd H⋯O and Csbnd H⋯C(π) hydrogen bonds in the crystal were confirmed by vibrational spectroscopic and DFT methods. The linear optical absorption characteristics of the solvent phase of CBMBSH were investigated using UV-Vis-NIR spectroscopic and TD-DFT approaches. The 2PA assisted RSA nonlinear absorption and the optical limiting properties of CBMBSH were studied using the open-aperture Z-scan method. The topological characteristics of the electron density have been determined using the quantum theory of atoms in molecules method.

  9. 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

    2015-01-01

    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.

  10. Photoelectron spectroscopic studies of 5-halouracil anions

    SciTech Connect

    Radisic, Dunja; Ko, Yeon Jae; Nilles, John M.; Stokes, Sarah T.; Bowen, Kit H.; Sevilla, Michael D.; Rak, Janusz

    2011-01-07

    The parent negative ions of 5-chlorouracil, UCl{sup -} and 5-fluorouracil, UF{sup -} have been studied using anion photoelectron spectroscopy in order to investigate the electrophilic properties of their corresponding neutral halouracils. The vertical detachment energies (VDE) of these anions and the adiabatic electron affinities (EA) of their neutral molecular counterparts are reported. These results are in good agreement with the results of previously published theoretical calculations. The VDE values for both UCl{sup -} and UF{sup -} and the EA values for their neutral molecular counterparts are much greater than the corresponding values for both anionic and neutral forms of canonical uracil and thymine. These results are consistent with the observation that DNA is more sensitive to radiation damage when thymine is replaced by halouracil. While we also attempted to prepare the parent anion of 5-bromouracil, UBr{sup -}, we did not observe it, the mass spectrum exhibiting only Br{sup -} fragments, i.e., 5-bromouracil apparently underwent dissociative electron attachment. This observation is consistent with a previous assessment, suggesting that 5-bromouracil is the best radio-sensitizer among these three halo-nucleobases.

  11. Photoelectron spectroscopic studies of 5-halouracil anions

    NASA Astrophysics Data System (ADS)

    Radisic, Dunja; Ko, Yeon Jae; Nilles, John M.; Stokes, Sarah T.; Sevilla, Michael D.; Rak, Janusz; Bowen, Kit H.

    2011-01-01

    The parent negative ions of 5-chlorouracil, UCl- and 5-fluorouracil, UF- have been studied using anion photoelectron spectroscopy in order to investigate the electrophilic properties of their corresponding neutral halouracils. The vertical detachment energies (VDE) of these anions and the adiabatic electron affinities (EA) of their neutral molecular counterparts are reported. These results are in good agreement with the results of previously published theoretical calculations. The VDE values for both UCl- and UF- and the EA values for their neutral molecular counterparts are much greater than the corresponding values for both anionic and neutral forms of canonical uracil and thymine. These results are consistent with the observation that DNA is more sensitive to radiation damage when thymine is replaced by halouracil. While we also attempted to prepare the parent anion of 5-bromouracil, UBr-, we did not observe it, the mass spectrum exhibiting only Br- fragments, i.e., 5-bromouracil apparently underwent dissociative electron attachment. This observation is consistent with a previous assessment, suggesting that 5-bromouracil is the best radio-sensitizer among these three halo-nucleobases.

  12. Quantum mechanical and spectroscopic (FT-IR, FT-Raman) study, NBO analysis, HOMO-LUMO, first order hyperpolarizability and molecular docking study of methyl[(3R)-3-(2-methylphenoxy)-3-phenylpropyl]amine by density functional method.

    PubMed

    Kuruvilla, Tintu K; Prasana, Johanan Christian; Muthu, S; George, Jacob; Mathew, Sheril Ann

    2018-01-05

    Quantum chemical techniques such as density functional theory (DFT) have become a powerful tool in the investigation of the molecular structure and vibrational spectrum and are finding increasing use in application related to biological systems. The Fourier transform infrared (FT-IR) and Fourier transform Raman (FT-Raman) techniques are employed to characterize the title compound. The vibrational frequencies were obtained by DFT/B3LYP calculations with 6-31G(d,p) and 6-311++G(d,p) as basis sets. The geometry of the title compound was optimized. The vibrational assignments and the calculation of Potential Energy Distribution (PED) were carried out using the Vibrational Energy Distribution Analysis (VEDA) software. Molecular electrostatic potential was calculated for the title compound to predict the reactive sites for electrophilic and nucleophilic attack. In addition, the first-order hyperpolarizability, HOMO and LUMO energies, Fukui function and NBO were computed. The thermodynamic properties of the title compound were calculated at different temperatures, revealing the correlations between heat capacity (C), entropy (S) and enthalpy changes (H) with temperatures. Molecular docking studies were also conducted as part of this study. The paper further explains the experimental results which are in line with the theoretical calculations and provide optimistic evidence through molecular docking that the title compound can act as a good antidepressant. It also provides sufficient justification for the title compound to be selected as a good candidate for further studies related to NLO properties. Copyright © 2017. Published by Elsevier B.V.

  13. Vibrational spectroscopic and DFT study of trimethoprim

    NASA Astrophysics Data System (ADS)

    Ungurean, Alia; Leopold, Nicolae; David, Leontin; Chiş, Vasile

    2013-02-01

    Structural investigations by different vibrational spectroscopic methods: FTIR, FT-Raman and surface-enhanced Raman scattering (SERS) spectroscopy, as well as density functional theory (DFT) calculations were performed on trimethoprim (5-(3,4,5-trimethoxybenzyl)pyrimidine-2,4-diamine). A reliable assignment of vibrational IR, Raman and SERS bands was possible by a proper choice of model used in quantum chemical calculations. Based on SERS spectrum analysis it is shown that the molecule is adsorbed on the silver surface through the pyrimidine ring, in a perpendicular orientation. Two theoretical models were used in order to simulate the silver surface and the interaction with trimethoprim molecule, the accuracy of the models being evaluated by comparing the predicted bands position of the two complexes with the SERS result.

  14. The Biophysical Probes 2-fluorohistidine and 4-fluorohistidine: Spectroscopic Signatures and Molecular Properties

    NASA Astrophysics Data System (ADS)

    Kasireddy, Chandana; Ellis, Jonathan M.; Bann, James G.; Mitchell-Koch, Katie R.

    2017-02-01

    Fluorinated amino acids serve as valuable biological probes, by reporting on local protein structure and dynamics through 19F NMR chemical shifts. 2-fluorohistidine and 4-fluorohistidine, studied here with DFT methods, have even more capabilities for biophysical studies, as their altered pKa values, relative to histidine, allow for studies of the role of proton transfer and tautomeric state in enzymatic mechanisms. Considering the two tautomeric forms of histidine, it was found that 2-fluorohistidine primarily forms the common (for histidine) τ-tautomer at neutral pH, while 4-fluorohistidine exclusively forms the less common π-tautomer. This suggests the two isomers of fluorohistidine can also serve as probes of tautomeric form within biomolecules, both by monitoring NMR chemical shifts and by potential perturbation of the tautomeric equilibrium within biomolecules. Fluorine also enables assignment of tautomeric states in crystal structures. The differences in experimental pKa values between the isomers was found to arise from solvation effects, providing insight into the polarization and molecular properties of each isomer. Results also encompass 13C and 19F NMR chemical shifts, from both tautomers of 2-fluorohistidine and 4-fluorohistidine in a number of different environments. This work can serve as a guide for interpretation of spectroscopic results in biophysical studies employing 2-fluorohistidine and 4-fluorohistidine.

  15. The Biophysical Probes 2-fluorohistidine and 4-fluorohistidine: Spectroscopic Signatures and Molecular Properties

    PubMed Central

    Kasireddy, Chandana; Ellis, Jonathan M.; Bann, James G.; Mitchell-Koch, Katie R.

    2017-01-01

    Fluorinated amino acids serve as valuable biological probes, by reporting on local protein structure and dynamics through 19F NMR chemical shifts. 2-fluorohistidine and 4-fluorohistidine, studied here with DFT methods, have even more capabilities for biophysical studies, as their altered pKa values, relative to histidine, allow for studies of the role of proton transfer and tautomeric state in enzymatic mechanisms. Considering the two tautomeric forms of histidine, it was found that 2-fluorohistidine primarily forms the common (for histidine) τ-tautomer at neutral pH, while 4-fluorohistidine exclusively forms the less common π-tautomer. This suggests the two isomers of fluorohistidine can also serve as probes of tautomeric form within biomolecules, both by monitoring NMR chemical shifts and by potential perturbation of the tautomeric equilibrium within biomolecules. Fluorine also enables assignment of tautomeric states in crystal structures. The differences in experimental pKa values between the isomers was found to arise from solvation effects, providing insight into the polarization and molecular properties of each isomer. Results also encompass 13C and 19F NMR chemical shifts, from both tautomers of 2-fluorohistidine and 4-fluorohistidine in a number of different environments. This work can serve as a guide for interpretation of spectroscopic results in biophysical studies employing 2-fluorohistidine and 4-fluorohistidine. PMID:28198426

  16. Synthesis, characterization and interaction studies of 1,3,4-oxadiazole derivatives of fatty acid with human serum albumin (HSA): A combined multi-spectroscopic and molecular docking study.

    PubMed

    Laskar, Khairujjaman; Alam, Parvez; Khan, Rizwan Hasan; Rauf, Abdul

    2016-10-21

    An efficient synthesis of fatty acid derivatives of 1,3,4-oxadiazole has been reported and comparative study between conventional heating to that of microwave irradiation also described. The newly synthesized compounds (2A-F) were characterized by FT-IR, (1)H NMR, (13)C NMR and mass spectral analysis. The binding interaction of (Z)-2-(heptadec-8'-enyl)-5-methyl-1,3,4-oxadiazole (2C) with human serum albumin (HSA) has been evaluated by UV, fluorescence, circular dichroism (CD) and molecular docking studies. Fluorescence results showed that compound 2C interacts with HSA through static quenching mechanism with binding affinity of 2 × 10(3) M(-1) and Gibbs free energy change (ΔG) was found to be -16.83 kJ mol(-1). Molecular docking studies have been performed to evaluate possible mode of interaction of compound 2C with HSA.

  17. 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

  18. Investigation of the interaction of naringin palmitate with bovine serum albumin: spectroscopic analysis and molecular docking.

    PubMed

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

    2013-01-01

    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. 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. 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 preparations may be clinically and practically significant

  19. 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.

  20. 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

  1. The ALMA Spectroscopic Survey in the Hubble Ultra Deep Field: Molecular Gas Reservoirs in High-redshift Galaxies

    NASA Astrophysics Data System (ADS)

    Decarli, Roberto; Walter, Fabian; Aravena, Manuel; Carilli, Chris; Bouwens, Rychard; da Cunha, Elisabete; Daddi, Emanuele; Elbaz, David; Riechers, Dominik; Smail, Ian; Swinbank, Mark; Weiss, Axel; Bacon, Roland; Bauer, Franz; Bell, Eric F.; Bertoldi, Frank; Chapman, Scott; Colina, Luis; Cortes, Paulo C.; Cox, Pierre; Gónzalez-López, Jorge; Inami, Hanae; Ivison, Rob; Hodge, Jacqueline; Karim, Alex; Magnelli, Benjamin; Ota, Kazuaki; Popping, Gergö; Rix, Hans-Walter; Sargent, Mark; van der Wel, Arjen; van der Werf, Paul

    2016-12-01

    We study the molecular gas properties of high-z galaxies observed in the ALMA Spectroscopic Survey (ASPECS) that targets an ˜1 arcmin2 region in the Hubble Ultra Deep Field (UDF), a blind survey of CO emission (tracing molecular gas) in the 3 and 1 mm bands. Of a total of 1302 galaxies in the field, 56 have spectroscopic redshifts and correspondingly well-defined physical properties. Among these, 11 have infrared luminosities {L}{IR}\\gt {10}11 {L}⊙ , i.e., a detection in CO emission was expected. Out of these, 7 are detected at various significance in CO, and 4 are undetected in CO emission. In the CO-detected sources, we find CO excitation conditions that are lower than those typically found in starburst/sub-mm galaxy/QSO environments. We use the CO luminosities (including limits for non-detections) to derive molecular gas masses. We discuss our findings in the context of previous molecular gas observations at high redshift (star formation law, gas depletion times, gas fractions): the CO-detected galaxies in the UDF tend to reside on the low-{L}{IR} envelope of the scatter in the {L}{IR}{--}{L}{CO}\\prime relation, but exceptions exist. For the CO-detected sources, we find an average depletion time of ˜1 Gyr, with significant scatter. The average molecular-to-stellar mass ratio ({M}{{H}2}/M *) is consistent with earlier measurements of main-sequence galaxies at these redshifts, and again shows large variations among sources. In some cases, we also measure dust continuum emission. On average, the dust-based estimates of the molecular gas are a factor ˜2-5× smaller than those based on CO. When we account for detections as well as non-detections, we find large diversity in the molecular gas properties of the high-redshift galaxies covered by ASPECS.

  2. Fluorescence probes of spectroscopic and dynamical aspects of molecular photoionization

    NASA Astrophysics Data System (ADS)

    Poliakoff, Erwin D.

    1988-11-01

    Studies were made of vibrationally resolved aspects of shape resonant excitation in the photoionization of N(2)0. This experiment was performed by generating dispersed fluorescence spectra from electronically excited photoions. These results are the first vibrationally resolved results on a polyatomic shape resonance. In vibrationally resolved measurements, different internuclear configurations are probed by sampling alternative vibrational levels of the ion. As a result, the continuum electron behavior can be mapped out most clearly, and the qualitative aspects of the electron ejection can be understood clearly. A central motivation for studying polyatomic shape resonances is that alternative vibrational modes may be explored, revealing facets that are nonexistent for diatomic systems, which are the only systems that have been characterized previously.

  3. 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.

  4. Spectroscopic Studies of Dehydrogenation of Ammonia Borane in Carbon Cryogel

    SciTech Connect

    Sepehri, Saghar; Feaver, Aaron M.; Shaw, Wendy J.; Howard, Christopher J.; Zhang, Qifeng; Autrey, Thomas; Cao, Guozhong

    2007-12-27

    The reaction pathways leading to the thermal decomposition of solid state ammonia borane (AB) incorporated in carbon cryogels (CC) have been studied by spectroscopic methods. The time dependent thermal decomposition was followed by in situ 11B NMR and showed a significant increase in hydrogen release kinetics. Both 11B NMR and Fourier Transform Infrared Spectroscopy (FTIR) show new reaction products formed in the thermal decomposition of AB-CC that are assigned to reactions with surface oxygen groups. The results indicate that incorporation of AB in CC enhance kinetics due to reactions with residual surface-bound oxygen functional groups. The formation of new products with surface-O-B bonds is consistent with the greater reaction exothermicity observed when hydrogen is released from AB-CC materials. Scanning electron microscopy (SEM) shows different morphology of AB in ammonia borane – carbon cryogel (AB-CC) nanocomposite as compared to neat AB. Support for this work is provided by NSF (DMR-0605159), WTC, and EnerG2 LLC as well as the DoE Center of Excellence in Chemical Hydrogen Storage funded by the DOE H2 Program. FTIR experiments were performed in Professor Zhang’s lab in MSE department at UW. Part of this research was performed in the William R. Wiley Environmental Molecular Sciences Laboratory, located at the Pacific Northwest National Laboratory, which is operated by the Battelle for the U.S. Department of Energy.

  5. Spectroscopic Studies of Double Beta Decays and MOON

    NASA Astrophysics Data System (ADS)

    Ejiri, H.

    2007-10-01

    This is a brief review of future spectroscopic experiments of neutrino-less double beta decays (0νββ) and the MOON (Mo Observatory Of Neutrinos) project. Spectroscopic 0νββ experiments of MOON, SuperNEMO and DCBA are planned to study Majorana masses in the quasi-degenerate (QD) and inverted mass hierarchy (IH) regions. MOON aims at 0νββ studies with the ν-mass sensitivities of 100-30 meV by means of a super ensemble of multi-layer modules, each being consist of a scintillator plate, two tracking detector planes and a thin ββ source film.

  6. Molecular assembly in synthesised hydrotalcites of formula Cu xZn 6- xAl 2(OH) 16(CO 3) · 4H 2O—a vibrational spectroscopic study

    NASA Astrophysics Data System (ADS)

    Frost, R. L.; Ding, Z.; Martens, W. N.; Johnson, T. E.; Kloprogge, J. Theo

    2003-01-01

    Infrared and Raman spectroscopy have been used to characterise synthetic hydrotalcites of formula Cu xZn 6- xAl 2(OH) 16(CO 3) · 4H 2O. The spectra have been used to assess the molecular assembly of the cations in the hydrotalcite structure. The spectra may be conveniently subdivided into spectral features based (a) upon the carbonate anion (b) the hydroxyl units (c) water units. The Raman spectra of the hydroxyl-stretching region enable bands to be assigned to the CuOH, ZnOH and AlOH units. It is proposed that in the hydrotalcites with minimal cationic replacement that the cations are arranged in a regular array. For the Cu xZn 6- xAl 2(OH) 16(CO 3) · 4H 2O hydrotalcites, spectroscopic evidence suggests that 'islands' of cations arte formed in the structure. In a similar fashion, the bands assigned to the interlayer water suggest that the water molecules are also in a regular well-structured arrangement. Bands are assigned to the hydroxyl stretching vibrations of water. Three types of water are identified (a) water hydrogen bonded to the interlayer carbonate ion (b) water hydrogen bonded to the hydrotalcite hydroxyl surface and (c) interlamellar water. It is proposed that the water is highly structured in the hydrotalcite as it is hydrogen bonded to both the carbonate anion and the hydroxyl surface.

  7. Spectroscopic and molecular characterization of the oligomeric antenna of the diatom Phaeodactylum tricornutum.

    PubMed

    Lepetit, Bernard; Volke, Daniela; Szabó, Milán; Hoffmann, Ralf; Garab, Gyözö; Wilhelm, Christian; Goss, Reimund

    2007-08-28

    The photosynthetic antenna system of diatoms contains fucoxanthin chlorophyll a/c binding proteins (FCPs), which are membrane intrinsic proteins showing high homology to the light harvesting complexes (LHC) of higher plants. In the present study, we used a mild solubilization of P. tricornutum thylakoid membranes in combination with sucrose density gradient centrifugation or gelfiltration and obtained an oligomeric FCP complex (FCPo). The spectroscopic characteristics and pigment stoichiometries of the FCPo complex were comparable to FCP complexes that were isolated after solubilization with higher detergent per chlorophyll ratios. The excitation energy transfer between the FCP-bound pigments was more efficient in the oligomeric FCPo complexes, indicating that these complexes may represent the native form of the diatom antenna system in the thylakoid membrane. Determination of the molecular masses of the two different FCP fractions by gelfiltration revealed that the FCP complexes consisted of trimers, whereas the FCPo complexes were either composed of six monomers or two tightly associated trimers. In contrast to vascular plants, stable functional monomers could not be isolated in P. tricornutum. Both types of FCP complexes showed two protein bands in SDS-gels with apparent molecular masses of 18 and 19 kDa, respectively. Sequence analysis by MS/MS revealed that the 19 kDa protein corresponded to the fcpC and fcpD genes, whereas the 18 kDa band contained the protein of the fcpE gene. The presence of an oligomeric antenna in diatoms is in line with the oligomeric organization of antenna complexes in different photoautotrophic groups.

  8. On-line separator for {gamma}-spectroscopic studies

    SciTech Connect

    Popeko, A. G.; Belozerov, A. V.; Chepigin, V. I.; Kabachenko, A. P.; Malyshev, O. N.; Shutov, A. V.; Svirikhin, A. I.; Yeremin, A. V.; Dorvaux, O.; Hauschild, K.; Korichi, A.; Lopez-Martens, A.

    2008-05-12

    We report about R and D of the new separator for spectroscopic studies which we plan to install at the beam of the modernized U400R FLNR cyclotron and which will allow to realize new possibilities of the JINR-IN2P3 collaboration project GABRIELA.

  9. On-line separator for γ-spectroscopic studies

    NASA Astrophysics Data System (ADS)

    Popeko, A. G.; Belozerov, A. V.; Chepigin, V. I.; Dorvaux, O.; Hauschild, K.; Kabachenko, A. P.; Korichi, A.; Lopez-Martens, A.; Malyshev, O. N.; Shutov, A. V.; Svirikhin, A. I.; Yeremin, A. V.

    2008-05-01

    We report about R&D of the new separator for spectroscopic studies which we plan to install at the beam of the modernized U400R FLNR cyclotron and which will allow to realize new possibilities of the JINR-IN2P3 collaboration project GABRIELA [1, 2].

  10. 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.}

  11. Vibrational spectroscopic studies, Fukui functions, HOMO-LUMO, NLO, NBO analysis and molecular docking study of (E)-1-(1,3-benzodioxol-5-yl)-4,4-dimethylpent-1-en-3-one, a potential precursor to bioactive agents

    NASA Astrophysics Data System (ADS)

    Al-Wabli, Reem I.; Resmi, K. S.; Sheena Mary, Y.; Yohannan Panicker, C.; Attia, Mohamed I.; El-Emam, Ali A.; Van Alsenoy, C.

    2016-11-01

    The FT-IR and FT-Raman spectra of (E)-1-(1,3-benzodioxol-5-yl)-4,4-dimethylpent-1-en-3-one were recorded and analyzed experimentally and theoretically. The observed experimental and theoretical wavenumbers were assigned using potential energy distribution. The NLO properties were evaluated by the determination of first and second hyperpolarizabilities of the title compound. From the frontier molecular orbital study, the HOMO centers over the entire molecule except the methyl groups, while the LUMO is over the entire molecule except the CH2 group with the dioxole ring and one of the methyl groups. From the MEP plot, it is evident that the negative region covers the carbonyl and Cdbnd C groups and the positive region is over CH2 groups. The Fukui functions are also reported. The calculated geometrical parameters are in agreement with the XRD results. From the molecular docking study, the docked ligand title compound forms a stable complex with the androgen receptor and gives a binding affinity value of -8.1 kcal/mol and the results suggest that the compound might exhibit inhibitory activity against androgen receptor.

  12. 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.

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

    PubMed

    Meierott, Stefan; Néel, Nicolas; Kröger, Jörg

    2016-07-07

    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.

  14. Vibrational and electronic spectroscopic studies of melatonin

    NASA Astrophysics Data System (ADS)

    Singh, Gurpreet; Abbas, J. M.; Dogra, Sukh Dev; Sachdeva, Ritika; Rai, Bimal; Tripathi, S. K.; Prakash, Satya; Sathe, Vasant; Saini, G. S. S.

    2014-01-01

    We report the infrared absorption and Raman spectra of melatonin recorded with 488 and 632.8 nm excitations in 3600-2700 and 1700-70 cm-1 regions. Further, we optimized molecular structure of the three conformers of melatonin within density functional theory calculations. Vibrational frequencies of all three conformers have also been calculated. Observed vibrational bands have been assigned to different vibrational motions of the molecules on the basis of potential energy distribution calculations and calculated vibrational frequencies. Observed band positions match well with the calculated values after scaling except Nsbnd H stretching mode frequencies. It is found that the observed and calculated frequencies mismatch of Nsbnd H stretching is due to intermolecular interactions between melatonin molecules.

  15. Halo Nucleus 11Be: A Spectroscopic Study via Neutron Transfer

    SciTech Connect

    Schmitt, Kyle; Jones, K. L.; Bey, A.; Ahn, S.H.; Bardayan, Daniel W; Blackmon, Jeffery C; Brown, S.; Chae, Kyung Yuk; Chipps, K.; Cizewski, J. A.; Kozub, R. L.; Liang, J Felix; Matei, Catalin; Matos, M.; Moazen, Brian H; Nesaraja, Caroline D; Nunes, F. M.; O'Malley, Patrick; Pain, Steven D; Peters, W. A.; Pittman, S. T.; Wilson, G.

    2012-01-01

    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 11Be, the spectroscopic factors for the two bound states remain poorly constrained. In the present work, the 10Be d;p reaction has been used in inverse kinematics at four beam energies to study the structure of 11Be. 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 n j 2s1=2 state coupled to the ground state of 10Be 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.

  16. Spectroscopic study of graphene oxide membranes exposed to ultraviolet light

    SciTech Connect

    Schwenzer, Birgit; Kaspar, Tiffany C.; Shin, Yongsoon; Gotthold, David W.

    2016-05-16

    Research on graphene oxide (GO) as anything but a precursor material for synthesizing graphene started to pick up in 20061,2 and was soon followed by a first report of freestanding GO membranes (also referred to as GO paper) from R. S. Ruoff’s group at Northwestern University.3 The first GO membranes were prepared by vacuum filtration. More recently, larger scale GO membranes have been prepared by tape casting4 and other methods.5 In step with the development of new fabrication techniques, GO membranes are now tested for a wide array of applications6 ranging from energy-related4,7 or biomedical8 applications to more conventional uses for filtration9 and dehumidification.10 For all these proposed and implemented applications it remains to be seen how sensitive each of them is with respect to chemical and physical changes of the GO membranes over time. In this study, we report the effects of UV exposure on 2D-hierarchically stacked (Fig. S1 in ESI†) GO membranes. Macroscopically observable changes, such as darkening and mechanical deformation, have been correlated to chemical changes at the molecular level through spectroscopic measurements. Not only do the results of this work offer insights into the stability of GO membranes under UV light, but the findings will enable researchers, who are studying the use of these materials for different applications, to better understand the shelf life and packaging requirements for GO membranes. Furthermore, our results demonstrate the feasibility of deep ultraviolet (DUV) photolithography for graphene oxide-based devices. This approach is readily scalable as opposed to previous reports on photolithographic patterned reduction of GO to graphene by AFM,11 electron-beam12 or with an extreme ultraviolet (λ = 46.9 nm) laser.13

  17. Effect of molecular conformation on spectroscopic properties of symmetrical Schiff bases derived from 1,4-phenylenediamine

    NASA Astrophysics Data System (ADS)

    Fang, Zhengjun; Cao, Chenzhong

    2013-03-01

    The relationship between the molecular conformation and spectroscopic properties of symmetrical bis-Schiff bases was explored experimentally. Seven samples of compounds p-X-C6H4CHdbnd NC6H4Ndbnd CHC6H4-p-X (X = OMe, Me, Et, Cl, F, CF3, or CN) were prepared for this study, and their crystal structures were measured by X-ray diffraction. Their λmax values in ethanol, acetonitrile, chloroform and cyclohexane solvents were measured, and their δC(Cdbnd N) values in chloroform-d were determined. The results show that the νmax is dependent on the substituents at the benzylidene ring and the dihedral angle τ of the titled molecules, and the term sin(τ) is suitable to modify the substituent effects on the νmax. However, experimental investigations indicate that the dihedral angle τ has a limited effect on the values of δC(Cdbnd N). This study provides a new understanding for the molecular conformation on spectroscopic properties of symmetrical Schiff bases.

  18. VCD spectroscopic and molecular dynamics analysis of the Trp-cage miniprotein TC5b.

    PubMed

    Copps, Jeffrey; Murphy, Richard F; Lovas, Sándor

    2007-01-01

    TC5b is a 20 residue polypeptide notable for its compact tertiary structure, a rarity for a short peptide. This structure is due to the "Trp-cage" motif, an association of aromatic, Pro, and Gly residues. The structure of TC5b has been fully characterized by NMR and electronic circular dichroism (ECD) studies, but has never been studied with vibrational circular dichroism (VCD) spectroscopy, which may reveal finer structure. In this study, we examine the VCD spectra of TC5b to characterize the spectroscopic signature of the peptide and its comprising structural elements. TC5b exhibited a negative-positive-negative triplet which is associated with alpha-helical structure in deuterated solvents but also signs of a polyproline II (PPII) helix in the amide I' region. Detection of this element was complicated by the aforementioned triplet form, as well as by an upfrequency shift in PPII helical elements due to the use of the deuterated organic solvents DMSO-d(6) and TFE-d(1). Nevertheless, while ECD spectra showed only alpha-helical structure for TC5b, VCD spectroscopy revealed a more complex structure which was in agreement with NMR results. VCD spectroscopy also showed a rapid conformational change of the peptide at temperatures above 35 degrees C in D(2)O and in aqueous solvent with greater than 75% DMSO-d(6) content. Molecular dynamics (MD) simulations to investigate this latter effect of DMSO-d(6) on TC5b were conducted in DMSO and 50% (v/v) DMSO in H(2)O. In DMSO unfolding of the peptide was rapid while in 50% (v/v) DMSO in H(2)O the unfolding was more gradual.

  19. Structural and spectroscopic studies of fluoroprotactinates.

    PubMed

    De Sio, Stéphanie M; Wilson, Richard E

    2014-02-03

    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.

  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. Binding of Tetracycline and Chlortetracycline to the Enzyme Trypsin: Spectroscopic and Molecular Modeling Investigations

    PubMed Central

    Chi, Zhenxing; Liu, Rutao; Yang, Hongxu; Shen, Hengmei; Wang, Jing

    2011-01-01

    Tetracycline (TC) and chlortetracycline (CTC) are common members of the widely used veterinary drug tetracyclines, the residue of which in the environment can enter human body, being potentially harmful. In this study, we establish a new strategy to probe the binding modes of TC and CTC with trypsin based on spectroscopic and computational modeling methods. Both TC and CTC can interact with trypsin with one binding site to form trypsin-TC (CTC) complex, mainly through van der Waals' interactions and hydrogen bonds with the affinity order: TC>CTC. The bound TC (CTC) can result in inhibition of trypsin activity with the inhibition order: CTC>TC. The secondary structure and the microenvironment of the tryptophan residues of trypsin were also changed. However, the effect of CTC on the secondary structure content of trypsin was contrary to that of TC. Both the molecular docking study and the trypsin activity experiment revealed that TC bound into S1 binding pocket, competitively inhibiting the enzyme activity, and CTC was a non-competitive inhibitor which bound to a non-active site of trypsin, different from TC due to the Cl atom on the benzene ring of CTC which hinders CTC entering into the S1 binding pocket. CTC does not hinder the binding of the enzyme substrate, but the CTC-trypsin-substrate ternary complex can not further decompose into the product. The work provides basic data for clarifying the binding mechanisms of TC (CTC) with trypsin and can help to comprehensively understanding of the enzyme toxicity of different members of tetracyclines in vivo. PMID:22205948

  2. Interaction between 8-methoxypsoralen and trypsin: Monitoring by spectroscopic, chemometrics and molecular docking approaches

    NASA Astrophysics Data System (ADS)

    Liu, Yingying; Zhang, Guowen; Zeng, Ni; Hu, Song

    2017-02-01

    8-Methoxypsoralen (8-MOP) is a naturally occurring furanocoumarin with various biological activities. However, there is little information on the binding mechanism of 8-MOP with trypsin. Here, the interaction between 8-MOP and trypsin in vitro was determined by multi-spectroscopic methods combined with the multivariate curve resolution-alternating least squares (MCR-ALS) chemometrics approach. An expanded UV-vis spectral data matrix was analysed by MCR-ALS, the concentration profiles and pure spectra for the three reaction species (trypsin, 8-MOP and 8-MOP-trypsin) were obtained to monitor the interaction between 8-MOP and trypsin. The fluorescence data suggested that a static type of quenching mechanism occurred in the binding of 8-MOP to trypsin. Hydrophobic interaction dominated the formation of the 8-MOP-trypsin complex on account of the positive enthalpy and entropy changes, and trypsin had one high affinity binding site for 8-MOP with a binding constant of 3.81 × 104 L mol- 1 at 298 K. Analysis of three dimensional fluorescence, UV-vis absorption and circular dichroism spectra indicated that the addition of 8-MOP induced the rearrangement of the polypeptides carbonyl hydrogen-bonding network and the conformational changes in trypsin. The molecular docking predicted that 8-MOP interacted with the catalytic residues His57, Asp102 and Ser195 in trypsin. The binding patterns and trypsin conformational changes may result in the inhibition of trypsin activity. This study has provided insights into the binding mechanism of 8-MOP with trypsin.

  3. 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.

  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 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.

  6. Integrated Spectroscopic Studies of Hydrous Sulfate Minerals

    NASA Technical Reports Server (NTRS)

    Dyar, M. D.; Lane, M. D.; Bishop, J. L.; OConnor, V.; Cloutis, E.; Hiroi, T.

    2005-01-01

    Sulfate minerals have been identified in Martian meteorites and on Mars using a suite of instruments aboard the MER rovers. These results have confirmed previous groundbased observations and orbital measurements that suggested their presence. The orbiting OMEGA instrument on Mars Express is also finding evidence for sulfate. In order to better interpret remote-sensing data, we present here the results of a coordinated visible/near infrared (VNIR) reflectance, Moussbauer (MB), and thermal emittance study of wellcharacterized hydrous sulfate minerals.

  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 Study of Microwave Induced Plasma

    SciTech Connect

    Jovicevic, S.

    2004-12-01

    The results of the spatial distribution studies of electron densities, excitation and rotational temperatures and atomic line intensities of various elements in an atmospheric pressure mini-MIP torch with tangential argon flow. The electron number density, ne, is determined from the width of the hydrogen H{beta} 486.13 nm line while excitation temperature, Texc, is evaluated from the Boltzmann plot of relative line intensities either of carrier gas-argon or neutral iron that is introduced in the form of aerosols in MIP, The rotational temperatures, Trot, are determined from the relative intensities of OH (R2 and Q1 branch) electronic band A2{sigma} - X2{pi} (0,0) and to N{sub 2}{sup +} first negative system B{sup 2} {sigma}{sub u}{sup +} - X{sup 2} {sigma}{sub g}{sup +} (P branch). For the selected input power of 100 W, the influence of hydrogen in the wet and desolvated aerosols and support gas and the corresponding changes of the electron density, excitation and rotational temperature distributions are studied. The influence of potassium, low ionization potential element, to the spatial distribution of ne, Texc and Trot is studied also. Spatial intensity distributions and maximum intensities for investigate atomic line are determinate for the same conditions.

  9. Spectroscopic Studies of Atmospheric Aerosol Chemistry

    NASA Astrophysics Data System (ADS)

    Wamsley, R.; Leather, K.; Horn, A. B.; Percival, C.

    2008-12-01

    Particles are ubiquitous in the troposphere and are involved in chemical and physical processes affecting the composition of the atmosphere, climate, cloud albedo and human health (Finlayson-Pitts and Pitts, 2000). Organic species, such as alcohols, carboxylic acids, ketones, aldehydes, aromatics, alkenes and alkanes, originate both from anthropogenic and natural sources and comprise a large component of atmospheric particles. Gas-phase species, such as ozone, can oxidize these organics, changing the particle's oxygen-to carbon ratio and potentially altering its hygroscopicity, viscosity, morphology and reactivity. One reaction in particular, that between ozone and oleic acid, has been the focus of several recent studies and extensively researched by Ziemann (2005). Oleic acid reacts readily with ozone and has a low vapor pressure making this reaction convenient to study in the laboratory and has become the benchmark for studying heterogeneous reactions representing the oxidative processing of atmospheric organic aerosols. A critical source of uncertainty in reactivity estimates is a lack of understanding of the mechanism through which some VOCs are oxidized. This knowledge gap is especially critical for aromatic compounds. Because the intermediate reaction steps and products of aromatics oxidation are unknown, chemical mechanisms incorporate parameters estimated from environmental chamber experiments to represent their overall contribution to ozone formation, e.g. Volkamer et al. ( 2006). Previous studies of uncertainties in incremental reactivity estimates for VOCs found that the representation of aromatics chemistry contributed significantly to the estimated 40 - 50% uncertainties in the incremental reactivities of common aromatic compounds Carter et al. (2002). This study shows development of an effective IR method that can monitor the reaction and hence obtain the kinetics of the ozonolysis of an aromatic compound in the aerosol phase. The development of such

  10. Study of Gallstones by Spectroscopic Methods

    NASA Astrophysics Data System (ADS)

    Pichugina, A. A.; Tsyro, L. V.; Afanasyev, D. A.; Kiselev, S. A.; Unger, F. G.

    2017-03-01

    We have conducted studies of cholesterol gallstones by electron paramagnetic resonance (EPR), x-ray diffraction (XRD), and nuclear magnetic resonance (1H NMR). The results obtained indicate that the cholesterol gallstone spectra are identical. We have used EPR to establish the presence in the gallstones of species containing open shell spin orbitals, which act as centers for colloidal particles. The 1H NMR spectra and the XRD data indicate the presence in the gallstones of cholesterol and structures representing a desmosterol transition, which form shells around the spin centers.

  11. 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.

  12. Spectroscopic studies of silver boro tellurite glasses

    NASA Astrophysics Data System (ADS)

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

    2014-04-01

    The FTIR absorption and Raman scattering studies were used to obtain the structural information of AgI-Ag2O-[(1-x)B2O3-xTeO2] (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 TeO2 on SBT glass system is that as increasing the concentration of TeO2 the band intensity at 707 cm-1 increase.

  13. Spectroscopic studies near the proton drip line

    SciTech Connect

    Toth, K.S. ); Moltz, D.M.; Nitschke, J.M.; Wilmarth, P.A. ); Robertson, J.D. )

    1990-01-01

    We have investigated nuclei close to the proton drip line by using heavy-ion fusion reactions to produce extremely neutron-deficient nuclides. Their nuclear decay properties were studied by using on-line isotope separators at Oak Ridge (UNISOR) and Berkeley (OASIS), the Oak Ridge National Laboratory velocity filter, and a fast helium-gas-jet transport system at Lawrence Berkeley Laboratory 88-Inch Cyclotron. Many isotopes, isomers, and {beta}-delayed-proton and {alpha}-particle emitters were discovered. This contribution summarizes three topics that are part of our overall program: decay rates of even-even {alpha}-particle emitters, mass excesses of {sup 181}Pb, {sup 182}Pb, and {sup 183}Pb, and {beta}-delayed proton emitters near N = 82. 14 refs., 6 figs.

  14. 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.

  15. Interactions of Isophorone Derivatives with DNA: Spectroscopic Studies

    PubMed Central

    Deiana, Marco; Matczyszyn, Katarzyna; Massin, Julien; Olesiak-Banska, Joanna; Andraud, Chantal; Samoc, Marek

    2015-01-01

    Interactions of three new isophorone derivatives, Isoa Isob and Isoc with salmon testes DNA have been investigated using UV-Vis, fluorescence and circular dichroism spectroscopic methods. All the studied compounds interact with DNA through intercalative binding mode. The stoichiometry of the isophorone/DNA adducts was found to be 1:1. The fluorescence quenching data revealed a binding interaction with the base pairs of DNA. The CD data indicate that all the investigated isophorones induce DNA modifications. PMID:26069963

  16. Spectroscopic Studies of Nearby Cool Stars: The DUNES Sample

    NASA Astrophysics Data System (ADS)

    Maldonado, J.; Martínez-Arnáiz, R. M.; Eiroa, C.; Montes, D.

    2009-02-01

    At the Universities of Madrid we are carrying out a systematic analysis of the spectroscopic properties of the nearby (d<25 pc), late-type stellar population with the aim of contributing to the knowledge of the stellar formation history in the solar neighbourhood. Part of our sample will be observed by DUNES, a Herschel OTKP aiming at detecting and studying cold, faint dust disks around nearby stars. In this contribution we present some preliminary results of the kinematics of the DUNES sample.

  17. Spectroscopic Studies of Nearby Cool Stars: The DUNES Sample

    NASA Astrophysics Data System (ADS)

    Maldonado, J.; Martinez-Arnáiz, R. M.; Eiroa, C.; Montes, D.

    At the universities of Madrid we are carrying out a systematic analysis of the spectroscopic properties of the nearby (d<25pc), late-type stellar population with the aim of contributing to the knowledge of the stellar formation history in the solar neighbourhood. Part of our sample will be observed by DUNES, a Herschel OTKP aiming at detecting and studying cold, faint dust disks around nearby stars. In this contribution we present some preliminary results on the kinematics of the DUNES sample.

  18. 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.

  19. 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.

  20. 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.

  1. Spectroscopic studies of alkaline activated slag geopolymers

    NASA Astrophysics Data System (ADS)

    Mozgawa, W.; Deja, J.

    2009-04-01

    In the work, results of structural studies of different geopolymers, obtained using a granulated blast furnace slag, are presented. The slag was subjected to an alkaline activation process. As activators, NaOH, Na 2CO 3 and liquid glass were applied. IR and NMR spectroscopy were the main experimental methods used, the results obtained were compared with XRD phase analysis and SEM observations. In the IR spectra of raw slag as well as in the spectra of products of paste hydration, the bands due to the characteristic vibrations of bonds observed in both types of oxygen bridges: Si-O-Si and Si-O-Al, were assigned. These bridges constitute basic structural units, forming tetrahedral geopolymer chains. It was found that the slag composition, mainly SiO 2/Al 2O 3 ratio and modification in oxides concentration, influences the presence of the bands connected with the phases (mainly C-S-H) formed during the hydration in the IR spectra. Additionally, significant effect of amorphous phases share on the spectra shape was established. 29Si and 27Al MAS-NMR spectra of initial slag geopolymers and pastes provided information concerning coordination of both atoms in the structures. It was revealed that the kind of slag geopolymers and the conditions of paste hydration influence connectedness of silicooxygen tetrahedra and coordination number of aluminium atoms. Based on IR spectra, it was also possible to determine the influence of the activator type, activation time and hydration conditions on the products formed. Significant changes were observed for the bands assigned to vibrations of carbonate and hydroxide groups. The changes were also noticed in the case of bands due to vibrations of silicate and aluminosilicate bonds.

  2. Metamictization of zircon: Raman spectroscopic study

    NASA Astrophysics Data System (ADS)

    Zhang, Ming; Salje, Ekhard K. H.; Farnan, Ian; Graeme-Barber, Ann; Daniel, Philippe; Ewing, Rodney C.; Clark, Andrew M.; Leroux, Hugues

    2000-02-01

    Raman spectroscopy of radiation-damaged natural zircon samples shows increased line broadening and shifts of phonon frequencies with increasing radiation dose. Stretching and bending frequencies of SiO4 tetrahedra soften dramatically with increasing radiation damage. The frequency shifts can be used to determine the degree of radiation damage. Broad spectral bands related to Si-O stretching vibrations between 900 and 1000 cm-1 were observed in metamict/amorphous zircon. The radiation-dose-independent spectral profiles and the coexistence of this broad background and relative sharp Raman modes in partially damaged samples indicate that these bands are correlated with amorphous domains in zircon. The spectral profiles of metamict zircon suggest that in comparison with silica, the SiO4 tetrahedra are less polymerized in metamict zircon. This study also shows that ZrO2 and SiO2 are not the principal products of metamictization in zircon. No indication of bulk chemical unmixing of zircon into ZrO2 and SiO2 was found in 26 samples with a large variation of radiation damage (maximum dose: 23.5 × 1018 icons/Journals/Common/alpha" ALT="alpha" ALIGN="TOP"/> -events g-1 ). Only one sample showed clearly, in all measured sample areas, extra sharp lines at 146, 260, 312, 460 and 642 cm-1 characteristic of tetragonal ZrO2 . The geological (and possibly artificial heating) history of this sample is not known. It is concluded that radiation damage without subsequent high temperature annealing does not cause unmixing of zircon into constituent oxides.

  3. Spectroscopic studies of cold, gas-phase biomolecular ions

    NASA Astrophysics Data System (ADS)

    Rizzo, Thomas R.; Stearns, Jaime A.; Boyarkin, Oleg V.

    While the marriage of mass spectrometry and laser spectroscopy is not new, developments over the last few years in this relationship have opened up new horizons for the spectroscopic study of biological molecules. The combination of electrospray ionisation for producing large biological molecules in the gas phase together with cooled ion traps and multiple-resonance laser schemes are allowing spectroscopic investigation of individual conformations of peptides with more than a dozen amino acids. Highly resolved infrared spectra of single conformations of such species provide important benchmarks for testing the accuracy of theoretical calculations. This review presents a number of techniques employed in our laboratory and in others for measuring the spectroscopy of cold, gas-phase protonated peptides. We show examples that demonstrate the power of these techniques and evaluate their extension to still larger biological molecules.

  4. 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

  5. Structure and vibrational spectroscopic study of alpha-tocopherol

    NASA Astrophysics Data System (ADS)

    Singh, Gurpreet; Sachdeva, Ritika; Rai, Bimal; Saini, G. S. S.

    2017-09-01

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

  6. 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.

  7. 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.

    PubMed

    Ji, Cuiying; Zhang, Xuewei; Yu, Peiqiang

    2016-03-05

    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.

  8. SpectraPlot.com: Integrated spectroscopic modeling of atomic and molecular gases

    NASA Astrophysics Data System (ADS)

    Goldenstein, Christopher S.; Miller, Victor A.; Mitchell Spearrin, R.; Strand, Christopher L.

    2017-10-01

    SpectraPlot is a web-based application for simulating spectra of atomic and molecular gases. At the time this manuscript was written, SpectraPlot consisted of four primary tools for calculating: (1) atomic and molecular absorption spectra, (2) atomic and molecular emission spectra, (3) transition linestrengths, and (4) blackbody emission spectra. These tools currently employ the NIST ASD, HITRAN2012, and HITEMP2010 databases to perform line-by-line simulations of spectra. SpectraPlot employs a modular, integrated architecture, enabling multiple simulations across multiple databases and/or thermodynamic conditions to be visualized in an interactive plot window. The primary objective of this paper is to describe the architecture and spectroscopic models employed by SpectraPlot in order to provide its users with the knowledge required to understand the capabilities and limitations of simulations performed using SpectraPlot. Further, this manuscript discusses the accuracy of several underlying approximations used to decrease computational time, in particular, the use of far-wing cutoff criteria.

  9. 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).

  10. 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.

  11. 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.

  12. 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.

  13. Deciphering the Positional Influence of the Hydroxyl Group in the Cinnamoyl Part of 3-Hydroxy Flavonoids for Structural Modification and Their Interaction with the Protonated and B Form of Calf Thymus DNA Using Spectroscopic and Molecular Modeling Studies.

    PubMed

    Pradhan, Ankur Bikash; Haque, Lucy; Bhuiya, Sutanwi; Ganguly, Aniruddha; Das, Suman

    2015-06-11

    Studies on the interaction of naturally occurring flavonoids with different polymorphic forms of nucleic acid are helpful for understanding the molecular aspects of binding mode and providing direction for the use and design of new efficient therapeutic agents. However, much less information is available on the interactions of these compounds with different polymorphic forms of DNA at the molecular level. In this report we investigated the interaction of two widely abundant dietary flavonoids quercetin (Q) and morin (M) with calf thymus (CT) DNA. Spectrophotometric, spectropolarimetric, viscosity measurement, and molecular docking simulation methods are used as tools to delineate the binding mode and probable location of the flavonoids and their effects on the stability and conformation of DNA. It is observed that in the presence of the protonated form of DNA the dual fluorescence of Q and M resulting from the excited-state intramolecular proton transfer (ESIPT) is modified significantly. Structural analysis showed Q and M binds weakly to the B form (groove binding) compared to the protonated form of CT DNA (electrostatic interaction). In both cases, Q binds strongly to both forms of DNA compared to M.

  14. Synthesis, spectroscopic (FT-IR, FT-Raman, NMR, UV-Visible), NLO, NBO, HOMO-LUMO, Fukui function and molecular docking study of (E)-1-(5-bromo-2-hydroxybenzylidene)semicarbazide

    NASA Astrophysics Data System (ADS)

    Raja, M.; Raj Muhamed, R.; Muthu, S.; Suresh, M.

    2017-08-01

    The title compound, (E)-1-(5-bromo-2-hydroxybenzylidene)semicarbazide (15BHS) was synthesized and characterized by FT-IR, FT-Raman, UV, 1HNMR and 13CNMR spectral analysis. The optimized molecular geometry, the vibrational wavenumbers, the infrared intensities and the Raman scattering activities were calculated by using density functional theory(DFT) B3LYP method with 6-311++G(d,p) basis set. The detailed interpretation of the vibrational spectra has been carried out by VEDA program. The calculated HOMO and LUMO energies show that charge transfer within the molecule. Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital analysis (NBO). The first order hyperpolarizability, Molecular electrostatic potential (MEP) and Fukui functions were also performed. To study the biological activity of the investigation molecule, molecular docking was done to identify the hydrogen bond lengths and binding energy with different antifungal proteins. The thermodynamic properties (heat capacity, entropy, and enthalpy) of the 15BHS at different temperatures have been calculated.

  15. Vibrational spectroscopic studies of newly developed synthetic biopolymers.

    PubMed

    Bista, Rajan K; Bruch, Reinhard F; Covington, Aaron M

    2010-05-01

    Vibrational spectroscopic techniques such as near-infrared (NIR), Fourier transform infrared (FTIR), and Raman spectroscopy are valuable diagnostic tools that can be used to elucidate comprehensive structural information of numerous biological samples. In this review article, we have highlighted the advantages of nanotechnology and biophotonics in conjunction with vibrational spectroscopic techniques in order to understand the various aspects of new kind of synthetic biopolymers termed as polyethylene glycol (PEG)ylated lipids. In contrast to conventional phospholipids, these novel lipids spontaneously form liposomes or nanovesicles upon hydration, without the supply of external activation energy. The amphiphiles considered in this study differ in their hydrophobic acyl chain length and contain different units of PEG hydrophilic headgroups. We have further explored the thermotropic phase behaviors and associated changes in the conformational order/disorder of such lipids by using variable-temperature FTIR and Raman spectroscopy. Phase transition temperature profiles and correlation between various spectral indicators have been identified by either monitoring the shifts in the vibrational peak positions or plotting vibrational peak intensity ratios in the C--H stretching region as a function of temperature. To supplement our observations of phase transformations, a thermodynamic approach known as differential scanning calorimetry (DSC) has been applied and revealed a good agreement with the infrared and Raman spectroscopic data. Finally, the investigation of thermal properties of lipids is extremely crucial for numerous purposes, thus the results obtained in this work may find application in a wide variety of studies including the development of PEGylated lipid based drug and substances delivery vehicles.

  16. The Origin, Composition and History of Comets from Spectroscopic Studies

    NASA Technical Reports Server (NTRS)

    Allamandola, L. J.

    1997-01-01

    A wealth of information essential to understanding the composition and physical structure of cometary ice and hence gain deep insight into the comet's origin and history, can be gleaned by carrying out a full range of spectroscopic studies on the returned sample. These studies ought to be among the first performed as they are generally non-destructive and will provide a broad data bank which will be crucial in planning subsequent analysis. Examples of the spectroscopic techniques along with relative sensitivities and transitions probed, are discussed. Different kind of "spectroscopy" is summarized, with emphasis placed on the kind of information each provides. Infrared spectroscopy should be the premier method of analysis as the mid-IR absorption spectrum of a substance contains more global information about the identity and structure of that material than any other property. In fact, the greatest strides in our understanding of the composition of interstellar ices (thought by many to be the primordial material from which comets have formed) have been taken during the past ten years or so because this was when high quality infrared spectra of the interstellar medium (ISM) first became available. The interpretation of the infrared spectra of mixtures, such as expected in comets, is often (not always) ambiguous. Consequently, a full range of other non-destructive, complementary spectroscopic measurements are required to fully characterize the material, to probe for substances for which the IR is not well suited and to lay the groundwork for future analysis. Given the likelihood that the icy component (including some of the organic and mineral phases) of the returned sample will be exceedingly complex, these techniques must be intensely developed over the next decade and then made ready to apply flawlessly to what will certainly be one of the most precious, and most challenging, samples ever analyzed.

  17. Studies of DNA-binding properties of lafutidine as adjuvant anticancer agent to calf thymus DNA using multi-spectroscopic approaches, NMR relaxation data, molecular docking and dynamical simulation.

    PubMed

    Yang, Hongqin; Tang, Peixiao; Tang, Bin; Huang, Yanmei; He, Jiawei; Li, Shanshan; Li, Hui

    2017-06-01

    The interactions between lafutidine (LAF) and calf thymus DNA (ctDNA) have been investigated both experimentally and theoretically. UV-vis absorption studies confirmed that LAF binds to ctDNA through non-covalent interactions. Fluorescence quenching and time-resolved fluorescence spectroscopy studies showed that the binding of LAF with ctDNA occurred through static quenching mechanism, resulting in the formation of a LAF-ctDNA complex. The binding constants (K) of the complex were found to be around 10(3)M(-1) via NMR relaxation rates and fluorescence data, and the calculated thermodynamic parameters indicated that hydrogen bonds and van der Waals forces played major roles in the binding of LAF to ctDNA. The changes in CD spectra indicated that LAF induced a slight perturbation on the base stacking and helicity of B-DNA. A comparative study of the LAF-ctDNA complex with respect to potassium iodide quenching experiments and competition displacement assays with ethidium bromide, acridine orange, and Hoechst 33258 probes suggested that LAF interacted with ctDNA by minor groove mode. Molecular docking analysis further supported the minor groove binding. Molecular dynamics simulation indicated that LAF depart from the C-G region of DNA, but it can steadily bind with the middle part of DNA composed by A-T base pairs. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. Interaction of an antiepileptic drug, lamotrigine with human serum albumin (HSA): Application of spectroscopic techniques and molecular modeling methods.

    PubMed

    Poureshghi, Fatemeh; Ghandforoushan, Parisa; Safarnejad, Azam; Soltani, Somaieh

    2017-01-01

    Lamotrigine (an epileptic drug) interaction with human serum albumin (HSA) was investigated by fluorescence, UV-Vis, FTIR, CD spectroscopic techniques, and molecular modeling methods. Binding constant (Kb) of 5.74×10(3) and number of binding site of 0.97 showed that there is a slight interaction between lamotrigine and HSA. Thermodynamic studies was constructed using the flourimetric titrations in three different temperatures and the resulted data used to calculate the parameters using Vant Hoff equation. Decreased Stern Volmer quenching constant by enhanced temperature revealed the static quenching mechanism. Negative standard enthalpy (ΔH) and standard entropy (ΔS) changes indicated that van der Waals interactions and hydrogen bonds were dominant forces which facilitate the binding of Lamotrigine to HSA, the results were confirmed by molecular docking studies which showed no hydrogen binding. The FRET studies showed that there is a possibility of energy transfer between Trp214 and lamotrigine. Also the binding of lamotrigine to HSA in the studied concentrations was not as much as many other drugs, but the secondary structure of the HSA was significantly changed following the interaction in a way that α-helix percentage was reduced from 67% to 57% after the addition of lamotrigine in the molar ratio of 4:1 to HSA. According to the docking studies, lamotrigine binds to IB site preferably.

  19. Experimental (FT-IR, FT-Raman, UV and NMR) and quantum chemical studies on molecular structure, spectroscopic analysis, NLO, NBO and reactivity descriptors of 3,5-Difluoroaniline.

    PubMed

    Pathak, S K; Srivastava, R; Sachan, A K; Prasad, O; Sinha, L; Asiri, A M; Karabacak, M

    2015-01-25

    Comprehensive investigation of geometrical and electronic structure in ground as well as the first excited state of 3,5-Difluoroaniline (C6H5NF2) was carried out. The experimentally observed spectral data (FT-TR and FT-Raman) of the title compound was compared with the spectral data obtained by DFT/B3LYP method using 6-311++G(d,p) basis set. The molecular properties like dipole moment, polarizability, first static hyperpolarizability, molecular electrostatic potential surface (MEPs), and contour map were calculated to get a better insight of the properties of the title molecule. Natural bond orbital (NBO) analysis was applied to study stability of the molecule arising from charge delocalization. UV-Vis spectrum of the title compound was also recorded and the electronic properties, such as Frontier orbitals and band gap energies were measured by TD-DFT approach. Total and partial density of state (TDOS and PDOS) and also overlap population density of state (OPDOS) diagrams analysis were presented. Global and local reactivity descriptors were computed to predict reactivity and reactive sites on the molecule. (1)H and (13)C NMR spectra by using gauge including atomic orbital (GIAO) method of studied compound were compared with experimental data obtained. Moreover, the thermodynamic properties were evaluated.

  20. 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.

    PubMed

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

    2015-02-05

    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, (1)H 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.

  1. Syntheses, spectroscopic characterization, thermal study, molecular modeling, and biological evaluation of novel Schiff's base benzil bis(5-amino-1,3,4-thiadiazole-2-thiol) with Ni(II), and Cu(II) metal complexes.

    PubMed

    Chandra, Sulekh; Gautam, Seema; Rajor, Hament Kumar; Bhatia, Rohit

    2015-02-25

    Novel Schiff's base ligand, benzil bis(5-amino-1,3,4-thiadiazole-2-thiol) was synthesized by the condensation of benzil and 5-amino-1,3,4-thiadiazole-2-thiol in 1:2 ratio. The structure of ligand was determined on the basis of elemental analyses, IR, (1)H NMR, mass, and molecular modeling studies. Synthesized ligand behaved as tetradentate and coordinated to metal ion through sulfur atoms of thiol ring and nitrogen atoms of imine group. Ni(II), and Cu(II) complexes were synthesized with this nitrogen-sulfur donor (N2S2) ligand. Metal complexes were characterized by elemental analyses, molar conductance, magnetic susceptibility measurements, IR, electronic spectra, EPR, thermal, and molecular modeling studies. All the complexes showed molar conductance corresponding to non-electrolytic nature, expect [Ni(L)](NO3)2 complex, which was 1:2 electrolyte in nature. [Cu(L)(SO4)] complex may possessed square pyramidal geometry, [Ni(L)](NO3)2 complex tetrahedral and rest of the complexes six coordinated octahedral/tetragonal geometry. Newly synthesized ligand and its metal complexes were examined against the opportunistic pathogens. Results suggested that metal complexes were more biological sensitive than free ligand.

  2. 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.

  3. FTIR Spectroscopic and Molecular Analysis during Differentiation of Pluripotent Stem Cells to Pancreatic Cells

    PubMed Central

    Mata-Miranda, Monica Maribel; Sanchez-Monroy, Virginia; Delgado-Macuil, Raul Jacobo; Perez-Ishiwara, David Guillermo

    2016-01-01

    Some of the greatest challenges in stem cells (SCs) biology and regenerative medicine are differentiation control of SCs and ensuring the purity of differentiated cells. In this work, we differentiated mouse pluripotent stem cells (mPSCs) toward pancreatic cells characterizing this differentiation process by molecular and spectroscopic technics. Both mPSCs and Differentiated Pancreatic Cells (DPCs) were subjected to a genetic, phenotypic, and biochemical analysis by real-time quantitative PCR (RT-qPCR), immunocytochemistry, and Fourier Transform Infrared (FTIR) spectroscopy. Cultured mPCSs expressed pluripotent genes and proteins (Nanog and SOX2). DPCs expressed endodermal genes (SOX17 and Pdx1) at day 11, an inductor gene of embryonic pancreas development (Pdx1) at day 17 and pancreas genes and proteins (Insulin and Glucagon) at day 21 of differentiation. Likewise, FTIR spectra of mPSCs and DPCs at different maturation stages (11, 17, and 21 days) were obtained and showed absorption bands related with different types of biomolecules. These FTIR spectra exhibited significant spectral changes agreeing with the differentiation process, particularly in proteins and nucleic acids bands. In conclusion, the obtained DPCs passed through the chronological stages of embryonic pancreas development and FTIR spectra provide a new biophysical parameter based on molecular markers indicating the differentiation process of mPSCs to specialized cells. PMID:27651798

  4. FTIR Spectroscopic and Molecular Analysis during Differentiation of Pluripotent Stem Cells to Pancreatic Cells.

    PubMed

    Vazquez-Zapien, Gustavo Jesus; Mata-Miranda, Monica Maribel; Sanchez-Monroy, Virginia; Delgado-Macuil, Raul Jacobo; Perez-Ishiwara, David Guillermo; Rojas-Lopez, Marlon

    2016-01-01

    Some of the greatest challenges in stem cells (SCs) biology and regenerative medicine are differentiation control of SCs and ensuring the purity of differentiated cells. In this work, we differentiated mouse pluripotent stem cells (mPSCs) toward pancreatic cells characterizing this differentiation process by molecular and spectroscopic technics. Both mPSCs and Differentiated Pancreatic Cells (DPCs) were subjected to a genetic, phenotypic, and biochemical analysis by real-time quantitative PCR (RT-qPCR), immunocytochemistry, and Fourier Transform Infrared (FTIR) spectroscopy. Cultured mPCSs expressed pluripotent genes and proteins (Nanog and SOX2). DPCs expressed endodermal genes (SOX17 and Pdx1) at day 11, an inductor gene of embryonic pancreas development (Pdx1) at day 17 and pancreas genes and proteins (Insulin and Glucagon) at day 21 of differentiation. Likewise, FTIR spectra of mPSCs and DPCs at different maturation stages (11, 17, and 21 days) were obtained and showed absorption bands related with different types of biomolecules. These FTIR spectra exhibited significant spectral changes agreeing with the differentiation process, particularly in proteins and nucleic acids bands. In conclusion, the obtained DPCs passed through the chronological stages of embryonic pancreas development and FTIR spectra provide a new biophysical parameter based on molecular markers indicating the differentiation process of mPSCs to specialized cells.

  5. 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.

  6. 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.

  7. Spectroscopic studies of interactions involving horseradish peroxidase and Tb3+.

    PubMed

    Guo, Shaofen; Zhou, Qing; Lu, Tianhong; Ding, Xiaolan; Huang, Xiaohua

    2008-09-01

    The spectroscopic properties of interactions involving horseradish peroxidase (HRP) and Tb3+ in the simulated physiological solution was investigated with some electrochemical and spectroscopic methods, such as cyclic voltammetry (CV), circular dichroism (CD), X-ray photoelectron spectroscopy (XPS) and synchronous fluorescence (SF). It was found that Tb3+ can coordinate with oxygen atoms in carbonyl groups in the peptide chain of HRP, form the complex of Tb3+ and HRP (Tb-HRP), and then lead to the conformation change of HRP. The increase in the random coil content of HRP can disturb the microstructure of the heme active center of HRP, in which the planarity of the porphyrin cycle in the heme group is increased and then the exposure extent of the electrochemical active center is decreased. Thus Tb3+ can inhibit the electrochemical reaction of HRP and its electrocatalytic activity for the reduction of H2O2 at the Au/Cys/GC electrode. The changes in the microstructure of HRP obstructed the electron transfer of Fe(III) in the porphyrin cycle of the heme group, thus HRP catalytic activity is inhibited. The inhibition effect of Tb3+ on HRP catalytic activity is increased with the increasing of Tb3+ concentration. This study would provide some references for better understanding the rare earth elements and heavy metals on peroxidase toxicity in living organisms.

  8. Novel dipodal Schiff base compounds: Synthesis, characterization and spectroscopic studies

    NASA Astrophysics Data System (ADS)

    Obali, Aslihan Yilmaz; Ucan, Halil Ismet

    2015-02-01

    Two novel dipodal Schiff base compounds 1,2-benzyloxy-bis-[2-(benzylideneamino)phenol, L1 and 1,2-benzyloxy-bis[3-(benzylideneamino)pyridine], L2 were synthesized. Their sensing actions were confirmed by UV-Vis absorbance and emission spectroscopic studies in presence of Cr(III), Mn(II), Fe(III), Co(II), Ni(II), Cu(II), Zn(II), Sn(II), Cd(II) and Pb(II) in methanol medium (1 × 10-4 M). It was found that the dipodal compounds can selectively bind to Cu(II) and Pb(II) metal ions with a significant change in its emission and absorption spectra, while the addition of other metal ions (Cr(III), Mn(II), Fe(III), Co(II), Ni(II), Cu(II), Zn(II), Sn(II), Cd(II) and Pb(II)) produces insignificant or minor changes. The host-guest complexes formed were determined by Job's plot method. As a chemosensor, L1 and L2 dipodal Schiff base compounds shows a specific selectivity towards Cu(II) and Pb(II) ions in according to all spectroscopic data.

  9. Electronic properties of diphenyl-s-tetrazine and some related oligomers. An spectroscopic and theoretical study

    NASA Astrophysics Data System (ADS)

    Moral, Mónica; García, Gregorio; Peñas, Antonio; Garzón, Andrés; Granadino-Roldán, José M.; Melguizo, Manuel; Fernández-Gómez, Manuel

    2012-10-01

    This work presents a theoretical and spectroscopic study on the electronic and structural properties of the diphenyl-s-tetrazine molecule (Ph2Tz) and some oligomeric derivatives. Ph2Tz was synthesized through a variation of Pinner-type reaction which uses N-acetylcysteine as catalyst. Insight into the structure and electronic properties of the title compound was obtained through IR, Raman, UV-Vis spectra in different solvents, and theoretical calculations. Theoretical studies have been extended to different n-mers derivatives up to an ideal molecular wire through the oligomeric approximation, predicting this way electronic properties such as LUMO energy levels, electron affinity and reorganization energy in order to assess their possible applications in molecular electronics.

  10. Interaction of anticancer drug clofarabine with human serum albumin and human α-1 acid glycoprotein. Spectroscopic and molecular docking approach.

    PubMed

    Ajmal, Mohammad Rehan; Nusrat, Saima; Alam, Parvez; Zaidi, Nida; Khan, Mohsin Vahid; Zaman, Masihuz; Shahein, Yasser E; Mahmoud, Mohamed H; Badr, Gamal; Khan, Rizwan Hasan

    2017-02-20

    The binding interaction between clofarabine, an important anticancer drug and two important carrier proteins found abundantly in human plasma, Human Serum Albumin (HSA) and α-1 acid glycoprotein (AAG) was investigated by spectroscopic and molecular modeling methods. The results obtained from fluorescence quenching experiments demonstrated that the fluorescence intensity of HSA and AAG is quenched by clofarabine and the static mode of fluorescence quenching is operative. UV-vis spectroscopy deciphered the formation of ground state complex between anticancer drug and the two studied proteins. Clofarabine was found to bind at 298K with both AAG and HSA with the binding constant of 8.128×10(3) and 4.120×10(3) for AAG and HSA, respectively. There is stronger interaction of clofarabine with AAG as compared to HSA. The Gibbs free energy change was found to be negative for the interaction of clofarabine with AAG and HSA indicating that the binding process is spontaneous. Binding of clofarabine with HSA and AAG induced ordered structures in both proteins and lead to molecular compaction. Clofarabine binds to HSA near to drug site II. Hydrogen bonding and hydrophobic interactions were the main bonding forces between HSA-clofarabine and AAG-clofarabine as revealed by docking results. This study suggests the importance of binding of anticancer drug to AAG spatially in the diseases like cancers where the plasma concentration of AAG increases many folds. Design of drug dosage can be adjusted accordingly to achieve optimal treatment outcome.

  11. Multi-spectroscopic methods combined with molecular modeling dissect the interaction mechanisms of ractopamine and calf thymus DNA.

    PubMed

    Chai, Jun; Wang, Juyuan; Xu, Qifei; Hao, Fang; Liu, Rutao

    2012-07-06

    The toxic interaction of ractopamine (RAC) with calf thymus DNA (ct DNA) was studied in vitro using multi-spectroscopic methods and molecular modeling methods. The hypochromic effect without a noticeable shift in UV-vis absorption indicated that the minor groove binding mode existed in the interaction between RAC and DNA. The fluorescence quenching of RAC was observed with the increasing addition of DNA and was proved to be the static quenching. The binding constant and the binding site sizes were 4.13 × 10(3) and 0.97, respectively. The thermodynamic calculation demonstrated that the hydrogen bond and van der Waals were main acting forces. This result further confirmed the existence of groove binding mode. Afterwards, we found another interaction mode, electrostatic binding mode through the fluorescence polarization, ionic effects and denatured DNA experiments. Circular dichroism spectroscopy (CD) was then employed to monitor the conformation changes of DNA. Molecular modeling studies illustrated the visual display of the binding mode and the detailed information of the H-bond.

  12. Precise Theoretical Study of Spectroscopic Constants in Diatomics

    NASA Astrophysics Data System (ADS)

    Skripnikov, L. V.; Petrov, A. N.; Titov, A. V.; Mosyagin, N. S.

    2013-06-01

    During the last decade a significant progress in methods of molecular spectroscopy was achieved. One of the most important applications of these methods is a measurement of an electron electric dipole moment in diatomic molecules and cations containing heavy elements. In order to speed up such experiments, which usually prepared for many years, one can apply accurate ab initio quantum-chemical methods to predict different spectroscopic constants of a molecule or cation under consideration: scheme of electronic terms, vibrational and rotation constants, hyperfine structure constants, g-factors, lifetimes etc. In such calculations both correlation and relativistic effects should be taken into account. This is not a trivial problem for systems containing transition elements and especially lanthanides and actinides. %Therefore, ``direct'' 4-component Hamiltonians are not always the best choice and some alternative We report results of our recent investigations of a number of diatomics including theoretical investigation of HfF^{+}. Details of used methods are discussed. K. C. Cossel, D. N. Gresh, L. C. Sinclair, T. Coffey, L. V. Skripnikov, A. N. Petrov, N. S. Mosyagin, A. V. Titov, R. W. Field, E. R. Meyer, E. A. Cornell and J. Ye, Chem. Phys. Lett., 546, 1 (2012).

  13. Evaluation of molecular assembly, spectroscopic interpretation, intra-/inter molecular hydrogen bonding and chemical reactivity of two pyrrole precursors

    NASA Astrophysics Data System (ADS)

    Rawat, Poonam; Singh, R. N.

    2014-10-01

    This paper describes the evaluation of conformational, spectroscopic, hydrogen bonding and chemical reactivity of pyrrole precursor: ethyl 3,5 dimethyl-1H-pyrrole-2-carboxylate (EDPC) and ethyl 3,4-dimethyl-4-acetyl-1H-pyrrole-2-carboxylate (EDAPC) for the convenient characterization, synthetic usefulness and comparative evaluations. All experimental spectral values of 1H NMR, UV-Vis and FT-IR spectra coincide well with calculated values by DFT. The orbital interactions in EDPC and EDAPC are found to lengthen their Nsbnd H and Cdbnd O bonds and lowers their vibrational frequencies (red shift) resulting to dimer formation. The QTAIM and NBO analyses provide the strength of interactions and charge transfer in the hydrogen bonding unit and stability of dimers. The binding energy of EDPC and EDPAC dimer are found to be 9.92, 10.22 kcal/mol, respectively. In EDPAC and EDPC dimer, hyperconjugative interactions between monomer units is due to n1(O) → σ*(Nsbnd H) that stabilize the molecule up to 9.7 and 9.3 kcal/mol, respectively. On evaluation of molecular electrostatic potential (MEP) and electronic descriptors for EDPC it has been found that it is a good precursor for synthesis of formyl and acetyl derivatives whereas EDAPC has been found to be a good precursor for synthesis of schiff base, hydrazones, hydrazide-hydrazones and chalcones.

  14. Confocal Raman spectroscopic analysis of cross-linked ultra-high molecular weight polyethylene for application in artificial hip joints.

    PubMed

    Pezzotti, Giuseppe; Kumakura, Tsuyoshi; Yamada, Kiyotaka; Tateiwa, Toshiyuki; Puppulin, Leonardo; Zhu, Wenliang; Yamamoto, Kengo

    2007-01-01

    Confocal spectroscopic techniques are applied to selected Raman bands to study the microscopic features of acetabular cups made of ultra-high molecular weight polyethylene (UHMWPE) before and after implantation in vivo. The micrometric lateral resolution of a laser beam focused on the polymeric surface (or subsurface) enables a highly resolved visualization of 2-D conformational population patterns, including crystalline, amorphous, orthorhombic phase fractions, and oxidation index. An optimized confocal probe configuration, aided by a computational deconvolution of the optical probe, allows minimization of the probe size along the in-depth direction and a nondestructive evaluation of microstructural properties along the material subsurface. Computational deconvolution is also attempted, based on an experimental assessment of the probe response function of the polyethylene Raman spectrum, according to a defocusing technique. A statistical set of high-resolution microstructural data are collected on a fully 3-D level on gamma-ray irradiated UHMWPE acetabular cups both as-received from the maker and after retrieval from a human body. Microstructural properties reveal significant gradients along the immediate material subsurface and distinct differences are found due to the loading history in vivo, which cannot be revealed by conventional optical spectroscopy. The applicability of the confocal spectroscopic technique is valid beyond the particular retrieval cases examined in this study, and can be easily extended to evaluate in-vitro tested components or to quality control of new polyethylene brands. Confocal Raman spectroscopy may also contribute to rationalize the complex effects of gamma-ray irradiation on the surface of medical grade UHMWPE for total joint replacement and, ultimately, to predict their actual lifetime in vivo.

  15. Time Domain Reflectometric and spectroscopic studies on toluene + butyronitrile solution

    NASA Astrophysics Data System (ADS)

    Karthick, N. K.; Arivazhagan, G.; Kumbharkhane, A. C.; Joshi, Y. S.; Kannan, P. P.

    2016-03-01

    The dielectric parameters of toluene + butyronitrile solution have been obtained by time domain reflectometry (TDR) technique in the frequency range from 10 MHz to 30 GHz at 298 K. Spectroscopic (FTIR and 13C NMR) studies have also been carried out on the solution and the results of the studies show that neat butyronitrile is self-associative through C-H⋯N contacts and weak intermolecular forces of C-H⋯N and C-H⋯π type are operative in the solution. The obtained dielectric parameters such as Kirkwood correlation factor g, relaxation time τ etc. have been analyzed in view of these weak intermolecular forces. The weak non-covalent interactions between heteromolecules appear to have no influence on the ideality of ɛm vs X2 curve of the solution. Heteromolecular entities with weak intermolecular forces experience larger hindrance leading to longer relaxation time τ.

  16. Spectroscopic study of demineralization and restoration processes in dental enamel

    NASA Astrophysics Data System (ADS)

    Sokolova, Tatiana N.; Surmenko, Elena L.; Tuchin, Valery V.; Kishen, A.; Chebotarevsky, Yu. V.

    2007-07-01

    The spectroscopic study of dental enamel by LIBS (laser induced breakdown spectroscopy), FTIR (Fourier transform infrared) and XRD (X-ray diffraction) are represented. The changes of enamel structure and composition in process of natural (caries) and artificial demineralization and restoration were studied. In comparison of sound and carious enamel LIBS showed a decrease of the content of Ca, P and change of the content of some other macro-and trace elements (Mn, Na, Fe, Zn etc). The character of the elemental composition variation was stipulated by the concrete disease. Analysis of FTIR and XRD spectra of dental samples, subjected to artificial demineralization and restoration, showed that restoration action reveals slower, than demineralization. And in some cases the damage of crystals after restoration is more significant than after demineralization.

  17. [Spectroscopic studies on transition metal ions in colored diamonds].

    PubMed

    Meng, Yu-Fei; Peng, Ming-Sheng

    2004-07-01

    Transition metals like nickel, cobalt and iron have been often used as solvent catalysts in high pressure high temperature (HPHT) synthesis of diamond, and nickel and cobalt ions have been found in diamond lattice. Available studies indicated that nickel and cobalt ions could enter the lattice as interstitial or substitutional impurities and form complexes with nitrogen. Polarized microscopy, SEM-EDS, EPR, PL and FTIR have been used in this study to investigate six fancy color natural and synthetic diamonds in order to determine the spectroscopic characteristics and the existing forms of transition metal ions in colored diamond lattice. Cobalt-related optical centers were first found in natural chameleon diamonds, and some new nickel and cobalt-related optical and EPR centers have also been detected in these diamond samples.

  18. Crystallographic and spectroscopic study on a known orally active progestin.

    PubMed

    Ferraboschi, Patrizia; Ciuffreda, Pierangela; Ciceri, Samuele; Grisenti, Paride; Castellano, Carlo; Meneghetti, Fiorella

    2015-12-01

    6,17α-Dimethyl-4,6-pregnadiene-3,20-dione (medrogestone, 2) is for a long time known steroid endowed with progestational activity. In order to study its crystallographic and NMR spectroscopic properties with the aim to fill the literature gap, we prepared medrogestone following a traditional procedure. A careful NMR study allowed the complete assignment of the (1)H and (13)C NMR signals not only of medrogestone but also of its synthetic intermediates. The structural and stereochemical characterizations of medrogestone together with its precursor 17α-methyl-3-ethoxy-pregna-3,5-dien-20-one were described by means of X-ray analysis, allowing a deepened conformational investigation.

  19. Investigation of the behavior of HSA upon binding to amlodipine and propranolol: Spectroscopic and molecular modeling approaches

    NASA Astrophysics Data System (ADS)

    Housaindokht, Mohammad Reza; Rouhbakhsh Zaeri, Zeinab; Bahrololoom, Mahmood; Chamani, Jamshid; Bozorgmehr, Mohammad Reza

    2012-01-01

    The interaction between human serum albumin (HSA) and two drugs - amlodipine and propranolol - was investigated using fluorescence, UV absorption and circular dichroism (CD) spectroscopy. In addition, the binding site was established by applying molecular modeling technique. Fluorescence data suggest that amlodipine will quench the intrinsic fluorescence of HSA; whereas propranolol enhances the fluorescence of HSA. The binding constants for the interaction of amlodipine and propranolol with HSA were found to be 3.63 × 10 5 M -1 and 2.29 × 10 4 M -1, respectively. The percentage of secondary structure feature of each one of the HSA-bound drugs, i.e. the α-helix content, was estimated empirically by circular dichroism. The results indicated that amlodipine causes an increase, and that propranolol leads to a decrease in α-helix content of HSA. The spectroscopic analysis indicates that the binding mechanisms of the two drugs are different from each other. The data obtained by the molecular modeling study indicated that these drugs bind, with different affinity, to different sites located in subdomain IIA and IIIA.

  20. Multi-spectroscopic and molecular modelling approach to investigate the interaction of riboflavin with human serum albumin.

    PubMed

    Alam, Md Maroof; Abul Qais, Faizan; Ahmad, Iqbal; Alam, Parvez; Hasan Khan, Rizwan; Naseem, Imrana

    2017-03-09

    Riboflavin (RF) plays an important role in various metabolic redox reactions in the form of flavin adenine dinucleotide and flavin mononucleotide. Human serum albumin (HSA) is an important protein involved in the transportation of drugs, hormones, fatty acid and other molecules which determine the biodistribution and physiological fate of these molecules. In this study, we have investigated the interaction of riboflavin RF with HSA under simulative physiological conditions using various biophysical, calorimetric and molecular docking techniques. Results demonstrate the formation of riboflavin-HSA complex with binding constant in the order of 10(4) M(-1). Fluorescence spectroscopy confirms intermediate strength having a static mode of quenching with stoichiometry of 1:1. Experimental results suggest that the binding site of riboflavin mainly resides in sub-domain IIA of HSA and that ligand interaction increases the α-helical content of HSA. These parameters were further verified by isothermal titration calorimetry ITC which confirms the thermodynamic parameters obtained by fluorescence spectroscopy. Molecular docking was employed to suggest a binding model. Based on thermodynamic, spectroscopic and computational observations it can be concluded that HSA-riboflavin complex is mainly stabilized by various non-covalent forces with binding energy of -7.2 kcal mol(-1).

  1. Extending the molecular size in accurate quantum-chemical calculations: the equilibrium structure and spectroscopic properties of uracil.

    PubMed

    Puzzarini, Cristina; Barone, Vincenzo

    2011-04-21

    The equilibrium structure of uracil has been investigated using both theoretical and experimental data. With respect to the former, quantum-chemical calculations at the coupled-cluster level in conjunction with a triple-zeta basis set have been carried out. Extrapolation to the basis set limit, performed employing the second-order Møller-Plesset perturbation theory, and inclusion of core-correlation and diffuse-function corrections have also been considered. Based on the available rotational constants for various isotopic species together with corresponding computed vibrational corrections, the semi-experimental equilibrium structure of uracil has been determined for the first time. Theoretical and semi-experimental structures have been found in remarkably good agreement, thus pointing out the limitations of previous experimental determinations. Molecular and spectroscopic properties of uracil have then been studied by means of the composite computational approach introduced for the molecular structure evaluation. Among the results achieved, we mention the revision of the dipole moment. On the whole, it has been proved that the computational procedure presented is able to provide parameters with the proper accuracy to support experimental investigations of large molecules of biological interest.

  2. Investigation of the behavior of HSA upon binding to amlodipine and propranolol: Spectroscopic and molecular modeling approaches.

    PubMed

    Housaindokht, Mohammad Reza; Rouhbakhsh Zaeri, Zeinab; Bahrololoom, Mahmood; Chamani, Jamshid; Bozorgmehr, Mohammad Reza

    2012-01-01

    The interaction between human serum albumin (HSA) and two drugs - amlodipine and propranolol - was investigated using fluorescence, UV absorption and circular dichroism (CD) spectroscopy. In addition, the binding site was established by applying molecular modeling technique. Fluorescence data suggest that amlodipine will quench the intrinsic fluorescence of HSA; whereas propranolol enhances the fluorescence of HSA. The binding constants for the interaction of amlodipine and propranolol with HSA were found to be 3.63×10(5)M(-1) and 2.29×10(4)M(-1), respectively. The percentage of secondary structure feature of each one of the HSA-bound drugs, i.e. the α-helix content, was estimated empirically by circular dichroism. The results indicated that amlodipine causes an increase, and that propranolol leads to a decrease in α-helix content of HSA. The spectroscopic analysis indicates that the binding mechanisms of the two drugs are different from each other. The data obtained by the molecular modeling study indicated that these drugs bind, with different affinity, to different sites located in subdomain IIA and IIIA. Copyright © 2011. Published by Elsevier B.V.

  3. Molecular structure and spectroscopic studies on novel complexes of coumarin-3-carboxylic acid with Ni(II), Co(II), Zn(II) and Mn(II) ions based on density functional theory.

    PubMed

    Creaven, B S; Devereux, M; Georgieva, I; Karcz, D; McCann, M; Trendafilova, N; Walsh, M

    2011-12-15

    Novel Ni(II), Co(II), Zn(II) and Mn(II) complexes of coumarin-3-carboxylic acid (HCCA) were studied at experimental and theoretical levels. The complexes were characterised by elemental analyses, FT-IR, (1)H NMR, (13)C NMR and UV-Vis spectroscopy and by magnetic susceptibility measurements. The binding modes of the ligand and the spin states of the metal complexes were established by means of molecular modelling of the complexes studied and calculation of their IR, NMR and absorption spectra at DFT(TDDFT)/B3LYP level. The experimental and calculated data verified high spin Ni(II), Co(II) and Mn(II) complexes and a bidentate binding through the carboxylic oxygen atoms (CCA2). The model calculations predicted pseudo octahedral trans-[M(CCA2)(2)(H(2)O)(2)] structures for the Zn(II), Ni(II) and Co(II) complexes and a binuclear [Mn(2)(CCA2)(4)(H(2)O)(2)] structure. Experimental and calculated (1)H, (13)C NMR, IR and UV-Vis data were used to distinguish the two possible bidentate binding modes (CCA1 and CCA2) as well as mononuclear and binuclear structures of the metal complexes.

  4. Molecular structure and spectroscopic studies on novel complexes of coumarin-3-carboxylic acid with Ni(II), Co(II), Zn(II) and Mn(II) ions based on density functional theory

    NASA Astrophysics Data System (ADS)

    Creaven, B. S.; Devereux, M.; Georgieva, I.; Karcz, D.; McCann, M.; Trendafilova, N.; Walsh, M.

    2011-12-01

    Novel Ni(II), Co(II), Zn(II) and Mn(II) complexes of coumarin-3-carboxylic acid (HCCA) were studied at experimental and theoretical levels. The complexes were characterised by elemental analyses, FT-IR, 1H NMR, 13C NMR and UV-Vis spectroscopy and by magnetic susceptibility measurements. The binding modes of the ligand and the spin states of the metal complexes were established by means of molecular modelling of the complexes studied and calculation of their IR, NMR and absorption spectra at DFT(TDDFT)/B3LYP level. The experimental and calculated data verified high spin Ni(II), Co(II) and Mn(II) complexes and a bidentate binding through the carboxylic oxygen atoms (CCA2). The model calculations predicted pseudo octahedral trans-[M(CCA2) 2(H 2O) 2] structures for the Zn(II), Ni(II) and Co(II) complexes and a binuclear [Mn 2(CCA2) 4(H 2O) 2] structure. Experimental and calculated 1H, 13C NMR, IR and UV-Vis data were used to distinguish the two possible bidentate binding modes (CCA1 and CCA2) as well as mononuclear and binuclear structures of the metal complexes.

  5. Theoretical and spectroscopic studies of pyridyl substituted bis-coumarins and their new neodymium (III) complexes

    NASA Astrophysics Data System (ADS)

    Kostova, Irena; Trendafilova, Natasha; Mihaylov, Tzvetan

    2005-07-01

    Ab initio, DFT and spectroscopic studies of 3,3'-( o-pyridinomethylene)di-[4-hydroxycoumarin], 3,3'-( m-pyridinomethylene)di-[4-hydroxycoumarin] and 3,3'-( p-pyridinomethylene)di-[4-hydroxycoumarin] were performed. The molecular and electronic structures of the compounds were investigated using accurate HF and B3LYP/6-31G(d) calculations. Molecular quantities as vertical ionization potential, electron affinity, electronegativity, hardness and electrophilicity indices of the neutral species were calculated and discussed. Molecular electrostatic potential was considered as an additional molecular characteristic for predicting the most probable sites for electrophilic attack. The molecular structure and quantities of the dianionic species, which are active in solution, were calculated and discussed. The theoretical results suggested that both carbonyl and both hydroxyl oxygen atoms are preferred binding sites for electrophilic attack, in particular for a metal coordination. Further, the coordination abilities of the compounds were studied in complexation reactions with Nd(III). Complexes of Nd(III) with o-, m- and p-3,3'-(pyridinomethylene)di-[4-hydroxycoumarin] were synthesized and characterized by different physicochemical methods: elemental analysis, IR, 1H NMR spectroscopies and mass spectral data. The experimental data confirmed the theoretical predictions that the ligands in Nd(III) complexes are tetradentate and bound the metal ion through both carbonyl and both deprotonated hydroxyl oxygen atoms.

  6. Binding interaction of atorvastatin with bovine serum albumin: Spectroscopic methods and molecular docking.

    PubMed

    Wang, Qi; Huang, Chuan-ren; Jiang, Min; Zhu, Ying-yao; Wang, Jing; Chen, Jun; Shi, Jie-hua

    2016-03-05

    The interaction of atorvastatin with bovine serum albumin (BSA) was investigated using multi-spectroscopic methods and molecular docking technique for providing important insight into further elucidating the store and transport process of atorvastatin in the body and the mechanism of action and pharmacokinetics. The experimental results revealed that the fluorescence quenching mechanism of BSA induced atorvastatin was a combined dynamic and static quenching. The binding constant and number of binding site of atorvastatin with BSA under simulated physiological conditions (pH=7.4) were 1.41 × 10(5) M(-1) and about 1 at 310K, respectively. The values of the enthalpic change (ΔH(0)), entropic change (ΔS(0)) and Gibbs free energy (ΔG(0)) in the binding process of atorvastatin with BSA at 310K were negative, suggesting that the binding process of atorvastatin and BSA was spontaneous and the main interaction forces were van der Waals force and hydrogen bonding interaction. Moreover, atorvastatin was bound into the subdomain IIA (site I) of BSA, resulting in a slight change of the conformation of BSA.

  7. Binding interaction of atorvastatin with bovine serum albumin: Spectroscopic methods and molecular docking

    NASA Astrophysics Data System (ADS)

    Wang, Qi; Huang, Chuan-ren; Jiang, Min; Zhu, Ying-yao; Wang, Jing; Chen, Jun; Shi, Jie-hua

    2016-03-01

    The interaction of atorvastatin with bovine serum albumin (BSA) was investigated using multi-spectroscopic methods and molecular docking technique for providing important insight into further elucidating the store and transport process of atorvastatin in the body and the mechanism of action and pharmacokinetics. The experimental results revealed that the fluorescence quenching mechanism of BSA induced atorvastatin was a combined dynamic and static quenching. The binding constant and number of binding site of atorvastatin with BSA under simulated physiological conditions (pH = 7.4) were 1.41 × 105 M- 1 and about 1 at 310 K, respectively. The values of the enthalpic change (ΔH0), entropic change (ΔS0) and Gibbs free energy (ΔG0) in the binding process of atorvastatin with BSA at 310 K were negative, suggesting that the binding process of atorvastatin and BSA was spontaneous and the main interaction forces were van der Waals force and hydrogen bonding interaction. Moreover, atorvastatin was bound into the subdomain IIA (site I) of BSA, resulting in a slight change of the conformation of BSA.

  8. Molecular structure and spectroscopic characterization of Carbamazepine with experimental techniques and DFT quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Suhasini, M.; Sailatha, E.; Gunasekaran, S.; Ramkumaar, G. R.

    2015-04-01

    A systematic vibrational spectroscopic assignment and analysis of Carbamazepine has been carried out by using FT-IR, FT-Raman and UV spectral data. The vibrational analysis were aided by electronic structure calculations - ab initio (RHF) and hybrid density functional methods (B3LYP) performed with standard basis set 6-31G(d,p). Molecular equilibrium geometries, electronic energies, natural bond order analysis, harmonic vibrational frequencies and IR intensities have been computed. A detailed interpretation of the vibrational spectra of the molecule has been made on the basis of the calculated Potential Energy Distribution (PED) by VEDA program. UV-visible spectrum of the compound was also recorded and the electronic properties, such as HOMO and LUMO energies and λmax were determined by HF/6-311++G(d,p) Time-Dependent method. The thermodynamic functions of the title molecule were also performed using the RHF and DFT methods. The restricted Hartree-Fock and density functional theory-based nuclear magnetic resonance (NMR) calculation procedure was also performed, and it was used for assigning the 13C and 1H NMR chemical shifts of Carbamazepine.

  9. Molecular structure and spectroscopic characterization of Carbamazepine with experimental techniques and DFT quantum chemical calculations.

    PubMed

    Suhasini, M; Sailatha, E; Gunasekaran, S; Ramkumaar, G R

    2015-04-15

    A systematic vibrational spectroscopic assignment and analysis of Carbamazepine has been carried out by using FT-IR, FT-Raman and UV spectral data. The vibrational analysis were aided by electronic structure calculations - ab initio (RHF) and hybrid density functional methods (B3LYP) performed with standard basis set 6-31G(d,p). Molecular equilibrium geometries, electronic energies, natural bond order analysis, harmonic vibrational frequencies and IR intensities have been computed. A detailed interpretation of the vibrational spectra of the molecule has been made on the basis of the calculated Potential Energy Distribution (PED) by VEDA program. UV-visible spectrum of the compound was also recorded and the electronic properties, such as HOMO and LUMO energies and λmax were determined by HF/6-311++G(d,p) Time-Dependent method. The thermodynamic functions of the title molecule were also performed using the RHF and DFT methods. The restricted Hartree-Fock and density functional theory-based nuclear magnetic resonance (NMR) calculation procedure was also performed, and it was used for assigning the (13)C and (1)H NMR chemical shifts of Carbamazepine. Copyright © 2015 Elsevier B.V. All rights reserved.

  10. Interaction between phillygenin and human serum albumin based on spectroscopic and molecular docking

    NASA Astrophysics Data System (ADS)

    Song, W.; Ao, M. Z.; Shi, Y.; Yuan, L. F.; Yuan, X. X.; Yu, L. J.

    2012-01-01

    In this paper, the interaction of human serum albumin (HSA) with phillygenin was investigated by fluorescence, circular dichroism (CD), UV-vis spectroscopic and molecular docking methods under physiological conditions. The Stern-Volmer analysis indicated that the fluorescence quenching of HSA by phillygenin resulted from static mechanism, and the binding constants were 1.71 × 10 5, 1.61 × 10 5 and 1.47 × 10 4 at 300, 305 and 310 K, respectively. The results of UV-vis spectra show that the secondary structure of the protein has been changed in the presence of phillygenin. The CD spectra showed that HSA conformation was altered by phillygenin with a major reduction of α-helix and an increase in β-sheet and random coil structures, indicating a partial protein unfolding. The distance between donor (HSA) and acceptor (phillygenin) was calculated to be 3.52 nm and the results of synchronous fluorescence spectra showed that binding of phillygenin to HSA can induce conformational changes in HSA. Molecular docking experiments found that phillygenin binds with HSA at IIIA domain of hydrophobic pocket with hydrogen bond interactions. The ionic bonds were formed with the O (4), O (5) and O (6) of phillygenin with nitrogen of ASN109, ARG186 and LEU115, respectively. The hydrogen bonds are formed between O (2) of phillygenin and SER419. In the presence of copper (II), iron (III) and alcohol, the apparent association constant KA and the number of binding sites of phillygenin on HSA were both decreased in the range of 88.84-91.97% and 16.09-18.85%, respectively. In view of the evidence presented, it is expected to enrich our knowledge of the interaction dynamics of phillygenin to the important plasma protein HSA, and it is also expected to provide important information of designs of new inspired drugs.

  11. Spectroscopic study of Gd nanostructures quantum confined in Fe corrals

    DOE PAGES

    Cao, R. X.; Sun, L.; Miao, B. F.; ...

    2015-07-10

    Low dimensional nanostructures have attracted attention due to their rich physical properties and potential applications. The essential factor for their functionality is their electronic properties, which can be modified by quantum confinement. Here the electronic states of Gd atom trapped in open Fe corrals on Ag(111) were studied via scanning tunneling spectroscopy. A single spectroscopic peak above the Fermi level is observed after Gd adatoms are trapped inside Fe corrals, while two peaks appear in empty corrals. The single peak position is close to the higher energy peak of the empty corrals. These findings, attributed to quantum confinement of themore » corrals and Gd structures trapped inside, are supported by tight-binding calculations. As a result, this demonstrates and provides insights into atom trapping in open corrals of various diameters, giving an alternative approach to modify the properties of nano-objects.« less

  12. Ultrasonic and spectroscopic studies on photoactivation of euglena

    NASA Astrophysics Data System (ADS)

    Saito, Mitsunori; Morita, Shin

    2006-12-01

    We studied the effect of the irradiation wavelength on the activity of photosynthetic euglena. The ultrasonic manipulation technique was used for both the activity evaluation and the movement restriction in the spectral measurements. Euglenas that had been preserved in darkness became inactive, and accordingly most of them were trapped by the ultrasonic standing wave (0.8mW/mm2). However, when they were exposed to light of 500 or 700nm wavelength (0.13W/m2), they became active enough to escape from the trapping. By contrast, irradiation at 550, 600, or 650nm wavelength had no effect on their activity. Spectroscopic measurements, which used to be difficult for locomotive microorganisms, were conducted successfully by trapping euglena at a node of the ultrasonic standing wave. The absorption bands were observed at around 500 or 700nm, which corresponded to the irradiation wavelengths that activated euglena.

  13. Raman spectroscopic study of cyclohexane at pressures below 1000 MPa

    NASA Astrophysics Data System (ADS)

    Qiao, Erwei; Zheng, Haifei

    2017-10-01

    At present, the room temperature freezing pressure of cyclohexane is still uncertain, and the phase transition pressure of solid I - solid III is not reliable at ambient temperature. In this work, we have performed a Raman spectroscopic study of cyclohexane in a Moissanite anvil cell at pressures below 1000 MPa at 25 °C, and analyzed the characteristic of Raman brands νs(CH2), νas(CH2) and νb(Ring). Two phase transition pressures 80 MPa and 550 MPa were determined by a quartz pressure gauge, and they are the room temperature freezing pressure of cyclohexane and the phase transition pressure of solid I to solid III, respectively. Furthermore, from the phase diagram of cyclohexane, it is inferred that pressure plays an important role on the stability of cyclohexane as the main constituent of oil, and it can be beneficial to understanding the formation, migration and preservation of petroleum in subterranean rock strata.

  14. A detailed spectroscopic study of an Italian fresco

    SciTech Connect

    Barilaro, Donatella; Crupi, Vincenza; Majolino, Domenico; Barone, Germana; Ponterio, Rosina

    2005-02-15

    In the present work we characterized samples of plasters and pictorial layers taken from a fresco in the Acireale Cathedral. The fresco represents the Coronation of Saint Venera, patron saint of this Ionian town. By performing a detailed spectroscopic analysis of the plaster preparation layer by Fourier-transform infrared (FTIR) spectroscopy and x-ray diffraction (XRD), and of the painting layer by FTIR and confocal Raman microspectroscopy, scanning electron microscopy+energy dispersive x-ray spectroscopy, and XRD, we were able to identify the pigments and the binders present. In particular, Raman investigation was crucial to the characterization of the pigments thanks to the high resolution of the confocal apparatus used. It is worth stressing that the simultaneous use of complementary techniques was able to provide more complete information for the conservation of the artifact we studied.

  15. Spectroscopic Capabilities of XMM for Stellar Coronal Studies

    NASA Astrophysics Data System (ADS)

    Pallavicini, R.

    The turn of the millennium will be a marvelous time for X-ray astronomy with the launch of powerful missions such as AXAF, XMM, and ASTRO-E. Stellar coronae, with their spectra rich in emission lines, will be primary targets to exploit the spectroscopic capabilities of these missions. In particular, the CCD cameras and reflection gratings on XMM will allow us to address a number of key questions in stellar coronal physics. The capabilities of XMM for the study of stellar coronae are illustrated by means of simulations of EPIC and RGS spectra for a variety of typical stellar coronal sources. The mission time-line and the policy for accessing the data are also briefly illustrated.

  16. Spectroscopic study of Gd nanostructures quantum confined in Fe corrals

    SciTech Connect

    Cao, R. X.; Sun, L.; Miao, B. F.; Li, Q. L.; Zheng, C.; Wu, D.; You, B.; Zhang, W.; Han, P.; Bader, S. D.; Zhang, W. Y.; Ding, H. F.

    2015-07-10

    Low dimensional nanostructures have attracted attention due to their rich physical properties and potential applications. The essential factor for their functionality is their electronic properties, which can be modified by quantum confinement. Here the electronic states of Gd atom trapped in open Fe corrals on Ag(111) were studied via scanning tunneling spectroscopy. A single spectroscopic peak above the Fermi level is observed after Gd adatoms are trapped inside Fe corrals, while two peaks appear in empty corrals. The single peak position is close to the higher energy peak of the empty corrals. These findings, attributed to quantum confinement of the corrals and Gd structures trapped inside, are supported by tight-binding calculations. As a result, this demonstrates and provides insights into atom trapping in open corrals of various diameters, giving an alternative approach to modify the properties of nano-objects.

  17. Spectroscopic studies of anthracyclines: Structural characterization and in vitro tracking

    NASA Astrophysics Data System (ADS)

    Szafraniec, Ewelina; Majzner, Katarzyna; Farhane, Zeineb; Byrne, Hugh J.; Lukawska, Malgorzata; Oszczapowicz, Irena; Chlopicki, Stefan; Baranska, Malgorzata

    2016-12-01

    A broad spectroscopic characterization, using ultraviolet-visible (UV-vis) and Fourier transform infrared absorption as well as Raman scattering, of two commonly used anthracyclines antibiotics (DOX) daunorubicin (DNR), their epimers (EDOX, EDNR) and ten selected analogs is presented. The paper serves as a comprehensive spectral library of UV-vis, IR and Raman spectra of anthracyclines in the solid state and in solution. The particular advantage of Raman spectroscopy for the measurement and analysis of individual antibiotics is demonstrated. Raman spectroscopy can be used to monitor the in vitro uptake and distribution of the drug in cells, using both 488 nm and 785 nm as source wavelengths, with submicrometer spatial resolution, although the cellular accumulation of the drug is different in each case. The high information content of Raman spectra allows studies of the drug-cell interactions, and so the method seems very suitable for monitoring drug uptake and mechanisms of interaction with cellular compartments at the subcellular level.

  18. Spectroscopic study of photo and thermal destruction of riboflavin

    NASA Astrophysics Data System (ADS)

    Astanov, Salikh; Sharipov, Mirzo Z.; Fayzullaev, Askar R.; Kurtaliev, Eldar N.; Nizomov, Negmat

    2014-08-01

    Influence of temperature and light irradiation on the spectroscopic properties of aqueous solutions of riboflavin was studied using linear dichroism method, absorption and fluorescence spectroscopy. It was established that in a wide temperature range 290-423 K there is a decline of absorbance and fluorescence ability, which is explained by thermodestruction of riboflavin. It is shown that the proportion of molecules, which have undergone degradation, are in the range of 4-28%, and depends on the concentration and quantity of temperature effects. Introduction of hydrochloric and sulfuric acids, as well as different metal ions leads to an increase in the photostability of riboflavin solutions by 2-2.5 times. The observed phenomena are explained by the formation protonation form of riboflavin and a complex between the metal ions and oxygen atoms of the carbonyl group of riboflavin, respectively.

  19. Raman spectroscopic study of "The Malatesta": a Renaissance painting?

    PubMed

    Edwards, Howell G M; Vandenabeele, Peter; Benoy, Timothy J

    2015-02-25

    Raman spectroscopic analysis of the pigments on an Italian painting described as a "Full Length Portrait of a Gentleman", known also as the "Malatesta", and attributed to the Renaissance period has established that these are consistent with the historical research provenance undertaken earlier. Evidence is found for the early 19th Century addition of chrome yellow to highlighted yellow ochre areas in comparison with a similar painting executed in 1801 by Sir Thomas Lawrence of John Kemble in the role of Hamlet, Prince of Denmark. The Raman data are novel in that no analytical studies have previously been made on this painting and reinforces the procedure whereby scientific analyses are accompanied by parallel historical research.

  20. Spectroscopic signatures of molecular orbitals in transition metal oxides with a honeycomb lattice

    NASA Astrophysics Data System (ADS)

    Pchelkina, Z. V.; Streltsov, S. V.; Mazin, I. I.

    2016-11-01

    A tendency to form benzenelike molecular orbitals has recently been shown to be a common feature of the 4 d and 5 d transition metal oxides with a honeycomb lattice. This tendency competes with other interactions such as the spin-orbit coupling and Hubbard correlations and can be partially or completely suppressed. In the calculations, SrRu2O6 presents the cleanest case of well-formed molecular orbitals so far; however, direct experimental evidence for or against this proposition has been missing. In this paper, we show that combined photoemission and optical studies can be used to identify molecular orbitals in SrRu2O6 . Symmetry-driven election selection rules suppress optical transitions between certain molecular orbitals, while photoemission and inverse photoemission measurements are insensitive to them. Comparing the photoemission and optical conductivity spectra, one should be able to observe clear signatures of molecular orbitals.

  1. Spectroscopic investigation (FT-IR and FT-Raman), vibrational assignments, HOMO-LUMO, NBO, MEP analysis and molecular docking study of 2-(4-hydroxyphenyl)-4,5-dimethyl-1H-imidazole 3-oxide

    NASA Astrophysics Data System (ADS)

    Benzon, K. B.; Varghese, Hema Tresa; Panicker, C. Yohannan; Pradhan, Kiran; Tiwary, Bipransh Kumar; Nanda, Ashis Kumar; Alsenoy, C. Van

    2015-07-01

    In this work, the vibrational spectral analysis was carried out using FT-IR and FT-Raman spectroscopy of 2-(4-hydroxyphenyl)-4,5-dimethyl-1H-imidazole 3-oxide. The computations were performed at DFT levels of theory to get the optimized geometry and vibrational frequencies of the normal modes of the title compound using Gaussian09 software. The complete vibrational assignments of frequencies were made on the basis of potential energy distribution. The calculated HOMO and LUMO energies show the chemical activity of the molecule. The stability of the molecule arising from hyper-conjugative interaction and charge delocalization has been analyzed using NBO analysis. The hyperpolarizability values are reported and the first hyperpolarizability of the title compound is 19.61 times that of standard NLO material urea. From the MEP plot, the negative charge covers the nitro group and the positive region is over the hydroxyl group and N-H part of the imidazole ring. The calculated 1H NMR results are in good agreement with experimental data. Molecular docking study is also reported.

  2. Spectroscopic, thermal, antimicrobial and molecular modeling studies of mononuclear pentafunctional Schiff base metal chelates derived from 5-acetyl-4-hydroxy-2H-1,3-thiazine-2,6(3H)-dione

    NASA Astrophysics Data System (ADS)

    Adly, Omima M. I.; Taha, Ali; Fahmy, Shery A.

    2015-03-01

    A new pentafunctional N3O2 Schiff base, H2L ligand, and its metal chelates with Cu(II), Ni(II), Co(II), VO(IV), Zn(II), Cd(II), Ce(III), Cr(III), Fe(III) and UO2(VI) have been synthesized and characterized by elemental analysis, spectral, molar conductance, magnetic and thermal gravimetric studies. The results showed that the complexes have octahedral geometry except UO2 complex which has pentagonal bipyramidal arrangement. The TGA analyses suggest high stability for most complexes followed by thermal decomposition in different steps. The kinetic and thermodynamic parameters for decomposition steps of metal complexes thermograms have been calculated. Molecular orbital calculations were performed for the ligand and its metal complexes by means of hyperchem 7.52 program on the bases of semiempirical PM3 level and the results were correlated with the experimental data. The antimicrobial activity of the synthesized compounds were tested in vitro against some Gram-positive and Gram-negative bacteria; yeast and fungus strains and the results were discussed in terms of extended Lewis acid-base interactions.

  3. Spectroscopic Studies of Quantum Well Structures in Pulsed Magnetic Fields

    NASA Astrophysics Data System (ADS)

    Perry, Clive H.

    1998-03-01

    Magneto-photoluminescence spectroscopy (MPS) at low temperatures is a powerful technique for investigating the ground and excited states of high quality quantum well-type semiconductor heterostructures. The spectra are strongly influenced by electron-electron interactions and the method offers a complimentary tool to electrical transport studies. We have established a MPS facility at NHMFL-LANL and have undertaken a comprehensive investigation of magneto-excitonic and Landau transitions in a large variety of undoped and doped (two-dimensional electron gas, 2DEG) GaAs/AlGaAs and InGaAs/GaAs quantum-well structures. Excitation energies are provided by UV, visible, and NIR lasers. Fiber optic probes are used to switch between steady state (to 18 tesla) and short-pulsed (to 65 tesla) magnetic fields applied perpendicular (Faraday geometry) and parallel (Voigt geometry) to the growth axis of the 2D layers. The experimental techniques, optical layout, and data acquisition are reviewed i n some detail. Short-pulse magnets require that the spectroscopic data acquisition to be obtained in a 2 ms time-frame in the 'flat-top' region at the peak of the field. A broad range of samples have been investigated as a function of temperature, sample geometry, and high pressure. Examples of MPL spectra of single and coupled double quantum wells, modulation-doped quantum wells, single interface structures, and other related semiconductor heterojunction structures are given. The recently commissioned long-pulse magnet at NHMFL-LANL offers several new exciting possibilities: (i) The long exponential decay associated with the crow-bar mode has the potential for spectroscopic studies from 60 -10 T in 0.5 T intervals from a single pulse. (ii) Field steps programmed to last from 100-500 ms or longer offer the opportunity for time-resolved MPL spectroscopy in the 60 - 10 T range.

  4. Spectroscopic study of the peculiar galaxy IC 883

    NASA Astrophysics Data System (ADS)

    Yakovleva, V. A.; Merkulova, O. A.; Karataeva, G. M.; Shalyapina, L. V.; Yablokova, N. V.; Burenkov, A. N.

    2016-04-01

    We analyze new optical spectroscopic observations obtained at the 6-m telescope of the Special Astrophysical Observatory of the Russian Academy of Sciences with the SCORPIO focal reducer (in the modes of a Fabry-Perot interferometer (FPI) and long-slit spectroscopy) and the Multi-Pupil Fiber Spectrograph for the galaxy IC 883. We have confirmed that the main body of the galaxy rotates around its minor axis. The positions of the dynamical axes of the stellar and gaseous components have been found to differ by ~10°. The velocities in the SE tail do not correspond to the circular rotation around the galaxy's minor axis. This structure is probably a fragment of an unwound curved spiral arm. Regions with high velocity dispersions and peculiarities in the velocity fields have been found along the minor axis. Our study of the age and metallicity of the galaxy's stellar population has shown that the mean values of these parameters in the stellar disk, except for the central region ( r ≤ 5"), are ≈1 Gyr and ≈-0.4 dex, respectively. Both young (2-5 × 108 yr) and old (5-10 × 109 yr) stellar populations are present in the circumnuclear region. Our analysis of the spectroscopic data for the bright feature 8" south of the nucleus coincident in position with a compact X-ray source has shown that this is apparently a dwarf galaxy or a remnant of a companion galaxy. Our FPI observations in the Hα emission line and direct images have revealed a region of ionized gas that together with the already known structures along the minor axis forms a clumpy tidal structure of ionized gas pulled from the companion galaxy. The results of our study confirm the previously proposed hypothesis that the observed peculiar structures were formed by the merger of two galaxies. However, it can be said that IC 883 does not belong to the class of polar-ring galaxies.

  5. Spectroscopic and molecular docking studies on the charge transfer complex of bovine serum albumin with quinone in aqueous medium and its influence on the ligand binding property of the protein

    NASA Astrophysics Data System (ADS)

    Satheshkumar, Angupillai; Elango, Kuppanagounder P.

    2014-09-01

    The spectral techniques such as UV-Vis, 1H NMR and fluorescence and electrochemical experiments have been employed to investigate the interaction between 2-methoxy-3,5,6-trichloro-1,4-benzoquinone (MQ; a water soluble quinone) and bovine serum albumin (BSA) in aqueous medium. The fluorescence of BSA was quenched by MQ via formation of a 1:1 BSA-MQ charge transfer adduct with a formation constant of 3.3 × 108 L mol-1. Based on the Forster’s theory the binding distance between them is calculated as 2.65 nm indicating high probability of binding. For the first time, influence of quinone on the binding property of various types of ligands such as aspirin, ascorbic acid, nicotinimide and sodium stearate has also been investigated. The results indicated that the strong and spontaneous binding existing between BSA and MQ, decreased the intensity of binding of these ligands with BSA. Since Tryptophan (Trp) is the basic residue present in BSA, a comparison between binding property of Trp-MQ adduct with that of BSA-MQ with these ligands has also been attempted. 1H NMR titration study indicated that the Trp forms a charge transfer complex with MQ, which reduces the interaction of Trp with the ligands. Molecular docking study supported the fact that the quinone interacts with the Trp212 unit of the BSA and the free energy change of binding (ΔG) for the BSA-MQ complex was found to be -46 kJ mol-1, which is comparable to our experimental free energy of binding (-49 kJ mol-1) obtained from fluorescence study.

  6. Spectroscopic and molecular docking studies on the charge transfer complex of bovine serum albumin with quinone in aqueous medium and its influence on the ligand binding property of the protein.

    PubMed

    Satheshkumar, Angupillai; Elango, Kuppanagounder P

    2014-09-15

    The spectral techniques such as UV-Vis, (1)H NMR and fluorescence and electrochemical experiments have been employed to investigate the interaction between 2-methoxy-3,5,6-trichloro-1,4-benzoquinone (MQ; a water soluble quinone) and bovine serum albumin (BSA) in aqueous medium. The fluorescence of BSA was quenched by MQ via formation of a 1:1 BSA-MQ charge transfer adduct with a formation constant of 3.3×10(8) L mol(-1). Based on the Forster's theory the binding distance between them is calculated as 2.65 nm indicating high probability of binding. For the first time, influence of quinone on the binding property of various types of ligands such as aspirin, ascorbic acid, nicotinimide and sodium stearate has also been investigated. The results indicated that the strong and spontaneous binding existing between BSA and MQ, decreased the intensity of binding of these ligands with BSA. Since Tryptophan (Trp) is the basic residue present in BSA, a comparison between binding property of Trp-MQ adduct with that of BSA-MQ with these ligands has also been attempted. 1H NMR titration study indicated that the Trp forms a charge transfer complex with MQ, which reduces the interaction of Trp with the ligands. Molecular docking study supported the fact that the quinone interacts with the Trp212 unit of the BSA and the free energy change of binding (ΔG) for the BSA-MQ complex was found to be -46 kJ mol(-1), which is comparable to our experimental free energy of binding (-49 kJ mol(-1)) obtained from fluorescence study.

  7. In situ real-time spectroscopic ellipsometry measurement for the investigation of molecular orientation in organic amorphous multilayer structures

    NASA Astrophysics Data System (ADS)

    Yokoyama, Daisuke; Adachi, Chihaya

    2010-06-01

    To investigate molecular orientation in organic amorphous films, in situ real-time spectroscopic ellipsometry measurements were performed during vacuum deposition. Three materials with different molecular shapes were adopted to confirm the generality of the molecular orientation. In all three cases, more than 200 000 values for the ellipsometric parameters measured during deposition were well simulated simultaneously over the entire spectral range and measurement period using a simple model where the films possessed homogeneous optical anisotropy. This demonstrated the homogeneity of the molecular orientation in the direction of film thickness. The molecular orientation can be controlled by the substrate temperature even in multilayer structures. It is also demonstrated that a "multilayer structure" can be fabricated using only one material, where each layer has different optical and electrical properties.

  8. Molecular orbital studies (hardness, chemical potential, electronegativity and electrophilicity), vibrational spectroscopic investigation and normal coordinate analysis of 5-{1-hydroxy-2-[(propan-2-yl)amino]ethyl}benzene-1,3-diol.

    PubMed

    Muthu, S; Renuga, S

    2014-01-24

    FT-IR and FT-Raman spectra of 5-{1-hydroxy-2-[(propan-2-yl) amino] ethyl} benzene-1,3-diol (abbrevi- 54 ated as HPAEBD) were recorded in the region 4000-450 cm(-1) and 4000-100 cm(-1) respectively. The structure of the molecule was optimized and the structural characteristics were determined by density functional theory (B3LYP) and HF method with 6-31 G(d,p) as basis set. The theoretical wave numbers were scaled and compared with experimental 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). Stability of the molecule arising from hyperconjugation and charge delocalization is confirmed by the natural bond orbital analysis (NBO). The results show that electron density (ED) in the σ antibonding orbitals and E (2) energies confirm the occurrence of intra molecular charge transfer (ICT) within the molecule. The molecule orbital contributions were studied by using the total (TDOS), sum of α and β electron (αβDOS) density of States. Mulliken population analysis of atomic charges is also calculated. The calculated HOMO and LUMO energy gap shows that charge transfer occurs within the molecule. The electron density-based local reactivity descriptors such as Fukui functions were calculated to explain the chemical selectivity or reactivity site in this compound. On the basis of vibrational analyses, the thermodynamic properties of title compound at different temperatures have been calculated.

  9. Electrochemical and spectroscopic study of octadecyltrimethylammonium bromide/DNA surfoplexes.

    PubMed

    Rodríguez-Pulido, Alberto; Aicart, Emilio; Junquera, Elena

    2009-04-21

    The use of cationic micelles consisting of octadecyltrimethylammonium bromide (C18TAB) to compact calf thymus DNA has been investigated in aqueous buffered solution at 310.15 K by means of conductometry, electrophoretic mobility, and several fluorescence spectroscopy methods. The results indicate that C18TAB micelles, consisting of 44 monomers on average, may compact DNA molecule by an electrostatic interaction that takes place at the cationic spherical micelle surface. The surfoplexes thus formed show a surface density charge that goes from negative to positive values at a Lmic/D mass ratio of around 1.0 (where Lmic and D are the masses of micellized cationic surfactant and DNA), called the isoneutrality ratio (Lmic/D)phi. Values of this characteristic parameter, determined in this work not only from the electrochemical experimental data but also from spectroscopic measurements, are in very good agreement with those ones calculated from molecular parameters and some other properties also obtained in this work. The electrostatic character of the DNA-micelle interaction has been confirmed by analyzing the decrease in fluorescence emission of the fluorophore ethidium bromide, EtBr, initially intercalated between DNA base pairs, as long as the surfoplexes are formed. Fluorescence anisotropy experiments have revealed that micelle packing becomes more rigid in the presence of DNA, but once the surfoplex is formed, the fluidity increases with the Lmic/D mass ratio, attaining its maximum when the isoneutrality ratio is exceeded. This fact, together with the net positive charge of the surfoplexes with the Lmic/D mass ratio over the isoneutrality ratio, makes this regimen of lipid and DNA content the optimum for efficiency in the transfection process.

  10. Synthesis, molecular structure, spectroscopic properties and stability of (Z)-N-methyl-C-2,4,6-trimethylphenylnitrone

    NASA Astrophysics Data System (ADS)

    Lasri, Jamal; Ismail, Ali I.; Haukka, Matti; Soliman, Saied M.

    2015-02-01

    New N-methyl-C-2,4,6-trimethylphenylnitrone 1 has been synthesized starting from N-methylhydroxylamine and mesitaldehyde. The product was fully characterized using different spectroscopic techniques; FTIR, NMR, UV-Vis, high resolution mass spectrometry and X-ray diffraction. The relative stability and percent of population of its two possible isomers (E and Z) were calculated using the B3LYP/6-311++G(d,p) method in gas phase and in solution. In agreement with the X-ray results, it was found that Z-isomer is the most stable one in both gas phase and solution. The molecular geometry, vibrational frequencies, gauge-including atomic orbital (GIAO), and chemical shift values were also calculated using the same level of theory. The TD-DFT results of the studied nitrone predicted a π-π∗ transition band at 285.1 nm (fosc = 0.3543) in the gas phase. The rest of the spectral bands undergo either hyperchromic or hypsochromic shifts in the presence of solvent. Polarizability and HOMO-LUMO gap values were used to predict the nonlinear optical properties (NLO) of the studied compound. NBO analysis has been used to determine the most accurate Lewis structure of the studied molecule.

  11. Fourier transform infrared vibrational spectroscopic imaging: integrating microscopy and molecular recognition.

    PubMed

    Levin, Ira W; Bhargava, Rohit

    2005-01-01

    The recent development of Fourier transform infrared (FTIR) spectroscopic imaging has enhanced our capability to examine, on a microscopic scale, the spatial distribution of vibrational spectroscopic signatures of materials spanning the physical and biomedical disciplines. Recent activity in this emerging area has concentrated on instrumentation development, theoretical analyses to provide guidelines for imaging practice, novel data processing algorithms, and the introduction of the technique to new fields. To illustrate the impact and promise of this spectroscopic imaging methodology, we present fundamental principles of the technique in the context of FTIR spectroscopy and review new applications in various venues ranging from the physical chemistry of macromolecular systems to the detection of human disease.

  12. Spectroscopic quantification of extremely rare molecular species in the presence of interfering optical absorption

    DOEpatents

    Ognibene, Ted; Bench, Graham; McCartt, Alan Daniel; Turteltaub, Kenneth; Rella, Chris W.; Tan, Sze; Hoffnagle, John A.; Crosson, Eric

    2017-05-09

    Optical spectrometer apparatus, systems, and methods for analysis of carbon-14 including a resonant optical cavity configured to accept a sample gas including carbon-14, an optical source configured to deliver optical radiation to the resonant optical cavity, an optical detector configured to detect optical radiation emitted from the resonant cavity and to provide a detector signal; and a processor configured to compute a carbon-14 concentration from the detector signal, wherein computing the carbon-14 concentration from the detector signal includes fitting a spectroscopic model to a measured spectrogram, wherein the spectroscopic model accounts for contributions from one or more interfering species that spectroscopically interfere with carbon-14.

  13. Molecular interaction of 2,4-diacetylphloroglucinol (DAPG) with human serum albumin (HSA): The spectroscopic, calorimetric and computational investigation

    NASA Astrophysics Data System (ADS)

    Pragna Lakshmi, T.; Mondal, Moumita; Ramadas, Krishna; Natarajan, Sakthivel

    2017-08-01

    Drug molecule interaction with human serum albumin (HSA) affects the distribution and elimination of the drug. The compound, 2,4-diacetylphloroglucinol (DAPG) has been known for its antimicrobial, antiviral, antihelminthic and anticancer properties. However, its interaction with HSA is not yet reported. In this study, the interaction between HSA and DAPG was investigated through steady-state fluorescence, time-resolved fluorescence (TRF), circular dichroism (CD), Fourier transform infrared (FT-IR) spectroscopy, isothermal titration calorimetry (ITC), molecular docking and molecular dynamics simulation (MDS). Fluorescence spectroscopy results showed the strong quenching of intrinsic fluorescence of HSA due to interaction with DAPG, through dynamic quenching mechanism. The compound bound to HSA with reversible and moderate affinity which explained its easy diffusion from circulatory system to target tissue. The thermodynamic parameters from fluorescence spectroscopic data clearly revealed the contribution of hydrophobic forces but, the role of hydrogen bonds was not negligible according to the ITC studies. The interaction was exothermic and spontaneous in nature. Binding with DAPG reduced the helical content of protein suggesting the unfolding of HSA. Site marker fluorescence experiments revealed the change in binding constant of DAPG in the presence of site I (warfarin) but not site II marker (ibuprofen) which confirmed that the DAPG bound to site I. ITC experiments also supported this as site I marker could not bind to HSA-DAPG complex while site II marker was accommodated in the complex. In silico studies further showed the lowest binding affinity and more stability of DAPG in site I than in site II. Thus the data presented in this study confirms the binding of DAPG to the site I of HSA which may help in further understanding of pharmacokinetic properties of DAPG.

  14. Laser irradiated gas jet: A spectroscopic experimental and theoretical study

    SciTech Connect

    Lee, R.W.; Matthews, D.L.; Koppel, L.; Busch, G.E.; Charatis, G.; Dunning, M.J.; Mayer, F.J.

    1983-09-01

    We present x-ray spectroscopic measurements of the longitudinal electron density profile and the longitudinal and transverse electron temperature profiles for a laser irradiated gas jet. We attempt to verify our spectroscopic method by laser interferometry and by comparison of inferred quantities to those determined from laser plasma interaction simulations. Because temperature profiles were time dependent, we used a theoretical time dependent radiation transport code to analyze the data.

  15. Spectroscopic Investigation of the Origin of Magnetic Bistability in Molecular Nanomagnets

    NASA Astrophysics Data System (ADS)

    van Slageren, Joris

    Molecular nanomagnets (MNMs) are coordination complexes consisting of one of more transition metal and/or f-element ions bridged and surrounded by organic ligands. Some of these can be magnetized in a magnetic field, and remain magnetized after the field is switched off. Because of this, MNMs have been proposed for magnetic data storage applications, where up to 1000 times higher data densities than currently possible can be obtained. Other MNMs were shown to display quantum coherence, and, as a consequence, are suitable as quantum bits. Quantum bits are the building blocks of a quantum computer, which will be able to carry out calculations that will never be possible with a conventional computer. The magnetic bistability of MNMs originates from the magnetic anisotropy of the magnetic ions, which creates an energy barrier between up and down orientations of the magnetic moment. Currently, most work in the area focuses on complexes of either lanthanide ions or low-coordinate transition metal ions. Synthetic chemical efforts have led to a large number of novel materials, but the rate of improvement has been slow. Therefore a better understanding of the origin of the magnetic anisotropy is clearly necessary. To this end we have applied a wide range of advanced spectroscopic techniques, ranging from different electron spin resonance techniques at frequencies up to the terahertz domain to optical techniques, including luminescence and magnetic circular dichroism spectroscopy. We will discuss two examples, one from the area of lanthanide MNMs, one a transition metal MNM (unpublished). This work was financially supported by DFG, DAAD and COST CM1006 EUFEN.

  16. In vitro drug interaction of levocetirizine and diclofenac: Theoretical and spectroscopic studies

    NASA Astrophysics Data System (ADS)

    Abo Dena, Ahmed S.; Abdel Gaber, Sara A.

    2017-06-01

    Levocetirizine dihydrochloride is known to interact with some anti-inflammatory drugs. We report here a comprehensive integrated theoretical and experimental study for the in vitro drug interaction between levocetirizine dihydrochloride (LEV) and diclofenac sodium (DIC). The interaction of the two drugs was confirmed by the molecular ion peak obtained from the mass spectrum of the product. Moreover, FTIR and 1HNMR spectra of the individual drugs and their interaction product were inspected to allocate the possible sites of interaction. In addition, quantum mechanical DFT calculations were performed to search for the interaction sites and to verify the types of interactions deduced from the spectroscopic studies such as charge-transfer and non-bonding π-π interactions. It was found that the studied drugs interact with each other in aqueous solution via four types of interactions, namely, ion-pair formation, three weak hydrogen bonds, non-bonding π-π interactions and charge-transfer from DIC to LEV.

  17. Molecular structure, spectroscopic properties, NLO, HOMO-LUMO and NBO analyses of 6-hydroxy-3(2H)-pyridazinone

    NASA Astrophysics Data System (ADS)

    Soliman, Saied M.; Albering, Jörg; Abu-Youssef, Morsy A. M.

    2015-02-01

    The molecular structure and relative stabilities of the six possible isomers of 6-hydroxy-3(2H)-pyridazinone (DHP) in the gas phase and in solutions of different polarities are predicted using the B3LYP/6-311++G(d,p) method. The oxo-hydroxo isomer is the most stable form in the gas phase and in solution. These results agree with our reported X-ray structure. The effect of solvents on the spectroscopic properties of the most stable isomer has been studied using the polarized continuum method (PCM) at the same level of theory. The vibrational spectra of the compound studied are calculated and compared with the experimentally measured FTIR spectra. The electronic spectra in gas phase and in solution were calculated using the TD-DFT method. The most intense absorption band is predicted at 312.4 nm and belongs mainly to a π → π* transition. In polar solvents, this spectral band undergoes a hypsochromic shift. Two stable dimer forms were calculated at same level of theory. Dimer A is more stable than dimer B, by 6.66 kcal mol-1. The former is stabilized by stronger Osbnd H⋯O H-bonds compared to the weaker Nsbnd H⋯O interactions in the latter. The effect of these H-bonding interactions on the molecular structure and vibrational spectra of these compounds are predicted. NBO analyses were carried out to investigate the stabilization energy of various inter- and intramolecular charge transfer interactions within the systems studied.

  18. Synthesis, spectroscopic (FT-IR, FT-Raman, NMR, UV-Visible), Fukui function, antimicrobial and molecular docking study of (E)-1-(3-bromobenzylidene)semicarbazide by DFT method

    NASA Astrophysics Data System (ADS)

    Raja, M.; Raj Muhamed, R.; Muthu, S.; Suresh, M.; Muthu, K.

    2017-02-01

    The title compound, (E)-1-(3-bromobenzylidene)semicarbazide (3BSC) was synthesized and characterized by FT-IR, FT-Raman, UV, 1HNMR and 13CNMR spectral analysis. The optimized molecular geometry, the vibrational wavenumbers, the infrared intensities and the Raman scattering activities were calculated by using density functional theory (DFT) B3LYP method with 6-311++G(d,p) basis set. The calculated HOMO and LUMO energies show that charge transfer within the molecule. Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital analysis (NBO). The hyperpolarizability calculation reveals the present material has a reasonably good propensity for nonlinear optical activity. Molecular electrostatic potential (MEP) and Fukui functions were also performed. The thermodynamic properties (heat capacity, entropy, and enthalpy) of the 3BSC at different temperatures have been calculated. The biological applications of 3BSC have been screened for its antimicrobial activity and found to exhibit antifungal and antibacterial effects. In addition, the Molecular docking was also performed for the different receptors.

  19. EPR Spectroscopic Studies of [FeFe]-Hydrogenase Maturation.

    PubMed

    Suess, Daniel L M; Britt, R David

    2015-09-01

    Proton reduction and H2 oxidation are key elementary reactions for solar fuel production. Hydrogenases interconvert H(+) and H2 with remarkable efficiency and have therefore received much attention in this context. For [FeFe]-hydrogenases, catalysis occurs at a unique cofactor called the H-cluster. In this article, we discuss ways in which EPR spectroscopy has elucidated aspects of the bioassembly of the H-cluster, with a focus on four case studies: EPR spectroscopic identification of a radical en route to the CO and CN(-) ligands of the H-cluster, tracing (57)Fe from the maturase HydG into the H-cluster, characterization of the auxiliary Fe-S cluster in HydG, and isotopic labeling of the CN(-) ligands of HydA for electronic structure studies of its Hox state. Advances in cell-free maturation protocols have enabled several of these mechanistic studies, and understanding H-cluster maturation may in turn provide insights leading to improvements in hydrogenase production for biotechnological applications.

  20. Characterization of water molecular state in in-vivo thick tissues using diffuse optical spectroscopic imaging

    NASA Astrophysics Data System (ADS)

    Chung, So Hyun

    Structural changes in water molecules are related to physiological, anatomical and pathological properties of tissues. Near infrared (NIR) optical absorption methods are sensitive to water; however, detailed characterization of water in thick tissues is difficult to achieve because subtle spectral shifts can be obscured by multiple light scattering. In the NIR, a water absorption peak is observed around 975 nm. The precise NIR peak's shape and position are highly sensitive to water molecular disposition. A bound water index (BWI) was developed that quantifies the spectral shift and shape changes observed in tissue water absorption spectra measured by broadband diffuse optical spectroscopic imaging (DOSI). DOSI quantitatively measures light absorption and scattering spectra in cm-deep tissues and therefore reveals bound water spectral shifts. BWI as a water state index was validated by comparing broadband DOSI to MRI and a conductivity cell using bound water phantoms. Non-invasive BWI measurements of malignant and normal tissues in 18 subjects showed a significantly higher fraction of free water in malignant tissues (p<0.0001) compared to normal tissues. BWI showed potential as a prognostic index based on high correlations with tumor grade and size. An algorithm for absolute temperature measurements in deep tissues was developed based on resolving opposing effects of water vibrational frequency shifts due to macromolecular binding. DOSI measures absolute temperature with a difference of 1.1+/-0.91°C from a thermistor. Deep tissue temperature measured in forearms during cold-stress was consistent with previously reported invasively-measured deep tissue temperature. Finally, the BWI was compared to Apparent Diffusion Coefficient (ADC) of diffusion weighted MRI in 9 breast cancer patients. The BWI and ADC correlated (R=0.8, p=<0.01) and both parameters decreased with increasing bulk water content in cancer tissues. Although BWI and ADC are positively correlated in

  1. Newly synthesized dihydroquinazoline derivative from the aspect of combined spectroscopic and computational study

    NASA Astrophysics Data System (ADS)

    El-Azab, Adel S.; Mary, Y. Sheena; Mary, Y. Shyma; Panicker, C. Yohannan; Abdel-Aziz, Alaa A.-M.; El-Sherbeny, Magda A.; Armaković, Stevan; Armaković, Sanja J.; Van Alsenoy, Christian

    2017-04-01

    In this work, spectroscopic characterization of 2-(2-(4-oxo-3-phenethyl-3,4-dihydroquinazolin-2-ylthio)ethyl)isoindoline-1,3-dione have been obtained with experimentally and theoretically. Complete assignments of fundamental vibrations were performed on the basis of the potential energy distribution of the vibrational modes and good agreement between the experimental and scaled wavenumbers has been achieved. Frontier molecular orbitals have been used as indicators of stability and reactivity. Intramolecular interactions have been investigated by NBO analysis. The dipole moment, linear polarizability and first and second order hyperpolarizability values were also computed. In order to determine molecule sites prone to electrophilic attacks DFT calculations of average local ionization energy (ALIE) and Fukui functions have been performed as well. Intra-molecular non-covalent interactions have been determined and analyzed by the analysis of charge density. Stability of title molecule have also been investigated from the aspect of autoxidation, by calculations of bond dissociation energies (BDE), and hydrolysis, by calculations of radial distribution functions after molecular dynamics (MD) simulations. In order to assess the biological potential of the title compound a molecular docking study towards breast cancer type 2 complex has been performed.

  2. Vibrational spectroscopic study of newly developed self-forming lipids and nanovesicles.

    NASA Astrophysics Data System (ADS)

    Bista, Rajan; Bruch, Reinhard

    2009-03-01

    We present the first experimental study of self-forming synthetic nanovesicles, trademarked as QuSomes, using vibrational spectroscopic techniques namely near-infrared (NIR) and laser tweezers Raman spectroscopy. Raman spectra of these new artificial nanovesicles suspended in Phosphate Buffered Saline (PBS) have been obtained by using an inverted confocal laser-tweezers-Raman-microscopy system in the spectral range of 3100 to 500 cm-1. This spectrometer works with an 80 mW diode-pumped solid-state laser, operating at a wavelength of 785 nm in the TEM00 mode. The laser is used both for optical trapping and Raman excitation. Similarly, NIR absorption spectra of these novel nanovesicles have been recorded in the spectral range of 9000-4800 cm-1 by using a new miniaturized micro-mirror spectrometer based on micro-optical-electro-mechanical systems (MOEMS) technology. In this work, we have found that the most prominent bands in the studied spectral region of Raman spectra are dominated by vibrational modes arising from C-C and CH2 bonds. Similarly, NIR spectra are primarily assigned as first and second overtone of C-H stretching mode and second overtone of C=O stretching mode. These spectroscopic techniques have proven to be an excellent tool to establish the fingerprint region revealing the molecular structure and conformation of QuSomes nanoparticles.

  3. Particle in a Disk: A Spectroscopic and Computational Laboratory Exercise Studying the Polycyclic Aromatic Hydrocarbon Corannulene

    ERIC Educational Resources Information Center

    Frey, E. Ramsey; Sygula, Andrzej; Hammer, Nathan I.

    2014-01-01

    This laboratory exercise introduces undergraduate chemistry majors to the spectroscopic and theoretical study of the polycyclic aromatic hydrocarbon (PAH), corannulene. Students explore the spectroscopic properties of corannulene using UV-vis and Raman vibrational spectroscopies. They compare their experimental results to simulated vibrational…

  4. Particle in a Disk: A Spectroscopic and Computational Laboratory Exercise Studying the Polycyclic Aromatic Hydrocarbon Corannulene

    ERIC Educational Resources Information Center

    Frey, E. Ramsey; Sygula, Andrzej; Hammer, Nathan I.

    2014-01-01

    This laboratory exercise introduces undergraduate chemistry majors to the spectroscopic and theoretical study of the polycyclic aromatic hydrocarbon (PAH), corannulene. Students explore the spectroscopic properties of corannulene using UV-vis and Raman vibrational spectroscopies. They compare their experimental results to simulated vibrational…

  5. Preferential binding of fisetin to the native state of bovine serum albumin: spectroscopic and docking studies.

    PubMed

    Singha Roy, Atanu; Pandey, Nitin Kumar; Dasgupta, Swagata

    2013-04-01

    We have investigated the binding of the biologically important flavonoid fisetin with the carrier protein bovine serum albumin using multi-spectroscopic and molecular docking methods. The binding constants were found to be in the order of 10(4) M(-1) and the number of binding sites was determined as one. MALDI-TOF analyses showed that one fisetin molecule binds to a single bovine serum albumin (BSA) molecule which is also supported by fluorescence quenching studies. The negative Gibbs free energy change (∆G°) values point to a spontaneous binding process which occurs through the presence of electrostatic forces with hydrophobic association that results in a positive entropy change (+51.69 ± 1.18 J mol(-1) K(-1)). The unfolding and refolding of BSA in urea have been studied in absence and presence of fisetin using steady-state fluorescence and lifetime measurements. Urea denaturation studies indicate that fisetin is gradually released from its binding site on the protein. In the absence of urea, an increase in temperature that causes denaturation of the protein results in the release of fisetin from its bound state indicating that fisetin binds only to the native state of the protein. The circular dichroism (CD) and Fourier transform infrared (FTIR) spectroscopic studies showed an increase in % α-helix content of BSA after binding with fisetin. Site marker displacement studies in accordance with the molecular docking results suggested that fisetin binds in close proximity of the hydrophobic cavity in site 1 (subdomain IIA) of the protein. The PEARLS (Program of Energetic Analysis of Receptor Ligand System) has been used to estimate the interaction energy of fisetin with BSA and the results are in good correlation with the experimental findings.

  6. Infrared Spectroscopic Studies with the Stratospheric Observatory for Infrared Astronomy (sofia)

    NASA Astrophysics Data System (ADS)

    Gehrz, R. D.; Becklin, E. E.

    2011-06-01

    The joint U.S. and German Stratospheric Observatory for Infrared Astronomy (SOFIA) will be a premier facility for studying the physics and chemistry of the interstellar medium and the stellar evolution process for many decades. SOFIA's first-generation instrument complement includes broadband imagers, moderate resolution spectrographs capable of resolving broad features due to dust and large molecules, and high resolution spectrometers suitable for kinematic studies of molecular and atomic gas lines at km/s resolution. SOFIA spectroscopic science applications will be discussed, with special emphasis on investigations related to infrared spectroscopy of astrophysical gas, grains, and ices. First light images and early science results related to these topics will be presented.

  7. Probing the mechanism of interaction of metoprolol succinate with human serum albumin by spectroscopic and molecular docking analysis.

    PubMed

    Pawar, Suma K; Jaldappagari, Seetharamappa

    2017-09-01

    In the present work, the mechanism of the interaction between a β1 receptor blocker, metoprolol succinate (MS) and human serum albumin (HSA) under physiological conditions was investigated by spectroscopic techniques, namely fluorescence, Fourier transform infra-red spectroscopy (FT-IR), fluorescence lifetime decay and circular dichroism (CD) as well as molecular docking and cyclic voltammetric methods. The fluorescence and lifetime decay results indicated that MS quenched the intrinsic intensity of HSA through a static quenching mechanism. The Stern-Volmer quenching constants and binding constants for the MS-HSA system at 293, 298 and 303 K were obtained from the Stern-Volmer plot. Thermodynamic parameters for the interaction of MS with HSA were evaluated; negative values of entropy change (ΔG°) indicated the spontaneity of the MS and HSA interaction. Thermodynamic parameters such as negative ΔH° and positive ΔS° values revealed that hydrogen bonding and hydrophobic forces played a major role in MS-HSA interaction and stabilized the complex. The binding site for MS in HSA was identified by competitive site probe experiments and molecular docking studies. These results indicated that MS was bound to HSA at Sudlow's site I. The efficiency of energy transfer and the distance between the donor (HSA) and acceptor (MS) was calculated based on the theory of Fosters' resonance energy transfer (FRET). Three-dimensional fluorescence spectra and CD results revealed that the binding of MS to HSA resulted in an obvious change in the conformation of HSA. Cyclic voltammograms of the MS-HSA system also confirmed the interaction between MS and HSA. Furthermore, the effects of metal ions on the binding of MS to HSA were also studied. Copyright © 2017 John Wiley & Sons, Ltd.

  8. Spectroscopic and DFT study of 3-quinolyl-α-aminophosphonates

    NASA Astrophysics Data System (ADS)

    Juribašić, Marina; Tušek-Božić, Ljerka

    2009-04-01

    Spectroscopic and DFT study of two types of 3-quinolyl-α-aminophosphonate derivatives obtained by one-pot microwave-assisted synthesis of quinoline-3-carboxaldehyde and aniline as well as 3-aminoquinoline and benzaldehyde, respectively, with diethyl phosphite, have been described. Besides the diethyl [α-anilino- N-(3-quinolylmethyl)]phosphonate ( 1) and diethyl [α-(3-quinolylamino)- N-benzyl]phosphonate ( 4) as the main reaction products, in both cases some unexpected monoester phosphonate derivatives were obtained as the by-products. In the first case along with diester 1, its corresponding monoethyl ester ( 2) and one monoethyl dihydrophosphonate-phosphate derivative ( 3) were formed, while in the second case diester 4 and a hydrogen phosphonamidate ( 5) were isolated. All quinoline-based α-aminophosphonates ( 1- 5) have been characterized by IR spectroscopy, and the results obtained are compared and discussed with those obtained by the NMR studies. Combining experimental IR, 1H and 13C NMR spectra with DFT calculations, most intensive IR spectral bands of diesters 1 and 4, along with 1H and 13C NMR resonances of 1, 2 and 4 derivatives, were assigned.

  9. Infrared Imaging, Spectroscopic, and Photometric Studies of Comets

    NASA Technical Reports Server (NTRS)

    Gehrz, Robert D.

    1997-01-01

    We have continued our program of infrared (IR) photometric, imaging, spectroscopic, and polarimetric temporal observations of comets to study the properties of comet dust and comet nuclei. During the first two years we digitized our IR data base on P/Halley and other recent comets to facilitate further analysis and comparison with other data bases, and found compelling evidence for the emission of a burst of small grains from P/Halley's nucleus at perihelion. We reported imaging and photometric observations of Comets Austin 1990 V and Swift-Tuttle 1992. The Swift-Tuttle 1992t observations included IR photometry, several 7-14 micron long-slit spectra of the coma and a time-sequence of more than 150 10 micron broadband images of the coma. An analysis of near-IR images of the inner coma of P/Halley obtained on three consecutive nights in 1986 March showed sunwardjets. We completed our analysis of IR imaging spectrosco-photometric data on comets. We also obtained observations of Comets Hyakutake 1996 B2 and Hale/Bopp 1995 01. We obtained infrared imaging, photometric, spectroscopic and polarimetric temporal observations of bright comets using a network of five telescopes, with emphasis on simultaneous observations of comets at many wavelengths with different instruments. Our program offers several unique advantages: 1) rapid observational response to new comets with dedicated infrared telescopes; 2) observations within a few degrees of the sun when comets are near perihelion and 3) access to advanced infrared array imagers and spectrometers. In particular, reduction, analysis, publication and archiving of our Jupiter/sl-9 and Comet Hyakutake infrared data received special emphasis. Instrumentation development included installation of the latest version of the innovative FORTH telescope control and a data acquisition system that enables us to control three telescopes remotely by telephone from anywhere in the world for comet observations in broad daylight. We have

  10. Interaction of collagen with chlorosulphonated paraffin tanning agents: Fourier transform infrared spectroscopic analysis and molecular dynamics simulations.

    PubMed

    Monti, Susanna; Bramanti, Emilia; Della Porta, Valentina; Onor, Massimo; D'Ulivo, Alessandro; Barone, Vincenzo

    2013-09-21

    The binding of chlorosulphonated paraffins to collagen triple helices is studied by means of classical molecular dynamics simulations and experimental spectroscopic techniques in order to disclose the principal characteristics of their interaction during the leather fattening process. Indeed, collagen is the main target to develop new leather modifying agents with specific characteristics, and an accurate design of the collagen binders, supported by predictive computational strategies, could be a successful tool to obtain new effective eco-compatible compounds able to impart to the leather the required functionalities and distinctive mechanical properties. Possible effects caused by the tanning agents on the collagen matrix have been identified from both experimental and theoretical points of view. Computational data in agreement with experiment have revealed that chlorosulphonated paraffins can interact favorably with the collagen residues having amine groups in their side chains (Arg, Lys, Asn and Gln) and reduce the tendency of the solvated collagen matrix to swell. However, the interference of chlorosulphonated paraffins with the unfolding process, which is operated mainly by the action of water, can be due both to covalent cross-linking of the collagen chains and intermolecular hydrogen bonding interactions involving also the hydroxyl groups of Hyp, Ser and Thr residues.

  11. Supramolecular interaction of gemifloxacin and hydroxyl propyl β-cyclodextrin spectroscopic characterization, molecular modeling and analytical application.

    PubMed

    Dsugi, Nuha Fathi Ali; Elbashir, Abdalla A; Suliman, Fakhr Eldin Osman

    2015-01-01

    The solid inclusion complex of gemifloxacin (GFX) and hydroxyl propyl β-cyclodextrin (HPβ-CD) was prepared and examined by UV-visible, FTIR, NMR, electrospray ionization mass spectrometry (ESI-MS) and fluorescence spectroscopy. The formation of inclusion complex has been confirmed on the basis of changes of spectroscopic properties. Further the interaction between GFX and HPβ-CD was studied using molecular modeling approaches. The results showed that HPβCD reacted with GFX to form a 1:1 host-guest inclusion complex. Based on the enhancement of the fluorescence intensity of GFX produced through complex formation, a simple, accurate, rapid and highly sensitive spectrofluorometric method for the determination of GFX in pharmaceutical formulation was developed. The linear relationships between the intensity and GFX concentration was obtained in the concentration range of 20-140 ng/mL with good correlation coefficients (0.9997). The limit of detection (LOD) was found to be 4 ng/mL. The proposed method was successfully applied to the analysis of GFX in pharmaceutical preparation. Copyright © 2015 Elsevier B.V. All rights reserved.

  12. Molecular basis of processing-induced changes in protein structure in relation to intestinal digestion in yellow and green type pea (Pisum sativum L.): A molecular spectroscopic analysis.

    PubMed

    Yu, Gloria Qingyu; Warkentin, Tom; Niu, Zhiyuan; Khan, Nazir A; Yu, Peiqiang

    2015-12-05

    The objectives of this study were (1) to quantify the protein inherent molecular structural features of green cotyledon (CDC Striker) and yellow cotyledon (CDC Meadow) pea (Pisum sativum L.) seeds using molecular spectroscopic technique (FT/IR-ATR); (2) measure the denaturation of protein molecular makeup in the two types of pea during dry roasting (120°C for 60 min), autoclaving (120°C for 60 min) or microwaving (for 5 min); and (3) correlate the heat-induced changes in protein molecular makeup to the corresponding changes in protein digestibility determined using modified three-step in vitro procedure. Compared with yellow-type, the green-type peas had higher (P<0.05) ratios of amide I to II peak height (1.698 vs. 1.805) and area (1.843 vs. 2.017). A significant correlation was observed between the amide I and II peak height (r=0.48) and peak area (r=-0.42) ratio with protein content. Compared with yellow-type, the green-type peas had lower (P<0.05) α-helix:β-sheet ratio (1.015 vs. 0.926), indicating varietal difference in protein secondary structure makeup. All processing applications increased α-helix:β-sheet ratio, with the largest (P<0.05) increase being observed with roasting and microwaving. The heat-induced changes in α-helix:β-sheet ratio was strongly correlated to intestinal digestibility of protein within the green (r=-0. 86) and yellow (r=0.81) pea-types. However, across the pea types the correlation was not significant. Principal component and hierarchical cluster analyses on the entire spectral data from the amide region (ca. 1727-1480 cm(-1)) were able to visualize and discriminate the structural difference between pea varieties and processing treatments. This study shows that the molecular spectroscopy can be used as a rapid tool to screen the protein value of raw and heat-treated peas. Copyright © 2015 Elsevier B.V. All rights reserved.

  13. In vitro spectroscopic study of piperine-encapsulated nanosize liposomes.

    PubMed

    Pentak, Danuta

    2016-03-01

    Black pepper is a source of effective antioxidants. It contains several powerful antioxidants and is thus one of the most important spices for preventing and curtailing oxidative stress. There is considerable interest in the development of a drug-delivery systems that would result in the selective delivery of antioxidants to tissues in sufficient concentrations to ameliorate oxidant-induced tissue injuries. Liposomes are biocompatible, biodegradable and nontoxic artificial phospholipid vesicles that offer the possibility of carrying hydrophilic, hydrophobic and amphiphilic molecules. This article focuses on the use of liposomes for the delivery of antioxidants in the prevention or treatment of pathological conditions related to oxidative stress. Liposome formulations of piperine were analyzed with various spectroscopic methods. The formulation with the highest entrapment efficiency (90.5%) was formulated with an L-α-phosphatidylcholine dipalmitoyl (DPPC):piperine, 30:1 molar ratio, and total lipid count of 19.47 mg/ml in the final liposomal preparation. The liposome formulation was found to be stable after storage at 4 °C, protected from light, for a minimum of 3 weeks. The incremental process of piperine penetration through the phospholipid membrane was analyzed using the FT-IR, UV-Vis and NMR methods. Temperature stability studies carried out at 37 °C showed the highest percentage of piperine release in the first 3 h of incubation.

  14. A spectroscopic study of the globular Cluster NGC 4147

    NASA Astrophysics Data System (ADS)

    Villanova, S.; Monaco, L.; Moni Bidin, C.; Assmann, P.

    2016-08-01

    We present the abundance analysis for a sample of 18 red giant branch stars in the metal-poor globular cluster NGC 4147 based on medium- and high-resolution spectra. This is the first extensive spectroscopic study of this cluster. We derive abundances of C, N, O, Na, Mg, Al, Si, Ca, Ti, Cr, Fe, Ni, Y, Ba, and Eu. We find a metallicity of [Fe/H] = -1.84 ± 0.02 and an α-enhancement of +0.38 ± 0.05 (errors on the mean), typical of halo globular clusters in this metallicity regime. A significant spread is observed in the abundances of light elements C, N, O, Na, and Al. In particular, we found an Na-O anticorrelation and Na-Al correlation. The cluster contains only ˜15 per cent of stars that belong to the first generation (Na-poor and O-rich). This implies that it suffered a severe mass-loss during its lifetime. Its [Ca/Fe] and [Ti/Fe] mean values agree better with the Galactic halo trend than with the trend of extragalactic environments at the cluster metallicity. This possibly suggests that NGC 4147 is a genuine Galactic object at odd with what claimed by some author that proposed the cluster to be member of the Sagittarius dwarf galaxy. An antirelation between the light s-process element Y and Na may also be present.

  15. Spectroscopic and Microscopic Study of Peroxyformic Pulping of Agave Waste.

    PubMed

    Hernández-Hernández, Hilda M; Chanona-Pérez, Jorge J; Vega, Alberto; Ligero, Pablo; Farrera-Rebollo, Reynold R; Mendoza-Pérez, Jorge A; Calderón-Domínguez, Georgina; Vera, Norma Güemes

    2016-10-01

    The peroxyformic process is based on the action of a carboxylic acid (mainly formic acid) and the corresponding peroxyacid. The influences of processing time (60-180 min), formic acid concentration (80-95%), temperature (60-80°C), and hydrogen peroxide concentration (2-4%) on peroxyformic pulping of agave leaves were studied by surface response methodology using a face-centered factorial design. Empirical models were obtained for the prediction of yield, κ number (KN) and pulp viscosity as functions of the aforementioned variables. Mathematical optimization enabled us to select a set of operational variables that produced the best fractionation of the material with the following results: pulp yield (26.9%), KN (3.6), and pulp viscosity (777 mL/g). Furthermore, this work allowed the description and evaluation of changes to the agave fibers during the fractionation process using different microscopic and spectroscopic techniques, and provided a comprehensive and qualitative view of the phenomena occurring in the delignification of agave fibers. The use of confocal and scanning electron microscopy provided a detailed understanding of the microstructural changes to the lignin and cellulose in the fibers throughout the process, whereas Raman spectroscopy and X-ray diffraction analysis indicated that cellulose in the pulp after treatment was mainly of type I.

  16. Spectroscopic studies of cryogenic fluids: Benzene in propane

    NASA Astrophysics Data System (ADS)

    Nowak, R.; Bernstein, E. R.

    1987-03-01

    Energy shifts and bandwidths for the 1B2u↔1A1g optical absorption and emission transitions of benzene dissolved in propane are presented as a function of pressure, temperature, and density. Both absorption and emission spectra exhibit shifts to lower energy as a function of density, whereas no shifts are observed if density is kept constant and temperature and pressure are varied simultaneously. Density is thus the fundamental microscopic parameter for energy shifts of optical transitions. The emission half-width is a linear function of both temperature and pressure but the absorption half-width is dependent only upon pressure. These results are interpreted qualitatively in terms of changes occurring in the intermolecular potentials of the ground and excited states. Both changes in shape of and separation between the ground and excited state potentials are considered as a function of density. Classical dielectric (Onsager-Böttcher), microscopic dielectric (Wertheim) and microscopic quantum statistical mechanical (Schweizer-Chandler) theories of solvent effects on solute electronic spectra are compared with the experimental results. Calculations suggest limited applicability of dielectric theories but good agreement between experiment and microscopic theory. The results demonstrate the usefulness of cryogenic solutions for high pressure, low temperature spectroscopic studies of liquids.

  17. Spectroscopic Study on the Interaction of 4-dimethylaminochalcones with Phospholipids

    NASA Astrophysics Data System (ADS)

    Tomečková, V.; Revická, M.; Sassen, A.; Veliká, B.; Stupák, M.; Perjési, P.

    2014-11-01

    The ultraviolet-visible and fluorescence spectroscopic properties of 4'-dimethylaminochalcone ( 1a) and its cyclic analogs 2a-4a have been studied in the presence of phospholipid vesicles (i.e., egg yolk lecithin and dipalmitoylpho sphatidylcholine), bovine serum albumin (BSA), and lipoprotein particles (i.e., bovine serum albumin plus egg yolk lecithin). The spectral results showed that compounds 1a-4a formed hydrophobic interactions with the phospholipids, lipoproteins, and BSA at the polar/nonpolar interface. Compounds 3a and 4a exhibited the strongest hydrophobic interactions of all of the compounds tested towards the phospholipids. Compound 2a gave the best fluorescent fluorophore indicating interactions with the lipids, lipoproteins, and proteins. Fluorescent microscopic imaging of breast cancer cells treated with compounds 1a-4a revealed that they could be used to stain all of the cellular components and destroy the nuclear structure. Compounds 1a-4a were found to be concentrated predominantly on the surfaces of the liposomes and lipoproteins.

  18. Vibrational spectroscopic study of vinyl substituted polycyclic aromatic hydrocarbons.

    PubMed

    Maurya, Anju; Rastogi, Shantanu

    2015-12-05

    The mid infrared emission features observed in various astrophysical sources are attributed to polycyclic aromatic hydrocarbon (PAH) molecules. The models of emission spectra from a collection of PAHs show uncertainty in matching the 6.2 μm feature. This indicates the need to consider a larger variety of PAHs and PAH derivatives. Chemical pathways towards formation of PAHs in the astrophysical environments involve vinyl substituted PAHs as intermediate products. Vibrational spectroscopic study of vinyl-PAHs is reported in the present work. The vinyl group is substituted at similar positions in eight different PAHs. The obtained optimized structures show that vinyl substitution at 2 position in acenes gives planar geometry, while all other vinyl-PAHs are non-planar. Infrared spectra is simulated for neutrals as well as for cations. The results are compared with the spectra of corresponding plain PAHs and analyzed for possible match with astrophysical observations. New features, due to vinyl group in the composite spectra, identified at 6.64, 6.92, 7.27, 8.77 and 10.35 μm fall close to some sub features of the observed emission spectra. The paper provides data that may be used in the emission models particularly along proto planetary nebulae type cool objects. Copyright © 2015 Elsevier B.V. All rights reserved.

  19. Spectroscopic Signatures and Structural Motifs of Dopamine: a Computational Study

    NASA Astrophysics Data System (ADS)

    Srivastava, Santosh Kumar; Singh, Vipin Bahadur

    2016-06-01

    Dopamine (DA) is an essential neurotransmitter in the central nervous system and it plays integral role in numerous brain functions including behaviour, cognition, emotion, working memory and associated learning. In the present work the conformational landscapes of neutral and protonated dopamine have been investigated in the gas phase and in aqueous solution by MP2 and DFT (M06-2X, ωB97X-D, B3LYP and B3LYP-D3) methods. Twenty lowest energy structures of neutral DA were subjected to geometry optimization and the gauche conformer, GIa, was found to be the lowest gas phase structure at the each level of theory in agreement with the experimental rotational spectroscopy. All folded gauche conformers (GI) where lone electron pair of the NH2 group is directed towards the π system of the aromatic ring ( 'non up' ) are found more stable in the gas phase. While in aqueous solution, all those gauche conformers (GII) where lone electron pair of the NH2 group is directed opposite from the π system of the aromatic ring ('up' structures) are stabilized significantly.Nine lowest energy structures, protonated at the amino group, are optimized at the same MP2/aug-cc-pVDZ level of theory. In the most stable gauche structures, g-1 and g+1, mainly electrostatic cation - π interaction is further stabilized by significant dispersion forces as predicted by the substantial differences between the DFT and dispersion corrected DFT-D3 calculations. In aqueous environment the intra-molecular cation- π distance in g-1 and g+1 isomers, slightly increases compared to the gas phase and the magnitude of the cation- π interaction is reduced relative to the gas phase, because solvation of the cation decreases its interaction energy with the π face of aromatic system. The IR intensity of the bound N-H+ stretching mode provides characteristic 'IR spectroscopic signatures' which can reflect the strength of cation- π interaction energy. The CC2 lowest lying S1 ( 1ππ* ) excited state of neutral

  20. A comparison investigation of DNP-binding effects to HSA and HTF by spectroscopic and molecular modeling techniques.

    PubMed

    Zolfagharzadeh, Mahboobeh; Pirouzi, Maliheh; Asoodeh, Ahmad; Saberi, Mohammad Reza; Chamani, Jamshidkhan

    2014-12-01

    This paper describes the interaction between 2,4-dinitrophenol (DNP) with the two drug carrier proteins - human serum albumin (HSA) and human holo transferrin (HTF). Hence, binding characteristics of DNP to HSA and HTF were analyzed by spectroscopic and molecular modeling techniques. Based on results obtained from fluorescence spectroscopy, DNP had a strong ability to quench the intrinsic fluorescence of HSA and HTF through a static quenching procedure. The binding constant and the number of binding sites were calculated as 2.3 × 10(11) M(-1) and .98 for HSA, and 1.7 × 10(11) M(-1) and 1.06 for HTF, respectively. In addition, synchronous fluorescence results showed that the microenvironment of Trp had a slight tendency of increasing its hydrophobicity, whereas the microenvironment of the Tyr residues of HSA did not change and that of HTF showed a significant trend (red shift of about 4 nm) of an increase in polarity. The distance between donor and acceptor was obtained by the Förster energy according to fluorescence resonance energy transfer, and was found to be 3.99 and 3.72 nm for HSA and HTF, respectively. The critical induced aggregation concentration (CCIAC) of the drug on both proteins was determined and confirmed by an inflection point of the zeta potential behavior. Circular dichroism data revealed that the presence of DNP caused a decrease of the α-helical content of HSA and HTF, and induced a remarkable mild denaturation of both proteins. The molecular modeling data confirmed our experimental results. This study is deemed useful for determining drug dosage.

  1. Interaction of bisphenol A with bovine hemoglobin using spectroscopic and molecular modeling methods.

    PubMed

    Fang, Xiaoyan; Cao, Shutao; Liu, Rutao

    2011-11-01

    The interaction of bisphenol A with bovine hemoglobin (BHb) under physiological conditions was investigated by using fluorescence, ultraviolet-visible (UV-Vis) absorption, circular dichroism (CD), and molecular modeling. The experimental results showed that BPA can bind with BHb to form a complex. The binding constant Ka and the number of binding sites n were calculated to be 1.49 × 10(5) L mol(-1) and 1, respectively. Molecular modeling study revealed that BPA bound into BHb central cavity, and the binding mode of BPA-BHb complex could be hydrogen bonding. The UV-Vis absorption and CD spectra indicated that the secondary structure of BHb was altered, which may affect physiological functions of hemoglobin. This work is helpful for clarifying the molecular toxic mechanism of BPA in vivo.

  2. Spectroscopic, structural and drug docking studies of carbocysteine

    NASA Astrophysics Data System (ADS)

    Manivannan, M.; Rajeshwaran, K.; Govindhan, R.; Karthikeyan, B.

    2017-09-01

    Carbocysteine or carbocisteine having the empirical formula C5H9NO4S,is one of the most therapeutically prescribed expectorant, sold under the brand name viz., Mucodyne (UK and India), Rhinathiol and Mucolite. In pediatric respiratory pathology, it can relieve the symptoms of obstructive pulmonary disease (COPD) and bronchiectasis. On the consideration of its extensive pharmaceutical usage and medicinal value, we have investigated its chemical structure and composition by employing various spectral techniques like 1H, 13C NMR, FT-IR,Raman, UV-Visible spectroscopy and powder X-ray diffraction method. Density Functional Theoretical (DFT) studies on its electronic structure is also carried out. Drug docking studies were carried out to ascertain the nature of molecular interaction with the biological protein system. Furthermore theoretical Raman spectrum of this molecule has been computed and compared with the experimental Raman spectrum. The forbidden energy gap between its frontier molecular orbitals, viz., HOMO-LUMO is calculated and correlated with its observed λmax value. Atomic orbitals which are mainly contributes to the frontier molecular orbitals were identified. Molecular electrostatic potential diagram has been mapped to explain its chemical activity. Based on the results, a suitable mechanism of its protein binding mode and drug action has been discussed.

  3. Spectroscopic study of humic acids fractionated by means of tangential ultrafiltration

    NASA Astrophysics Data System (ADS)

    Francioso, O.; Sánchez-Cortés, S.; Casarini, D.; Garcia-Ramos, J. V.; Ciavatta, C.; Gessa, C.

    2002-05-01

    Different chemical and spectroscopic techniques—diffuse reflectance infrared Fourier transform (DRIFT), surface-enhanced Raman spectroscopy (SERS), and 1H, 13C nuclear magnetic resonance (NMR) have been applied to investigate a peat humic acid (HA) separated by tangential ultrafiltration into different nominal molecular weight (NMW) fractions. Each fraction analyzed showed a characteristic DRIFT and NMR pattern. High nominal molecular weight fractions were mainly characterized by long chains of methyl and methylene groups and poorly substituted aromatic rings, while in low nominal molecular weight fractions (L-NMW), phenolic and oxygen-containing groups were predominant. A comparative study on fractions before and after treatment with 0.5 M HCl was carried out. Purified fractions showed either an increase in the carboxylate and phenolic OH groups or an improvement in signal-to-noise ratio of their NMR spectra. The SERS study of NMW fractions allowed significative information on structure and conformation of these fractions. In particular, L-NMW fractions showed a great structural modification, when different alkaline extractants or treatment with HCl were used. Humic-like substances obtained by catechol and gallic acid polymerization on metal surface were investigated using SERS. The SERS spectra of these polymers were compared and discussed with those of NMW HA fractions.

  4. Photoacoustic FTIR spectroscopic study of undisturbed human cortical bone

    NASA Astrophysics Data System (ADS)

    Gu, Chunju; Katti, Dinesh R.; Katti, Kalpana S.

    2013-02-01

    Chemical pretreatment has been the prevailing sample preparation procedure for infrared (IR) spectroscopic studies on bone. However, experiments have indicated that chemical pretreatment can potentially affect the interactions between the components. Typically the IR techniques have involved transmission experiments. Here we report experimental studies using photoacoustic Fourier transform infrared spectroscopy (PA-FTIR). As a nondestructive technique, PA-FTIR can detect absorbance spectrum from a sample at controllable sampling depth and with little or no sample preparation. Additionally, the coupling inert gas, helium, which is utilized in the PA-FTIR system, can inhibit bacteria growth of bone by displacing oxygen. Therefore, we used this technique to study the undisturbed human cortical bone. It is found that photoacoustic mode (linear-scan, LS-PA-FTIR) can obtain basically similar spectra of bone as compared to the traditional transmission mode, but it seems more sensitive to amide III and ν2 carbonate bands. The ν3 phosphate band is indicative of detailed mineral structure and symmetry of native bone. The PA-FTIR depth profiling experiments on human cortical bone also indicate the influence of water on OH band and the cutting effects on amide I and mineral bands. Our results indicate that phosphate ion geometry appears less symmetric in its undisturbed state as detected by the PA-FTIR as compared to higher symmetry observed using transmission techniques on disturbed samples. Moreover, the PA-FTIR spectra indicate a band at 1747 cm-1 possibly resulting from Cdbnd O stretching of lipids, cholesterol esters, and triglycerides from the arteries. Comparison of the spectra in transverse and longitudinal cross-sections demonstrates that, the surface area of the longitudinal section bone appears to have more organic matrix exposed and with higher mineral stoichiometry.

  5. Spectroscopic investigations and molecular docking study of (2E)-1-(4-Chlorophenyl)-3-[4-(propan-2-yl)phenyl]prop-2-en-1-one using quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Parveen, Shana; Al-Alshaikh, Monirah A.; Panicker, C. Yohannan; El-Emam, Ali A.; Salian, Vinutha V.; Narayana, B.; Sarojini, B. K.; van Alsenoy, C.

    2016-09-01

    In this work, the vibrational spectral analysis was carried out using FT-IR and FT-Raman spectroscopy of (2E)-1-(4-Chlorophenyl)-3-[4-(propan-2-yl)phenyl]prop-2-en-1-one. The computations were performed at DFT level of theory to get the optimizedgeometry and vibrational wave numbers of the normal modes of the title compound using Gaussian09 software. The complete vibrational assignments of wave numbers were made on the basis of potential energy distribution. The calculated HOMO and LUMO energies show chemical activity of the molecule. The stability of the molecule arising from hyper-conjugative interaction and charge delocalization has been analyzed using NBO analysis. The hyperpolarizability values are reported and the first hyperpolarizability of the title compound is 83.85 times that of standard NLO material urea. From the MEP plot, the negative electrostatic potential regions are mainly localized over the carbonyl group, the phenyl rings and are possible sites for electrophilic attack. The positive regions are localized over all the hydrogen atoms and are possible sites for nucleophilic attack. The molecular docking results suggest that the compound might exhibit inhibitory activity against lymphocyte-specific kinase and may results in design of novel T-cell immunosuppressants.

  6. Investigation on the protein-binding properties of icotinib by spectroscopic and molecular modeling method

    NASA Astrophysics Data System (ADS)

    Zhang, Hua-xin; Xiong, Hang-xing; Li, Li-wei

    2016-05-01

    Icotinib is a highly-selective epidermal growth factor receptor tyrosine kinase inhibitor with preclinical and clinical activity in non-small cell lung cancer, which has been developed as a new targeted anti-tumor drug in China. In this work, the interaction of icotinib and human serum albumin (HSA) were studied by three-dimensional fluorescence spectra, ultraviolet spectra, circular dichroism (CD) spectra, molecular probe and molecular modeling methods. The results showed that icotinib binds to Sudlow's site I in subdomain IIA of HSA molecule, resulting in icotinib-HSA complexes formed at ground state. The number of binding sites, equilibrium constants, and thermodynamic parameters of the reaction were calculated at different temperatures. The negative enthalpy change (ΔHθ) and entropy change (ΔSθ) indicated that the structure of new complexes was stabilized by hydrogen bonds and van der Waals power. The distance between donor and acceptor was calculated according to Förster's non-radiation resonance energy transfer theory. The structural changes of HSA caused by icotinib binding were detected by synchronous spectra and circular dichroism (CD) spectra. Molecular modeling method was employed to unfold full details of the interaction at molecular level, most of which could be supported by experimental results. The study analyzed the probability that serum albumins act as carriers for this new anticarcinogen and provided fundamental information on the process of delivering icotinib to its target tissues, which might be helpful in understanding the mechanism of icotinib in cancer therapy.

  7. Investigation on the protein-binding properties of icotinib by spectroscopic and molecular modeling method.

    PubMed

    Zhang, Hua-xin; Xiong, Hang-xing; Li, Li-wei

    2016-05-15

    Icotinib is a highly-selective epidermal growth factor receptor tyrosine kinase inhibitor with preclinical and clinical activity in non-small cell lung cancer, which has been developed as a new targeted anti-tumor drug in China. In this work, the interaction of icotinib and human serum albumin (HSA) were studied by three-dimensional fluorescence spectra, ultraviolet spectra, circular dichroism (CD) spectra, molecular probe and molecular modeling methods. The results showed that icotinib binds to Sudlow's site I in subdomain IIA of HSA molecule, resulting in icotinib-HSA complexes formed at ground state. The number of binding sites, equilibrium constants, and thermodynamic parameters of the reaction were calculated at different temperatures. The negative enthalpy change (ΔH(θ)) and entropy change (ΔS(θ)) indicated that the structure of new complexes was stabilized by hydrogen bonds and van der Waals power. The distance between donor and acceptor was calculated according to Förster's non-radiation resonance energy transfer theory. The structural changes of HSA caused by icotinib binding were detected by synchronous spectra and circular dichroism (CD) spectra. Molecular modeling method was employed to unfold full details of the interaction at molecular level, most of which could be supported by experimental results. The study analyzed the probability that serum albumins act as carriers for this new anticarcinogen and provided fundamental information on the process of delivering icotinib to its target tissues, which might be helpful in understanding the mechanism of icotinib in cancer therapy.

  8. Interaction of coomassie brilliant blue G250 with human serum albumin: Probing of the binding mechanism and binding site by spectroscopic and molecular modeling methods

    NASA Astrophysics Data System (ADS)

    Li, Yue-Sheng; Ge, Yu-Shu; Zhang, Yue; Zhang, Ai-Qing; Sun, Shao-Fa; Jiang, Feng-Lei; Liu, Yi

    2010-04-01

    The interaction between coomassie brilliant blue G250 and human serum albumin was investigated by spectroscopic methods such as fluorescence quenching, synchronous fluorescence , 3D fluorescence spectra, circular dichroism spectra and UV-vis absorption as well as molecular modeling. The fluorescence quenching of human serum albumin by coomassie brilliant blue G250 was attributed to static interaction. The binding reaction was mainly enthalpy-driven. Both van der Waals and hydrogen bonding forces played major roles in stabilizing the coomassie brilliant blue G250-human serum albumin complex. The Stern-Volmer quenching constant ( KSV) and corresponding thermodynamic parameters (Δ HΘ, Δ GΘ and Δ SΘ) were determined. Site marker competitive experiments indicated that coomassie brilliant blue G250 bound to site I (subdomain IIA) of human serum albumin. Molecular docking study further confirmed the binding mode obtained by experimental study. The conformational investigation demonstrated very minor micro-environmental and conformational changes in human serum albumin molecules.

  9. Spectroscopic studies on 9H-carbazole-9-(4-phenyl) boronic acid pinacol ester by DFT method

    NASA Astrophysics Data System (ADS)

    Sas, E. B.; Kurt, M.; Can, M.; Horzum, N.; Atac, A.

    2016-08-01

    9H-Carbazole-9-(4-phenyl) boronic acid pinacol ester (9-CPBAPE) molecule was investigated by FT-IR, Raman, UV-vis, 1H and 13C NMR spectra. FT-IR, FT-Raman and dispersive Raman spectra were recorded in the solid phase. 1H, 13C NMR and UV-vis spectra were recorded in dimethyl sulfoxide (DMSO) solution. The results of theoretical calculations for the spectra of the title molecule were compared with the experimental spectra. The highest occupied molecular orbital (HOMO) the lowest unoccupied molecular orbital (LUMO) and molecular electrostatic potential (MEP) analyses were performed. The theoretical calculations for the molecular structure and spectroscopic studies were performed with DFT (B3LYP) and 6-311G (d,p) basis set calculations using the Gaussian 09 program. The total (TDOS), partial (PDOS) density of state and overlap population density of state (OPDOS) diagrams analyses were performed using GaussSum 2.2 program.

  10. Lead sorption on ruthenium oxide: a macroscopic and spectroscopic study.

    PubMed

    Scheckel, Kirk G; Impellitteri, Christopher A; Ryan, James A

    2004-05-15

    The sorption and desorption of Pb on RuO2.xH2O were examined kinetically and thermodynamically via spectroscopic and macroscopic investigations. X-ray absorption spectroscopy (XAS) was employed to determine the sorption mechanism with regard to identity and interaction of nearest atomic neighbors, bond distances (R), and coordination numbers (N). The kinetics of the Pb-Ru-oxide sorption reaction are rapid with the equilibrium loading of Pb on the surface achieving approximately 1:1 wt/wt (129 micromol m(-2)). XAS data indicate that Pb adsorbed as bidentate innersphere complexes with first shell Pb-O parameters of RPb-O = 2.27 A and NPb-O = 2.1-2.5. Pb-Ru interatomic associations suggest two distinct bidentate surface coordinations of Pb to edges (RPb-RuI approximately 3.38 A, NPb-RuI approximately 1.0) and shared corners (RPb-RuII approximately 4.19 A, NPb-RuII approximately 0.8) on RuO2 octahedra (cassiterite-like structure), and an additional second neighbor backscattering of Pb indicates the formation of Pb-Pb dimers (RPb-Pb degrees 3.89 A, NPb-Pb approximately 0.9). Desorption studies as a function of aging time (1 h to 1 year) using a continuous stirred-flow reactor with a background electrolyte (0.01 M NaNO3, pH 6) demonstrated that Pb was tightly bound (99.7-99.9% retained). The Pb sorption capacity and retention on RuO2.xH2O is greater than that of other metal oxides examined in the literature. The results of this study imply that RuO2.xH2O may serve as a high capacity remediation treatment media.

  11. Effect of temperature on the methotrexate BSA interaction: Spectroscopic study

    NASA Astrophysics Data System (ADS)

    Sułkowska, A.; Maciążek, M.; Równicka, J.; Bojko, B.; Pentak, D.; Sułkowski, W. W.

    2007-05-01

    Rheumatoid arthritis (RA) is an autoimmune and chronic inflammatory illness which affects about one percent of the world's population. Methotrexate (4-amino-10-methylfolic acid) (MTX) also known as amethopterin is commonly used to treat rheumatoid arthritis (RA). It is transported in the circulary system as a complex with serum albumin. The aim of this study was to investigate the interactions of MTX with transporting protein with the use of spectroscopic methods. The binding of MTX to bovine serum albumin (BSA) was studied by monitoring the changes in the emission fluorescence spectra of protein in the presence of MTX at excitation wavelength of 280 nm and 295 nm. The quenching of protein fluorescence at temperature range from 298 K to 316 K was observed. Energy transfer between methotrexate and fluorophores contained in the serum albumin structure was found at the molar ratio MTX:BSA 7.5:1. The relative fluorescence intensity of BSA decreases with increase of temperature. Similar results were observed for BSA excited with 280 nm and 295 nm at the same temperature range. The presence of MTX seems to prevent these changes. Temperature dependence of the binding constant has been presented. The binding and quenching constants for equilibrium complex were calculated using Scatchard and Stern-Volmer method, respectively. The results show that MTX forms π-π complex with aromatic amino acid residues of BSA. The binding site for MTX on BSA was found to be situated in the hydrophobic IIA or IB subdomain where the Trps were located. The spontaneity of MTX-BSA complex formation in the temperature range 298-316 K was ascertained.

  12. A spectroscopic study of anomalous stellar populations in M67

    NASA Astrophysics Data System (ADS)

    McGahee, Courtney Elizabeth

    A population of stars exists in the old, open cluster M67, whose photometry, color magnitude diagram locations and associated evolutionary states cannot be explained by current, standard single star evolution theory. These stars are often referred to as "yellow straggler" stars. Yellow stragglers have been identified in multiple star clusters suggesting that these stars constitute a real population. Additionally, according to independent studies, at least some of the yellow straggler stars in M67 are likely cluster members. Therefore, cluster non-membership is not a sufficient explanation for the observed anomalous photometry of these stars. It is possible that the yellow stragglers occupy their precarious color magnitude diagram positions as a result of the evolution of mass transfer blue straggler stars. These are stars which have been formed by Roche Lobe overflow mass transfer in close binary systems. If this the case for the yellow stragglers, it is hypothesized that they could potentially exhibit two spectroscopic characteristics that can be indicative of this type of mass transfer system. Specifically, variable radial velocities can be used to indicate that the yellow stragglers exist in binary systems and enhancements of s-process elements in yellow stragglers can indicate Roche Lobe overflow mass transfer from a once asymptotic giant branch star which has since evolved into a white dwarf. This dissertation details the radial velocity survey and the chemical abundance analysis that have been conducted to investigate the yellow stragglers with regard to this hypothesis. The radial velocity survey revealed that eight of the ten yellow stragglers studied exhibit variable radial velocities indicating that the yellow straggler population of M67 possess a high binary frequency. However, the chemical abundance analysis revealed that none of the yellow stragglers exhibited enhancements of the s-process elements Y and Ba. Therefore, a history which involves Roche

  13. The spectroscopic study of building composites containing natural sorbents

    NASA Astrophysics Data System (ADS)

    Król, M.; Mozgawa, W.

    2011-08-01

    This work presents the results of FT-IR spectroscopic studies of heavy metal cations (Ag +, Pb 2+, Zn 2+, Cd 2+ and Cr 3+) immobilization from aqueous solutions on natural sorbents. The sorption has been conducted on sodium forms of zeolite (clinoptilolite) and clay minerals (mixtures containing mainly montmorillonite and kaolinite) which have been separated from natural Polish deposit. In the next part of the work both sorbents were used to obtain new building composites. It was proven those heavy metal cations' sorption causes changes in IR spectra of the zeolite and clay minerals. These alterations are dependent on the way the cations were sorbed. In the case of zeolite, variations of the bands corresponding to the characteristic ring vibrations have been observed. These rings occur in pseudomolecular complexes 4-4-1 (built of alumino- and silicooxygen tetrahedra) which constitute the secondary building units (SBU) and form spatial framework of the zeolite. The most significant changes have been determined in the region of pseudolattice vibrations (650-700 cm -1). In the instance of clay minerals, changes in the spectra occur at two ranges: 1200-800 cm -1 - the range of the bands assigned to asymmetric Si-O(Si,Al) and bending Al-OH vibrations and 3800-3000 cm -1 - the range of the bands originating from OH - groups stretching vibrations. Next results indicate possibilities of applying the used natural sorbents for the obtainment of new building materials having favourable composition and valuable properties. The zeolite was used for obtaining autoclaved materials with an addition of CaO, and the clay minerals for ceramic sintered materials with an addition of quartz and clinoptilolite were produced. FT-IR studies were also conducted on the obtained materials.

  14. Synthesis, Spectroscopic, Structural and Quantum Chemical Studies of a New Imine Oxime and Its Palladium(II) Complex: Hydrolysis Mechanism.

    PubMed

    Kaya, Yunus; Yilmaz, Veysel T; Buyukgungor, Orhan

    2016-01-21

    In this work, we report synthesis, crystallographic, spectroscopic and quantum chemical studies of a new imine oxime, namely (4-nitro-phenyl)-(1-phenyl-ethylimino)-acetaldehyde oxime (nppeieoH). Spectroscopic and X-ray diffraction studies showed that nppeieoH is hydrolyzed in aqueous solution, forming nitroisonitrosoacetophenone (ninap) and the hydrolysis product binds to Pd(II) to yield [Pd(nppeieo)(ninap)]. The mechanism of the hydrolysis reaction has been theoretically investigated in detail, using density functional theory (DFT) with the B3LYP method. The vibrational and the electronic spectra of nppeieoH and its Pd(II) complex, the HOMO and LUMO analysis, Mulliken atomic charges and molecular electrostatic potential were also performed. The predicted nonlinear optical properties of both compounds are higher than those of urea.

  15. LEAD SORPTION ON RUTHENIUM OXIDE: A MACROSCOPIC AND SPECTROSCOPIC STUDY

    EPA Science Inventory

    The sorption and desorption of Pb on RuO2 xH2O were examined kinetically and thermodynamically via spectroscopic and macroscopic investigations. X-ray absorption spectroscopy (XAS) was employed to determine the sorption mechanism with regard to identity of nearest atomic neighbo...

  16. LEAD SORPTION ON RUTHENIUM OXIDE: A MACROSCOPIC AND SPECTROSCOPIC STUDY

    EPA Science Inventory

    The sorption and desorption of Pb on RuO2 xH2O were examined kinetically and thermodynamically via spectroscopic and macroscopic investigations. X-ray absorption spectroscopy (XAS) was employed to determine the sorption mechanism with regard to identity of nearest atomic neighbo...

  17. Synthesis, spectroscopic, DFT and in vitro biological studies of vanadium(III) complexes of aryldithiocarbonates

    NASA Astrophysics Data System (ADS)

    Andotra, Savit; Kumar, Sandeep; Kour, Mandeep; Vikas; Chayawan; Sharma, Vishal; Jaglan, Sundeep; Pandey, Sushil. K.

    2017-06-01

    Vanadium(III) tris(dithiocarbonates), [(ROCS2)3V] (R = o-, m-, p-CH3C6H4 and 4-Cl-3-CH3C6H3) and donor stabilized addition complexes [(ROCS2)2V(Cl)·L] [L = NC5H5 or P(C6H5)3] were synthesized and characterized by elemental analyses, IR, mass, TGA/DTA, SEM magnetic susceptibility and heteronuclear NMR (1H, 13C and 31P) spectroscopic studies. The cytotoxicity of the complexes was measured in vitro using the cultivated human cell lines. In addition, the antioxidant activities of the ligands and its vanadium complexes were also investigated through their scavenging effect on DPPH radicals. The antimicrobial activity of ligands and some complexes has been conducted against three bacterial strains and fungus. The density functional theory (DFT) calculations of ligands and vanadium complexes were performed by the DFT/B3LYP/LANL2DZ method to obtain the optimized molecular geometry, vibrational frequencies, the highest occupied molecular orbital (HOMO), the lowest unoccupied molecular orbital (LUMO), thermodynamic properties and various other quantum-mechanical parameters.

  18. Spectroscopic Evidence for Room Temperature Interaction of Molecular Oxygen with Cobalt Porphyrin Linker Sites within a Metal-Organic Framework.

    PubMed

    Lahanas, Nicole; Kucheryavy, Pavel; Lockard, Jenny V

    2016-10-17

    Metalloporphyrin-based metal-organic frameworks offer a promising platform for developing solid-state porous materials with accessible, coordinatively unsaturated metal sites. Probing small-molecule interactions at the metalloporphyrin sites within these materials on a molecular level under ambient conditions is crucial for both understanding and ultimately harnessing this functionality for potential catalytic purposes. Co-PCN-222, a metal-organic framework based on cobalt(II) porphyrin linkers. is investigated using in situ UV-vis diffuse-reflectance and X-ray absorption spectroscopy. Spectroscopic evidence for the axial interaction of diatomic oxygen with the framework's open metalloporphyrin sites at room temperature is presented and discussed.

  19. Optical and spectroscopic study of erbium doped calcium borotellurite glasses

    NASA Astrophysics Data System (ADS)

    Gomes, J. F.; Lima, A. M. O.; Sandrini, M.; Medina, A. N.; Steimacher, A.; Pedrochi, F.; Barboza, M. J.

    2017-04-01

    In this study, 10CaF2 - (29.9-0.4x)CaO - (60-0.6x)B2O3 - xTeO2 - 0,1Er2O3 (x = 10, 16, 22, 30 and 50 mol %) glasses were synthesized, and their optical and spectroscopic properties were investigated. X-ray diffraction, density, glass transition temperature (Tg), crystallization temperature (Tx), refraction index, luminescence, radiative lifetime and optical absorption measurements were carried out. Molar volume (Vm), thermal stability (Tx-Tg), electronic polarizability (αm), optical bang gap energy (Eg) and Judd-Ofelt (JO) parameters Ωt (2,4,6) were also calculated. The results are discussed in terms of tellurium oxide content. The increase of TeO2 in the glasses composition increases density, refractive index and electronic polarizability. The optical band gap energy decreases varying from 3.37 to 2.71 eV for the glasses with 10 and 50 mol% of TeO2, respectively. The optical absorption coefficient spectra show characteristic bands of Er3+ ions. Furthermore, these spectra in NIR region show a decrease of hydroxyl groups as a function of TeO2 addition. Luminescence intensity and radiative lifetimes at 1530 nm show an increasing with the TeO2 content. The JO parameters of Er:CaBTeX glasses follow the trend Ω2 > Ω4 > Ω6 and the quality factor values (Ω4/Ω6) were between 1.37 and 3.07. By comparing the measured lifetime with the calculated radiative decay time, quantum efficiency was calculated. The luminescence emission intensity at 1530 nm decreases with the increase of temperature. The lifetime values show a slight trend to decrease with the temperature increase, from 300 to 420 K, for all the samples.

  20. Vibrational spectroscopic studies of Isoleucine by quantum chemical calculations.

    PubMed

    Moorthi, P P; Gunasekaran, S; Ramkumaar, G R

    2014-04-24

    In this work, we reported a combined experimental and theoretical study on molecular structure, vibrational spectra and NBO analysis of Isoleucine (2-Amino-3-methylpentanoic acid). The optimized molecular structure, vibrational frequencies, corresponding vibrational assignments, thermodynamics properties, NBO analyses, NMR chemical shifts and ultraviolet-visible spectral interpretation of Isoleucine have been studied by performing MP2 and DFT/cc-pVDZ level of theory. The FTIR, FT-Raman spectra were recorded in the region 4000-400 cm(-1) and 3500-50 cm(-1) respectively. The UV-visible absorption spectra of the compound were recorded in the range of 200-800 nm. Computational calculations at MP2 and B3LYP level with basis set of cc-pVDZ is employed in complete assignments of Isoleucine molecule on the basis of the potential energy distribution (PED) of the vibrational modes, calculated using VEDA-4 program. The calculated wavenumbers are compared with the experimental values. The difference between the observed and calculated wavenumber values of most of the fundamentals is very small. (13)C and (1)H nuclear magnetic resonance chemical shifts of the molecule were calculated using the gauge independent atomic orbital (GIAO) method and compared with experimental results. The formation of hydrogen bond was investigated in terms of the charge density by the NBO calculations. Based on the UV spectra and TD-DFT calculations, the electronic structure and the assignments of the absorption bands were carried out. Besides, molecular electrostatic potential (MEP) were investigated using theoretical calculations.

  1. Evaluation of the binding of perfluorinated compound to pepsin: Spectroscopic analysis and molecular docking.

    PubMed

    Yue, Yuanyuan; Sun, Yangyang; Yan, Xuyang; Liu, Jianming; Zhao, Shufang; Zhang, Jia

    2016-10-01

    In this paper, we investigated the binding mode of perfluorooctanoic acid (PFOA) and perfluorononanoic acid (PFNA) to pepsin using spectroscopies and molecular docking methods. Fluorescence quenching study indicated that their different ability to bind with pepsin. Meanwhile, time-resolved fluorescence measurements established that PFOA and PFNA quenched the fluorescence intensity of pepsin through the mechanism of static quenching. The thermodynamic parameters showed that hydrophobic forces were the main interactions. Furthermore, UV-vis, FTIR, three-dimensional fluorescence and molecular docking result indicated that PFCs impact the conformation of pepsin and PFOA was more toxic than PFNA. The conformational transformation of PFOA/PFNA-pepsin was confirmed through the quantitative analysis of the CD spectra. The present studies offer the theory evidence to analyze environmental safety and biosecurity of PFCs on proteases. Copyright © 2016 Elsevier Ltd. All rights reserved.

  2. Spectroscopic Photoacoustic Molecular Imaging of Breast Cancer using a B7-H3-targeted ICG Contrast Agent

    PubMed Central

    Wilson, Katheryne E.; Bachawal, Sunitha V.; Abou-Elkacem, Lotfi; Jensen, Kristen; Machtaler, Steven; Tian, Lu; Willmann, Jürgen K.

    2017-01-01

    Purpose: Breast cancer imaging methods lack diagnostic accuracy, in particular for patients with dense breast tissue, and improved techniques are critically needed. The purpose of this study was to evaluate antibody-indocyanine green (ICG) conjugates, which undergo dynamic absorption spectrum shifts after cellular endocytosis and degradation, and spectroscopic photoacoustic (sPA) imaging to differentiate normal breast tissue from breast cancer by imaging B7-H3, a novel breast cancer associated molecular target. Methods: Quantitative immunohistochemical staining of endothelial and epithelial B7-H3 expression was assessed in 279 human breast tissue samples, including normal (n=53), benign lesions (11 subtypes, n=129), and breast cancers (4 subtypes, n=97). After absorption spectra of intracellular and degraded B7-H3-ICG and Isotype control-ICG (Iso-ICG) were characterized, sPA imaging in a transgenic murine breast cancer model (FVB/N-Tg(MMTVPyMT)634Mul) was performed and compared to imaging of control conditions [B7-H3-ICG in tumor negative animals (n=60), Iso-ICG (n=30), blocking B7-H3+B7-H3-ICG (n=20), and free ICG (n=20)] and validated with ex vivo histological analysis. Results: Immunostaining showed differential B7-H3 expression on both the endothelium and tumor epithelium in human breast cancer with an area under the ROC curve of 0.93 to differentiate breast cancer vs non-cancer. Combined in vitro/in vivo imaging showed that sPA allowed specific B7-H3-ICG detection down to the 13 nM concentration and differentiation from Iso-ICG. sPA molecular imaging of B7-H3-ICG showed a 3.01-fold (P<0.01) increase in molecular B7-H3-ICG signal in tumors compared to control conditions. Conclusions: B7-H3 is a promising target for both vascular and epithelial sPA imaging of breast cancer. Leveraging antibody-ICG contrast agents and their dynamic optical absorption spectra allows for highly specific sPA imaging of breast cancer. PMID:28529630

  3. Vibrational spectroscopic and computational studies on diisopropylammonium bromide

    NASA Astrophysics Data System (ADS)

    Sahoo, Shradhanjali; Ravindran, T. R.; Chandra, Sharat; Sarguna, R. M.; Das, B. K.; Sairam, T. N.; Sivasubramanian, V.; Thirmal, C.; Murugavel, P.

    2017-09-01

    Diisopropylammonium bromide (DIPAB) can be crystallized either in an orthorhombic (P212121) or in a monoclinic (P21) structure at room temperature depending on synthesis conditions. The non-polar orthorhombic structure exhibits a subtle, irreversible transformation into the ferroelectric monoclinic-II (m-II) phase above 421 K. At a slightly higher temperature of 426 K this m-II (P21) phase reversibly transforms into a disordered, paraelectric monoclinic-I (P21/m) structure. We synthesized DIPAB in the orthorhombic structure, heated it to obtain the m-II phase and carried out a systematic study of their Raman and IR spectra. We obtained the phonon irreducible representations from factor group analysis of the orthorhombic and m-II structures based on the reported structural information. DIPAB is an organic molecular crystal, and the vibrational spectra in the intramolecular region (200-3500 cm- 1) of the two different phases are identical to each other, indicating weak inter-molecular interactions in both crystalline structures. In the low wavenumber region (10-150 cm- 1) the Raman spectra of the two phases are different due to their sensitivity to molecular environment. We also carried out first principles calculations using Gaussian 09 and CASTEP codes to analyze the vibrational frequencies. Mode assignments were facilitated by isolated molecule calculations that are also in good agreement with intramolecular vibrations, whereas CASTEP (solid state) results could explain the external modes.

  4. Spectroscopic studies of cathode materials for lithium-ion batteries

    NASA Astrophysics Data System (ADS)

    Totir, Dana Alexa

    2000-10-01

    Structural changes that occur during electrochemical cycling of lithium-ion battery cathode materials have been investigated using in situ spectroscopic techniques. A new method was developed for the preparation of carbon and binder free cathodes utilizing powder materials of interest for commercial batteries. The extraordinary quality of the cyclic voltammetric curves recorded for this type of electrodes during the in situ measurements allows direct correlations to be made between the state of charge of the material and its structural and electronic characteristics. LiCoO2, LiMn2O4 and LiCo0.15Ni 0.85O2 electrodes were evaluated using cycling voltammetry and the mean diffusion coefficient for Li-ions in the lattice (DLi) was calculated for LiMn2O4. LiMn2O4 electrodes prepared by this technique have been studied in situ using Mn K-edge XAS. Data analysis for the species formed at different potentials indicated a contraction of the lattice associated with the increase in the oxidation state of manganese. In situ Raman spectra of particles of LiMn2O 4, and LiCoO2 embedded in Au and also of KS-44 graphite and carbon microfibers MCF28 embedded in thermally annealed Ni have been recorded as a function of the applied potential. Fe K-edge XAFS of pyrite electrodes in a Li/PEO(LiClO4)/FeS 2 cell and S K-edge XANES measurements of a FeS2 electrode in a non-aqueous electrolyte have been acquired as a function of the state of charge. The studies have clearly evidenced the formation of metallic Fe and Li2S as intermediates after 4 e- discharge and the formation of Li2FeS2 after 2 e- recharge. While Fe K-edge studies have indicated that there is no change in the Fe environment and oxidation state upon 4 e- recharge, the results obtained from S K-edge studies are inconclusive for this stage. Finally, in situ Co K-edge XAFS data were obtained for the first time during the electrochemical cycling of electrodeposited Co(OH) 2 films in alkaline solutions. The results support

  5. Molecular recognition and binding of beta-lactamase II from Bacillus cereus with penicillin V and sulbactam by spectroscopic analysis in combination with docking simulation.

    PubMed

    Zhang, Yeli; Qiao, Pan; Li, Shuaihua; Feng, Xuan; Bian, Liujiao

    2017-02-10

    The molecular recognition and binding interaction of beta-lactamase II from Bacillus cereus (Bc II) with penicillin V (PV) and sulbactam (Sul) at 277 K were studied by spectroscopic analysis and molecular docking. The results showed that a non-fluorescence static complex was separately formed between Bc II and two ligands, the molecular ratio of Bc II to PV or Sul was both 1:1 in the binding and the binding constants were 2.00 × 10(6) and 3.98 × 10(5) (L/mol), respectively. The negative free energy changes and apparent activation energies indicated that both the binding processes were spontaneous. Molecular docking showed that in the binding process, the whole Sul molecule entered into the binding pocket of Bc II while only part of the whole PV molecule entered into the pocket due to a long side chain, and electrostatic interactions were the major contribution to the binding processes. In addition, a weak conformational change of Bc II was also observed in the molecular recognition and binding process of Bc II with PV or Sul. This study may provide some valuable information for exploring the recognition and binding of proteins with ligands in the binding process and for the design of novel super-antibiotics.

  6. Characterization of the Interaction between Eupatorin and Bovine Serum Albumin by Spectroscopic and Molecular Modeling Methods

    PubMed Central

    Xu, Hongliang; Yao, Nannan; Xu, Haoran; Wang, Tianshi; Li, Guiying; Li, Zhengqiang

    2013-01-01

    This study investigated the interaction between eupatorin and bovine serum albumin (BSA) using ultraviolet-visible (UV-vis) absorption, fluorescence, synchronous fluorescence, circular dichroism (CD) spectroscopies, and molecular modeling at pH 7.4. Results of UV-vis and fluorescence spectroscopies illustrated that BSA fluorescence was quenched by eupatorin via a static quenching mechanism. Thermodynamic parameters revealed that hydrophobic and electrostatic interactions played major roles in the interaction. Moreover, the efficiency of energy transfer, and the distance between BSA and acceptor eupatorin, were calculated. The effects of eupatorin on the BSA conformation were analyzed using UV-vis, CD, and synchronous fluorescence. Finally, the binding of eupatorin to BSA was modeled using the molecular docking method. PMID:23839090

  7. Computational and Spectroscopic Investigations of the Molecular Scale Structure and Dynamics of Geologically Important Fluids and Mineral-Fluid Interfaces

    SciTech Connect

    R. James Kirkpatrick; Andrey G. Kalinichev

    2008-11-25

    significantly larger systems. These calculations have allowed us, for the first time, to study the effects of metal cations with different charges and charge density on the NOM aggregation in aqueous solutions. Other computational work has looked at the longer-time-scale dynamical behavior of aqueous species at mineral-water interfaces investigated simultaneously by NMR spectroscopy. Our experimental NMR studies have focused on understanding the structure and dynamics of water and dissolved species at mineral-water interfaces and in two-dimensional nano-confinement within clay interlayers. Combined NMR and MD study of H2O, Na+, and Cl- interactions with the surface of quartz has direct implications regarding interpretation of sum frequency vibrational spectroscopic experiments for this phase and will be an important reference for future studies. We also used NMR to examine the behavior of K+ and H2O in the interlayer and at the surfaces of the clay minerals hectorite and illite-rich illite-smectite. This the first time K+ dynamics has been characterized spectroscopically in geochemical systems. Preliminary experiments were also performed to evaluate the potential of 75As NMR as a probe of arsenic geochemical behavior. The 75As NMR study used advanced signal enhancement methods, introduced a new data acquisition approach to minimize the time investment in ultra-wide-line NMR experiments, and provides the first evidence of a strong relationship between the chemical shift and structural parameters for this experimentally challenging nucleus. We have also initiated a series of inelastic and quasi-elastic neutron scattering measurements of water dynamics in the interlayers of clays and layered double hydroxides. The objective of these experiments is to probe the correlations of water molecular motions in confined spaces over the scale of times and distances most directly comparable to our MD simulations and on a time scale different than that probed by NMR. This work is being done

  8. Spectroscopic studies of uranium species for environmental decontamination applications

    NASA Astrophysics Data System (ADS)

    Eng, Charlotte

    After the Cold War, Department of Energy began to concentrate its efforts on cleanup of former nuclear material processing facilities, especially uranium-contaminated groundwater and soil. This research aims to study uranium association to both organic and inorganic compounds found in the contaminated environment in the hopes that the information gathered can be applied to the development and optimization of cost-effective remediation techniques. Spectroscopic and electrochemical methods will be employed to examine the behavior of uranium in given conditions to further our understanding of its impact on the environment. Uranium found in groundwater and soil bind with various ligands, especially organic ligands present in the environment due to natural sources (e.g. metabolic by-products or degradation of plants and animals) or man-made sources (e.g. chelating agents used in operating or cleanup of uranium processing facilities). We selected reasonable analogs of naturally occurring matter and studied their structure, chemical and electrochemical behavior and found that the structure of uranyl complexes depends heavily on the nature of the ligand and environmental factors such as pH. Association of uranium-organic complexes with anaerobic bacteria, Clostridium sp. was studied to establish if the bacteria can effectively bioreduce uranium while going through normal bacterial activity. It was found that the nature of the organic ligand affected the bioavailability and toxicity of the uranium on the bacteria. In addition, we have found that the type of iron corrosion products and uranyl species present on the surface of corroded steel depended on various environmental factors, which subsequently affected the removal rate of uranium by a citric acid/hydrogen peroxide/deionized water cleaning process. The method was found to remove uranium from only the topmost corrosion layers and residual uranium could be found (a) deeper in the corrosion layers where it is occluded by

  9. X-ray spectroscopic studies of secondary battery materials

    NASA Astrophysics Data System (ADS)

    Kostov, Svilen Dimitar

    1998-09-01

    X-ray spectroscopic methods, both NEXAFS and EXAFS were used in the study of the structural and electronic properties of different types of new battery materials. NEXAFS analysis of the spectra of Lisb{1-x}CoO2 secondary battery cathodes revealed that the addition of Li proceeds is strongly correlated to the increase in electronic charge on the Co ion. A structural phase transition is confirmed for x=0.5. The presence of Mnsp{+2} is detected in the conventionally made LiMnOsb2 cathodes but not in ones prepared according to the new ADL process. Lisb{x}Vsb6Osb{13} cathode material, where 0≤ x≤6, was measured using x-ray absorption, EPR and NMR techniques. The intercalation mechanism involves a conversion of Vsp{+5} to Vsp{+4} in Vsb6Osb{13} until the composition Lisb2Vsb6Osb{13} is reached. Further addition of lithium is accompanied by the conversion of Vsp{+4} to Vsp{+3} until Lisb8Vsb6Osb{13} is reached. The process is complicated and involves structural phase changes and increasing structural disorder within the multi-phase system as Li concentration is increased. Studies of LiNi/CoOsb2 intercalation cathodes prepared by a novel sol-gel technique suggests that although the partial substitution of Co for Ni stabilizes the system by removing Nisp{+2}, a Jahn-Teller type structural distortion in the predominantly Nisp{=3} system persists. In-situ EXAFS measurements of the pyrite cathode in a new Li/CPE/FeSsb2 showed two distinct environments of the Fe ion, which were interpreted as those of metallic Fe and residual FeSsb2 at high lithium concentration, and Lisb2FeSsb2 and residual FeSsb2 at low lithium concentration. The formation of FeS was not detected. A new type of hydrogen ion battery incorporating a MnSOsb4sp&*slash;Hsb2O based cathode and polymer electrolyte was also studied. Heavily cycled and discharged cathodes showed an almost identical Mn local structure to that of single cycled ones. The Mn environment becomes very different in the charged cathodes

  10. Spectroscopic Studies of the Several Isomers of UO3

    SciTech Connect

    Sweet, Lucas E.; Reilly, Dallas D.; Abrecht, David G.; Buck, Edgar C.; Meier, David E.; Su, Yin-Fong; Brauer, Carolyn S.; Schwantes, Jon M.; Tonkyn, Russell G.; Szecsody, James E.; Blake, Thomas A.; Johnson, Timothy J.

    2013-09-26

    Uranium trioxide is known to adopt seven different structural forms. While these structural forms have been well characterized using x-ray or neutron diffraction techniques, little work has been done to characterize their spectroscopic properties, particularly of the pure phases. Since the structural isomers of UO3 all have similar thermodynamic stabilities and most tend to hydrolyze under open atmospheric conditions, mixtures of UO3 phases and the hydrolysis products are common. Much effort went into isolating pure phases of UO3. Utilizing x-ray diffraction as a sample identification check, UV/Vis/NIR spectroscopic signatures of α-UO3, β-UO3, γ-UO3 and UO2(OH)2 products were obtained. The spectra of the pure phases can now be used to characterize typical samples of UO3, which are often mixtures of isomers.

  11. Structural, spectroscopic and theoretical study of novel ephedrinum salt

    NASA Astrophysics Data System (ADS)

    Ivanova, B.; Kolev, T.; Lamshöft, M.; Mayer-Figge, H.; Seidel, R.; Sheldrick, W. S.; Spiteller, M.

    2010-05-01

    Ephedrinum violurate dihydrate was synthesized, spectroscopically and structural elucidated. The data are compared with those of the free-base ephedrine hemihydrate. Discussion on the stable conformer of the ephedrinum cation is carried out. Quantum chemical calculations were performed for the theoretical elucidation of the conformational preference of the ephedrinum cation and its vibrational properties. The model systems neutral ephedrine hemihydrate ( 1) and violurate salt dihydrate ( 2) are elucidated.

  12. The electronic structure of pyracene: a spectroscopic and computational study.

    PubMed

    Auerswald, Johannes; Engels, Bernd; Fischer, Ingo; Gerbich, Thiemo; Herterich, Jörg; Krueger, Anke; Lang, Melanie; Schmitt, Hans-Christian; Schon, Christof; Walter, Christof

    2013-06-07

    We report a synthetic, spectroscopic and computational study of the polycyclic aromatic molecule pyracene, which contains aliphatic five-membered rings annealed to a naphthalene chromophore. An improved route to synthesize the compound is described. Gas-phase IR and solid-state Raman spectra agree with a ground-state D2h structure. The electronically excited S1 A(1)B3u state has been studied by resonance-enhanced multiphoton ionisation. An adiabatic excitation energy T0 = 30,798 cm(-1) (3.818 eV) was determined. SCS-ADC(2) calculations found a D2h minimum energy structure of the S1 state and yielded an excitation energy of +3.98 eV, including correction for zero point vibrational energy. The spectrum shows a rich low-frequency vibrational structure that can be assigned to the overtones of out-of-plane deformation modes of the five-membered rings by comparison with computations. The appearance of these modes as well as the frequency reduction in the excited state indicate that the potential in the S1 state is very flat. At higher excess energies most bands can be assigned to fundamentals, overtones and combination bands of either totally symmetric ag modes or of b2g modes that appear due to vibronic coupling. Lifetimes between 43 ns and 76 ns were measured for a number of vibronic bands. For the S2 state an equilibrium geometry with a non-planar carbon framework was computed. In addition a signal from the pyracene dimer was present.