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Sample records for investigate molecular structure

  1. Theoretical investigation of the molecular structure of the isoquercitrin molecule

    NASA Astrophysics Data System (ADS)

    Cornard, J. P.; Boudet, A. C.; Merlin, J. C.

    1999-09-01

    Isoquercitrin is a glycosilated flavonoid that has received a great deal of attention because of its numerous biological effects. We present a theoretical study on isoquercitrin using both empirical (Molecular Mechanics (MM), with MMX force field) and quantum chemical (AM1 semiempirical method) techniques. The most stable structures of the molecule obtained by MM calculations have been used as input data for the semiempirical treatment. The position and orientation of the glucose moiety with regard to the remainder of the molecule have been investigated. The flexibility of isoquercitrin principally lies in rotations around the inter-ring bond and the sugar link. In order to know the structural modifications generated by the substitution by a sugar, geometrical parameters of quercetin (aglycon) and isoquercitrin have been compared. The good accordance between theoretical and experimental electronic spectra permits to confirm the reliability of the structural model.

  2. Optical investigation of molecular structure of sophisticated materials for photonics

    NASA Astrophysics Data System (ADS)

    Gnyba, Marcin; Keraenen, Mikko

    2003-10-01

    Permanent development of photonics stimulates a searching for new materials, which have better optical, mechanical and electrical properties. One of the new classes of materials with large application and development potential are hybrid polymers, synthesized in sol-gel technology. Thanks to incorporation of organic components into an in organic network, a combination of advantages of both class of materials became available. Properties of hybrids may be formed in wide range. These materials can be used in photonics to produce planar waveguides, lenses, Bragg gratings and components for integrated optics. Moreover, dielectric layers, coatings and packaging are made from hybrids. Additionally, research to apply them in optical fiber sensors (including bio-sensors) and solid state lasers is underway. However, to obtain a high quality product, a strict control of its molecular structure must be ensured. This is a very difficult task, because of a sophisticated structure of hybrid polymers. To address these problems, optical, non-destructive measurement techniques such as Raman and infrared spectroscopy were used. They are compementary methods, so their simultaneous application, as it was shown in this paper, can significantly increase the amoung of information about molecular structure of materials and process of their synthesis.

  3. Molecular tools for investigating ANME community structure and function

    SciTech Connect

    Hallam, Steven J.; Page, Antoine P.; Constan, Lea; Song, Young C.; Norbeck, Angela D.; Brewer, Heather M.; Pasa-Tolic, Ljiljana

    2011-05-20

    Methane production and consumption in anaerobic marine sediments 1 is catalyzed by a series of reversible tetramethanopterin (H4MPT)-linked C1 transfer reactions. Although many of these reactions are conserved between one-carbon compound utilizing microorganisms, two remain diagnostic for archaeal methane metabolism. These include reactions catalyzed by N5-methyltetrahydromethanopterin: coenzyme M methyltransferase and methyl coenzyme M reductase. The latter enzyme is central to C-H bond formation and cleavage underlying methanogenic and reverse methanogenic phenotypes. Here we describe a set of novel tools for the detection and functional analysis of H4MPT-linked C1 transfer reactions mediated by uncultivated anaerobic methane oxidizing archaea (ANME). These tools include polymerase chain reaction primers targeting ANME methyl coenzyme M reductase subunit A subgroups and protein extraction methods from marine sediments compatible with high-resolution mass spectrometry for profiling population structure and functional dynamics. [910, 1,043

  4. Teaching Structure-Property Relationships: Investigating Molecular Structure and Boiling Point

    ERIC Educational Resources Information Center

    Murphy, Peter M.

    2007-01-01

    A concise, well-organized table of the boiling points of 392 organic compounds has facilitated inquiry-based instruction in multiple scientific principles. Many individual or group learning activities can be derived from the tabulated data of molecular structure and boiling point based on the instructor's education objectives and the students'…

  5. Investigating molecular structures: Rapidly examining molecular fingerprints through fast passage broadband fourier transform microwave spectroscopy

    NASA Astrophysics Data System (ADS)

    Grubbs, Garry Smith Smitty, II

    Microwave spectroscopy is a gas phase technique typically geared toward measuring the rotational transitions of molecules. The information contained in this type of spectroscopy pertains to a molecules structure, both geometric and electronic, which give insight into a molecule's chemistry. Typically this type of spectroscopy is high resolution, but narrowband ≤1 MHz in frequency. This is achieved by tuning a cavity, exciting a molecule with electromagnetic radiation in the microwave region, turning the electromagnetic radiation off, and measuring a signal from the molecular relaxation in the form of a free induction decay (FID). The FID is then Fourier transformed to give a frequency of the transition. "Fast passage" is defined as a sweeping of frequencies through a transition at a time much shorter (≤10 mus) than the molecular relaxation (≈100 mus). Recent advancements in technology have allowed for the creation of these fast frequency sweeps, known as "chirps", which allow for broadband capabilities. This work presents the design, construction, and implementation of one such novel, high-resolution microwave spectrometer with broadband capabilities. The manuscript also provides the theory, technique, and motivations behind building of such an instrument. In this manuscript it is demonstrated that, although a gas phase technique, solids, liquids, and transient species may be studied with the spectrometer with high sensitivity, making it a viable option for many molecules wanting to be rotationally studied. The spectrometer has a relative correct intensity feature that, when coupled with theory, may ease the difficulty in transition assignment and facilitate dynamic chemical studies of the experiment. Molecules studied on this spectrometer have, in turn, been analyzed and assigned using common rotational spectroscopic analysis. Detailed theory on the analysis of these molecules has been provided. Structural parameters such as rotational constants and

  6. Using solvents with different molecular sizes to investigate the structure of Antheraea pernyi silk.

    PubMed

    Wang, Yu; Porter, David; Shao, Zhengzhong

    2013-11-11

    The interaction between silk and polar solvents of different molecular size can be an important tool for understanding the structural features of natural silk; in particular, the disordered regions associated with the key property of mechanical toughness. In this work, we investigate the transitions induced in the tensile performance and structure of as-reeled Antheraea pernyi silks from different silkworms by a range of solvents that can only soften the protein chains in the amorphous regions. The results indicate that polar solvents with different molecular sizes affect the silk to different degrees, and silks with slightly different structures display significantly different tensile performance in the same solvent. The solvent molecular size is quantitatively correlated with the accessible volume in the amorphous regions before and after the yield point, which suggests that the volume accessible to the solvent molecules decreases as the solvent radius increases. Moreover, silks with more ordered structure (less free volume) in the amorphous regions are less sensitive to solvents than those with more disordered structures. However, silks with higher free volume have higher toughness due to the greater strain to failure.

  7. Spectroscopic and structural investigation of interaction product of 8-mercaptoquinoline with molecular iodine

    NASA Astrophysics Data System (ADS)

    Chernov'yants, Margarita S.; Starikova, Zoya A.; Karginova, Anastasia O.; Kolesnikova, Tatiana S.; Tereznikov, Alexander Yu.

    2013-11-01

    The behavior of 8-mercaptoquinoline, which is a potential antithyroid drug toward molecular iodine was investigated. The ability of 8-mercaptoquinoline to form the outer-sphere charge-transfer complex C9H7NS·I2 with iodine molecular in dilute chloroform solution has been studied by UV/vis spectroscopy (lg β = 3.14). The crystal structure of the new salt 8-(quinoline-8-yldisulfonyl)quinolinium triiodide - product of irreversible oxidation of 8-mercaptoquinoline was determined by X-ray diffraction. Intramolecular hydrogen bond of N-H⋯N type is presented in the organic cation. The triiodide ion is the nearly centrosymmetrical anion. The 8-(quinoline-8-yldisulfanyl)quinolinium cations form dimers through π-π-stacking interaction between quinolinium rings. The reduced intramolecular interactions are observed between iodine - sulfur atoms and iodine-hydrogen atoms with shortened contacts (less of sum of van-der-waals contacts).

  8. First principles investigations of electronic structure and transport properties of graphitic structures and single molecular junctions

    NASA Astrophysics Data System (ADS)

    Owens, Jonathan R.

    properties of the IV curves of single molecule nano-junctions. Specifically, these systems consist of a zinc-porphyrin molecule coupled between two gold electrodes, i.e., a nano-gap. The first observation we want to explain is the asymmetric nature of the experimental IV curve for this porphyrin system, where the IV curve is skewed heavily to the negative bias region. Using a plane-wave DFT calculation, we present the density of states of the porphyrin molecule (both in the presence and absence of the electrodes) and indeed see highly delocalized states (as confirmed by site-projection of the DOS) only in the negative bias region, meaning that the channels with high transmission probability reside there, in agreement with experimental observation. The next problem studied pertains to observed switching in an experimentally-measured IV curve, this time of a longer zinc porphyrin molecule, still within a gold nano-gap. The switching behavior is observed only at 300K, not at 4.2K. The temperature-dependance of this problem renders our previous toolset of DFT calculations void; DFT is a ground-state theory. Instead, we employ a density functional-based tight-binding (DFTB) approach in a molecular dynamics simulation. Basically, the structural configuration evaluated at each time step is based on a tight-binding electronic structure calculation, instead of a typical MD force field. Trajectories are presented at varying temperatures and electric field strengths. Indeed, we observe a conformation of the porphyrin molecule between two configurations of the dihedral angle of the central nitrogen ring, ±15. {o} at 300K, but not 4.2K. These confirmations are equally likely, i.e., the structure assumes these configurations an equal number of teams, meaning the average structure has an angle of 0. {o}. After computing the DOS of all three aforementioned configurations (0. {text{o}} and ±15. {text{o}}), we indeed see a difference between the DOS curves at ±15. {text{o}} (which are

  9. Investigation of Terminal Group Effect on Electron Transport Through Open Molecular Structures

    NASA Astrophysics Data System (ADS)

    C. Preferencial, Kala; P. Aruna, Priya; John Thiruvadigal, D.

    2013-05-01

    The effect of terminal groups on the electron transport through metal-molecule-metal system has been investigated using nonequilibrium Green's function (NEGF) formalism combined with extended Huckel theory (EHT). Au-molecule-Au junctions are constructed with borazine and BCN unit structure as core molecule and sulphur (S), oxygen (O), selenium (Se) and cyano-group (CN) as terminal groups. The electron transport characteristics of the borazine and BCN molecular systems are analyzed through the transmission spectra and the current-voltage curve. The results demonstrate that the terminal groups modifying the transport behaviors of these systems in a controlled way. Our result shows that, selenium is the best linker to couple borazine to Au electrode and oxygen is the best one to couple BCN to Au electrode. Furthermore, the results of borazine systems are compared with that of BCN molecular systems and are discussed. Simulation results show that the conductance through BCN molecular systems is four times larger than the borazine molecular systems. Negative differential resistance behavior is observed with borazine-CN system and the saturation feature appears in BCN systems.

  10. Molecular structure and spectral investigations of 3,5-Di-tert-butyl-o-benzoquinone

    NASA Astrophysics Data System (ADS)

    Yilmaz, M.; Aydin, B.; Dogan, O.; Dereli, O.

    2017-01-01

    Conformational analysis of 3,5-Di-tert-butyl-o-benzoquinone molecule was performed and two stable conformers were determined by B3LYP/6-311++G(d,p). Using the most stable one, molecular structural parameters, vibrational frequencies were calculated by B3LYP/6-311++G(d,p), B3LYP/6-31G(d) and BLYP/6-31G(d,p) levels of theory. The FT-IR spectrum of the compound was recorded in the region 4000-550 cm-1. The Raman spectrum was also recorded in the region 3500-100 cm-1. Calculated results were compared with experimental counterparts. The best results were obtained from B3LYP/6-311++G(d,p) calculations. Experimental 13C and 1H NMR data of tittle compound were taken from literature and the calculated results compared with these data. Vibrational and NMR band assignments were performed. HOMO-LUMO energies, molecular electrostatic potentials and thermodynamic properties were also given for further investigations of our structure.

  11. Structural analysis and investigation of molecular properties of Cefpodoxime acid, a third generation antibiotic

    NASA Astrophysics Data System (ADS)

    Suganthi, S.; Balu, P.; Sathyanarayanamoorthi, V.; Kannappan, V.; Kamil, M. G. Mohamed; Kumar, R.

    2016-03-01

    Extensive quantum mechanical studies are carried out on Cefpodoxime acid (CA), a new generation drug by Hartree-Fock (HF) and B3LYP methods to understand the structural and spectral characteristics of the molecule. The most stable geometry of the molecule was optimized and the bond parameters were reported. The spectroscopic properties of this pharmaceutically important compound were investigated by FT-IR, FT-Raman, UV and 1H NMR techniques. The scaled vibrational frequencies of CA in the ground state are calculated by HF and B3LYP methods with 6-311++G (d, p) basis set and compared with the observed FT-IR and FT-Raman spectra. The vibrational spectral analysis indicates the presence of two intra molecular hydrogen bonds in the molecule which is supported by theoretical study. 1H NMR chemical shifts (δ) were calculated for the CA molecule and compared with the experimental values. The theoretical electronic absorption spectral data in water and ethanol solvents were computed by TD-DFT method. UV-Vis absorption spectra of CA are recorded in these two solvents and compared with theoretical spectra. The spectral data and natural bond orbital (NBO) analysis confirm the occurrence of intra molecular interactions in CA. The electronic distribution, in conjunction with electrophilicity index of CA was used to establish the active site and type of interaction between CA and beta lactamases. Mulliken population analysis on atomic charges is also carried out and thermodynamic properties of the title compound are calculated.

  12. Theoretical investigation of the molecular structures and excitation spectra of triphenylamine and its derivatives

    NASA Astrophysics Data System (ADS)

    Sumimoto, Michinori; Yokogawa, Daisuke; Komeda, Masahiro; Yamamoto, Hidetoshi; Hori, Kenji; Fujimoto, Hitoshi

    2011-10-01

    The molecular geometries, electronic structures, and excitation energies of NPh 3, NPh 2Me, NPhMe 2, and NMe 3, were investigated using DFT and post-Hartree Fock methods. When the structural stabilities of these compounds were compared to results obtained by using MP4(SDQ) method, it was confirmed that the optimized geometries by using MP2 method were sufficiently reliable. The excited states with large oscillator strengths consisted of transition components from the HOMO. It should be noted that the orbitals of the nitrogen atom mix with the π-orbital of the phenyl group in an anti-bonding way in the HOMO, and the orbital energy increases with this mixing. The unoccupied orbitals are generated from bonding and anti-bonding type interactions between the π-orbitals of the phenyl groups; therefore, the number of phenyl groups strongly affects the energy diagram of the compounds studied. The differences in the energy diagram cause a spectral change in these compounds in the ultraviolet region.

  13. Molecular structure activity on pharmaceutical applications of Phenacetin using spectroscopic investigation

    NASA Astrophysics Data System (ADS)

    Madanagopal, A.; Periandy, S.; Gayathri, P.; Ramalingam, S.; Xavier, S.

    2017-01-01

    The pharmaceutical compound; Phenacetin was investigated by analyzing FT-IR, FT-Raman and 1H &13C NMR spectra. The hybrid efficient computational calculations performed for computing physical and chemical parameters. The cause of pharmaceutical activity due to the substitutions; carboxylic, methyl and amine groups in appropriate positions on the pedestal compound was deeply investigated. Moreover, 13C NMR and 1H NMR chemical shifts correlated with TMS standard to explain the truth of compositional ratio of base and ligand groups. The bathochromic shift due to chromophores over the energy levels in UV-Visible region was strongly emphasized the Anti-inflammatory chemical properties. The chemical stability was pronounced by the strong kubo gap which showed the occurring of charge transformation within the molecule. The occurrence of the chemical reaction was feasibly interpreted by Gibbs free energy profile. The standard vibrational analysis stressed the active participation of composed ligand groups for the existence of the analgesic as well as antipyretic properties of the Phenacetin compound. The strong dipole interaction energy utilization for the transition among non-vanishing donor and acceptor for composition of the molecular structure was interpreted.

  14. 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.

  15. Molecular structure and spectral (FT-IR, Raman) investigations of 3-aminocoumarin

    NASA Astrophysics Data System (ADS)

    Dereli, Ömer

    2016-05-01

    The molecular structure of 3-Aminocoumarin was determined by conformational analysis. Conformational space was scanned by conformer distribution option of Spartan 08 program package using Merck Molecular Force Field (MMFF) method. Then obtained conformers were optimized by B3LYP/6-311++ G( d, p) and B3LYP/6-311 G( d, p) levels of Density Functional Theory. As a result of these calculations, only one conformer was determined. Vibrational frequencies of this conformer were calculated by Gaussian 03 program package using the same levels of geometry optimizations. The FT-IR and Raman spectra of 3-Aminocoumarin were recorded and compared with the calculated values. Consequently, a good agreement between experimental and the calculated values were founded. Molecular electrostatic potentials (MEPs), HOMO-LUMO energies, thermodynamic properties and Mulliken atomic charges were also covered in this study.

  16. Molecular polymorphism: microwave spectra, equilibrium structures, and an astronomical investigation of the HNCS isomeric family.

    PubMed

    McGuire, Brett A; Martin-Drumel, Marie-Aline; Thorwirth, Sven; Brünken, Sandra; Lattanzi, Valerio; Neill, Justin L; Spezzano, Silvia; Yu, Zhenhong; Zaleski, Daniel P; Remijan, Anthony J; Pate, Brooks H; McCarthy, Michael C

    2016-08-10

    The rotational spectra of thioisocyanic acid (HNCS), and its three energetic isomers (HSCN, HCNS, and HSNC) have been observed at high spectral resolution by a combination of chirped-pulse and Fabry-Pérot Fourier-transform microwave spectroscopy between 6 and 40 GHz in a pulsed-jet discharge expansion. Two isomers, thiofulminic acid (HCNS) and isothiofulminic acid (HSNC), calculated here to be 35-37 kcal mol(-1) less stable than the ground state isomer HNCS, have been detected for the first time. Precise rotational, centrifugal distortion, and nitrogen hyperfine coupling constants have been determined for the normal and rare isotopic species of both molecules; all are in good agreement with theoretical predictions obtained at the coupled cluster level of theory. On the basis of isotopic spectroscopy, precise molecular structures have been derived for all four isomers by correcting experimental rotational constants for the effects of rotation-vibration interaction calculated theoretically. Formation and isomerization pathways have also been investigated; the high abundance of HSCN relative to ground state HNCS, and the detection of strong lines of SH using CH3CN and H2S, suggest that HSCN is preferentially produced by the radical-radical reaction HS + CN. A radio astronomical search for HSCN and its isomers has been undertaken toward the high-mass star-forming region Sgr B2(N) in the Galactic Center with the 100 m Green Bank Telescope. While we find clear evidence for HSCN, only a tentative detection of HNCS is proposed, and there is no indication of HCNS or HSNC at the same rms noise level. HSCN, and tentatively HNCS, displays clear deviations from a single-excitation temperature model, suggesting weak masing may be occurring in some transitions in this source.

  17. 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.

  18. Molecular Modeling of Myrosinase from Brassica oleracea: A Structural Investigation of Sinigrin Interaction

    PubMed Central

    Natarajan, Sathishkumar; Thamilarasan, Senthil Kumar; Park, Jong-In; Chung, Mi-Young; Nou, Ill-Sup

    2015-01-01

    Myrosinase, which is present in cruciferous plant species, plays an important role in the hydrolysis of glycosides such as glucosinolates and is involved in plant defense. Brassicaceae myrosinases are diverse although they share common ancestry, and structural knowledge about myrosinases from cabbage (Brassica oleracea) was needed. To address this, we constructed a three-dimensional model structure of myrosinase based on Sinapis alba structures using Iterative Threading ASSEmbly Refinement server (I-TASSER) webserver, and refined model coordinates were evaluated with ProQ and Verify3D. The resulting model was predicted with β/α fold, ten conserved N-glycosylation sites, and three disulfide bridges. In addition, this model shared features with the known Sinapis alba myrosinase structure. To obtain a better understanding of myrosinase–sinigrin interaction, the refined model was docked using Autodock Vina with crucial key amino acids. The key nucleophile residues GLN207 and GLU427 were found to interact with sinigrin to form a hydrogen bond. Further, 20-ns molecular dynamics simulation was performed to examine myrosinase–sinigrin complex stability, revealing that residue GLU207 maintained its hydrogen bond stability throughout the entire simulation and structural orientation was similar to that of the docked state. This conceptual model should be useful for understanding the structural features of myrosinase and their binding orientation with sinigrin. PMID:26703735

  19. 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

  20. Structure of Penta-Alanine Investigated by Two-Dimensional Infrared Spectroscopy and Molecular Dynamics Simulation.

    PubMed

    Feng, Yuan; Huang, Jing; Kim, Seongheun; Shim, Ji Hyun; MacKerell, Alexander D; Ge, Nien-Hui

    2016-06-23

    We have studied the structure of (Ala)5, a model unfolded peptide, using a combination of 2D IR spectroscopy and molecular dynamics (MD) simulation. Two different isotopomers, each bis-labeled with (13)C═O and (13)C═(18)O, were strategically designed to shift individual site frequencies and uncouple neighboring amide-I' modes. 2D IR spectra taken under the double-crossed ⟨π/4, -π/4, Y, Z⟩ polarization show that the labeled four-oscillator systems can be approximated by three two-oscillator systems. By utilizing the different polarization dependence of diagonal and cross peaks, we extracted the coupling constants and angles between three pairs of amide-I' transition dipoles through spectral fitting. These parameters were related to the peptide backbone dihedral angles through DFT calculated maps. The derived dihedral angles are all located in the polyproline-II (ppII) region of the Ramachandran plot. These results were compared to the conformations sampled by Hamiltonian replica-exchange MD simulations with three different CHARMM force fields. The C36 force field predicted that ppII is the dominant conformation, consistent with the experimental findings, whereas C22/CMAP predicted similar population for α+, β, and ppII, and the polarizable Drude-2013 predicted dominating β structure. Spectral simulation based on MD representative conformations and structure ensembles demonstrated the need to include multiple 2D spectral features, especially the cross-peak intensity ratio and shape, in structure determination. Using 2D reference spectra defined by the C36 structure ensemble, the best spectral simulation is achieved with nearly 100% ppII population, although the agreement with the experimental cross-peak intensity ratio is still insufficient. The dependence of population determination on the choice of reference structures/spectra and the current limitations on theoretical modeling relating peptide structures to spectral parameters are discussed. Compared

  1. Investigation on critical structural motifs of ligands for triggering glucocorticoid receptor nuclear migration through molecular docking simulations.

    PubMed

    Liu, Ya-Lin; Jang, Soonmin; Wang, Shih-Min; Chen, Chiu-Hao; Li, Feng-Yin

    2016-06-01

    The glucocorticoid receptor (GR), a transcription factor regulating gene expression in a ligand-dependent fashion, is known for flexibility in adapting various ligands with their structures ranging from steroid to non-steroid. However, in our previous study, GR shows a stringent discrimination against a set of steroid ligands with highly similar structures for triggering its nuclear migration. In order to resolve this puzzle, we employed molecular docking simulations to investigate the origin of this structural discrimination. By analyzing the docking orientations and the related ligand-GR interaction patterns, we found that the hydrophilicity mismatch between the docking ligand and the GR ligand-binding site is the main cause combined with the steric hindrance and structural rigidness of these steroid ligands. Furthermore, we utilized this knowledge to rationalize how the structure-binding interaction of non-steroid ligands triggers GR nuclear migration with their structures available in Protein Data Bank.

  2. Chemical and structural investigation of lipid nanoparticles: drug-lipid interaction and molecular distribution

    NASA Astrophysics Data System (ADS)

    Anantachaisilp, Suranan; Meejoo Smith, Siwaporn; Treetong, Alongkot; Pratontep, Sirapat; Puttipipatkhachorn, Satit; Rungsardthong Ruktanonchai, Uracha

    2010-03-01

    Lipid nanoparticles are a promising alternative to existing carriers in chemical or drug delivery systems. A key challenge is to determine how chemicals are incorporated and distributed inside nanoparticles, which assists in controlling chemical retention and release characteristics. This study reports the chemical and structural investigation of γ-oryzanol loading inside a model lipid nanoparticle drug delivery system composed of cetyl palmitate as solid lipid and Miglyol 812® as liquid lipid. The lipid nanoparticles were prepared by high pressure homogenization at varying liquid lipid content, in comparison with the γ-oryzanol free systems. The size of the lipid nanoparticles, as measured by the photon correlation spectroscopy, was found to decrease with increased liquid lipid content from 200 to 160 nm. High-resolution proton nuclear magnetic resonance (1H-NMR) measurements of the medium chain triglyceride of the liquid lipid has confirmed successful incorporation of the liquid lipid in the lipid nanoparticles. Differential scanning calorimetric and powder x-ray diffraction measurements provide complementary results to the 1H-NMR, whereby the crystallinity of the lipid nanoparticles diminishes with an increase in the liquid lipid content. For the distribution of γ-oryzanol inside the lipid nanoparticles, the 1H-NMR revealed that the chemical shifts of the liquid lipid in γ-oryzanol loaded systems were found at rather higher field than those in γ-oryzanol free systems, suggesting incorporation of γ-oryzanol in the liquid lipid. In addition, the phase-separated structure was observed by atomic force microscopy for lipid nanoparticles with 0% liquid lipid, but not for lipid nanoparticles with 5 and 10% liquid lipid. Raman spectroscopic and mapping measurements further revealed preferential incorporation of γ-oryzanol in the liquid part rather than the solid part of in the lipid nanoparticles. Simple models representing the distribution of γ-oryzanol and

  3. Investigation of mechanical strength of 2D nanoscale structures using a molecular dynamics based computational intelligence approach

    NASA Astrophysics Data System (ADS)

    Garg, A.; Vijayaraghavan, V.; Wong, C. H.; Tai, K.; Singru, Pravin M.; Mahapatra, S. S.; Sangwan, K. S.

    2015-09-01

    A molecular dynamics (MD) based computational intelligence (CI) approach is proposed to investigate the Young modulus of two graphene sheets: Armchair and Zigzag. In this approach, the effect of aspect ratio, the temperature, the number of atomic planes and the vacancy defects on the Young modulus of two graphene sheets are first analyzed using the MD simulation. The data obtained using the MD simulation is then fed into the paradigm of a CI cluster comprising of genetic programming, which was specifically designed to formulate the explicit relationship of Young modulus of two graphene structures. We find that the MD-based-CI model is able to model the Young modulus of two graphene structures very well, which compiles in good agreement with that of experimental results obtained from the literature. Additionally, we also conducted sensitivity and parametric analysis and found that the number of defects has the most dominating influence on the Young modulus of two graphene structures.

  4. Structural aspects of the solvation shell of lysine and acetylated lysine: A Car-Parrinello and classical molecular dynamics investigation

    SciTech Connect

    Carnevale, V.; Raugei, S.

    2009-12-14

    Lysine acetylation is a post-translational modification, which modulates the affinity of protein-protein and/or protein-DNA complexes. Its crucial role as a switch in signaling pathways highlights the relevance of charged chemical groups in determining the interactions between water and biomolecules. A great effort has been recently devoted to assess the reliability of classical molecular dynamics simulations in describing the solvation properties of charged moieties. In the spirit of these investigations, we performed classical and Car-Parrinello molecular dynamics simulations on lysine and acetylated-lysine in aqueous solution. A comparative analysis between the two computational schemes is presented with a focus on the first solvation shell of the charged groups. An accurate structural analysis unveils subtle, yet statistically significant, differences which are discussed in connection to the significant electronic density charge transfer occurring between the solute and the surrounding water molecules.

  5. Structural aspects of the solvation shell of lysine and acetylated lysine: A Car-Parrinello and classical molecular dynamics investigation.

    PubMed

    Carnevale, V; Raugei, S

    2009-12-14

    Lysine acetylation is a post-translational modification, which modulates the affinity of protein-protein and/or protein-DNA complexes. Its crucial role as a switch in signaling pathways highlights the relevance of charged chemical groups in determining the interactions between water and biomolecules. A great effort has been recently devoted to assess the reliability of classical molecular dynamics simulations in describing the solvation properties of charged moieties. In the spirit of these investigations, we performed classical and Car-Parrinello molecular dynamics simulations on lysine and acetylated-lysine in aqueous solution. A comparative analysis between the two computational schemes is presented with a focus on the first solvation shell of the charged groups. An accurate structural analysis unveils subtle, yet statistically significant, differences which are discussed in connection to the significant electronic density charge transfer occurring between the solute and the surrounding water molecules.

  6. Synthesis, molecular structure investigations and antimicrobial activity of 2-thioxothiazolidin-4-one derivatives

    NASA Astrophysics Data System (ADS)

    Barakat, Assem; Al-Najjar, Hany J.; Al-Majid, Abdullah Mohammed; Soliman, Saied M.; Mabkhot, Yahia Nasser; Al-Agamy, Mohamed H. M.; Ghabbour, Hazem A.; Fun, Hoong-Kun

    2015-02-01

    A variety of 2-thioxothiazolidin-4-one derivatives were prepared and their in vitro antimicrobial activities were studied. Most of these compounds showed significant antibacterial activity specifically against Gram-positive bacteria, among which compounds 4a,e,g, 5b,e,g,h and 6f exhibit high levels of antimicrobial activity against Bacillus subtilis ATCC 10400 with Minimum Inhibitory Concentration (MIC) value of 16 μg/mL. All compounds have antifungal activity against Candida albicans. Unfortunately, however, none of the compounds were active against Gram-negative bacteria. The chemical structure of 3 was confirmed by X-ray single crystal diffraction technique. DFT calculations of 3 have been performed on the free C10H7Cl2NO2S2, 3a and the H-bonded complex, C10H7Cl2NO2S2·H2O, 3b to explore the effect of the H-bonding interactions on the geometric and electronic properties of the studied systems. A small increase in bond length was observed in the C12-O6 due to the H-bonding interactions between 3a and water molecule. MEP study has been used to recognize the most reactive sites towards electrophilic and nucleophilic attacks as well as the possible sites for the H-bonding interactions. The TD-DFT calculations have been used to predict theoretically the electronic spectra of the studied compound. The most intense transition band is predicted at 283.9 nm due to the HOMO-2/HOMO-1 to LUMO transitions. NBO analyses were carried out to investigate the stabilization energy of the various intramolecular charge transfer interactions within the studied molecules.

  7. Investigating the Interaction Pattern and Structural Elements of a Drug-Polymer Complex at the Molecular Level.

    PubMed

    Nie, Haichen; Mo, Huaping; Zhang, Mingtao; Song, Yang; Fang, Ke; Taylor, Lynne S; Li, Tonglei; Byrn, Stephen R

    2015-07-06

    Strong associations between drug and polymeric carriers are expected to contribute to higher drug loading capacities and better physical stability of amorphous solid dispersions. However, molecular details of the interaction patterns and underlying mechanisms are still unclear. In the present study, a series of amorphous solid dispersions of clofazimine (CLF), an antileprosy drug, were prepared with different polymers by applying the solvent evaporation method. When using hypromellose phthalate (HPMCP) as the carrier, the amorphous solid dispersion system exhibits not only superior drug loading capacity (63% w/w) but also color change due to strong drug-polymer association. In order to further explain these experimental observations, the interaction between CLF and HPMCP was investigated in a nonpolar volatile solvent system (chloroform) prior to forming the solid dispersion. We observed significant UV/vis and (1)H NMR spectral changes suggesting the protonation of CLF and formation of ion pairs between CLF and HPMCP in chloroform. Furthermore, nuclear Overhauser effect spectroscopy (NOESY) and diffusion order spectroscopy (DOSY) were employed to evaluate the strength of associations between drug and polymers, as well as the molecular mobility of CLF. Finally, by correlating the experimental values with quantum chemistry calculations, we demonstrate that the protonated CLF is binding to the carboxylate group of HPMCP as an ion pair and propose a possible structural model of the drug-polymer complex. Understanding the drug and carrier interaction patterns from a molecular perspective is critical for the rational design of new amorphous solid dispersions.

  8. A molecular dynamics investigation of the influence of water structure on ion conduction through a carbon nanotube.

    PubMed

    Liu, L; Patey, G N

    2017-02-21

    Molecular dynamics simulations are employed to investigate pressure-driven water and ion transport through a (9,9) carbon nanotube (CNT). We consider NaCl solutions modeled with both the TIP3P and TIP4P/2005 water models. Concentrations range from 0.25 to 2.8 mol l(-1) and temperatures from 260 to 320 K are considered. We discuss the influences on flow rates of continuum hydrodynamic considerations and molecular structural effects. We show that the flow rate of water, sodium, and chloride ions through the CNT is strongly model dependent, consistent with earlier simulations of pure water conduction. To remove the effects of different water flow rates, and clearly expose the influence of other factors on ion flow, we calculate ion transport efficiencies. Ion transport efficiencies are much smaller for TIP4P/2005 solutions than for those using the TIP3P model. Particularly at lower temperatures, the ion transport efficiencies for the TIP4P/2005 model are small, despite the fact that the nanotube conducts water at a significant rate. We trace the origin of small ion transport efficiencies to the presence of ring-like water structures within the CNT. Such structures occur commonly for the TIP4P/2005 model, but less frequently for TIP3P. The water structure acts to reduce ion "solvation" within the CNT, posing an additional barrier to ion entry and transport. Our results demonstrate that increasing the water structure within the CNT by decreasing the temperature strongly inhibits ion conduction, while still permitting significant water transport.

  9. A molecular dynamics investigation of the influence of water structure on ion conduction through a carbon nanotube

    NASA Astrophysics Data System (ADS)

    Liu, L.; Patey, G. N.

    2017-02-01

    Molecular dynamics simulations are employed to investigate pressure-driven water and ion transport through a (9,9) carbon nanotube (CNT). We consider NaCl solutions modeled with both the TIP3P and TIP4P/2005 water models. Concentrations range from 0.25 to 2.8 mol l-1 and temperatures from 260 to 320 K are considered. We discuss the influences on flow rates of continuum hydrodynamic considerations and molecular structural effects. We show that the flow rate of water, sodium, and chloride ions through the CNT is strongly model dependent, consistent with earlier simulations of pure water conduction. To remove the effects of different water flow rates, and clearly expose the influence of other factors on ion flow, we calculate ion transport efficiencies. Ion transport efficiencies are much smaller for TIP4P/2005 solutions than for those using the TIP3P model. Particularly at lower temperatures, the ion transport efficiencies for the TIP4P/2005 model are small, despite the fact that the nanotube conducts water at a significant rate. We trace the origin of small ion transport efficiencies to the presence of ring-like water structures within the CNT. Such structures occur commonly for the TIP4P/2005 model, but less frequently for TIP3P. The water structure acts to reduce ion "solvation" within the CNT, posing an additional barrier to ion entry and transport. Our results demonstrate that increasing the water structure within the CNT by decreasing the temperature strongly inhibits ion conduction, while still permitting significant water transport.

  10. Molecular tools for investigating microbial community structure and function in oxygen-deficient marine waters.

    PubMed

    Hawley, Alyse K; Kheirandish, Sam; Mueller, Andreas; Leung, Hilary T C; Norbeck, Angela D; Brewer, Heather M; Pasa-Tolic, Ljiljana; Hallam, Steven J

    2013-01-01

    Water column oxygen (O2)-deficiency shapes food-web structure by progressively directing nutrients and energy away from higher trophic levels into microbial community metabolism resulting in fixed nitrogen loss and greenhouse gas production. Although respiratory O2 consumption during organic matter degradation is a natural outcome of a productive surface ocean, global-warming-induced stratification intensifies this process leading to oxygen minimum zone (OMZ) expansion. Here, we describe useful tools for detection and quantification of potential key microbial players and processes in OMZ community metabolism including quantitative polymerase chain reaction primers targeting Marine Group I Thaumarchaeota, SUP05, Arctic96BD-19, and SAR324 small-subunit ribosomal RNA genes and protein extraction methods from OMZ waters compatible with high-resolution mass spectrometry for profiling microbial community structure and functional dynamics.

  11. Structural basis of type 2A von Willebrand disease investigated by molecular dynamics simulations and experiments.

    PubMed

    Interlandi, Gianluca; Ling, Minhua; Tu, An Yue; Chung, Dominic W; Thomas, Wendy E

    2012-01-01

    The hemostatic function of von Willebrand factor is downregulated by the metalloprotease ADAMTS13, which cleaves at a unique site normally buried in the A2 domain. Exposure of the proteolytic site is induced in the wild-type by shear stress as von Willebrand factor circulates in blood. Mutations in the A2 domain, which increase its susceptibility to cleavage, cause type 2A von Willebrand disease. In this study, molecular dynamics simulations suggest that the A2 domain unfolds under tensile force progressively through a series of steps. The simulation results also indicated that three type 2A mutations in the C-terminal half of the A2 domain, L1657I, I1628T and E1638K, destabilize the native state fold of the protein. Furthermore, all three type 2A mutations lowered in silico the tensile force necessary to undock the C-terminal helix α6 from the rest of the A2 domain, the first event in the unfolding pathway. The mutations F1520A, I1651A and A1661G were also predicted by simulations to destabilize the A2 domain and facilitate exposure of the cleavage site. Recombinant A2 domain proteins were expressed and cleavage assays were performed with the wild-type and single-point mutants. All three type 2A and two of the three predicted mutations exhibited increased rate of cleavage by ADAMTS13. These results confirm that destabilization of the helix α6 in the A2 domain facilitates exposure of the cleavage site and increases the rate of cleavage by ADAMTS13.

  12. Complementarity of real-time neutron and synchrotron radiation structural investigations in molecular biology

    SciTech Connect

    Aksenov, V. L.; Kiselev, M. A.

    2010-12-15

    General problems of the complementarity of different physical methods and specific features of the interaction between neutron and matter and neutron diffraction with respect to the time of flight are discussed. The results of studying the kinetics of structural changes in lipid membranes under hydration and self-assembly of the lipid bilayer in the presence of a detergent are reported. The possibilities of the complementarity of neutron diffraction and X-ray synchrotron radiation and developing a free-electron laser are noted.

  13. Structural and thermodynamic investigations on the aggregation and folding of acylphosphatase by molecular dynamics simulations and solvation free energy analysis.

    PubMed

    Chong, Song-Ho; Lee, Chewook; Kang, Guipeun; Park, Mirae; Ham, Sihyun

    2011-05-11

    Protein engineering method to study the mutation effects on muscle acylphosphatase (AcP) has been actively applied to describe kinetics and thermodynamics associated with AcP aggregation as well as folding processes. Despite the extensive mutation experiments, the molecular origin and the structural motifs for aggregation and folding kinetics as well as thermodynamics of AcP have not been rationalized at the atomic resolution. To this end, we have investigated the mutation effects on the structures and thermodynamics for the aggregation and folding of AcP by using the combination of fully atomistic, explicit-water molecular dynamics simulations, and three-dimensional reference interaction site model theory. The results indicate that the A30G mutant with the fastest experimental aggregation rate displays considerably decreased α1-helical contents as well as disrupted hydrophobic core compared to the wild-type AcP. Increased solvation free energy as well as hydrophobicity upon A30G mutation is achieved due to the dehydration of hydrophilic side chains in the disrupted α1-helix region of A30G. In contrast, the Y91Q mutant with the slowest aggregation rate shows a non-native H-bonding network spanning the mutation site to hydrophobic core and α1-helix region, which rigidifies the native state protein conformation with the enhanced α1-helicity. Furthermore, Y91Q exhibits decreased solvation free energy and hydrophobicity compared to wild type due to more exposed and solvated hydrophilic side chains in the α1-region. On the other hand, the experimentally observed slower folding rates in both mutants are accompanied by decreased helicity in α2-helix upon mutation. We here provide the atomic-level structures and thermodynamic quantities of AcP mutants and rationalize the structural origin for the changes that occur upon introduction of those mutations along the AcP aggregation and folding processes.

  14. Molecular monolayer structures formed on vicinal surfaces as investigated by scanning tunneling microscopy

    NASA Astrophysics Data System (ADS)

    Avila-Bront, Lynna Gabriela

    The increasing demand for efficient cancer treatment inspired the researchers for new investigations about an alternative treatment of cancer. Microwave ablation is the newest ablation technique to cure cancer. This method is minimally noninvasive and inexpensive compared to the other methods. However, current microwave ablation systems suffer due to narrow band nature of the antenna (dipole or slot) placed at the tip of the probe. Therefore, this study developed an ultra-wide band ablation probe that operates from 300 MHz to 10 GHz. For this purpose, a small wide band antenna is designed to place at the tip of the probe and fabricated. These probes are tested at ISM frequencies (2.4 GHz and 5.8 GHz) in skin mimicking gels and pig liver. Microwave ablation probe design, simulation results, and experiment results are provided in this thesis.

  15. Structure investigation of three hydrazones Schiff's bases by spectroscopic, thermal and molecular orbital calculations and their biological activities.

    PubMed

    Belal, Arafa A M; Zayed, M A; El-Desawy, M; Rakha, Sh M A H

    2015-03-05

    Three Schiff's bases AI (2(1-hydrazonoethyl)phenol), AII (2, 4-dibromo 6-(hydrazonomethyl)phenol) and AIII (2(hydrazonomethyl)phenol) were prepared as new hydrazone compounds via condensation reactions with molar ratio (1:1) of reactants. Firstly by reaction of 2-hydroxy acetophenone solution and hydrazine hydrate; it gives AI. Secondly condensation between 3,5-dibromo-salicylaldehyde and hydrazine hydrate gives AII. Thirdly condensation between salicylaldehyde and hydrazine hydrate gives AIII. The structures of AI-AIII were characterized by elemental analysis (EA), mass (MS), FT-IR and (1)H NMR spectra, and thermal analyses (TG, DTG, and DTA). The activation thermodynamic parameters, such as, ΔE(∗), ΔH(∗), ΔS(∗) and ΔG(∗) were calculated from the TG curves using Coats-Redfern method. It is important to investigate their molecular structures to know the active groups and weak bond responsible for their biological activities. Consequently in the present work, the obtained thermal (TA) and mass (MS) practical results are confirmed by semi-empirical MO-calculations (MOCS) using PM3 procedure. Their biological activities have been tested in vitro against Escherichia coli, Proteus vulgaris, Bacillissubtilies and Staphylococcus aurous bacteria in order to assess their anti-microbial potential.

  16. Structure investigation of three hydrazones Schiff's bases by spectroscopic, thermal and molecular orbital calculations and their biological activities

    NASA Astrophysics Data System (ADS)

    Belal, Arafa A. M.; Zayed, M. A.; El-Desawy, M.; Rakha, Sh. M. A. H.

    2015-03-01

    Three Schiff's bases AI (2(1-hydrazonoethyl)phenol), AII (2, 4-dibromo 6-(hydrazonomethyl)phenol) and AIII (2(hydrazonomethyl)phenol) were prepared as new hydrazone compounds via condensation reactions with molar ratio (1:1) of reactants. Firstly by reaction of 2-hydroxy acetophenone solution and hydrazine hydrate; it gives AI. Secondly condensation between 3,5-dibromo-salicylaldehyde and hydrazine hydrate gives AII. Thirdly condensation between salicylaldehyde and hydrazine hydrate gives AIII. The structures of AI-AIII were characterized by elemental analysis (EA), mass (MS), FT-IR and 1H NMR spectra, and thermal analyses (TG, DTG, and DTA). The activation thermodynamic parameters, such as, ΔE∗, ΔH∗, ΔS∗ and ΔG∗ were calculated from the TG curves using Coats-Redfern method. It is important to investigate their molecular structures to know the active groups and weak bond responsible for their biological activities. Consequently in the present work, the obtained thermal (TA) and mass (MS) practical results are confirmed by semi-empirical MO-calculations (MOCS) using PM3 procedure. Their biological activities have been tested in vitro against Escherichia coli, Proteus vulgaris, Bacillissubtilies and Staphylococcus aurous bacteria in order to assess their anti-microbial potential.

  17. 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

  18. Molecular-scale investigations of structures and surface charge distribution of surfactant aggregates by three-dimensional force mapping

    SciTech Connect

    Suzuki, Kazuhiro; Oyabu, Noriaki; Matsushige, Kazumi; Yamada, Hirofumi; Kobayashi, Kei

    2014-02-07

    Surface charges on nanoscale structures in liquids, such as biomolecules and nano-micelles, play an essentially important role in their structural stability as well as their chemical activities. These structures interact with each other through electric double layers (EDLs) formed by the counter ions in electrolyte solution. Although static-mode atomic force microscopy (AFM) including colloidal-probe AFM is a powerful technique for surface charge density measurements and EDL analysis on a submicron scale in liquids, precise surface charge density analysis with single-nanometer resolution has not been made because of its limitation of the resolution and the detection sensitivity. Here we demonstrate molecular-scale surface charge measurements of self-assembled micellar structures, molecular hemicylinders of sodium dodecyl sulfate (SDS), by three-dimensional (3D) force mapping based on frequency modulation AFM. The SDS hemicylindrical structures with a diameter of 4.8 nm on a graphite surface were clearly imaged. We have succeeded in visualizing 3D EDL forces on the SDS hemicylinder surfaces and obtaining the molecular-scale charge density for the first time. The results showed that the surface charge on the trench regions between the hemicylinders was much smaller than that on the hemicylinder tops. The method can be applied to a wide variety of local charge distribution studies, such as spatial charge variation on a single protein molecule.

  19. A Combination of Hand-Held Models and Computer Imaging Programs Helps Students Answer Oral Questions about Molecular Structure and Function: A Controlled Investigation of Student Learning

    ERIC Educational Resources Information Center

    Harris, Michelle A.; Peck, Ronald F.; Colton, Shannon; Morris, Jennifer; Neto, Elias Chaibub; Kallio, Julie

    2009-01-01

    We conducted a controlled investigation to examine whether a combination of computer imagery and tactile tools helps introductory cell biology laboratory undergraduate students better learn about protein structure/function relationships as compared with computer imagery alone. In all five laboratory sections, students used the molecular imaging…

  20. Investigation of solvent polarity effect on molecular structure and vibrational spectrum of xanthine with the aid of quantum chemical computations.

    PubMed

    Polat, Turgay; Yıldırım, Gurcan

    2014-04-05

    The main scope of this study is to determine the effects of 8 solvents on the geometric structure and vibrational spectra of the title compound, xanthine, by means of the DFT/B3LYP level of theory in the combination with the polarizable conductor continuum model (CPCM) for the first time. After determination of the most-steady state (favored structure) of the xanthine molecule, the role of the solvent polarity on the SCF energy (for the molecule stability), atomic charges (for charge distribution) and dipole moments (for molecular charge transfer) belonging to tautomer is discussed in detail. The results obtained indicate not only the presence of the hydrogen bonding and strong intra-molecular charge transfer (ICT) in the compound but the increment of the molecule stability with the solvent polarity, as well. Moreover, it is noted that the optimized geometric parameters and the theoretical vibrational frequencies are in good agreement with the available experimental results found in the literature. In fact, the correlations between the experimental and theoretical findings for the molecular structures improve with the enhancement of the solvent polarity. At the same time, the dimer forms of the xanthine compound are simulated to describe the effect of intermolecular hydrogen bonding on the molecular geometry and vibrational frequencies. It is found that the CO and NH stretching vibrations shift regularly to lower frequency value with higher IR intensity as the dielectric medium enhances systematically due to the intermolecular NH⋯O hydrogen bonds. Theoretical vibrational spectra are also assigned based on the potential energy distribution (PED) using the VEDA 4 program.

  1. Understanding molecular structure from molecular mechanics.

    PubMed

    Allinger, Norman L

    2011-04-01

    Molecular mechanics gives us a well known model of molecular structure. It is less widely recognized that valence bond theory gives us structures which offer a direct interpretation of molecular mechanics formulations and parameters. The electronic effects well-known in physical organic chemistry can be directly interpreted in terms of valence bond structures, and hence quantitatively calculated and understood. The basic theory is outlined in this paper, and examples of the effects, and their interpretation in illustrative examples is presented.

  2. INVESTIGATION OF MOLECULAR CLOUD STRUCTURE AROUND INFRARED BUBBLES: CARMA OBSERVATIONS OF N14, N22, AND N74

    SciTech Connect

    Sherman, Reid A.

    2012-11-20

    We present CARMA observations in 3.3 mm continuum and several molecular lines of the surroundings of N14, N22, and N74, three infrared bubbles from the GLIMPSE catalog. We have discovered 28 compact continuum sources and confirmed their associations with the bubbles using velocity information from HCO{sup +} and HCN. We have also mapped small-scale structures of N{sub 2}H{sup +} emission in the vicinity of the bubbles. By combining our data with survey data from GLIMPSE, MIPSGAL, BGPS, and MAGPIS, we establish about half of our continuum sources as star-forming cores. We also use survey data with the velocity information from our molecular line observations to describe the morphology of the bubbles and the nature of the fragmentation. We conclude from the properties of the continuum sources that N74 likely is at the near kinematic distance, which was previously unconfirmed. We also present tentative evidence of molecular clouds being more fragmented on bubble rims compared to dark clouds, suggesting that triggered star formation may occur, though our findings do not conform to a classic collect-and-collapse model.

  3. Structural investigations of E. Coli dihydrolipoamide dehydrogenase in solution: Small-angle X-ray scattering and molecular docking

    NASA Astrophysics Data System (ADS)

    Dadinova, L. A.; Rodina, E. V.; Vorobyeva, N. N.; Kurilova, S. A.; Nazarova, T. I.; Shtykova, E. V.

    2016-05-01

    Dihydrolipoamide dehydrogenase from Escherichia coli (LpD) is a bacterial enzyme that is involved in the central metabolism and shared in common between the pyruvate dehydrogenase and 2-oxoglutarate dehydrogenase complexes. In the crystal structure, E. coli LpD is known to exist as a dimer. The present work is focused on analyzing the solution structure of LpD by small-angle X-ray scattering, molecular docking, and analytical ultracentrifugation. It was shown that in solution LpD exists as an equilibrium mixture of a dimer and a tetramer. The presence of oligomeric forms is determined by the multifunctionality of LpD in the cell, in particular, the required stoichiometry in the complexes.

  4. Validity assessment of the detection method of maize event Bt10 through investigation of its molecular structure.

    PubMed

    Milcamps, Anne; Rabe, Scott; Cade, Rebecca; De Framond, Anic J; Henriksson, Peter; Kramer, Vance; Lisboa, Duarte; Pastor-Benito, Susana; Willits, Michael G; Lawrence, David; Van den Eede, Guy

    2009-04-22

    In March 2005, U.S. authorities informed the European Commission of the inadvertent release of unauthorized maize GM event Bt10 in their market and subsequently the grain channel. In the United States measures were taken to eliminate Bt10 from seed and grain supplies; in the European Union an embargo for maize gluten and brewer's grain import was implemented unless certified of Bt10 absence with a Bt10-specific PCR detection method. With the aim of assessing the validity of the Bt10 detection method, an in-depth analysis of the molecular organization of the genetic modification of this event was carried out by both the company Syngenta, who produced the event, and the European Commission Joint Research Centre, who validated the detection method. Using a variety of molecular analytical tools, both organizations found the genetic modification of event Bt10 to be very complex in structure, with rearrangements, inversions, and multiple copies of the structural elements (cry1Ab, pat, and the amp gene), interspersed with small genomic maize fragments. Southern blot analyses demonstrated that all Bt10 elements were found tightly linked on one large fragment, including the region that would generate the event-specific PCR amplicon of the Bt10 detection method. This study proposes a hypothetical map of the insert of event Bt10 and concludes that the validated detection method for event Bt10 is fit for its purpose.

  5. Molecular Investigations of the Structure and Function of the Protein Phosphatase 1-Spinophilin-Inhibitor 2 Heterotrimeric Complex

    SciTech Connect

    Dancheck, B.; Allaire, M.; Ragusa, M.J.; Nairn, A.C.; Page, R.; Peti, W.

    2011-01-06

    Regulation of the major Ser/Thr phosphatase protein phosphatase 1 (PP1) is controlled by a diverse array of targeting and inhibitor proteins. Though many PP1 regulatory proteins share at least one PP1 binding motif, usually the RVxF motif, it was recently discovered that certain pairs of targeting and inhibitor proteins bind PP1 simultaneously to form PP1 heterotrimeric complexes. To date, structural information for these heterotrimeric complexes and, in turn, how they direct PP1 activity is entirely lacking. Using a combination of NMR spectroscopy, biochemistry, and small-angle X-ray scattering (SAXS), we show that major structural rearrangements in both spinophilin (targeting) and inhibitor 2 (I-2, inhibitor) are essential for the formation of the heterotrimeric PP1-spinophilin-I-2 (PSI) complex. The RVxF motif of I-2 is released from PP1 during the formation of PSI, making the less prevalent SILK motif of I-2 essential for complex stability. The release of the I-2 RVxF motif allows for enhanced flexibility of both I-2 and spinophilin in the heterotrimeric complex. In addition, we used inductively coupled plasma atomic emission spectroscopy to show that PP1 contains two metals in both heterodimeric complexes (PP1-spinophilin and PP1-I-2) and PSI, demonstrating that PSI retains the biochemical characteristics of the PP1-I-2 holoenzyme. Finally, we combined the NMR and biochemical data with SAXS and molecular dynamics simulations to generate a structural model of the full heterotrimeric PSI complex. Collectively, these data reveal the molecular events that enable PP1 heterotrimeric complexes to exploit both the targeting and inhibitory features of the PP1-regulatory proteins to form multifunctional PP1 holoenzymes.

  6. A nuclear Overhauser effect investigation of the molecular and electronic structure of the heme crevice in lactoperoxidase

    SciTech Connect

    Thanabal, V.; La Mar, G.N. )

    1989-08-22

    The proton homonuclear nuclear Overhauser effect, NOE, in conjunction with paramagnetic-induced dipolar relaxation, is utilized to assign resonances and to probe the molecular and electronic structures of the heme cavity in the low-spin cyanide complex of resting-state bovine lactoperoxidase, LPO-CN. Predominantly primary NOEs were detected in spite of the large molecular weight of the enzyme, which demonstrates again the advantage of paramagnetism suppressing spin diffusion in large proteins. Both of the nonlabile ring protons of a coordinated histidine are located at resonance positions consistent with a deprotonated imidazole. Several methylene proton pairs are identified, of which the most strongly hyperfine-shifted pair is assigned to the unusual chemically functionalized 8-(mercaptomethylene) group of the prosthetic group. The large 8-(mercaptomethylene) proton contact shifts relative to that of the only resolved heme methyl signal are rationalized by the additive perturbations on the rhombic asymmetry of the functionalization of the 8-position and the alignment of the axial histidyl imidazole projection along a vector passing through pyrrole A and C of the prosthetic group. Such a stereochemistry is consistent with the resolution of only a single heme methyl group, 3-CH{sub 3}, as observed. A pair of hyperfine-shifted methylene protons, as well as a low-field hyperfine-shifted labile proton signal, exhibit dipolar connectivities similar to those previously reported for the distal arginine and histidine, respectively, of horseradish peroxidase suggesting that these catalytically relevant residues may also exist in LPO.

  7. Molecular-level investigation into copper complexes on vermiculite: effect of reduction of structural iron on copper complexation.

    PubMed

    Furnare, Luca J; Vailionis, Arturas; Strawn, Daniel G

    2005-09-01

    In this paper we present results that describe the speciation of Cu sorbed to the clay mineral vermiculite, with special attention to the effects of reduction on Cu sorption complexes. Sorption complexes were studied using powdered extended X-ray absorption fine structure (EXAFS) spectroscopy, polarized EXAFS spectroscopy, and X-ray diffraction (XRD). Ionic strength (I), background ion, and clay reduction (structural iron) were varied in the sorption samples. At low I EXAFS results indicate that Cu was surrounded by up to six water molecules sorbed in the interlayer of reduced vermiculite. EXAFS results from Cu-equilibrated reduced vermiculite with high I Ca background electrolyte revealed that Cu was surrounded by 4 O atoms at 1.95 Angatroms and 8 second shell O atoms at 3.14 Angstroms. Angular dependence of the second shell O atoms interpreted from the polarized-EXAFS spectra indicated that the atoms are out of plane from the basal plane of the vermiculite (inclined approximately 25 degrees from the ab plane). The local atomic environment and angular dependence of the EXAFS spectra suggest that the Cu atoms are adsorbed above the hexagonal cavities of the reduced clay mineral and form a Cu dimer in the interlayer. This adsorption mechanism was not observed in the non-reduced vermiculite under identical equilibration conditions. Our results provide molecular level evidence that Cu sorption mechanisms on vermiculite are dependent on solution conditions, such as redox potential and background electrolyte. These results can be used to develop better models of Cu sorption mechanisms on clay mineral surfaces.

  8. Testing the limits of sensitivity in a solid-state structural investigation by combined X-ray powder diffraction, solid-state NMR, and molecular modelling.

    PubMed

    Filip, Xenia; Borodi, Gheorghe; Filip, Claudiu

    2011-10-28

    A solid state structural investigation of ethoxzolamide is performed on microcrystalline powder by using a multi-technique approach that combines X-ray powder diffraction (XRPD) data analysis based on direct space methods with information from (13)C((15)N) solid-state Nuclear Magnetic Resonance (SS-NMR) and molecular modeling. Quantum chemical computations of the crystal were employed for geometry optimization and chemical shift calculations based on the Gauge Including Projector Augmented-Wave (GIPAW) method, whereas a systematic search in the conformational space was performed on the isolated molecule using a molecular mechanics (MM) approach. The applied methodology proved useful for: (i) removing ambiguities in the XRPD crystal structure determination process and further refining the derived structure solutions, and (ii) getting important insights into the relationship between the complex network of non-covalent interactions and the induced supra-molecular architectures/crystal packing patterns. It was found that ethoxzolamide provides an ideal case study for testing the accuracy with which this methodology allows to distinguish between various structural features emerging from the analysis of the powder diffraction data.

  9. A Theoretical Investigation of the Structure and Reactivity of the Molecular Constituents of Oil Sand and Oil Shale

    SciTech Connect

    Parish, Carol A.

    2016-11-28

    We used a variety of small organic models of asphaltenes to investigate the molecular mechanism for the high temperature decomposition that would take place as part of the oil refinery process. We determined that the decomposition is initiated via four different types of hydrogen migration reactions. According to the energetics of the reactions, the dominant 1,2-H shift mechanism involves two competitive product channels, namely, C2H2 + CH2CS and CS + CH3CCH. The minor channels include the formation of CS + CH2CCH2, H2S + C4H2, HCS + CH2CCH, CS + CH2CHCH, H + C4H3S, and HS + C4H3. We also investigated the alkyl substitution effect by exploring the decomposition pathways of models with alkyl arms. The energetics of such systems were very similar to that for unsubstituted model compounds, which suggests that asphaltene alkylation may not play a significant role in the decomposition of asphaltene compounds. This work was published in the Journal of Physical Chemistry A 2011, 115, 2882-2891. A MECHANISTIC STUDY OF THE 2-THIENYLMETHYL + HO2 RADICAL RECOMBINATION REACTION Radicals are molecules which contain single electrons. They are very reactive. Radical recombination reactions are important in the combustion of fuel oils. Shale oil contains radicals. We used quantum mechanics to explore the reactivity of shale oil model radical compounds. Seventeen product channels corresponding to either addition/elimination or direct hydrogen abstraction were characterized. Direct hydrogen abstraction proceeds via a weakly bonded complex, which leads to 2-methylthiophene, 2-methylene-2,3-dihydrothiophene or 2-methylene-2,5-dihydrothiophene depending upon the 2-thienylmethyl radical reaction site. The addition pathway for the two radical reactants is barrierless with the formation of three adducts, as distinguished by HO

  10. Structure investigation of codeine drug using mass spectrometry, thermal analyses and semi-emperical molecular orbital (MO) calculations

    NASA Astrophysics Data System (ADS)

    Zayed, M. A.; Hawash, M. F.; Fahmey, M. A.

    2006-05-01

    Codeine is an analgesic with uses similar to morphine, but it has a mild sedative effect. It is preferable used as phosphate form and it is often administrated by mouth with aspirin or paracetamol. Therefore, it is important to investigate its structure to know the active groups and weak bonds responsible for its medical activity. Consequently in the present work, codeine was investigated by mass spectrometry and thermal analyses (TG, DTG and DTA) and confirming by semi-empirical MO-calculation (PM3 method) in the neutral and positively charged forms of the drug. Some results of studying the d-block element complexes of codeine were used to declare the relationship between drug structure and its chemical reactivity in vitro system. The mass spectra and thermal analyses fragmentation pathways were proposed and compared to each other to select the most suitable scheme representing the correct fragmentation of this drug. From EI mass spectra, the main primary cleavage site of the charged drug molecule is that due to β-cleavage to nitrogen atom in its skeleton. It occurs in two parallel mechanisms with the same possibility, i.e. no difference in appearance activation energy between them. In the neutral drug form the primary site cleavage is that occurs in the ether ring. Thermal analyses of the neutral form of the drug revealed the high response of the drug to the temperature variation with very fast rate. It decomposed in several sequential steps in the temperature range 200-600 °C. The initial thermal fragments are very similar to that obtained by mass spectrometric fragmentation. Therefore, comparison between mass and thermal helps in selection of the proper pathway representing the fragmentation of this drug. This comparison successfully confirmed by MOC. These calculations give the bond order, charge distribution, heat of formation and possible hybridization of some atoms in different position of the drug skeleton. This helps the successful choice of the weakest

  11. An investigations on the molecular structure, FT-IR, FT-Raman and NMR spectra of 1-(p-tolylsulfonyl) pyrrole by theoretical and experimental approach.

    PubMed

    Erdogdu, Y; Saglam, S; Gulluoglu, M T

    2015-07-05

    Fourier-Transform-Infrared, Fourier-Transform-Raman and Nuclear Magnetic Rezonans spectra of 1-(p-tolylsulfonyl) pyrrole molecule have been recorded. In the powder form, vibrational spectra of 1-(p-tolylsulfonyl) pyrrol molecule were investigated in the region 4000-400 cm(-1) and 3500-50 cm(-1), respectively. The conformational analysis, geometrical structure, molecular electrostatic potential map, HOMO-LUMO and vibrational spectroscopic properties of the isolated 1-(p-tolylsulfonyl) pyrrole molecule have also been carried out at the Molecular Mechanic and Density Functional Theory approaches. Density Functional Theory results have been associated with Scaled Quantum Mechanics Force Field for fitting between the theoretical and the experimental frequencies.

  12. 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.

  13. Electrostatic guidelines and molecular tailoring for density functional investigation of structures and energetics of (Li)n clusters

    NASA Astrophysics Data System (ADS)

    K. V., Jovan Jose; Gadre, Shridhar R.

    2008-10-01

    A molecular electrostatic potential (MESP)-guided method for building metal aggregates is proposed and tested on prototype lithium (Li)n clusters from n =4 to 58. The smaller clusters are subsequently subjected to direct density functional theory based geometry optimization, while the larger ones are optimized via molecular tailoring approach (MTA). The calculations are performed using PW91-PW91 as well as B3LYP functionals, and the trends in the interaction energies are found to be similar. The MESP-guided model for building metal clusters is validated by comparing the resulting cluster geometries with the ones reported in the literature up to n =20. A comparison of the ionization potential and polarizability (up to n =22) with their experimental counterparts shows a fairly good agreement. A new MTA-based scheme for calculating the ionization potential and polarizability values of large metal clusters is proposed and tested on Li40 and Li58 clusters. Further, the existence of "magic numbered clusters" up to n =22 is justified in terms of "maximum hardness principle" as well based on molecular electron density topography and distance descriptors.

  14. Investigation of the local structure of mixtures of an ionic liquid with polar molecular species through molecular dynamics: cluster formation and angular distributions.

    PubMed

    Carrete, Jesús; Méndez-Morales, Trinidad; Cabeza, Óscar; Lynden-Bell, Ruth M; Gallego, Luis J; Varela, Luis M

    2012-05-24

    In this work, we used molecular dynamics simulations to analyze in detail the spatial distributions of the different constituents in mixtures of 1-butyl-3-methylimidazolium tetrafluoroborate with three polar molecular species: water and two alcohols of different chain lengths (methanol and ethanol). In particular, we report results regarding the influence of the chosen species and its concentration on the formation of ionic and molecular clusters over the whole miscibility range, as well as on the angular distribution of polar molecules around the anion and the cation in these systems. Both analyses showed that addition of a molecular species breaks down the polar network of the pure ionic liquid in clusters whose mean size decreases progressively as more molecules are added. At very high concentrations of the molecular species, the ions are found to be isolated in mixtures with water and methanol, but they tend to form pairs in ethanol. In mixtures with water we identified large clusters that form a water network at very high water concentrations, while at low water concentrations polar molecules tend to form smaller aggregates. In contrast, in mixtures with alkanols there is no evidence of the formation of large alcohol clusters at any concentration. Spatial order in alcohol was also studied by means of the Kirkwood G factor, reaching the conclusion that the angular correlations which appear in pure alcohols due to dipole interactions are destroyed by the ionic liquid, even when present only in tiny amounts.

  15. 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.

  16. A dynamic structural model of expanded RNA CAG repeats: a refined X-ray structure and computational investigations using molecular dynamics and umbrella sampling simulations.

    PubMed

    Yildirim, Ilyas; Park, HaJeung; Disney, Matthew D; Schatz, George C

    2013-03-06

    One class of functionally important RNA is repeating transcripts that cause disease through various mechanisms. For example, expanded CAG repeats can cause Huntington's and other disease through translation of toxic proteins. Herein, a crystal structure of r[5'UUGGGC(CAG)3GUCC]2, a model of CAG expanded transcripts, refined to 1.65 Å resolution is disclosed that shows both anti-anti and syn-anti orientations for 1 × 1 nucleotide AA internal loops. Molecular dynamics (MD) simulations using AMBER force field in explicit solvent were run for over 500 ns on the model systems r(5'GCGCAGCGC)2 (MS1) and r(5'CCGCAGCGG)2 (MS2). In these MD simulations, both anti-anti and syn-anti AA base pairs appear to be stable. While anti-anti AA base pairs were dynamic and sampled multiple anti-anti conformations, no syn-anti ↔ anti-anti transformations were observed. Umbrella sampling simulations were run on MS2, and a 2D free energy surface was created to extract transformation pathways. In addition, an explicit solvent MD simulation over 800 ns was run on r[5'GGGC(CAG)3GUCC]2, which closely represents the refined crystal structure. One of the terminal AA base pairs (syn-anti conformation), transformed to anti-anti conformation. The pathway followed in this transformation was the one predicted by umbrella sampling simulations. Further analysis showed a binding pocket near AA base pairs in syn-anti conformations. Computational results combined with the refined crystal structure show that global minimum conformation of 1 × 1 nucleotide AA internal loops in r(CAG) repeats is anti-anti but can adopt syn-anti depending on the environment. These results are important to understand RNA dynamic-function relationships and to develop small molecules that target RNA dynamic ensembles.

  17. A dynamic structural model of expanded RNA CAG repeats: A refined X-ray structure and computational investigations using molecular dynamics and umbrella sampling simulations

    PubMed Central

    Yildirim, Ilyas; Park, Hajeung; Disney, Matthew D.; Schatz, George C.

    2013-01-01

    One class of functionally important RNA is repeating transcripts that cause disease through various mechanisms. For example, expanded r(CAG) repeats can cause Huntington’s and other disease through translation of toxic proteins. Herein, crystal structure of r[5ʹUUGGGC(CAG)3GUCC]2, a model of CAG expanded transcripts, refined to 1.65 Å resolution is disclosed that show both anti-anti and syn-anti orientations for 1×1 nucleotide AA internal loops. Molecular dynamics (MD) simulations using Amber force field in explicit solvent were run for over 500 ns on model systems r(5ʹGCGCAGCGC)2 (MS1) and r(5ʹCCGCAGCGG)2 (MS2). In these MD simulations, both anti-anti and syn-anti AA base pairs appear to be stable. While anti-anti AA base pairs were dynamic and sampled multiple anti-anti conformations, no syn-anti↔anti-anti transformations were observed. Umbrella sampling simulations were run on MS2, and a 2D free energy surface was created to extract transformation pathways. In addition, over 800 ns explicit solvent MD simulation was run on r[5ʹGGGC(CAG)3GUCC]2, which closely represents the refined crystal structure. One of the terminal AA base pairs (syn-anti conformation), transformed to anti-anti conformation. The pathway followed in this transformation was the one predicted by umbrella sampling simulations. Further analysis showed a binding pocket near AA base pairs in syn-anti conformations. Computational results combined with the refined crystal structure show that global minimum conformation of 1×1 nucleotide AA internal loops in r(CAG) repeats is anti-anti but can adopt syn-anti depending on the environment. These results are important to understand RNA dynamic-function relationships and develop small molecules that target RNA dynamic ensembles. PMID:23441937

  18. Structural investigations into the binding mode of novel neolignans Cmp10 and Cmp19 microtubule stabilizers by in silico molecular docking, molecular dynamics, and binding free energy calculations.

    PubMed

    Tripathi, Shubhandra; Kumar, Akhil; Kumar, B Sathish; Negi, Arvind S; Sharma, Ashok

    2016-06-01

    Microtubule stabilizers provide an important mode of treatment via mitotic cell arrest of cancer cells. Recently, we reported two novel neolignans derivatives Cmp10 and Cmp19 showing anticancer activity and working as microtubule stabilizers at micromolar concentrations. In this study, we have explored the binding site, mode of binding, and stabilization by two novel microtubule stabilizers Cmp10 and Cmp19 using in silico molecular docking, molecular dynamics (MD) simulation, and binding free energy calculations. Molecular docking studies were performed to explore the β-tubulin binding site of Cmp10 and Cmp19. Further, MD simulations were used to probe the β-tubulin stabilization mechanism by Cmp10 and Cmp19. Binding affinity was also compared for Cmp10 and Cmp19 using binding free energy calculations. Our docking results revealed that both the compounds bind at Ptxl binding site in β-tubulin. MD simulation studies showed that Cmp10 and Cmp19 binding stabilizes M-loop (Phe272-Val288) residues of β-tubulin and prevent its dynamics, leading to a better packing between α and β subunits from adjacent tubulin dimers. In addition, His229, Ser280 and Gln281, and Arg278, Thr276, and Ser232 were found to be the key amino acid residues forming H-bonds with Cmp10 and Cmp19, respectively. Consequently, binding free energy calculations indicated that Cmp10 (-113.655 kJ/mol) had better binding compared to Cmp19 (-95.216 kJ/mol). This study provides useful insight for better understanding of the binding mechanism of Cmp10 and Cmp19 and will be helpful in designing novel microtubule stabilizers.

  19. Structural investigation of zymogenic and activated forms of human blood coagulation factor VIII: a computational molecular dynamics study

    PubMed Central

    2010-01-01

    Background Human blood coagulation factor VIII (fVIII) is a large plasma glycoprotein with sequential domain arrangement in the order A1-a1-A2-a2-B-a3-A3-C1-C2. The A1, A2 and A3 domains are interconnected by long linker peptides (a1, a2 and a3) that possess the activation sites. Proteolysis of fVIII zymogen by thrombin or factor Xa results in the generation of the activated form (fVIIIa) which serves as a critical co-factor for factor IXa (fIXa) enzyme in the intrinsic coagulation pathway. Results In our efforts to elucidate the structural differences between fVIII and fVIIIa, we developed the solution structural models of both forms, starting from an incomplete 3.7 Å X-ray crystal structure of fVIII zymogen, using explicit solvent MD simulations. The full assembly of B-domainless single-chain fVIII was built between the A1-A2 (Ala1-Arg740) and A3-C1-C2 (Ser1669-Tyr2332) domains. The structural dynamics of fVIII and fVIIIa, simulated for over 70 ns of time scale, enabled us to evaluate the integral motions of the multi-domain assembly of the co-factor and the possible coordination pattern of the functionally important calcium and copper ion binding in the protein. Conclusions MD simulations predicted that the acidic linker peptide (a1) between the A1 and A2 domains is largely flexible and appears to mask the exposure of putative fIXa enzyme binding loop (Tyr555-Asp569) region in the A2 domain. The simulation of fVIIIa, generated from the zymogen structure, predicted that the linker peptide (a1) undergoes significant conformational reorganization upon activation by relocating completely to the A1-domain. The conformational transition led to the exposure of the Tyr555-Asp569 loop and the surrounding region in the A2 domain. While the proposed linker peptide conformation is predictive in nature and warrants further experimental validation, the observed conformational differences between the zymogen and activated forms may explain and support the large body of

  20. Functional and Structural Analyses of CYP1B1 Variants Linked to Congenital and Adult-Onset Glaucoma to Investigate the Molecular Basis of These Diseases

    PubMed Central

    Chakrabarti, Saikat; Ray, Kunal

    2016-01-01

    Glaucoma, the leading cause of irreversible blindness, appears in various forms. Mutations in CYP1B1 result in primary congenital glaucoma (PCG) by an autosomal recessive mode of inheritance while it acts as a modifier locus for primary open angle glaucoma (POAG). We investigated the molecular basis of the variable phenotypes resulting from the defects in CYP1B1 by using subclones of 23 CYP1B1 mutants reported in glaucoma patients, in a cell based system by measuring the dual activity of the enzyme to metabolize both retinol and 17β-estradiol. Most variants linked to POAG showed low steroid metabolism while null or very high retinol metabolism was observed in variants identified in PCG. We examined the translational turnover rates of mutant proteins after the addition of cycloheximide and observed that the levels of enzyme activity mostly corroborated the translational turnover rate. We performed extensive normal mode analysis and molecular-dynamics-simulations-based structural analyses and observed significant variation of fluctuation in certain segmental parts of the mutant proteins, especially at the B-C and F-G loops, which were previously shown to affect the dynamic behavior and ligand entry/exit properties of the cytochrome P450 family of proteins. Our molecular study corroborates the structural analysis, and suggests that the pathologic state of the carrier of CYP1B1 mutations is determined by the allelic state of the gene. To our knowledge, this is the first attempt to dissect biological activities of CYP1B1 for correlation with congenital and adult onset glaucomas. PMID:27243976

  1. Basic amphipathic model peptides: Structural investigations in solution, studied by circular dichroism, fluorescence, analytical ultracentrifugation and molecular modelling

    NASA Astrophysics Data System (ADS)

    Mangavel, C.; Sy, D.; Reynaud, J. A.

    1999-05-01

    A twenty amino acid residue long amphipathic peptide made of ten leucine and ten lysine residues and four derivatives, in which a tryptophan, as a fluorescent probe, is substituted for a leucine, are studied. The peptides in water are mainly in an unordered conformation (~90%), and undergo a two state reversible transition upon heating, leading to a partially helical conformation (cold denaturation). Time resolved fluorescence results show that fluorescence decay for the four Trp containing peptides is best described by triple fluorescence decay kinetics. In TFE/water mixture, peptides adopt a single α-helix conformation but the Leu-Trp9 substitution leads to an effective helix destabilizing effect. In salted media, the peptides are fully helical and present a great tendency to self associate by bringing the hydrophobic faces of helices into close contact. This proceeds in non-cooperative multisteps leading to the formation of α helix aggregates with various degrees of complexation. Using modelling, the relative hydrophobic surface areas accessible to water molecules in n-mer structures are calculated and discussed. Nous avons étudié un peptide amphipathique composé de dix lysine et dix leucine, ainsi que quatre dérivés comportant un résidu tryptophane pour les études par fluorescence. Dans l'eau, les peptides ne sont pas structurés (~90%), et se structurent partiellement en hélice α par chauffage (dénaturation froide). Les mesures de déclin de fluorescence font apparaître une cinétique à trois temps de vie. Dans un mélange eau/TFE, les peptides adoptent une conformation en hélice α, mais la substitution Leu-Trp9 possède un effet déstabilisant. En mileu salin, les peptides sont totalement hélicoïdaux et ont tendance à s'agréger de façon à regrouper leur face hydrophobe. Ce processus se fait en plusieurs étapes avec des agrégats de taille variable. L'existence de tels agrégats est discutée sur la base de la modélisation mol

  2. Synthesis, crystal structure analysis, spectral investigations, DFT computations and molecular dynamics and docking study of 4-benzyl-5-oxomorpholine-3-carbamide, a potential bioactive agent

    NASA Astrophysics Data System (ADS)

    Murthy, P. Krishna; Sheena Mary, Y.; Shyma Mary, Y.; Panicker, C. Yohannan; Suneetha, V.; Armaković, Stevan; Armaković, Sanja J.; Van Alsenoy, C.; Suchetan, P. A.

    2017-04-01

    4-benzyl-5-oxomorpholine-3-carbamide has been synthesized; single crystals were grown by slow evaporation solution growth technique at room temperature and characterized by single crystal X-ray diffraction, FT-IR, FT-Raman and 1H-NMR. The compound crystallizes in the monoclinic space group P21/n. The molecular geometry of the compound was optimized by using Density Functional Theory (DFT/B3LYP) method with 6-311++G(d,p) basis set in the ground state and geometric parameters are in agreement with the X-ray analysis results of the structure. The experimental vibrational spectra were compared with the calculated spectra and each vibrational wave number was assigned on the basis of potential energy distribution (PED). The electronic and charge transfer properties have been explained on the basis of highest occupied molecular orbital's (HOMOs) and lowest unoccupied molecular orbital's (LUMOs). Besides molecular electrostatic potential (MEP), frontier molecular orbital's (FMOs), some global reactivity descriptors, thermodynamic properties, non-linear optical (NLO) behavior and Mullikan charge analysis of the title compound were computed with the same method in gas phase, theoretically. Potential reactive sites of the title compound have been identified by average local ionization energy and Fukui functions, both mapped to the electron density surface. Bond dissociation energies for all single acyclic bonds have been calculated in order to investigate autoxidation and degradation properties of the title compound. Atoms with pronounced interactions with water molecules have been detected by calculations of radial distribution functions after molecular dynamics simulations. The experimental results are compared with the theoretical calculations using DFT methods for the fortification of the paper. Further the docking studies revealed that the title compound as a docked ligand forms a stable complex with pyrrole inhibitor with a binding affinity value of -7.5 kcal/mol. This

  3. Spectroscopic and molecular structure investigation of the phosphorus-containing G‧2 dendrimer with terminal aldehyde groups using DFT method

    NASA Astrophysics Data System (ADS)

    Furer, V. L.; Vandyukov, A. E.; Majoral, J. P.; Caminade, A. M.; Kovalenko, V. I.

    2015-02-01

    The FTIR and FT Raman spectra of the second generation dendrimer G‧2 built from thiophosphoryl core with terminal aldehyde groups have been recorded. The structural optimization and normal mode analysis were performed for model compound C, consisting of thiophosphoryl core, one branch with three repeated units, and four 4-oxybenzaldehyde terminal groups on the basis of the density functional theory (DFT) at the PBE/TZ2P level. The vibrational frequencies, infrared and Raman intensities for the t,g,g- and t,-g,g-conformers of the terminal groups were calculated. The t,g,g-conformer is 2.0 kcal/mol less stable compared to t,-g,g-conformer. A reliable assignment of the fundamental bands observed in the experimental IR and Raman spectra of dendrimer was achieved. For the low generations (G‧1 to G‧3) the disk form of studied dendrimer molecules is the most probable. For higher generations, the shape of dendrimer molecules will be that of a cauliflower.

  4. Probing the molecular and electronic structure of norhipposudoric and hipposudoric acids from the red sweat of Hippopotamus amphibius: a DFT investigation.

    PubMed

    Galasso, Vinicio; Pichierri, Fabio

    2009-03-19

    Molecular structure and tautomeric/conformational preferences of norhipposudoric and hipposudoric acids, the recently isolated pigments of the Hippopotamus amphibius' sweat, were investigated using the density functional theory (DFT) PBE0 formalism. Among a large variety of possible structures, two similar keto-enol tautomer/conformers are nearly isoenergetic and markedly more stable than the others both in the gas phase and aqueous solution. The bulk solvent effect was accounted for with the polarizable continuum model (PCM). A distinctive structural feature is the strong intramolecular hydrogen bonding in the keto-enol O-H...O bridge, as shown by analysis of the atoms-in-molecules topological properties of the electron density. To elucidate the claimed strong acidity of these pigments, the site-specific microscopic dissociation constants were also calculated using the cluster-continuum model, a hybrid approach based on inclusion of explicit solvent molecules and solvation of the cluster by the dielectric continuum. Notably, the first deprotonation should occur predominantly from the enolic group with a remarkably low pk(i) value. This factor could play an important role in the potent antibiotic activity of the pigments. The absorption spectra of the undissociated and dissociated compounds in aqueous solution were interpreted with time-dependent DFT/PCM calculations. The pi-pi* diquinoid excitations, mainly occurring in the fluorenoid nucleus, are the major contributors to the color and strong absorption bands in the UVA and UVB regions, which are closely related to the efficient sunscreen activity exerted by the pigments.

  5. Structural changes of humic acids from sinking organic matter and surface sediments investigated by advanced solid-state NMR: Insights into sources, preservation and molecularly uncharacterized components

    NASA Astrophysics Data System (ADS)

    Mao, Jingdong; Tremblay, Luc; Gagné, Jean-Pierre

    2011-12-01

    Knowledge of the structural changes that particulate organic matter (POM) undergoes in natural systems is essential for determining its reactivity and fate. In the present study, we used advanced solid-state NMR techniques to investigate the chemical structures of sinking particulate matter collected at different depths as well as humic acids (HAs) extracted from these samples and underlying sediments from the Saguenay Fjord and the St. Lawrence Lower Estuary (Canada). Compared to bulk POM, HAs contain more non-polar alkyls, aromatics, and aromatic C-O, but less carbohydrates (or carbohydrate-like structures). In the two locations studied, the C and N contents of the samples (POM and HAs) decreased with depth and after deposition onto sediments, leaving N-poor but O-enriched HAs and suggesting the involvement of partial oxidation reactions during POM microbial degradation. Advanced NMR techniques revealed that, compared to the water-column HAs, sedimentary HAs contained more protonated aromatics, non-protonated aromatics, aromatic C-O, carbohydrates (excluding anomerics), anomerics, OC q, O-C q-O, OCH, and OCH 3 groups, but less non-polar alkyls, NCH, and mobile CH 2 groups. These results are consistent with the relatively high reactivity of lipids and proteins or peptides. In contrast, carbohydrate-like structures were selectively preserved and appeared to be involved in substitution and copolymerization reactions. Some of these trends support the selective degradation (or selective preservation) theory. The results provide insights into mechanisms that likely contribute to the preservation of POM and the formation of molecules that escape characterization by traditional methods. Despite the depletion of non-polar alkyls with depth in HAs, a significant portion of their general structure survived and can be assigned to a model phospholipid. In addition, little changes in the connectivities of different functional groups were observed. Substituted and copolymerized

  6. Dynamic molecular graphs: "hopping" structures.

    PubMed

    Cortés-Guzmán, Fernando; Rocha-Rinza, Tomas; Guevara-Vela, José Manuel; Cuevas, Gabriel; Gómez, Rosa María

    2014-05-05

    This work aims to contribute to the discussion about the suitability of bond paths and bond-critical points as indicators of chemical bonding defined within the theoretical framework of the quantum theory of atoms in molecules. For this purpose, we consider the temporal evolution of the molecular structure of [Fe{C(CH2 )3 }(CO)3 ] throughout Born-Oppenheimer molecular dynamics (BOMD), which illustrates the changing behaviour of the molecular graph (MG) of an electronic system. Several MGs with significant lifespans are observed across the BOMD simulations. The bond paths between the trimethylenemethane and the metallic core are uninterruptedly formed and broken. This situation is reminiscent of a "hopping" ligand over the iron atom. The molecular graph wherein the bonding between trimethylenemethane and the iron atom takes place only by means of the tertiary carbon atom has the longest lifespan of all the considered structures, which is consistent with the MG found by X-ray diffraction experiments and quantum chemical calculations. In contrast, the η(4) complex predicted by molecular-orbital theory has an extremely brief lifetime. The lifespan of different molecular structures is related to bond descriptors on the basis of the topology of the electron density such as the ellipticities at the FeCH2 bond-critical points and electron delocalisation indices. This work also proposes the concept of a dynamic molecular graph composed of the different structures found throughout the BOMD trajectories in analogy to a resonance hybrid of Lewis structures. It is our hope that the notion of dynamic molecular graphs will prove useful in the discussion of electronic systems, in particular for those in which analysis on the basis of static structures leads to controversial conclusions.

  7. Structural investigation of nanocrystalline graphene grown on (6√3 × 6√3)R30°-reconstructed SiC surfaces by molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Schumann, T.; Dubslaff, M.; Oliveira, M. H., Jr.; Hanke, M.; Fromm, F.; Seyller, T.; Nemec, L.; Blum, V.; Scheffler, M.; Lopes, J. M. J.; Riechert, H.

    2013-12-01

    Growth of nanocrystalline graphene films on (6√3 × 6√3)R30°-reconstructed SiC surfaces was achieved by molecular beam epitaxy, enabling the investigation of quasi-homoepitaxial growth. The structural quality of the graphene films, which is investigated by Raman spectroscopy, increases with growth time. X-ray photoelectron spectroscopy proves that the SiC surface reconstruction persists throughout the growth process and that the synthesized films consist of sp2-bonded carbon. Interestingly, grazing incidence x-ray diffraction measurements show that the graphene domains possess one single in-plane orientation, are aligned to the substrate, and offer a noticeably contracted lattice parameter of 2.450 Å. We correlate this contraction with theoretically calculated reference values (all-electron density functional calculations based on the van der Waals corrected Perdew-Burke-Ernzerhof functional) for the lattice parameter contraction induced in ideal, free-standing graphene sheets by: substrate-induced buckling, the edges of limited-size flakes and typical point defects (monovacancies, divacancies, Stone-Wales defects).

  8. A molecular dynamics investigation of the structural and dynamic properties of the ionic liquid 1-n-butyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide.

    PubMed

    Liu, Hongjun; Maginn, Edward

    2011-09-28

    Molecular dynamics simulations have been performed to investigate the structure and dynamics of the ionic liquid, 1-n-butyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide ([C(4)mim][Tf(2)N]) in the temperature range of 283-460 K. Extensive analysis was carried out to characterize a number of structural and dynamic features. Transport properties were computed using a variety of equilibrium methods that employed the Green-Kubo and Einstein formulations. Nonequilibrium techniques were also used. In general, different methods mostly yielded consistent results, although some differences were observed. Computed self-diffusivities and ionic conductivities tended to be slightly lower than experimental values, while computed viscosities were significantly higher than experiment. Computed thermal conductivities agreed reasonably well with experimental data. Despite these discrepancies, the simulations capture the experimental temperature-dependent trends for all these transport properties. Single ion dynamics were studied by examining diffusional anisotropy, the self-part of the van Hove function, non-Gaussian parameters, and incoherent intermediate scattering functions. It is found that cations diffuse faster than anions and are more dynamically heterogeneous. A clear anisotropy is revealed in cation displacement, with the motion normal to the imidazolium ring plane being the most hindered and the motion along the alkyl chain in the plane of the ring being the most facile. Cations structurally relax faster than anions but they rotationally relax slower than anions. There is a pronounced temperature dependence to the rotational anisotropy of the cations, but only a weak temperature dependence for the anions. The ionic conductivity deviates from the Nernst-Einstein relation due to the correlated motion of cations and anions. The results suggest that the dynamical behavior of this and related ionic liquids is extremely complex and consists of many different modes with

  9. A molecular dynamics investigation of the structural and dynamic properties of the ionic liquid 1-n-butyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide

    NASA Astrophysics Data System (ADS)

    Liu, Hongjun; Maginn, Edward

    2011-09-01

    Molecular dynamics simulations have been performed to investigate the structure and dynamics of the ionic liquid, 1-n-butyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide ([C4mim][Tf2N]) in the temperature range of 283-460 K. Extensive analysis was carried out to characterize a number of structural and dynamic features. Transport properties were computed using a variety of equilibrium methods that employed the Green-Kubo and Einstein formulations. Nonequilibrium techniques were also used. In general, different methods mostly yielded consistent results, although some differences were observed. Computed self-diffusivities and ionic conductivities tended to be slightly lower than experimental values, while computed viscosities were significantly higher than experiment. Computed thermal conductivities agreed reasonably well with experimental data. Despite these discrepancies, the simulations capture the experimental temperature-dependent trends for all these transport properties. Single ion dynamics were studied by examining diffusional anisotropy, the self-part of the van Hove function, non-Gaussian parameters, and incoherent intermediate scattering functions. It is found that cations diffuse faster than anions and are more dynamically heterogeneous. A clear anisotropy is revealed in cation displacement, with the motion normal to the imidazolium ring plane being the most hindered and the motion along the alkyl chain in the plane of the ring being the most facile. Cations structurally relax faster than anions but they rotationally relax slower than anions. There is a pronounced temperature dependence to the rotational anisotropy of the cations, but only a weak temperature dependence for the anions. The ionic conductivity deviates from the Nernst-Einstein relation due to the correlated motion of cations and anions. The results suggest that the dynamical behavior of this and related ionic liquids is extremely complex and consists of many different modes with

  10. Investigation of the retention behavior of structurally diverse drugs on alpha(1) acid glycoprotein column: insight on the molecular factors involved and correlation with protein binding data.

    PubMed

    Chrysanthakopoulos, Marios; Vallianatou, Theodosia; Giaginis, Costas; Tsantili-Kakoulidou, Anna

    2014-08-18

    Retention of 49 structurally diverse drugs on alpha1 acid glycoprotein column was investigated under different chromatographic conditions. Acetonitrile and 2-propanol were used as organic modifiers at different percentages and the pH was adjusted at 7.0 using PBS. Analysis of extrapolated and isocratic retention in terms of lipophilicity and electrostatic interactions revealed significant effect of the nature and percentage of organic modifier, which was attributed to the different shielding degree of the charged sites on the stationary phase by the buffer constituents. AGP retention factors were compared to HSA retention factors analyzed previously. Application of LSER analysis, extended to incorporate fractions ionized, demonstrated hydrogen bond acidity, dipolarity/polarizability and excess molar refraction as the most significant parameters for all AGP chromatographic indices, elucidating the differentiation of AGP retention from octanol-water partitioning and HSA retention. An attempt to correlate AGP chromatographic indices to AGP association constants, available in literature, supported the importance of stationary shielding in retention mechanism. Thus, isocratic retention factors logk10(ACN)(AGP) show a moderate but still better performance than lipophilicity in the case of A variant and may be a useful tool for the estimation of relevant association constants. For F1/S binding simulation lower stationary phase shielding is needed to obtain a significant two term regression equation, where logk20(ACN)(AGP) exerts a secondary contribution next to the most important bulk effect expressed by molecular weight.

  11. A combination of hand-held models and computer imaging programs helps students answer oral questions about molecular structure and function: a controlled investigation of student learning.

    PubMed

    Harris, Michelle A; Peck, Ronald F; Colton, Shannon; Morris, Jennifer; Chaibub Neto, Elias; Kallio, Julie

    2009-01-01

    We conducted a controlled investigation to examine whether a combination of computer imagery and tactile tools helps introductory cell biology laboratory undergraduate students better learn about protein structure/function relationships as compared with computer imagery alone. In all five laboratory sections, students used the molecular imaging program, Protein Explorer (PE). In the three experimental sections, three-dimensional physical models were made available to the students, in addition to PE. Student learning was assessed via oral and written research summaries and videotaped interviews. Differences between the experimental and control group students were not found in our typical course assessments such as research papers, but rather were revealed during one-on-one interviews with students at the end of the semester. A subset of students in the experimental group produced superior answers to some higher-order interview questions as compared with students in the control group. During the interview, students in both groups preferred to use either the hand-held models alone or in combination with the PE imaging program. Students typically did not use any tools when answering knowledge (lower-level thinking) questions, but when challenged with higher-level thinking questions, students in both the control and experimental groups elected to use the models.

  12. Students' Understanding of Molecular Structure Representations

    ERIC Educational Resources Information Center

    Ferk, Vesna; Vrtacnik, Margareta; Blejec, Andrej; Gril, Alenka

    2003-01-01

    The purpose of the investigation was to determine the meanings attached by students to the different kinds of molecular structure representations used in chemistry teaching. The students (n = 124) were from primary (aged 13-14 years) and secondary (aged 17-18 years) schools and a university (aged 21-25 years). A computerised "Chemical…

  13. Trigonal Mn3 and Co3 clusters supported by weak-field ligands: a structural, spectroscopic, magnetic, and computational investigation into the correlation of molecular and electronic structure.

    PubMed

    Fout, Alison R; Xiao, Dianne J; Zhao, Qinliang; Harris, T David; King, Evan R; Eames, Emily V; Zheng, Shao-Liang; Betley, Theodore A

    2012-10-01

    Transamination of divalent transition metal starting materials (M(2)(N(SiMe(3))(2))(4), M = Mn, Co) with hexadentate ligand platforms (R)LH(6) ((R)LH(6) = MeC(CH(2)NPh-o-NR)(3) where R = H, Ph, Mes (Mes = Mesityl)) or (H,Cy)LH(6) = 1,3,5-C(6)H(9)(NHPh-o-NH(2))(3) with added pyridine or tertiary phosphine coligands afforded trinuclear complexes of the type ((R)L)Mn(3)(py)(3) and ((R)L)Co(3)(PMe(2)R')(3) (R' = Me, Ph). While the sterically less encumbered ligand varieties, (H)L or (Ph)L, give rise to local square-pyramidal geometries at each of the bound metal atoms, with four anilides forming an equatorial plane and an exogenous pyridine or phosphine in the apical site, the mesityl-substituted ligand ((Mes)L) engenders local tetrahedral coordination. Both the neutral Mn(3) and Co(3) clusters feature S = (1)/(2) ground states, as determined by direct current (dc) magnetometry, (1)H NMR spectroscopy, and low-temperature electron paramagnetic resonance (EPR) spectroscopy. Within the Mn(3) clusters, the long internuclear Mn-Mn separations suggest minimal direct metal-metal orbital overlap. Accordingly, fits to variable-temperature magnetic susceptibility data reveal the presence of weak antiferromagnetic superexchange interactions through the bridging anilide ligands with exchange couplings ranging from J = -16.8 to -42 cm(-1). Conversely, the short Co-Co interatomic distances suggest a significant degree of direct metal-metal orbital overlap, akin to the related Fe(3) clusters. With the Co(3) series, the S = (1)/(2) ground state can be attributed to population of a single molecular orbital manifold that arises from mixing of the metal- and o-phenylenediamide (OPDA) ligand-based frontier orbitals. Chemical oxidation of the neutral Co(3) clusters affords diamagnetic cationic clusters of the type [((R)L)Co(3)(PMe(2)R)(3)](+). Density functional theory (DFT) calculations on the neutral (S = (1)/(2)) and cationic (S = 0) Co(3) clusters reveal that oxidation occurs at an

  14. Pressure-induced structural changes in the network-forming isostatic glass GeSe4: An investigation by neutron diffraction and first-principles molecular dynamics

    NASA Astrophysics Data System (ADS)

    Bouzid, Assil; Pizzey, Keiron J.; Zeidler, Anita; Ori, Guido; Boero, Mauro; Massobrio, Carlo; Klotz, Stefan; Fischer, Henry E.; Bull, Craig L.; Salmon, Philip S.

    2016-01-01

    The changes to the topological and chemical ordering in the network-forming isostatic glass GeSe4 are investigated at pressures up to ˜14.4 GPa by using a combination of neutron diffraction and first-principles molecular dynamics. The results show a network built from corner- and edge-sharing Ge(Se1 /2)4 tetrahedra, where linkages by Se2 dimers or longer Sen chains are prevalent. These linkages confer the network with a local flexibility that helps to retain the network connectivity at pressures up to ˜8 GPa, corresponding to a density increase of ˜37 % . The network reorganization at constant topology maintains a mean coordination number n ¯≃2.4 , the value expected from mean-field constraint-counting theory for a rigid stress-free network. Isostatic networks may therefore remain optimally constrained to avoid stress and retain their favorable glass-forming ability over a large density range. As the pressure is increased to around 13 GPa, corresponding to a density increase of ˜49 % , Ge(Se1 /2)4 tetrahedra remain as the predominant structural motifs, but there is an appearance of 5-fold coordinated Ge atoms and homopolar Ge-Ge bonds that accompany an increase in the fraction of 3-fold coordinated Se atoms. The band gap energy decreases with increasing pressure, and midgap states appear at pressures beyond ˜6.7 GPa. The latter originate from undercoordinated Se atoms that terminate broken Sen chains.

  15. Using Carbon-14 Isotope Tracing to Investigate Molecular Structure Effects of the Oxygenate Dibutyl Maleate on Soot Emissions from a DI Diesel Engine

    SciTech Connect

    Buchholz, B A; Mueller, C J; Upatnieks, A; Martin, G C; Pitz, W J; Westbrook, C K

    2004-01-07

    The effect of oxygenate molecular structure on soot emissions from a DI diesel engine was examined using carbon-14 ({sup 14}C) isotope tracing. Carbon atoms in three distinct chemical structures within the diesel oxygenate dibutyl maleate (DBM) were labeled with {sup 14}C. The {sup 14}C from the labeled DBM was then detected in engine-out particulate matter (PM), in-cylinder deposits, and CO{sub 2} emissions using accelerator mass spectrometry (AMS). The results indicate that molecular structure plays an important role in determining whether a specific carbon atom either does or does not form soot. Chemical-kinetic modeling results indicate that structures that produce CO{sub 2} directly from the fuel are less effective at reducing soot than structures that produce CO before producing CO{sub 2}. Because they can follow individual carbon atoms through a real combustion process, {sup 14}C isotope tracing studies help strengthen the connection between actual engine emissions and chemical-kinetic models of combustion and soot formation/oxidation processes.

  16. Techniques for Investigating Molecular Toxicology of Nanomaterials.

    PubMed

    Wang, Yanli; Li, Chenchen; Yao, Chenjie; Ding, Lin; Lei, Zhendong; Wu, Minghong

    2016-06-01

    Nanotechnology has been a rapidly developing field in the past few decades, resulting in the more and more exposure of nanomaterials to human. The increased applications of nanomaterials for industrial, commercial and life purposes, such as fillers, catalysts, semiconductors, paints, cosmetic additives and drug carriers, have caused both obvious and potential impacts on human health and environment. Nanotoxicology is used to study the safety of nanomaterials and has grown at the historic moment. Molecular toxicology is a new subdiscipline to study the interactions and impacts of materials at the molecular level. To better understand the relationship between the molecular toxicology and nanomaterials, this review summarizes the typical techniques and methods in molecular toxicology which are applied when investigating the toxicology of nanomaterials and include six categories: namely; genetic mutation detection, gene expression analysis, DNA damage detection, chromosomal aberration analysis, proteomics, and metabolomics. Each category involves several experimental techniques and methods.

  17. Electronic structure investigation of biphenylene films

    NASA Astrophysics Data System (ADS)

    Totani, R.; Grazioli, C.; Zhang, T.; Bidermane, I.; Lüder, J.; de Simone, M.; Coreno, M.; Brena, B.; Lozzi, L.; Puglia, C.

    2017-02-01

    Photoelectron Spectroscopy (PS) and Near-Edge X-ray Absorption Fine Structure (NEXAFS) spectroscopy have been used to investigate the occupied and empty density of states of biphenylene films of different thicknesses, deposited onto a Cu(111) crystal. The obtained results have been compared to previous gas phase spectra and single molecule Density Functional Theory (DFT) calculations to get insights into the possible modification of the molecular electronic structure in the film induced by the adsorption on a surface. Furthermore, NEXAFS measurements allowed characterizing the variation of the molecular arrangement with the film thickness and helped to clarify the substrate-molecule interaction.

  18. 2004 Reversible Associations in Structure & Molecular Biology

    SciTech Connect

    Edward Eisenstein Nancy Ryan Gray

    2005-03-23

    The Gordon Research Conference (GRC) on 2004 Gordon Research Conference on Reversible Associations in Structure & Molecular Biology was held at Four Points Sheraton, CA, 1/25-30/2004. The Conference was well attended with 82 participants (attendees list attached). The attendees represented the spectrum of endeavor in this field coming from academia, industry, and government laboratories, both U.S. and foreign scientists, senior researchers, young investigators, and students.

  19. FT-IR and FT-Raman, NMR and UV spectroscopic investigation and hybrid computational (HF and DFT) analysis on the molecular structure of mesitylene

    NASA Astrophysics Data System (ADS)

    Kose, E.; Atac, A.; Karabacak, M.; Nagabalasubramanian, P. B.; Asiri, A. M.; Periandy, S.

    2013-12-01

    The spectroscopic properties of mesitylene were investigated by FT-IR, FT-Raman, UV, 1H and 13C NMR techniques. The geometrical parameters and energies have been obtained from density functional theory (DFT) B3LYP method and Hartree-Fock (HF) method with 6-311++G(d,p) and 6-311G(d,p) basis sets calculations. The geometry of the molecule was fully optimized, vibrational spectra were calculated and fundamental vibrations were assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method and PQS program. Total and partial density of state (TDOS and PDOS) and also overlap population density of state (OPDOS) diagrams analysis were presented. 13C and 1H NMR chemical shifts were calculated by using the gauge-invariant atomic orbital (GIAO) method. The electronic properties, such as excitation energies, oscillator strength, wavelengths, HOMO and LUMO energies, were performed by time-dependent density functional theory (TD-DFT) results complements with the experimental findings. The results of the calculations were applied to simulate spectra of the title compound, which show excellent agreement with observed spectra. Besides, frontier molecular orbitals (FMO), molecular electrostatic potential (MEP) and thermodynamic properties were performed. Reduced density gradient (RDG) of the mesitylene was also given to investigate interactions of the molecule.

  20. FT-IR and FT-Raman, NMR and UV spectroscopic investigation and hybrid computational (HF and DFT) analysis on the molecular structure of mesitylene.

    PubMed

    Kose, E; Atac, A; Karabacak, M; Nagabalasubramanian, P B; Asiri, A M; Periandy, S

    2013-12-01

    The spectroscopic properties of mesitylene were investigated by FT-IR, FT-Raman, UV, (1)H and (13)C NMR techniques. The geometrical parameters and energies have been obtained from density functional theory (DFT) B3LYP method and Hartree-Fock (HF) method with 6-311++G(d,p) and 6-311G(d,p) basis sets calculations. The geometry of the molecule was fully optimized, vibrational spectra were calculated and fundamental vibrations were assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method and PQS program. Total and partial density of state (TDOS and PDOS) and also overlap population density of state (OPDOS) diagrams analysis were presented. (13)C and (1)H NMR chemical shifts were calculated by using the gauge-invariant atomic orbital (GIAO) method. The electronic properties, such as excitation energies, oscillator strength, wavelengths, HOMO and LUMO energies, were performed by time-dependent density functional theory (TD-DFT) results complements with the experimental findings. The results of the calculations were applied to simulate spectra of the title compound, which show excellent agreement with observed spectra. Besides, frontier molecular orbitals (FMO), molecular electrostatic potential (MEP) and thermodynamic properties were performed. Reduced density gradient (RDG) of the mesitylene was also given to investigate interactions of the molecule.

  1. Molecular dynamics investigations on the effect of D amino acid substitution in a triple-helix structure and the stability of collagen.

    PubMed

    Punitha, V; Raman, S Sundar; Parthasarathi, R; Subramanian, V; Rao, J Raghava; Nair, Balachandran Unni; Ramasami, T

    2009-07-02

    Studies on the structure and stability of peptides and proteins during l-->d configurational change are certainly important for the designing of peptides with new biological activity and protein engineering. The l-->d amino acid (d AA) changes have been observed in aged proteins such as collagen. Hence, in this study, an attempt has been made to explore the effect of the replacement of l amino acid (l AA) in the model collagen-like peptides with d AA and the origin of structural stability (destability) has been traced using the molecular dynamics (MD) method employing the AMBER force field. Our results reveal that the substitution of d AA produces a large local disruption to the triple-helical structure. Formation of a kink (bulge) at the site of substitution is observed from the detailed analysis of MD trajectory. However, this local perturbation of kinked helix changes the direction of the helices and affects the relative orientation of the respective AA residues for helix-helix interaction, enough to affect the overall stability of the model collagen-like peptide. The destabilization energy per d Ala substitution is 7.87 kcal/mol, which is similar to the value for the Gly-->Ala mutation in collagen. Since the Gly-->Ala mutation is involved in genetic disorders such as osteogenesis imperfecta (OI), the l-->d configurational change may produce a similar effect on collagen.

  2. The influence of the substitution pattern on the molecular conformation of ureido-1,2,5-oxadiazoles, related to STAT3 inhibitors: chemical behavior and structural investigation.

    PubMed

    Villa, Stefania; Masciocchi, Daniela; Gelain, Arianna; Meneghetti, Fiorella

    2012-07-01

    Signal transducer and activator of transcription 3 (STAT3) is a protein constitutively activated by aberrant upstream tyrosine kinase activities in a broad spectrum of human solid and blood tumors. Therefore, the availability of drugs affecting STAT3 may have important therapeutic potential for the treatment of cancer. Pursuing our efforts in exploring the influence of the substitution pattern of the ureido 1,2,5-oxadiazole moiety on the molecular conformation, new compounds substituted at positions 3 and 4 on the furazane ring were synthesized. The inhibition properties vs. STAT3 of the novel compounds were evaluated in a dual-luciferase assay, using HCT-116 cells, and the results evidenced a moderate activity only for the compounds endowed with a planar arrangement. Crystallographic studies of the new derivatives were performed in order to evidence the peculiar chemical behavior and to evaluate how structural modulations affected the biological properties.

  3. Laboratory investigation of the contribution of complex aromatic/aliphatic polycyclic hybrid molecular structures to interstellar ultraviolet extinction and infrared emission

    NASA Technical Reports Server (NTRS)

    Arnoult, K. M.; Wdowiak, T. J.; Beegle, L. W.

    2000-01-01

    , provide insight into possible molecular structure details of newly formed hydrocarbon-rich interstellar dust and its transformation into aged material that becomes resident in the interstellar medium. Specifically the presence of naphthalene-like and butadiene-like conjugated structures as chromophores for the 2175 angstroms ultraviolet extinction feature is indicated.

  4. Synthesis, characterization and quantum chemical investigation of molecular structure and vibrational spectra of 2,5-dichloro-3,6-bis-(methylamino)1,4-benzoquinone

    NASA Astrophysics Data System (ADS)

    Gautam, Bhanu Pratap Singh; Srivastava, Mayuri; Prasad, R. L.; Yadav, R. A.

    2014-08-01

    2,5-Dichloro-3,6-bis-methylamino-[1,4]benzoquinone has been synthesized by condensing methyl amine hydrochloride with chloranil in presence of condensing agent sodium acetate. FT-IR (4000-400 cm-1) and FT-Raman (4000-400 cm-1) spectral measurements of dmdb have been done. Ab initio and DFT (B3LYP/6-311+G**) calculations have been performed giving energies, optimized structures, harmonic vibrational frequencies, infrared intensities and Raman activities. The optimized molecular structure of the compound is found to possess C2h point group symmetry. A detailed interpretation of the observed IR and Raman spectra of dmdb is reported on the basis of the calculated potential energy distribution. Stability of the molecule arising from hyper conjugative interactions, charge delocalization has been analyzed using NBO analysis. The HOMO and LUMO energy gap reveals that the energy gap reflects the chemical activity of the molecule. The thermodynamic functions of the title compound have also been computed.

  5. Theoretical investigation of the molecular, electronic structures and vibrational spectra of a series of first transition metal phthalocyanines by Z. Liu et al.

    NASA Astrophysics Data System (ADS)

    Sumimoto, Michinori; Kawashima, Yukio; Hori, Kenzi; Fujimoto, Hitoshi

    2008-11-01

    A recent papar by Lui et al. [Z. Liu, X. Zhang, Y. Zhang, J. Jiang, Spectrochim. Acta A 67 (2007) 1232] reported on the theoretical investigations of the fully optimized geometries and electronic structures of iron (II) phthalocyanine (FePc) with the singlet spin state carried out with the restricted density functional theory (DFT) method, where the B3LYP functional was adopted for the exchange-correlation term; however, the triplet spin state was experimentally reported, and we also obtained the triplet spin state by the unrestricted DFT calculations.

  6. Synthesis, molecular structure, spectral investigation on (E)-1-(4-bromophenyl)-3-(4-(dimethylamino)phenyl)prop-2-en-1-one

    NASA Astrophysics Data System (ADS)

    Asiri, A. M.; Karabacak, M.; Sakthivel, S.; Al-youbi, A. O.; Muthu, S.; Hamed, S. A.; Renuga, S.; Alagesan, T.

    2016-01-01

    In this work, an organic nonlinear optical material (E)-1-(4-bromophenyl)-3-(4-(dimethylamino)phenyl)prop-2-en-1-one (C17H16NOBr) was synthesized by reacting 4-bromoacetophenone and N,N-dimethyl benzaldehyde in ethanol in the presence of sodium hydroxide. FT-IR and FT-Raman spectra were recorded in the region 4000-500 cm-1 and 4000-50 cm-1, respectively. The structural and spectroscopic data of the molecule in the ground state were calculated by using density functional method (B3LYP) with 6-311++G(d,p) basis set. The vibrational frequencies were calculated and compared with the experimental frequencies, which yield good agreement between observed and calculated frequencies. The infrared and Raman spectra were also predicted from the calculated intensities. 1H NMR spectrum was recorded in CDCl3 and 1H NMR chemical shifts of the molecule were calculated using the gauge independent atomic orbital (GIAO) method. UV-visible spectrum of the compound was recorded in water in the range of 200-800 nm and the electronic properties were calculated by time-dependent density functional theory (TD-DFT) approach. Besides, Mulliken atomic charges, molecular electrostatic potential (MEP) were performed. Nonlinear optical features and thermodynamic properties were also outlined theoretically. The geometric parameters, energies, harmonic vibrational frequencies, chemical shifts and absorption wavelengths were compared with the available experimental data of the molecule. Comprehensive theoretical and experimental structural studies on the molecule were carried out by FT-IR, FT-Raman, NMR and UV spectrometry.

  7. Theoretical and experimental investigations on molecular structure of 7-Chloro-9-phenyl-2,3-dihydroacridin-4(1H)-one with cytotoxic studies

    NASA Astrophysics Data System (ADS)

    Satheeshkumar, Rajendran; Shankar, Ramasamy; Kaminsky, Werner; Kalaiselvi, Sivalingam; Padma, Viswanadha Vijaya; Rajendra Prasad, Karnam Jayarampillai

    2016-04-01

    7-Chloro-9-phenyl-2,3-dihydroacridin-4(1H)-one (3) is synthesized from 2-amino-5-chlorobenzophenone (1) and 1,2-cyclohexanedione (2) in the presence of catalyst InCl3. FT-IR, FT-Raman and FT-NMR spectra of molecule 3 have been recorded and the structure was confirmed by single crystal X-ray diffraction. CDCl3 and DMSO-d6 FT-NMR spectra and 1H and 13C NMR chemical shifts have been measured in molecule 3 and calculated at the B3LYP/6-311G (d,p) and MO6-2x/6-311G (d,p) levels of theory. Similarly calculated vibrational frequencies were found in good agreement with experimental findings. The optimized geometry of molecule 3 was compared with experimental XRD values. DFT calculations of the molecular electrostatic potential (MEP) and HOMO - LUMO frontier orbitals identified chemically active sites of molecule 3 responsible for its bioactivity. The title compound, 3 exhibits higher cytotoxicity in Human breast cancer cells (MCF-7) compared to human lung adenocarcinoma cells (A549).

  8. Evaluating Agronomic Performance and Investigating Molecular Structure of Drought and Heat Tolerant Wild Alfalfa (Medicago sativa L.) Collection from the Southeastern Turkey.

    PubMed

    Basbag, Mehmet; Aydin, Ali; Sakiroglu, Muhammet

    2017-02-01

    Drought is a major stress factor for agricultural production including alfalfa production. One way to counterbalance the yield losses is the introgression of drought tolerant germplasm into breeding programs. As an effort to exploit such germplasm, 16 individual plants were selected from the Southeastern Turkey from their natural habitat and clonally propagated in field trials with an ultimate goal to use the germplasm as parents for releasing a synthetic cultivar. Forage yield and forage quality traits were evaluated and molecular genetic diversity among genotypes were determined using inter simple sequence repeat markers. Genotypes showed a variation from growth habit to yield and quality traits indicating sufficient phenotypic variation for diverse breeding efforts (for grazing or harvesting) and long term selection schemes. A large amount of genetic variation was observed even with a limited number of marker and genotypes. However, no pattern of spatial genetic structure was observed for the scale of the study when genetic variation is linked to the geographic origin. We conclude that ex situ natural variation provides a wealth of germplasm that could be incorporated into breeding programs aiming to improve drought tolerance. We also suggest an extensive collection of seeds/plant tissue from unique plants with desirable traits rather than putting more efforts to create a spatial germplasm sampling efforts in narrow regions.

  9. A New Approach for Investigating the Molecular Recognition of Protein: Toward Structure-Based Drug Design Based on the 3D-RISM Theory.

    PubMed

    Kiyota, Yasuomi; Yoshida, Norio; Hirata, Fumio

    2011-11-08

    A new approach to investigate a molecular recognition process of protein is presented based on the three-dimensional reference interaction site model (3D-RISM) theory, a statistical mechanics theory of molecular liquids. Numerical procedure for solving the conventional 3D-RISM equation consists of two steps. In step 1, we solve ordinary RISM (or 1D-RISM) equations for a solvent mixture including target ligands in order to obtain the density pair correlation functions (PCF) among molecules in the solution. Then, we solve the 3D-RISM equation for a solute-solvent system to find three-dimensional density distribution functions (3D-DDF) of solvent species around a protein, using PCF obtained in the first step. A key to the success of the method was to regard a target ligand as one of "solvent" species. However, the success is limited due to a difficulty of solving the 1D-RISM equation for a solvent mixture, including large ligand molecules. In the present paper, we propose a method which eases the limitation concerning solute size in the conventional method. In this approach, we solve a solute-solute 3D-RISM equations for a protein-ligand system in which both proteins and ligands are regarded as "solutes" at infinite dilution. The 3D- and 1D-RISM equations are solved for protein-solvent and ligand-solvent systems, respectively, in order to obtain the 3D- and 1D-DDF of solvent around the solutes, which are required for solving the solute-solute 3D-RISM equation. The method is applied to two practical and noteworthy examples concerning pharmaceutical design. One is an odorant binding protein in the Drosophila melanogaster , which binds an ethanol molecule. The other is phospholipase A2, which is known as a receptor of acetylsalicylic acid or aspirin. The result indicates that the method successfully reproduces the binding mode of the ligand molecules in the binding sites measured by the experiments.

  10. Molecular structure investigation of neutral, dimer and anion forms of 3,4-pyridinedicarboxylic acid: a combined experimental and theoretical study.

    PubMed

    Karabacak, Mehmet; Bilgili, Sibel; Atac, Ahmet

    2015-01-25

    In this study, the structural and vibrational analysis of 3,4-pyridinedicarboxylic acid (3,4-PDCA) are presented using experimental techniques as FT-IR, FT-Raman, NMR, UV and quantum chemical calculations. FT-IR and FT-Raman spectra of 3,4-pyridinedicarboxylic acid in the solid phase are recorded in the region 4000-400 cm(-1) and 4000-50 cm(-1), respectively. The geometrical parameters and energies of all different and possible monomer, dimer, anion(-1) and anion(-2) conformers of 3,4-PDCA are obtained from Density Functional Theory (DFT) with B3LYP/6-311++G(d,p) basis set. There are sixteen conformers (C1C16) for this molecule (neutral form). The most stable conformer of 3,4-PDCA is the C1 conformer. The complete assignments are performed on the basis of the total energy distribution (TED) of the vibrational modes calculated with scaled quantum mechanics (SQM) method. (1)H and (13)C NMR spectra are recorded and the chemical shifts are calculated by using DFT/B3LYP methods with 6-311++G(d,p) basis set. The UV absorption spectrum of the studied compound is recorded in the range of 200-400 nm by dissolved in ethanol. The optimized geometric parameters were compared with experimental data via the X-ray results derived from complexes of this molecule. In addition these, molecular electrostatic potential (MEP), thermodynamic and electronic properties, HOMO-LUMO energies and Mulliken atomic charges, are performed.

  11. Molecular structure investigation of neutral, dimer and anion forms of 3,4-pyridinedicarboxylic acid: A combined experimental and theoretical study

    NASA Astrophysics Data System (ADS)

    Karabacak, Mehmet; Bilgili, Sibel; Atac, Ahmet

    2015-01-01

    In this study, the structural and vibrational analysis of 3,4-pyridinedicarboxylic acid (3,4-PDCA) are presented using experimental techniques as FT-IR, FT-Raman, NMR, UV and quantum chemical calculations. FT-IR and FT-Raman spectra of 3,4-pyridinedicarboxylic acid in the solid phase are recorded in the region 4000-400 cm-1 and 4000-50 cm-1, respectively. The geometrical parameters and energies of all different and possible monomer, dimer, anion-1 and anion-2 conformers of 3,4-PDCA are obtained from Density Functional Theory (DFT) with B3LYP/6-311++G(d,p) basis set. There are sixteen conformers (C1sbnd C16) for this molecule (neutral form). The most stable conformer of 3,4-PDCA is the C1 conformer. The complete assignments are performed on the basis of the total energy distribution (TED) of the vibrational modes calculated with scaled quantum mechanics (SQM) method. 1H and 13C NMR spectra are recorded and the chemical shifts are calculated by using DFT/B3LYP methods with 6-311++G(d,p) basis set. The UV absorption spectrum of the studied compound is recorded in the range of 200-400 nm by dissolved in ethanol. The optimized geometric parameters were compared with experimental data via the X-ray results derived from complexes of this molecule. In addition these, molecular electrostatic potential (MEP), thermodynamic and electronic properties, HOMO-LUMO energies and Mulliken atomic charges, are performed.

  12. Experimental and theoretical investigation of the molecular structure, conformational stability, hyperpolarizability, electrostatic potential, thermodynamic properties and NMR spectra of pharmaceutical important molecule: 4‧-Methylpropiophenone

    NASA Astrophysics Data System (ADS)

    Karunakaran, V.; Balachandran, V.

    2014-07-01

    Combined experimental and theoretical studies have been performed on the structure and vibrational spectra (IR and Raman spectra) of 4‧-methylpropiophenone (MPP). The FT-IR and FT-Raman spectra of 4‧-methylpropiophenone (MPP) have been recorded in the region 4000-400 cm-1 and 3500-100 cm-1, respectively. The harmonic vibrational frequencies were calculated and the scaled values have been compared with experimental FT-IR and FT-Raman spectra. A detailed interpretation of the infrared and Raman spectra of MPP are also reported based on total energy distribution (TED). The observed and the calculated frequencies are found to be in good agreement. The 1H and 13C NMR chemical shifts have been calculated by Gauge-Independent Atomic Orbital (GIAO) method with B3LYP/6-311++G(d,p). The natural bond orbital (NBO), natural hybrid orbital (NHO) analysis and electronic properties, such as HOMO and LUMO energies, were performed by DFT approach. The calculated HOMO and LUMO energies show that charge transfer occurs within molecule. The first order hyperpolarizability (β0) of the novel molecular system and related properties (βtot, α0 and Δα) of MPP are calculated using DFT/6-311++G(d,p) method on the finite-field approach. The Mulliken charges, the values of electric dipole moment (μ) of the molecule were computed using DFT calculations. The thermodynamic functions of the title compound were also performed at the above method and basis set.

  13. Development of molecular markers and preliminary investigation of the population structure and mating system in one lineage of black morel (Morchella elata) in the Pacific Northwestern USA.

    PubMed

    Pagliaccia, Deborah; Douhan, Greg W; Douhan, LeAnn; Peever, Tobin L; Carris, Lori M; Kerrigan, Julia L

    2011-01-01

    Phylogenetic analysis of LSU/ITS sequence data revealed two distinct lineages among 44 morphologically similar fruiting bodies of natural black morels (Morchella elata group) sampled at three non-burn locations in the St Joe and Kanisku National Forests in northern Idaho. Most of the sampled isolates (n = 34) represented a dominant LSU/ITS haplotype present at all three sites and identical to the Mel-12 phylogenetic lineage (GU551425) identified in a previous study. Variation at 1-3 nucleotide sites was detected among a small number of isolates (n = 6) within this well supported clade (94%). Four isolates sampled from a single location were in a well supported clade (97%) distinct from the dominant haplotypes and may represent a previously un-sampled, cryptic phylogenetic species. Species-specific SNP and SCAR markers were developed for Mel-12 lineage isolates by cloning and sequencing AFLP amplicons, and segregation of AFLP markers were studied from single ascospore isolates from individual fruiting bodies. Based on the segregation of AFLP markers within single fruiting bodies, split decomposition analyses of two SCAR markers, and population genetic analyses of SNP, SCAR, and AFLP markers, it appears that members of the Morchella sp. Mel-12 phylogenetic lineage are heterothallic and outcross in nature similar to yellow morels. This is the first set of locus-specific molecular markers that has been developed for any Morchella species, to our knowledge. These markers will prove to be valuable tools to study mating system, gene flow and genetic structure of black morels at various spatial scales with field-collected fruiting bodies and eliminate the need to culture samples in vitro.

  14. A high-resolution near-edge x-ray absorption fine structure investigation of the molecular orientation in the pentacene/poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) pentacene/system.

    PubMed

    Casu, M B; Cosseddu, P; Batchelor, D; Bonfiglio, A; Umbach, E

    2008-01-07

    We present x-ray photoemission spectroscopy and highly resolved near-edge x-ray absorption fine structure spectroscopy measurements taken on pentacene thin films of different thicknesses deposited on a spin coated poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) substrate. Thin films of pentacene were prepared by using organic molecular beam deposition in situ using strictly controlled evaporation conditions. Our investigations show that pentacene thin films on PEDOT:PSS are characterized by upright standing molecules. Due to the strong dichroic behavior, the calculated values of the molecular orientation give a clear indication not only of the real molecular arrangement in the films but also of a high orientational order. This high degree of molecular orientation order is a characteristic already of the first layer. The films show the tendency to grow on the PEDOT:PSS substrate following an island-fashion mode, with a relatively narrow intermixing zone at the interface between the pentacene and the polymer blend. The peculiarity of the growth of pentacene on PEDOT:PSS is due to the fact that the substrate does not offer any template for the nucleated films and thus exerts a lateral order toward the crystal structure arrangement. Under these conditions, the upright orientation of the molecules in the films minimizes the energy required for the system stability.

  15. Preparation and structure investigation of novel Schiff bases using spectroscopic, thermal analyses and molecular orbital calculations and studying their biological activities.

    PubMed

    Zayed, Ehab M; Zayed, M A; El-Desawy, M

    2015-01-05

    Two novel Schiff's bases (EB1 and L1) as new macrocyclic compounds were prepared via condensation reactions between bisaldehyde (2,2'-(ethane-1,2-diylbis(oxy))dibenzaldehyde): firstly with hydrazine carbothioamide to give (EB1), secondly with 4,6-diaminopyrimidine-2-thiol to give (L1). EB1 has a general formula C₁₈H₂₀N₆O₂S₂ of mole mass=416.520, and IUPAC name ((N,N'Z,N,N'E)-N,N'-(((ethane1,2diylbis(oxy))bis(2,1phenylene))bis(methanylylidene))bis(1hydrazinylmethanethioamide). L1 has a general formula C₂₀H₁₆N₄O₂S of mole mass=376.10; and IUPAC name 1,2-bis(2-vinylphenoxy)ethane4,6-diaminopyrimidine-2-thiol). The structures of the compounds obtained were characterized based on elemental analysis, FT-IR and (1)H NMR spectra, mass, and thermogravimetric analysis (TG, DTG). The activation thermodynamic parameters, such as, ΔE(*), ΔH(*), ΔS(*) and ΔG(*) were calculated from the TG curves using Coats-Redfern method. It is important to investigate their structures to know the active groups and weak bond responsible for their biological activities. The obtained thermal (TA) and mass (MS) practical results are confirmed by semi-empirical MO-calculation using PM3 procedure, on the neutral and positively charged forms of these novel Schiff bases. Therefore, comparison between MS and TA helps in selection of the proper pathway representing the decomposition of these compounds to give indication about their structures and consequently their biological activities. Their biological activities have been tested in vitro against Escherichia coli, Proteus vulgaris, Bacillissubtilies and Staphylococcus aurous bacteria in order to assess their antimicrobial potential.

  16. Preparation and structure investigation of novel Schiff bases using spectroscopic, thermal analyses and molecular orbital calculations and studying their biological activities

    NASA Astrophysics Data System (ADS)

    Zayed, Ehab M.; Zayed, M. A.; El-Desawy, M.

    2015-01-01

    Two novel Schiff's bases (EB1 and L1) as new macrocyclic compounds were prepared via condensation reactions between bisaldehyde (2,2‧-(ethane-1,2-diylbis(oxy))dibenzaldehyde): firstly with hydrazine carbothioamide to give (EB1), secondly with 4,6-diaminopyrimidine-2-thiol to give (L1). EB1 has a general formula C18H20N6O2S2 of mole mass = 416.520, and IUPAC name ((N,N‧Z,N,N‧E)-N,N‧-(((ethane1,2diylbis(oxy))bis(2,1phenylene))bis(methanylylidene))bis(1hydrazinylmethanethioamide). L1 has a general formula C20H16N4O2S of mole mass = 376.10; and IUPAC name 1,2-bis(2-vinylphenoxy)ethane4,6-diaminopyrimidine-2-thiol). The structures of the compounds obtained were characterized based on elemental analysis, FT-IR and 1H NMR spectra, mass, and thermogravimetric analysis (TG, DTG). The activation thermodynamic parameters, such as, ΔE*, ΔH*, ΔS* and ΔG* were calculated from the TG curves using Coats-Redfern method. It is important to investigate their structures to know the active groups and weak bond responsible for their biological activities. The obtained thermal (TA) and mass (MS) practical results are confirmed by semi-empirical MO-calculation using PM3 procedure, on the neutral and positively charged forms of these novel Schiff bases. Therefore, comparison between MS and TA helps in selection of the proper pathway representing the decomposition of these compounds to give indication about their structures and consequently their biological activities. Their biological activities have been tested in vitro against Escherichia coli, Proteus vulgaris, Bacillissubtilies and Staphylococcus aurous bacteria in order to assess their antimicrobial potential.

  17. Investigation of glassy state molecular motions in thermoset polymers

    NASA Astrophysics Data System (ADS)

    Tu, Jianwei

    This dissertation presents the investigation of the glassy state molecular motions in isomeric thermoset epoxies by means of solid-state deuterium (2H) NMR spectroscopy technique. The network structure of crosslinked epoxies was altered through monomer isomerism; specifically, diglycidyl ether of bisphenol A (DGEBA) was cured with isomeric amine curatives, i.e., the meta-substituted diaminodiphenylsulfone (33DDS) and para-substituted diaminodiphenylsulfone (44DDS). The use of structural isomerism provided a path way for altering macroscopic material properties while maintaining identical chemical composition within the crosslinked networks. The effects of structural isomerism on the glassy state molecular motions were studied using solid-state 2H NMR spectroscopy, which offers unrivaled power to monitor site-specific molecular motions. Three distinctive molecular groups on each isomeric network, i.e., the phenylene rings in the bisphenol A structure (BPA), the phenylene rings in the diaminodiphenylsulfone structure (DDS), and the hydroxypropoyl ether group (HPE) have been selectively deuterated for a comprehensive study of the structure-dynamics- property relationships in thermoset epoxies. Quadrupolar echo experiments and line shape simulations were employed as the main research approach to gain both qualitative and quantitative motional information of the epoxy networks in the glassy state. Quantitative information on the geometry and rate of the molecular motions allows the elucidation of the relationship between molecular motions and macro physical properties and the role of these motions in the mechanical relaxation. Specifically, it is revealed that both the BPA and HPE moieties in the isomeric networks have almost identical behaviors in the deep glassy state, which indicates that the molecular motions in the glassy state are localized, and the correlation length of the motions does not exceed the length of the DGEBA repeat unit. BPA ring motions contribute

  18. Molecular structure investigation of organic cocrystals of 1,10-phenanthroline-5,6-dione with aryloxyacetic acid: a combined experimental and theoretical study.

    PubMed

    Suresh Kumar, G S; Muthu Prabhu, A Antony; Bhuvanesh, N; Ronica, X A V; Kumaresan, S

    2014-11-11

    Two organic cocrystals namely, 1,10-phenanthroline-5,6-dione:2-naphthoxyacetic acid [(phendione)(2-naa)] (1) and 1,10-phenanthroline-5,6-dione:2-formylphenoxyacetic acid [(phendione)(2-fpaa)] (2) were synthesized and studied by single crystal XRD, FT-IR, NMR, thermogravimetric, and powder X-ray diffraction analysis. The molecular properties of cocrystals were studied using density functional theory (DFT), basis set B3LYP/6-31G(d,p). Both cocrystals are stabilized through intermolecular hydrogen bonding (OH⋯N). The total electron density and molecular electrostatic potential surfaces of the cocrystals were constructed by NBO analysis using B3LYP/6-31G(d,p) method to display the electrostatic potential (electron+nuclei) distribution. The energy gap between HOMO and LUMO was measured for both cocrystals.

  19. Molecular structure investigation of organic cocrystals of 1,10-phenanthroline-5,6-dione with aryloxyacetic acid: A combined experimental and theoretical study

    NASA Astrophysics Data System (ADS)

    Suresh Kumar, G. S.; Antony Muthu Prabhu, A.; Bhuvanesh, N.; Ronica, X. A. V.; Kumaresan, S.

    2014-11-01

    Two organic cocrystals namely, 1,10-phenanthroline-5,6-dione:2-naphthoxyacetic acid [(phendione)(2-naa)] (1) and 1,10-phenanthroline-5,6-dione:2-formylphenoxyacetic acid [(phendione)(2-fpaa)] (2) were synthesized and studied by single crystal XRD, FT-IR, NMR, thermogravimetric, and powder X-ray diffraction analysis. The molecular properties of cocrystals were studied using density functional theory (DFT), basis set B3LYP/6-31G(d,p). Both cocrystals are stabilized through intermolecular hydrogen bonding (Osbnd H⋯N). The total electron density and molecular electrostatic potential surfaces of the cocrystals were constructed by NBO analysis using B3LYP/6-31G(d,p) method to display the electrostatic potential (electron + nuclei) distribution. The energy gap between HOMO and LUMO was measured for both cocrystals.

  20. Algorithmic dimensionality reduction for molecular structure analysis.

    PubMed

    Brown, W Michael; Martin, Shawn; Pollock, Sara N; Coutsias, Evangelos A; Watson, Jean-Paul

    2008-08-14

    Dimensionality reduction approaches have been used to exploit the redundancy in a Cartesian coordinate representation of molecular motion by producing low-dimensional representations of molecular motion. This has been used to help visualize complex energy landscapes, to extend the time scales of simulation, and to improve the efficiency of optimization. Until recently, linear approaches for dimensionality reduction have been employed. Here, we investigate the efficacy of several automated algorithms for nonlinear dimensionality reduction for representation of trans, trans-1,2,4-trifluorocyclo-octane conformation--a molecule whose structure can be described on a 2-manifold in a Cartesian coordinate phase space. We describe an efficient approach for a deterministic enumeration of ring conformations. We demonstrate a drastic improvement in dimensionality reduction with the use of nonlinear methods. We discuss the use of dimensionality reduction algorithms for estimating intrinsic dimensionality and the relationship to the Whitney embedding theorem. Additionally, we investigate the influence of the choice of high-dimensional encoding on the reduction. We show for the case studied that, in terms of reconstruction error root mean square deviation, Cartesian coordinate representations and encodings based on interatom distances provide better performance than encodings based on a dihedral angle representation.

  1. Molecular modeling of nucleic acid structure

    PubMed Central

    Galindo-Murillo, Rodrigo; Bergonzo, Christina

    2013-01-01

    This unit is the first in a series of four units covering the analysis of nucleic acid structure by molecular modeling. This unit provides an overview of computer simulation of nucleic acids. Topics include the static structure model, computational graphics and energy models, generation of an initial model, and characterization of the overall three-dimensional structure. PMID:18428873

  2. Investigation of PDE5/PDE6 and PDE5/PDE11 selective potent tadalafil-like PDE5 inhibitors using combination of molecular modeling approaches, molecular fingerprint-based virtual screening protocols and structure-based pharmacophore development.

    PubMed

    Kayık, Gülru; Tüzün, Nurcan Ş; Durdagi, Serdar

    2017-12-01

    The essential biological function of phosphodiesterase (PDE) type enzymes is to regulate the cytoplasmic levels of intracellular second messengers, 3',5'-cyclic guanosine monophosphate (cGMP) and/or 3',5'-cyclic adenosine monophosphate (cAMP). PDE targets have 11 isoenzymes. Of these enzymes, PDE5 has attracted a special attention over the years after its recognition as being the target enzyme in treating erectile dysfunction. Due to the amino acid sequence and the secondary structural similarity of PDE6 and PDE11 with the catalytic domain of PDE5, first-generation PDE5 inhibitors (i.e. sildenafil and vardenafil) are also competitive inhibitors of PDE6 and PDE11. Since the major challenge of designing novel PDE5 inhibitors is to decrease their cross-reactivity with PDE6 and PDE11, in this study, we attempt to identify potent tadalafil-like PDE5 inhibitors that have PDE5/PDE6 and PDE5/PDE11 selectivity. For this aim, the similarity-based virtual screening protocol is applied for the "clean drug-like subset of ZINC database" that contains more than 20 million small compounds. Moreover, molecular dynamics (MD) simulations of selected hits complexed with PDE5 and off-targets were performed in order to get insights for structural and dynamical behaviors of the selected molecules as selective PDE5 inhibitors. Since tadalafil blocks hERG1 K channels in concentration dependent manner, the cardiotoxicity prediction of the hit molecules was also tested. Results of this study can be useful for designing of novel, safe and selective PDE5 inhibitors.

  3. An integrated experimental and theoretical investigation of the vibrational modes and molecular structure of a chelate, tetraaqua cysteine aluminum(III).

    PubMed

    Tenório, Thaís; Tenório, André

    2015-03-05

    The complex formed by Al(3+) and cysteine in aqueous solution has been studied by potentiometry, Raman spectroscopy and DFT calculations (DFT:B3LYP/6-311++G(∗∗)). Atomic charges, frontier molecular orbitals, electrostatic potential contour surface, electrostatic potential map and donor-acceptor second order perturbative energies were examined. The [Al(Cys)(H2O)4](2+) complex adopts a distorted octahedral geometry. Cysteine should act as a bidentate ligand through the oxygen of the carboxylate and the nitrogen of the amino group. The molecule has high HOMO-LUMO energy gap, intense intramolecular charge transfer and positive electrostatic potential.

  4. Investigation of superlattice device structures

    NASA Technical Reports Server (NTRS)

    Gergis, I. S.; Manasevit, H. M.; Lin, A. L.; Jones, A. B.

    1985-01-01

    This report describes the investigation of growth properties, and the structure of epitaxial multilayer Si(Si(1x)Ge(x)) films grown on bulk Silicon Substrates. It also describes the fabrication and characterization of MOSFET and MESFET devices made on these epitaxial films. Films were grown in a CVD reactor using hydrides of Si and Ge with H2 and He as carrier gases. Growth temperatures were between 900 C and 1050 C with most films grown at 1000 C. Layer thickness was between 300A and 2000A and total film thickness was between 0.25 micro m and 7 micro m. The Ge content (X) in the alloy layers was between .05 and 0.2. N-type multilayer films grown on (100) p-type Si showed Hall mobility in the range 1000 to 1500 sq cm/v for an average carrier concentration of approx. 10 to the 16th power/cu cm. This is up to 50% higher than the Hall mobility observed in epitaxial Si films grown under the same conditions and with the same average carrier concentration. The mobility enhancement occurred in films with average carrier concentration (n) from 0.7 x 10 to the 16th power to 2 x 10 to the 17th power/cu cm, and total film thickness greater than 1.0 micro m. No mobility enhancement was seen in n-type multilayer films grown on (111) Si or in p-type multilayer films. The structure of the films was investigated was using SEM, TEM, AES, SIMS, and X-ray double crystal diffraction techniques. The film composition profile (AES, SIMS) showed that the transition region between layers is of the order of about 100A. The TEM examination revealed a well defined layered structure with fairly sharp interfaces and good crystalline quality. It also showed that the first few layers of the film (closest to the substrate) are uneven, most probably due to the initial growth pattern of the epitaxial film where growth occurs first in isolated islands that eventually growth and coalesce. The X-ray diffraction measurement determined the elastic strain and strain relief in the alloy layers of the film

  5. The Molecular Structure of Penicillin

    NASA Astrophysics Data System (ADS)

    Bentley, Ronald

    2004-10-01

    The chemical structure of penicillin was determined between 1942 and 1945 under conditions of secrecy established by the U.S. and U.K. governments. The evidence was not published in the open literature but as a monograph. This complex volume does not present a structure proof that can be readily comprehended by a student. In this article, a basic structural proof for the penicillin molecule is provided, emphasizing the chemical work. The stereochemistry of penicillin is also described, and various rearrangements are considered on the basis of the accepted β-lactam structure.

  6. One Pot Selective Arylation of 2-Bromo-5-Chloro Thiophene; Molecular Structure Investigation via Density Functional Theory (DFT), X-ray Analysis, and Their Biological Activities

    PubMed Central

    Rasool, Nasir; Kanwal, Aqsa; Rasheed, Tehmina; Ain, Quratulain; Mahmood, Tariq; Ayub, Khurshid; Zubair, Muhammad; Khan, Khalid Mohammed; Arshad, Muhammad Nadeem; M. Asiri, Abdullah; Zia-Ul-Haq, Muhammad; Jaafar, Hawa Z. E.

    2016-01-01

    Synthesis of 2,5-bisarylthiophenes was accomplished by sequential Suzuki cross coupling reaction of 2-bromo-5-chloro thiophenes. Density functional theory (DFT) studies were carried out at the B3LYP/6-31G(d, p) level of theory to compare the geometric parameters of 2,5-bisarylthiophenes with those from X-ray diffraction results. The synthesized compounds are screened for in vitro bacteria scavenging abilities. At the concentration of 50 and 100 μg/mL, compounds 2b, 2c, 2d, 3c, and 3f with IC50-values of 51.4, 52.10, 58.0, 56.2, and 56.5 μg/mL respectively, were found most potent against E. coli. Among all the synthesized compounds 2a, 2d, 3c, and 3e with the least values of IC50 77, 76.26, 79.13 μg/mL respectively showed significant antioxidant activities. Almost all of the compounds showed good antibacterial activity against Escherichia coli, whereas 2-chloro-5-(4-methoxyphenyl) thiophene (2b) was found most active among all synthesized compound with an IC50 value of 51.4 μg/mL. All of the synthesized compounds were screened for nitric oxide scavenging activity as well. Frontier molecular orbitals (FMOs) and molecular electrostatic potentials of the target compounds were also studied theoretically to account for their relative reactivity PMID:27367666

  7. Experimental Investigations of Transport and Optical Properties of 3-5 Quantum Well Structures Grown Via Molecular Beam Epitaxy under Optimal Growth Conditions

    DTIC Science & Technology

    1989-04-18

    Mariott Hotel , CA), SPIE Vol. 946, p.1 5 0 (1988). 13. W.C. Tang, Pudong Lao, and A. Madhukar, "Optical Investigation of Resonant Mixing Between...Superconductors; Physics and Device Applications", (13-18 March, 1988, Newport Beach Mariott Hotel , CA), SPIE Vol. 943, p.170 (1988). 14. F.J. Grunthaner...Newport Beach Mariott Hotel , CA). 4. W.C. Tang, Pudong Lao, and A. Madhukar, "Optical Investigation of Resonant Mixing Between Electronic and Optical

  8. Molecular Contamination Investigation Facility (MCIF) Capabilities

    NASA Technical Reports Server (NTRS)

    Soules, David M.

    2013-01-01

    This facility was used to guide the development of ASTM E 1559 center dot Multiple Quartz Crystal Microbalances (QCMs), large sample and spectral effects capability center dot Several instrumented, high vacuum chamber systems are used to evaluate the molecular outgassing characteristics of materials, flight components and other sensitive surfaces. Test materials for spacecraft/instrument selection center.Test flight components for acceptable molecular outgas levels center dot Determine time/temperature vacuum bake-out requirements center. Data used to set limits for use of materials and specific components center. Provide Input Data to Contamination Transport Models -Applied to numerous flight projects over the past 20 years.

  9. Molecular & Genetic Investigation of Tau in Chronic Traumatic Encephalopathy

    DTIC Science & Technology

    2015-10-01

    AWARD NUMBER: W81XWH-14-1-0399 TITLE: Molecular & Genetic Investigation of Tau in Chronic Traumatic Encephalopathy PRINCIPAL INVESTIGATOR: John F...Include area code) October 2015 Annual Report 30 Sep 2014 - 29 Sep 2015 Molecular & Genetic Investigation of Tau in Chronic Traumatic Encephalopathy John...encephalopathy (CTE), but the underlying molecular changes remain unclear. Here, biochemical and genetic studies that deepen our understanding of the

  10. The Molecular Structure of Penicillin

    ERIC Educational Resources Information Center

    Bentley, Ronald

    2004-01-01

    Overviews of the observations that constitute a structure proof for penicillin, specifically aimed at the general student population, are presented. Melting points and boiling points were criteria of purity and a crucial tool was microanalysis leading to empirical formulas.

  11. Structure and Dynamics of Cellulose Molecular Solutions

    NASA Astrophysics Data System (ADS)

    Wang, Howard; Zhang, Xin; Tyagi, Madhusudan; Mao, Yimin; Briber, Robert

    Molecular dissolution of microcrystalline cellulose has been achieved through mixing with ionic liquid 1-Ethyl-3-methylimidazolium acetate (EMIMAc), and organic solvent dimethylformamide (DMF). The mechanism of cellulose dissolution in tertiary mixtures has been investigated by combining quasielastic and small angle neutron scattering (QENS and SANS). As SANS data show that cellulose chains take Gaussian-like conformations in homogenous solutions, which exhibit characteristics of having an upper critical solution temperature, the dynamic signals predominantly from EMIMAc molecules indicate strong association with cellulose in the dissolution state. The mean square displacement quantities support the observation of the stoichiometric 3:1 EMIMAc to cellulose unit molar ratio, which is a necessary criterion for the molecular dissolution of cellulose. Analyses of dynamics structure factors reveal the temperature dependence of a slow and a fast process for EMIMAc's bound to cellulose and in DMF, respectively, as well as a very fast process due possibly to the rotational motion of methyl groups, which persisted to near the absolute zero.

  12. Structured Molecular Gas Reveals Galactic Spiral Arms

    NASA Astrophysics Data System (ADS)

    Sawada, Tsuyoshi; Hasegawa, Tetsuo; Koda, Jin

    2012-11-01

    We explore the development of structures in molecular gas in the Milky Way by applying the analysis of the brightness distribution function and the brightness distribution index (BDI) in the archival data from the Boston University-Five College Radio Astronomy Observatory 13CO J = 1-0 Galactic Ring Survey. The BDI measures the fractional contribution of spatially confined bright molecular emission over faint emission extended over large areas. This relative quantity is largely independent of the amount of molecular gas and of any conventional, pre-conceived structures, such as cores, clumps, or giant molecular clouds. The structured molecular gas traced by higher BDI is located continuously along the spiral arms in the Milky Way in the longitude-velocity diagram. This clearly indicates that molecular gas changes its structure as it flows through the spiral arms. Although the high-BDI gas generally coincides with H II regions, there is also some high-BDI gas with no/little signature of ongoing star formation. These results support a possible evolutionary sequence in which unstructured, diffuse gas transforms itself into a structured state on encountering the spiral arms, followed by star formation and an eventual return to the unstructured state after the spiral arm passage.

  13. STRUCTURED MOLECULAR GAS REVEALS GALACTIC SPIRAL ARMS

    SciTech Connect

    Sawada, Tsuyoshi; Hasegawa, Tetsuo; Koda, Jin

    2012-11-01

    We explore the development of structures in molecular gas in the Milky Way by applying the analysis of the brightness distribution function and the brightness distribution index (BDI) in the archival data from the Boston University-Five College Radio Astronomy Observatory {sup 13}CO J = 1-0 Galactic Ring Survey. The BDI measures the fractional contribution of spatially confined bright molecular emission over faint emission extended over large areas. This relative quantity is largely independent of the amount of molecular gas and of any conventional, pre-conceived structures, such as cores, clumps, or giant molecular clouds. The structured molecular gas traced by higher BDI is located continuously along the spiral arms in the Milky Way in the longitude-velocity diagram. This clearly indicates that molecular gas changes its structure as it flows through the spiral arms. Although the high-BDI gas generally coincides with H II regions, there is also some high-BDI gas with no/little signature of ongoing star formation. These results support a possible evolutionary sequence in which unstructured, diffuse gas transforms itself into a structured state on encountering the spiral arms, followed by star formation and an eventual return to the unstructured state after the spiral arm passage.

  14. Molecular interactions investigated with DFT calculations of QTAIM and NBO analyses: An application to dimeric structures of rice α-amylase/subtilisin inhibitor

    NASA Astrophysics Data System (ADS)

    Astani, Elahe K.; Hadipour, Nasser L.; Chen, Chun-Jung

    2017-03-01

    Characterization of the dimer interactions at the dimeric interface of the crystal structure of rice α-amylase/subtilisin inhibitor (RASI) were performed using the quantum theory of atoms in molecules (QTAIM) and natural bonding orbital (NBO) analyses at the density-functional theory (DFT) level. The results revealed that Gly27 and Arg151 of chain A are the main residues involved in hydrogen bonds, dipole-dipole, and charge-dipole interactions with Gly64, Ala66, Ala67 and Arg81 of chain B at the dimeric interface. Calcium ion of chain A plays the significant role in the stability of the dimeric structure through a strong charge-charge interaction with Ala66.

  15. NBO, NMR, UV, FT-IR, FT-Raman spectra and molecular structure (monomeric and dimeric structures) investigation of 4-Chloro-3,5-Xylenol: a combined experimental and theoretical study.

    PubMed

    Arivazhagan, M; Gayathri, R

    2013-12-01

    In this work, a joint experimental (FTIR and FT-Raman) and theoretical (DFT and ab initio) study on the structure and the vibrations of 4-Chloro-3,5-Xylenol (CXL) are compared and analyzed. CXL is a chlorinated phenolic antiseptic which is a bactericide against most gram-positive bacteria. The first hyperpolarizability (β0) of this novel molecular system and related non-linear properties of CXL are calculated using HF/6-311++G(d,p) method on the finite-field approach. The energy and oscillator strength calculated using absorption spectra (UV-Vis spectrum), this spectral analysis confirms the charge transfer of the molecule. The theoretical (13)C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by Gauge Including Atomic Orbital (GIAO) method, to analyze the molecular environment as well as the delocalization activities of electron clouds. The directly calculated ionization potential (IP), electron affinity (EA), electronegativity (χ), chemical hardness (η), first electron excitation energy (τ) and electrophilicity index (ω) as well as local reactivity (S) analyzed using HOMO and LUMO energies; the energy band gap are also determined. NBO analysis shows that charge in electron density(ED) in the σ(*) and π(*) antibonding orbitals and E((2)) energies confirms the occurrence of ICT (Intramolecular Charge Transfer) within the molecule. Inter molecular hydrogen bonds exist between -OH group, give the evidence for the formation of dimer entities in the title molecule. The influences of chlorine atom, hydroxyl group and methyl group on the geometry of benzene and its normal modes of vibrations (monomer and dimer of CXL) have also been discussed. Finally the calculated results were applied to simulate Infrared and Raman spectra of the title molecule which show good agreement with observed spectra.

  16. Experimental Investigations of Transport and Optical Properties of III-V Quantum Well Structures Grown Via Molecular Beam Epitaxy Under Optimal Growth Conditions

    DTIC Science & Technology

    1990-06-01

    March, 1988, Newport Beach Mariott Hotel , CA). 4. W.C Tang, Pudong Lao, and A. Madhukar, "Optical Investigation of Resonant Mixing Between Electronic...and Device Applications", (13-18 March, 1988, Newport Beach Mariott Hotel , CA). III. ST JDENTS/POST-DO CS TRAINED: 1. Mr. Nam-Min Cho (Ph.D. Oct. 1988...Semiconductors and Superconductors: Physics and Device Applications" (13-18 March, 1988, Newport Beach Mario« Hotel , CA), SPIE Vol. 946, p.150 (1988

  17. ESR and X-ray Structure Investigations on the Binding and Mechanism of Inhibition of the Native State of Myeloperoxidase with Low Molecular Weight Fragments

    SciTech Connect

    Chavali, Balagopalakrishna; Masquelin, Thierry; Nilges, Mark J.; Timm, David E.; Stout, Stephanie L.; Matter, William F.; Jin, Najia; Jadhav, Prabhakar K.; Deng, Gary G.

    2015-05-19

    As an early visitor to the injured loci, neutrophil-derived human Myeloperoxidase (hMPO) offers an attractive protein target to modulate the inflammation of the host tissue through suitable inhibitors. We describe a novel methodology of using low temperature ESR spectroscopy (6 K) and FAST™ technology to screen a diverse series of small molecules that inhibit the peroxidase function through reversible binding to the native state of MPO. Also, our initial efforts to profile molecules on the inhibition of MPO-initiated nitration of the Apo-A1 peptide (AEYHAKATEHL) assay showed several potent (with sub-micro molar IC50s) but spurious inhibitors that either do not bind to the heme pocket in the enzyme or retain high (>50 %) anti oxidant potential. Such molecules when taken forward for X-ray did not yield inhibitor-bound co-crystals. We then used ESR to confirm direct binding to the native state enzyme, by measuring the binding-induced shift in the electronic parameter g to rank order the molecules. Molecules with a higher rank order—those with g-shift Rrelative ≥15—yielded well-formed protein-bound crystals (n = 33 structures). The co-crystal structure with the LSN217331 inhibitor reveals that the chlorophenyl group projects away from the heme along the edges of the Phe366 and Phe407 side chain phenyl rings thereby sterically restricting the access to the heme by the substrates like H2O2. Both ESR and antioxidant screens were used to derive the mechanism of action (reversibility, competitive substrate inhibition, and percent antioxidant potential). In conclusion, our results point to a viable path forward to target the native state of MPO to tame local inflammation.

  18. ESR and X-ray Structure Investigations on the Binding and Mechanism of Inhibition of the Native State of Myeloperoxidase with Low Molecular Weight Fragments

    DOE PAGES

    Chavali, Balagopalakrishna; Masquelin, Thierry; Nilges, Mark J.; ...

    2015-05-19

    As an early visitor to the injured loci, neutrophil-derived human Myeloperoxidase (hMPO) offers an attractive protein target to modulate the inflammation of the host tissue through suitable inhibitors. We describe a novel methodology of using low temperature ESR spectroscopy (6 K) and FAST™ technology to screen a diverse series of small molecules that inhibit the peroxidase function through reversible binding to the native state of MPO. Also, our initial efforts to profile molecules on the inhibition of MPO-initiated nitration of the Apo-A1 peptide (AEYHAKATEHL) assay showed several potent (with sub-micro molar IC50s) but spurious inhibitors that either do not bindmore » to the heme pocket in the enzyme or retain high (>50 %) anti oxidant potential. Such molecules when taken forward for X-ray did not yield inhibitor-bound co-crystals. We then used ESR to confirm direct binding to the native state enzyme, by measuring the binding-induced shift in the electronic parameter g to rank order the molecules. Molecules with a higher rank order—those with g-shift Rrelative ≥15—yielded well-formed protein-bound crystals (n = 33 structures). The co-crystal structure with the LSN217331 inhibitor reveals that the chlorophenyl group projects away from the heme along the edges of the Phe366 and Phe407 side chain phenyl rings thereby sterically restricting the access to the heme by the substrates like H2O2. Both ESR and antioxidant screens were used to derive the mechanism of action (reversibility, competitive substrate inhibition, and percent antioxidant potential). In conclusion, our results point to a viable path forward to target the native state of MPO to tame local inflammation.« less

  19. Structure investigations on oxygen fluorides.

    PubMed

    Marx, Rupert; Seppelt, Konrad

    2015-12-07

    The crystal structure of O2F2 is obtained at -180 °C. In the solid state the molecule has the typical hydrogen peroxide structure that has been established long ago by electron diffraction and microwave spectroscopy. OF2 melts at -223.8 °C, so its structure is determined by powder X-ray data. The structure differs from the solid state structures of ozone and Br2O. O2F in its dissolved form as O2(+) HnFn+1(-) oxidizes palladium to the four valence state, as found some time ago. The first product formed at low temperatures is (O2(+)H3Pd2F12(-))n.

  20. A molecular phylogenetic investigation of zoothamnium (ciliophora, peritrichia, sessilida).

    PubMed

    Clamp, John C; Williams, Daniel

    2006-01-01

    The gene coding for 18S small subunit ribosomal RNA (ssu rRNA) was sequenced in seven free-living, marine species of the sessiline peritrich genus Zoothamnium. These were Zoothamnium niveum, Zoothamnium alternans, Zoothamnium pelagicum, and four unidentified species. The ssu rRNA gene also was sequenced in Vorticella convallaria, Vorticella microstoma, and in an unidentified, freshwater species of Vorticella. Phylogenetic trees were constructed using these new sequences to test a previously published phylogenetic association between Zoothamnium arbuscula, currently in the family Zoothamniidae, and peritrichs in the family Vorticellidae. Trees constructed by means of neighbor-joining, maximum parsimony, maximum likelihood, and Bayesian inference methods all had similar topologies. The seven new sequences of Zoothamnium species grouped into three well-supported clades, each of which contained a diversity of morphological types. The three clades formed a poorly supported, larger clade that was deeply divergent from Z. arbuscula, which remained more closely associated with vorticellid peritrichs. It is apparent that Zoothamnium is a richly diverse genus and that a much more intensive investigation, involving both morphological and molecular data and a wider selection of species, will be necessary to resolve its phylogeny. A greater amount of molecular diversity than is predicted by morphological data exists within all major clades of sessiline peritrichs that have been included in molecular phylogenies, indicating that characteristics of stalk and peristomial structure traditionally used to differentiate taxa at the generic level and above may not be uniformly reliable.

  1. Structure investigations of group 13 organometallic carboxylates.

    PubMed

    Justyniak, Iwona; Prochowicz, Daniel; Tulewicz, Adam; Bury, Wojciech; Goś, Piotr; Lewiński, Janusz

    2017-01-17

    The octet-compliant group 13 organometallics with highly polarized bonds in the metal coordination sphere exhibit a significant tendency to maximize their coordination number through the formation of adducts with a wide range of neutral donor ligands or by self-association to give aggregates containing tetrahedral and higher coordinated aluminium centres, and even in some cases molecular complexes equilibrate with ionic species of different coordination numbers of the metal centre. This work provides a comprehensive overview of the structural chemistry landscape of the group 13 carboxylates. Aside from a more systematic approach to the general structural chemistry of the title compounds, the structure investigations of [R2M(μ-O2CPh)]2-type benzoate complexes (where M = B, Al and Ga) and their Lewis acid-base adducts [(R2M)(μ-O2CPh)(py-Me)] are reported. DFT calculations were also performed to obtain a more in-depth understanding of both the changes in the bonding of group 13 organometallic carboxylate adducts with a pyridine ligand.

  2. Structure and kinematics of molecular jets

    NASA Astrophysics Data System (ADS)

    Snell, R. L.

    1986-04-01

    Observational studies of the structure and kinematics of the supersonic molecular gas in star-forming regions are reviewed. These studies have suggested that the bulk of the high-velocity gas may be ambient-cloud material swept up by a collimated stellar wind. The actual structures of these outflows, however, are poorly understood. One source that may provide a better understanding of molecular outflows is that in the nearby dark cloud LDN 1551. New observations of this outflow are presented and discussed in context of the models proposed by Snell and Schloerb.

  3. On the emergence of molecular structure

    SciTech Connect

    Matyus, Edit; Reiher, Markus; Hutter, Juerg; Mueller-Herold, Ulrich

    2011-05-15

    The structure of (a{sup {+-}},a{sup {+-}},b{sup {+-}})-type Coulombic systems is characterized by the effective ground-state density of the a-type particles, computed via nonrelativistic quantum mechanics without introduction of the Born-Oppenheimer approximation. A structural transition is observed when varying the relative mass of the a- and b-type particles, e.g., between atomic H{sup -} and molecular H{sub 2}{sup +}. The particle-density profile indicates a molecular-type behavior for the positronium ion, Ps{sup -}.

  4. Reverse engineering chemical structures from molecular descriptors : how many solutions?

    SciTech Connect

    Brown, William Michael; Martin, Shawn Bryan; Faulon, Jean-Loup Michel

    2005-06-01

    Physical, chemical and biological properties are the ultimate information of interest for chemical compounds. Molecular descriptors that map structural information to activities and properties are obvious candidates for information sharing. In this paper, we consider the feasibility of using molecular descriptors to safely exchange chemical information in such a way that the original chemical structures cannot be reverse engineered. To investigate the safety of sharing such descriptors, we compute the degeneracy (the number of structure matching a descriptor value) of several 2D descriptors, and use various methods to search for and reverse engineer structures. We examine degeneracy in the entire chemical space taking descriptors values from the alkane isomer series and the PubChem database. We further use a stochastic search to retrieve structures matching specific topological index values. Finally, we investigate the safety of exchanging of fragmental descriptors using deterministic enumeration.

  5. Speculations on the molecular structure of eumelanin.

    PubMed

    Swift, J A

    2009-04-01

    Eumelanin is the polymeric black pigment commonly found in hair and skin. Its chemical intractability, to all but vigorous oxidizing agents, has hindered satisfactory understanding of its molecular structure. It is well-established that the immediate precursor to polymerization, indole-5,6-quinone (IQ), is biosynthesized from the amino acid tyrosine. Current views are that the polymer consists of single bond connections between random indole and degraded indole units. In this paper, an alternative chemical scheme for the polymerization of IQ is proposed based upon the original suggestion by Horner in 1949 that a Diels-Alder (D-A) reaction might be involved. The proposed basic chemical scheme for eumelanin formation is that D-A addition occurs specifically between the 2- and 3-positions of one IQ molecule and the 7- and 4- positions respectively of a second IQ molecule, that the ensuing diketo bridge is oxidized to carboxyl groups and that, by decarboxylation and aromatization, a fused indole dimer is produced. It is envisaged that, by further D-A addition of more IQ molecules, oligomers of greater molecular mass are produced. Calculations based on published bond lengths and angles for the indole nucleus show that oligomeric units containing a total of up to 11 fused indoles could be packed into a flat circular disc of 20 A diameter. The discs of the extensively conjugated polymer are envisaged to be stacked above each other by pi-pi interaction and with a spacing of 3.4 A to produce cylindrical units, the mass density of which is calculated to be 1.54 gm cm(-3); approximating with actual physical measurements. The size and shape of the predicted cylinders are in concordance with those observed in atomic force microscope investigations of eumelanin proto-particles. The model is also in agreement with published experimental data that 2/3rds of the carbon dioxide liberated during eumelanin formation derives from positions 5- and 6- of the IQ molecule.

  6. Molecular docking to ensembles of protein structures.

    PubMed

    Knegtel, R M; Kuntz, I D; Oshiro, C M

    1997-02-21

    Until recently, applications of molecular docking assumed that the macromolecular receptor exists in a single, rigid conformation. However, structural studies involving different ligands bound to the same target biomolecule frequently reveal modest but significant conformational changes in the target. In this paper, two related methods for molecular docking are described that utilize information on conformational variability from ensembles of experimental receptor structures. One method combines the information into an "energy-weighted average" of the interaction energy between a ligand and each receptor structure. The other method performs the averaging on a structural level, producing a "geometry-weighted average" of the inter-molecular force field score used in DOCK 3.5. Both methods have been applied in docking small molecules to ensembles of crystal and solution structures, and we show that experimentally determined binding orientations and computed energies of known ligands can be reproduced accurately. The use of composite grids, when conformationally different protein structures are available, yields an improvement in computational speed for database searches in proportion to the number of structures.

  7. Molecular Association and Structure of Hydrogen Peroxide.

    ERIC Educational Resources Information Center

    Giguere, Paul A.

    1983-01-01

    The statement is sometimes made in textbooks that liquid hydrogen peroxide is more strongly associated than water, evidenced by its higher boiling point and greater heat of vaporization. Discusses these and an additional factor (the nearly double molecular mass of the peroxide), focusing on hydrogen bonds and structure of the molecule. (JN)

  8. Investigation of coal structure. Final report

    SciTech Connect

    Nishioka, Masaharu

    1994-03-01

    A better understanding of coal structure is the first step toward more effective utilization of the most abundant hydrocarbon resource. Detailed characterization of coal structure is very difficult, even with today`s highly developed analytical techniques. This is primarily due to the amorphous nature of these high-molecular-weight mixtures. Coal has a polymeric character and has been popularly represented as a three-dimensional cross-linked network. There is, however, little or no information which positively verifies this model. The principal objective of this research was to further investigate the physical structure of coal and to determine the extent to which coal molecules may be covalently cross-linked and/or physically associated. Two common characterization methods, swellability and extractability, were used. A technique modifying the conventional swelling procedure was established to better determine network or associated model conformation. A new method for evaluating coal swelling involving laser scattering has also been developed. The charge-transfer interaction is relatively strong in high-volatile bituminous coal. Soaking in the presence of electron donors and acceptors proved effective for solubilizing the coal, but temperatures in excess of 200 C were required. More than 70 wt% of the coal was readily extracted with pyridine after soaking. Associative/dissociative equilibria of coal molecules were observed during soaking. From these results, the associated model has gained credibility over the network model as the representative structure of coal. Significant portions of coal molecules are unquestionably physically associated, but the overall extent is not known at this time.

  9. Quantum-chemical investigations of small molecular anions

    NASA Astrophysics Data System (ADS)

    Botschwina, P.; Seeger, S.; Mladenović, M.; Schulz, B.; Horn, M.; Schmatz, S.; Flügge, J.; Oswald, R.

    Dedicated to Dr Gerhard Herzberg on the occasion of his 90th birthday Recent large-scale ab initio calculations for small negative molecular ions are reviewed. Accurate equilibrium geometries are established for several species like NH2-, HCC-, NO2-, CH2N- C5- and C6-. Predictions are made for various spectroscopic properties like vibrational frequencies, rotational constants and infrared intensities. The effects of a shallow energy minimum in the T-shaped configuration on the rovibrational term energies of HCC - are investigated. The calculated vibrational structures of the photoelectron spectra of SiH3- and CH2N - are in very good agreement with the experiment. The present calculations support the assignment of an absorption observed at 608 nm in a neon matrix to the

  10. Molecular structures and intramolecular dynamics of pentahalides

    NASA Astrophysics Data System (ADS)

    Ischenko, A. A.

    2017-03-01

    This paper reviews advances of modern gas electron diffraction (GED) method combined with high-resolution spectroscopy and quantum chemical calculations in studies of the impact of intramolecular dynamics in free molecules of pentahalides. Some recently developed approaches to the electron diffraction data interpretation, based on direct incorporation of the adiabatic potential energy surface parameters to the diffraction intensity are described. In this way, complementary data of different experimental and computational methods can be directly combined for solving problems of the molecular structure and its dynamics. The possibility to evaluate some important parameters of the adiabatic potential energy surface - barriers to pseudorotation and saddle point of intermediate configuration from diffraction intensities in solving the inverse GED problem is demonstrated on several examples. With increasing accuracy of the electron diffraction intensities and the development of the theoretical background of electron scattering and data interpretation, it has become possible to investigate complex nuclear dynamics in fluxional systems by the GED method. Results of other research groups are also included in the discussion.

  11. Structural and electronic properties of Si n, Si n+, and AlSi n-1 (n=2-13) clusters: theoretical investigation based on ab initio molecular orbital theory.

    PubMed

    Nigam, Sandeep; Majumder, Chiranjib; Kulshreshtha, S K

    2004-10-22

    The geometric and electronic structures of Si(n), Si(n) (+), and AlSi(n-1) clusters (2< or =n< or =13) have been investigated using the ab initio molecular orbital theory under the density functional theory formalism. The hybrid exchange-correlation energy function (B3LYP) and a standard split-valence basis set with polarization functions [6-31G(d)] were employed for this purpose. Relative stabilities of these clusters have been analyzed based on their binding energies, second difference in energy (Delta (2)E) and fragmentation behavior. The equilibrium geometry of the neutral and charged Si(n) clusters show similar structural growth. However, significant differences have been observed in the electronic structure leading to their different stability pattern. While for neutral clusters, the Si(10) is magic, the extra stability of the Si(11) (+) cluster over the Si(10) (+) and Si(12) (+) bears evidence for the magic behavior of the Si(11) (+) cluster, which is in excellent agreement with the recent experimental observations. Similarly for AlSi(n-1) clusters, which is isoelectronic with Si(n) (+) clusters show extra stability of the AlSi(10) cluster suggesting the influence of the electronic structures for different stabilities between neutral and charged clusters. The ground state geometries of the AlSi(n-1) clusters show that the impurity Al atom prefers to substitute for the Si atom, that has the highest coordination number in the host Si(n) cluster. The fragmentation behavior of all these clusters show that while small clusters prefers to evaporate monomer, the larger ones dissociate into two stable clusters of smaller size.

  12. Structural investigation of hybrid nanocomposites

    NASA Astrophysics Data System (ADS)

    Lo Celso, F.; Triolo, A.; Negroni, F.; Hainbuchner, M.; Baron, M.; Strunz, P.; Rauch, H.; Triolo, R.

    Ultra small (USANS) and small angle neutron scattering (SANS) techniques were employed to study an elastomer styrene-butadiene, where two kinds of silica fillers have been added in different amounts. Small silica-particle fillers are expected to modify morphological and mechanical properties when dispersed in the copolymer matrix. The USANS and SANS techniques can span a wide range of momentum transfer, investigating morphological properties of the filled elastomer over a number of decades in length scale. Surface and mass fractal behavior has been observed over different length scales.

  13. Electronic structure investigations of quasicrystals

    NASA Astrophysics Data System (ADS)

    Rotenberg, E.; Theis, W.; Horn, K.

    2004-08-01

    We present a review of the determination of density of states (DOS) of quasicrystals using valence band photoemission spectroscopy. The absence of fine or spiky structure in the angle-integrated DOS of quasicrystals suggests the possibility of delocalized electronic states. These were confirmed with angle-resolved photoemission studies, which clearly establish the presence of dispersing features attributed to momentum-dependent bandstructure. Such dispersing states are observed not only for deeper-lying sp states, but also for d-derived bands near the Fermi level. Data from three different high symmetry surfaces of decagonal Al-Ni-Co, an ideal model system, are presented. We find that only a few dominant reciprocal lattice vectors are sufficient to describe the quasiperiodic potential, and the implications for electronic properties are discussed.

  14. The Global Coronal Structure Investigation

    NASA Technical Reports Server (NTRS)

    Golub, Leon

    1998-01-01

    During the past year we have completed the changeover from the NIXT program to the new TXI sounding rocket program. The NIXT effort, aimed at evaluating the viability of the remaining portions of the NIXT hardware and design, has been finished and the portions of the NIXT which are viable and flightworthy, such as filters, mirror mounting hardware, electronics and telemetry interface systems, are now part of the new rocket payload. The backup NIXT multilayer-coated x-ray telescope and its mounting hardware have been completely fabricated and are being stored for possible future use in the TXI rocket. The H-alpha camera design is being utilized in the TXI program for real-time pointing verification and control via telemetry. A new H-alpha camera has been built, with a high-resolution RS170 CCD camera output. Two papers, summarizing scientific results from the NIXT rocket program, have been written and published this year: 1. "The Solar X-ray Corona," by L. Golub, Astrophysics and Space Science, 237, 33 (1996). 2. "Difficulties in Observing Coronal Structure," Keynote Paper, Proceedings STEPWG1 Workshop on Measurements and Analyses of the Solar 3D Magnetic Field, Solar Physics, 174, 99 (1997).

  15. Structural effects in molecular metal halides.

    PubMed

    Hargittai, Magdolna

    2009-03-17

    Metal halides are a relatively large class of inorganic compounds that participate in many industrial processes, from halogen metallurgy to the production of semiconductors. Because most metal halides are ionic crystals at ambient conditions, the term "molecular metal halides" usually refers to vapor-phase species. These gas-phase molecules have a special place in basic research because they exhibit the widest range of chemical bonding from the purely ionic to mostly covalent bonding through to weakly interacting systems. Although our focus is basic research, knowledge of the structural and thermodynamic properties of gas-phase metal halides is also important in industrial processes. In this Account, we review our most recent work on metal halide molecular structures. Our studies are based on electron diffraction and vibrational spectroscopy, and increasingly, we have augmented our experimental work with quantum chemical computations. Using both experimental and computational techniques has enabled us to determine intriguing structural effects with better accuracy than using either technique alone. We loosely group our discussion based on structural effects including "floppiness", relativistic effects, vibronic interactions, and finally, undiscovered molecules with computational thermodynamic stability. Floppiness, or serious "nonrigidity", is a typical characteristic of metal halides and makes their study challenging for both experimentalists and theoreticians. Relativistic effects are mostly responsible for the unique structure of gold and mercury halides. These molecules have shorter-than-expected bonds and often have unusual geometrical configurations. The gold monohalide and mercury dihalide dimers and the molecular-type crystal structure of HgCl(2) are examples. We also examined spin-orbit coupling and the possible effect of the 4f electrons on the structure of lanthanide trihalides. Unexpectedly, we found that the geometry of their dimers depends on the f

  16. Creep rupture of fiber bundles: A molecular dynamics investigation

    NASA Astrophysics Data System (ADS)

    Linga, G.; Ballone, P.; Hansen, Alex

    2015-08-01

    The creep deformation and eventual breaking of polymeric samples under a constant tensile load F is investigated by molecular dynamics based on a particle representation of the fiber bundle model. The results of the virtual testing of fibrous samples consisting of 40 000 particles arranged on Nc=400 chains reproduce characteristic stages seen in the experimental investigations of creep in polymeric materials. A logarithmic plot of the bundle lifetime τ versus load F displays a marked curvature, ruling out a simple power-law dependence of τ on F . A power law τ ˜F-4 , however, is recovered at high load. We discuss the role of reversible bond breaking and formation on the eventual fate of the sample and simulate a different type of creep testing, imposing a constant stress rate on the sample up to its breaking point. Our simulations, relying on a coarse-grained representation of the polymer structure, introduce new features into the standard fiber bundle model, such as real-time dynamics, inertia, and entropy, and open the way to more detailed models, aiming at material science aspects of polymeric fibers, investigated within a sound statistical mechanics framework.

  17. Structural and electronic properties of Si(n), Si(n)-, and PSi(n-1) clusters (2 < or = n < or = 13): Theoretical investigation based on ab initio molecular orbital theory.

    PubMed

    Nigam, Sandeep; Majumder, Chiranjib; Kulshreshtha, S K

    2006-08-21

    The geometric and electronic structures of Si(n), Si(n)-, and PSi(n-1) clusters (2 < or = n < or = 13) have been investigated using the ab initio molecular orbital theory formalism. The hybrid exchange-correlation energy functional (B3LYP) and a standard split-valence basis set with polarization functions (6-31+G(d)) were employed to optimize geometrical configurations. The total energies of the lowest energy isomers thus obtained were recalculated at the MP2/aug-cc-pVTZ level of theory. Unlike positively charged clusters, which showed similar structural behavior as that of neutral clusters [Nigam et al., J. Chem. Phys. 121, 7756 (2004)], significant geometrical changes were observed between Si(n) and Si(n)- clusters for n = 6, 8, 11, and 13. However, the geometries of P substituted silicon clusters show similar growth as that of negatively charged Si(n) clusters with small local distortions. The relative stability as a function of cluster size has been verified based on their binding energies, second difference in energy (Delta2 E), and fragmentation behavior. In general, the average binding energy of Si(n)- clusters is found to be higher than that of Si(n) clusters. For isoelectronic PSi(n-1) clusters, it is found that although for small clusters (n < 4) substitution of P atom improves the binding energy of Si(n) clusters, for larger clusters (n > or = 4) the effect is opposite. The fragmentation behavior of these clusters reveals that while small clusters prefer to evaporate monomer, the larger ones dissociate into two stable clusters of smaller size. The adiabatic electron affinities of Si(n) clusters and vertical detachment energies of Si(n)- clusters were calculated and compared with available experimental results. Finally, a good agreement between experimental and our theoretical results suggests good prediction of the lowest energy isomeric structures for all clusters calculated in the present study.

  18. Structure and dynamics of layered molecular assemblies

    NASA Astrophysics Data System (ADS)

    Horne, Jennifer Conrad

    This dissertation focuses on the goal of understanding and controlling layered material properties from a molecular perspective. With this understanding, materials can be synthetically tailored to exhibit predetermined bulk properties. This investigation describes the optical response of a family of metal-phosphonate (MP) monolayers and multilayers, materials that are potentially useful because the films are easy to synthesize and are chemically and thermally stable. MP films have shown potential in a variety of chemical sensing and optical applications, and in this dissertation, the suitability of MP films for optical information storage is explored For this application, the extent of photonic energy transport within and between optically active layers is an important factor in determining the stability and specificity of optical modifications made to a material. Intralayer and interlayer energy transport processes can be studied selectively in MP films because the composition, and thus the properties, of each layer are controlled synthetically. It was determined by fluorescence relaxation dynamics in conjunction with atomic force microscopy (AFM) that the substrate and layer morphologies are key factors in determining the layer optical and physical properties. The initial MP layers in a multilayer are structurally heterogeneous, characterized by randomly distributed islands that are ~50 A in diameter. The population dynamics measured for these layers are non-exponential, chromophore concentration-independent, and identical for two different chromophores. The data is explained in the context of an excitation hopping model in a system where the surface is characterized by islands of aggregated chromophores as well as non-aggregated monomers. Within a MP monolayer, the dynamics are dominated by intra-island excitation hopping. Forster (dipolar) energy transfer between the energetically overlapped chromophores does not play a significant role in determining the

  19. Investigating the Structure of X(4140) in QCD

    NASA Astrophysics Data System (ADS)

    Dağ, H.; Türkan, A.

    2017-03-01

    In this work, the masses of the ground states coupling to molecular or tetraquark currents with JPC = 0++, 1++, 2++ are studied to investigate the structure of X(4140) exotic meson observed at J/ψϕ invariant mass spectrum. We found that all currents predict ground states with masses of the same magnitude, which might be inter-pereted as the existance of at least three exotic structures with degenerate mass.

  20. Investigation of high hole mobility In{sub 0.41}Ga{sub 0.59}Sb/Al{sub 0.91}Ga{sub 0.09}Sb quantum well structures grown by molecular beam epitaxy

    SciTech Connect

    Wang, Juan; Xing, Jun-Liang; Xiang, Wei; Wang, Guo-Wei; Xu, Ying-Qiang; Ren, Zheng-Wei; Niu, Zhi-Chuan

    2014-02-03

    Modulation-doped In{sub 0.41}Ga{sub 0.59}Sb/Al{sub 0.91}Ga{sub 0.09}Sb quantum-well (QW) structures were grown by molecular beam epitaxy. Cross-sectional transmission electron microscopy and atomic force microscopy studies show high crystalline quality and smooth surface morphology. X-ray diffraction investigations confirm 1.94% compressive strain within In{sub 0.41}Ga{sub 0.59}Sb channel. High room temperature hole mobility with high sheet density of 1000 cm{sup 2}/Vs, 0.877 × 10{sup 12}/cm{sup 2}, and 965 cm{sup 2}/Vs, 1.112 × 10{sup 12}/cm{sup 2} were obtained with different doping concentrations. Temperature dependent Hall measurements show different scattering mechanisms on hole mobility at different temperature range. The sheet hole density keeps almost constantly from 300 K to 77 K. This study shows great potential of In{sub 0.41}Ga{sub 0.59}Sb/Al{sub 0.91}Ga{sub 0.09}Sb QW for high-hole-mobility device applications.

  1. Investigation of Ribosomes Using Molecular Dynamics Simulation Methods.

    PubMed

    Makarov, G I; Makarova, T M; Sumbatyan, N V; Bogdanov, A A

    2016-12-01

    The ribosome as a complex molecular machine undergoes significant conformational changes while synthesizing a protein molecule. Molecular dynamics simulations have been used as complementary approaches to X-ray crystallography and cryoelectron microscopy, as well as biochemical methods, to answer many questions that modern structural methods leave unsolved. In this review, we demonstrate that all-atom modeling of ribosome molecular dynamics is particularly useful in describing the process of tRNA translocation, atomic details of behavior of nascent peptides, antibiotics, and other small molecules in the ribosomal tunnel, and the putative mechanism of allosteric signal transmission to functional sites of the ribosome.

  2. Structures of High Density Molecular Fluids

    SciTech Connect

    Baer, B; Cynn, H; Iota, V; Yoo, C-S

    2002-02-01

    The goal of this proposal is to develop an in-situ probe for high density molecular fluids. We will, therefore, use Coherent Anti-Stokes Raman Spectroscopy (CARS) applied to laser heated samples in a diamond-anvil cell (DAC) to investigate molecular fluids at simultaneous conditions of high temperatures (T > 2000K) and high pressures (P > 10 GPa.) Temperatures sufficient to populate vibrational levels above the ground state will allow the vibrational potential to be mapped by CARS. A system capable of heating and probing these samples will be constructed. Furthermore, the techniques that enable a sample to be sufficiently heated and probed while held at static high pressure in a diamond-anvil-cell will be developed. This will be an in-situ investigation of simple molecules under conditions relevant to the study of detonation chemistry and the Jovain planet interiors using state of the art non-linear spectroscopy, diamond-anvil-cells, and laser heating technology.

  3. Molecular Dynamics Modeling of Hydrated Calcium-Silicate-Hydrate (CSH) Cement Molecular Structure

    DTIC Science & Technology

    2014-08-30

    properties of key hydrated cement constituent calcium-silicate-hydrate (CSH) at the molecular, nanometer scale level. Due to complexity, still unknown...public release; distribution is unlimited. Molecular Dynamics Modeling of Hydrated Calcium-Silicate- Hydrate (CSH) Cement Molecular Structure The views... Cement Molecular Structure Report Title Multi-scale modeling of complex material systems requires starting from fundamental building blocks to

  4. Ab initio study of structural and mechanical property of solid molecular hydrogens

    NASA Astrophysics Data System (ADS)

    Ye, Yingting; Yang, Li; Yang, Tianle; Nie, Jinlan; Peng, Shuming; Long, Xinggui; Zu, Xiaotao; Du, Jincheng

    2015-06-01

    Ab initio calculations based on density functional theory (DFT) were performed to investigate the structural and the elastic properties of solid molecular hydrogens (H2). The influence of molecular axes of H2 on structural relative stabilities of hexagonal close-packed (hcp) and face-centered cubic (fcc) structured hydrogen molecular crystals were systematically investigated. Our results indicate that for hcp structures, disordered hydrogen molecule structure is more stable, while for fcc structures, Pa3 hydrogen molecular crystal is most stable. The cohesive energy of fcc H2 crystal was found to be lower than hcp. The mechanical properties of fcc and hcp hydrogen molecular crystals were obtained, with results consistent with previous theoretical calculations. In addition, the effects of zero point energy (ZPE) and van der Waals (vdW) correction on the cohesive energy and the stability of hydrogen molecular crystals were systematically studied and discussed.

  5. Molecular, Functional, and Structural Imaging of Major Depressive Disorder.

    PubMed

    Zhang, Kai; Zhu, Yunqi; Zhu, Yuankai; Wu, Shuang; Liu, Hao; Zhang, Wei; Xu, Caiyun; Zhang, Hong; Hayashi, Takuya; Tian, Mei

    2016-06-01

    Major depressive disorder (MDD) is a significant cause of morbidity and mortality worldwide, correlating with genetic susceptibility and environmental risk factors. Molecular, functional, and structural imaging approaches have been increasingly used to detect neurobiological changes, analyze neurochemical correlates, and parse pathophysiological mechanisms underlying MDD. We reviewed recent neuroimaging publications on MDD in terms of molecular, functional, and structural alterations as detected mainly by magnetic resonance imaging (MRI) and positron emission tomography. Altered structure and function of brain regions involved in the cognitive control of affective state have been demonstrated. An abnormal default mode network, as revealed by resting-state functional MRI, is likely associated with aberrant metabolic and serotonergic function revealed by radionuclide imaging. Further multi-modal investigations are essential to clarify the characteristics of the cortical network and serotonergic system associated with behavioral and genetic variations in MDD.

  6. Insights into molecular structure and digestion rate of oat starch.

    PubMed

    Xu, Jinchuan; Kuang, Qirong; Wang, Kai; Zhou, Sumei; Wang, Shuo; Liu, Xingxun; Wang, Shujun

    2017-04-01

    The in vitro digestibility of oat starch and its relationship with starch molecular structure was investigated. The in vitro digestion results showed that the first-order kinetic constant (k) of oat starches (OS-1 and OS-2) was lower than that of rice starch. The size of amylose chains, amylose content and degree of branching (DB) of amylopectin in oat starch were significantly higher than the corresponding parameters in rice starch. The larger molecular size of oat starch may account for its lower digestion rate. The fine structure of amylopectin showed that oat starch had less chains of DP 6-12 and DP>36, which may explain the small difference in digestion rate between oat and rice starch. The biosynthesis model from oat amylopectin fine structure data suggested a lower starch branching enzyme (SBE) activity and/or a higher starch synthase (SS) activity, which may decrease the DB of oat starch and increase its digestion rate.

  7. [Molecular genetic investigation of sugar beet (Beta vulgaris L.)].

    PubMed

    Butorina, A K; Kornienko, A V

    2011-10-01

    Molecular genetic studies of sugar beet (Beta vulgaris L.) are reviewed as a basis for the development of genomics of this species. The methods used to study structural and functional genomics are considered. The results and their application to increase the efficiency of sugar beet breeding are discussed.

  8. Isotope effects in water as investigated by neutron diffraction and path integral molecular dynamics

    NASA Astrophysics Data System (ADS)

    Zeidler, Anita; Salmon, Philip S.; Fischer, Henry E.; Neuefeind, Jörg C.; Simonson, J. Mike; Markland, Thomas E.

    2012-07-01

    The structures of heavy and light water at 300 K were investigated by using a joint approach in which the method of neutron diffraction with oxygen isotope substitution was complemented by path integral molecular dynamics simulations. The diffraction results, which give intra-molecular O-D and O-H bond distances of 0.985(5) and 0.990(5) Å, were found to be in best agreement with those obtained by using the flexible anharmonic TTM3-F water model. Both techniques show a difference of ≃ 0.5% between the O-D and O-H intra-molecular bond lengths, and the results support a competing quantum effects model for water in which its structural and dynamical properties are governed by an offset between intra-molecular and inter-molecular quantum contributions. Further consideration of the O-O correlations is needed in order to improve agreement with experiment.

  9. Molecular structure and elastic properties of thermotropic liquid crystals: integrated molecular dynamics--statistical mechanical theory vs molecular field approach.

    PubMed

    Ilk Capar, M; Nar, A; Ferrarini, A; Frezza, E; Greco, C; Zakharov, A V; Vakulenko, A A

    2013-03-21

    The connection between the molecular structure of liquid crystals and their elastic properties, which control the director deformations relevant for electro-optic applications, remains a challenging objective for theories and computations. Here, we compare two methods that have been proposed to this purpose, both characterized by a detailed molecular level description. One is an integrated molecular dynamics-statistical mechanical approach, where the bulk elastic constants of nematics are calculated from the direct correlation function (DCFs) and the single molecule orientational distribution function [D. A. McQuarrie, Statistical Mechanics (Harper & Row, New York, 1973)]. The latter is obtained from atomistic molecular dynamics trajectories, together with the radial distribution function, from which the DCF is then determined by solving the Ornstein-Zernike equation. The other approach is based on a molecular field theory, where the potential of mean torque experienced by a mesogen in the liquid crystal phase is parameterized according to its molecular surface. In this case, the calculation of elastic constants is combined with the Monte Carlo sampling of single molecule conformations. Using these different approaches, but the same description, at the level of molecular geometry and torsional potentials, we have investigated the elastic properties of the nematic phase of two typical mesogens, 4'-n-pentyloxy-4-cyanobiphenyl and 4'-n-heptyloxy-4-cyanobiphenyl. Both methods yield K3(bend) >K1 (splay) >K2 (twist), although there are some discrepancies in the average elastic constants and in their anisotropy. These are interpreted in terms of the different approximations and the different ways of accounting for the structural properties of molecules in the two approaches. In general, the results point to the role of the molecular shape, which is modulated by the conformational freedom and cannot be fully accounted for by a single descriptor such as the aspect ratio.

  10. Molecular structure and elastic properties of thermotropic liquid crystals: Integrated molecular dynamics—Statistical mechanical theory vs molecular field approach

    NASA Astrophysics Data System (ADS)

    Capar, M. Ilk; Nar, A.; Ferrarini, A.; Frezza, E.; Greco, C.; Zakharov, A. V.; Vakulenko, A. A.

    2013-03-01

    The connection between the molecular structure of liquid crystals and their elastic properties, which control the director deformations relevant for electro-optic applications, remains a challenging objective for theories and computations. Here, we compare two methods that have been proposed to this purpose, both characterized by a detailed molecular level description. One is an integrated molecular dynamics-statistical mechanical approach, where the bulk elastic constants of nematics are calculated from the direct correlation function (DCFs) and the single molecule orientational distribution function [D. A. McQuarrie, Statistical Mechanics (Harper & Row, New York, 1973)]. The latter is obtained from atomistic molecular dynamics trajectories, together with the radial distribution function, from which the DCF is then determined by solving the Ornstein-Zernike equation. The other approach is based on a molecular field theory, where the potential of mean torque experienced by a mesogen in the liquid crystal phase is parameterized according to its molecular surface. In this case, the calculation of elastic constants is combined with the Monte Carlo sampling of single molecule conformations. Using these different approaches, but the same description, at the level of molecular geometry and torsional potentials, we have investigated the elastic properties of the nematic phase of two typical mesogens, 4'-n-pentyloxy-4-cyanobiphenyl and 4'-n-heptyloxy-4-cyanobiphenyl. Both methods yield K3(bend) >K1 (splay) >K2 (twist), although there are some discrepancies in the average elastic constants and in their anisotropy. These are interpreted in terms of the different approximations and the different ways of accounting for the structural properties of molecules in the two approaches. In general, the results point to the role of the molecular shape, which is modulated by the conformational freedom and cannot be fully accounted for by a single descriptor such as the aspect ratio.

  11. Mechanical properties of borophene films: a reactive molecular dynamics investigation

    NASA Astrophysics Data System (ADS)

    Quy Le, Minh; Mortazavi, Bohayra; Rabczuk, Timon

    2016-11-01

    The most recent experimental advances could provide ways for the fabrication of several atomic thick and planar forms of boron atoms. For the first time, we explore the mechanical properties of five types of boron films with various vacancy ratios ranging from 0.1-0.15, using molecular dynamics simulations with ReaxFF force field. It is found that the Young’s modulus and tensile strength decrease with increasing the temperature. We found that boron sheets exhibit an anisotropic mechanical response due to the different arrangement of atoms along the armchair and zigzag directions. At room temperature, 2D Young’s modulus and fracture stress of these five sheets appear in the range 63-136 N m-1 and 12-19 N m-1, respectively. In addition, the strains at tensile strength are in the ranges of 9%-14%, 11%-19%, and 10%-16% at 1, 300, and 600 K, respectively. This investigation not only reveals the remarkable stiffness of 2D boron, but establishes relations between the mechanical properties of the boron sheets to the loading direction, temperature and atomic structures.

  12. Evolution & Phylogenetic Analysis: Classroom Activities for Investigating Molecular & Morphological Concepts

    ERIC Educational Resources Information Center

    Franklin, Wilfred A.

    2010-01-01

    In a flexible multisession laboratory, students investigate concepts of phylogenetic analysis at both the molecular and the morphological level. Students finish by conducting their own analysis on a collection of skeletons representing the major phyla of vertebrates, a collection of primate skulls, or a collection of hominid skulls.

  13. Molecular and electronic structure of electroactive self-assembled monolayers

    NASA Astrophysics Data System (ADS)

    Méndez De Leo, Lucila P.; de la Llave, Ezequiel; Scherlis, Damián; Williams, Federico J.

    2013-03-01

    Self-assembled monolayers (SAMs) containing electroactive functional groups are excellent model systems for the formation of electronic devices by self-assembly. In particular ferrocene-terminated alkanethiol SAMs have been extensively studied in the past. However, there are still open questions related with their electronic structure including the influence of the ferrocene group in the SAM-induced work function changes of the underlying metal. We have thus carried out a thorough experimental and theoretical investigation in order to determine the molecular and electronic structure of ferrocene-terminated alkanethiol SAMs on Au surfaces. In agreement with previous studies we found that the Fc-containing alkanethiol molecules adsorb forming a thiolate bond with the Au surface with a molecular geometry 30° tilted with respect to the surface normal. Measured surface coverages indicate the formation of a compact monolayer. We found for the first time that the ferrocene group has little influence on the observed work function decrease which is largely determined by the alkanethiol. Furthermore, the ferrocene moiety lies 14 Å above the metal surface covalently bonded to the alkanethiol SAM and its HOMO is located at -1.6 eV below the Fermi level. Our results provide new valuable insight into the molecular and electronic structure of electroactive SAMs which are of fundamental importance in the field of molecular electronics.

  14. Molecular and electronic structure of electroactive self-assembled monolayers.

    PubMed

    Méndez De Leo, Lucila P; de la Llave, Ezequiel; Scherlis, Damián; Williams, Federico J

    2013-03-21

    Self-assembled monolayers (SAMs) containing electroactive functional groups are excellent model systems for the formation of electronic devices by self-assembly. In particular ferrocene-terminated alkanethiol SAMs have been extensively studied in the past. However, there are still open questions related with their electronic structure including the influence of the ferrocene group in the SAM-induced work function changes of the underlying metal. We have thus carried out a thorough experimental and theoretical investigation in order to determine the molecular and electronic structure of ferrocene-terminated alkanethiol SAMs on Au surfaces. In agreement with previous studies we found that the Fc-containing alkanethiol molecules adsorb forming a thiolate bond with the Au surface with a molecular geometry 30° tilted with respect to the surface normal. Measured surface coverages indicate the formation of a compact monolayer. We found for the first time that the ferrocene group has little influence on the observed work function decrease which is largely determined by the alkanethiol. Furthermore, the ferrocene moiety lies 14 Å above the metal surface covalently bonded to the alkanethiol SAM and its HOMO is located at -1.6 eV below the Fermi level. Our results provide new valuable insight into the molecular and electronic structure of electroactive SAMs which are of fundamental importance in the field of molecular electronics.

  15. Rheological investigation of highly filled polymers: Effect of molecular weight

    NASA Astrophysics Data System (ADS)

    Hnatkova, Eva; Hausnerova, Berenika; Hales, Andrew; Jiranek, Lukas; Vera, Juan Miguel Alcon

    2015-04-01

    The paper deals with rheological properties of highly filled polymers used in powder injection molding. Within the experimental framework seven PIM feedstocks based on superalloy Inconel 718 powder were prepared. Each feedstock contains the fixed amount of powder loading and the same composition of binder system consisting of three components: polyethylene glycol (PEG) differing in molecular weight, poly (methyl methacrylate) (PMMA) and stearic acid (SA). The aim is to investigate the influence of PEG's molecular weight on the flow properties of feedstocks. Non-Newtonian indices, representing the shear rate sensitivity of the feedstocks, are obtained from a polynomial fit, and found to vary within measured shear rates range from 0.2 to 0.8. Temperature effect is considered via activation energies, showing decreasing trend with increasing of molecular weight of PEG (except of feedstock containing 1,500 g.mol-1 PEG).

  16. Molecular structure of the collagen triple helix.

    PubMed

    Brodsky, Barbara; Persikov, Anton V

    2005-01-01

    The molecular conformation of the collagen triple helix confers strict amino acid sequence constraints, requiring a (Gly-X-Y)(n) repeating pattern and a high content of imino acids. The increasing family of collagens and proteins with collagenous domains shows the collagen triple helix to be a basic motif adaptable to a range of proteins and functions. Its rodlike domain has the potential for various modes of self-association and the capacity to bind receptors, other proteins, GAGs, and nucleic acids. High-resolution crystal structures obtained for collagen model peptides confirm the supercoiled triple helix conformation, and provide new information on hydrogen bonding patterns, hydration, sidechain interactions, and ligand binding. For several peptides, the helix twist was found to be sequence dependent, and such variation in helix twist may serve as recognition features or to orient the triple helix for binding. Mutations in the collagen triple-helix domain lead to a variety of human disorders. The most common mutations are single-base substitutions that lead to the replacement of one Gly residue, breaking the Gly-X-Y repeating pattern. A single Gly substitution destabilizes the triple helix through a local disruption in hydrogen bonding and produces a discontinuity in the register of the helix. Molecular information about the collagen triple helix and the effect of mutations will lead to a better understanding of function and pathology.

  17. Growth mechanism, electronic spectral investigation and molecular orbital studies of L-prolinium phosphate.

    PubMed

    Liu, Xiaojing; Sun, Xin; Xu, Xijin; Sun, Ping

    2015-01-01

    By using atomic force microscopy, birth and spread has proved to be the primary growth mechanism for L-prolinium phosphate (LPP). The phenomenon of newly formed islands expanding to the edge of the preceding terrace was observed. The optimized molecular structure and the molecular properties were calculated by density functional theory method. Natural bond orbital analysis was carried out to demonstrate the various inter and intramolecular interactions that are responsible for the stabilization of LPP leading to high NLO activity. Molecular electrostatic potential, frontier molecular orbital analysis and thermodynamic properties were investigated to get a better insight of the molecular properties. Global and local reactivity descriptors were computed to predict the reactivity and reactive sites on the molecules. Non-linear optical (NLO) properties such as the total dipole moment (μ) and first order hyperopolarizability (β) were also calculated to predict NLO behavior.

  18. Theoretical investigations on the molecular structure, vibrational spectra, HOMO-LUMO analyses and NBO study of 1-[(Cyclopropylmethoxy)methyl]-5-ethyl-6-(4-methylbenzyl)-1,2,3,4-tetrahydropyrimidine-2,4-dione.

    PubMed

    Al-Abdullah, Ebtehal S; Mary, Y Sheena; Panicker, C Yohannan; El-Brollosy, Nasser R; El-Emam, Ali A; Van Alsenoy, Christian; Al-Saadi, Abdulaziz A

    2014-12-10

    The FT-IR and FT-Raman spectra of 1-[(Cyclopropylmethoxy)methyl]-5-ethyl-6-(4-methylbenzyl)-1,2,3,4-tetrahydropyrimidine-2,4-dione were recorded. In this work, experimental and theoretical study on the molecular structure and vibrational wavenumbers of the title compound are presented. The vibrational wavenumbers were obtained theoretically at the DFT level and were compared with the experimental results. The study is extended to calculate the HOMO-LUMO energy gap, NBO, mapped molecular electrostatic potential and first hyperpolarizability. The calculated first hyperpolarizability of the title compound is 9.15 times that of urea and hence the title compound and the series of compounds it represents are attractive candidates for further studies in non linear optical applications. In the title compound, the HOMO of π nature is delocalized over the phenyl ring while the LUMO is located over the pyrimidine ring. The inter-molecular hydrogen bonding at O7 and N1H25 positions in each monomer give rise to a C2-symmetry dimer which is predicted to be about 10kcalmol(-1) more stable than the monomeric form.

  19. Theoretical investigations on the molecular structure, vibrational spectra, HOMO-LUMO analyses and NBO study of 1-[(Cyclopropylmethoxy)methyl]-5-ethyl-6-(4-methylbenzyl)-1,2,3,4-tetrahydropyrimidine-2,4-dione

    NASA Astrophysics Data System (ADS)

    Al-Abdullah, Ebtehal S.; Mary, Y. Sheena; Panicker, C. Yohannan; El-Brollosy, Nasser R.; El-Emam, Ali A.; Van Alsenoy, Christian; Al-Saadi, Abdulaziz A.

    2014-12-01

    The FT-IR and FT-Raman spectra of 1-[(Cyclopropylmethoxy)methyl]-5-ethyl-6-(4-methylbenzyl)-1,2,3,4-tetrahydropyrimidine-2,4-dione were recorded. In this work, experimental and theoretical study on the molecular structure and vibrational wavenumbers of the title compound are presented. The vibrational wavenumbers were obtained theoretically at the DFT level and were compared with the experimental results. The study is extended to calculate the HOMO-LUMO energy gap, NBO, mapped molecular electrostatic potential and first hyperpolarizability. The calculated first hyperpolarizability of the title compound is 9.15 times that of urea and hence the title compound and the series of compounds it represents are attractive candidates for further studies in non linear optical applications. In the title compound, the HOMO of π nature is delocalized over the phenyl ring while the LUMO is located over the pyrimidine ring. The inter-molecular hydrogen bonding at O7 and N1sbnd H25 positions in each monomer give rise to a C2-symmetry dimer which is predicted to be about 10 kcal mol-1 more stable than the monomeric form.

  20. Investigating the Web Structure by Isolated Stars

    NASA Astrophysics Data System (ADS)

    Uno, Yushi; Ota, Yoshinobu; Uemichi, Akio

    The link structure of the Web is generally represented by the webgraph, and it is often used for web structure mining that mainly aims to find hidden communities on the Web. In this paper, we identify a common frequent substructure and give it a formal graph definition, which we call an isolated star (i-star), and propose an efficient enumeration algorithm of i-stars. We then investigate the structure of the Web by enumerating i-stars from real web data. As a result, we observed that most i-stars correspond to index structures in single domains, while some of them are verified to be candidates of communities, which implies the validity of i-stars as useful substructure for web structure mining and link spam detecting. We also observed that the distributions of i-star sizes show power-law, which is another new evidence of the scale-freeness of the webgraph.

  1. Structures of the substrate-free and product-bound forms of HmuO, a heme oxygenase from corynebacterium diphtheriae: x-ray crystallography and molecular dynamics investigation.

    PubMed

    Unno, Masaki; Ardèvol, Albert; Rovira, Carme; Ikeda-Saito, Masao

    2013-11-29

    Heme oxygenase catalyzes the degradation of heme to biliverdin, iron, and carbon monoxide. Here, we present crystal structures of the substrate-free, Fe(3+)-biliverdin-bound, and biliverdin-bound forms of HmuO, a heme oxygenase from Corynebacterium diphtheriae, refined to 1.80, 1.90, and 1.85 Å resolution, respectively. In the substrate-free structure, the proximal and distal helices, which tightly bracket the substrate heme in the substrate-bound heme complex, move apart, and the proximal helix is partially unwound. These features are supported by the molecular dynamic simulations. The structure implies that the heme binding fixes the enzyme active site structure, including the water hydrogen bond network critical for heme degradation. The biliverdin groups assume the helical conformation and are located in the heme pocket in the crystal structures of the Fe(3+)-biliverdin-bound and the biliverdin-bound HmuO, prepared by in situ heme oxygenase reaction from the heme complex crystals. The proximal His serves as the Fe(3+)-biliverdin axial ligand in the former complex and forms a hydrogen bond through a bridging water molecule with the biliverdin pyrrole nitrogen atoms in the latter complex. In both structures, salt bridges between one of the biliverdin propionate groups and the Arg and Lys residues further stabilize biliverdin at the HmuO heme pocket. Additionally, the crystal structure of a mixture of two intermediates between the Fe(3+)-biliverdin and biliverdin complexes has been determined at 1.70 Å resolution, implying a possible route for iron exit.

  2. Investigation of Chiral Molecular Micelles by NMR Spectroscopy and Molecular Dynamics Simulation

    PubMed Central

    Morris, Kevin F.; Billiot, Eugene J.; Billiot, Fereshteh H.; Lipkowitz, Kenny B.; Southerland, William M.; Fang, Yayin

    2013-01-01

    NMR spectroscopy and molecular dynamics (MD) simulation analyses of the chiral molecular micelles poly-(sodium undecyl-(L,L)-leucine-valine) (poly-SULV) and poly-(sodium undecyl-(L,L)- valine-leucine) (poly-(SUVL)) are reported. Both molecular micelles are used as chiral selectors in electrokinetic chromatography and each consists of covalently linked surfactant chains with chiral dipeptide headgroups. To provide experimental support for the structures from MD simulations, NOESY spectra were used to identify protons in close spatial proximity. Results from the NOESY analyses were then compared to radial distribution functions from MD simulations. In addition, the hydrodynamic radii of both molecular micelles were calculated from NMR-derived diffusion coefficients. Corresponding radii from the MD simulations were found to be in agreement with these experimental results. NMR diffusion experiments were also used to measure association constants for polar and non-polar binaphthyl analytes binding to both molecular micelles. Poly(SUVL) was found to bind the non-polar analyte enantiomers more strongly, while the more polar analyte enantiomers interacted more strongly with poly(SULV). MD simulations in tum showed that poly(SUL V) had a more open structure that gave greater access for water molecules to the dipeptide headgroup region. PMID:23991355

  3. Investigating bias in squared regression structure coefficients

    PubMed Central

    Nimon, Kim F.; Zientek, Linda R.; Thompson, Bruce

    2015-01-01

    The importance of structure coefficients and analogs of regression weights for analysis within the general linear model (GLM) has been well-documented. The purpose of this study was to investigate bias in squared structure coefficients in the context of multiple regression and to determine if a formula that had been shown to correct for bias in squared Pearson correlation coefficients and coefficients of determination could be used to correct for bias in squared regression structure coefficients. Using data from a Monte Carlo simulation, this study found that squared regression structure coefficients corrected with Pratt's formula produced less biased estimates and might be more accurate and stable estimates of population squared regression structure coefficients than estimates with no such corrections. While our findings are in line with prior literature that identified multicollinearity as a predictor of bias in squared regression structure coefficients but not coefficients of determination, the findings from this study are unique in that the level of predictive power, number of predictors, and sample size were also observed to contribute bias in squared regression structure coefficients. PMID:26217273

  4. Investigating bias in squared regression structure coefficients.

    PubMed

    Nimon, Kim F; Zientek, Linda R; Thompson, Bruce

    2015-01-01

    The importance of structure coefficients and analogs of regression weights for analysis within the general linear model (GLM) has been well-documented. The purpose of this study was to investigate bias in squared structure coefficients in the context of multiple regression and to determine if a formula that had been shown to correct for bias in squared Pearson correlation coefficients and coefficients of determination could be used to correct for bias in squared regression structure coefficients. Using data from a Monte Carlo simulation, this study found that squared regression structure coefficients corrected with Pratt's formula produced less biased estimates and might be more accurate and stable estimates of population squared regression structure coefficients than estimates with no such corrections. While our findings are in line with prior literature that identified multicollinearity as a predictor of bias in squared regression structure coefficients but not coefficients of determination, the findings from this study are unique in that the level of predictive power, number of predictors, and sample size were also observed to contribute bias in squared regression structure coefficients.

  5. MOLECULAR INTERACTION POTENTIALS FOR THE DEVELOPMENT OF STRUCTURE-ACTIVITY RELATIONSHIPS

    EPA Science Inventory

    Abstract
    One reasonable approach to the analysis of the relationships between molecular structure and toxic activity is through the investigation of the forces and intermolecular interactions responsible for chemical toxicity. The interaction between the xenobiotic and the bio...

  6. Shock induced phase transition of water: Molecular dynamics investigation

    SciTech Connect

    Neogi, Anupam; Mitra, Nilanjan

    2016-02-15

    Molecular dynamics simulations were carried out using numerous force potentials to investigate the shock induced phenomenon of pure bulk liquid water. Partial phase transition was observed at single shock velocity of 4.0 km/s without requirement of any external nucleators. Change in thermodynamic variables along with radial distribution function plots and spectral analysis revealed for the first time in the literature, within the context of molecular dynamic simulations, the thermodynamic pathway leading to formation of ice VII from liquid water on shock loading. The study also revealed information for the first time in the literature about the statistical time-frame after passage of shock in which ice VII formation can be observed and variations in degree of crystallinity of the sample over the entire simulation time of 100 ns.

  7. State of water, molecular structure, and cytotoxicity of silk hydrogels.

    PubMed

    Numata, Keiji; Katashima, Takuya; Sakai, Takamasa

    2011-06-13

    A novel technique was developed to regulate the bulk water content of silk hydrogels by adjusting the concentrations of silk proteins, which is helpful to investigate the effects of the state of water in polymeric hydrogel on its biological functions, such as cytotoxicity. Gelation of the silk hydrogel was induced with ethanol and its gelation behavior was analyzed by rheometry. The silk hydrogels prepared at various silk concentrations were characterized with respect to their water content, molecular and network structures, state of water, mechanical properties, and cytotoxicity to human mesenchymal stem cells. The network structure of silk hydrogel was heterogeneous with β-sheet and fibrillar structures. The influence of the state of water in the silk hydrogel on the cytotoxicity was recognized by means of differential scanning calorimetry and cell proliferation assay, which revealed that the bound water will support cell-adhesion proteins in the cellular matrix to interact with the surface of the silk hydrogels.

  8. 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.

  9. Optical properties and structural investigations of (11-22)-oriented GaN/Al{sub 0.5}Ga{sub 0.5}N quantum wells grown by molecular beam epitaxy

    SciTech Connect

    Rosales, Daniel; Gil, Bernard; Bretagnon, Thierry; Brault, Julien; Vennéguès, Philippe; Nemoz, Maud; Mierry, Philippe de; Damilano, Benjamin; Massies, Jean; Bigenwald, Pierre

    2015-07-14

    We have grown (11-22)-oriented GaN/Al{sub 0.5}Ga{sub 0.5}N quantum wells (QWs) using molecular beam epitaxy on GaN (11-22)-oriented templates grown by metal-organic vapor phase epitaxy on m-plane oriented sapphire substrates. The performance of epitaxial growth of GaN/Al{sub 0.5}Ga{sub 0.5}N heterostructures on the semi-polar orientation (11-22) in terms of surface roughness and structural properties, i.e., strain relaxation mechanisms is discussed. In addition, high resolution transmission electron microscopy reveals very smooth QW interfaces. The photoluminescence of such samples are strictly originating from radiative recombination of free excitons for temperatures above 100 K. At high temperature, the population of localized excitons, moderately trapped (5 meV) at low temperature, is negligible.

  10. Filamentary structure in the Orion molecular cloud

    NASA Technical Reports Server (NTRS)

    Bally, J.; Langer, W. D.; Bally, J.; Langer, W. D.; Bally, J.; Langer, W. D.

    1986-01-01

    A large scale 13CO map (containing 33,000 spectra) of the giant molecular cloud located in the southern part of Orion is presented which contains the Orion Nebula, NGC1977, and the LI641 dark cloud complex. The overall structure of the cloud is filamentary, with individual features having a length up to 40 times their width. This morphology may result from the effects of star formation in the region or embedded magnetic fields in the cloud. We suggest a simple picture for the evolution of the Orion-A cloud and the formation of the major filament. A rotating proto-cloud (counter rotating with respect to the galaxy) contians a b-field aligned with the galaxtic plane. The northern protion of this cloud collapsed first, perhaps triggered by the pressure of the Ori I OB association. The magnetic field combined with the anisotropic pressure produced by the OB-association breaks the symmetry of the pancake instability, a filament rather than a disc is produced. The growth of instabilities in the filament formed sub-condensations which are recent sites of star formation.

  11. The Determination of Molecular Structure from Rotational Spectra

    DOE R&D Accomplishments Database

    Laurie, V. W.; Herschbach, D. R.

    1962-07-01

    An analysis is presented concerning the average molecular configuration variations and their effects on molecular structure determinations. It is noted that the isotopic dependence of the zero-point is often primarily governed by the isotopic variation of the average molecular configuration. (J.R.D.)

  12. Polymorphism and disorder in caffeine: Dielectric investigation of molecular mobilities

    NASA Astrophysics Data System (ADS)

    Descamps, M.; Decroix, A. A.

    2014-12-01

    Using dielectric relaxation data we have characterized the molecular mobilities of caffeine both in phase I (stable and metastable) and in phase II. In phase I effects of sublimation and phase transformation kinetics were carefully considered. In plane rotational motions were followed on a wide temperature range. A noticeable antiferroelectric short range order developing at the approach of the glass-like transition is characterized. Condition for occurrence of a critical-like behaviour is discussed. At high temperature the emergence of an additional ultra slow relaxation process is highlighted. Possible molecular mechanisms are proposed for both processes. In phase II the existence of a less intense relaxation process is confirmed. Close similarity with the main process developing in phase I hints at a common origin of the dipolar motions. Careful consideration of recent structure determinations leads to suggest that this process is associated to similar molecular in plane rotations but developing at the surface of crystalline samples. Lower cooperativity at the surface is reflected in the smaller activation entropy of the relaxation.

  13. Structural investigation of californium under pressure

    NASA Astrophysics Data System (ADS)

    Heathman, S.; Le Bihan, T.; Yagoubi, S.; Johansson, B.; Ahuja, R.

    2013-06-01

    The high-pressure structural behavior of californium has been studied experimentally and theoretically up to 100 GPa. A valence change from divalent to trivalent forms was observed under modest pressure revealing californium to be the only actinide to exhibit more than one metallic valence at near to ambient conditions as is the case for cerium in the lanthanide series. Three metallic valencies and four different crystallographic phases were observed in californium as a function of pressure. High-pressure techniques, synchrotron radiation, and ab initio electronic structure calculations of total energies were used to investigate the material and to determine the role which californium's 5f electrons play in influencing these transitions. The crystallographic structures observed are similar to those found in the preceding actinide elements, curium and americium, with the initially localized 5f states becoming completely delocalized under the influence of high pressure.

  14. Investigations of ice nanoparticles and aerosols in molecular beams

    NASA Astrophysics Data System (ADS)

    Farnik, Michal

    2015-03-01

    We have recently set up a versatile experiment which allows for different experiments with molecular clusters and nanoparticles in molecular beams. Here we concentrate on the experiments with ice nanoparticles (large water clusters (H2O)N, N ~ 102-103) doped with atmospherically relevant molecules, e.g., hydrogen halides, CFCs, nitric acid, NxOy, etc. Such species are relevant to ozone depletion and other atmospheric processes. We investigate (1) the UV-photochemistry using velocity map imaging techniques, and (2) the uptake cross section for the molecules on the ice nanoparticles from velocity measurements. In addition, we record (3) mass spectra of the particles implementing different ionization methods: electron ionization (EI) at variable electron energies, photoionization, and special method of electron photodetachment after Na-doping (NaPI). The unique combination of all these different methods performed with the same nanoparticles provides detailed molecular level information about the studied species and their (photo)physics and chemistry. In particular, an investigation of mixed water-nitric acid particles by means of EI and NaPI revealed the prominent role of the HNO3 molecule as the condensation nuclei. The uptake of atmospheric molecules by ice nanoparticles has been studied, and the pickup cross sections for some molecules exceed significantly the geometrical sizes of the ice nanoparticles. It has been argued that the large particles composed of several hundred water molecules which grow in the supersonic expansions tend to have highly irregular shapes -nanosnowflakes. Photodissociation of hydrogen halides on ice nanoparticles has been investigated, and shown to proceed via excitation of acidically dissociated ion pair and subsequent biradical generation and H3O dissociation. The photodissociation of CF2Cl2 molecules in clusters leads to efficient Cl-fragment caging caused by formation of halogen bond. Grant agency of the Czech Republic, Grant No.: 14

  15. Molecular cloning of chicken aggrecan. Structural analyses.

    PubMed Central

    Chandrasekaran, L; Tanzer, M L

    1992-01-01

    The large, aggregating chondroitin sulphate proteoglycan of cartilage, aggrecan, has served as a generic model of proteoglycan structure. Molecular cloning of aggrecans has further defined their amino acid sequences and domain structures. In this study, we have obtained the complete coding sequence of chicken sternal cartilage aggrecan by a combination of cDNA and genomic DNA sequencing. The composite sequence is 6117 bp in length, encoding 1951 amino acids. Comparison of chicken aggrecan protein primary structure with rat, human and bovine aggrecans has disclosed both similarities and differences. The domains which are most highly conserved at 70-80% identity are the N-terminal domains G1 and G2 and the C-terminal domain G3. The chondroitin sulphate domain of chicken aggrecan is smaller than that of rat and human aggrecans and has very distinctive repeat sequences. It has two separate sections, one comprising 12 consecutive Ser-Gly-Glu repeats of 20 amino acids each, adjacent to the other which has 23 discontinuous Ser-Gly-Glu repeats of 10 amino acids each; this latter region, N-terminal to the former one, appears to be unique to chicken aggrecan. The two regions contain a total of 94 potential chondroitin sulphate attachment sites. Genomic comparison shows that, although chicken exons 11-14 are identical in size to the rat and human exons, chicken exon 10 is the smallest of the three species. This is also reflected in the size of its chondroitin sulphate coding region and in the total number of Ser-Gly pairs. The putative keratan sulphate domain shows 31-45% identity with the other species and lacks the repetitive sequences seen in the others. In summary, while the linear arrangement of specific domains of chicken aggrecan is identical to that in the aggrecans of other species, and while there is considerable identity of three separate domains, chicken aggrecan demonstrates unique features, notably in its chondroitin sulphate domain and its keratan sulphate

  16. Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations.

    PubMed

    Dal Peraro, Matteo; Ruggerone, Paolo; Raugei, Simone; Gervasio, Francesco Luigi; Carloni, Paolo

    2007-04-01

    Density functional theory (DFT)-based Car-Parrinello molecular dynamics (CPMD) simulations describe the time evolution of molecular systems without resorting to a predefined potential energy surface. CPMD and hybrid molecular mechanics/CPMD schemes have recently enabled the calculation of redox properties of electron transfer proteins in their complex biological environment. They provided structural and spectroscopic information on novel platinum-based anticancer drugs that target DNA, also setting the basis for the construction of force fields for the metal lesion. Molecular mechanics/CPMD also lead to mechanistic hypotheses for a variety of metalloenzymes. Recent advances that increase the accuracy of DFT and the efficiency of investigating rare events are further expanding the domain of CPMD applications to biomolecules.

  17. Kinetic Effects of Aromatic Molecular Structures on Diffusion Flame Extinction

    SciTech Connect

    Won, Sang Hee; Dooley, S.; Dryer, F. L.; Ju, Yiguang

    2011-01-01

    Kinetic effects of aromatic molecular structures for jet fuel surrogates on the extinction of diffusion flames have been investigated experimentally and numerically in the counterflow configuration for toluene, n-propylbenzene, 1,2,4-trimethylbenzene, and 1,3,5-trimethylbenzene. Quantitative measurement of OH concentration for aromatic fuels was conducted by directly measuring the quenching rate from the emission lifetimes of OH planar laser induced fluorescence (LIF). The kinetic models for toluene and 1,2,4-trimethylbenzene were validated against the measurements of extinction strain rates and LIF measurements. A semi-detailed n-propylbenzene kinetic model was developed and tested. The experimental results showed that the extinction limits are ranked from highest to lowest as n-propylbenzene, toluene, 1,2,4-trimethylbenzene, and 1,3,5-trimethylbenzene. The present models for toluene and n-propylbenzene agree reasonably well with the measurements, whereas the model for 1,2,4-trimethylbenzene under-estimates extinction limits. Kinetic pathways of OH production and consumption were analyzed to investigate the impact of fuel fragmentation on OH formation. It was found that, for fuels with different molecular structures, the fuel decomposition pathways and their propagation into the formation of radical pool play an important role to determine the extinction limits of diffusion flames. Furthermore, OH concentrations were found to be representative of the entire radical pool concentration, the balance between chain branching and propagation/termination reactions and the balance between heat production from the reaction zone and heat losses to the fuel and oxidizer sides. Finally, a proposed “OH index,” was defined to demonstrate a linear correlation between extinction strain rate and OH index and fuel mole fraction, suggesting that the diffusion flame extinctions for the tested aromatic fuels can be determined by the capability of a fuel to establish a radical pool

  18. Identification of a Conserved 8 aa Insert in the PIP5K Protein in the Saccharomycetaceae family of Fungi and the Molecular Dynamics Simulations and Structural Analysis to investigate its Potential Functional Role.

    PubMed

    Khadka, Bijendra; Gupta, Radhey S

    2017-04-13

    Homologs of the phosphatidylinositol-4-phosphate-5-kinase (PIP5K), which controls a multitude of essential cellular functions, contain a 8 aa insert in a conserved region that is specific for the Saccharomycetaceae family of fungi. Using structures of human PIP4K proteins as templates, structural models were generated of the Saccharomyces cerevisiae and human PIP5K proteins. In the modeled S. cerevisiae PIP5K, the 8 aa insert forms a surface exposed loop, present on the same face of the protein as the activation loop of the kinase domain. Electrostatic potential analysis indicates that the residues from 8 aa conserved loop form a highly-positively charged surface patch, which through electrostatic interaction with the anionic portions of phospholipid head groups, is expected to play a role in the membrane interaction of the yeast PIP5K. To unravel this prediction, molecular dynamics (MD) simulations were carried out to examine the binding interaction of PIP5K, either containing or lacking the conserved signature insert (CSI), with two different membrane lipid bilayers. The results from MD studies provide insights concerning the mechanistic of interaction of PIP5K with lipid bilayer, and support the contention that the identified 8 aa conserved insert in fungal PIP5K plays an important role in the binding of this protein with membrane surface. This article is protected by copyright. All rights reserved.

  19. Investigation on the binding interaction between silybin and pepsin by spectral and molecular docking.

    PubMed

    Zeng, Hua-jin; You, Jing; Liang, Hui-li; Qi, Tingting; Yang, Ran; Qu, Ling-bo

    2014-06-01

    In this study, the binding mode of silybin with pepsin was investigated by spectroscopic and molecular docking methods. Silybin can interact with pepsin to form a silybin-pepsin complex. The binding constant, number of binding sites and thermodynamic parameters were measured, which indicated that silybin could spontaneously bind with pepsin mainly through hydrophobic interaction with one binding site. Molecular docking results revealed that silybin bound into the pepsin cavity site. Synchronous fluorescence and three-dimensional fluorescence results provide data concerning conformational and some micro-environmental changes of pepsin. Furthermore, in order to reveal whether the binding process can inhibit the activity of pepsin in vivo, the effect of silybin on pepsin activity in rat was investigated. The present study provides direct evidence at a molecular level to show that exposure to silybin could induce changes in the enzyme pepsin structure and function.

  20. Biological spectra analysis: Linking biological activity profiles to molecular structure

    PubMed Central

    Fliri, Anton F.; Loging, William T.; Thadeio, Peter F.; Volkmann, Robert A.

    2005-01-01

    Establishing quantitative relationships between molecular structure and broad biological effects has been a longstanding challenge in science. Currently, no method exists for forecasting broad biological activity profiles of medicinal agents even within narrow boundaries of structurally similar molecules. Starting from the premise that biological activity results from the capacity of small organic molecules to modulate the activity of the proteome, we set out to investigate whether descriptor sets could be developed for measuring and quantifying this molecular property. Using a 1,567-compound database, we show that percent inhibition values, determined at single high drug concentration in a battery of in vitro assays representing a cross section of the proteome, provide precise molecular property descriptors that identify the structure of molecules. When broad biological activity of molecules is represented in spectra form, organic molecules can be sorted by quantifying differences between biological spectra. Unlike traditional structure–activity relationship methods, sorting of molecules by using biospectra comparisons does not require knowledge of a molecule's putative drug targets. To illustrate this finding, we selected as starting point the biological activity spectra of clotrimazole and tioconazole because their putative target, lanosterol demethylase (CYP51), was not included in the bioassay array. Spectra similarity obtained through profile similarity measurements and hierarchical clustering provided an unbiased means for establishing quantitative relationships between chemical structures and biological activity spectra. This methodology, which we have termed biological spectra analysis, provides the capability not only of sorting molecules on the basis of biospectra similarity but also of predicting simultaneous interactions of new molecules with multiple proteins. PMID:15625110

  1. Giant Molecular Cloud Structure and Evolution

    NASA Technical Reports Server (NTRS)

    Hollenbach, David (Technical Monitor); Bodenheimer, P. H.

    2003-01-01

    Bodenheimer and Burkert extended earlier calculations of cloud core models to study collapse and fragmentation. The initial condition for an SPH collapse calculation is the density distribution of a Bonnor-Ebert sphere, with near balance between turbulent plus thermal energy and gravitational energy. The main parameter is the turbulent Mach number. For each Mach number several runs are made, each with a different random realization of the initial turbulent velocity field. The turbulence decays on a dynamical time scale, leading the cloud into collapse. The collapse proceeds isothermally until the density has increased to about 10(exp 13) g cm(exp -3). Then heating is included in the dense regions. The nature of the fragmentation is investigated. About 15 different runs have been performed with Mach numbers ranging from 0.3 to 3.5 (the typical value observed in molecular cloud cores is 0.7). The results show a definite trend of increasing multiplicity with increasing Mach number (M), with the number of fragments approximately proportional to (1 + M). In general, this result agrees with that of Fisher, Klein, and McKee who published three cases with an AMR grid code. However our results show that there is a large spread about this curve. For example, for M=0.3 one case resulted in no fragmentation while a second produced three fragments. Thus it is not only the value of M but also the details of the superposition of the various velocity modes that play a critical role in the formation of binaries. Also, the simulations produce a wide range of separations (10-1000 AU) for the multiple systems, in rough agreement with observations. These results are discussed in two conference proceedings.

  2. Structural investigation of protein kinase C inhibitors.

    PubMed

    Barak, D; Shibata, M; Rein, R

    1991-01-01

    The phospholipid and Ca2+ dependent protein kinase (PKC) plays an essential role in a variety of cellular events. Inhibition of PKC was shown to arrest growth in tumor cell cultures making it a target for possible antitumor therapy. Calphostins are potent inhibitors of PKC with high affinity for the enzyme regulatory site. Structural characteristics of calphostins, which confer the inhibitory activity, are investigated by comparing their optimized structures with the existing models for PKC activation. The resulting model of inhibitory activity assumes interaction with two out of the three electrostatic interaction sites postulated for activators. The model shows two sites of hydrophobic interaction and enables the inhibitory activity of gossypol to be accounted for.

  3. Structural investigation of protein kinase C inhibitors

    NASA Technical Reports Server (NTRS)

    Barak, D.; Shibata, M.; Rein, R.

    1991-01-01

    The phospholipid and Ca2+ dependent protein kinase (PKC) plays an essential role in a variety of cellular events. Inhibition of PKC was shown to arrest growth in tumor cell cultures making it a target for possible antitumor therapy. Calphostins are potent inhibitors of PKC with high affinity for the enzyme regulatory site. Structural characteristics of calphostins, which confer the inhibitory activity, are investigated by comparing their optimized structures with the existing models for PKC activation. The resulting model of inhibitory activity assumes interaction with two out of the three electrostatic interaction sites postulated for activators. The model shows two sites of hydrophobic interaction and enables the inhibitory activity of gossypol to be accounted for.

  4. Investigation of Y/SBA Composite Molecular Sieves Morphology Control and Catalytic Performance for n-Pentane Aromatization

    PubMed Central

    Shi, Chun-Wei; Wu, Wen-Yuan; Li, Shuai; Bian, Xue; Zhao, Shan-lin; Pei, Ming-Yuan

    2016-01-01

    Using Y molecular sieve as the core, Y/SBA-15 composite molecular sieves were prepared by different crystallization methods in the paper. The growth process and morphologies of the composite molecular sieves were controlled by adjusting the synthesis factors. The structures and acidity of two kinds of composite molecular sieves were characterized by X-ray diffraction (XRD), N2 adsorption/desorption, transmission electron microscopy (TEM), and NH3-TPD. The catalysis performances of the composite molecular sieves were investigated in the aromatization reaction of n-pentane. The results indicated that the desired core-shell composite molecular sieves were obtained when the crystallization conditions were 36 hours, 100 °C and secondary crystallization. The aromatization results showed that core-shell composite molecular sieves had better selectivity for producing high application value xylenes compared to mixed-crystal composite molecular sieves. PMID:27029526

  5. Structure investigations of PP-PA blends

    NASA Astrophysics Data System (ADS)

    Janicki, Jaroslaw; Wlochowicz, Andrzej; Slusarczyk, Czeslaw

    1997-02-01

    In the paper we have used the SAXS method in order to determine the supermolecular structure parameters, including the transition layer thickness, of polypropylene/polyamide-6 (PP/PA) blends. The transition layer thickness has been obtained by means of two methods elaborated by Koberstein and co-workers and by Ruland, respectively. Both these methods assume that changes of the electron density in the transition region can be described by a Gaussian function with a standard deviation (sigma) . The parameter (sigma) have been determined graphically from the appropriate plots. Then, the thickness of the phase boundary E was estimated as (root)12(sigma) . The investigated PP/PA blends are multiphase systems and the problem of determination of the boundary width is more complicated because the meaning of Porod's law must be considered with caution. This problem is discussed based on wide range of the investigated samples prepared over various pressure and crystallization temperature conditions.

  6. Molecular clouds and galactic spiral structure

    NASA Technical Reports Server (NTRS)

    Dame, T. M.

    1984-01-01

    Galactic CO line emission at 115 GHz was surveyed in order to study the distribution of molecular clouds in the inner galaxy. Comparison of this survey with similar H1 data reveals a detailed correlation with the most intense 21 cm features. To each of the classical 21 cm H1 spiral arms of the inner galaxy there corresponds a CO molecular arm which is generally more clearly defined and of higher contrast. A simple model is devised for the galactic distribution of molecular clouds. The modeling results suggest that molecular clouds are essentially transient objects, existing for 15 to 40 million years after their formation in a spiral arm, and are largely confined to spiral features about 300 pc wide.

  7. Ab initio investigation of benzene clusters: Molecular tailoring approach

    NASA Astrophysics Data System (ADS)

    Mahadevi, A. Subha; Rahalkar, Anuja P.; Gadre, Shridhar R.; Sastry, G. Narahari

    2010-10-01

    An exhaustive study on the clusters of benzene (Bz)n, n =2-8, at MP2/6-31++G∗∗ level of theory is reported. The relative strengths of CH-π and π-π interactions in these aggregates are examined, which eventually govern the pattern of cluster formation. A linear scaling method, viz., molecular tailoring approach (MTA), is efficiently employed for studying the energetics and growth patterns of benzene clusters consisting up to eight benzene (Bz) units. Accuracy of MTA-based calculations is appraised by performing the corresponding standard calculations wherever possible, i.e., up to tetramers. For benzene tetramers, the error introduced in energy is of the order of 0.1 mH (˜0.06 kcal/mol). Although for higher clusters the error may build up, further corrections based on many-body interaction energy analysis substantially reduce the error in the MTA-estimate. This is demonstrated for a prototypical case of benzene hexamer. A systematic way of building up a cluster of n monomers (n-mer) which employs molecular electrostatic potential of an (n -1)-mer is illustrated. The trends obtained using MTA method are essentially identical to those of the standard methods in terms of structure and energy. In summary, this study clearly brings out the possibility of effecting such large calculations, which are not possible conventionally, by the use of MTA without a significant loss of accuracy.

  8. Investigation of ``shears'' structure in ^110In

    NASA Astrophysics Data System (ADS)

    Chiara, C. J.; Fossan, D. B.; Lafosse, D. R.; Schnare, H.; Vaska, P.; Frauendorf, S.; Mullins, S. M.; Hackman, G.; Prévost, D.; Waddington, J. C.; Janzen, V. P.; Radford, D. C.; Ward, D.; Wadsworth, R.; Paul, E. S.

    1997-04-01

    The high-spin structure of ^110In has been investigated using the ^96Zr(^19F,5n) reaction. A thin-target experiment using an 85 MeV beam provided by the Chalk River TASCC facility yielded 50 million γ-γ coincidence events with the 8π spectrometer. In addition, a backed-target experiment using a 72 MeV beam provided by the SUNY at Stony Brook LINAC facility yielded 150 million events with the Stony Brook BGO-suppressed Ge spectrometer. A partial level scheme has been established in which two new γ-ray sequences have been observed in ^110In in addition to extending collective structures from earlier studies(R. Béraud, et al., J. Phys. (Paris), Colloq C-10), 159 (1980). The ΔI=1 bands involving high-K g_9/2 proton-hole orbitals and low-K g_7/2 and h_11/2 proton and neutron orbitals have been investigated as possible ``shears bands'' and compared with calculations made using the Tilted Axis Cranking (TAC) theory(S. Frauendorf, Nucl. Phys. A557), 259c (1993).

  9. Molecular structures, charge distributions, and vibrational analyses of the tetracoordinate Cu(II), Zn(II), Cd(II), and Hg(II) bromide complexes of p-toluidine investigated by density functional theory in comparison with experiments

    NASA Astrophysics Data System (ADS)

    Bardakçı, Tayyibe; Kumru, Mustafa; Altun, Ahmet

    2016-07-01

    The Cu(II), Zn(II), Cd(II), and Hg(II) bromide complexes of p-toluidine have been studied with B3LYP calculations by using def2-TZVP basis set at the metal atoms and using def2-TZVP and 6-311G+(d,p) basis sets at the remaining atoms. Both basis set combinations give analogous results, which validate the use of quickly converging 6-311G+(d,p) basis set in future studies. The molecular structures, atomic charge and spin distributions, and harmonic vibrational frequencies of the complexes have been calculated. The Zn, Cd and Hg complexes have been found to have distorted tetrahedral environments around the metal atoms whereas Cu complex has a square planar geometry. The NBO charge analysis have been found more accurate and less misleading compared with the Mulliken scheme. The present vibrational spectra calculations allow accurate assignment of the vibrational bands, which otherwise assigned tentatively in previous experimental-only studies.

  10. Structural modifications of 4-aryl-4-oxo-2-aminylbutanamides and their acetyl- and butyrylcholinesterase inhibitory activity. Investigation of AChE-ligand interactions by docking calculations and molecular dynamics simulations.

    PubMed

    Vitorović-Todorović, Maja D; Koukoulitsa, Catherine; Juranić, Ivan O; Mandić, Ljuba M; Drakulić, Branko J

    2014-06-23

    Congeneric set of thirty-eight 4-aryl-4-oxo-2-(N-aryl/cycloalkyl)butanamides has been designed, synthesized and evaluated for acetyl- and butyrylcholinesterase inhibitory activity. Structural variations included cycloalkylamino group attached to C2 position of butanoyl moiety, and variation of amido moiety of molecules. Twelve compounds, mostly piperidino and imidazolo derivatives, inhibited AChE in low micromolar range, and were inactive toward BChE. Several N-methylpiperazino derivatives showed inhibition of BChE in low micromolar or submicromolar concentrations, and were inactive toward AChE. Therefore, the nature of the cycloalkylamino moiety governs the AChE/BChE selectivity profile of compounds. The most active AChE inhibitor showed mixed-type inhibition modality, indicating its binding to free enzyme and to enzyme-substrate complex. Thorough docking calculations of the seven most potent AChE inhibitors from the set, showed that the hydrogen bond can be formed between amide -NH- moiety of compounds and -OH group of Tyr 124. The 10 ns unconstrained molecular dynamic simulation of the AChE-compound 18 complex shows that this interaction is the most persistent. This is, probably, the major anchoring point for the binding.

  11. An investigation of molecular dynamics simulation and molecular docking: interaction of citrus flavonoids and bovine β-lactoglobulin in focus.

    PubMed

    Sahihi, M; Ghayeb, Y

    2014-08-01

    Citrus flavonoids are natural compounds with important health benefits. The study of their interaction with a transport protein, such as bovine β-lactoglobulin (BLG), at the atomic level could be a valuable factor to control their transport to biological sites. In the present study, molecular docking and molecular dynamics simulation methods were used to investigate the interaction of hesperetin, naringenin, nobiletin and tangeretin as citrus flavonoids and BLG as transport protein. The molecular docking results revealed that these flavonoids bind in the internal cavity of BLG and the BLG affinity for binding the flavonoids follows naringenin>hesperetin>tangeretin>nobiletin. The docking results also indicated that the BLG-flavonoid complexes are stabilized through hydrophobic interactions, hydrogen bond interactions and π-π stacking interactions. The analysis of molecular dynamics (MD) simulation trajectories showed that the root mean square deviation (RMSD) of various systems reaches equilibrium and fluctuates around the mean value at various times. Time evolution of the radius of gyration, total solvent accessible surface of the protein and the second structure of protein showed as well that BLG and BLG-flavonoid complexes were stable around 2500ps, and there was not any conformational change as for BLG-flavonoid complexes. Further, the profiles of atomic fluctuations indicated the rigidity of the ligand binding site during the simulation.

  12. Structural investigations of lead-strontium fluoroapatites

    SciTech Connect

    Badraoui, Bechir; Aissa, Abdallah; Bigi, Adriana; Debbabi, Mongi; Gazzano, Massimo . E-mail: gazzano@isof.cnr.it

    2006-10-15

    Solid solutions in the system Pb{sub (10-x)}Sr {sub x} (PO{sub 4}){sub 6}F{sub 2}, 0{<=}x{<=}10, were obtained as apatitic phases from aqueous medium. They were investigated by X-ray diffraction, chemical analysis and infrared (IR) spectroscopy. The results of the structural refinements indicated that the substitution of lead by strontium induces a regular decrease of the lattice constant 'a' and a preferential strontium distribution in site M(1). A progressive shift of the F{sup -} ion position along the apatitic channel was detected and confirmed by IR evidence. The different character of the M-F and M-O interactions was invoked to justify the structural differences observed as a function of composition. - Graphical abstract: The structural refinements carried out on five Pb{sub (10-x)}Sr {sub x} (PO{sub 4}){sub 6}F{sub 2} samples evidence preferential distribution of cations in metal sites and a progressive shift of the F{sup -} ion.

  13. Thermal and molecular investigation of laser tissue welding

    SciTech Connect

    Small, W., IV

    1998-06-01

    Despite the growing number of successful animal and human trials, the exact mechanisms of laser tissue welding remain unknown. Furthermore, the effects of laser heating on tissue on the molecular scale are not fully understood. To address these issues, a multi-front attack oil both extrinsic (solder/patch mediated) and intrinsic (laser only) tissue welding was launched using two-color infrared thermometry, computer modeling, weld strength assessment, biochemical assays, and vibrational spectroscopy. The coupling of experimentally measured surface temperatures with the predictive numerical simulations provided insight into the sub-surface dynamics of the laser tissue welding process. Quantification of the acute strength of the welds following the welding procedure enabled comparison among trials during an experiment, with previous experiments, and with other studies in the literature. The acute weld integrity also provided an indication of tile probability of long-term success. Molecular effects induced In the tissue by laser irradiation were investigated by measuring tile concentrations of specific collagen covalent crosslinks and characterizing the Fourier-Transform infrared (FTIR) spectra before and after the laser exposure.

  14. Phenol-formaldehyde resins: A quantitative NMR study of molecular structure and molecular dynamics

    NASA Astrophysics Data System (ADS)

    Ottenbourgs, Benjamin Tony

    Phenol-formaldehyde (PF) resins have been the subject of this work. 13C liquid-state and solid-state NMR has been used to investigate the molecular structure of mainly novolak and partially of resole resins. 1H wideline in combination with 13C solid-state NMR relaxometry has been applied to study the curing and the molecular dynamics of phenolic resins. It was the intention to provide an insight in the relationship between resin composition, resin structure and subsequent resin properties (by means of the molecular dynamics). An improved 13C liquid-state NMR quantification technique of novolaks in THF-CDCl3 solutions is demonstrated. Full quantitative 13C liquid-state spectra of phenol-formaldehyde resins with high signal- to-noise ratio were obtained by using chromium acetylacetonate under optimized spectral conditions within a few hours spectrometer time. Attached proton test (APT) spectra enabled proper peak assignments in the region with significant overlap. For several novolaks, prepared under different catalytic conditions, the degree of polymerization, degree of branching, number average molecular weight, isomeric distribution, and the number of unreacted ortho and para phenol ring positions was determined with a reduced margin of error, by analyzing and integrating the 13C spectra. The power of 13C solid-state NMR in the analysis of cured PF resins is shown. Particular importance was ascribed to the question of the quantifiability of the experiments when it was desired to measure the degree of conversion by means of a 13C CP/MAS contact time study. The network structure present, and thus also the mechanical properties, is critically dependent upon the final degree of conversion obtained after curing. The degree of conversion, which depended on the cure conditions (cure temperature, cure pressure and cure time), was limited by vitrification as was demonstrated by DSC experiments. Changes in the spin-lattice relaxation time T 1H were observed, providing

  15. A survey of quantitative descriptions of molecular structure.

    PubMed

    Guha, Rajarshi; Willighagen, Egon

    2012-01-01

    Numerical characterization of molecular structure is a first step in many computational analysis of chemical structure data. These numerical representations, termed descriptors, come in many forms, ranging from simple atom counts and invariants of the molecular graph to distribution of properties, such as charge, across a molecular surface. In this article we first present a broad categorization of descriptors and then describe applications and toolkits that can be employed to evaluate them. We highlight a number of issues surrounding molecular descriptor calculations such as versioning and reproducibility and describe how some toolkits have attempted to address these problems.

  16. Investigation of multilayer painting by means of molecular spectroscopy

    NASA Astrophysics Data System (ADS)

    Kadikova, I. F.; Grigorieva, I. A.

    2016-12-01

    The study of paintings' layer structure under microscope was implemented in the early XX century; since that time method of cross-section preparation as well as composition of embedded materials changed and capabilities of optical microscopy broadened. Nevertheless, until recently cross-sections were prepared only for analysis of paintings' layer-specific structure, morphological and technological features, tracks of restoration treatments. Examination of chemical composition required additional sampling as well as division of these samples layer by layer in order to determine pigments and binding media; these procedures didn't always lead to proper results. Micro-Raman and micro-FTIR spectroscopy allow carrying out investigation of painting cross-sections without any additional preliminary sampling; this is shown on example of investigation of a number of paintings.

  17. Attosecond time-resolved imaging of molecular structure by photoelectron holography.

    PubMed

    Bian, Xue-Bin; Bandrauk, André D

    2012-06-29

    Dynamic imaging of the molecular structure of H(2)(+) is investigated by attosecond photoelectron holography. The interference between direct (reference) and backward rescattered (signal) photoelectrons in attosecond photoelectron holography reveals the birth time of both channels and the spatial information of molecular structure. This is confirmed by simulations with a semiclassical model and numerical solutions of the corresponding time-dependent Schrödinger equation, suggesting an attosecond time-resolved way of imaging molecular structure obtained from laser induced rescattering of ionized electrons. It is shown that both short and long rescattered electron trajectories can be imaged from the momentum distribution.

  18. A First-principles Molecular Dynamics Investigation of Superionic Conductivity

    NASA Astrophysics Data System (ADS)

    Wood, Brandon; Marzari, Nicola

    2007-03-01

    Superionic materials---solids with liquid-like transport properties---have found widespread use in a variety of applications in fuel cells, switches, sensors, and batteries. However, reasons for fast-ion conduction in such materials, as well as the specific atomistic mechanisms involved, remain ill understood. Our work uses first-principles molecular dynamics to illuminate the mechanisms, pathways, and motivations for superionic conductivity in two materials representing different classes of ion conductors: α-AgI, an archetypal Type-I superionic; and CsHSO4, an anhydrous solid-state electrolyte candidate for hydrogen fuel cells. For α-AgI, we trace common pathways for silver ion conduction and discuss how a chemical signature in the electronic structure relates to enhanced silver ion mobility. We also characterize the dynamical lattice structure in the superionic phase and present the likely motivations for its existence. For CsHSO4, we isolate the dominant atomistic mechanisms involved in superprotonic conduction and discuss the effect of correlated diffusive events in enhancing proton transport. We also offer a detailed description of the dynamics of the hydrogen bond network topology in the course of proton diffusion and discuss the relevance of atomistic processes with competing timescales in facilitating proton transport.

  19. The molecular structure of waxy maize starch nanocrystals.

    PubMed

    Angellier-Coussy, Hélène; Putaux, Jean-Luc; Molina-Boisseau, Sonia; Dufresne, Alain; Bertoft, Eric; Perez, Serge

    2009-08-17

    The insoluble residues obtained by submitting amylopectin-rich native starch granules from waxy maize to a mild acid hydrolysis consist of polydisperse platelet nanocrystals that have retained the allomorphic type of the parent granules. The present investigation is a detailed characterization of their molecular composition. Two major groups of dextrins were found in the nanocrystals and were isolated. Each group was then structurally characterized using beta-amylase and debranching enzymes (isoamylase and pullulanase) in combination with anion-exchange chromatography. The chain lengths of the dextrins in both groups corresponded with the thickness of the crystalline lamellae in the starch granules. Only approximately 62 mol% of the group of smaller dextrins with an average degree of polymerization (DP) 12.2 was linear, whereas the rest consisted of branched dextrins. The group of larger dextrins (DP 31.7) apparently only consisted of branched dextrins, several of which were multiply branched molecules. It was shown that many of the branch linkages were resistant to the action of the debranching enzymes. The distribution of branched molecules in the two populations of dextrins suggested that the nanocrystals possessed a regular and principally homogeneous molecular structure.

  20. Structure, molecular evolution, and hydrolytic specificities of largemouth bass pepsins.

    PubMed

    Miura, Yoko; Suzuki-Matsubara, Mieko; Kageyama, Takashi; Moriyama, Akihiko

    2016-02-01

    The nucleotide sequences of largemouth bass pepsinogens (PG1, 2 and 3) were determined after molecular cloning of the respective cDNAs. Encoded PG1, 2 and 3 were classified as fish pepsinogens A1, A2 and C, respectively. Molecular evolutionary analyses show that vertebrate pepsinogens are classified into seven monophyletic groups, i.e. pepsinogens A, F, Y (prochymosins), C, B, and fish pepsinogens A and C. Regarding the primary structures, extensive deletion was obvious in S'1 loop residues in fish pepsin A as well as tetrapod pepsin Y. This deletion resulted in a decrease in hydrophobic residues in the S'1 site. Hydrolytic specificities of bass pepsins A1 and A2 were investigated with a pepsin substrate and its variants. Bass pepsins preferred both hydrophobic/aromatic residues and charged residues at the P'1 sites of substrates, showing the dual character of S'1 sites. Thermodynamic analyses of bass pepsin A2 showed that its activation Gibbs energy change (∆G(‡)) was lower than that of porcine pepsin A. Several sites of bass pepsin A2 moiety were found to be under positive selection, and most of them are located on the surface of the molecule, where they are involved in conformational flexibility. The broad S'1 specificity and flexible structure of bass pepsin A2 are thought to cause its high proteolytic activity.

  1. Numerical Investigation of Josephson Junction Structures

    SciTech Connect

    Hristov, I.; Dimova, S.; Boyadjiev, T.

    2009-10-29

    Multilayered long Josephson Junction Structures form an interesting physical system where both nonlinearity and interaction between subsystems play an important role. Such systems allow to study physical effects that do not occur in single Josephson junction.The Sakai-Bodin-Pedersen model--a system of perturbed sine-Gordon equations--is used to study the dynamic states of stacks of inductively coupled long Josephson Junctions (LJJs). The corresponding static problem is numerically investigated as well. In order to study the stability of possible static solutions a Sturm-Liouville problem is generated and solved.The transitions from static to dynamic state and the scenario of these transitions are analyzed depending on the model parameters. Different physical characteristics--current-voltage characteristics, individual instant voltages and internal magnetic fields, are calculated and interpreted.

  2. Molecular road ecology: exploring the potential of genetics for investigating transportation impacts on wildlife.

    PubMed

    Balkenhol, Niko; Waits, Lisette P

    2009-10-01

    Transportation infrastructures such as roads, railroads and canals can have major environmental impacts. Ecological road effects include the destruction and fragmentation of habitat, the interruption of ecological processes and increased erosion and pollution. Growing concern about these ecological road effects has led to the emergence of a new scientific discipline called road ecology. The goal of road ecology is to provide planners with scientific advice on how to avoid, minimize or mitigate negative environmental impacts of transportation. In this review, we explore the potential of molecular genetics to contribute to road ecology. First, we summarize general findings from road ecology and review studies that investigate road effects using genetic data. These studies generally focus only on barrier effects of roads on local genetic diversity and structure and only use a fraction of available molecular approaches. Thus, we propose additional molecular applications that can be used to evaluate road effects across multiple scales and dimensions of the biodiversity hierarchy. Finally, we make recommendations for future research questions and study designs that would advance molecular road ecology. Our review demonstrates that molecular approaches can substantially contribute to road ecology research and that interdisciplinary, long-term collaborations will be particularly important for realizing the full potential of molecular road ecology.

  3. Atomic scale structure investigations of epitaxial Fe/Cr multilayers

    NASA Astrophysics Data System (ADS)

    Kąc, M.; Morgiel, J.; Polit, A.; Zabila, Y.; Marszałek, M.

    2014-06-01

    Fe/Cr multilayers were deposited by molecular beam epitaxy on the MgO(1 0 0) substrate. Structural properties of the samples were analyzed by low energy electron diffraction, high resolution transmission electron microscopy (HRTEM), as well as by X-ray reflectivity, conversion electron Mössbauer spectroscopy (CEMS) and Auger electron spectroscopy. Investigations revealed multilayered system built of well-ordered Fe and Cr thin films with (1 0 0) orientation. A high geometrical perfection of the system, i.e. planar form of interfaces and reproducible thickness of layers, was also proven. Fe/Cr interface roughness was determined to be 2-3 atomic layers. CEMS studies allowed to analyze at atomic scale the structure of buried Fe/Cr interfaces, as well as to distinguish origin of interface roughness. Roughnesses resulting from interface corrugations and from the Fe-Cr interdiffusion at interfaces were observed. Fe/Cr multilayers showed strong antiferromagnetic coupling of Fe layers.

  4. Hydration structure of salt solutions from ab initio molecular dynamics

    SciTech Connect

    Bankura, Arindam; Carnevale, Vincenzo; Klein, Michael L.

    2013-01-07

    The solvation structures of Na{sup +}, K{sup +}, and Cl{sup -} ions in aqueous solution have been investigated using density functional theory (DFT) based Car-Parrinello (CP) molecular dynamics (MD) simulations. CPMD trajectories were collected for systems containing three NaCl or KCl ion pairs solvated by 122 water molecules using three different but commonly employed density functionals (BLYP, HCTH, and PBE) with electron correlation treated at the level of the generalized gradient approximation (GGA). The effect of including dispersion forces was analyzed through the use of an empirical correction to the DFT-GGA scheme. Special attention was paid to the hydration characteristics, especially the structural properties of the first solvation shell of the ions, which was investigated through ion-water radial distribution functions, coordination numbers, and angular distribution functions. There are significant differences between the present results obtained from CPMD simulations and those provided by classical MD based on either the CHARMM force field or a polarizable model. Overall, the computed structural properties are in fair agreement with the available experimental results. In particular, the observed coordination numbers 5.0-5.5, 6.0-6.4, and 6.0-6.5 for Na{sup +}, K{sup +}, and Cl{sup -}, respectively, are consistent with X-ray and neutron scattering studies but differ somewhat from some of the many other recent computational studies of these important systems. Possible reasons for the differences are discussed.

  5. Hydration structure of salt solutions from ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Bankura, Arindam; Carnevale, Vincenzo; Klein, Michael L.

    2013-01-01

    The solvation structures of Na^+, K^+, and Cl^- ions in aqueous solution have been investigated using density functional theory (DFT) based Car-Parrinello (CP) molecular dynamics (MD) simulations. CPMD trajectories were collected for systems containing three NaCl or KCl ion pairs solvated by 122 water molecules using three different but commonly employed density functionals (BLYP, HCTH, and PBE) with electron correlation treated at the level of the generalized gradient approximation (GGA). The effect of including dispersion forces was analyzed through the use of an empirical correction to the DFT-GGA scheme. Special attention was paid to the hydration characteristics, especially the structural properties of the first solvation shell of the ions, which was investigated through ion-water radial distribution functions, coordination numbers, and angular distribution functions. There are significant differences between the present results obtained from CPMD simulations and those provided by classical MD based on either the CHARMM force field or a polarizable model. Overall, the computed structural properties are in fair agreement with the available experimental results. In particular, the observed coordination numbers 5.0-5.5, 6.0-6.4, and 6.0-6.5 for Na^+, K^+, and Cl^-, respectively, are consistent with X-ray and neutron scattering studies but differ somewhat from some of the many other recent computational studies of these important systems. Possible reasons for the differences are discussed.

  6. Hydration structure of salt solutions from ab initio molecular dynamics.

    PubMed

    Bankura, Arindam; Carnevale, Vincenzo; Klein, Michael L

    2013-01-07

    The solvation structures of Na(+), K(+), and Cl(-) ions in aqueous solution have been investigated using density functional theory (DFT) based Car-Parrinello (CP) molecular dynamics (MD) simulations. CPMD trajectories were collected for systems containing three NaCl or KCl ion pairs solvated by 122 water molecules using three different but commonly employed density functionals (BLYP, HCTH, and PBE) with electron correlation treated at the level of the generalized gradient approximation (GGA). The effect of including dispersion forces was analyzed through the use of an empirical correction to the DFT-GGA scheme. Special attention was paid to the hydration characteristics, especially the structural properties of the first solvation shell of the ions, which was investigated through ion-water radial distribution functions, coordination numbers, and angular distribution functions. There are significant differences between the present results obtained from CPMD simulations and those provided by classical MD based on either the CHARMM force field or a polarizable model. Overall, the computed structural properties are in fair agreement with the available experimental results. In particular, the observed coordination numbers 5.0-5.5, 6.0-6.4, and 6.0-6.5 for Na(+), K(+), and Cl(-), respectively, are consistent with X-ray and neutron scattering studies but differ somewhat from some of the many other recent computational studies of these important systems. Possible reasons for the differences are discussed.

  7. Structural investigation of Mimosa pudica Linn fibre

    NASA Astrophysics Data System (ADS)

    Patra, S. R.; Pattojoshi, P.; Tiwari, T. N.; Mallick, B.

    2016-12-01

    Sensitive plant (Mimosa pudica Linn.) fibre is a natural fibre with electrically conductive property. Because of its electro-active sensing nature, it has been found very interesting among physicists, chemists, biologists, material scientists and technologists. So far as our knowledge is concerned; there is no report on the X-ray structure of M. pudica fibre using diffraction technique. In the present report, the M. pudica fibre has been extracted from the stem of the herb by sinking the stem in 10% NaOH solution for one week. The diffraction pattern of the fibre is found out to be cellulose-I. The effect of the fibre structure and its orientation due to different mounting have been investigated using X-ray diffraction technique. The I max of cellulose-I has been observed along (002) and (10overline{1)} for the perpendicular and parallel mounting of the native-fibre, respectively. Full width at half maxima of the diffraction profile turns out to be decreased with fibre orientation. Dimension of crystallite size D hkl estimated in the perpendicular mounting D_{hkl}^{ bot } is more as compared to that of the parallel mounting D_{hkl}^{{^{allel } }} . The smallest crystallite sizes observed in both parallel and perpendicular mounting are 18.78 and 30.78 Å respectively. It is expected that the present study may help to analyse the X-ray diffraction of fibre materials in general and natural fibres in particular.

  8. Structural investigation of Mimosa pudica Linn fibre

    NASA Astrophysics Data System (ADS)

    Patra, S. R.; Pattojoshi, P.; Tiwari, T. N.; Mallick, B.

    2017-04-01

    Sensitive plant ( Mimosa pudica Linn.) fibre is a natural fibre with electrically conductive property. Because of its electro-active sensing nature, it has been found very interesting among physicists, chemists, biologists, material scientists and technologists. So far as our knowledge is concerned; there is no report on the X-ray structure of M. pudica fibre using diffraction technique. In the present report, the M. pudica fibre has been extracted from the stem of the herb by sinking the stem in 10% NaOH solution for one week. The diffraction pattern of the fibre is found out to be cellulose-I. The effect of the fibre structure and its orientation due to different mounting have been investigated using X-ray diffraction technique. The I max of cellulose-I has been observed along (002) and (10\\overline{1)} for the perpendicular and parallel mounting of the native-fibre, respectively. Full width at half maxima of the diffraction profile turns out to be decreased with fibre orientation. Dimension of crystallite size D hkl estimated in the perpendicular mounting D_{hkl}^{ \\bot } is more as compared to that of the parallel mounting D_{hkl}^{{^{allel } }}. The smallest crystallite sizes observed in both parallel and perpendicular mounting are 18.78 and 30.78 Å respectively. It is expected that the present study may help to analyse the X-ray diffraction of fibre materials in general and natural fibres in particular.

  9. Electronic and Magnetic Structure of Octahedral Molecular Sieves

    NASA Astrophysics Data System (ADS)

    Morey-Oppenheim, Aimee M.

    The major part of this research consists of magnetic and electronic studies of metal doped cryptomelane-type manganese oxide octahedral molecular sieves (KOMS-2). The second part of this study involves the magnetic characterization of cobalt doped MCM-41 before and after use in the synthesis of single walled carbon nanotubes. Manganese oxides have been used widely as bulk materials in catalysis, chemical sensors, and batteries due to the wide range of possible stable oxidation states. The catalytic function of manganese oxides is further tuned by doping the material with numerous transition metals. It is of particular interest the oxidation states of Mn present after doping. New titrations to determine the oxidation state of Mn were investigated. To further examine the structure of KOMS-2, the magnetic contribution of dopant metals was also examined. The KOMS-2 structure having both diamagnetic and paramagnetic metal ions substitutions was studied. MCM-41 with the incorporation of cobalt into the structure was analyzed for its magnetic properties. The material undergoes significant structural change during the synthesis of single walled carbon nanotubes. It was the focus of this portion of the research to do a complete magnetic profile of both the before and after reaction material.

  10. Molecular Modeling and Experimental Investigations of Nonlinear Optical Compounds Monosubstituted Derivatives of Dicyanovinylbenzene

    NASA Technical Reports Server (NTRS)

    Timofeeva, Tatiana V.; Nesterov, Vladimir N.; Antipin, Mikhail Yu.; Clark, Ronald D.; Sanghadasa, Mohan; Cardelino, Beatriz H.; Moore, Craig E.; Frazier, Donald O.

    1999-01-01

    A search for potential nonlinear optical compounds was performed using the Cambridge Structure Database and molecular modeling. We investigated a series of monosubstituted derivatives of dicyanovinylbenzene, since the nonlinear optical (NLO) properties of such derivatives (o-methoxy-dicyanovinylbenzene, DIVA) were studied earlier. The molecular geometry of these compounds was investigated with x-ray analysis and discussed along with the results of molecular mechanics and ab initio quantum chemical calculations. The influence of crystal packing on the planarity of the molecules of this series has been revealed. Two new compounds from the series studied, ortho-F and para-Cl-dicyanovinylbenzene, according to powder measurements, were found to be NLO compounds in the crystal state about 10 times more active than urea. The peculiarities of crystal structure formation in the framework of balance between van der Waals and electrostatic interactions have been discussed. The crystal shape of DIVA and two new NLO compounds have been calculated on the basis of the known crystal structure.

  11. Colour Chemistry, Part I, Principles, Colour, and Molecular Structure

    ERIC Educational Resources Information Center

    Hallas, G.

    1975-01-01

    Discusses various topics in color chemistry, including the electromagnetic spectrum, the absorption and reflection of light, additive and subtractive color mixing, and the molecular structure of simple colored substances. (MLH)

  12. An investigation of the preparation of high molecular weight perfluorocarbon polyethers

    NASA Technical Reports Server (NTRS)

    Watts, R. O.; Tarrant, P.

    1972-01-01

    High molecular weight perfluorocarbon polyether gums were obtained by photolysis of perfluorodienes and discyl fluorides containing a perfluorocarbon polyether backbond. The materials obtained are represented by chemical formulas. A method was developed whereby reactive acyl fluoride and trifluorovinyl end groups are converted into inert structures. In order to investigate the possible preparation of difunctional molecules which may be useful in polymer synthesis, the reactions of hexafluoropropene oxide (HFPO) with Grignard and organolithium reagents have been studied. Reactions of various nucleophilic reagents with HFPO were also investigated.

  13. Yield and Failure Behavior Investigated for Cross-Linked Phenolic Resins Using Molecular Dynamics

    NASA Technical Reports Server (NTRS)

    Monk, Joshua D.; Lawson, John W.

    2016-01-01

    Molecular dynamics simulations were conducted to fundamentally evaluate the yield and failure behavior of cross-linked phenolic resins at temperatures below the glass transition. Yield stress was investigated at various temperatures, strain rates, and degrees of cross-linking. The onset of non-linear behavior in the cross-linked phenolic structures was caused by localized irreversible molecular rearrangements through the rotation of methylene linkers followed by the formation or annihilation of neighboring hydrogen bonds. The yield stress results, with respect to temperature and strain rate, could be fit by existing models used to describe yield behavior of amorphous glasses. The degree of cross-linking only indirectly influences the maximum yield stress through its influence on glass transition temperature (Tg), however there is a strong relationship between the degree of cross-linking and the failure mechanism. Low cross-linked samples were able to separate through void formation, whereas the highly cross-linked structures exhibited bond scission.

  14. Diffusion and structure in silica liquid: a molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Hung, P. K.; Hong, N. V.; Vinh, L. T.

    2007-11-01

    Diffusion and structure in liquid silica under pressure have been investigated by a molecular dynamics model of 999 atoms with the inter-atomic potentials of van Beest, Kramer and van Santen. The simulation reveals that silica liquid is composed of the species SiO4, SiO5 and SiO6 with a fraction dependent on pressure. The density as well as volume of voids can be expressed as a linear function of the fraction of those species. Low-density liquid is mainly constructed of SiO4 and has a large number of O- and Si-voids and a large void tube. This tube contains most O-voids and is spread over the whole system. The anomalous diffusion behavior is observed and discussed.

  15. Investigation of the Molecular Response of Belugas to Stressors

    DTIC Science & Technology

    2014-09-30

    To apply molecular methods to describe and quantify changes in the expression of immunological “stress” markers in peripheral blood from captive and...wild belugas. 4. To apply molecular methods to describe and quantify the expression of immunological markers in skin. 5. To correlate the...molecular marker to be used in this study. Being a part of vertebrate innate immune system, Toll-like receptors are located at the direct interface

  16. Investigation of the Composition and Formation Constant of Molecular Complexes

    PubMed Central

    Sahai, R.; Loper, G. L.; Lin, S. H.; Eyring, H.

    1974-01-01

    It has been the purpose of the present paper to investigate and explore the conditions under which the linear relation between Δ/CD0 and Δ in the Hanna-Ashbaugh-Foster-Fyfe equation for the evaluation of equilibrium constants holds, (CD0 is initial concentration of a donor and Δ is the observed chemical shift relative to the chemical shift of the acceptor) to obtain the equation representing the exact linear relation between Δ/CD0 and Δ, when the linear relation between Δ/CD0 and Δ holds, and to discuss how to use the Job method in nuclear magnetic resonance measurements to determine the stoichiometry of molecular complexes. We have found that the conventional belief that CD0 should always be chosen to be much greater than CA0 (initial concentration of acceptor) is not necessarily always true and the exact linear relation between Δ/CD0 and Δ is represented by the equation Δ/CD0 = K1Δ0/(1 + K1CA0) - K1Δ/(1 + K1CA0)2, where K1 is the formation constant of the complex. It is shown that in the Job method of nuclear magnetic resonance measurements one has to plot ΔCA0 against the mole fraction, and the mole fraction at the maximum should give us the composition of the complex. Theoretical results have been verified experimentally on the weak interaction between naphthalene and methyl iodide. PMID:16592155

  17. Investigation of synthetic molecular recognition for biosensing applications

    NASA Astrophysics Data System (ADS)

    Stratis-Cullum, Dimitra N.; McMasters, Sun; Sooter, Letha J.; Pellegrino, Paul M.

    2007-04-01

    A fundamental understanding of the factors which influence binding performance is critical to any technology or methodology relying on molecular recognition of a specific target species. For the Army, there is a growing need for a basic understanding of these interactions with traditional recognition elements (e.g., antibodies) in non-traditional environmental conditions, such as with new and emerging threats. There is a similar need for building a base of knowledge on non-traditional affinity ligands that are biomimetic or biosynthetic in nature. In this paper, specific research at the Army Research Laboratory towards the development, evaluation and use of synthetic affinity ligands for sensing applications is discussed. This includes the results of our investigations of aptamer-based affinity ligands targeting Campylobacter jejuni. Using capillary electrophoretic techniques, the relative binding affinities of the aptamer ligands towards the target pathogen as well as the degree of cross-reactivity with other food borne-pathogens (i.e., Escherichia coli O157:H7 and Salmonella typhimurium) were evaluated. Current progress towards the development of synthetic affinity ligands for sensing applications will also be discussed.

  18. Synthesis, spectroscopic investigations (X-ray, NMR and TD-DFT), antimicrobial activity and molecular docking of 2,6-bis(hydroxy(phenyl)methyl)cyclohexanone.

    PubMed

    Barakat, Assem; Ghabbour, Hazem A; Al-Majid, Abdullah Mohammed; Soliman, Saied M; Ali, M; Mabkhot, Yahia Nasser; Shaik, Mohammed Rafi; Fun, Hoong-Kun

    2015-07-21

    The synthesis of 2,6-bis(hydroxy(phenyl)methyl)cyclohexanone 1 is described. The molecular structure of the title compound 1 was confirmed by NMR, FT-IR, MS, CHN microanalysis, and X-ray crystallography. The molecular structure was also investigated by a set of computational studies and found to be in good agreement with the experimental data obtained from the various spectrophotometric techniques. The antimicrobial activity and molecular docking of the synthesized compound was investigated.

  19. Molecular Dynamics Investigation of the Substrate Binding Mechanism in Carboxylesterase

    SciTech Connect

    Chen, Qi; Luan, Zheng-Jiao; Cheng, Xiaolin; Xu, Jian-He

    2015-02-25

    A recombinant carboxylesterase, cloned from Pseudomonas putida and designated as rPPE, is capable of catalyzing the bioresolution of racemic 2-acetoxy-2-(2 -chlorophenyl)acetate (rac-AcO-CPA) with excellent (S)-enantioselectivity. Semi-rational design of the enzyme showed that the W187H variant could increase the activity by ~100-fold compared to the wild type (WT) enzyme. In this study, we performed all-atom molecular dynamics (MD) simulations of both apo-rPPE and rPPE in complex with (S)-AcO-CPA to gain insights into the origin of the increased catalysis in the W187H mutant. Moreover, our results show differential binding of (S)-AcO-CPA in the WT and W187H enzymes, especially the interactions of the substrate with the two active site residues Ser159 and His286. The replacement of Trp187 by His leads to considerable structural rearrangement in the active site of W187H. Unlike in the WT rPPE, the cap domain in the W187 mutant shows an open conformation in the simulations of both apo and substrate-bound enzymes. This open conformation exposes the catalytic triad to the solvent through a water accessible channel, which may facilitate the entry of the substrate and/or the exit of the product. Binding free energy calculations confirmed that the substrate binds more strongly in W187H than in WT. Based on these computational results, furthermore, we predicted that the mutations W187Y and D287G might also be able to increase the substrate binding, thus improve the enzyme s catalytic efficiency. Experimental binding and kinetic assays on W187Y and D287G show improved catalytic efficiency over WT, but not W187H. Contrary to our prediction, W187Y shows slightly decreased substrate binding coupled with a 100 fold increase in turn-over rate, while in D287G the substrate binding is 8 times stronger but with a slightly reduced turn-over rate. Finally, our work provides important molecular-level insights into the binding of the (S)-AcO-CPA substrate to carboxylesterase r

  20. Molecular Dynamics Investigation of the Substrate Binding Mechanism in Carboxylesterase

    DOE PAGES

    Chen, Qi; Luan, Zheng-Jiao; Cheng, Xiaolin; ...

    2015-02-25

    A recombinant carboxylesterase, cloned from Pseudomonas putida and designated as rPPE, is capable of catalyzing the bioresolution of racemic 2-acetoxy-2-(2 -chlorophenyl)acetate (rac-AcO-CPA) with excellent (S)-enantioselectivity. Semi-rational design of the enzyme showed that the W187H variant could increase the activity by ~100-fold compared to the wild type (WT) enzyme. In this study, we performed all-atom molecular dynamics (MD) simulations of both apo-rPPE and rPPE in complex with (S)-AcO-CPA to gain insights into the origin of the increased catalysis in the W187H mutant. Moreover, our results show differential binding of (S)-AcO-CPA in the WT and W187H enzymes, especially the interactions of themore » substrate with the two active site residues Ser159 and His286. The replacement of Trp187 by His leads to considerable structural rearrangement in the active site of W187H. Unlike in the WT rPPE, the cap domain in the W187 mutant shows an open conformation in the simulations of both apo and substrate-bound enzymes. This open conformation exposes the catalytic triad to the solvent through a water accessible channel, which may facilitate the entry of the substrate and/or the exit of the product. Binding free energy calculations confirmed that the substrate binds more strongly in W187H than in WT. Based on these computational results, furthermore, we predicted that the mutations W187Y and D287G might also be able to increase the substrate binding, thus improve the enzyme s catalytic efficiency. Experimental binding and kinetic assays on W187Y and D287G show improved catalytic efficiency over WT, but not W187H. Contrary to our prediction, W187Y shows slightly decreased substrate binding coupled with a 100 fold increase in turn-over rate, while in D287G the substrate binding is 8 times stronger but with a slightly reduced turn-over rate. Finally, our work provides important molecular-level insights into the binding of the (S)-AcO-CPA substrate to carboxylesterase r

  1. Instructional Approach to Molecular Electronic Structure Theory

    ERIC Educational Resources Information Center

    Dykstra, Clifford E.; Schaefer, Henry F.

    1977-01-01

    Describes a graduate quantum mechanics projects in which students write a computer program that performs ab initio calculations on the electronic structure of a simple molecule. Theoretical potential energy curves are produced. (MLH)

  2. Conformation of receptor-associated PGI2: An investigation by molecular modeling

    NASA Astrophysics Data System (ADS)

    Tsai, Ah-lim; Strobel-Jager, Eva; Wu, Kenneth K.

    1991-04-01

    To elucidate the conformation of receptor-associated prostacyclin (PGI2), we first performed structure-activity correlation analysis of over 200 PGI2 analogues and derived from this analysis several crucial features pertaining to structural requirements for PGI2 activity [Ah-lim Tsai and Kenneth K. Wu, Eicosanoids, 2 (1989) 131-143]. These structural features proved to be useful guidelines for selecting `model molecules' for further investigations by molecular mechanics. By properly selecting four analogues with either rigid or uniquely oriented α-side chain structure for geometric fitting, we succeeded in maximally minimizing the degree of freedom of the carboxylate terminus of PGI2. We were able to define the spatial relationship among the four critical functional groups, i.e., C1-COOH, C6a-O, C11-OH and C15-OH. More information is needed, however, to define the geometry of the ω-side chain, particularly for the moiety beyond C15. Nevertheless, results from structure-activity correlation analysis and molecular modeling provide useful information regarding the conformation of receptor-associated PGI2, which assumes an `elongated' conformation instead of the traditional `hairpin' structure.

  3. Hygrothermal aging effects on buried molecular structures at epoxy interfaces.

    PubMed

    Myers, John N; Zhang, Chi; Lee, Kang-Wook; Williamson, Jaimal; Chen, Zhan

    2014-01-14

    Interfacial properties such as adhesion are determined by interfacial molecular structures. Adhesive interfaces in microelectronic packages that include organic polymers such as epoxy are susceptible to delamination during accelerated stress testing. Infrared-visible sum frequency generation vibrational spectroscopy (SFG) and attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR) were used to study molecular structures at buried epoxy interfaces during hygrothermal aging to relate molecular structural changes at buried interfaces to decreases in macroscopic adhesion strength. SFG peaks associated with strongly hydrogen bonded water were detected at hydrophilic epoxy interfaces. Ordered interfacial water was also correlated to large decreases in interfacial adhesion strength that occurred as a result of hygrothermal aging, which suggests that water diffused to the interface and replaced original hydrogen bond networks. No water peaks were observed at hydrophobic epoxy interfaces, which was correlated with a much smaller decrease in adhesion strength from the same aging process. ATR-FTIR water signals observed in the epoxy bulk were mainly contributed by relatively weakly hydrogen bonded water molecules, which suggests that the bulk and interfacial water structure was different. Changes in interfacial methyl structures were observed regardless of the interfacial hydrophobicity which could be due to water acting as a plasticizer that restructured both the bulk and interfacial molecular structure. This research demonstrates that SFG studies of molecular structural changes at buried epoxy interfaces during hygrothermal aging can contribute to the understanding of moisture-induced failure mechanisms in electronic packages that contain organic adhesives.

  4. FT-IR, FT-Raman, UV, NMR spectra and molecular structure investigation of (E)-2-(3-chloropyrazin-2-yl)-1-(3-ethyl-2, 6-diphenyl piperidin-4-ylidene) hydrazine: A combined experimental and theoretical study

    NASA Astrophysics Data System (ADS)

    Therasa Alphonsa, A.; Loganathan, C.; Athavan Alias Anand, S.; Kabilan, S.

    2015-11-01

    This work presents the characterization of (E)-2-(3-chloropyrazin-2-yl)-1-(3-ethyl-2, 6-diphenyl piperidin-4-ylidene) hydrazine (HDE) by quantum chemical calculations and spectral techniques. The structure was investigated by FT-IR, FT-Raman, UV-vis and NMR techniques. The geometrical parameters and energies have been obtained from Density functional theory (DFT) B3LYP (6-31G (d, p)) basis set calculations. The geometry of the molecule was fully optimized, vibrational spectra were calculated and fundamental vibrations were assigned on the basis of total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. 1H and 13C NMR chemical shifts of the molecule were calculated using Gauge-independent atomic orbital method (GIAO). The electronic properties such as excitation energies, wavelength, HOMO, LUMO energies performed by Time dependent density functional theory (TD-DFT) results complements with the experimental findings. NBO analysis has been performed for analyzing charge delocalization throughout the molecule. The calculation results were applied to simulate spectra of the title compound, which show excellent agreement with observed spectra. To provide information about the interactions between human cytochrome protein and the novel compound theoretically, docking studies were carried out using Schrödinger software.

  5. First Investigations on the Pantasma Structure (Nicaragua)

    NASA Astrophysics Data System (ADS)

    Rochette, P.; Beck, P.; Debaille, V.; Devouard, B.; Moustard, F.; Nomade, S.; Cornec, J.

    2016-08-01

    The 13 km diameter structure of Pantasma occurs in subhorizontal volcanics. Morphology, structure and deformation are compatible with a Quaternary impact. Recovered glass pebbles appear to be impact generated.

  6. Molecular Epidemiology Investigation of Obesity and Lethal Prostate Cancer

    DTIC Science & Technology

    2015-09-01

    in the field of molecular epidemiology. During the award period the PI performed research incorporating tissue -level biomarker data into...Using whole transcriptome gene expression profiling data, she identified a chromatin gene signature that is enriched in the tumor tissue of overweight...prostate cancer, obesity, tissue biomarkers, gene expression, growth factor signaling, inflammation, angiogenesis, molecular epidemiology 16

  7. Effect of valence of lanthanide ion and molecular symmetry in polyoxotungstoborate on the molecular structure and spectrochemical properties

    NASA Astrophysics Data System (ADS)

    Iijima, Jun; Naruke, Haruo

    2017-01-01

    The compound K9(NH4)H[CeIV(α-BW11O39)(W5O18)]·16H2O (1) was successfully isolated and structurally characterized. The structural investigation revealed that 1 displayed a less molecular distortion, whereas Ln3+-analogs exhibited a large molecular distortion. IR spectroscopy demonstrated that the spectral patterns of 1 and Ce3+-analog were depending on each valence of Ce (IV/III). 11B-NMR spectroscopy showed that a decrease in site symmetry of B atom in the polyoxotungstoborate was related with an increase in a half width of NMR peak. There is a difference in molecular distortion between 1 and Ce3+-analog, but they have similar large half widths because of the same site symmetry of B atom. The 4f electron in Ce atom exhibited less effect on the chemical shift.

  8. An Investigation of College Chemistry Students' Understanding of Structure-Property Relationships

    ERIC Educational Resources Information Center

    Cooper, Melanie M.; Corley, Leah M.; Underwood, Sonia M.

    2013-01-01

    The connection between the molecular-level structure of a substance and its macroscopic properties is a fundamental concept in chemistry. Students in college-level general and organic chemistry courses were interviewed to investigate how they used structure-property relationships to predict properties such as melting and boiling points. Although…

  9. Tyrosine aminotransferase: biochemical and structural properties and molecular dynamics simulations

    SciTech Connect

    Mehere, P.; Robinson, H.; Han, Q.; Lemkul, J. A.; Vavricka, C. J.; Bevan, D. R.; Li, J.

    2010-11-01

    Tyrosine aminotransferase (TAT) catalyzes the transamination of tyrosine and other aromatic amino acids. The enzyme is thought to play a role in tyrosinemia type II, hepatitis and hepatic carcinoma recovery. The objective of this study is to investigate its biochemical and structural characteristics and substrate specificity in order to provide insight regarding its involvement in these diseases. Mouse TAT (mTAT) was cloned from a mouse cDNA library, and its recombinant protein was produced using Escherichia coli cells and purified using various chromatographic techniques. The recombinant mTAT is able to catalyze the transamination of tyrosine using {alpha}-ketoglutaric acid as an amino group acceptor at neutral pH. The enzyme also can use glutamate and phenylalanine as amino group donors and p-hydroxy-phenylpyruvate, phenylpyruvate and alpha-ketocaproic acid as amino group acceptors. Through macromolecular crystallography we have determined the mTAT crystal structure at 2.9 {angstrom} resolution. The crystal structure revealed the interaction between the pyridoxal-5'-phosphate cofactor and the enzyme, as well as the formation of a disulphide bond. The detection of disulphide bond provides some rational explanation regarding previously observed TAT inactivation under oxidative conditions and reactivation of the inactive TAT in the presence of a reducing agent. Molecular dynamics simulations using the crystal structures of Trypanosoma cruzi TAT and human TAT provided further insight regarding the substrate-enzyme interactions and substrate specificity. The biochemical and structural properties of TAT and the binding of its cofactor and the substrate may help in elucidation of the mechanism of TAT inhibition and activation.

  10. Tyrosine Aminotransferase: Biochemical and Structural Properties and Molecular Dynamics Simulations

    SciTech Connect

    P Mehere; Q Han; J Lemkul; C Vavricka; H Robinson; D Bevan; J Li

    2011-12-31

    Tyrosine aminotransferase (TAT) catalyzes the transamination of tyrosine and other aromatic amino acids. The enzyme is thought to play a role in tyrosinemia type II, hepatitis and hepatic carcinoma recovery. The objective of this study is to investigate its biochemical and structural characteristics and substrate specificity in order to provide insight regarding its involvement in these diseases. Mouse TAT (mTAT) was cloned from a mouse cDNA library, and its recombinant protein was produced using Escherichia coli cells and purified using various chromatographic techniques. The recombinant mTAT is able to catalyze the transamination of tyrosine using {alpha}-ketoglutaric acid as an amino group acceptor at neutral pH. The enzyme also can use glutamate and phenylalanine as amino group donors and p-hydroxy-phenylpyruvate, phenylpyruvate and alpha-ketocaproic acid as amino group acceptors. Through macromolecular crystallography we have determined the mTAT crystal structure at 2.9 {angstrom} resolution. The crystal structure revealed the interaction between the pyridoxal-5'-phosphate cofactor and the enzyme, as well as the formation of a disulphide bond. The detection of disulphide bond provides some rational explanation regarding previously observed TAT inactivation under oxidative conditions and reactivation of the inactive TAT in the presence of a reducing agent. Molecular dynamics simulations using the crystal structures of Trypanosoma cruzi TAT and human TAT provided further insight regarding the substrate-enzyme interactions and substrate specificity. The biochemical and structural properties of TAT and the binding of its cofactor and the substrate may help in elucidation of the mechanism of TAT inhibition and activation.

  11. Structural investigation of a new antimicrobial thiazolidine compound

    NASA Astrophysics Data System (ADS)

    Cozar, I. B.; Pırnǎu, A.; Vedeanu, N.; Nastasǎ, C.

    2013-11-01

    Thiazoles and their derivatives have attracted the interest over the last decades because of their varied biological activities: antibacterial, antiviral, antifungal, inflammation or in the treatment of allergies. A new synthesized compound 3-[2-(4-Methyl-2-phenyl-thiazol-5-yl)-2-oxo-ethyl]-thazolidine-2,4-dione was investigated by FT-IR, FT-Raman, 1H, 13C NMR spectroscopies and also by DFT calculations at B3LYP/6-31G(d) level of theory. The very good correlation found between the experimental and theoretical data shows that the optimized molecular structure is very close to reality. Also the NMR spectra show a monomeric behaviour of this compound in solutions.

  12. DFT investigation on the electronic structure of Faujasite

    NASA Astrophysics Data System (ADS)

    Popeneciu, Horea; Calborean, Adrian; Tudoran, Cristian; Buimaga-Iarinca, Luiza

    2013-11-01

    We report here first-principle pseudopotential DFT calculations to investigate relevant aspects of the electronic structure of zeolites based FAU. Fundamental molecular issues of the band-gap and electronic population analysis were reviewed under GGA/RPBE level of theory, corroborated with a DZP basis set and Troullier-Martins norm conserving pseudo-potentials. The atom-projected density of states and the analysis of HOMO-LUMO frontier orbitals at Gamma point were performed. Their electronic transfers are discussed through the alignment and relative positions of orbitals in order to determine the way that the molecule interacts with adsorbed molecules and other practical applications. Mulliken population analysis was employed for describing atomic charge distribution in the chosen systems.

  13. Structural investigation of a new antimicrobial thiazolidine compound

    SciTech Connect

    Cozar, I. B.; Pîrnău, A.; Vedeanu, N.; Nastasă, C.

    2013-11-13

    Thiazoles and their derivatives have attracted the interest over the last decades because of their varied biological activities: antibacterial, antiviral, antifungal, inflammation or in the treatment of allergies. A new synthesized compound 3-[2-(4-Methyl-2-phenyl-thiazol-5-yl)-2-oxo-ethyl]-thazolidine-2,4-dione was investigated by FT-IR, FT-Raman, {sup 1}H, {sup 13}C NMR spectroscopies and also by DFT calculations at B3LYP/6-31G(d) level of theory. The very good correlation found between the experimental and theoretical data shows that the optimized molecular structure is very close to reality. Also the NMR spectra show a monomeric behaviour of this compound in solutions.

  14. Marine Biotoxins: Laboratory Culture and Molecular Structure

    DTIC Science & Technology

    1991-01-21

    toxins that are associated with the human fish intoxication known as ciguatera , ciguatoxin and maitotoxin. of unknown structure at the outset of this...87-C-7210 Appendix A. Bibliography 1. Ciguatera - what we know and what we would like to know. P.J. Scheuer in "Mycotoxins and Phycotoxins 󈨜". (S...Mycotoxins, and Phycotoxins, Tokyo. Japan, August 1988. 2. Third International Conference on Ciguatera , Puerto Rico. April 1990. C. Personnel Receiving Pay

  15. Marine Toxins Origin, Structure, and Molecular Pharmacology

    DTIC Science & Technology

    1990-01-01

    thin-layer chromatography (TLC) were instrumental in the initial isolation and purification processes. Mass spectrometry (MS), infrared spectroscopy ...Frederick, MD 21701-5011 Methods of detection, metabolism, and pathophysiology of the brevetoxins, PbTx-2 and PbTx-3, are summarized. Infrared spectros...1R), circular dichroism (CD), nuclear magnetic resonance spectroscopy (NMR), and X-ray crystal- lography all played important roles in structure

  16. Molecular Eigensolution Symmetry Analysis and Fine Structure

    PubMed Central

    Harter, William G.; Mitchell, Justin C.

    2013-01-01

    Spectra of high-symmetry molecules contain fine and superfine level cluster structure related to J-tunneling between hills and valleys on rovibronic energy surfaces (RES). Such graphic visualizations help disentangle multi-level dynamics, selection rules, and state mixing effects including widespread violation of nuclear spin symmetry species. A review of RES analysis compares it to that of potential energy surfaces (PES) used in Born–Oppenheimer approximations. Both take advantage of adiabatic coupling in order to visualize Hamiltonian eigensolutions. RES of symmetric and D2 asymmetric top rank-2-tensor Hamiltonians are compared with Oh spherical top rank-4-tensor fine-structure clusters of 6-fold and 8-fold tunneling multiplets. Then extreme 12-fold and 24-fold multiplets are analyzed by RES plots of higher rank tensor Hamiltonians. Such extreme clustering is rare in fundamental bands but prevalent in hot bands, and analysis of its superfine structure requires more efficient labeling and a more powerful group theory. This is introduced using elementary examples involving two groups of order-6 (C6 and D3~C3v), then applied to families of Oh clusters in SF6 spectra and to extreme clusters. PMID:23344041

  17. Molecular sonography with targeted microbubbles: current investigations and potential applications.

    PubMed

    Hwang, Misun; Lyshchik, Andrej; Fleischer, Arthur C

    2010-06-01

    Sonography using targeted microbubbles affords a variety of diagnostic and potentially therapeutic clinical applications. It provides a whole new world of functional information at the cellular and molecular level. This information can then be used to diagnose and possibly prevent diseases at early stages as well as devise therapeutic strategies at the molecular level. It is also useful in monitoring tumor response to therapy and devising treatment timing and plans based on the molecular state of an individual's health. Moreover, targeted microbubble-enhanced sonography has several advantages over other imaging modalities, including widespread availability, low cost, fast acquisition times, and lack of radiation risk. These traits are likely to advance it as one of the imaging methods of choice in future clinical trials examining the impact of molecular imaging on treatment outcome. This review describes the fundamental concepts of targeted microbubble-enhanced sonography as well as its potential clinical applications.

  18. Ionization probes of molecular structure and chemistry

    SciTech Connect

    Johnson, P.M.

    1993-12-01

    Various photoionization processes provide very sensitive probes for the detection and understanding of the spectra of molecules relevant to combustion processes. The detection of ionization can be selective by using resonant multiphoton ionization or by exploiting the fact that different molecules have different sets of ionization potentials. Therefore, the structure and dynamics of individual molecules can be studied even in a mixed sample. The authors are continuing to develop methods for the selective spectroscopic detection of molecules by ionization, and to use these methods for the study of some molecules of combustion interest.

  19. DFT study of the effect of substitution on the molecular structure of copper phthalocyanine

    NASA Astrophysics Data System (ADS)

    Kaur, Prabhjot; Sachdeva, Ritika; Singh, Sukhwinder; Saini, G. S. S.

    2016-05-01

    To study the effect of sulfonic acid group as substituent on the molecular structure of an organic compound copper Phthalocyanine, the optimized geometry, mulliken charges, energies and dipole momemts of copper phthalocyanine and copper phthalocyaninetetrasulfonic acid tetra sodium salt have been investigated using density functional theory. Also to predict the change in reactive sites after substitution, molecular electrostatic potential maps for both the molecules have been calculated.

  20. Relation between photochromic properties and molecular structures in salicylideneaniline crystals.

    PubMed

    Johmoto, Kohei; Ishida, Takashi; Sekine, Akiko; Uekusa, Hidehiro; Ohashi, Yuji

    2012-06-01

    The crystal structures of the salicylideneaniline derivatives N-salicylidene-4-tert-butyl-aniline (1), N-3,5-di-tert-butyl-salicylidene-3-methoxyaniline (2), N-3,5-di-tert-butyl-salicylidene-3-bromoaniline (3), N-3,5-di-tert-butyl-salicylidene-3-chloroaniline (4), N-3,5-di-tert-butyl-salicylidene-4-bromoaniline (5), N-3,5-di-tert-butyl-salicylidene-aniline (6), N-3,5-di-tert-butyl-salicylidene-4-carboxyaniline (7) and N-salicylidene-2-chloroaniline (8) were analyzed by X-ray diffraction analysis at ambient temperature to investigate the relationship between their photochromic properties and molecular structures. A clear correlation between photochromism and the dihedral angle of the two benzene rings in the salicylideneaniline derivatives was observed. Crystals with dihedral angles less than 20° were non-photochromic, whereas those with dihedral angles greater than 30° were photochromic. Crystals with dihedral angles between 20 and 30° could be either photochromic or non-photochromic. Inhibition of the pedal motion by intra- or intermolecular steric hindrance, however, can result in non-photochromic behaviour even if the dihedral angle is larger than 30°.

  1. Syntheses and molecular structures of new cali.

    PubMed

    Attner, J; Radius, U

    2001-01-01

    An unusual disproportionation reaction of the molybdenum(IV) and tungsten(IV) chlorides [MCl4L2] (M=Mo, L=Et2S, Et2O; M=W; L= Et2S) in the presence of p-tBu-calix[4]arene (Cax(OH)4) and triethylamine leads to d0 complexes [(CaxO4)[CaxO2(OH)2]M] (1) and d3 compounds (HNEt3)2[(CaxO4)2M2] (2). Complexes la (M = Mo), 1b (M = W), and the HCl adduct of 2a (M = Mo) have been structurally characterized. Compound 1a represents one of the few examples of a well-characterized molybdenum(VI) hexa-alkoxide complex of the type [Mo(OR)6]. Isolation and structural characterization of the side product [(CaxO4W)[kappa2(O)-kappa1(O)-CaxO3(OH)](CaxO4WCl)] (3) suggests the intermediacy of chloro-containing calix[4]arene complexes in these reaction mixtures. The reaction of 1a with HCI provides [CaxO4MoCl2] (4a), the first well-defined example of a mixed molybdenum(VI) alkoxide halide compound of the general formula [MoClx(OR)6-x].

  2. First-principles investigation of iron pentacarbonyl molecular solid phases at high pressure

    NASA Astrophysics Data System (ADS)

    Cong, Kien Nguyen; Steele, Brad A.; Landerville, Aaron C.; Oleynik, Ivan I.

    2017-01-01

    The polymeric phases of carbon monoxide (p-CO), an extended non-molecular solid, represent a new class of low-Z energetic materials. The presence of transition metal ions is believed to stabilize polymeric carbon monoxide (p-CO) at ambient conditions. Since p-CO forms at high pressures, it becomes important to investigate the high-pressure behavior of one of the potential precursors, iron pentacarbonyl Fe(CO)5. In this work, a first-principles evolutionary structure search method is used to determine the crystal phases of Fe(CO)5 at high pressure. The calculations predict the crystal structure of Phase I in agreement with experiment. Moreover, the previously unidentified crystal structure of Phase II is found. The calculated pressure-dependent Raman spectra are used to demonstrate that the changes in Raman spectra as a function of pressure observed in recent experiment can be explained without invoking a phase transition to a new phase III.

  3. Molecular arrangement investigation of copper phthalocyanine grown on hydrogen passivated Si(1 1 1) surfaces

    NASA Astrophysics Data System (ADS)

    Arbi, I.; Ben Hamada, B.; Souissi, A.; Menzli, S.; Ben Azzouz, C.; Laribi, A.; Akremi, A.; Chefi, C.

    2014-06-01

    Chemical, electronic and structural properties of ultra thin films of copper phthalocyanine (CuPc) grown on hydrogen passivated silicon (1 1 1) surfaces were investigated in situ by X-ray photoelectron spectroscopy (XPS), ultraviolet photoemission spectroscopy (UPS), X-ray photoelectron diffraction (XPD) and electron diffraction (LEED). The early stages of copper phthalocyanine adsorption (1-2) were characterized by the saturation of surface defects and by a flat lying disposition on the surface. Upon further CuPc coverage, the passivation of Si surfaces resulted in the molecule taking a standing position in films. The molecular packing deduced from these studies appears very close to the one in the bulk α phase of CuPc. The work function of the films was found to be decreasing during the growth and was correlated with the molecular orientation.

  4. Electronic and molecular structure of carbon grains

    NASA Technical Reports Server (NTRS)

    Almloef, Jan; Luethi, Hans-Peter

    1990-01-01

    Clusters of carbon atoms have been studied with large-scale ab initio calculations. Planar, single-sheet graphite fragments with 6 to 54 atoms were investigated, as well as the spherical C(sub 60) Buckminsterfullerene molecule. Polycyclic aromatic hydrocarbons (PAHs) have also been considered. Thermodynamic differences between diamond- and graphite-like grains have been studied in particular. Saturation of the peripheral bonds with hydrogen is found to provide a smooth and uniform convergence of the properties with increasing cluster size. For the graphite-like clusters the convergence to bulk values is much slower than for the three-dimensional complexes.

  5. FT-IR, FT-Raman, UV, NMR spectra, molecular structure, ESP, NBO and HOMO-LUMO investigation of 2-methylpyridine 1-oxide: a combined experimental and DFT study.

    PubMed

    Shoba, D; Periandi, S; Boomadevi, S; Ramalingam, S; Fereyduni, E

    2014-01-24

    In this paper, the equilibrium geometry, bonding features, vibrational frequencies, (1)H and (13)C chemical shift values, molecular electrostatic potential maps, HOMO-LUMO energies and several thermodynamic parameters of title compound in the ground state have been calculated by using the density functional method with 6-31G(d,p) and 6-311G(d,p) basis sets. A detailed interpretation of the infrared and Raman spectra of 2-methylpyridine 1-oxide was reported. Furthermore, natural bond orbitals were performed in this work. The theoretical results showed an excellent agreement with the experimental values.

  6. Microwave spectrum and molecular structure of PNO

    NASA Astrophysics Data System (ADS)

    Okabayashi, Toshiaki; Yamazaki, Emi; Tanimoto, Mitsutoshi

    1999-08-01

    The microwave spectra of P14N16O and its isotopomers P15N16O and P14N18O were observed in a dc glow discharge plasma of a mixture of nitric oxide and hydrogen gases over solid red phosphorus placed on the stainless steel electrode. Rotational transitions of the parent P14N16O species were measured in the ground state as well as in the vibrationally excited ν1 (PN str.), ν2 (bend), and 2ν2 states. The l=0 substate of the 2ν2 state interacts with the ν1 state through a Fermi resonance. The rotational constants determined for the ground states of the three isotopomers yield the substitution structure, rs(PN)=151.6516(87) pm and rs(NO)=119.5025(80) pm.

  7. Connecting the density structure of molecular clouds with star formation

    NASA Astrophysics Data System (ADS)

    Kainulainen, Jouni

    In the current paradigm of turbulence-regulated interstellar medium (ISM), star formation rates of entire galaxies are intricately linked to the density structure of the individual molecular clouds. This density structure is essentially encapsulated in the probability distribution function of volume densities (ρ-PDF), which directly affects the star formation rates predicted by analytic models. Contrasting its fundamental role, the ρ-PDF function has remained virtually unconstrained by observations. I describe in this contribution the recent progress in attaining observational constraints for the column density PDFs (N-PDFs) of molecular clouds that function as a proxy of the ρ-PDFs. Specifically, observational works point towards a universal correlation between the shape of the N-PDFs and star formation activity in molecular clouds. The correlation is in place from the scales of a parsec up to the scales of entire galaxies, making it a fundamental, global link between the ISM structure and star formation.

  8. Molecular structure of vapor-deposited amorphous selenium

    NASA Astrophysics Data System (ADS)

    Goldan, A. H.; Li, C.; Pennycook, S. J.; Schneider, J.; Blom, A.; Zhao, W.

    2016-10-01

    The structure of amorphous selenium is clouded with much uncertainty and contradictory results regarding the dominance of polymeric chains versus monomer rings. The analysis of the diffraction radial distribution functions are inconclusive because of the similarities between the crystalline allotropes of selenium in terms of the coordination number, bond length, bond angle, and dihedral angle. Here, we took a much different approach and probed the molecular symmetry of the thermodynamically unstable amorphous state via analysis of structural phase transformations. We verified the structure of the converted metastable and stable crystalline structures using scanning transmission electron microscopy. In addition, given that no experimental technique can tell us the exact three-dimensional atomic arrangements in glassy semiconductors, we performed molecular-dynamic simulations using a well-established empirical three-body interatomic potential. We developed a true vapor-deposited process for the deposition of selenium molecules onto a substrate using empirical molecular vapor compositions and densities. We prepared both vapor-deposited and melt-quenched samples and showed that the simulated radial distribution functions match very well to experiment. The combination of our experimental and molecular-dynamic analyses shows that the structures of vapor- and melt-quenched glassy/amorphous selenium are quite different, based primarily on rings and chains, respectively, reflecting the predominant structure of the parent phase in its thermodynamic equilibrium.

  9. Synchrotron based mass spectrometry to investigate the molecular properties of mineral-organic associations

    SciTech Connect

    Liu, Suet Yi; Kleber, Markus; Takahashi, Lynelle K.; Nico, Peter; Keiluweit, Marco; Ahmed, Musahid

    2013-04-01

    Soil organic matter (OM) is important because its decay drives life processes in the biosphere. Analysis of organic compounds in geological systems is difficult because of their intimate association with mineral surfaces. To date there is no procedure capable of quantitatively separating organic from mineral phases without creating artifacts or mass loss. Therefore, analytical techniques that can (a) generate information about both organic and mineral phases simultaneously and (b) allow the examination of predetermined high-interest regions of the sample as opposed to conventional bulk analytical techniques are valuable. Laser Desorption Synchrotron Postionization (synchrotron-LDPI) mass spectrometry is introduced as a novel analytical tool to characterize the molecular properties of organic compounds in mineral-organic samples from terrestrial systems, and it is demonstrated that when combined with Secondary Ion Mass Spectrometry (SIMS), can provide complementary information on mineral composition. Mass spectrometry along a decomposition gradient in density fractions, verifies the consistency of our results with bulk analytical techniques. We further demonstrate that by changing laser and photoionization energies, variations in molecular stability of organic compounds associated with mineral surfaces can be determined. The combination of synchrotron-LDPI and SIMS shows that the energetic conditions involved in desorption and ionization of organic matter may be a greater determinant of mass spectral signatures than the inherent molecular structure of the organic compounds investigated. The latter has implications for molecular models of natural organic matter that are based on mass spectrometric information.

  10. Synthesis, crystal structure analysis, spectral investigations, DFT computations, Biological activities and molecular docking of methyl(2E)-2-{[N-(2-formylphenyl)(4-methylbenzene) sulfonamido]methyl}-3-(4-fluorophenyl)prop-2-enoate, a potential bioactive agent

    NASA Astrophysics Data System (ADS)

    Murugavel, S.; Vetri Velan, V.; Kannan, Damodharan; Bakthadoss, Manickam

    2016-03-01

    The title compound methyl(2E)-2-{[N-(2-formylphenyl) (4-methylbenzene)sulfonamido]methyl}-3-(4-fluorophenyl) prop-2-enoate (MFMSF) has been synthesized and single crystals were grown by slow evaporation solution growth technique at room temperature. The grown crystals were characterized by FTIR, 1H NMR, 13C NMR, and single crystal X-ray diffraction. In the crystal, molecules are linked by intermolecular C-H…O hydrogen bonds forming a two-dimensional supramolecular network along [110] direction. The molecular geometry was also optimized using density functional theory (DFT/B3LYP) method with the 6-311G (d,p) basis set in ground state and compared with the experimental data. The entire vibrational assignments of wave numbers were made on the basis of potential energy distribution (PED) by VEDA 4 programme. Stability of the molecule arising from hyper conjugative interactions, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. In addition, NLO, MEP, Mulliken, thermodynamic properties, HOMO and LUMO energy gap were theoretically predicted. The global chemical reactivity descriptors are calculated for MFMSF and used to predict their relative stability and reactivity. The antibacterial activity of the compound was also tested against various pathogens. The molecular docking studies concede that title compound may exhibit PBP-2X inhibitor activity.

  11. Molecular and chemical investigations and comparisons of biomaterials for ocular surface regeneration.

    PubMed

    Kim, Yeon-Hee; Jin, Kyung-Hyun; Kim, Jae Hyung; Park, Dong Jin; Choi, Samjin; Park, Hun-Kuk

    2014-03-01

    This study investigated and compared the ultrastructural and chemical properties of representative biomaterials for ocular surface regeneration: a human amniotic membrane (AM) in a basal plate, a human AM in reflected chorion, a preserved AM, and a human corneo-scleral tissue. Assessments of the morphological differences in the extracellular matrices were evaluated by hematoxylin-eosin, Masson's trichrome (for total collagen), and picrosirius-red (for newly synthesized collagen) staining. Assessments of the changes in the molecular structures and chemical compositions of the biomaterials for ocular surface regeneration were evaluated by Raman spectroscopy. A placental AM (52 %) was a dense and thick collagenous structure compared to a reflected AM (23 %). The spectroscopy did not obtain any structural information for a preserved AM. The cornea group (100 %, control) and sclera group (104 %) showed the collagen lamellae and interfibrillar spacing, and a slight inflammatory reaction with more fibrous and granulomatous tissues. There was a formation of newly synthesized collagen in a placental AM, while there were few collagen components in a reflected AM. Human AM tissues showed consistent Raman spectra and the characteristic collagen bands, similar to the corneal and scleral tissues. Therefore, these findings suggest that human placental AM and reflected AM are structurally suitable for scleral and corneal surface regeneration, respectively, while human placental or preserved AM and reflected AM are molecularly and chemically suitable for corneal and scleral surface regeneration, respectively.

  12. Molecular investigation on the interaction of spermine with proteinase K by multispectroscopic techniques and molecular simulation studies.

    PubMed

    Hosseini-Koupaei, Mansoore; Shareghi, Behzad; Saboury, Ali Akbar; Davar, Fateme

    2017-01-01

    The alteration in structure, function and stability of proteinase K in the presence of spermine was investigated using spectroscopic methods and simulation techniques. The stability and enzyme activity of proteinase K-spermine complex were significantly enhanced as compared to that of the pure enzyme. The increase in the value of Vmax and the catalytic efficiency of Proteinase K in presence of spermine confirmed that the polyamine could bring the enzyme hyperactivation. UV-vis spectroscopy, intrinsic fluorescence and circular dichroism methods demonstrated that the binding of spermine changed the microenvironment and structure of proteinase K. The fluorescence studies, showing that spermine quenched the intensity of proteinase K with static mechanism. Thermodynamic parameters analysis suggested that hydrogen bond and van der Waals forces play a key role in complex stability which is in agreement with modeling studies. The CD spectra represented the secondary structure alteration of proteinase K with an increase in α-helicity and a decrease in β-sheet of proteinase K upon spermine conjugation. The molecular simulation results proposed that spermine could interact with proteinase K spontaneously at single binding site, which is in agreement with spectroscopic results. This agreement between experimental and theoretical results may be a worth method for protein-ligand complex studies.

  13. Investigation of the torsional barrier of EDOT using molecular mechanics and DFT methods.

    PubMed

    Durães, Jussara A; da Silva Filho, Demétrio A; Ceschin, Artemis M; Sales, Maria J A; Martins, João B L

    2014-08-01

    When heterocyclic monomers are polymerized by electrochemical or chemical methods, they form fully conjugated polymers which have a wide range of applications due to their outstanding electronic properties. Among this class of compounds, thiophene derivatives are widely used due to their chemical stability and synthesis flexibility. With the goal to investigate the torsion barrier of polymer chains, a few units of 3,4-ethylenedioxythiophene (EDOT) were chosen and submitted to molecular mechanics (MM), density functional theory (DFT) and coupled cluster CCSD(T) calculations. This study helps to understand the performance and transferability of force fields used in molecular mechanics and molecular dynamics simulations often used to describe structure-property relationships of those systems. Determination of inter-ring torsion angle was performed in a comparative study using both force field, DFT and CCSD(T) methods. A good agreement was noticed between MM and QC results and highlights the importance of the description of the interactions involving the oxygen atoms present in the structure of EDOT. These observations are related to the α,α-coupling that occurs between the monomer units and yields a linear polymer. DFT HOMO and LUMO orbitals were also presented. Finally, UV-vis spectra of EDOT units were obtained using several levels of theory by means of time-dependent DFT calculations (TD-DFT).

  14. Molecular Evolution, Structure, and Function of Peroxidasins

    PubMed Central

    Soudi, Monika; Zamocky, Marcel; Jakopitsch, Christa; Furtmüller, Paul G; Obinger, Christian

    2012-01-01

    Peroxidasins represent the subfamily 2 of the peroxidase-cyclooxygenase superfamily and are closely related to chordata peroxidases (subfamily 1) and peroxinectins (subfamily 3). They are multidomain proteins containing a heme peroxidase domain with high homology to human lactoperoxidase that mediates one- and two-electron oxidation reactions. Additional domains of the secreted and glycosylated metalloproteins are type C-like immunoglobulin domains, typical leucine-rich repeats, as well as a von Willebrand factor C module. These are typical motifs of extracellular proteins that mediate protein–protein interactions. We have reconstructed the phylogeny of this new family of oxidoreductases and show the presence of four invertebrate clades as well as one vertebrate clade that includes also two different human representatives. The variability of domain assembly in the various clades was analyzed, as was the occurrence of relevant catalytic residues in the peroxidase domain based on the knowledge of catalysis of the mammalian homologues. Finally, the few reports on expression, localization, enzymatic activity, and physiological roles in the model organisms Drosophila melanogaster, Caenorhabditis elegans, and Homo sapiens are critically reviewed. Roles attributed to peroxidasins include antimicrobial defense, extracellular matrix formation, and consolidation at various developmental stages. Many research questions need to be solved in future, including detailed biochemical/physical studies and elucidation of the three dimensional structure of a model peroxidasin as well as the relation and interplay of the domains and the in vivo functions in various organisms including man. PMID:22976969

  15. Importance of Molecular Structure on the Thermophoresis of Binary Mixtures.

    PubMed

    Kumar, Pardeep; Goswami, Debabrata

    2014-12-26

    Using thermal lens spectroscopy, we study the role of molecular structural isomers of butanol on the thermophoresis (or Soret effect) of binary mixtures of methanol in butanol. In this study, we show that the thermal lens signal due to the Soret effect changes its sign for all the different concentrations of binary mixtures of butanol with methanol except for the one containing tertiary-butanol. The magnitude and sign of the Soret coefficients strongly depend on the molecular structure of the isomers of butanol in the binary mixture with methanol. This isomerization dependence is in stark contrast to the expected mass dependence of the Soret effect.

  16. Molecular structure and exciton dynamics in organic conjugated polymers

    NASA Astrophysics Data System (ADS)

    Thomas, Alan K.

    Intermolecular electronic interactions, dipole coupling and orbital overlap, caused by pi-pi stacking in organic conjugated polymers lead to unique structures and properties that can be harnessed for optoelectronic applications. These interactions define structure-function relationships in amorphous and aggregated forms of polymers in the solid state and determine their efficiencies and functionality in electronic devices, from transistors to solar cells. Organic polymer electronic device performance depends critically upon electronic coupling between monomer units -mediated by conformation and packing characteristics - that dictates electronic properties like conductivity and capacitance as well as electronic processes, such as charge carrier generation and transport. This dissertation demonstrates how electronic processes in conjugated polymers are mediated by subtle inter- and intra-chain electronic interactions imparted by the conformational degrees of freedom within their solid state structure and how this effects device performance. To initiate this investigation into structure-function relationships, an examination of nanoparticles representing two limiting aggregation states of the conjugated polymer poly(3-hexylthiophene) (P3HT) was conducted. These aggregates are defined by their predominate form of electronic coupling, inter- or intrachain, called H- and J-aggregates respectively. H- or J-aggregates of P3HT were embedded in an insulating matrix and time-resolved fluorescence intensity modulation spectroscopy was utilized to uncover the existence of efficient singlet-triplet quenching in J aggregates not present in H-aggregates. These studies were extended by examining P3HT H-and J-aggregates under applied electric fields in capacitor type devices using multiple time-resolved and steady-state spectroscopic techniques. These experiments reveal electronic couplings in J aggregates that shift excited state population towards a majority composed of long lived

  17. Investigating the influence of effective parameters on molecular characteristics of bovine serum albumin nanoparticles

    NASA Astrophysics Data System (ADS)

    Rohiwal, S. S.; Satvekar, R. K.; Tiwari, A. P.; Raut, A. V.; Kumbhar, S. G.; Pawar, S. H.

    2015-04-01

    The protein nanoparticles formulation is a challenging task as they are prone to undergo conformational transitions while processing which may affect bioavailability for bioactive compounds. Herein, a modified desolvation method is employed to prepare Bovine Serum Albumin nanoparticles, with controllable particle size ranging from 100 to 300 nm and low polydispersity index. The factors influencing the size and structure of BSA NPs viz. protein concentration, pH and the conditions for purification are well investigated. The structure of BSA NPs is altered due to processing, and may affect the effective binding ability with drugs and bioactive compounds. With that aims, investigations of molecular characteristics of BSA NPs are carried out in detail by using spectroscopic techniques. UV-visible absorption and Fourier Transform Infrared demonstrate the alteration in protein structure of BSA NPs whereas the FT-Raman spectroscopy investigates changes in the secondary and tertiary structures of the protein. The conformational changes of BSA NPs are observed by change in fluorescence intensity and emission maximum wavelength of tryptophan residue by fluorescence spectroscopy. The field emission scanning electron and atomic force microscopy micrographs confirm the size and semi-spherical morphology of the BSA NPs. The effect of concentration and pH on particle size distribution is studied by particle size analyzer.

  18. Nuclear-structure investigations on spherical nuclei

    SciTech Connect

    Heisenberg, J.

    1982-01-01

    Nuclear structure research at the University of New Hampshire is reported. Energy level studies using electron inelastic scattering and electron-induced fission are briefly discussed. Also, the theoretical studies are outlined including exchange current calculations, shell model RPA calculations, and self-consistent RPA. Publications are listed. (WHK)

  19. Structural and dipolar fluctuations in liquid water: A Car-Parrinello molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Skarmoutsos, Ioannis; Masia, Marco; Guardia, Elvira

    2016-03-01

    A Car-Parrinello molecular dynamics simulation was performed to investigate the local tetrahedral order, molecular dipole fluctuations and their interrelation with hydrogen bonding in liquid water. Water molecules were classified in three types, exhibiting low, intermediate and high tetrahedral order. Transitions from low to high tetrahedrally ordered structures take place only through transitions to the intermediate state. The molecular dipole moments depend strongly on the tetrahedral order and hydrogen bonding. The average dipole moment of water molecules with a strong tetrahedral order around them comes in excellent agreement with previous estimations of the dipole moment of ice Ih molecules.

  20. From non-random molecular structure to life and mind

    NASA Technical Reports Server (NTRS)

    Fox, S. W.

    1989-01-01

    The evolutionary hierarchy molecular structure-->macromolecular structure-->protobiological structure-->biological structure-->biological functions has been traced by experiments. The sequence always moves through protein. Extension of the experiments traces the formation of nucleic acids instructed by proteins. The proteins themselves were, in this picture, instructed by the self-sequencing of precursor amino acids. While the sequence indicated explains the thread of the emergence of life, protein in cellular membrane also provides the only known material basis for the emergence of mind in the context of emergence of life.

  1. ALMA Reveals Internal Structure of Molecular Clouds in the LMC

    NASA Astrophysics Data System (ADS)

    Sawada, T.; Hasegawa, T.; Koda, J.

    2015-12-01

    We carried out high-resolution (0.7 pc) CO J=1-0 mosaic observations of five giant molecular clouds, which cover a wide range of evolutionary stages based on their associations to recent star formation, in the Large Magellanic Cloud with ALMA. The observations revealed a variety of spatial structures of the gas, from faint and diffuse emission to bright and compact structures. The variation of structures, which is similar to that seen in the Milky Way, is quantified by the brightness distribution function (BDF) and brightness distribution index (BDI) established in our prior studies. The structured molecular gas may indicate the readiness for, rather than the outcome of, star formation.

  2. Investigating Molecular Kinetics by Variationally Optimized Diffusion Maps.

    PubMed

    Boninsegna, Lorenzo; Gobbo, Gianpaolo; Noé, Frank; Clementi, Cecilia

    2015-12-08

    Identification of the collective coordinates that describe rare events in complex molecular transitions such as protein folding has been a key challenge in the theoretical molecular sciences. In the Diffusion Map approach, one assumes that the molecular configurations sampled have been generated by a diffusion process, and one uses the eigenfunctions of the corresponding diffusion operator as reaction coordinates. While diffusion coordinates (DCs) appear to provide a good approximation to the true dynamical reaction coordinates, they are not parametrized using dynamical information. Thus, their approximation quality could not, as yet, be validated, nor could the diffusion map eigenvalues be used to compute relaxation rate constants of the system. Here we combine the Diffusion Map approach with the recently proposed Variational Approach for Conformation Dynamics (VAC). Diffusion Map coordinates are used as a basis set, and their optimal linear combination is sought using the VAC, which employs time-correlation information on the molecular dynamics (MD) trajectories. We have applied this approach to ultra-long MD simulations of the Fip35 WW domain and found that the first DCs are indeed a good approximation to the true reaction coordinates of the system, but they could be further improved using the VAC. Using the Diffusion Map basis, excellent approximations to the relaxation rates of the system are obtained. Finally, we evaluate the quality of different metric spaces and find that pairwise minimal root-mean-square deviation performs poorly, while operating in the recently introduced kinetic maps based on the time-lagged independent component analysis gives the best performance.

  3. Origin and structure of polar domains in doped molecular crystals

    PubMed Central

    Meirzadeh, E.; Azuri, I.; Qi, Y.; Ehre, D.; Rappe, A. M.; Lahav, M.; Kronik, L.; Lubomirsky, I.

    2016-01-01

    Doping is a primary tool for the modification of the properties of materials. Occlusion of guest molecules in crystals generally reduces their symmetry by the creation of polar domains, which engender polarization and pyroelectricity in the doped crystals. Here we describe a molecular-level determination of the structure of such polar domains, as created by low dopant concentrations (<0.5%). The approach comprises crystal engineering and pyroelectric measurements, together with dispersion-corrected density functional theory and classical molecular dynamics calculations of the doped crystals, using neutron diffraction data of the host at different temperatures. This approach is illustrated using centrosymmetric α-glycine crystals doped with minute amounts of different L-amino acids. The experimentally determined pyroelectric coefficients are explained by the structure and polarization calculations, thus providing strong support for the local and global understanding of how different dopants influence the properties of molecular crystals. PMID:27824050

  4. Molecular structure of DNA by scanning tunneling microscopy.

    PubMed

    Cricenti, A; Selci, S; Felici, A C; Generosi, R; Gori, E; Djaczenko, W; Chiarotti, G

    1989-09-15

    Uncoated DNA molecules marked with an activated tris(l-aziridinyl) phosphine oxide (TAPO) solution were deposited on gold substrates and imaged in air with the use of a high-resolution scanning tunneling microscope (STM). Constant-current and gap-modulated STM images show clear evidence of the helicity of the DNA structure: pitch periodicity ranges from 25 to 35 angstroms, whereas the average diameter is 20 angstroms. Molecular structure within a single helix turn was also observed.

  5. Molecular Structure of DNA by Scanning Tunneling Microscopy

    NASA Astrophysics Data System (ADS)

    Cricenti, A.; Selci, S.; Felici, A. C.; Generosi, R.; Gori, E.; Djaczenko, W.; Chiarotti, G.

    1989-09-01

    Uncoated DNA molecules marked with an activated tris(1-aziridinyl) phosphine oxide (TAPO) solution were deposited on gold substrates and imaged in air with the use of a high-resolution scanning tunneling microscope (STM). Constant-current and gap-modulated STM images show clear evidence of the helicity of the DNA structure: pitch periodicity ranges from 25 and 35 angstroms, whereas the average diameter is 20 angstroms. Molecular structure within a single helix turn was also observed.

  6. Structure and photochromic properties of molybdenum-containing silica gels obtained by molecular-lamination method

    SciTech Connect

    Belotserkovskaya, N.G.; Dobychin, D.P.; Pak, V.N.

    1992-05-10

    The structure and physicochemical properties of molybdenum-containing silica gels obtained by molecular lamination have been studied quite extensively. Up to the present, however, no studies have been made of the influence of the pore structure of the original silica gel on the structure and properties of molybdenum-containing silica gels (MSG). The problem is quite important, since molybdenum silicas obtained by molecular lamination may find applications in catalysis and as sensors of UV radiation. In either case, the structure of the support is not a factor to be ignored. Here, the authors are reporting on an investigation of the structure of MSG materials with different pore structures and their susceptibility to reduction of the Mo(VI) oxide groupings when exposed to UV radiation. 16 refs., 2 figs., 2 tabs.

  7. Vibrational spectroscopic and structural investigations on fullerene: A DFT approach

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

    The molecular structure of fullerene (C60) molecule was optimized by the DFT/B3LYP method with 6-31G and 6-31G(d,p) basis sets using Gaussian 09 program. The vibrational frequencies were calculated for the optimized molecular structure of the molecule. The calculated vibrational frequencies confirm that the molecular structure of the molecule was located at the minimum energy potential energy surface. The calculated vibrational frequencies were assigned on the basis of functional group analysis and also confirmed using the GaussView 05 software. The frontier molecular orbitals analysis was carried out. The FMOs related molecular properties were predicted. The higher ionization potential, higher electron affinity, higher softness, lower band gap energy and lower hardness values were obtained, which confirm that the fullerene molecule has a higher molecular reactivity. The Mulliken atomic charge distribution of the molecule was also calculated. Hence, these results play an important role due to its potential applications as drug delivery devices.

  8. Electronic Structure Investigation of Doping C60 with Metal Oxide

    NASA Astrophysics Data System (ADS)

    Wang, Chenggong; Gao, Yongli

    2014-03-01

    Fullerene (C60) has been used extensively as an acceptor material in organic photovoltaic (OPV) cells. Other applications including n-channel organic thin film transistors (OTFT) and C60 based organic superconductors have been reported more than a decade ago. We have investigated p-doping of C60 with molybdenum oxide (MoOx) with ultra-violet photoemission spectroscopy (UPS), inverse photoemission spectroscopy (IPES) and atomic force microscopy (AFM). Both surface doping and bulk doping by MoOx are studied. It was found that the thermally evaporated MoOx inter-layer substantially increased the surface workfunction. This increased surface workfunction strongly attract electrons towards the MoOx layer at the C60/MoOx interface, resulting in strong inversion of C60. Energy levels of C60 relax gradually as the thickness of C60 increases. An exceptionally long (greater than 400 Angstrom) band bending is observed during this relaxation in C60. Such a long band bending has not been observed for other organic/MoOx interface. For the bulk doping, MoOx doping ratios from 1% to over 100% were investigated. The saturation occurs at approximately 20 %, when the highest occupied molecular level (HOMO) of C60 starts to be pinned at the Fermi level. These studies demonstrate effective ways to manipulate the electronic structures of the fullerene. This work is supported by the National Science Foundation Grant No. DMR-1303742.

  9. Investigate the Binding of Catechins to Trypsin Using Docking and Molecular Dynamics Simulation

    PubMed Central

    Cui, Fengchao; Yang, Kecheng; Li, Yunqi

    2015-01-01

    To explore the inhibitory mechanism of catechins for digestive enzymes, we investigated the binding mode of catechins to a typical digestive enzyme-trypsin and analyzed the structure-activity relationship of catechins, using an integration of molecular docking, molecular dynamics simulation and binding free energy calculation. We found that catechins with different structures bound to a conservative pocket S1 of trypsin, which is comprised of residues 189–195, 214–220 and 225–228. In the trypsin-catechin complexes, Asp189 by forming strong hydrogen bonding, and Gln192, Trp215 and Gly216 through hydrophobic interactions, all significantly contribute to the binding of catechins. The number and the position of hydroxyl and aromatic groups, the structure of stereoisomers, and the orientation of catechins in the binding pocket S1 of trypsin all affect the binding affinity. The binding affinity is in the order of Epigallocatechin gallate (EGCG) > Epicatechin gallate (ECG) > Epicatechin (EC) > Epigallocatechin (EGC), and 2R-3R EGCG shows the strongest binding affinity out of other stereoisomers. Meanwhile, the synergic conformational changes of residues and catechins were also analyzed. These findings will be helpful in understanding the knowledge of interactions between catechins and trypsin and referable for the design of novel polyphenol based functional food and nutriceutical formulas. PMID:25938485

  10. Connecting molecular structure and exciton diffusion length in rubrene derivatives.

    PubMed

    Mullenbach, Tyler K; McGarry, Kathryn A; Luhman, Wade A; Douglas, Christopher J; Holmes, Russell J

    2013-07-19

    Connecting molecular structure and exciton diffusion length in rubrene derivatives demonstrates how the diffusion length of rubrene can be enhanced through targeted functionalization aiming to enhance self-Förster energy transfer. Functionalization adds steric bulk, forcing the molecules farther apart on average, and leading to increased photoluminescence efficiency. A diffusion length enhancement greater than 50% is realized over unsubstituted rubrene.

  11. Elucidation of Drug Metabolite Structural Isomers Using Molecular Modeling Coupled with Ion Mobility Mass Spectrometry.

    PubMed

    Reading, Eamonn; Munoz-Muriedas, Jordi; Roberts, Andrew D; Dear, Gordon J; Robinson, Carol V; Beaumont, Claire

    2016-02-16

    Ion mobility-mass spectrometry (IM-MS) in combination with molecular modeling offers the potential for small molecule structural isomer identification by measurement of their gas phase collision cross sections (CCSs). Successful application of this approach to drug metabolite identification would facilitate resource reduction, including animal usage, and may benefit other areas of pharmaceutical structural characterization including impurity profiling and degradation chemistry. However, the conformational behavior of drug molecules and their metabolites in the gas phase is poorly understood. Here the gas phase conformational space of drug and drug-like molecules has been investigated as well as the influence of protonation and adduct formation on the conformations of drug metabolite structural isomers. The use of CCSs, measured from IM-MS and molecular modeling information, for the structural identification of drug metabolites has also been critically assessed. Detection of structural isomers of drug metabolites using IM-MS is demonstrated and, in addition, a molecular modeling approach has been developed offering rapid conformational searching and energy assessment of candidate structures which agree with experimental CCSs. Here it is illustrated that isomers must possess markedly dissimilar CCS values for structural differentiation, the existence and extent of CCS differences being ionization state and molecule dependent. The results present that IM-MS and molecular modeling can inform on the identity of drug metabolites and highlight the limitations of this approach in differentiating structural isomers.

  12. An experimental and theoretical investigation of Acenaphthene-5-boronic acid: conformational study, NBO and NLO analysis, molecular structure and FT-IR, FT-Raman, NMR and UV spectra.

    PubMed

    Karabacak, Mehmet; Sinha, Leena; Prasad, Onkar; Asiri, Abdullah M; Cinar, Mehmet

    2013-11-01

    The solid state Fourier transform infrared (FT-IR) and FT-Raman spectra of Acenaphthene-5-boronic acid (AN-5-BA), have been recorded in the range 4000-400cm(-1) and 4000-10cm(-1), respectively. Density functional theory (DFT), with the B3LYP functional was used for the optimization of the ground state geometry and simulation of the infrared and Raman spectra of the molecule. The vibrational wave numbers and their assignments were examined theoretically using the Gaussian 09 set of quantum chemistry codes and the normal modes were assigned by a scaled quantum mechanical (SQM) force field approach. Hydrogen-bonded dimer of AN-5-BA, optimized by counterpoise correction, has also been studied by B3LYP at the 6-311++G(d,p) level and the effects of molecular association through O-H⋯O hydrogen bonding have been discussed. The (1)H and (13)C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by Gauge-Including Atomic Orbital (GIAO) method. Natural bond orbital (NBO) analysis has been applied to study stability of the molecule arising from charge delocalization. UV 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. The first order hyperpolarizability 〈β〉, its components and associated properties such as average polarizability and anisotropy of the polarizability (α and Δα) of AN-5-BA was calculated using the finite-field approach.

  13. Investigation of Nuclear Partonic Structure. Final Report

    SciTech Connect

    Crawford, Henry J.; Engelage, J. M.

    2016-08-30

    Our research program had two primary goals during the period of this grant, to search for new and rare particles produced in high-energy nuclear collisions and to understand the internal structure of nuclear matter. We have developed electronics to pursue these goals at the Relativistic Heavy Ion Collider (RHIC) in the Solenoidal Tracker at RHIC (STAR) experiment and the AnDY experiment. Our results include discovery of the anti-hyper-triton, anti- 3Λ-barH, which opened a new branch on the chart of the nuclides, and the anti-alpha, anti- 4He, the heaviest form of anti-matter yet seen, as well as uncovering hints of gluon saturation in cold nuclear matter and observation of jets in polarized proton-proton collisions that will be used to probe orbital motion inside protons.

  14. The Venus SAGE Atmospheric Structure Investigation

    NASA Technical Reports Server (NTRS)

    Colaprete, Anthony; Crisp, Dave; LaBaw, Clayton; Morse, Stephanie

    2005-01-01

    Experiment goals and objectives are: a) To accurately define the state properties as a function of altitude from below the 10(exp -4) mb level (approx.150 km) to 92 bars (surface); b) To measure the stability of the atmosphere, and identify convective layers and stable layers, where they exist; c) To detect cloud levels from changes in the lapse rate at their boundaries; d) To provide state properties within the cloud levels, and thus provide supplementary information on cloud composition; e) To search for and characterize wave structure within the atmosphere; f) To search for and measure the intensity and scale of turbulence; g) To measure descent and surface wind speed and direction; h) To provide Lander altitude and attitude during decent for descent imaging analysis; and i) To provide a back-up landing sensor.

  15. Single Molecule Switches and Molecular Self-Assembly: Low Temperature STM Investigations and Manipulations

    SciTech Connect

    Iancu, Violeta

    2006-08-01

    This dissertation is devoted to single molecule investigations and manipulations of two porphyrin-based molecules, chlorophyll-a and Co-popphyrin. The molecules are absorbed on metallic substrates and studied at low temperatures using a scanning tunneling microscope. The electronic, structural and mechanical properties of the molecules are investigated in detail with atomic level precision. Chlorophyll-a is the key ingredient in photosynthesis processes while Co-porphyrin is a magnetic molecule that represents the recent emerging field of molecular spintronics. Using the scanning tunneling microscope tip and the substrate as electrodes, and the molecules as active ingredients, single molecule switches made of these two molecules are demonstrated. The first switch, a multiple and reversible mechanical switch, is realized by using chlorophyll-a where the energy transfer of a single tunneling electron is used to rotate a C-C bond of the molecule's tail on a Au(111) surface. Here, the det

  16. Investigation of deformation mechanisms of staggered nanocomposites using molecular dynamics

    NASA Astrophysics Data System (ADS)

    Mathiazhagan, S.; Anup, S.

    2016-08-01

    Biological materials with nanostructure of regularly or stair-wise staggered arrangements of hard platelets reinforced in a soft protein matrix have superior mechanical properties. Applications of these nanostructures to ceramic matrix composites could enhance their toughness. Using molecular dynamics simulations, mechanical behaviour of the bio-inspired nanocomposites is studied. Regularly staggered model shows better flow behaviour compared to stair-wise staggered model due to the symmetrical crack propagation along the interface. Though higher stiffness and strength are obtained for stair-wise staggered models, rapid crack propagation reduces the toughness. Arresting this crack propagation could lead to superior mechanical properties in stair-wise staggered models.

  17. Molecular Population Genetic Structure in the Piping Plover

    USGS Publications Warehouse

    Miller, Mark P.; Haig, Susan M.; Gratto-Trevor, Cheri L.; Mullins, Thomas D.

    2009-01-01

    The Piping Plover (Charadrius melodus) is a migratory shorebird currently listed as Endangered in Canada and the U.S. Great Lakes, and threatened throughout the remainder of its U.S. breeding and winter range. In this study, we undertook the first comprehensive molecular genetic-based investigation of Piping Plovers. Our primary goals were to (1) address higher level subspecific taxonomic issues, (2) characterize population genetic structure, and (3) make inferences regarding past bottlenecks or population expansions that have occurred within this species. Our analyses included samples of individuals from 23 U.S. States and Canadian Provinces, and were based on mitochondrial DNA sequences (580 bp, n = 245 individuals) and eight nuclear microsatellite loci (n = 229 individuals). Our findings illustrate strong support for separate Atlantic and Interior Piping Plover subspecies (C. m. melodus and C. m. circumcinctus, respectively). Birds from the Great Lakes region were allied with the Interior subspecies group and should be taxonomically referred to as C. m. circumcinctus. Population genetic analyses suggested that genetic structure was stronger among Atlantic birds relative to the Interior group. This pattern indicates that natal and breeding site fidelity may be reduced among Interior birds. Furthermore, analyses suggested that Interior birds have previously experienced genetic bottlenecks, whereas no evidence for such patterns existed among the Atlantic subspecies. Likewise, genetic analyses indicated that the Great Lakes region has experienced a population expansion. This finding may be interpreted as population growth following a previous bottleneck event. No genetic evidence for population expansions was found for Atlantic, Prairie Canada, or U.S. Northern Great Plains individuals. We interpret our population history insights in light of 25 years of Piping Plover census data. Overall, differences observed between Interior and Atlantic birds may reflect

  18. Designing π-stacked molecular structures to control heat transport through molecular junctions

    SciTech Connect

    Kiršanskas, Gediminas; Li, Qian; Solomon, Gemma C.; Flensberg, Karsten; Leijnse, Martin

    2014-12-08

    We propose and analyze a way of using π stacking to design molecular junctions that either enhance or suppress a phononic heat current, but at the same time remain conductors for an electric current. Such functionality is highly desirable in thermoelectric energy converters, as well as in other electronic components where heat dissipation should be minimized or maximized. We suggest a molecular design consisting of two masses coupled to each other with one mass coupled to each lead. By having a small coupling (spring constant) between the masses, it is possible to either reduce or perhaps more surprisingly enhance the phonon conductance. We investigate a simple model system to identify optimal parameter regimes and then use first principle calculations to extract model parameters for a number of specific molecular realizations, confirming that our proposal can indeed be realized using standard molecular building blocks.

  19. Extracting Structure Parameters of Dimers for Molecular Tunneling Ionization Model

    NASA Astrophysics Data System (ADS)

    Song-Feng, Zhao; Fang, Huang; Guo-Li, Wang; Xiao-Xin, Zhou

    2016-03-01

    We determine structure parameters of the highest occupied molecular orbital (HOMO) of 27 dimers for the molecular tunneling ionization (so called MO-ADK) model of Tong et al. [Phys. Rev. A 66 (2002) 033402]. The molecular wave functions with correct asymptotic behavior are obtained by solving the time-independent Schrödinger equation with B-spline functions and molecular potentials which are numerically created using the density functional theory. We examine the alignment-dependent tunneling ionization probabilities from MO-ADK model for several molecules by comparing with the molecular strong-field approximation (MO-SFA) calculations. We show the molecular Perelomov-Popov-Terent'ev (MO-PPT) can successfully give the laser wavelength dependence of ionization rates (or probabilities). Based on the MO-PPT model, two diatomic molecules having valence orbital with antibonding systems (i.e., Cl2, Ne2) show strong ionization suppression when compared with their corresponding closest companion atoms. Supported by National Natural Science Foundation of China under Grant Nos. 11164025, 11264036, 11465016, 11364038, the Specialized Research Fund for the Doctoral Program of Higher Education of China under Grant No. 20116203120001, and the Basic Scientific Research Foundation for Institution of Higher Learning of Gansu Province

  20. Structural investigation into physiological DNA phosphorothioate modification

    PubMed Central

    Lan, Wenxian; Hu, Zhongpei; Shen, Jie; Wang, Chunxi; Jiang, Feng; Liu, Huili; Long, Dewu; Liu, Maili; Cao, Chunyang

    2016-01-01

    DNA phosphorothioate (PT) modification, with sulfur replacing a nonbridging phosphate oxygen in a sequence and stereo specific manner, is a novel physiological variation in bacteria. But what effects on DNA properties PT modification has is still unclear. To address this, we prepared three double-stranded (ds) DNA decamers, d(CGPXGCCGCCGA) with its complementary strand d(TCGGCGPXGCCG) (where X = O or S, i.e., PT-free dsDNA, [Sp, Sp]-PT dsDNA or [Rp, Rp]-PT dsDNA) located in gene of Streptomyces lividans. Their melting temperature (Tm) measurement indicates that [Rp, Rp]-PT dsDNA is most unstable. Their electron transfer potential detection presents an order of anti-oxidation properties: Sp-PT DNA > Rp-PT DNA > PT-free DNA. Their NMR structures demonstrate that PT modification doesn’t change their B-form conformation. The sulfur in [Rp, Rp]-PT dsDNA locates in the major groove, with steric effects on protons in the sugar close to modification sites, resulting in its unstability, and facilitating its selectively interactions with ScoMcrA. We thought that PT modification was dialectical to the bacteria. It protects the hosting bacteria by working as antioxidant against H2O2, and acts as a marker, directing restriction enzyme observed in other hosts, like ScoMcrA, to correctly cleave the PT modified DNA, so that bacteria cannot spread and survive. PMID:27169778

  1. Molecular design for growth of supramolecular membranes with hierarchical structure.

    PubMed

    Zha, R Helen; Velichko, Yuri S; Bitton, Ronit; Stupp, Samuel I

    2016-02-07

    Membranes with hierarchical structure exist in biological systems, and bio-inspired building blocks have been used to grow synthetic analogues in the laboratory through self-assembly. The formation of these synthetic membranes is initiated at the interface of two aqueous solutions, one containing cationic peptide amphiphiles (PA) and the other containing the anionic biopolymer hyaluronic acid (HA). The membrane growth process starts within milliseconds of interface formation and continues over much longer timescales to generate robust membranes with supramolecular PA-HA nanofibers oriented orthogonal to the interface. Computer simulation indicates that formation of these hierarchically structured membranes requires strong interactions between molecular components at early time points in order to generate a diffusion barrier between both solutions. Experimental studies using structurally designed PAs confirm simulation results by showing that only PAs with high ζ potential are able to yield hierarchically structured membranes. Furthermore, the chemical structure of such PAs must incorporate residues that form β-sheets, which facilitates self-assembly of long nanofibers. In contrast, PAs that form low aspect ratio nanostructures interact weakly with HA and yield membranes that exhibit non-fibrous fingering protrusions. Furthermore, experimental results show that increasing HA molecular weight decreases the growth rate of orthogonal nanofibers. This result is supported by simulation results suggesting that the thickness of the interfacial contact layer generated immediately after initiation of self-assembly increases with polymer molecular weight.

  2. Investigation of molecular penetration depth variation with SMBI fluxes

    NASA Astrophysics Data System (ADS)

    Zhou, Yu-Lin; Wang, Zhan-Hui; Xu, Min; Wang, Qi; Nie, Lin; Feng, Hao; Sun, Wei-Guo

    2016-09-01

    We study the molecular penetration depth variation with the SMBI fluxes. The molecular transport process and the penetration depth during SMBI with various injection velocities and densities are simulated and compared. It is found that the penetration depth of molecules strongly depends on the radial convective transport of SMBI and it increases with the increase of the injection velocity. The penetration depth does not vary much once the SMBI injection density is larger than a critical value due to the dramatic increase of the dissociation rate on the fueling path. An effective way to improve the SMBI penetration depth has been predicted, which is SMBI with a large radial injection velocity and a lower molecule injection density than the critical density. Project supported by the National Natural Science Foundation of China (Grant Nos. 11375053, 11575055, 11405022, and 11405112), the Chinese National Fusion Project for ITER (Grant Nos. 2013GB107001 and 2013GB112005), the International S&T Cooperation Program of China (Grant No. 2015DFA61760), and the Funds of the Youth Innovation Team of Science and Technology in Sichuan Province of China (Grant No. 2014TD0023).

  3. Photoelectron Angular Distribution and Molecular Structure in Multiply Charged Anions

    SciTech Connect

    Xing, Xiaopeng; Wang, Xue B.; Wang, Lai S.

    2009-02-12

    Photoelectrons emitted from multiply charged anions (MCAs) carry information of the intramolecular Coulomb repulsion (ICR), which is dependent on molecular structures. Using photoelectron imaging, we observed the effects of ICR on photoelectron angular distributions (PAD) of the three isomers of benzene dicarboxylate dianions C6H4(CO2)22– (o-, m- and p-BDC2–). Photoelectrons were observed to peak along the laser polarization due to the ICR, but the anisotropy was the largest for p-BDC2–, followed by the m- and o-isomer. The observed anisotropy is related to the direction of the ICR or the detailed molecular structures, suggesting that photoelectron imaging may allow structural information to be obtained for complex multiply charged anions.

  4. MOLVIE: an interactive visualization environment for molecular structures.

    PubMed

    Sun, Huandong; Li, Ming; Xu, Ying

    2003-05-01

    A Molecular visualization interactive environment (MOLVIE), is designed to display three-dimensional (3D) structures of molecules and support the structural analysis and research on proteins. The paper presents the features, design considerations and applications of MOLVIE, especially the new functions used to compare the structures of two molecules and view the partial fragment of a molecule. Being developed in JAVA, MOLVIE is platform-independent. Moreover, it may run on a webpage as an applet for remote users. MOLVIE is available at http://www.cs.ucsb.edu/~mli/Bioinf/software/index.html.

  5. Cytoskeleton Molecular Motors: Structures and Their Functions in Neuron.

    PubMed

    Xiao, Qingpin; Hu, Xiaohui; Wei, Zhiyi; Tam, Kin Yip

    2016-01-01

    Cells make use of molecular motors to transport small molecules, macromolecules and cellular organelles to target region to execute biological functions, which is utmost important for polarized cells, such as neurons. In particular, cytoskeleton motors play fundamental roles in neuron polarization, extension, shape and neurotransmission. Cytoskeleton motors comprise of myosin, kinesin and cytoplasmic dynein. F-actin filaments act as myosin track, while kinesin and cytoplasmic dynein move on microtubules. Cytoskeleton motors work together to build a highly polarized and regulated system in neuronal cells via different molecular mechanisms and functional regulations. This review discusses the structures and working mechanisms of the cytoskeleton motors in neurons.

  6. Three-dimensional depth profiling of molecular structures.

    PubMed

    Wucher, A; Cheng, J; Zheng, L; Winograd, N

    2009-04-01

    Molecular time of flight secondary ion mass spectrometry (ToF-SIMS) imaging and cluster ion beam erosion are combined to perform a three-dimensional chemical analysis of molecular films. The resulting dataset allows a number of artifacts inherent in sputter depth profiling to be assessed. These artifacts arise from lateral inhomogeneities of either the erosion rate or the sample itself. Using a test structure based on a trehalose film deposited on Si, we demonstrate that the "local" depth resolution may approach values which are close to the physical limit introduced by the information depth of the (static) ToF-SIMS method itself.

  7. Cytoskeleton Molecular Motors: Structures and Their Functions in Neuron

    PubMed Central

    Xiao, Qingpin; Hu, Xiaohui; Wei, Zhiyi; Tam, Kin Yip

    2016-01-01

    Cells make use of molecular motors to transport small molecules, macromolecules and cellular organelles to target region to execute biological functions, which is utmost important for polarized cells, such as neurons. In particular, cytoskeleton motors play fundamental roles in neuron polarization, extension, shape and neurotransmission. Cytoskeleton motors comprise of myosin, kinesin and cytoplasmic dynein. F-actin filaments act as myosin track, while kinesin and cytoplasmic dynein move on microtubules. Cytoskeleton motors work together to build a highly polarized and regulated system in neuronal cells via different molecular mechanisms and functional regulations. This review discusses the structures and working mechanisms of the cytoskeleton motors in neurons. PMID:27570482

  8. Spatially resolved dynamic structure factor of finite systems from molecular dynamics simulations

    SciTech Connect

    Raitza, Thomas; Roepke, Gerd; Reinholz, Heidi; Morozov, Igor

    2011-09-15

    The dynamical response of metallic clusters up to 10{sup 3} atoms is investigated using the restricted molecular dynamics simulations scheme. Exemplarily, a sodium like material is considered. Correlation functions are evaluated to investigate the spatial structure of collective electron excitations and the optical response of laser-excited clusters. In particular, the spectrum of bilocal correlation functions shows resonances representing different modes of collective excitations inside the nano plasma. The spatial structure, the resonance energy, and the width of the eigenmodes have been investigated for various values of electron density, temperature, cluster size, and ionization degree. Comparison with bulk properties is performed and the dispersion relation of collective excitations is discussed.

  9. Experimental investigations of 3 mm aperture PPLN structures

    NASA Astrophysics Data System (ADS)

    Kolker, D.; Pronyushkina, A.; Boyko, A.; Kostyukova, N.; Trashkeev, S.; Nuyshkov, B.; Shur, V.

    2017-01-01

    We are reporting about investigation of domestic 3 mm aperture periodically polled lithium niobate (PPLN) structures for cascaded mid-IR OPO. Wide aperture periodically poled MgO-doped lithium niobate (LiNbO3) structures at multigrating, fan-out and multi fan-out configuration were prepared at “Labfer LTD”. Laser source based on such structures can be used for special applications. Four different PPLN structures were investigated and effective aperture for effective pumping was defined.

  10. Study on molecular structure, spectroscopic investigation (IR, Raman and NMR), vibrational assignments and HOMO-LUMO analysis of L-sodium folinate using DFT: a combined experimental and quantum chemical approach.

    PubMed

    Li, Linwei; Cai, Tiancheng; Wang, Zhiqiang; Zhou, Zhixu; Geng, Yiding; Sun, Tiemin

    2014-01-01

    In the present work, an exhaustive conformational search of N-[4-[[(2-amino-5-formyl-(6S)-3,4,5,6,7,8-hexahydro-4-oxo-6-pteridinyl)methyl]amino]benzoyl]-L-glutamic acid disodium salt (L-SF) has been preformed. The optimized structure of the molecule, vibrational frequencies and NMR spectra studies have been calculated by density functional theory (DFT) using B3LYP method with the 6-311++G (d, p) basis set. IR and FT-Raman spectra for L-SF have been recorded in the region of 400-4000 cm(-1) and 100-3500 cm(-1), respectively. 13C and 1H NMR spectra were recorded and 13C and 1H nuclear magnetic resonance chemical shifts of the molecule were calculated based on the gauge-independent atomic orbital (GIAO) method. Finally all of the calculation results were applied to simulate IR, Raman, 1H NMR and 13C NMR spectrum of the title compound which showed excellent agreement with observed spectrum. Furthermore, reliable vibrational assignments which have been made on the basis of potential energy distribution (PED) and characteristic vibratinonal absorption bands of the title compound in IR and Raman have been figured out. HOMO-LUMO energy and Mulliken atomic charges have been evaluated, either.

  11. Investigating the Lithospheric Structure of Southern Madagascar

    NASA Astrophysics Data System (ADS)

    Tilmann, F. J.; Yuan, X.; Rumpker, G.; Heit, B.; Rambolamana, G.; Rindraharisaona, E.; Priestley, K. F.

    2013-12-01

    eastern part of the study area, where there is some so-far poorly characterised seismicity. We will present preliminary results on the lithospheric crust and mantle structure based on surface wave dispersion and waveform modelling, focussing on the contrast between the metamorphic areas in the east and the presumably stretched regions in the west. Station distribution Red diamonds: Temporary Broadband Light red squares: Short period Green: permanent stations Other temporary experiments: Open dark blue boxes: RHUM-RUM stations Open light blue boxes: MACOMO stations

  12. A Self-Assisting Protein Folding Model for Teaching Structural Molecular Biology.

    PubMed

    Davenport, Jodi; Pique, Michael; Getzoff, Elizabeth; Huntoon, Jon; Gardner, Adam; Olson, Arthur

    2017-04-04

    Structural molecular biology is now becoming part of high school science curriculum thus posing a challenge for teachers who need to convey three-dimensional (3D) structures with conventional text and pictures. In many cases even interactive computer graphics does not go far enough to address these challenges. We have developed a flexible model of the polypeptide backbone using 3D printing technology. With this model we have produced a polypeptide assembly kit to create an idealized model of the Triosephosphate isomerase mutase enzyme (TIM), which forms a structure known as TIM barrel. This kit has been used in a laboratory practical where students perform a step-by-step investigation into the nature of protein folding, starting with the handedness of amino acids to the formation of secondary and tertiary structure. Based on the classroom evidence we collected, we conclude that these models are valuable and inexpensive resource for teaching structural molecular biology.

  13. Challenges and novel approaches for investigating molecular mediation

    PubMed Central

    Richmond, R.C.; Hemani, G.; Tilling, K.; Davey Smith, G.; Relton, C.L.

    2016-01-01

    Understanding mediation is useful for identifying intermediates lying between an exposure and an outcome which, when intervened upon, will block (some or all of) the causal pathway between the exposure and outcome. Mediation approaches used in conventional epidemiology have been adapted to understanding the role of molecular intermediates in situations of high-dimensional omics data with varying degrees of success. In particular, the limitations of observational epidemiological study including confounding, reverse causation and measurement error can afflict conventional mediation approaches and may lead to incorrect conclusions regarding causal effects. Solutions to analysing mediation which overcome these problems include the use of instrumental variable methods such as Mendelian randomization, which may be applied to evaluate causality in increasingly complex networks of omics data. PMID:27439390

  14. [Mitochondrial diseases: molecular mechanisms, clinical presentations and diagnosis investigations].

    PubMed

    Auré, Karine; Jardel, Claude; Lombès, Anne

    2005-09-01

    Mitochondrial diseases are relatively common inherited metabolic diseases due to mitochondrial respiratory chain dysfunction. Their clinical presentation is extremely diverse, multisystemic or confined to a single tissue, sporadic or transmitted, by maternal or mendelian inheritance. The diagnosis of mitochondrial disorders is difficult. It is based upon several types of clues both clinical (family history, type of symptoms but also their association in syndromic presentation,...) and biological (alteration of the lactate metabolism, brain imaging, morphological alterations especially of muscle tissue). The diagnosis relies upon the demonstration of a defect of the respiratory chain activities and/or upon the identification of the underlying genetic alteration. Molecular diagnosis remains quite difficult and up to-date concerns essentially mitochondrial DNA mutations. On one hand, clinical and biological presentations as well as enzymatic defects lack specificity. On the other hand, candidate genes are very numerous and part of them are probably still unknown.

  15. A molecular dynamics investigation of surface reconstruction on magnetite (001)

    NASA Astrophysics Data System (ADS)

    Rustad, J. R.; Wasserman, E.; Felmy, A. R.

    1999-07-01

    Molecular dynamics calculations using analytical potential functions with polarizable oxygen ions have been used to identify a novel mode of reconstruction on the half-occupied tetrahedral layer termination of the magnetite (Fe 3O 4) (001) surface. In the proposed reconstruction, the twofold coordinated iron ion in the top monolayer rotates downward to occupy a vacant half-octahedral site in the plane of the second-layer iron ions. At the same time, half of the tetrahedral iron ions in the third iron layer are pushed upward to occupy an adjacent octahedral vacancy at the level of the second-layer iron ions. The other half of the third-layer iron ions remain roughly in their original positions. The proposed reconstruction is consistent with recent low-energy electron diffraction and X-ray photoelectron spectroscopy results. It also provides a compelling interpretation for the arrangement of atoms suggested by high-resolution scanning-tunneling microscopy studies.

  16. A Structural and Molecular Approach for the Study Biomarkers

    NASA Technical Reports Server (NTRS)

    Thomas-Keprta, Kathie; Vali, Hojatollah; Sears, S. Kelly; Roh, Yul

    2001-01-01

    Investigation of the nucleation and growth of crystals in both abiotic and biotic systems is critical to seemingly diverse disciplines of geology, biology, environmental science, and astrobiology. While there are abundant studies devoted to the determination of the structure and composition of inorganic crystals, as well as to the development of thermodynamic and kinetic models, it is only recently that research efforts have been directed towards understanding mineralization in biological systems (i.e., biomineralization). Biomineralization refers to the processes by which living organisms form inorganic solids. Studies of the processes of biomineralization under low temperature aqueous conditions have focused primarily on magnetite forming bacteria and shell forming marine organisms. Many of the biological building materials consist of inorganic minerals (calcium carbonate, calcium phosphate, silica or iron oxide) intricately combined with organic polymers (like proteins). More recently, efforts have been undertaken to explore the nature of biological activities in ancient rocks. In the absence of well-preserved microorganisms or genetic material required for the polmerase chain reaction (PCR) method in molecular phylogenetic studies, using biominerals as biomarkers offers an alternative approach for the recognition of biogenic activity in both terrestrial and extraterrestrial environments. The primary driving force in biomineralization is the interaction between organic and inorganic phases. Thus, the investigation of the ultrastructure and the nature of reactions at the molecular level occurring at the interface between inorganic and organic phases is essential to understanding the processes leading to the nucleation and growth of crystals. It is recognized that crystal surfaces can serve as the substrate for the organization of organic molecules that lead to the formation of polymers and other complex organic molecules, and in discussions of the origins of life

  17. Investigating the Lithospheric Structure of Southern Madagascar

    NASA Astrophysics Data System (ADS)

    Tilmann, Frederik; Yuan, Xiaohui; Rümpker, Georg; Gerard, Rambolamana; Elisa, Rindraharisaona; Priestley, Keith

    2014-05-01

    study area, where there is some so-far poorly characterised seismicity. We present preliminary results on the lithospheric crust and mantle structure based on surface wave dispersion and waveform modelling, focussing on the contrast between the metamorphic areas in the east and the presumably stretched regions in the west. Interstation Green's functions have been obtained from all pairs of vertical broadband records, with coherent Rayleigh waves being identifiable for periods of 3-40 s. In addition, two-station phase dispersion measurements have allowed us to determine phase dispersion between 25 and 60 s. The ambient noise and earthquake data both indicate a slow-down of surface propagation in the western part of the array for periods < 40-45 s, but faster propagation in the western part for periods >45 s.

  18. Molecular dynamics simulations of soliton-like structures in a dusty plasma medium

    SciTech Connect

    Tiwari, Sanat Kumar Das, Amita; Sen, Abhijit; Kaw, Predhiman

    2015-03-15

    The existence and evolution of soliton-like structures in a dusty plasma medium are investigated in a first principles approach using molecular dynamic (MD) simulations of particles interacting via a Yukawa potential. These localized structures are found to exist in both weakly and strongly coupled regimes with their structures becoming sharper as the correlation effects between the dust particles get stronger. A surprising result, compared to fluid simulations, is the existence of rarefactive soliton-like structures in our non-dissipative system, a feature that arises from the charge conjugation symmetry property of the Yukawa fluid. Our simulation findings closely resemble many diverse experimental results reported in the past.

  19. Solution structures and molecular interactions of selective melanocortin receptor antagonists.

    PubMed

    Lee, Chul-Jin; Yun, Ji-Hye; Lim, Sung-Kil; Lee, Weontae

    2010-12-01

    The solution structures and inter-molecular interaction of the cyclic melanocortin antagonists SHU9119, JKC363, HS014, and HS024 with receptor molecules have been determined by NMR spectroscopy and molecular modeling. While SHU9119 is known as a nonselective antagonist, JKC363, HS014, and HS024 are selective for the melanocortin subtype-4 receptor (MC4R) involved in modulation of food intake. Data from NMR and molecular dynamics suggest that the conformation of the Trp9 sidechain in the three MC4R-selective antagonists is quite different from that of SHU9119. This result strongly supports the concept that the spatial orientation of the hydrophobic aromatic residue is more important for determining selectivity than the presence of a basic, "arginine-like" moiety responsible for biological activity. We propose that the conformation of hydrophobic residues of MCR antagonists is critical for receptor-specific selectivity.

  20. Study of the structuring of pure molecular liquids

    NASA Astrophysics Data System (ADS)

    Letamendia, L.; Duplessix, R.; Nouchi, G.; Vaucamps, C.

    Recent experiments have shown that changes in the slope of specific heat variation as a function of temperature in liquids are not always regular. In this study, the authors consider the possibility that fluid structure can change with temperature, by shifting from one form to another. They study such molecular liquids as benzene, hexafluorobenzene, and quinoleine using Rayleigh-Brillouin and depolarized Rayleigh diffusion, and total intensity diffusion. The authors clearly found anomalies for all collective properties of the medium in the liquids studied, though purely molecular properties were undisturbed. The accidents observed occurred at the same temperatures, whatever the collective or intermolecular property under study. But it took some time (several hours) for them to manifest themselves, which suggests that molecular liquids are characterized by a long thermodynamic equilibrium. Results also show a disturbance in hydrodynamic state at accident temperatures, which are similar to those generated by long spatial correlation processes.

  1. Molecular structures in the charmonium spectrum: the XYZ puzzle

    NASA Astrophysics Data System (ADS)

    Ortega, P. G.; Entem, D. R.; Fernández, F.

    2013-06-01

    We study in the framework of a constituent quark model the possible contributions of molecular structures to the XYZ charmonium-like states. We analyze simultaneously the c\\bar{c} structures and the possible molecular components in the coupled channel formalism. In the 1++ sector two states appear which could be identified with X(3872) and X(3940). The recently confirmed X(3915) state appears as a mixture of c\\bar{c} and D\\bar{D} components as a JPC = 0++ state in agreement with the new measurements. A second broad resonance which may correspond with the so-called Y(3940) state is found with these quantum numbers. In the JPC = 1-- sector we also found significant contributions of the molecular structures which may affect the phenomenology. In particular the study allows us to understand the G(3900) state recently observed in Belle and BaBar. All these resonances together with the prediction of the model of a c\\bar{c} structure for Z(3930) provide a reasonable scenario for the so-called XYZ states with masses near 3.9 GeV.

  2. Molecular-Level Investigations of Nucleation Mechanisms and Kinetics of Formation of Environmental Nanoparticles

    SciTech Connect

    Young-Shin Jun; Glenn A. Waychunas

    2007-04-19

    Environmental nanoparticles are often poorly-crystalline or metastable structures, whose kinetics of formation and growth are poorly understood. Further, the sorption or growth of nanoparticles on mineral surfaces may control the mineral surface's reactivity and modify its ability to influence contaminant transport. Due to the characteristic length scale, a holistic understanding of the nucleation mechanisms and kinetics of nanoparticle formation on mineral surfaces is difficult to achieve with traditional methodology. In this work, our intent is to determine the molecular nature of nucleation on surfaces, the kinetics of surface nucleation and growth, and the effect of crystal surface topology using new synchrotron-based techniques. We have approached these objectives by: (1) combining state-of-the-art crystal-truncation rod diffraction (CTR) and grazing incidence x-ray absorption fine structure spectroscopy (GIXAS) techniques to investigate the three-dimensional molecular-scale geometry of silicate monomer sorption on the r-plane of hematite; and (2) developing a new grazing-incidence small angle x-ray scattering (GISAXS) setup at SSRL (0.08 nm{sup -1} < q < 8 nm{sup -1}) to explore the initial development of environmental nanoparticles on various mineral surfaces. This study also includes complementary techniques such as atomic force microscopy (AFM), bulk SAXS, dynamic light scattering (DLS), XRD, and TEM.

  3. Investigation on surface molecular conformations and pervaporation performance of the poly(vinyl alcohol) (PVA) membrane.

    PubMed

    Zhang, Wei; Zhang, Zhennan; Wang, Xinping

    2009-05-01

    A simple method of changing pre-treatment temperature in the course of film formation was used to tune the surface structures of PVA membranes. Surface structure and property of the resulting membranes were characterized by X-ray photoelectron spectroscopy (XPS), sum frequency generation (SFG) vibrational spectroscopy, and contact angle measurements. The results show that PVA have different molecular conformations at the membrane surface while those membranes were prepared at different pre-treatment temperature. At higher pre-treatment temperatures, polar acetoxyl residues and hydroxyl groups of the PVA chains oriented in a more orderly fashion, as induced by the faster evaporation of water. When the membranes were in air, CH(3) groups adjacent to the acetoxyl groups covered the surface in order to minimize the surface free energy, while backbones of the PVA were rarely observed. These surfaces exhibited a hydrophilic nature upon contact with water due to rapid surface reconstruction. Conversely, at lower pre-treatment temperatures, the backbone CH(2) groups dominated the surface, forming a less hydrophilic surface. When the PVA membranes were employed to separate ethanol/water mixtures, it was found that the PVA membranes with more hydrophilic surface exhibited higher water selectivity. Our investigation indicates that molecular conformations on the membrane surface have considerable influence on pervaporation performance.

  4. Multi-Probe Investigation of Proteomic Structure of Pathogens

    SciTech Connect

    Malkin, A J; Plomp, M; Leighton, T J; Vogelstein, B; Wheeler, K E

    2008-01-24

    Complete genome sequences are available for understanding biotransformation, environmental resistance and pathogenesis of microbial, cellular and pathogen systems. The present technological and scientific challenges are to unravel the relationships between the organization and function of protein complexes at cell, microbial and pathogens surfaces, to understand how these complexes evolve during the bacterial, cellular and pathogen life cycles, and how they respond to environmental changes, chemical stimulants and therapeutics. In particular, elucidating the molecular structure and architecture of human pathogen surfaces is essential to understanding mechanisms of pathogenesis, immune response, physicochemical interactions, environmental resistance and development of countermeasures against bioterrorist agents. The objective of this project was to investigate the architecture, proteomic structure, and function of bacterial spores through a combination of high-resolution in vitro atomic force microscopy (AFM) and AFM-based immunolabeling with threat-specific antibodies. Particular attention in this project was focused on spore forming Bacillus species including the Sterne vaccine strain of Bacillus anthracis and the spore forming near-neighbor of Clostridium botulinum, C. novyi-NT. Bacillus species, including B. anthracis, the causative agent of inhalation anthrax are laboratory models for elucidating spore structure/function. Even though the complete genome sequence is available for B. subtilis, cereus, anthracis and other species, the determination and composition of spore structure/function is not understood. Prof. B. Vogelstein and colleagues at the John Hopkins University have recently developed a breakthrough bacteriolytic therapy for cancer treatment (1). They discovered that intravenously injected Clostridium novyi-NT spores germinate exclusively within the avascular regions of tumors in mice and destroy advanced cancerous lesions. The bacteria were also

  5. Excitation energies of a water-bridged twisted retinal structure in the bacteriorhodopsin proton pump: a theoretical investigation.

    PubMed

    Wolter, Tino; Welke, Kai; Phatak, Prasad; Bondar, Ana-Nicoleta; Elstner, Marcus

    2013-08-14

    The first proton transfer in the bacteriorhodopsin photocycle takes place during the L → M transition. Structural details of the pre proton transfer L intermediate have been investigated using experiments and computations. Here, we assess L-state structural models by performing hybrid quantum mechanical/molecular mechanical molecular dynamics and excitation energy calculations. The computations suggest that a water-bridged twisted retinal structure gives the closest agreement with the experimental L/bR shift in the excitation energy.

  6. Improving structure-based function prediction using molecular dynamics

    PubMed Central

    Glazer, Dariya S.; Radmer, Randall J.; Altman, Russ B.

    2009-01-01

    Summary The number of molecules with solved three-dimensional structure but unknown function is increasing rapidly. Particularly problematic are novel folds with little detectable similarity to molecules of known function. Experimental assays can determine the functions of such molecules, but are time-consuming and expensive. Computational approaches can identify potential functional sites; however, these approaches generally rely on single static structures and do not use information about dynamics. In fact, structural dynamics can enhance function prediction: we coupled molecular dynamics simulations with structure-based function prediction algorithms that identify Ca2+ binding sites. When applied to 11 challenging proteins, both methods showed substantial improvement in performance, revealing 22 more sites in one case and 12 more in the other, with a modest increase in apparent false positives. Thus, we show that treating molecules as dynamic entities improves the performance of structure-based function prediction methods. PMID:19604472

  7. Structural investigations and morphology of tomato fruit starch.

    PubMed

    Luengwilai, Kietsuda; Beckles, Diane M

    2009-01-14

    The physicochemical properties of starch from tomato (Solanum lycopersicum L.) pericarp and columella of cv. Moneymaker fruit at 28 days post anthesis (DPA) were investigated, providing the first description of the composition and structure of tomato fruit starch. Starch granules from pericarp were mainly polygonal, 13.5-14.3 microm, and increased in size through development, being largest in ripening fruit. Amylopectin content was 81-83% and was of molecular weight 1.01 x 10(8) g/mol; the phosphorus content was 139 ppm, and starch showed a C-type pattern with crystallinity of 30%. Starch characteristics were similar in columella except granule size (16.8-17.8 microm) and crystallinity (40%), although 6-fold more starch accumulated in the pericarp. Solara, a high-sugar tomato cultivar, was also studied to determine if this affects starch granule architecture. There were few differences from Moneymaker, except that Solara columella starch crystallinity was lower (26%), and more starch granule-intrinsic proteins could be extracted by sodium dodecyl sulfate-polyacrylamide gel electrophoresis.

  8. Investigation of the influence factors of polyethylene molecule encapsulated into carbon nanotubes by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Li, Qun; He, Guofang; Zhao, Rengao; Li, Yanfei

    2011-09-01

    In this work, the influence factors, namely chirality, temperature, radius and surface chemical modification, of the interaction energy for polyethylene (PE) molecule encapsulated into single-walled carbon nanotubes (SWNTs) had been investigated by molecular mechanics (MM) and molecular dynamics (MD) simulation. The results showed that all these factors would influence the interaction energy between PE and SWNTs. The interaction energy between PE molecule and the armchair SWNTs is largest among eight kinds of chiral SWNTs. The interaction energy decreases with the increase of temperature or the SWNT radius. The methyl, phenyl, hydroxyl, carboxyl, -F, and amino groups, have been introduced onto the surface of the SWNTs by the simulation software and the influence of SWNT chemical modification has also been investigated. The interaction energy between PE and chemically modified SWNTs is larger than that between PE and pristine SWNTs, and increases with increasing the concentration of the modified groups monotonously. In addition, the group electronegativity and van der Waals force will affect the interaction energy between PE and chemically modified SWNTs greatly, which can be attributed to the electronic structures of the chemically modified groups. This study can provide some useful suggestions for the composite material design and drug transport.

  9. The liquid structure of tetrachloroethene: Molecular dynamics simulations and reverse Monte Carlo modeling with interatomic potentials

    NASA Astrophysics Data System (ADS)

    Gereben, Orsolya; Pusztai, László

    2013-10-01

    The liquid structure of tetrachloroethene has been investigated on the basis of measured neutron and X-ray scattering structure factors, applying molecular dynamics simulations and reverse Monte Carlo (RMC) modeling with flexible molecules and interatomic potentials. As no complete all-atom force field parameter set could be found for this planar molecule, the closest matching all-atom Optimized Potentials for Liquid Simulations (OPLS-AA) intra-molecular parameter set was improved by equilibrium bond length and angle parameters coming from electron diffraction experiments [I. L. Karle and J. Karle, J. Chem. Phys. 20, 63 (1952)]. In addition, four different intra-molecular charge distribution sets were tried, so in total, eight different molecular dynamics simulations were performed. The best parameter set was selected by calculating the mean square difference between the calculated total structure factors and the corresponding experimental data. The best parameter set proved to be the one that uses the electron diffraction based intra-molecular parameters and the charges qC = 0.1 and qCl = -0.05. The structure was further successfully refined by applying RMC computer modeling with flexible molecules that were kept together by interatomic potentials. Correlation functions concerning the orientation of molecular axes and planes were also determined. They reveal that the molecules closest to each other exclusively prefer the parallel orientation of both the molecular axes and planes. Molecules forming the first maximum of the center-center distribution have a preference for <30° and >60° axis orientation and >60° molecular plane arrangement. A second coordination sphere at ˜11 Å and a very small third one at ˜16 Å can be found as well, without preference for any axis or plane orientation.

  10. A Structural and Molecular Approach for the Study Biomarkers

    NASA Technical Reports Server (NTRS)

    Thomas-Keprta, Kathie; Vali, Hojatollah; Sears, S. Kelly; Roh, Yul

    2001-01-01

    Investigation of the nucleation and growth of crystals in both abiotic and biotic systems is critical to seemingly diverse disciplines of geology, biology, environmental science, and astrobiology. While there are abundant studies devoted to the determination of the structure and composition of inorganic crystals, as well as to the development of thermodynamic and kinetic models, it is only recently that research efforts have been directed towards understanding mineralization in biological systems (i.e., biomineralization). Biomineralization refers to the processes by which living organisms form inorganic solids. Studies of the processes of biomineralization under low temperature aqueous conditions have focused primarily on magnetite forming bacteria and shell forming marine organisms. Many of the biological building materials consist of inorganic minerals (calcium carbonate, calcium phosphate, silica or iron oxide) intricately combined with organic polymers (like proteins). More recently, efforts have been undertaken to explore the nature of biological activities in ancient rocks. In the absence of well-preserved microorganisms or genetic material required for the polmerase chain reaction (PCR) method in molecular phylogenetic studies, using biominerals as biomarkers offers an alternative approach for the recognition of biogenic activity in both terrestrial and extraterrestrial environments. The primary driving force in biomineralization is the interaction between organic and inorganic phases. Thus, the investigation of the ultrastructure and the nature of reactions at the molecular level occurring at the interface between inorganic and organic phases is essential to understanding the processes leading to the nucleation and growth of crystals. It is recognized that crystal surfaces can serve as the substrate for the organization of organic molecules that lead to the formation of polymers and other complex organic molecules, and in discussions of the origins of life

  11. Molecular dynamics investigation of the interaction of dislocations with carbides in BCC Fe

    NASA Astrophysics Data System (ADS)

    Granberg, F.; Terentyev, D.; Nordlund, K.

    2015-06-01

    Different types of carbides are present in many steels used as structural materials. To safely use steel in demanding environments, like nuclear power plants, it is important to know how defects will affect the mechanical properties of the material. In this study, the effect of carbide precipitates on the edge dislocation movement is investigated. Three different types of carbides were investigated by means of molecular dynamics, with a Tersoff-like bond order interatomic potential by Henriksson et al. The obstacles were 4 nm in diameter and were of Fe3C- (cementite-), Fe23C6- and Cr23C6-type. The critical unpinning stress was calculated for each type at different temperatures, to get the temperature-dependent obstacle strength. The results showed a decreasing critical stress with increasing temperature, consistent with previous studies. The critical unpinning stress was seen to be dependent on the type of carbide, but the differences were small. A difference was also observed between the obstacles with the same structure, but with different composition. This study shows the relation between the existing Cr23C6 carbide and the experimentally non-existing Fe23C6 carbide, which needs to be used as a model system for investigations with interatomic potentials not able to describe the interaction of Cr in the Fe-C-system. We found the difference to be a between 7% and 10% higher critical unpinning stress for the chromium carbide, than for the iron carbide of the same type.

  12. Dynamic Wetting on Graphene-Coated Surface: Molecular Dynamics Investigation

    NASA Astrophysics Data System (ADS)

    Hung, Shih-Wei; Shiomi, Junichiro

    2015-11-01

    Wettability of graphene-coated surface gained significant attention recently due to discussion on the ``transparency'' (whether the wetting characteristics follow that of graphene or the underlying surface) and practical applications of graphene. In terms of static contact angle, the wettability of graphene-coated surfaces have been widely studied by experiments, simulations, and theory in recent years. However, the studies of dynamic wetting on graphene-coated surfaces are limited. In the present study, molecular dynamics simulation was performed to study the dynamic wetting of water droplet on graphene-coated surfaces from a microscopic point of view. The results show that the degree of similarity between the spreading behavior on graphene-coated surface and that on pure graphene (or that on the underlying surface) depends on time, i.e. how nonequilibrium the interface dynamics is. We also found that this feature can be altered by introducing defects into graphene. The work is partially supported by Grant-in-Aid for JSPS Fellows 26-04364 and JST CREST.

  13. Molecular solutes in ionic liquids: a structural perspective.

    PubMed

    Pádua, Agílio A H; Costa Gomes, Margarida F; Canongia Lopes, José N A

    2007-11-01

    Understanding physicochemical properties of ionic liquids is important for their rational use in extractions, reactions, and other applications. Ionic liquids are not simple fluids: their ions are generally asymetric, flexible, with delocalized electrostatic charges, and available in a wide variety. It is difficult to capture their subtle properties with models that are too simplistic. Molecular simulation using atomistic force fields, which describe structures and interactions in detail, is an excellent tool to gain insights into their liquid-state organization, how they solvate different compounds, and what molecular factors determine their properties. The identification of certain ionic liquids as self-organized phases, with aggregated nonpolar and charged domains, provides a new way to interpret the solvation and structure of their mixtures. Many advances are the result of a successful interplay between experiment and modeling, possible in this field where none of the two methodologies had a previous advance.

  14. Molecular modelling of miraculin: Structural analyses and functional hypotheses.

    PubMed

    Paladino, Antonella; Costantini, Susan; Colonna, Giovanni; Facchiano, Angelo M

    2008-02-29

    Miraculin is a plant protein that displays the peculiar property of modifying taste by swiching sour into a sweet taste. Its monomer is flavourless at all pH as well as at high concentration; the dimer form elicits its taste-modifying activity at acidic pH; a tetrameric form is also reported as active. Two histidine residues, located in exposed regions, are the main responsible of miraculin activity, as demonstrated by mutagenesis studies. Since structural data of miraculin are not available, we have predicted its three-dimensional structure and simulated both its dimer and tetramer forms by comparative modelling and molecular docking techniques. Finally, molecular dynamics simulations at different pH conditions have indicated that at acidic pH the dimer assumes a widely open conformation, in agreement with the hypotheses coming from other studies.

  15. Molecular self-assembly for biological investigations and nanoscale lithography

    NASA Astrophysics Data System (ADS)

    Cheunkar, Sarawut

    Small, diffusible molecules when recognized by their binding partners, such as proteins and antibodies, trigger enzymatic activity, cell communication, and immune response. Progress in analytical methods enabling detection, characterization, and visualization of biological dynamics at the molecular level will advance our exploration of complex biological systems. In this dissertation, analytical platforms were fabricated to capture membrane-associated receptors, which are essential proteins in cell signaling pathways. The neurotransmitter serotonin and its biological precursor were immobilized on gold substrates coated with self-assembled monolayers (SAMs) of oligo(ethylene glycol)alkanethiols and their reactive derivatives. The SAM-coated substrates present the biologically selective affinity of immobilized molecules to target native membrane-associated receptors. These substrates were also tested for biospecificity using antibodies. In addition, small-molecule-functionalized platforms, expressing neurotransmitter pharmacophores, were employed to examine kinetic interactions between G-protein-coupled receptors and their associated neurotransmitters. The binding interactions were monitored using a quartz crystal microbalance equipped with liquid-flow injection. The interaction kinetics of G-protein-coupled serotonin 1A receptor and 5-hydroxytyptophan-functionalized surfaces were studied in a real-time, label-free environment. Key binding parameters, such as equilibrium dissociation constants, binding rate constants, and dissociative half-life, were extracted. These parameters are critical for understanding and comparing biomolecular interactions in modern biomedical research. By integrating self-assembly, surface functionalization, and nanofabrication, small-molecule microarrays were created for high-throughput screening. A hybrid soft-lithography, called microcontact insertion printing, was used to pattern small molecules at the dilute scales necessary for highly

  16. Molecular dynamics investigation of mechanisms of femtosecond laser ablation

    NASA Astrophysics Data System (ADS)

    Cheng, Changrui

    Laser micro-machining has been widely applied for material processing in many industries. A phenomenon called "laser ablation" is usually involved in the laser micro-machining process. Laser ablation is the process of material removal after the irradiation of a laser beam onto the material. It is commonly characterized by small temporal and spatial scales, extremely high material temperature and pressure, and strong non-equilibrium thermodynamic state. In this work, molecular dynamics (MD) simulation is conducted to study the femtosecond laser ablation of metals (nickel and copper) and dielectrics (fused silica, or glass). The laser heating and the ablation processes are numerically modeled, and the computation is accelerated by parallel processing technique. Both the pair-wise Morse potential and the many-body EAM (Embedded-Atom Method) potential are employed for metals. In the simulation of fused silica, the BKS (van Beest, Kramer and van Santen) potential is used, and the generation of free electrons, the energy transport from laser beam to free electrons and energy coupling between electrons and the lattice are considered. The main goal of this work is to illustrate the detailed processes of femtosecond laser ablation and to study its mechanisms. From the MD results, it is found that the mechanism of femtosecond laser ablation is strongly dependent on the laser fluences. For metals, low fluence laser ablation is mainly through phase explosion (homogeneous gas bubble nucleation), while spinodal decomposition is responsible for high fluence ablation. Ablation mechanism is determined by whether or not the material (liquid) temperature exceeds the critical temperature. For fused silica, the generation and existence of free electrons are found to affect ablation significantly, especially at low fluence, where Coulomb explosion is found to play an important role in material separation.

  17. Nanoparticle Probes for Structural and Functional Photoacoustic Molecular Tomography

    PubMed Central

    Chen, Haobin; Yuan, Zhen; Wu, Changfeng

    2015-01-01

    Nowadays, nanoparticle probes have received extensive attention largely due to its potential biomedical applications in structural, functional, and molecular imaging. In addition, photoacoustic tomography (PAT), a method based on the photoacoustic effect, is widely recognized as a robust modality to evaluate the structure and function of biological tissues with high optical contrast and high acoustic resolution. The combination of PAT with nanoparticle probes holds promises for detecting and imaging diseased tissues or monitoring their treatments with high sensitivity. This review will introduce the recent advances in the emerging field of nanoparticle probes and their preclinical applications in PAT, as well as relevant perspectives on future development. PMID:26609534

  18. FilFinder: Filamentary structure in molecular clouds

    NASA Astrophysics Data System (ADS)

    Koch, Eric W.; Rosolowsky, Erik W.

    2016-08-01

    FilFinder extracts and analyzes filamentary structure in molecular clouds. In particular, it is capable of uniformly extracting structure over a large dynamical range in intensity. It returns the main filament properties: local amplitude and background, width, length, orientation and curvature. FilFinder offers additional tools to, for example, create a filament-only image based on the properties of the radial fits. The resulting mask and skeletons may be saved in FITS format, and property tables may be saved as a CSV, FITS or LaTeX table.

  19. Molecular dynamics investigation of the grain boundary migration hysteresis of nanocrystalline Ni under cyclic shear loading

    NASA Astrophysics Data System (ADS)

    Wang, Peng; Yang, Xinhua; Peng, Di

    2017-02-01

    The deformation behavior and grain boundary (GB) response of nanocrystalline Ni under cyclic shear loading are investigated by molecular dynamics simulations. The GB migration hysteresis phenomenon, in which the GB migration displacement lags behind the change in nominal shear strain, is observed in the symmetric tilt GBs for the first time. The elementary structure transformation occurring at the two end segments of the observed GB during GB migration produces a disordered and irreversible state, while the transformation in the middle segment is reversible. Both dislocation retraction and nucleation occur during unloading. Relatively large cyclic strain amplitudes lead to disordered GB segments of greater length, such that the residual GB migration displacement increases with increasing cyclic amplitude. GB migration hysteresis vanishes after the GB becomes immobile owing to a cyclic shear induced transition to a disordered state along its entire length.

  20. [Investigation on bioactive protective function of amino acids to insulin by molecular simulation].

    PubMed

    Li, Daixi; Zhai, Zhen; Guo, Baisong; Liu, Baolin; Zhang, Yan; Yu, Huaxing; Liu, Li; Yang, Chunsheng

    2014-08-01

    Heat sensitive protein medicines are increasingly exhibiting their critical importance on treatment of various diseases at present. But their popularization and application meet a great challenge because of their heat instability. In the present study, insulin was taken as a heat sensitive protein medicine and amino acid as bio-protective agent in order to investigate if these amino acids can protect the insulin from losing its bioactivity due to desiccation. The experiment was performed by using replica exchange molecular simulation (REMD) method and Gromacs software with Gromos96 (53a6) force field. The REMD results indicated that these amino acids could protect the bioactive structure of insulin during desiccation. The configurations of the protected insulin were preserved very well. Those results proved that amino acid is a kind of good bioactive protective agent for the heat sensitive protein medicines.

  1. Investigating Actinide Molecular Adducts From Absorption Edge Spectroscopy

    SciTech Connect

    Den Auwer, C.; Conradson, S.D.; Guilbaud, P.; Moisy, P.; Mustre de Leon, J.; Simoni, E.; /SLAC, SSRL

    2006-10-27

    Although Absorption Edge Spectroscopy has been widely applied to the speciation of actinide elements, specifically at the L{sub III} edge, understanding and interpretation of actinide edge spectra are not complete. In that sense, semi-quantitative analysis is scarce. In this paper, different aspects of edge simulation are presented, including semi-quantitative approaches. Comparison is made between various actinyl (U, Np) aquo or hydroxy compounds. An excursion into transition metal osmium chemistry allows us to compare the structurally related osmyl and uranyl hydroxides. The edge shape and characteristic features are discussed within the multiple scattering picture and the role of the first coordination sphere as well as contributions from the water solvent are described.

  2. Hierarchical QSAR technology based on the Simplex representation of molecular structure

    NASA Astrophysics Data System (ADS)

    Kuz'min, V. E.; Artemenko, A. G.; Muratov, E. N.

    2008-06-01

    This article is about the hierarchical quantitative structure-activity relationship technology (HiT QSAR) based on the Simplex representation of molecular structure (SiRMS) and its application for different QSAR/QSP(property)R tasks. The essence of this technology is a sequential solution (with the use of the information obtained on the previous steps) to the QSAR problem by the series of enhanced models of molecular structure description [from one dimensional (1D) to four dimensional (4D)]. It is a system of permanently improved solutions. In the SiRMS approach, every molecule is represented as a system of different simplexes (tetratomic fragments with fixed composition, structure, chirality and symmetry). The level of simplex descriptors detailing increases consecutively from the 1D to 4D representation of the molecular structure. The advantages of the approach reported here are the absence of "molecular alignment" problems, consideration of different physical-chemical properties of atoms (e.g. charge, lipophilicity, etc.), the high adequacy and good interpretability of obtained models and clear ways for molecular design. The efficiency of the HiT QSAR approach is demonstrated by comparing it with the most popular modern QSAR approaches on two representative examination sets. The examples of successful application of the HiT QSAR for various QSAR/QSPR investigations on the different levels (1D-4D) of the molecular structure description are also highlighted. The reliability of developed QSAR models as predictive virtual screening tools and their ability to serve as the base of directed drug design was validated by subsequent synthetic and biological experiments, among others. The HiT QSAR is realized as a complex of computer programs known as HiT QSAR software that also includes a powerful statistical block and a number of useful utilities.

  3. Sculpting Molecular Potentials to Design Optimized Materials: The Inverse Design of New Molecular Structures

    DTIC Science & Technology

    2010-05-10

    Miloradovic, A. Persoons, T . Verbiest, M. J . Therien, and K. Clays, "Molecular Symmetry and Solution Phase Structure Interrogated by Hyper-Raleigh...34 Nano Lett., 8, 2814-2818 (2008).  T . V. Duncan, K. Song, S.- T . Hung, I. Miloradovic, A. Persoons, T . Verbiest, M. J . Therien, and K. Clays...Beratan, Weitao Yang, Michael J . Therien, Koen Clays Duke University Office of Research Support Duke University Durham, NC 27705 - REPORT

  4. Investigation of structural behavior of candidate Space Station structure

    NASA Technical Reports Server (NTRS)

    Hedgepeth, John M.; Miller, Richard K.

    1989-01-01

    Quantitative evaluations of the structural loads, stiffness and deflections of an example Space Station truss due to a variety of influences, including manufacturing tolerances, assembly operations, and operational loading are reported. The example truss is a dual-keel design composed of 5-meter-cube modules. The truss is 21 modules high and 9 modules wide, with a transverse beam 15 modules long. One problem of concern is the amount of mismatch which will be expected when the truss is being erected on orbit. Worst-case thermal loading results in less than 0.5 inch of mismatch. The stiffness of the interface is shown to be less than 100 pounds per inch. Thus, only moderate loads will be required to overcome the mismatch. The problem of manufacturing imperfections is analyzed by the Monte Carlo approach. Deformations and internal loads are obtained for ensembles of 100 example trusses. All analyses are performed on a personal computer. The necessary routines required to supplement commercially available programs are described.

  5. Molecular structures of amyloid and prion fibrils: consensus versus controversy.

    PubMed

    Tycko, Robert; Wickner, Reed B

    2013-07-16

    Many peptides and proteins self-assemble into amyloid fibrils. Examples include mammalian and fungal prion proteins, polypeptides associated with human amyloid diseases, and proteins that may have biologically functional amyloid states. To understand the propensity for polypeptides to form amyloid fibrils and to facilitate rational design of amyloid inhibitors and imaging agents, it is necessary to elucidate the molecular structures of these fibrils. Although fibril structures were largely mysterious 15 years ago, a considerable body of reliable structural information about amyloid fibril structures now exists, with essential contributions from solid state nuclear magnetic resonance (NMR) measurements. This Account reviews results from our laboratories and discusses several structural issues that have been controversial. In many cases, the amino acid sequences of amyloid fibrils do not uniquely determine their molecular structures. Self-propagating, molecular-level polymorphism complicates the structure determination problem and can lead to apparent disagreements between results from different laboratories, particularly when different laboratories study different polymorphs. For 40-residue β-amyloid (Aβ₁₋₄₀) fibrils associated with Alzheimer's disease, we have developed detailed structural models from solid state NMR and electron microscopy data for two polymorphs. These polymorphs have similar peptide conformations, identical in-register parallel β-sheet organizations, but different overall symmetry. Other polymorphs have also been partially characterized by solid state NMR and appear to have similar structures. In contrast, cryo-electron microscopy studies that use significantly different fibril growth conditions have identified structures that appear (at low resolution) to be different from those examined by solid state NMR. Based on solid state NMR and electron paramagnetic resonance (EPR) measurements, the in-register parallel β-sheet organization

  6. Cloning Yeast Actin cDNA Leads to an Investigative Approach for the Molecular Biology Laboratory

    ERIC Educational Resources Information Center

    Black, Michael W.; Tuan, Alice; Jonasson, Erin

    2008-01-01

    The emergence of molecular tools in multiple disciplines has elevated the importance of undergraduate laboratory courses that train students in molecular biology techniques. Although it would also be desirable to provide students with opportunities to apply these techniques in an investigative manner, this is generally not possible in the…

  7. 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.

  8. Molecular dynamics investigations of BioH protein substrate specificity for biotin synthesis.

    PubMed

    Xue, Qiao; Cui, Ying-Lu; Zheng, Qing-Chuan; Zhang, Hong-Xing

    2016-05-01

    BioH, an enzyme of biotin synthesis, plays an important role in fatty acid synthesis which assembles the pimelate moiety. Pimeloyl-acyl carrier protein (ACP) methyl ester, which is long known to be a biotin precursor, is the physiological substrate of BioH. Azelayl methyl ester, which has a longer chain than pimeloyl methyl ester, conjugated to ACP is also indeed accepted by BioH with very low rate of hydrolysis. To date, the substrate specificity for BioH and the molecular origin for the experimentally observed rate changes of hydrolysis by the chain elongation have remained elusive. To this end, we have investigated chain elongation effects on the structures by using the fully atomistic molecular dynamics simulations combined with binding free energy calculations. The results indicate that the substrate specificity is determined by BioH together with ACP. The added two methylenes would increase the structural flexibility by protein motions at the interface of ACP and BioH, instead of making steric clashes with the side chains of the BioH hydrophobic cavity. On the other hand, the slower hydrolysis of azelayl substrate is suggested to be associated with the loose of contacts between BioH and ACP, and with the lost electrostatic interactions of two ionic/hydrogen bonding networks at the interface of the two proteins. The present study provides important insights into the structure-function relationships of the complex of BioH with pimeloyl-ACP methyl ester, which could contribute to further understanding about the mechanism of the biotin synthetic pathway, including the catalytic role of BioH.

  9. Profiling of the molecular weight and structural isomer abundance of macroalgae-derived phlorotannins.

    PubMed

    Heffernan, Natalie; Brunton, Nigel P; FitzGerald, Richard J; Smyth, Thomas J

    2015-01-16

    Phlorotannins are a group of complex polymers of phloroglucinol (1,3,5-trihydroxybenzene) unique to macroalgae. These phenolic compounds are integral structural components of the cell wall in brown algae, but also play many secondary ecological roles such as protection from UV radiation and defense against grazing. This study employed Ultra Performance Liquid Chromatography (UPLC) with tandem mass spectrometry to investigate isomeric complexity and observed differences in phlorotannins derived from macroalgae harvested off the Irish coast (Fucus serratus, Fucus vesiculosus, Himanthalia elongata and Cystoseira nodicaulis). Antioxidant activity and total phenolic content assays were used as an index for producing phlorotannin fractions, enriched using molecular weight cut-off dialysis with subsequent flash chromatography to profile phlorotannin isomers in these macroalgae. These fractions were profiled using UPLC-MS with multiple reaction monitoring (MRM) and the level of isomerization for specific molecular weight phlorotannins between 3 and 16 monomers were determined. The majority of the low molecular weight (LMW) phlorotannins were found to have a molecular weight range equivalent to 4-12 monomers of phloroglucinol. The level of isomerization within the individual macroalgal species differed, resulting in substantially different numbers of phlorotannin isomers for particular molecular weights. F. vesiculosus had the highest number of isomers of 61 at one specific molecular mass, corresponding to 12 phloroglucinol units (PGUs). These results highlight the complex nature of these extracts and emphasize the challenges involved in structural elucidation of these compounds.

  10. A 3D visualization system for molecular structures

    NASA Technical Reports Server (NTRS)

    Green, Terry J.

    1989-01-01

    The properties of molecules derive in part from their structures. Because of the importance of understanding molecular structures various methodologies, ranging from first principles to empirical technique, were developed for computing the structure of molecules. For large molecules such as polymer model compounds, the structural information is difficult to comprehend by examining tabulated data. Therefore, a molecular graphics display system, called MOLDS, was developed to help interpret the data. MOLDS is a menu-driven program developed to run on the LADC SNS computer systems. This program can read a data file generated by the modeling programs or data can be entered using the keyboard. MOLDS has the following capabilities: draws the 3-D representation of a molecule using stick, ball and ball, or space filled model from Cartesian coordinates, draws different perspective views of the molecule; rotates the molecule on the X, Y, Z axis or about some arbitrary line in space, zooms in on a small area of the molecule in order to obtain a better view of a specific region; and makes hard copy representation of molecules on a graphic printer. In addition, MOLDS can be easily updated and readily adapted to run on most computer systems.

  11. Structural characterization of polymorphs and molecular complexes of finasteride

    NASA Astrophysics Data System (ADS)

    Wawrzycka, Irena; Stȩpniak, Krystyna; Matyjaszczyk, Sławomir; Kozioł, Anna E.; Lis, Tadeusz; Abboud, Khalil A.

    1999-01-01

    The molecular structure of finasteride, 17 β-( N-tert-butylcarbamoyl)-4-aza-5 α-androst-1-en-3-one, and structures of three related crystalline forms have been determined by X-ray analysis. The rigid steroid skeleton of the molecule adopts a half-chair/chair/chair/half-chair conformation. Two peptide groups, one cyclic (lactam) in the ring A and a second being a part of the substituent at C17, are the main factors influencing intermolecular contacts. Different hydrogen-bond interactions of these hydrophilic groups are observed in the crystal structures. An infinite ribbon of finasteride molecules is formed between lactam groups in the orthorhombic homomolecular crystal ( 1) obtained from an ethanol solution. The linear molecular complex finasteride-acetic acid ( 1a) is connected by hydrogen bonds between the lactam of finasteride and the carboxyl group of acetic acid. The crystallization from an ethyl acetate solution gives a complex structure of bis-finasteride monohydrate ethyl acetate clathrate ( 1b) with guest molecule disordered in channels. Crystals of a second (monoclinic) finasteride polymorph ( 2) were obtained during thermal decomposition of 1a, and sublimation of 1, 1a and 1b. Two polymorphic forms show different IR spectra.

  12. Molecular Investigations into the Mechanics of a Muscle Anchoring Complex

    PubMed Central

    Bodmer, Nicholas K.; Theisen, Kelly E.; Dima, Ruxandra I.

    2015-01-01

    The titin-telethonin complex, essential for anchoring filaments in the Z-disk of the sarcomere, is composed of immunoglobulin domains. Surprisingly, atomic force microscopy experiments showed that it resists forces much higher than the typical immunoglobulin domain and that the force distribution is unusually broad. To investigate the origin of this behavior, we developed a multiscale simulation approach, combining minimalist and atomistic models (SOP-AT). By following the mechanical response of the complex on experimental timescales, we found that the mechanical stability of titin-telethonin is modulated primarily by the strength of contacts between telethonin and the two titin chains, and secondarily by the timescales of conformational excursions inside telethonin and the pulled titin domains. Importantly, the conformational transitions executed by telethonin in simulations support its proposed role in mechanosensing. Our SOP-AT computational approach thus provides a powerful tool for the exploration of the link between conformational diversity and the broadness of the mechanical response, which can be applied to other multidomain complexes. PMID:25954889

  13. Structural and spectral characterizations of C1C2 channelrhodopsin and its mutants by molecular simulations

    NASA Astrophysics Data System (ADS)

    Kamiya, Motoshi; Kato, Hideaki E.; Ishitani, Ryuichiro; Nureki, Osamu; Hayashi, Shigehiko

    2013-01-01

    Molecular dynamics (MD) simulations and excitation energy calculations of C1C2 chimera channelrhodopsin, a light-gated ion channel protein utilized as a biotechnological tool for optogenetics, based on a protein structure determined recently by X-ray crystallography were performed to investigate its structural and spectral properties. The MD simulations showed stability of hydrogen-bonds responsible for the channel gating observed in the crystallographic structural model. Analysis of electrostatic contribution of the surrounding protein groups to the absorption energy proposes several site-specific mutations that shift absorption maxima significantly, and provides a clear and controlled guide for engineering design of color variant proteins utilized in optogenetics.

  14. Atomic structure evolution during solidification of liquid niobium from ab initio molecular dynamics simulations

    SciTech Connect

    Debela, T. T.; Wang, X. D.; Cao, Q. P.; Zhang, D. X.; Wang, S. Y.; Wang, Cai-Zhuang; Jiang, J. Z.

    2013-12-12

    Atomic structure transitions of liquid niobium during solidification, at different temperatures from 3200 to 1500 K, were studied by using ab initio molecular dynamics simulations. The local atomic structure variations with temperature are investigated by using the pair-correlation function, the structure factor, the bond-angle distribution function, the Honeycutt–Anderson index, Voronoi tessellation and the cluster alignment methods. Our results clearly show that, upon quenching, the icosahedral short-range order dominates in the stable liquid and supercooled liquid states before the system transforms to crystalline body-center cubic phase at a temperature of about 1830 K.

  15. Efficient electronic structure calculation for molecular ionization dynamics at high x-ray intensity

    PubMed Central

    Hao, Yajiang; Inhester, Ludger; Hanasaki, Kota; Son, Sang-Kil; Santra, Robin

    2015-01-01

    We present the implementation of an electronic-structure approach dedicated to ionization dynamics of molecules interacting with x-ray free-electron laser (XFEL) pulses. In our scheme, molecular orbitals for molecular core-hole states are represented by linear combination of numerical atomic orbitals that are solutions of corresponding atomic core-hole states. We demonstrate that our scheme efficiently calculates all possible multiple-hole configurations of molecules formed during XFEL pulses. The present method is suitable to investigate x-ray multiphoton multiple ionization dynamics and accompanying nuclear dynamics, providing essential information on the chemical dynamics relevant for high-intensity x-ray imaging. PMID:26798806

  16. Large Molecule Structures by Broadband Fourier Transform Molecular Rotational Spectroscopy

    NASA Astrophysics Data System (ADS)

    Evangelisti, Luca; Seifert, Nathan A.; Spada, Lorenzo; Pate, Brooks

    2016-06-01

    Fourier transform molecular rotational resonance spectroscopy (FT-MRR) using pulsed jet molecular beam sources is a high-resolution spectroscopy technique that can be used for chiral analysis of molecules with multiple chiral centers. The sensitivity of the molecular rotational spectrum pattern to small changes in the three dimensional structure makes it possible to identify diastereomers without prior chemical separation. For larger molecules, there is the additional challenge that different conformations of each diastereomer may be present and these need to be differentiated from the diastereomers in the spectral analysis. Broadband rotational spectra of several larger molecules have been measured using a chirped-pulse FT-MRR spectrometer. Measurements of nootkatone (C15H22O), cedrol (C15H26O), ambroxide (C16H28O) and sclareolide (C16H26O2) are presented. These spectra are measured with high sensitivity (signal-to-noise ratio near 1,000:1) and permit structure determination of the most populated isomers using isotopic analysis of the 13C and 18O isotopologues in natural abundance. The accuracy of quantum chemistry calculations to identify diastereomers and conformers and to predict the dipole moment properties needed for three wave mixing measurements is examined.

  17. Discovering structural alerts for mutagenicity using stable emerging molecular patterns.

    PubMed

    Métivier, Jean-Philippe; Lepailleur, Alban; Buzmakov, Aleksey; Poezevara, Guillaume; Crémilleux, Bruno; Kuznetsov, Sergei O; Le Goff, Jérémie; Napoli, Amedeo; Bureau, Ronan; Cuissart, Bertrand

    2015-05-26

    This study is dedicated to the introduction of a novel method that automatically extracts potential structural alerts from a data set of molecules. These triggering structures can be further used for knowledge discovery and classification purposes. Computation of the structural alerts results from an implementation of a sophisticated workflow that integrates a graph mining tool guided by growth rate and stability. The growth rate is a well-established measurement of contrast between classes. Moreover, the extracted patterns correspond to formal concepts; the most robust patterns, named the stable emerging patterns (SEPs), can then be identified thanks to their stability, a new notion originating from the domain of formal concept analysis. All of these elements are explained in the paper from the point of view of computation. The method was applied to a molecular data set on mutagenicity. The experimental results demonstrate its efficiency: it automatically outputs a manageable number of structural patterns that are strongly related to mutagenicity. Moreover, a part of the resulting structures corresponds to already known structural alerts. Finally, an in-depth chemical analysis relying on these structures demonstrates how the method can initiate promising processes of chemical knowledge discovery.

  18. Heat-induced changes to lipid molecular structure in Vimy flaxseed: Spectral intensity and molecular clustering

    NASA Astrophysics Data System (ADS)

    Yu, Peiqiang; Damiran, Daalkhaijav

    2011-06-01

    Autoclaving was used to manipulate nutrient utilization and availability. The objectives of this study were to characterize any changes of the functional groups mainly associated with lipid structure in flaxseed ( Linum usitatissimum, cv. Vimy), that occurred on a molecular level during the treatment process using infrared Fourier transform molecular spectroscopy. The parameters included lipid CH 3 asymmetric (ca. 2959 cm -1), CH 2 asymmetric (ca. 2928 cm -1), CH 3 symmetric (ca. 2871 cm -1) and CH 2 symmetric (ca. 2954 cm -1) functional groups, lipid carbonyl C dbnd O ester group (ca. 1745 cm -1), lipid unsaturation group (CH attached to C dbnd C) (ca. 3010 cm -1) as well as their ratios. Hierarchical cluster analysis (CLA) and principal components analysis (PCA) were conducted to identify molecular spectral differences. Flaxseed samples were kept raw for the control or autoclaved in batches at 120 °C for 20, 40 or 60 min for treatments 1, 2 and 3, respectively. Molecular spectral analysis of lipid functional group ratios showed a significant decrease ( P < 0.05) in the CH 2 asymmetric to CH 3 asymmetric stretching band peak intensity ratios for the flaxseed. There were linear and quadratic effects ( P < 0.05) of the treatment time from 0, 20, 40 and 60 min on the ratios of the CH 2 asymmetric to CH 3 asymmetric stretching vibration intensity. Autoclaving had no significant effect ( P > 0.05) on lipid carbonyl C dbnd O ester group and lipid unsaturation group (CH attached to C dbnd C) (with average spectral peak area intensities of 138.3 and 68.8 IR intensity units, respectively). Multivariate molecular spectral analyses, CLA and PCA, were unable to make distinctions between the different treatment original spectra at the CH 3 and CH 2 asymmetric and symmetric region (ca. 2988-2790 cm -1). The results indicated that autoclaving had an impact to the mid-infrared molecular spectrum of flaxseed to identify heat-induced changes in lipid conformation. A future study

  19. Evolution of molecular crystal optical phonons near structural phase transitions

    NASA Astrophysics Data System (ADS)

    Michki, Nigel; Niessen, Katherine; Xu, Mengyang; Markelz, Andrea

    Molecular crystals are increasingly important photonic and electronic materials. For example organic semiconductors are lightweight compared to inorganic semiconductors and have inexpensive scale up processing with roll to roll printing. However their implementation is limited by their environmental sensitivity, in part arising from the weak intermolecular interactions of the crystal. These weak interactions result in optical phonons in the terahertz frequency range. We examine the evolution of intermolecular interactions near structural phase transitions by measuring the optical phonons as a function of temperature and crystal orientation using terahertz time-domain spectroscopy. The measured orientation dependence of the resonances provides an additional constraint for comparison of the observed spectra with the density functional calculations, enabling us to follow specific phonon modes. We observe crystal reorganization near 350 K for oxalic acid as it transforms from dihydrate to anhydrous form. We also report the first THz spectra for the molecular crystal fructose through its melting point.

  20. The molecular structure of the left-handed supra-molecular helix of eukaryotic polyribosomes

    NASA Astrophysics Data System (ADS)

    Myasnikov, Alexander G.; Afonina, Zhanna A.; Ménétret, Jean-François; Shirokov, Vladimir A.; Spirin, Alexander S.; Klaholz, Bruno P.

    2014-11-01

    During protein synthesis, several ribosomes bind to a single messenger RNA (mRNA) forming large macromolecular assemblies called polyribosomes. Here we report the detailed molecular structure of a 100 MDa eukaryotic poly-ribosome complex derived from cryo electron tomography, sub-tomogram averaging and pseudo-atomic modelling by crystal structure fitting. The structure allowed the visualization of the three functional parts of the polysome assembly, the central core region that forms a rather compact left-handed supra-molecular helix, and the more open regions that harbour the initiation and termination sites at either ends. The helical region forms a continuous mRNA channel where the mRNA strand bridges neighbouring exit and entry sites of the ribosomes and prevents mRNA looping between ribosomes. This structure provides unprecedented insights into protein- and RNA-mediated inter-ribosome contacts that involve conserved sites through 40S subunits and long protruding RNA expansion segments, suggesting a role in stabilizing the overall polyribosomal assembly.

  1. Three decades of structure- and property-based molecular design.

    PubMed

    Müller, Klaus

    2014-01-01

    Roche has pioneered structure- and property-based molecular design to drug discovery. While this is an ongoing development, the past three decades feature key events that have revolutionized the way drug discovery is conducted in Big Pharma industry. It has been a great privilege to have been involved in this transformation process, to have been able to collaborate with, direct, guide, or simply encourage outstanding experts in various disciplines to build and further develop what has become a major pillar of modern small-molecule drug discovery. This article is an account of major events that took place since the early decision of Roche to implement computer-assisted molecular modeling 32 years ago and is devoted to the key players involved. It highlights the internal build-up of structural biology, with protein X-ray structure determination at its core, and the early setup of bioinformatics. It describes the strategic shift to large compound libraries and high-throughput screening with the development of novel compound storage and ultra-high-throughput screening facilities, as well as the strategic return to focused screening of small motif-based compound libraries. These developments were accompanied by the rise of miniaturized parallel compound property analytics which resulted in a major paradigm shift in medicinal chemistry from linear to multi-dimensional lead optimization. The rapid growth of huge collections of property data stimulated the development of various novel data mining concepts with 'matched molecular pair' analysis and novel variants thereof playing crucial roles. As compound properties got more prominent in molecular design, exploration of specific structural motifs for property modulation became a research activity complementary to target-oriented medicinal chemistry. The exploration of oxetane is given as an example. For the sake of brevity, this account cannot detail all further developments that have taken place in each individual area of

  2. Structure of a molecular liquid GeI4

    NASA Astrophysics Data System (ADS)

    Fuchizaki, Kazuhiro; Sakagami, Takahiro; Kohara, Shinji; Mizuno, Akitoshi; Asano, Yuta; Hamaya, Nozomu

    2016-11-01

    A molecular liquid GeI4 is a candidate that undergoes a pressure-induced liquid-to-liquid phase transition. This study establishes the reference structure of the low-pressure liquid phase. Synchrotron x-ray diffraction measurements were carried out at several temperatures between the melting and the boiling points under ambient pressure. The molecule has regular tetrahedral symmetry, and the intramolecular Ge-I length of 2.51 Å is almost temperature-independent within the measured range. A reverse Monte Carlo (RMC) analysis is employed to find that the distribution of molecular centers remains self-similar against heating, and thus justifying the length-scaling method adopted in determining the density. The RMC analysis also reveals that the vertex-to-face orientation of the nearest molecules are not straightly aligned, but are inclined at about 20 degrees, thereby making the closest intermolecular I-I distance definitely shorter than the intramolecular one. The prepeak observed at  ˜1 Å-1 in the structural factor slightly shifts and increases in height with increasing temperature. The origin of the prepeak is clearly identified to be traces of the 111 diffraction peak in the crystalline state. The prepeak, assuming the residual spatial correlation between germanium sites in the densest direction, thus shifts toward lower wavenumbers with thermal expansion. The aspect that a relative reduction in molecular size associated with the volume expansion is responsible for the increase in the prepeak’s height is confirmed by a simulation, in which the molecular size is changed.

  3. Structure-based molecular modeling approaches to GPCR oligomerization.

    PubMed

    Kaczor, Agnieszka A; Selent, Jana; Poso, Antti

    2013-01-01

    Classical structure-based drug design techniques using G-protein-coupled receptors (GPCRs) as targets focus nearly exclusively on binding at the orthosteric site of a single receptor. Dimerization and oligomerization of GPCRs, proposed almost 30 years ago, have, however, crucial relevance for drug design. Targeting these complexes selectively or designing small molecules that affect receptor-receptor interactions might provide new opportunities for novel drug discovery. In order to study the mechanisms and dynamics that rule GPCRs oligomerization, it is essential to understand the dynamic process of receptor-receptor association and to identify regions that are suitable for selective drug binding, which may be determined with experimental methods such as Förster resonance energy transfer (FRET) or Bioluminescence resonance energy transfer (BRET) and computational sequence- and structure-based approaches. The aim of this chapter is to provide a comprehensive description of the structure-based molecular modeling methods for studying GPCR dimerization, that is, protein-protein docking, molecular dynamics, normal mode analysis, and electrostatics studies.

  4. [Cajal bodies and histone locus bodies: molecular structure and function].

    PubMed

    Khodiuchenko, T A; Krasikova, A V

    2014-01-01

    The review provides modern classification of evolutionarily conserved coilin-containing nuclear bodies of somatic and germ cells that is based on the characteristic features of their molecular composition and the nature of their functions. The main differences between Cajal bodies and histone locus bodies, which are involved in the biogenesis of small nuclear spliceosomal and nucleolar RNAs and in the 3'-end processing of histone precursor messenger RNA, respectively, are considered. It is shown that a significant contribution to the investigation of the diversity of coilin-containing bodies was made by the studies on the architecture of the RNA processing machinery in oocyte nuclei in a number of model organisms. The characteristics features of the molecular composition of coilin-containing bodies in the nuclei of growing oocytes (the so-called germinal vesicles) of vertebrates, including amphibians and birds, are described.

  5. Structural characterization of interfacial n-octanol and 3-octanol using molecular dynamic simulations.

    PubMed

    Napoleon, Raeanne L; Moore, Preston B

    2006-03-02

    Structurally isomeric octanol interfacial systems, water/vapor, 3-octanol/vapor, n-octanol/vapor, 3-octanol/water, and n-octanol/water are investigated at 298 K using molecular dynamics simulation techniques. The present study is intended to investigate strongly associated liquid/liquid interfaces and probe the atomistic structure of these interfaces. The octanol and water molecules were initially placed randomly into a box and were equilibrated using constant pressure techniques to minimize bias within the initial conditions as well as to fully sample the structural conformations of the interface. An interface formed via phase separation during equilibration and resulted in a slab geometry with a molecularly sharp interface. However, some water molecules remained within the octanol phase with a mole fraction of 0.12 after equilibration. The resulting "wet" octanol interfaces were analyzed using density profiles and orientational order parameters. Our results support the hypothesis of an ordered interface only 1 or 2 molecular layers deep before bulk properties are reached for both the 3-octanol and water systems. However, in contrast to most other interfacial systems studied by molecular dynamics simulations, the n-octanol interface extends for several molecular layers. The octanol hydroxyl groups form a hydrogen-bonding network with water which orders the surface molecules toward a preferred direction and produces a hydrophilic/hydrophobic layering. The ordered n-octanol produces an oscillating low-high density of oxygen atoms out of phase with a high-low density of carbon atoms, consistent with an oscillating dielectric. In contrast, the isomeric 3-octanol has only a single carbon-rich layer directly proximal to the interface, which is a result of the different molecular topology. Both 3-octanol and n-octanol roughen the water interface with respect to the water/vapor interface. The "wet" octanol phases, in the octanol/water systems reach bulk properties in a

  6. Structural and energy properties of interstitial molecular hydrogen in single-crystal silicon

    SciTech Connect

    Melnikov, V. V.

    2015-06-15

    The structural and energy characteristics of interstitial molecular hydrogen in single-crystal silicon are theoretically studied. The dependence of the potential energy of the system on the position and orientation of the interstitial defect is investigated, and the mechanism of interaction of a hydrogen molecule with a silicon crystal is considered. A three-dimensional model is employed to calculate the energy spectrum of H{sub 2} in Si, and the obtained dispersion law is analyzed.

  7. Bohm's Quantum Potential and the Visualization of Molecular Structure

    NASA Technical Reports Server (NTRS)

    Levit, Creon; Chancellor, Marisa K. (Technical Monitor)

    1997-01-01

    David Bohm's ontological interpretation of quantum theory can shed light on otherwise counter-intuitive quantum mechanical phenomena including chemical bonding. In the field of quantum chemistry, Richard Bader has shown that the topology of the Laplacian of the electronic charge density characterizes many features of molecular structure and reactivity. Visual and computational examination suggests that the Laplacian of Bader and the quantum potential of Bohm are morphologically equivalent. It appears that Bohmian mechanics and the quantum potential can make chemistry as clear as they makes physics.

  8. Structurally Defined Molecular Hypervalent Iodine Catalysts for Intermolecular Enantioselective Reactions

    PubMed Central

    Haubenreisser, Stefan; Wöste, Thorsten H.; Martínez, Claudio; Ishihara, Kazuaki

    2015-01-01

    Abstract Molecular structures of the most prominent chiral non‐racemic hypervalent iodine(III) reagents to date have been elucidated for the first time. The formation of a chirally induced supramolecular scaffold based on a selective hydrogen‐bonding arrangement provides an explanation for the consistently high asymmetric induction with these reagents. As an exploratory example, their scope as chiral catalysts was extended to the enantioselective dioxygenation of alkenes. A series of terminal styrenes are converted into the corresponding vicinal diacetoxylation products under mild conditions and provide the proof of principle for a truly intermolecular asymmetric alkene oxidation under iodine(I/III) catalysis. PMID:26596513

  9. Relationship between antimold activity and molecular structure of cinnamaldehyde analogues.

    PubMed

    Zhang, Yuanyuan; Li, Shujun; Kong, Xianchao

    2013-03-01

    A quantitative structure-activity relationship (QSAR) modeling of the antimold activity of cinnamaldehyde analogues against of Aspergillus niger and Paecilomyces variotii was presented. The molecular descriptors of cinnamaldehyde analogues were calculated by the CODESSA program, and these descriptors were selected by best multi-linear regression method (BMLR). Satisfactory multilinear regression models of Aspergillus niger and Paecilomyces variotii were obtained with R(2)=0.9099 and 0.9444, respectively. The models were also satisfactorily validated using internal validation and leave one out validation. The QSAR models provide the guidance for further synthetic work.

  10. Structural Organization of {pi} Conjugated Highly Luminescent Molecular Material

    SciTech Connect

    Toudic, B.; Limelette, P.; Le Gac, F.; Moreac, A.; Rabiller, P.; Froyer, G.

    2005-11-18

    We report on striking evidence for a room temperature structural phase instability in p-hexaphenyl, inducing a nonplanar conformation of the molecules. Solid state proton NMR and single crystal x-ray diffraction allow the analysis of the organization, the individual dynamics and the involved symmetry breaking. The analysis of Raman spectra above and below room temperature reveals a singular behavior suggesting a modification of the overlap between the electronic wave function induced by the nonplanarity. These results provide a new basis to answer fundamental issues related to molecular and electronic materials and, in particular, luminescent organic devices.

  11. The role of molecular epidemiology in contact investigations: a US perspective.

    PubMed

    Daley, C L; Kawamura, L M

    2003-12-01

    Preventing tuberculosis (TB) transmission through treatment of active cases and contact investigation is the highest priority of TB control programs in the United States. The role of contact investigation is becoming increasingly important as the number of TB cases declines nationally. However, the effectiveness of contact investigation has been difficult to assess because, prior to the availability of molecular genotyping techniques, levels of transmission were crudely measurable. Epidemiological links within and outside the traditional concentric circle approach are limited by the quality of the contact investigation, the skill and knowledge of the investigator and the information provided by the patient. Molecular epidemiology has added a new dimension by enabling the recognition of unsuspected transmission, likely locations of transmission, and quantification of the extent of transmission that is occurring within a given population. In the future, as real-time genotyping becomes more available, the role of molecular epidemiology is likely to expand.

  12. Effects of the Terminal Structure, Purity, and Molecular Weight of an Amorphous Conjugated Polymer on Its Photovoltaic Characteristics.

    PubMed

    Kuwabara, Junpei; Yasuda, Takeshi; Takase, Naoto; Kanbara, Takaki

    2016-01-27

    The photovoltaic characteristics of an amorphous polymer containing EDOT and fluorene units were investigated. In particular, the effects of the terminal structure, residual amount of Pd, and molecular weight were systematically investigated. Direct arylation polycondensation of EDOT followed by an established purification method readily afforded polymers with different terminal structures, Pd contents, and molecular weights. Of these factors, the terminal structure of the polymer was a crucial factor affecting the photovoltaic characteristics. For example, the polymer with a Br terminal had a PCE of 2.9% in bulk-heterojunction organic photovoltaics (BHJ OPVs) with a fullerene derivative, whereas the polymer without a Br terminal had a PCE of 4.6% in the same cell configuration. The decreased Pd residues and high molecular weights of the polymers increased the long-term stability of the devices. Moreover, BHJ OPVs containing the high-molecular-weight polymer could be fabricated with an environmentally friendly nonhalogenated solvent.

  13. Molecular and electronic structures of cerium and cerium suboxide clusters

    NASA Astrophysics Data System (ADS)

    Kafader, Jared O.; Topolski, Josey E.; Jarrold, Caroline Chick

    2016-10-01

    The anion photoelectron (PE) spectra of Ce2Oy- (y = 1, 2), Ce3Oy- (y = 0-4), Ce4Oy- (y = 0-2), and Ce5Oy- (y = 1, 2) are reported and analyzed with supporting results from density functional theory calculations. The PE spectra all exhibit an intense electronic transition to the neutral ground state, all falling in the range of 0.7 to 1.1 eV electron binding energy, with polarization dependence consistent with detachment from diffuse Ce 6s-based molecular orbitals. There is no monotonic increase in electron affinity with increasing oxidation. A qualitative picture of how electronic structure evolves with an oxidation state emerges from comparison between the spectra and the computational results. The electronic structure of the smallest metallic cluster observed in this study, Ce3, is similar to the bulk structure in terms of atomic orbital occupancy (4f 5d2 6s). Initial cerium cluster oxidation involves largely ionic bond formation via Ce 5d and O 2p orbital overlap (i.e., larger O 2p contribution), with Ce—O—Ce bridge bonding favored over Ce=O terminal bond formation. With subsequent oxidation, the Ce 5d-based molecular orbitals are depleted of electrons, with the highest occupied orbitals described as diffuse Ce 6s based molecular orbitals. In the y ≤ (x + 1) range of oxidation states, each Ce center has a singly occupied non-bonding 4f orbital. The PE spectrum of Ce3O4- is unique in that it exhibits a single nearly vertical transition. The highly symmetric structure predicted computationally is the same structure determined from Ce3O4+ IR predissociation spectra [A. M. Burow et al., Phys. Chem. Chem. Phys. 13, 19393 (2011)], indicating that this structure is stable in -1, 0, and +1 charge states. Spectra of clusters with x ≥ 3 exhibit considerable continuum signal above the ground state transition; the intensity of the continuum signal decreases with increasing oxidation. This feature is likely the result of numerous quasi-bound anion states or two

  14. Solid-State Spectroscopic Investigation of Molecular Interactions between Clofazimine and Hypromellose Phthalate in Amorphous Solid Dispersions.

    PubMed

    Nie, Haichen; Su, Yongchao; Zhang, Mingtao; Song, Yang; Leone, Anthony; Taylor, Lynne S; Marsac, Patrick J; Li, Tonglei; Byrn, Stephen R

    2016-11-07

    It has been technically challenging to specify the detailed molecular interactions and binding motif between drugs and polymeric inhibitors in the solid state. To further investigate drug-polymer interactions from a molecular perspective, a solid dispersion of clofazimine (CLF) and hypromellose phthalate (HPMCP), with reported superior amorphous drug loading capacity and physical stability, was selected as a model system. The CLF-HPMCP interactions in solid dispersions were investigated by various solid state spectroscopic methods including ultraviolet-visible (UV-vis), infrared (IR), and solid-state NMR (ssNMR) spectroscopy. Significant spectral changes suggest that protonated CLF is ionically bonded to the carboxylate from the phthalyl substituents of HPMCP. In addition, multivariate analysis of spectra was applied to optimize the concentration of polymeric inhibitor used to formulate the amorphous solid dispersions. Most interestingly, proton transfer between CLF and carboxylic acid was experimentally investigated from 2D (1)H-(1)H homonuclear double quantum NMR spectra by utilizing the ultrafast magic-angle spinning (MAS) technique. The molecular interaction pattern and the critical bonding structure in CLF-HPMCP dispersions were further delineated by successfully correlating ssNMR findings with quantum chemistry calculations. These high-resolution investigations provide critical structural information on active pharmaceutical ingredient-polymer interaction, which can be useful for rational selection of appropriate polymeric carriers, which are effective crystallization inhibitors for amorphous drugs.

  15. Molecular dynamics simulation and NMR investigation of the association of the β-blockers atenolol and propranolol with a chiral molecular micelle

    NASA Astrophysics Data System (ADS)

    Morris, Kevin F.; Billiot, Eugene J.; Billiot, Fereshteh H.; Hoffman, Charlene B.; Gladis, Ashley A.; Lipkowitz, Kenny B.; Southerland, William M.; Fang, Yayin

    2015-08-01

    Molecular dynamics simulations and NMR spectroscopy were used to compare the binding of two β-blocker drugs to the chiral molecular micelle poly-(sodium undecyl-(L)-leucine-valine). The molecular micelle is used as a chiral selector in capillary electrophoresis. This study is part of a larger effort to understand the mechanism of chiral recognition in capillary electrophoresis by characterizing the molecular micelle binding of chiral compounds with different geometries and charges. Propranolol and atenolol were chosen because their structures are similar, but their chiral interactions with the molecular micelle are different. Molecular dynamics simulations showed both propranolol enantiomers inserted their aromatic rings into the molecular micelle core and that (S)-propranolol associated more strongly with the molecular micelle than (R)-propranolol. This difference was attributed to stronger molecular micelle hydrogen bonding interactions experienced by (S)-propranolol. Atenolol enantiomers were found to bind near the molecular micelle surface and to have similar molecular micelle binding free energies.

  16. Investigation of ethanol infiltration into demineralized dentin collagen fibrils using molecular dynamics simulations.

    PubMed

    Jee, Sang Eun; Zhou, Jienfeng; Tan, Jianquo; Breschi, Lorenzo; Tay, Franklin R; Grégoire, Geneviève; Pashley, David H; Jang, Seung Soon

    2016-05-01

    The purpose of this study is to investigate the interaction of neat ethanol with bound and non-bound water in completely demineralized dentin that is fully hydrated, using molecular dynamics (MD) simulation method. The key to creating ideal resin-dentin bonds is the removal of residual free water layers and its replacement by ethanol solvent in which resin monomers are soluble, using the ethanol wet-bonding technique. The test null hypotheses were that ethanol cannot remove any collagen-bound water, and that ethanol cannot infiltrate into the spacing between collagen triple helix due to narrow interlayer spacing. Collagen fibrillar structures of overlap and gap regions were constructed by aligning the collagen triple helix of infinite length in hexagonal packing. Three layers of the water molecules were specified as the layers of 0.15-0.22nm, 0.22-0.43nm and 0.43-0.63nm from collagen atoms by investigating the water distribution surrounding collagen molecules. Our simulation results show that ethanol molecules infiltrated into the intermolecular spacing in the gap region, which increased due to the lateral shrinkage of the collagen structures in contact with ethanol solution, while there was no ethanol infiltration observed in the overlap region. Infiltrated ethanol molecules in the gap region removed residual water molecules via modifying mostly the third water layer (50% decrease), which would be considered as a loosely-bound water layer. The first and second hydration layers, which would be considered as tightly bound water layers, were not removed by the ethanol molecules, thus maintaining the helical structures of the collagen molecules.

  17. Molecular structure of uranium carbides: isomers of UC3.

    PubMed

    Zalazar, M Fernanda; Rayón, Víctor M; Largo, Antonio

    2013-03-21

    In this article, the most relevant isomers of uranium tricarbide are studied through quantum chemical methods. It is found that the most stable isomer has a fan geometry in which the uranium atom is bonded to a quasilinear C3 unit. Both, a rhombic and a ring CU(C2) structures are found about 104-125 kJ/mol higher in energy. Other possible isomers including linear geometries are located even higher. For each structure, we provide predictions for those molecular properties (vibrational frequencies, IR intensities, dipole moments) that could eventually help in their experimental detection. We also discuss the possible routes for the formation of the different UC3 isomers as well as the bonding situation by means of a topological analysis of the electron density.

  18. Crystal and molecular structures of new enantiopure quinuclidines.

    PubMed

    Kania, Iwona; Stadnicka, Katarzyna; Oleksyn, Barbara J

    2004-03-01

    X-ray crystal structure analysis was performed on single crystals of two diastereomeric enantiopure quinuclidines, (3R,8R)-3-vinyl-8-hydroxymethyl-quinuclidine (quincoridine, QCD) and (3R,8S)-3-vinyl-8-hydroxymethyl-quinuclidine (quincorine, QCI) as their salts with tartaric and p-toluenesulphonate anions, respectively. The molecules of these quinuclidine derivatives are considered here as fragments of the Cinchona alkaloids, quinidine and quinine. A comparison of the conformational features of QCD, QCI, and Cinchona alkaloids in the crystalline state shows that the molecular geometry of the title compounds is similar to that of threo-alkaloids (e.g., R,R isomer of epicinchonine) rather than to quinidine and quinine. The packing of the molecules in both structures is dominated by intermolecular hydrogen bonds.

  19. Raman spectroscopy based investigation of molecular changes associated with an early stage of dengue virus infection

    NASA Astrophysics Data System (ADS)

    Bilal, Maria; Bilal, Muhammad; Saleem, Muhammad; Khurram, Muhammad; Khan, Saranjam; Ullah, Rahat; Ali, Hina; Ahmed, Mushtaq; Shahzada, Shaista; Ullah Khan, Ehsan

    2017-04-01

    Raman spectroscopy based investigations of the molecular changes associated with an early stage of dengue virus infection (DENV) using a partial least squares (PLS) regression model is presented. This study is based on non-structural protein 1 (NS1) which appears after three days of DENV infection. In total, 39 blood sera samples were collected and divided into two groups. The control group contained samples which were the negative for NS1 and antibodies and the positive group contained those samples in which NS1 is positive and antibodies were negative. Out of 39 samples, 29 Raman spectra were used for the model development while the remaining 10 were kept hidden for blind testing of the model. PLS regression yielded a vector of regression coefficients as a function of Raman shift, which were analyzed. Cytokines in the region 775–875 cm‑1, lectins at 1003, 1238, 1340, 1449 and 1672 cm‑1, DNA in the region 1040–1140 cm‑1 and alpha and beta structures of proteins in the region 933–967 cm‑1 have been identified in the regression vector for their role in an early stage of DENV infection. Validity of the model was established by its R-square value of 0.891. Sensitivity, specificity and accuracy were 100% each and the area under the receiver operator characteristic curve was found to be 1.

  20. Alphavirus protease inhibitors from natural sources: A homology modeling and molecular docking investigation.

    PubMed

    Byler, Kendall G; Collins, Jasmine T; Ogungbe, Ifedayo Victor; Setzer, William N

    2016-10-01

    Alphaviruses such as Chikungunya virus (CHIKV), O'Nyong-Nyong virus (ONNV), Ross River virus (RRV), Eastern equine encephalitis virus (EEEV), Venezuelan equine encephalitis virus (VEEV), and Western equine encephalitis virus (WEEV), are mosquito-transmitted viruses that can cause fevers, rash, and rheumatic diseases (CHIKV, ONNV, RRV) or potentially fatal encephalitis (EEEV, VEEV, WEEV) in humans. These diseases are considered neglected tropical diseases for which there are no current antiviral therapies or vaccines available. The alphavirus non-structural protein 2 (nsP2) contains a papain-like protease, which is considered to be a promising target for antiviral drug discovery. In this work, molecular docking analyses have been carried out on a library of 2174 plant-derived natural products (290 alkaloids, 664 terpenoids, 1060 polyphenolics, and 160 miscellaneous phytochemicals) with the nsP2 proteases of CHIKV, ONNV, RRV, EEEV, VEEV, WEEV, as well as Aura virus (AURV), Barmah Forest Virus (BFV), Semliki Forest virus (SFV), and Sindbis virus (SINV) in order to identity structural scaffolds for inhibitor design or discovery. Of the 2174 phytochemicals examined, a total of 127 showed promising docking affinities and poses to one or more of the nsP2 proteases, and this knowledge can be used to guide experimental investigation of potential inhibitors.

  1. Investigations of the plasma and structure based accelerators

    SciTech Connect

    Shvets, Gennady

    2012-08-30

    The objective of our research during the reported period was three-fold: (a) theoretical investigation of novel mechanisms of injection into laser wake field accelerators; (b) theoretical investigation of single-shot frequency domain diagnostics of relativistic plasma wakes, specifically in the context of spatio-temporal evolution of the plasma bubble;(c) experimental and theoretical investigation of laser-driven accelerating structure, specifically in the context of the Surface Wave Accelerator Based on SiC (SWABSIC).

  2. Noninvasive structural, functional, and molecular imaging in drug development.

    PubMed

    Rudin, Markus

    2009-06-01

    Modern drug research is mechanism-based and the development of disease modifying therapies involves the identification of molecular key players in the pathological cascade. Today, noninvasive imaging tools enable the visualization and quantitative assessment of the expression of molecular targets, of their interaction with potential ligands, as well as of the functional consequence of this interaction at a molecular (e.g. activation of signaling cascades), cellular, metabolic, physiological, and morphological level in a temporo-spatially resolved manner. The ability to gather such information from the intact organism with all regulatory processes in place renders imaging highly attractive for the biomedical researcher and for the drug developer in particular. Molecular imaging is potentially capable of providing this information. Today, proof-of-principle has been established that imaging is in fact adding value to the drug discovery and development processes. Numerous studies have used structural and functional imaging readouts to document therapy efficacy, mainly during lead optimization. Similarly, major efforts have been devoted to the development and evaluation of imaging biomarkers that might serve as early readouts for therapy response with the potential of being used in the clinical drug evaluation thereby facilitating translational research. In this contribution, we illustrate the role and potential of imaging in modern drug discovery and development with selected examples. Yet, despite its huge potential the impact of imaging on drug discovery has been modest in the past; potential reasons will be discussed. Nevertheless, noninvasive imaging methods are rapidly evolving and it is beyond doubt that their importance for biomedical research will increase.

  3. Rattlesnake Neurotoxin Structure, Mechanism of Action, Immunology and Molecular Biology

    DTIC Science & Technology

    1992-09-10

    Revised 1985). For the protection of human subjects, the investigator(s) adhered to policies of applicable Federal Law 45 CFR 46. condurting research...trial crystallization studies. Sequencing of the basic subunit of Mojave toxin was also proposed in this application , to facilitate our x-ray structural...hydroxysuccinimidyl-4-azidobenzoate ( HSAB ), to synaptosomes and synaptosomal membranes yielded bands on SDS-PAGE migrating at 102kD, equating to a 88kD

  4. A nanostructural investigation of glassy gelatin oligomers: molecular organization and interactions with low molecular weight diluents

    NASA Astrophysics Data System (ADS)

    Roussenova, M.; Enrione, J.; Diaz-Calderon, P.; Taylor, A. J.; Ubbink, J.; Alam, M. A.

    2012-03-01

    The effects of low molecular weight diluents (namely water and glycerol) on the nanostructure and thermodynamic state of low water content gelatin matrices are explored systematically by combining positron annihilation lifetime spectroscopy (PALS) with calorimetric measurements. Bovine gelatin matrices with a variation in the glycerol content (0-10 wt.%) are equilibrated in a range of water activities (aw = 0.11-0.68, T = 298 K). Both water and glycerol reduce the glass transition temperature, Tg, and the temperature of dissociation of the ordered triple helical segments, Tm, while having no significant effect on the level of re-naturation of the gelatin matrices. Our PALS measurements show that over the concentration range studied, glycerol acts as a packing enhancer and in the glassy state it causes a nonlinear decrease in the average hole size, vh, of the gelatin matrices. Finally, we report complex changes in vh for the gelatin matrices as a function of the increasing level of hydration. At low water contents (Qw ˜ 0.01-0.10), water acts as a plasticizer, causing a systematic increase in vh. Conversely, for water contents higher than Qw ˜ 0.10, vh is found to decrease, as small clusters of water begin to form between the polypeptide chains.

  5. Numerical investigations of flow structure in gas turbine shroud gap

    NASA Astrophysics Data System (ADS)

    Wasilczuk, F.; Flaszyński, P.; Doerffer, P.

    2016-10-01

    The structure of the flow in the labyrinth sealing of an axial gas turbine was investigated by means of numerical simulations. Additionally, the flow structure for two- and three-dimensional axisymmetric models was compared. The porous disc as a model for the pressure drop relevant to the obtained in the cascade was proposed and tested. Several flow structure features existing in the sealing cavities are investigated: vortical structure and separation bubble on the rib and the correlation between the pressure drop and the clearance size. The carried out investigations indicate that the innovation aimed at decreasing the leakage flow through implementation of the flow control devices is possible. Furthermore the comparison between 2D and 3D models shows good agreement, thus application of less demanding 2D model introduces negligible differences. It is shown that the proposed porous disc model applied to mimic pressure drop in cascade can be effectively used for rotor blade sealing simulations.

  6. Theoretical Study of Donor - Spacer - Acceptor Structure Molecule for Molecular Rectifier

    NASA Astrophysics Data System (ADS)

    Mizuseki, Hiroshi; Kenji, Niimura; Belosludov, Rodion; Farajian, Amir; Kawazoe, Yoshiyuki

    2003-03-01

    Recently, the molecular electronics has attracted strong attention as a ``post-silicone technology'' to establish a future nanoscale electronic devices. To realize this molecular device, unimolecular rectifiering function is one of the most important constituents in nanotechnology [C. Majumder, H. Mizuseki, and Y. Kawazoe, Molecular Scale Rectifier: Theoretical Study, J. Phys. Chem. A, 105 (2001) 9454-9459.]. In the present study, the geometric and electronic structure of alkyl derivative C37H50N4O4 (PNX) molecule, (donor - spacer - acceptor), a leading candidate of molecular rectifying device, has been investigated theoretically using ab initio quantum mechanical calculation. The results suggest that in such donor-acceptor molecular complexes, while the lowest unoccupied orbital concentrates on the acceptor subunit, the highest occupied molecular orbital is localized on the donor subunit. The approximate potential differences for optimized PNX molecule have been estimated at the B3PW91/6-311g++(d,p) level of theory, which achieves quite good agreement with experimentally reported results. This study was performed through Special Coordination Funds for Promoting Science and Technology of the Ministry of Education, Culture, Sports, Science and Technology of the Japanese Government.

  7. Molecular dynamics simulations of H2 adsorption in tetramethyl ammonium lithium phthalocyanine crystalline structures.

    PubMed

    Lamonte, Kevin; Gómez Gualdrón, Diego A; Cabrales-Navarro, Fredy A; Scanlon, Lawrence G; Sandi, Giselle; Feld, William; Balbuena, Perla B

    2008-12-11

    Tetramethyl ammonium lithium phthalocyanine is explored as a potential material for storage of molecular hydrogen. Density functional theory calculations are used to investigate the molecular structure and the dimer conformation. Additional scans performed to determine the interactions of a H2 molecule located at various distances from the molecular sites are used to generate a simple force field including dipole-induced-dipole interactions. This force field is employed in molecular dynamics simulations to calculate adsorption isotherms at various pressures. The regions of strongest adsorption are quantified as functions of temperature, pressure, and separation between molecules in the adsorbent phase, and compared to the regions of strongest binding energy as given by the proposed force field. It is found that the total adsorption could not be predicted only from the spatial distribution of the strongest binding energies; the available volume is the other contributing factor even if the volume includes regions of much lower binding energy. The results suggest that the complex anion is primarily involved in the adsorption process with molecular hydrogen, whereas the cation serves to provide access for hydrogen adsorption in both sides of the anion molecular plane, and spacing between the planes.

  8. Anti-cancer chalcones: Structural and molecular target perspectives.

    PubMed

    Mahapatra, Debarshi Kar; Bharti, Sanjay Kumar; Asati, Vivek

    2015-06-15

    Chalcone or (E)-1,3-diphenyl-2-propene-1-one scaffold remained a fascination among researchers in the 21st century due to its simple chemistry, ease of synthesis and a wide variety of promising biological activities. Several natural and (semi) synthetic chalcones have shown anti-cancer activity due to their inhibitory potential against various targets namely ABCG2/P-gp/BCRP, 5α-reductase, aromatase, 17-β-hydroxysteroid dehydrogenase, HDAC/Situin-1, proteasome, VEGF, VEGFR-2 kinase, MMP-2/9, JAK/STAT signaling pathways, CDC25B, tubulin, cathepsin-K, topoisomerase-II, Wnt, NF-κB, B-Raf and mTOR etc. In this review, a comprehensive study on molecular targets/pathways involved in carcinogenesis, mechanism of actions (MOAs), structure activity relationships (SARs) and patents granted have been highlighted. With the knowledge of molecular targets, structural insights and SARs, this review may be helpful for (medicinal) chemists to design more potent, safe, selective and cost effective anti-cancer chalcones.

  9. THE INVESTIGATION OF STRUCTURAL PROPERTIES AND CHEMICAL TRANSFORMATIONS OF CARBAZOLE AND SOME OF ITS DERIVATIVES

    DTIC Science & Technology

    AZOLES, ALKYL RADICALS, AMIDES, CHEMICAL RADICALS, CHEMICAL REACTIONS , GLYCINE, HETEROCYCLIC COMPOUNDS, METHYL RADICALS, MOLECULAR STRUCTURE, ULTRAVIOLET SPECTROPHOTOMETERS, ULTRAVIOLET SPECTROSCOPY.

  10. Influence of free surface nanorelief on the rear spallation threshold: Molecular-dynamics investigation

    NASA Astrophysics Data System (ADS)

    Mayer, Alexander E.; Ebel, Andrej A.

    2016-10-01

    By means of molecular dynamics simulation, we investigate the interaction of picosecond-duration compression pulses excited by a flat impactor with flat and nano-structured rear surfaces of copper and aluminum samples. It is shown that protrusions on the rear surface can increase the threshold value of the impact velocity, leading to spallation. As the shock wave reaches the perturbed rear surface, an unloading on the lateral surfaces of the protrusions begins; it leads to an intensive plastic deformation in the surface layer of metal. A part of the compression pulse energy is spent on the plastic deformation that restricts the rarefaction wave amplitude and suppresses the spall fracture. An increase in threshold velocity can be observed for all investigated thicknesses of the targets. The increase is substantial with respect to comparability between the protrusion height and the compression pulse width (the impactor thickness). Another condition is the ratio of the protrusion cross-section to the total surface area, which should be neither small nor large-approximately 0.3-0.4 for the best case. At high protrusion heights (higher than the compression pulse width), as well as at large protrusion cross sections, instability develops on the rear surface of the target and is accompanied by mass ejection. The instability violates the rear surface integrity and restricts the threshold velocity, although the loss of integrity in this case goes through mass ejection, not spallation.

  11. The Molecular Structure of a Phosphatidylserine Bilayer Determined by Scattering and Molecular Dynamics Simulations

    SciTech Connect

    Pan, Jianjun; Cheng, Xiaolin; Monticelli, Luca; Heberle, Frederick A; Kucerka, Norbert; Tieleman, D. Peter; Katsaras, John

    2014-01-01

    Phosphatidylserine (PS) lipids play essential roles in biological processes, including enzyme activation and apoptosis. We report on the molecular structure and atomic scale interactions of a fluid bilayer composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (POPS). A scattering density profile model, aided by molecular dynamics (MD) simulations, was developed to jointly refine different contrast small-angle neutron and X-ray scattering data, which yielded a lipid area of 62.7 A2 at 25 C. MD simulations with POPS lipid area constrained at different values were also performed using all-atom and aliphatic united-atom models. The optimal simulated bilayer was obtained using a model-free comparison approach. Examination of the simulated bilayer, which agrees best with the experimental scattering data, reveals a preferential interaction between Na+ ions and the terminal serine and phosphate moieties. Long-range inter-lipid interactions were identified, primarily between the positively charged ammonium, and the negatively charged carboxylic and phosphate oxygens. The area compressibility modulus KA of the POPS bilayer was derived by quantifying lipid area as a function of surface tension from area-constrained MD simulations. It was found that POPS bilayers possess a much larger KA than that of neutral phosphatidylcholine lipid bilayers. We propose that the unique molecular features of POPS bilayers may play an important role in certain physiological functions.

  12. Establishing whether the structural feature controlling the mechanical properties of starch films is molecular or crystalline.

    PubMed

    Li, Ming; Xie, Fengwei; Hasjim, Jovin; Witt, Torsten; Halley, Peter J; Gilbert, Robert G

    2015-03-06

    The effects of molecular and crystalline structures on the tensile mechanical properties of thermoplastic starch (TPS) films from waxy, normal, and high-amylose maize were investigated. Starch structural variations were obtained through extrusion and hydrothermal treatment (HTT). The molecular and crystalline structures were characterized using size-exclusion chromatography and X-ray diffractometry, respectively. TPS from high-amylose maize showed higher elongation at break and tensile strength than those from normal maize and waxy maize starches when processed with 40% plasticizer. Within the same amylose content, the mechanical properties were not affected by amylopectin molecular size or the crystallinity of TPS prior to HTT. This lack of correlation between the molecular size, crystallinity and mechanical properties may be due to the dominant effect of the plasticizer on the mechanical properties. Further crystallization of normal maize TPS by HTT increased the tensile strength and Young's modulus, while decreasing the elongation at break. The results suggest that the crystallinity from the remaining ungelatinized starch granules has less significant effect on the mechanical properties than that resulting from starch recrystallization, possibly due to a stronger network from leached-out amylose surrounding the remaining starch granules.

  13. Structure of the thermolabile mutant aldolase B, A149P: molecular basis of hereditary fructose intolerance.

    PubMed

    Malay, Ali D; Allen, Karen N; Tolan, Dean R

    2005-03-18

    Hereditary fructose intolerance (HFI) is a potentially lethal inborn error in metabolism caused by mutations in the aldolase B gene, which is critical for gluconeogenesis and fructose metabolism. The most common mutation, which accounts for 53% of HFI alleles identified worldwide, results in substitution of Pro for Ala at position 149. Structural and functional investigations of human aldolase B with the A149P substitution (AP-aldolase) have shown that the mutation leads to losses in thermal stability, quaternary structure, and activity. X-ray crystallography is used to reveal the structural basis of these perturbations. Crystals of AP-aldolase are grown at two temperatures (4 degrees C and 18 degrees C), and the structure solved to 3.0 angstroms resolution, using the wild-type structure as the phasing model. The structures reveal that the single residue substitution, A149P, causes molecular disorder around the site of mutation (residues 148-159), which is propagated to three adjacent beta-strand and loop regions (residues 110-129, 189-199, 235-242). Disorder in the 110-129-loop region, which comprises one subunit-subunit interface, provides an explanation for the disrupted quaternary structure and thermal instability. Greater structural perturbation, particularly at a Glu189-Arg148 salt bridge in the active-site architecture, is observed in the structure determined at 18 degrees C, which could explain the temperature-dependent loss in activity. The disorder revealed in these structures is far greater than that predicted by homology modeling and underscores the difficulties in predicting perturbations of protein structure and function by homology modeling alone. The AP-aldolase structure reveals the molecular basis of a hereditary disease and represents one of only a few structures known for mutant proteins at the root of the thousands of other inherited disorders.

  14. Molecular dynamics simulation of the structure and dynamics of 5-HT3 serotonin receptor

    NASA Astrophysics Data System (ADS)

    Antonov, M. Yu.; Popinako, A. V.; Prokopiev, G. A.

    2016-10-01

    In this work, we investigated structure, dynamics and ion transportation in transmembrane domain of the 5-HT3 serotonin receptor. High-resolution (0.35 nm) structure of the 5-HT3 receptor in complex with stabilizing nanobodies was determined by protein crystallography in 2014 (Protein data bank (PDB) code 4PIR). Transmembrane domain of the structure was prepared in complex with explicit membrane environment (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC)) and solvent (TIP3P water model). Molecular dynamics protocols for simulation and stabilization of the transmembrane domain of the 5-HT3 receptor model were developed and 60 ns simulation of the structure was conducted in order to explore structural parameters of the system. We estimated the mean force profile for Na+ ions using umbrella sampling method.

  15. Maintain rigid structures in Verlet based cartesian molecular dynamics simulations.

    PubMed

    Tao, Peng; Wu, Xiongwu; Brooks, Bernard R

    2012-10-07

    An algorithm is presented to maintain rigid structures in Verlet based cartesian molecular dynamics (MD) simulations. After each unconstrained MD step, the coordinates of selected particles are corrected to maintain rigid structures through an iterative procedure of rotation matrix computation. This algorithm, named as SHAPE and implemented in CHARMM program suite, avoids the calculations of Lagrange multipliers, so that the complexity of computation does not increase with the number of particles in a rigid structure. The implementation of this algorithm does not require significant modification of propagation integrator, and can be plugged into any cartesian based MD integration scheme. A unique feature of the SHAPE method is that it is interchangeable with SHAKE for any object that can be constrained as a rigid structure using multiple SHAKE constraints. Unlike SHAKE, the SHAPE method can be applied to large linear (with three or more centers) and planar (with four or more centers) rigid bodies. Numerical tests with four model systems including two proteins demonstrate that the accuracy and reliability of the SHAPE method are comparable to the SHAKE method, but with much more applicability and efficiency.

  16. On the vibration of double-walled carbon nanotubes using molecular structural and cylindrical shell models

    NASA Astrophysics Data System (ADS)

    Ansari, R.; Rouhi, S.; Aryayi, M.

    2016-01-01

    The vibrational behavior of double-walled carbon nanotubes is studied by the use of the molecular structural and cylindrical shell models. The spring elements are employed to model the van der Waals interaction. The effects of different parameters such as geometry, chirality, atomic structure and end constraint on the vibration of nanotubes are investigated. Besides, the results of two aforementioned approaches are compared. It is indicated that by increasing the nanotube side length and radius, the computationally efficient cylindrical shell model gives rational results.

  17. Molecular dynamics simulations of the structure evolutions of Cu-Zr metallic glasses under irradiation

    NASA Astrophysics Data System (ADS)

    Lang, Lin; Tian, Zean; Xiao, Shifang; Deng, Huiqiu; Ao, Bingyun; Chen, Piheng; Hu, Wangyu

    2017-02-01

    Molecular dynamics simulations have been performed to investigate the structural evolution of Cu64.5Zr35.5 metallic glasses under irradiation. The largest standard cluster analysis (LSCA) method was used to quantify the microstructure within the collision cascade regions. It is found that the majority of clusters within the collision cascade regions are full and defective icosahedrons. Not only the smaller structures (common neighbor subcluster) but also primary clusters greatly changed during the collision cascades; while most of these radiation damages self-recover quickly in the following quench states. These findings indicate the Cu-Zr metallic glasses have excellent irradiation-resistance properties.

  18. Molecular and Cellular Quantitative Microscopy: theoretical investigations, technological developments and applications to neurobiology

    NASA Astrophysics Data System (ADS)

    Esposito, Alessandro

    2006-05-01

    This PhD project aims at the development and evaluation of microscopy techniques for the quantitative detection of molecular interactions and cellular features. The primarily investigated techniques are Fαrster Resonance Energy Transfer imaging and Fluorescence Lifetime Imaging Microscopy. These techniques have the capability to quantitatively probe the biochemical environment of fluorophores. An automated microscope capable of unsupervised operation has been developed that enables the investigation of molecular and cellular properties at high throughput levels and the analysis of cellular heterogeneity. State-of-the-art Förster Resonance Energy Transfer imaging, Fluorescence Lifetime Imaging Microscopy, Confocal Laser Scanning Microscopy and the newly developed tools have been combined with cellular and molecular biology techniques for the investigation of protein-protein interactions, oligomerization and post-translational modifications of α-Synuclein and Tau, two proteins involved in Parkinson’s and Alzheimer’s disease, respectively. The high inter-disciplinarity of this project required the merging of the expertise of both the Molecular Biophysics Group at the Debye Institute - Utrecht University and the Cell Biophysics Group at the European Neuroscience Institute - Gαttingen University. This project was conducted also with the support and the collaboration of the Center for the Molecular Physiology of the Brain (Göttingen), particularly with the groups associated with the Molecular Quantitative Microscopy and Parkinson’s Disease and Aggregopathies areas. This work demonstrates that molecular and cellular quantitative microscopy can be used in combination with high-throughput screening as a powerful tool for the investigation of the molecular mechanisms of complex biological phenomena like those occurring in neurodegenerative diseases.

  19. Investigation of the radiation-stimulated oxidation of sulfide by molecular oxygen

    SciTech Connect

    Muratbekov, M.B.; Beremzhanov, B.A.; Koroleva, G.Y.

    1986-07-01

    In order to determine the possibility of radiation stimulation of the oxidation of dissolved sulfide by molecular oxygen and to consider the mechanism from the standpoint of radiation chemical concepts, the authors investigated the radiation-stimulated oxidation of sulfide by molecular oxygen at pH 13. The kinetics were studied according to the decrease in oxygen with the aid of a gasometric set up.

  20. Theoretical Investigation Leading to Energy Storage in Atomic and Molecular Systems

    DTIC Science & Technology

    1990-12-01

    maintenance of equivalent quality of calculation for nuclear geometries differing in the nature or number of chemical bonds ; (iii) ability to describe...function. In order to calculate properties for such states, or to investigate the formation of molecular bonds , one often needs multiconfiguration wave...of calculating one-electron properties and analyzing molecular charge distributions, and various ’post-SCF’ stages, beginning with a 4- index

  1. Self-structured surface patterns on molecular azo glass films induced by laser light irradiation.

    PubMed

    Yin, Jianjun; Ye, Gang; Wang, Xiaogong

    2010-05-04

    In this work, formation of photoinduced self-structured surface pattern and its correlation with chromophoric structures were studied by using a series of star-shaped azo compounds, which exist as stable molecular glass at room temperature. For the synthesis, a star-shaped precursor (Tr-AN) was prepared by a ring-open reaction between 1, 3, 5-triglycidyl isocyanurate and N-methylaniline. The star-shaped azo compounds were then synthesized through azo-coupling reactions between the precursor and diazonium salts of 4-nitroaniline, 2-methyl-4-nitroaniline, and 4-aminobenzonitrile, respectively. Through these steps, three azo compounds were obtained to bear different donor-acceptor type azo chromophores at the peripheral positions. The formation of the photoinduced self-structured patterns was investigated by irradiating solid thin films of the molecular azo glass with a uniform laser beam (532 nm, 200 mW/cm(2)) at normal incidence. For comparison, formation of surface-relief-gratings (SRGs) was also investigated by exposing the thin films to an interference pattern of the laser beams (532 nm, 80 mW/cm(2)). The results show that SRGs can be inscribed on the films of all three star-shaped azo compounds, but self-structured surface patterns is only observed on film of the azo compound containing 4-cyanoazobenzene moieties (Tr-AZ-CN) under the same irradiation condition. The electron-withdrawing groups, which control the absorption band position, show a significant influence on both the self-structured pattern formation and SRG inscription rate. Under proper experimental conditions, both self-structured surface pattern and SRG can simultaneously be observed on the Tr-AZ-CN films. The observations can lead to a deeper understanding of the photoinduced effects, especially their correlation with molecular structures.

  2. IRT in the investigation of buildings and historic structures

    NASA Astrophysics Data System (ADS)

    Avdelidis, Nicolas P.; Moropoulou, Antonia

    2004-04-01

    Although, the efficiency of IRT (infrared thermography) as a NDT & E technique in the literature it is well documented, in the investigation of historic structures, where a restoration or conservation treatment can cause irreversible damage to the structure, it is considered to be of most importance. IRT is a non-destructive investigation technique that can be widely used due to the outstanding advantages that offers in a number of applications and specifically in the assessment of structural materials and techniques. In the present work, both IRT approaches, passive and active, were used, depending on the application, for the investigation of traditional-historical materials and structures. IRT was applied on restoration and traditional-historic materials and structures for the evaluation of conservation interventions (materials and techniques) concerning cleaning of architectural surfaces, restoration of masonries by repair mortars, as well as the disclosure of tesserae on plastered mosaic surfaces. For this reason, diagnostic studies on historical sites and structures took place. Wherever necessary, the emissivity values of the investigated materials were taken into account, after their determination in the laboratory on representative samples. Furthermore, in order to obtain useful information from the IRT surveys various properties (thermal, optical, physical) of the examined materials were taken into account. The outcome of this work provides strong evidence that IRT is an effective technique for the evaluation of historic buildings and sites.

  3. An Investigation of Molecular Docking and Molecular Dynamic Simulation on Imidazopyridines as B-Raf Kinase Inhibitors.

    PubMed

    Xie, Huiding; Li, Yupeng; Yu, Fang; Xie, Xiaoguang; Qiu, Kaixiong; Fu, Jijun

    2015-11-16

    In the recent cancer treatment, B-Raf kinase is one of key targets. Nowadays, a group of imidazopyridines as B-Raf kinase inhibitors have been reported. In order to investigate the interaction between this group of inhibitors and B-Raf kinase, molecular docking, molecular dynamic (MD) simulation and binding free energy (ΔGbind) calculation were performed in this work. Molecular docking was carried out to identify the key residues in the binding site, and MD simulations were performed to determine the detail binding mode. The results obtained from MD simulation reveal that the binding site is stable during the MD simulations, and some hydrogen bonds (H-bonds) in MD simulations are different from H-bonds in the docking mode. Based on the obtained MD trajectories, ΔGbind was computed by using Molecular Mechanics Generalized Born Surface Area (MM-GBSA), and the obtained energies are consistent with the activities. An energetic analysis reveals that both electrostatic and van der Waals contributions are important to ΔGbind, and the unfavorable polar solvation contribution results in the instability of the inhibitor with the lowest activity. These results are expected to understand the binding between B-Raf and imidazopyridines and provide some useful information to design potential B-Raf inhibitors.

  4. An Investigation of Molecular Docking and Molecular Dynamic Simulation on Imidazopyridines as B-Raf Kinase Inhibitors

    PubMed Central

    Xie, Huiding; Li, Yupeng; Yu, Fang; Xie, Xiaoguang; Qiu, Kaixiong; Fu, Jijun

    2015-01-01

    In the recent cancer treatment, B-Raf kinase is one of key targets. Nowadays, a group of imidazopyridines as B-Raf kinase inhibitors have been reported. In order to investigate the interaction between this group of inhibitors and B-Raf kinase, molecular docking, molecular dynamic (MD) simulation and binding free energy (ΔGbind) calculation were performed in this work. Molecular docking was carried out to identify the key residues in the binding site, and MD simulations were performed to determine the detail binding mode. The results obtained from MD simulation reveal that the binding site is stable during the MD simulations, and some hydrogen bonds (H-bonds) in MD simulations are different from H-bonds in the docking mode. Based on the obtained MD trajectories, ΔGbind was computed by using Molecular Mechanics Generalized Born Surface Area (MM-GBSA), and the obtained energies are consistent with the activities. An energetic analysis reveals that both electrostatic and van der Waals contributions are important to ΔGbind, and the unfavorable polar solvation contribution results in the instability of the inhibitor with the lowest activity. These results are expected to understand the binding between B-Raf and imidazopyridines and provide some useful information to design potential B-Raf inhibitors. PMID:26580609

  5. Investigations on structural thinning in deformation machining stretching mode

    NASA Astrophysics Data System (ADS)

    Singh, Arshpreet; Nirala, Harish Kumar; Agrawal, Anupam

    2016-10-01

    Deformation machining is a combination of thin structure machining and single point incremental forming/bending. This process enables the creation of monolithic, complex structures and geometries, which are difficult or sometimes impossible to manufacture employing conventional manufacturing techniques. Section thinning of the formed structure is a measure of process formability and influences the strength and stiffness of the formed component. In this study, experimental and finite element investigations on structural thinning in Deformation machining stretching mode have been performed. Structural thinning was found out to be highly non uniform along the forming depth at varying forming angles. A compensation strategy in thin structure machining has been proposed for uniform section thickness in incremental forming.

  6. Molecular Clouds in the North American and Pelican Nebulae: Structures

    NASA Astrophysics Data System (ADS)

    Zhang, Shaobo; Xu, Ye; Yang, Ji

    2014-03-01

    We present observations of a 4.25 deg2 area toward the North American and Pelican Nebulae in the J = 1-0 transitions of 12CO, 13CO, and C18O. Three molecules show different emission areas with their own distinct structures. These different density tracers reveal several dense clouds with a surface density of over 500 M ⊙ pc-2 and a mean H2 column density of 5.8, 3.4, and 11.9 × 1021 cm-2 for 12CO, 13CO, and C18O, respectively. We obtain a total mass of 5.4 × 104 M ⊙ (12CO), 2.0 × 104 M ⊙ (13CO), and 6.1 × 103 M ⊙ (C18O) in the complex. The distribution of excitation temperature shows two phases of gas: cold gas (~10 K) spreads across the whole cloud; warm gas (>20 K) outlines the edge of the cloud heated by the W80 H II region. The kinetic structure of the cloud indicates an expanding shell surrounding the ionized gas produced by the H II region. There are six discernible regions in the cloud: the Gulf of Mexico, Caribbean Islands and Sea, and Pelican's Beak, Hat, and Neck. The areas of 13CO emission range within 2-10 pc2 with mass of (1-5) × 103 M ⊙ and line width of a few km s-1. The different line properties and signs of star-forming activity indicate they are in different evolutionary stages. Four filamentary structures with complicated velocity features are detected along the dark lane in LDN 935. Furthermore, a total of 611 molecular clumps within the 13CO tracing cloud are identified using the ClumpFind algorithm. The properties of the clumps suggest that most of the clumps are gravitationally bound and at an early stage of evolution with cold and dense molecular gas.

  7. Mathematical analysis of compressive/tensile molecular and nuclear structures

    NASA Astrophysics Data System (ADS)

    Wang, Dayu

    Mathematical analysis in chemistry is a fascinating and critical tool to explain experimental observations. In this dissertation, mathematical methods to present chemical bonding and other structures for many-particle systems are discussed at different levels (molecular, atomic, and nuclear). First, the tetrahedral geometry of single, double, or triple carbon-carbon bonds gives an unsatisfying demonstration of bond lengths, compared to experimental trends. To correct this, Platonic solids and Archimedean solids were evaluated as atoms in covalent carbon or nitrogen bond systems in order to find the best solids for geometric fitting. Pentagonal solids, e.g. the dodecahedron and icosidodecahedron, give the best fit with experimental bond lengths; an ideal pyramidal solid which models covalent bonds was also generated. Second, the macroscopic compression/tension architectural approach was applied to forces at the molecular level, considering atomic interactions as compressive (repulsive) and tensile (attractive) forces. Two particle interactions were considered, followed by a model of the dihydrogen molecule (H2; two protons and two electrons). Dihydrogen was evaluated as two different types of compression/tension structures: a coaxial spring model and a ring model. Using similar methods, covalent diatomic molecules (made up of C, N, O, or F) were evaluated. Finally, the compression/tension model was extended to the nuclear level, based on the observation that nuclei with certain numbers of protons/neutrons (magic numbers) have extra stability compared to other nucleon ratios. A hollow spherical model was developed that combines elements of the classic nuclear shell model and liquid drop model. Nuclear structure and the trend of the "island of stability" for the current and extended periodic table were studied.

  8. Roles of water in protein structure and function studied by molecular liquid theory.

    PubMed

    Imai, Takashi

    2009-01-01

    The roles of water in the structure and function of proteins have not been completely elucidated. Although molecular simulation has been widely used for the investigation of protein structure and function, it is not always useful for elucidating the roles of water because the effect of water ranges from atomic to thermodynamic level. The three-dimensional reference interaction site model (3D-RISM) theory, which is a statistical-mechanical theory of molecular liquids, can yield the solvation structure at the atomic level and calculate the thermodynamic quantities from the intermolecular potentials. In the last few years, the author and coworkers have succeeded in applying the 3D-RISM theory to protein aqueous solution systems and demonstrated that the theory is useful for investigating the roles of water. This article reviews some of the recent applications and findings, which are concerned with molecular recognition by protein, protein folding, and the partial molar volume of protein which is related to the pressure effect on protein.

  9. Molecular investigation of a dicentric 13;17 chromosome found in a 21-week gestation fetus with multiple congenital abnormalities.

    PubMed

    Cockwell, A E; Maloney, V K; Thomas, N S; Smith, E L; Gonda, P; Bass, P; Crolla, J A

    2006-01-01

    We report a 21-week gestation fetus terminated because of multiple congenital abnormalities seen on ultrasound scan, including ventriculomegaly, possible clefting of the hard palate, cervical hemivertebrae, micrognathia, abnormal heart, horseshoe kidney and a 2-vessel umbilical cord. On cytogenetic examination, the fetus was found to have a male karyotype with 45 chromosomes with a dicentric chromosome, which appeared to consist of the long arms of chromosomes 13 and 17. Molecular genetic investigations and fluorescence in situ hybridization (FISH) unexpectedly showed that the derivative chromosome contained two interstitial blocks of chromosome 17 short arm sequences, totalling approximately 7 Mb, between the two centromeres. This effectively made the fetus monosomic for approximately 15 Mb of 17p without the concurrent trisomy for another chromosome normally seen following malsegregation of reciprocal translocations. It also illustrates the complexity involved in the formation of some structurally abnormal chromosomes, which can only be resolved by detailed molecular investigations.

  10. Phase-transition properties of glycerol-dipalmitate lipid bilayers investigated using molecular dynamics simulation.

    PubMed

    Laner, Monika; Hünenberger, Philippe H

    2015-06-01

    The phase- and phase-transition properties of glycerol-dipalmitate (GDP) bilayer patches are investigated using molecular dynamics simulations. This permits to characterize the influence of introducing a second aliphatic lipid tail by comparison to previously reported simulations of glycerol-1-monopalmitate (GMP). To this purpose, a set of 67 simulations (up to 300ns duration) of 2×8×8GDP bilayer patches are performed, considering the two GDP isomers glycerol-1,3-dipalmitate (13GDP) and glycerol-1,2-dipalmitate (12GDP; racemic), two hydration levels (12GDP only), and temperatures in the range 250-370K. In agreement with experiment, the GDP simulations reveal an increase in the main transition temperature by about 25K relative to GMP, and the occurrence of non-bilayer phases at high temperatures (inverted-cylinder or stacked phases). Structurally, the GDP system tends to evidence a tighter packing of the chains, a reduced extent of tilting, increased order parameters and a reduced fluidity. These differences are easily interpreted in terms of two key changes in molecular properties when going from GMP to GDP: (i) the reduction of the headgroup polarity and hydration (from two free hydroxyl groups to a single one); (ii) the increase in the effective tail cross-section relative to the (hydrated) headgroup cross-section, conferring to GDP a particular wedge shape. These two effects contribute to the relative instability of the liquid-crystalline phase, the stability being recovered in nature when the diglyceride headgroup is functionalized by a bulky or/and polar substituent.

  11. Metal ion mediated molecularly imprinted polymer for selective capturing antibiotics containing beta-diketone structure.

    PubMed

    Qu, Shanshan; Wang, Xiaobo; Tong, Changlun; Wu, Jianmin

    2010-12-24

    A new molecularly imprinted polymer (MIP) targeting to quinolones (Qs) and tetracyclines (TCs) was synthesized using itaconic acid (ITA) and ciprofloxacin (CIP) as a functional monomer and template molecule, respectively. Factors affecting the overall performance of MIP were investigated, and the results showed that Fe(3+) ion play a vital role in the formation of MIP with high molecular imprinting effect. Meanwhile, the chelating ability of monomer, species of template molecule, as well as the molar ratio of monomer and template also contribute to the performance of the obtained MIP. Cyclic voltammetry verified that, with the participation of Fe(3+) ions, a ternary complex of ITA-Fe(3+)-CIP could be formed before polymerization. Compared with conventional MIP prepared from commonly used monomer, methacrylic acid (MAA), the new MIP show significantly enhanced molecular imprinting effect and higher capacity for specific adsorption of target compounds as revealed by static and dynamic binding experiments. The MIP was successfully used as solid-phase extraction (SPE) adsorbent for enriching a broad spectrum of antibiotics containing beta-diketone structure from surface water sample. HPLC detection showed that high recovery rate (78.6-113.6%) was found in these spiked antibiotics, whereas recovery rate for the non structurally related drugs, epinephrine (EP) and dopamine (DOPA), was very low (4.7-7.6%) on the MIP cartridges. The results demonstrate that the MIP prepared by the strategy proposed in this work, could specifically target to a series of structurally related antibiotics containing beta-diketone structure.

  12. Crystal and electronic structures of substituted halide perovskites based on density functional calculation and molecular dynamics

    NASA Astrophysics Data System (ADS)

    Takaba, Hiromitsu; Kimura, Shou; Alam, Md. Khorshed

    2017-03-01

    Durability of organo-lead halide perovskite are important issue for its practical application in a solar cells. In this study, using density functional theory (DFT) and molecular dynamics, we theoretically investigated a crystal structure, electronic structure, and ionic diffusivity of the partially substituted cubic MA0.5X0.5PbI3 (MA = CH3NH3+, X = NH4+ or (NH2)2CH+ or Cs+). Our calculation results indicate that a partial substitution of MA induces a lattice distortion, resulting in preventing MA or X from the diffusion between A sites in the perovskite. DFT calculations show that electronic structures of the investigated partially substituted perovskites were similar with that of MAPbI3, while their bandgaps slightly decrease compared to that of MAPbI3. Our results mean that partial substitution in halide perovskite is effective technique to suppress diffusion of intrinsic ions and tune the band gap.

  13. Theoretical investigation of energy storage in atomic and molecular systems: Metastable molecular fuels

    NASA Astrophysics Data System (ADS)

    Saxon, Roberta P.

    1990-12-01

    Ion-pair species bound by the coulomb attraction between a stable positive and stable negative ion have been investigated theoretically as candidate high-energy fuels that could form the basis of new propulsion schemes. Theoretical results for H3O, Li3H, and H3F are presented along with specific impulse, I(sub sp), predictions based on calculated energies. The ion-pair local minimum on the first excited potential surface of H3O is found to be unstable with respect to dissociation to H2 + H + O. The ion-pair state of H3F has a double degenerate imaginary frequency. These results support the general conclusion that ion-pair states based on the H3 cation will not be stable because back-charge transfer to H3(+) leads to neutral H3, which is unstable with respect to H2 + H. However, the ion-pair state of Li3H is found to be a local minimum with a very small barrier to conversion to the lower energy planar form. Even the lowest energy form of Li3H as an additive to hydrogen is predicted to provide a 16 percent improvement in I(sub sp).

  14. Structured illumination microscopy for vibrational molecular imaging (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Watanabe, Kozue; Palonpon, Almar F.; Smith, Nicholas I.; Chiu, Liang-da; Kasai, Atsushi; Hashimoto, Hitoshi; Kawata, Satoshi; Fujita, Katsumasa

    2016-09-01

    Raman microscopy is a powerful tool for analytical imaging. The wavelength shift of Raman scattering corresponds to molecular vibrational energy. Therefore, we can access rich chemical information, such as distribution, concentration, and chemical environment of sample molecules. Despite these strengths of Raman microscopy, the spatial resolution has been a limiting factor for many practical applications. In this study, we developed a large-area, high-resolution Raman microscope by utilizing structured illumination microscopy (SIM) to overcome the spatial resolution limit. A structured line-illumination (SLI) Raman microscope was constructed. The structured illumination is introduced along the line direction by the interference of two line-shaped beams. In SIM, the spatial frequency mixing between structured illumination and Raman scattering from the sample allows access to the high spatial frequency information beyond the conventional cut-off. As a result, the FWHM of 40-nm fluorescence particle images showed a clear resolution enhancement in the line direction: 366 nm in LI and 199 nm in SLI microscope. Using the developed microscope, we successfully demonstrated high-resolution Raman imaging of various kinds of specimens, such as few-layer graphene, graphite, mouse brain tissue, and polymer nanoparticles. The high resolution Raman images showed the capability to extract original spectral features from the mixed Raman spectra of a multi-component sample because of the enhanced spatial resolution, which is advantageous in observing complex spectral features. The Raman microscopy technique reported here enables us to see the detailed chemical structures of chemical, biological, and medical samples with a spatial resolution smaller than 200 nm.

  15. Molecular and structural insight into plasmodium falciparum RIO2 kinase.

    PubMed

    Chouhan, Devendra K; Sharon, Ashoke; Bal, Chandralata

    2013-02-01

    Among approximately 65 kinases of the malarial genome, RIO2 (right open reading frame) kinase belonging to the atypical class of kinase is unique because along with a kinase domain, it has a highly conserved N-terminal winged helix (wHTH) domain. The wHTH domain resembles the wing like domain found in DNA binding proteins and is situated near to the kinase domain. Ligand binding to this domain may reposition the kinase domain leading to inhibition of enzyme function and could be utilized as a novel allosteric site to design inhibitor. In the present study, we have generated a model of RIO2 kinase from Plasmodium falciparum utilizing multiple modeling, simulation approach. A novel putative DNA-binding site is identified for the first time in PfRIO2 kinase to understand the DNA binding events involving wHTH domain and flexible loop. Induced fit DNA docking followed by minimization, molecular dynamics simulation, energetic scoring and binding mode studies are used to reveal the structural basis of PfRIO2-ATP-DNA complex. Ser105 as a potential site of phosphorylation is revealed through the structural studies of ATP binding in PfRIO2. Overall the present study discloses the structural facets of unknown PfRIO2 complex and opens an avenue toward exploration of novel drug target.

  16. Transmission electron microscopy in molecular structural biology: A historical survey.

    PubMed

    Harris, J Robin

    2015-09-01

    In this personal, historic account of macromolecular transmission electron microscopy (TEM), published data from the 1940s through to recent times is surveyed, within the context of the remarkable progress that has been achieved during this time period. The evolution of present day molecular structural biology is described in relation to the associated biological disciplines. The contribution of numerous electron microscope pioneers to the development of the subject is discussed. The principal techniques for TEM specimen preparation, thin sectioning, metal shadowing, negative staining and plunge-freezing (vitrification) of thin aqueous samples are described, with a selection of published images to emphasise the virtues of each method. The development of digital image analysis and 3D reconstruction is described in detail as applied to electron crystallography and reconstructions from helical structures, 2D membrane crystals as well as single particle 3D reconstruction of icosahedral viruses and macromolecules. The on-going development of new software, algorithms and approaches is highlighted before specific examples of the historical progress of the structural biology of proteins and viruses are presented.

  17. Structural and molecular interrogation of intact biological systems

    PubMed Central

    Chung, Kwanghun; Wallace, Jenelle; Kim, Sung-Yon; Kalyanasundaram, Sandhiya; Andalman, Aaron S.; Davidson, Thomas J.; Mirzabekov, Julie J.; Zalocusky, Kelly A.; Mattis, Joanna; Denisin, Aleksandra K.; Pak, Sally; Bernstein, Hannah; Ramakrishnan, Charu; Grosenick, Logan; Gradinaru, Viviana; Deisseroth, Karl

    2014-01-01

    Obtaining high-resolution information from a complex system, while maintaining the global perspective needed to understand system function, represents a key challenge in biology. Here we address this challenge with a method (termed CLARITY) for the transformation of intact tissue into a nanoporous hydrogel-hybridized form (crosslinked to a three-dimensional network of hydrophilic polymers) that is fully assembled but optically transparent and macromolecule-permeable. Using mouse brains, we show intact-tissue imaging of long-range projections, local circuit wiring, cellular relationships, subcellular structures, protein complexes, nucleic acids and neurotransmitters. CLARITY also enables intact-tissue in situ hybridization, immunohistochemistry with multiple rounds of staining and de-staining in non-sectioned tissue, and antibody labelling throughout the intact adult mouse brain. Finally, we show that CLARITY enables fine structural analysis of clinical samples, including non-sectioned human tissue from a neuropsychiatric-disease setting, establishing a path for the transmutation of human tissue into a stable, intact and accessible form suitable for probing structural and molecular underpinnings of physiological function and disease. PMID:23575631

  18. Solving structures of protein complexes by molecular replacement with Phaser

    SciTech Connect

    McCoy, Airlie J.

    2007-01-01

    Four case studies in using maximum-likelihood molecular replacement, as implemented in the program Phaser, to solve structures of protein complexes are described. Molecular replacement (MR) generally becomes more difficult as the number of components in the asymmetric unit requiring separate MR models (i.e. the dimensionality of the search) increases. When the proportion of the total scattering contributed by each search component is small, the signal in the search for each component in isolation is weak or non-existent. Maximum-likelihood MR functions enable complex asymmetric units to be built up from individual components with a ‘tree search with pruning’ approach. This method, as implemented in the automated search procedure of the program Phaser, has been very successful in solving many previously intractable MR problems. However, there are a number of cases in which the automated search procedure of Phaser is suboptimal or encounters difficulties. These include cases where there are a large number of copies of the same component in the asymmetric unit or where the components of the asymmetric unit have greatly varying B factors. Two case studies are presented to illustrate how Phaser can be used to best advantage in the standard ‘automated MR’ mode and two case studies are used to show how to modify the automated search strategy for problematic cases.

  19. Molecular structure and dynamical properties of niosome bilayers with and without cholesterol incorporation: A molecular dynamics simulation study

    NASA Astrophysics Data System (ADS)

    Ritwiset, Aksornnarong; Krongsuk, Sriprajak; Johns, Jeffrey Roy

    2016-09-01

    Niosomes are non-ionic surfactant vesicles having a bilayer structure formed by self-assembly of hydrated surfactants, usually with cholesterol incorporation. Stability and mechanical properties of niosomes strongly depend on type of non-ionic surfactants and compositions used. In this study we present the structural and dynamical properties of niosome bilayers composed of sorbitan monostearate (Span60) with 0% and 50% cholesterol compositions which are investigated by using molecular dynamics simulations. The simulations reveal that niosome bilayer without cholesterol prefer to form in the gel phase with a higher order structure, while in the presence of cholesterol the bilayer exhibits more fluidity having a less ordered structure. The niosome bilayer with 50% cholesterol inclusion shows an increase of area per lipid (∼11%) and thickness (∼39%) compared with the niosome bilayer without cholesterol. The Span60 tailgroup orientation of the niosome bilayers without cholesterol exhibits more tilt (34.5o ± 0.5) than that of the bilayer with 50% cholesterol (15.4o ± 0.8). Additionally, our results show that the addition of cholesterol to the bilayer causes the higher in lateral and transverse diffusion, as well as an increase in the hydrogen bond number between Span60 and water. Such characteristics not only enhance the niosome stability but also increase the fluidity, which are necessary for the niosomal drug delivery.

  20. Guiding Molecular Motors with Nano-Imprinted Structures

    NASA Astrophysics Data System (ADS)

    Bunk, Richard; Carlberg, Patrick; Månsson, Alf; Nicholls, Ian A.; Omling, Pär; Sundberg, Mark; Tågerud, Sven; Montelius, Lars

    2005-05-01

    This work, for the first time, demonstrates that nano-imprinted samples, with 100 nm wide polymer lines, can act as guides for molecular motors consisting of motor proteins actin and myosin. The motor protein function was characterized using fluorescence microscopy and compared to actomyosin motility on non-structured nitrocellulose surfaces. Our results open for further use of the nano-imprint technique in the production of disposable chips for bio-nanotechnological applications and miniaturized biological test systems. We discuss how the nano-imprinted motor protein assay system may be optimized and also how it compares to previously tested assay systems involving low-resolution UV-lithography and low throughput but high-resolution electron beam lithography.

  1. The molecular structure of naphthalene by electron diffraction

    NASA Astrophysics Data System (ADS)

    Ketkar, S. N.; Fink, M.

    1981-11-01

    The molecular structure of gaseous naphthalene has been studied by electron diffraction at a nozzle tip temperature of about 25°C. The molecule has D 2h symmetry to within experimental error. The results for the distances ( ra), bond angle and r.m.s. amplitude ( l) are r(CH) = 1.092(6) Å, r(C 9C 1) = 1.422(2) Å, r(C 1C 2) = 1.381(2) Å, r(C 2C 3) = 1.417(4) Å, r(C 10C 9) = 1.412(8) Å, ∠C 10C 9C 1 = 119.5(3)°, ∠CCH = 119.9(7)°, l(CH) = 0.076(6) Å, l(CC) = 0.047(2) Å.

  2. Crystal and molecular structure of three biologically active nitroindazoles

    NASA Astrophysics Data System (ADS)

    Cabildo, Pilar; Claramunt, Rosa M.; López, Concepción; García, M. Ángeles; Pérez-Torralba, Marta; Pinilla, Elena; Torres, M. Rosario; Alkorta, Ibon; Elguero, José

    2011-01-01

    3-Bromo-1-methyl-7-nitro-1 H-indazole ( 1), 3-bromo-2-methyl-7-nitro-2 H-indazole ( 2) and 3,7-dinitro-1(2) H-indazole ( 3) have been synthesized and characterized by X-ray diffraction, 13C and 15N NMR spectroscopy in solution and in solid-state. The dihedral angles obtained in the crystal structures are in good agreement with the molecular parameters calculated using DFT B3LYP calculations employing the 6-311++G(d,p) basis set. Compounds 1 and 2 present intermolecular halogen bonds between the bromine and the oxygen atoms of the nitro group and in compound 3 inter- and intramolecular hydrogen bonding exists.

  3. A systematic investigation of the preparation and properties of composite carbon molecular sieves containing inorganic oxides

    NASA Technical Reports Server (NTRS)

    Foley, Henry C.

    1990-01-01

    The objective of this research is to define the methodology for the preparation and characterization of new carbon-based molecular sieves with composite structures. Carbon molecular sieves have found increasing application in the field of separation and purification of gases. These materials are relatively easy to prepare and their surfaces can be modified to some extent. It is expected that by combining inorganic oxides with the carbonaceous structure one can begin to design composite materials with a wider range of possible chemical and physical properties. In this way, the IOM-CMS materials may confer distinct advantages over pure carbon molecular sieves, not just for separation, but also for catalysis. The most recent results in the design and characterization of these IOM-CMS materials are reviewed and summarized. Directions for further research are also presented.

  4. Molecular interactions of organic molecules at the air/water interface investigated by sum frequency generation vibrational spectroscopy.

    PubMed

    Wang, Wenting; Ye, Shuji

    2017-02-08

    The molecular structure and dynamics of organic molecules at the aqueous interface have attracted a number of investigations owing to their importance and specific nature. However, there are relatively few studies on the direct characterization of the molecular interactions at the air/water interface because they are extremely difficult to measure in experiments. In this study, we use dibutyl ester molecules (R1CO2R2O2CR1) as a model of organic molecules, and investigate their molecular structure and interactions using sum frequency generation vibrational spectroscopy. We demonstrate that the molecular interactions can be estimated by measuring the intensity ratio of the symmetric stretching (ν1) and Fermi resonant bands (2ν2) of methyl groups. Here, dibutyl ester molecules are widely used as plasticizers in polymers to improve the properties of the plastics and polymers. It is found that the orientation angles of the tailed methyl groups at the air/water interface decrease from 34° to 19° when the chain length of R2 increases from 0 to 8. The total intermolecular interactions of the dibutyl ester molecules decrease as the chain length of R2 increases because the van der Waals interactions between the hydrocarbon chains increase, while the hydrogen bond interactions between the carbonyl group and water molecules decrease. Our study demonstrates the stability of ester-based plasticizers in polymers can be well predicted from the intensity ratio of the ν1 and 2ν2 bands of methyl group. Such an intensity ratio can be thus used as an effective vibrational optical ruler for characterizing molecular interactions between plasticizers and polymers.

  5. Application of molecular dynamics simulations for structural studies of carbon nanotubes.

    PubMed

    Bródka, A; Kołoczek, J; Burian, A

    2007-01-01

    Molecular dynamics studies based on the Brenner-Tersoff second-generation reactive empirical bond order potential and the Lennard-Jones carbon-carbon potential for intra- and inter-layer interactions have been performed for carbon nanotubes. These potentials reproduce reasonably the carbon-carbon distances and inter-layer spacing. The structure factors and the reduced radial distribution functions computed from the cartesian coordinates, resulting from energy minimisation and molecular dynamics simulations at 2 K and 300 K have been obtained for two models of two- and five-wall carbon nanotubes containing defects in the form of five and seven membered carbon rings. The results of computations have been compared with experimental data obtained from neutron and X-ray diffraction. The energy relaxation and the molecular dynamics simulations at 2 K and 300 K with appropriate values of the Debye-Waller factor lead practically to the same results which are in a good agreement with the experimental data indicating that molecular dynamics reproduce all structure features of the investigated carbon nanotubes together with thermal oscillations. Possible applications of this approach for other carbon nanotubes and related materials have been also discussed.

  6. Quantum chemical density functional theory studies on the molecular structure and vibrational spectra of mannitol.

    PubMed

    Moorthi, P P; Gunasekaran, S; Swaminathan, S; Ramkumaar, G R

    2015-02-25

    A collective experimental and theoretical study was conducted on the molecular structure and vibrational spectra of mannitol. The FT-IR and FT-Raman spectra of mannitol were recorded in the solid phase. The molecular geometry, vibrational frequencies, thermodynamic functions and atomic charges of mannitol in the ground state have been calculated by using the ab initio HF (Hartree-Fock) and density functional methods (B3LYP) invoking cc-pVDZ basis set. The complete vibrational assignments were performed on the basis of Total Energy Distribution (TED) of the vibrational modes. The UV absorption spectra of the title compound dissolved in water. Natural bond orbital analysis has been carried out to explain the charge transfer or delocalization of charge due to the intra-molecular interactions. The (1)H and (13)C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by GIAO methods. The first order hyperpolarizability (β0) of this novel molecular system and related properties (β, α0 and Δα) of mannitol are calculated using B3LYP/cc-pVDZ and HF/cc-pVDZ methods on the finite-field approach. By using TD-DFT calculation, electronic absorption spectra of the title compound have been predicted and a good agreement with experimental one is established. In addition, the molecular electrostatic potential (MEP) have been investigated using theoretical calculations, the calculated HOMO and LUMO energies shows that the charge transfer within the molecule.

  7. Molecular dynamics simulations on local structure and diffusion in liquid Ti x Al 1- x alloys

    NASA Astrophysics Data System (ADS)

    Xia, J. H.; Liu, C. S.; Cheng, Z. F.; Shi, D. P.

    2011-10-01

    The microscopic structure and dynamics of liquid Ti xAl 1- x alloys together with pure liquid Ti and Al metals were investigated by means of molecular dynamics simulations. This work gives the structural properties, including pair-correlation function, bond-angle distribution function, HA and Voronoi indices, and their composition dependence. The dynamical properties have also been studied. The calculated pair-correlation function, bond-angle distribution function, and HA and Voronoi indices suggest that the stoichiometric composition Ti 0.75Al 0.25 exhibits a different local structure order compared with other concentrations, which help us understand the appearance of the minimum diffusion coefficient at this composition. These results indicate that the mobility of atoms strongly depends on their atomic local structure.

  8. Molecular dynamics investigation of the effect of copper nanoparticle on the solid contact between friction surfaces

    NASA Astrophysics Data System (ADS)

    Hu, Chengzhi; Bai, Minli; Lv, Jizu; Liu, Hao; Li, Xiaojie

    2014-12-01

    This study investigated the effect of copper (Cu) nanoparticles on the solid contact between friction surfaces by applying a molecular dynamics method to reveal the mechanisms responsible for the favorable friction properties of nanoparticles. Two models were built, which were named model A (without Cu) and model B (with Cu), respectively. The differences in the mechanical properties between these two models were compared. The simulation results demonstrated that the improvement in friction properties by Cu nanoparticles was more obvious at low velocity than at high velocity. At low velocity, a Cu nano-film was formed on the friction surface, which accommodated the velocity gradient and plastic deformation. Due to the good lubrication effect of the nano-film, the plastic deformation, defect structures and friction force of model B were improved compared with model A. Under high velocity conditions, a transfer layer appeared adjacent to the interface in both models. Because of this, the friction forces of the two models decreased with increased velocity. The fluid mechanics theory was used to explain why the friction force in model B was lower than that in model A at high velocity. The effect of the load on friction properties was also analyzed and the results showed that the mechanisms of anti-wear and friction reduction by Cu nanoparticles under a low load were the same as those under a high load.

  9. Investigation of imprinting parameters and their recognition nature for quinine-molecularly imprinted polymers

    NASA Astrophysics Data System (ADS)

    He, Jian-feng; Zhu, Quan-hong; Deng, Qin-ying

    2007-08-01

    A series of molecularly imprinted polymers (MIPs) was prepared using quinine as the template molecules by bulk polymerization. The presence of monomer-template solution complexes in non-covalent MIPs systems has been verified by both fluorescence and UV-vis spectrometric detection. The influence of different synthetic conditions (porogen, functional monomer, cross-linkers, initiation methods, monomer-template ratio, etc.) on recognition properties of the polymers was investigated. Scatchard analysis revealed that two classes of binding sites were formed in the imprinted polymer. The corresponding dissociation constants were estimated to be 45.00 μmol l -1 and 1.42 mmol l -1, respectively, by utilizing a multi-site recognition model. The binding characteristics of the imprinted polymers were explored in various solvents using equilibrium binding experiments. In the organic media, results suggested that polar interactions (hydrogen bonding, ionic interactions, etc.) between acidic monomer/polymer and template molecules were mainly responsible for the recognition, whereas in aqueous media, hydrophobic interactions had a remarkable non-specific contribution to the overall binding. The specificity of MIP was evaluated by rebinding the other structurally similar compounds. The results indicated that the imprinted polymers exhibited an excellent stereo-selectivity toward quinine.

  10. Laboratory spectra of C60 and related molecular structures

    NASA Technical Reports Server (NTRS)

    Janca, J.; Solc, M.; Vetesnik, M.

    1994-01-01

    The electronic spectra of fullerene structures in high frequency discharge are studied in the plasma chemistry laboratory of the Faculty of Science of Masaryk University in Brno. The ultraviolet and visual spectra are investigated in order to be compared with the diffuse interstellar bands and interpreted within the theory of quantum mechanics. The preliminary results of the study are presented here in the form of a poster.

  11. Molecular structure of cyclic deoxydiadenylic acid at atomic resolution.

    PubMed

    Frederick, C A; Coll, M; van der Marel, G A; van Boom, J H; Wang, A H

    1988-11-01

    The molecular structure of a small cyclic nucleotide, cyclic deoxydiadenylic acid, has been determined by single-crystal X-ray diffraction analysis and refined to an R factor of 7.8% at 1.0-A resolution. The crystals are in the monoclinic space group C2 with unit cell dimensions of a = 24.511 (3) A, b = 24.785 (3) A, c = 13.743 (3) A, and beta = 94.02 (2) degrees. The structure was solved by the direct methods program SHELXS-86. There are 2 independent cyclic d(ApAp) molecules, 2 hydrated magnesium ions, and 26 water molecules in the asymmetric unit of the unit cell. The two cyclic d(ApAp) molecules have similar conformations within their 12-membered sugar-phosphate backbone ring, but they have quite different appearances due to the different glycosyl torsion angles that make one molecule more compact and the other extended and open. Three of the four deoxyribose rings are in the less common C3'-endo conformation. All four phosphate groups have their phosphodiester torsion angles alpha/zeta in the gauche(+)/gauche(+) conformation. One of the cyclic d(ApAp) molecules associates with another symmetry-related molecule to form a self-intercalated dimer that is a stable structure in solution, as observed in NMR studies. Many interesting intermolecular interactions, including base-base stacking, ribose-base stacking, base pairing, base-phosphate hydrogen bonding, and metal ion-phosphate interactions, are found in the crystal lattice. This structure may be relevant for understanding the conformational potentiality of an endogenous biological regulator of cellulose synthesis, cyclic (GpGp).

  12. The Latent Structure of Psychopathy in Youth: A Taxometric Investigation

    ERIC Educational Resources Information Center

    Vasey, Michael W.; Kotov, Roman; Frick, Paul J.; Loney, Bryan R.

    2005-01-01

    Using taxometric procedures, the latent structure of psychopathy was investigated in two studies of children and adolescents. Prior studies have identified a taxon (i.e., a natural category) associated with antisocial behavior in adults as well as children and adolescents. However, features of this taxon suggest that it is not psychopathy but…

  13. New AFM Techniques for Investigating Molecular Growth Mechanisms of Protein Crystals

    NASA Technical Reports Server (NTRS)

    Li, Huayu; Nadarajah, Arunan; Konnert, John H.; Pusey, Marc L.

    1998-01-01

    Atomic Force Microscopy (AFM) has emerged as a powerful technique for investigating protein crystal growth. Earlier AFM studies were among the first to demonstrate that these crystals grew by dislocation and 2D nucleation growth mechanisms [1]. These investigations were restricted to the micron range where only surface features, such as dislocation hillocks and 2D islands are visible. Most AFM instruments can scan at higher resolutions and have the potential to resolve individual protein molecules at nanometer ranges. Such scans are essential for determining the molecular packing arrangements on crystal faces and for probing the growth process at the molecular level. However, at this resolution the AFM tip influences the image produced, with the resulting image being a convolution of the tip shape and the surface morphology [2]. In most studies this problem is resolved by deconvoluting the image to obtain the true surface morphology. Although deconvolution routines work reasonably well for simple one- dimensional shapes, for complex surfaces this approach does not produce accurate results. In this study we devised a new approach which takes advantage of the precise molecular order of crystal surfaces, combined with the knowledge of individual molecular shapes from the crystallographic data of the protein and the AFM tip shape. This information is used to construct expected theoretical AFM images by convoluting the tip shape with the constructed crystal surface shape for a given surface packing arrangement. By comparing the images from actual AFM scans with the constructed ones for different possible surface packing arrangements, the correct packing arrangement can be conclusively determined. This approach was used in this study to determine the correct one from two possible packing arrangements on (I 10) faces of tetragonal lysozyme crystals. Another novel AFM technique was also devised to measure the dimension of individual growth units of the crystal faces

  14. Derivatives of Ergot-alkaloids: Molecular structure, physical properties, and structure-activity relationships

    NASA Astrophysics Data System (ADS)

    Ivanova, Bojidarka B.; Spiteller, Michael

    2012-09-01

    A comprehensive screening of fifteen functionalized Ergot-alkaloids, containing bulk aliphatic cyclic substituents at D-ring of the ergoline molecular skeleton was performed, studying their structure-active relationships and model interactions with α2A-adreno-, serotonin (5HT2A) and dopamine D3 (D3A) receptors. The accounted high affinity to the receptors binding loops and unusual bonding situations, joined with the molecular flexibility of the substituents and the presence of proton accepting/donating functional groups in the studied alkaloids, may contribute to further understanding the mechanisms of biological activity in vivo and in predicting their therapeutic potential in central nervous system (CNS), including those related the Schizophrenia. Since the presented correlation between the molecular structure and properties, was based on the comprehensively theoretical computational and experimental physical study on the successfully isolated derivatives, through using routine synthetic pathways in a relatively high yields, marked these derivatives as 'treasure' for further experimental and theoretical studied in areas such as: (a) pharmacological and clinical testing; (b) molecular-drugs design of novel psychoactive substances; (c) development of the analytical protocols for determination of Ergot-alkaloids through a functionalization of the ergoline-skeleton, and more.

  15. Investigating the Postmortem Molecular Biology of Cartilage and its Potential Forensic Applications.

    PubMed

    Bolton, Shawna N; Whitehead, Michael P; Dudhia, Jayesh; Baldwin, Timothy C; Sutton, Raul

    2015-07-01

    This study investigated the postmortem molecular changes that articular cartilage undergoes following burial. Fresh pig trotters were interred in 30-cm-deep graves at two distinct locations exhibiting dissimilar soil environments for up to 42 days. Extracts of the metacarpophalangeal (MCP) and metatarsophalangeal (MTP) joint cartilage from trotters disinterred weekly over 6 weeks were analyzed by Western blot against the monoclonal antibody 2-B-6 to assess aggrecan degradation. In both soil conditions, aggrecan degradation by-products of decreasing molecular size and complexity were observed up to 21 days postmortem. Degradation products were undetected after this time and coincided with MCP/MTP joint exposure to the soil environment. These results show that cartilage proteoglycans undergo an ordered molecular breakdown, the analysis of which may have forensic applications. This model may prove useful for use as a human model and for forensic investigations concerning crimes against animals and the mortality of endangered species.

  16. Structural and vibrational spectroscopy investigation of the 5-[(diphenyl) amino] isophthalic acid molecule

    NASA Astrophysics Data System (ADS)

    Kurt, M.; Şaş, E. Babur; Can, M.; Okur, S.; Icli, S.; Demic, S.

    2014-10-01

    The molecular structure and vibrations of 5-(diphenyl) amino] isophthalic acid (DPIFA) were investigated by different spectroscopic techniques (such as infrared and Raman). FT-IR, FT-Raman and dispersive Raman spectra were recorded in the solid phase. HOMO-LUMO 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. After optimizing the geometry of the molecule, vibration wavenumbers and fundamental vibrations wavenumbers were assigned on the basis of the potential energy distribution (PED) of the vibrational modes calculated with VEDA 4 program. The results of theoretical calculations for the spectra of the title compound were compared with the observed spectra.

  17. Structural and molecular basis of starch viscosity in hexaploid wheat.

    PubMed

    Ral, J-P; Cavanagh, C R; Larroque, O; Regina, A; Morell, M K

    2008-06-11

    Wheat starch is considered to have a low paste viscosity relative to other starches. Consequently, wheat starch is not preferred for many applications as compared to other high paste viscosity starches. Increasing the viscosity of wheat starch is expected to increase the functionality of a range of wheat flour-based products in which the texture is an important aspect of consumer acceptance (e.g., pasta, and instant and yellow alkaline noodles). To understand the molecular basis of starch viscosity, we have undertaken a comprehensive structural and rheological analysis of starches from a genetically diverse set of wheat genotypes, which revealed significant variation in starch traits including starch granule protein content, starch-associated lipid content and composition, phosphate content, and the structures of the amylose and amylopectin fractions. Statistical analysis highlighted the association between amylopectin chains of 18-25 glucose residues and starch pasting properties. Principal component analysis also identified an association between monoesterified phosphate and starch pasting properties in wheat despite the low starch-phosphate level in wheat as compared to tuber starches. We also found a strong negative correlation between the phosphate ester content and the starch content in flour. Previously observed associations between internal starch granule fatty acids and the swelling peak time and pasting temperature have been confirmed. This study has highlighted a range of parameters associated with increased starch viscosity that could be used in prebreeding/breeding programs to modify wheat starch pasting properties.

  18. Structural and electronic properties of Diisopropylammonium bromide molecular ferroelectric crystal

    NASA Astrophysics Data System (ADS)

    Alsaad, A.; Qattan, I. A.; Ahmad, A. A.; Al-Aqtash, N.; Sabirianov, R. F.

    2015-10-01

    We report the results of ab-initio calculations based on Generalized Gradient Approximation (GGA) and hybrid functional (HSE06) of electronic band structure, density of states and partial density of states to get a deep insight into structural and electronic properties of P21 ferroelectric phase of Diisopropylammonium Bromide molecular crystal (DIPAB). We found that the optical band gap of the polar phase of DIPAB is ∼ 5 eV confirming it as a good dielectric. Examination of the density of states and partial density of states reveal that the valence band maximum is mainly composed of bromine 4p orbitals and the conduction band minimum is dominated by carbon 2p, carbon 2s, and nitrogen 2s orbitals. A unique aspect of P21 ferroelectric phase is the permanent dipole within the material. We found that P21 DIPAB has a spontaneous polarization of 22.64 consistent with recent findings which make it good candidate for the creation of ferroelectric tunneling junctions (FTJs) which have the potential to be used as memory devices.

  19. Molecular Structures and Interactions in the Yeast Kinetochore

    PubMed Central

    Cho, U.-S.; Corbett, K.D.; Al-Bassam, J.; Bellizzi, J.J.; De Wulf, P.; Espelin, C.W.; Miranda, J.J.; Simons, K.; Wei, R.R.; Sorger, P.K.; Harrison, S.C.

    2011-01-01

    Kinetochores are the elaborate protein assemblies that attach chromosomes to spindle microtubules in mitosis and meiosis. The kinetochores of point-centromere yeast appear to represent an elementary module, which repeats a number of times in kinetochores assembled on regional centromeres. Structural analyses of the discrete protein subcomplexes that make up the budding-yeast kinetochore have begun to reveal principles of kinetochore architecture and to uncover molecular mechanisms underlying functions such as transmission of tension and establishment and maintenance of bipolar attachment. The centromeric DNA is probably wrapped into a compact organization, not only by a conserved, centromeric nucleosome, but also by interactions among various other DNA-bound kinetochore components. The rod-like, heterotetrameric Ndc80 complex, roughly 600 Å long, appears to extend from the DNA-proximal assembly to the plus end of a microtubule, to which one end of the complex is known to bind. Ongoing structural studies will clarify the roles of a number of other well-defined complexes. PMID:21467141

  20. Bonding and structure in dense multi-component molecular mixtures

    SciTech Connect

    Meyer, Edmund R.; Ticknor, Christopher; Bethkenhagen, Mandy; Hamel, Sebastien; Redmer, Ronald; Kress, Joel D.; Collins, Lee A.

    2015-10-30

    We have performed finite-temperature density functional theory molecular dynamics simulations on dense methane, ammonia, and water mixtures (CH4:NH3:H2O) for various compositions and temperatures (2000 K ≤ T ≤ 10000 K) that span a set of possible conditions in the interiors of ice-giant exoplanets. The equation-of-state, pair distribution functions, and bond autocorrelation functions (BACF) were used to probe the structure and dynamics of these complex fluids. In particular, an improvement to the choice of the cutoff in the BACF was developed that allowed analysis refinements for density and temperature effects. We note the relative changes in the nature of these systems engendered by variations in the concentration ratios. As a result, a basic tenet emerges from all these comparisons that varying the relative amounts of the three heavy components (C,N,O) can effect considerable changes in the nature of the fluid and may in turn have ramifications for the structure and composition of various planetary layers.

  1. Chitosan Molecular Structure as a Function of N-Acetylation

    SciTech Connect

    Franca, Eduardo F.; Freitas, Luiz C.; Lins, Roberto D.

    2011-07-01

    Molecular dynamics simulations have been carried out to characterize the structure and solubility of chitosan nanoparticle-like structures as a function of the deacetylation level (0, 40, 60, and 100%) and the spatial distribution of the N-acetyl groups in the particles. The polysaccharide chains of highly N-deacetylated particles where the N-acetyl groups are uniformly distributed present a high flexibility and preference for the relaxed two-fold helix and five-fold helix motifs. When these groups are confined to a given region of the particle, the chains adopt preferentially a two-fold helix with f and w values close to crystalline chitin. Nanoparticles with up to 40% acetylation are moderately soluble, forming stable aggregates when the N-acetyl groups are unevenly distributed. Systems with 60% or higher N-acetylation levels are insoluble and present similar degrees of swelling regardless the distribution of their N-acetyl groups. Overall particle solvation is highly affected by electrostatic forces resulting from the degree of acetylation. The water mobility and orientation around the polysaccharide chains affects the stability of the intramolecular O3- HO3(n) ... O5(n+ 1) hydrogen bond, which in turn controls particle aggregation.

  2. Bonding and structure in dense multi-component molecular mixtures

    DOE PAGES

    Meyer, Edmund R.; Ticknor, Christopher; Bethkenhagen, Mandy; ...

    2015-10-30

    We have performed finite-temperature density functional theory molecular dynamics simulations on dense methane, ammonia, and water mixtures (CH4:NH3:H2O) for various compositions and temperatures (2000 K ≤ T ≤ 10000 K) that span a set of possible conditions in the interiors of ice-giant exoplanets. The equation-of-state, pair distribution functions, and bond autocorrelation functions (BACF) were used to probe the structure and dynamics of these complex fluids. In particular, an improvement to the choice of the cutoff in the BACF was developed that allowed analysis refinements for density and temperature effects. We note the relative changes in the nature of these systemsmore » engendered by variations in the concentration ratios. As a result, a basic tenet emerges from all these comparisons that varying the relative amounts of the three heavy components (C,N,O) can effect considerable changes in the nature of the fluid and may in turn have ramifications for the structure and composition of various planetary layers.« less

  3. Molecular structure of tetramethylgermane from gas electron diffraction

    NASA Astrophysics Data System (ADS)

    Csákvári, Éva; Rozsondai, Béla; Hargittai, István

    1991-05-01

    The molecular structure of Ge(CH 3) 4 has been determined from gas-phase electron diffraction augmented by a normal coordinate analysis. Assuming tetrahedral symmetry for the germanium bond configuration, the following structural parameters are found: rg(GeC) = 1.958 ± 0.004 Å, rg(CH) = 1.111 ± 0.003 Å and ∠(GeCH) = 110.7 ± 0.2° ( R=4.0%). The methyl torsional barrier V 0 is estimated to be 1.3 kJ mol -1 on the basis of an effective angle of torsion 23.0 ± 1.5°, from the staggered form, yielded directly by the analysis. The GeC bond length of Ge(CH 3) 4 is the same, within experimental error, as that of Ge(C 6H 5) 4 and is in agreement with the prediction of a modified Schomaker-Stevenson relationship.

  4. Magnetic Field Structure in Molecular Clouds by Polarization Measurements

    NASA Astrophysics Data System (ADS)

    Chen, W. P.; Su, B. H.; Eswaraiah, C.; Pandey, A. K.; Wang, C. W.; Lai, S. P.; Tamura, M.; Sato, S.

    2015-03-01

    We report on a program to delineate magnetic field structure inside molecular clouds by optical and infrared polarization observations. An ordered magnetic field inside a dense cloud may efficiently align the spinning dust grains to cause a detectable level of optical and near-infrared polarization of otherwise unpolarized background starlight due to dichroic extinction. The near-infrared polarization data were taken by SIRPOL mounted on IRSF in SAAO. Here we present the SIRPOL results in RCW 57, for which the magnetic field is oriented along the cloud filaments, and in Carina Nebula, for which no intrinsic polarization is detected in the turbulent environment. We further describe TRIPOL, a compact and efficient polarimer to acquire polarized images simultaneously at g', r', and i' bands, which is recently developed at Nagoya University for adaption to small-aperture telescopes. We show how optical observations probe the translucent outer parts of a cloud, and when combining with infrared observations probing the dense parts, and with millimeter and submillimeter observations to sutdy the central embedded protostar, if there is one, would yield the magnetic field structure on different length scales in the star-formation process.

  5. Molecular clouds in the North American and Pelican Nebulae: structures

    SciTech Connect

    Zhang, Shaobo; Xu, Ye; Yang, Ji

    2014-03-01

    We present observations of a 4.25 deg{sup 2} area toward the North American and Pelican Nebulae in the J = 1-0 transitions of {sup 12}CO, {sup 13}CO, and C{sup 18}O. Three molecules show different emission areas with their own distinct structures. These different density tracers reveal several dense clouds with a surface density of over 500 M {sub ☉} pc{sup –2} and a mean H{sub 2} column density of 5.8, 3.4, and 11.9 × 10{sup 21} cm{sup –2} for {sup 12}CO, {sup 13}CO, and C{sup 18}O, respectively. We obtain a total mass of 5.4 × 10{sup 4} M {sub ☉} ({sup 12}CO), 2.0 × 10{sup 4} M {sub ☉} ({sup 13}CO), and 6.1 × 10{sup 3} M {sub ☉} (C{sup 18}O) in the complex. The distribution of excitation temperature shows two phases of gas: cold gas (∼10 K) spreads across the whole cloud; warm gas (>20 K) outlines the edge of the cloud heated by the W80 H II region. The kinetic structure of the cloud indicates an expanding shell surrounding the ionized gas produced by the H II region. There are six discernible regions in the cloud: the Gulf of Mexico, Caribbean Islands and Sea, and Pelican's Beak, Hat, and Neck. The areas of {sup 13}CO emission range within 2-10 pc{sup 2} with mass of (1-5) × 10{sup 3} M {sub ☉} and line width of a few km s{sup –1}. The different line properties and signs of star-forming activity indicate they are in different evolutionary stages. Four filamentary structures with complicated velocity features are detected along the dark lane in LDN 935. Furthermore, a total of 611 molecular clumps within the {sup 13}CO tracing cloud are identified using the ClumpFind algorithm. The properties of the clumps suggest that most of the clumps are gravitationally bound and at an early stage of evolution with cold and dense molecular gas.

  6. Investigation on a new scleroglucan/borax hydrogel: structure and drug release.

    PubMed

    Palleschi, Antonio; Coviello, Tommasina; Bocchinfuso, Gianfranco; Alhaique, Franco

    2006-09-28

    The aim of this work is to elucidate the structure of the new hydrogel prepared with scleroglucan (Sclg) and borax, suitable for drug delivery, applying theoretical approaches, and to explain its very peculiar swelling. The possible linkages with borate ions have been investigated and original parameters for the 4,6-gluco-borate moiety have been introduced. The structures relative to the Sclg chains in the presence of borax and the possible mutual arrangements among the triple helices are given. According to molecular dynamics simulations, the most probable assembly of the chains in the network is proposed, without and in the presence of three tested model drugs with different molecular dimensions: theophylline (TPH), Vitamin B12 (Vit. B12) and myoglobin (MGB). The hydrogel supramolecular structure, formed via chemical and physical linkages among the polysaccharidic chains, is built up taking into account the steric hindrance of the entrapped molecules. It is shown that molecular dynamics analysis can be a useful tool capable to shed some light on the anomalous swelling of the hydrogel, suitable for drug release, giving a new insight on the network structure and the release rate of the guest molecules.

  7. Partially collapsed cristobalite structure in the non molecular phase V in CO2

    PubMed Central

    Santoro, Mario; Gorelli, Federico A.; Bini, Roberto; Haines, Julien; Cambon, Olivier; Levelut, Claire; Montoya, Javier A.; Scandolo, Sandro

    2012-01-01

    Non molecular CO2 has been an important subject of study in high pressure physics and chemistry for the past decade opening up a unique area of carbon chemistry. The phase diagram of CO2 includes several non molecular phases above 30 GPa. Among these, the first discovered was CO2-V which appeared silica-like. Theoretical studies suggested that the structure of CO2-V is related to that of β-cristobalite with tetrahedral carbon coordination similar to silicon in SiO2, but reported experimental structural studies have been controversial. We have investigated CO2-V obtained from molecular CO2 at 40–50 GPa and T > 1500 K using synchrotron X-ray diffraction, optical spectroscopy, and computer simulations. The structure refined by the Rietveld method is a partially collapsed variant of SiO2 β-cristobalite, space group , in which the CO4 tetrahedra are tilted by 38.4° about the c-axis. The existence of CO4 tetrahedra (average O-C-O angle of 109.5°) is thus confirmed. The results add to the knowledge of carbon chemistry with mineral phases similar to SiO2 and potential implications for Earth and planetary interiors. PMID:22431594

  8. Investigations on Binding Pattern of Kinase Inhibitors with PPARγ: Molecular Docking, Molecular Dynamic Simulations, and Free Energy Calculation Studies

    PubMed Central

    Mazumder, Mohit; Das, Umashankar; Gourinath, Samudrala

    2017-01-01

    Peroxisome proliferator-activated receptor gamma (PPARγ) is a potential target for the treatment of several disorders. In view of several FDA approved kinase inhibitors, in the current study, we have investigated the interaction of selected kinase inhibitors with PPARγ using computational modeling, docking, and molecular dynamics simulations (MDS). The docked conformations and MDS studies suggest that the selected KIs interact with PPARγ in the ligand binding domain (LBD) with high positive predictive values. Hence, we have for the first time shown the plausible binding of KIs in the PPARγ ligand binding site. The results obtained from these in silico investigations warrant further evaluation of kinase inhibitors as PPARγ ligands in vitro and in vivo. PMID:28321247

  9. Synchrotron-based and globar-sourced molecular (micro)spectroscopy contributions to advances in new hulless barley (with structure alteration) research on molecular structure, molecular nutrition, and nutrient delivery.

    PubMed

    Yang, Ling; Yu, Peiqiang

    2017-01-02

    This paper aimed to review synchrotron-based and globar-sourced molecular infrared (micro)spectroscopy contributions to advances in new hulless barley (with structure alteration) research on molecular structure, molecular nutrition, and nutrient delivery in ruminants. It reviewed recent progress in barley varieties, its utilization for animal and human, inherent structure features and chemical make-up, evaluation and research methodology, breeding progress, rumen degradation, and intestinal digestion. The emphasis of this review was focused on the effect of alteration of carbohydrate traits of newly developed hulless barley on molecular structure changes and nutrient delivery and quantification of the relationship between molecular structure features and changes and truly absorbed nutrient supply to ruminants. This review provides an insight into how inherent structure changes on a molecular basis affect nutrient utilization and availability in ruminants.

  10. A Molecular Dynamics Study on the Local Structure of Liquid-Vapor Interface of Water and L-J Fluid

    NASA Astrophysics Data System (ADS)

    Kikugawa, Gota; Takagi, Shu; Matsumoto, Yoichiro; Ohara, Taku

    Microscopic structures of a liquid-vapor interface are investigated by molecular dynamics simulations. In the previous studies, we proposed the local and instantaneous definition of the interface at the molecular level, which can capture the thermal fluctuation of the interface. By using this definition, the layering structure of water molecules at the interface was found, in other words, the structurization phenomena of water at the molecular level were clearly seen as usually found at the liquid-solid interface. In this study, we investigated the liquid-vapor interface of Lenard-Jones fluid. The effect of well depth of L-J potential parameter on the structure was also studied. Although the structurization was found at the L-J fluid as well as water, characteristic of this structure was clearly different from that of water. We consider that the difference is ascribed to the intrinsic structure of liquid and associative trend of molecules. We also discussed the anisotropic characteristics of the molecular diffusion at the interface. The anisotropy of the translational diffusion at the interface of water is stronger than that of the L-J fluid.

  11. Investigation of Buckling Behavior of Composite Shell Structures with Cutouts

    NASA Astrophysics Data System (ADS)

    Arbelo, Mariano A.; Herrmann, Annemarie; Castro, Saullo G. P.; Khakimova, Regina; Zimmermann, Rolf; Degenhardt, Richard

    2015-12-01

    Thin-walled cylindrical composite shell structures can be applied in space applications, looking for lighter and cheaper launcher transport system. These structures are prone to buckling under axial compression and may exhibit sensitivity to geometrical imperfections. Today the design of such structures is based on NASA guidelines from the 1960's using a conservative lower bound curve generated from a database of experimental results. In this guideline the structural behavior of composite materials may not be appropriately considered since the imperfection sensitivity and the buckling load of shells made of such materials depend on the lay-up design. It is clear that with the evolution of the composite materials and fabrication processes this guideline must be updated and / or new design guidelines investigated. This need becomes even more relevant when cutouts are introduced to the structure, which are commonly necessary to account for access points and to provide clearance and attachment points for hydraulic and electric systems. Therefore, it is necessary to understand how a cutout with different dimensions affects the buckling load of a thin-walled cylindrical shell structure in combination with other initial geometric imperfections. In this context, this paper present some observations regarding the buckling load behavior vs. cutout size and radius over thickness ratio, of laminated composite curved panels and cylindrical shells, that could be applied in further recommendations, to allow identifying when the buckling of the structure is dominated by the presence of the cutout or by other initial imperfections.

  12. A reassessment of the molecular structure-functional relationships of the inhaled general anaesthetics.

    PubMed

    Halsey, M J

    1984-01-01

    The importance of structure-activity relationships in the inhaled general anaesthetic agents may have been underestimated in the elucidation of the central and peripheral mechanisms of general anaesthesia. It is true that there is no single spatial arrangement of atoms in a molecule that is essential for anaesthetic activity; the "anesthesiophore", as it was termed, is a myth. However, the chemical structure of a compound is directly related to its physical properties which in turn are one of the major determinants in the molecular mechanisms. Second, chemical structures are the major factors in the physical, chemical and biological stability of the anaesthetics; in particular the electron distributions, bond densities and net atomic charges determine the extent and mode of biotransformation. Some of the evidence for the importance of structure in the anesthetic "side effects" on circulation, respiration and neuroelectric irritability is presented. An example of the detailed structural-molecular studies is provided by the nuclear magnetic resonance investigations of anaesthetic conformational perturbations of haemoglobin which we have used as a model system for elucidating the ground rules of anaesthetic-protein interactions.

  13. STRUCTURAL BIOLOGY AND MOLECULAR MEDICINE RESEARCH PROGRAM (LSBMM)

    SciTech Connect

    Eisenberg, David S.

    2008-07-15

    The UCLA-DOE Institute of Genomics and Proteomics is an organized research unit of the University of California, sponsored by the Department of Energy through the mechanism of a Cooperative Agreement. Today the Institute consists of 10 Principal Investigators and 7 Associate Members, developing and applying technologies to promote the biological and environmental missions of the Department of Energy, and 5 Core Technology Centers to sustain this work. The focus is on understanding genomes, pathways and molecular machines in organisms of interest to DOE, with special emphasis on developing enabling technologies. Since it was founded in 1947, the UCLA-DOE Institute has adapted its mission to the research needs of DOE and its progenitor agencies as these research needs have changed. The Institute started as the AEC Laboratory of Nuclear Medicine, directed by Stafford Warren, who later became the founding Dean of the UCLA School of Medicine. In this sense, the entire UCLA medical center grew out of the precursor of our Institute. In 1963, the mission of the Institute was expanded into environmental studies by Director Ray Lunt. I became the third director in 1993, and in close consultation with David Galas and John Wooley of DOE, shifted the mission of the Institute towards genomics and proteomics. Since 1993, the Principal Investigators and Core Technology Centers are entirely new, and the Institute has separated from its former division concerned with PET imaging. The UCLA-DOE Institute shares the space of Boyer Hall with the Molecular Biology Institute, and assumes responsibility for the operation of the main core facilities. Fig. 1 gives the organizational chart of the Institute. Some of the benefits to the public of research carried out at the UCLA-DOE Institute include the following: The development of publicly accessible, web-based databases, including the Database of Protein Interactions, and the ProLinks database of genomicly inferred protein function linkages

  14. Prediction of molecular properties including symmetry from quantum-based molecular structural formulas, VIF.

    PubMed

    Alia, Joseph D; Vlaisavljevich, Bess; Abbot, Matthew; Warneke, Hallie; Mastin, Tyson

    2008-10-09

    Structurally covariant valency interaction formulas, VIF, gain chemical significance by comparison with resonance structures and natural bond orbital, NBO, bonding schemes and at the same time allow for additional prediction such as symmetry of ring systems and destabilization of electron pairs with respect to reference energy of -1/2 Eh. Comparisons are based on three chemical interpretations of Sinanoğlu's theory of structural covariance: (1) sets of structurally covariant quantum structural formulas, VIF, are interpreted as the same quantum operator represented in linearly related basis frames; (2) structurally covariant VIF pictures are interpreted as sets of molecular species with similar energy; and (3) the same VIF picture can be interpreted as different quantum operators, one-electron density or Hamiltonian; for example. According to these three interpretations, bond pair, lone pair, and free radical electrons understood in terms of a localized orbital representation are recognized as having energies above, below, or equal to a predetermined reference, frequently-1/2 Eh. The probable position of electron pairs and radical electrons is predicted. The selectivity of concerted ring closures in allyl anion and cation is described. Symmetries of conjugated ring systems are predicted according to their numbers of pi-electrons and spin-multiplicity. The pi-distortivity of benzene is predicted.The 3c/2e- H-bridging bonds in diborane are derived in a natural way according to the notion that the bridging bonds will have delocalizing interactions between them consistent with results of the NBO method. Key chemical bonding motifs are described using VIF. These include 2c/1e-, 2c/2e-, 2c/3e-, 3c/2e-, 3c/3e-,3c/4e-, 4n antiaromatic, and 4n+2 aromatic bonding systems. Some common organic functional groups are represented as VIF pictures and because these pictures can be interpreted simultaneously as one-electron density and Hamiltonian operators, the valence shell

  15. Pure and Modified Co-Poly(amide-12-b-ethylene oxide) Membranes for Gas Separation Studied by Molecular Investigations

    PubMed Central

    De Lorenzo, Luana; Tocci, Elena; Gugliuzza, Annarosa; Drioli, Enrico

    2012-01-01

    This paper deals with a theoretical investigation of gas transport properties in a pure and modified PEBAX block copolymer membrane with N-ethyl-o/p-toluene sulfonamide (KET) as additive molecules. Molecular dynamics simulations using COMPASS force field, Gusev-Suter Transition State Theory (TST) and Monte Carlo methods were used. Bulk models of PEBAX and PEBAX/KET in different copolymer/additive compositions were assembled and analyzed to evaluate gas permeability and morphology to characterize structure-performance relationships. PMID:24958285

  16. Investigating Structure and Dynamics of Atg8 Family Proteins.

    PubMed

    Weiergräber, O H; Schwarten, M; Strodel, B; Willbold, D

    2017-01-01

    Atg8 family members were the first autophagy-related proteins to be investigated in structural detail and continue to be among the best-understood molecules of the pathway. In this review, we will first provide a concise outline of the major methods that are being applied for structural characterization of these proteins and the complexes they are involved in. This includes a discussion of the strengths and limitations associated with each method, along with guidelines for successful adoption to a specific problem. Subsequently, we will present examples illustrating the application of these techniques, with a particular focus on the complementarity of information they provide.

  17. Terahertz Spectroscopy Applied for Investigation of Water Structure.

    PubMed

    Penkov, Nikita; Shvirst, Nikolay; Yashin, Valery; Fesenko, Eugeny; Fesenko, Eugeny

    2015-10-01

    The absorption spectra of liquid water and various aqueous solutions were analyzed in a terahertz frequency domain (from 6 to 200 cm(-1)) which characterize the collective dynamics of water molecules. Particular attention was paid to the relaxation process in the range of ∼6-80 cm(-1). The physical essence of this process on the molecular level is still unclear. We found that the amplitude of this relaxation process correlates with the degree of destruction of water structure. The obtained data allowed us to interpret this process as a monomolecular relaxation of free water molecules. On the basis of a consideration of the water polarization in the electric field, we proposed a method of calculation of the amount of free water molecules in solution.

  18. Acid-catalyzed furfurly alcohol polymerization : characterizations of molecular structure and thermodynamic properties.

    SciTech Connect

    Kim, T.; Assary, R. S.; Marshall, C. L.; Gosztola, D. J.; Curtiss, L. A.; Stair, P. C.

    2011-01-01

    The liquid-phase polymerization of furfuryl alcohol catalyzed by sulfuric acid catalysts and the identities of molecular intermediates were investigated by using Raman spectroscopy and density functional theory calculation. At room temperature, with an acid catalyst, a vigorous furfuryl alcohol polymerization reaction was observed, whereas even at a high water concentration, furfuryl alcohol was very stable in the absence of an acid catalyst. Theoretical studies were carried out to investigate the thermodynamics of protonation of furfuryl alcohol, initiation of polymerization, and formation of conjugated dienes and diketonic species by using the B3LYP level of theory. A strong aliphatic C=C band observed in the calculated and measured Raman spectra provided crucial evidence to understand the polymerization reaction mechanism. It is confirmed that the formation of a conjugated diene structure rather than a diketone structure is involved in the furfuryl alcohol polymerization reaction.

  19. Acid-catalyzed Furfuryl Alcohol Polymerization: Characterizations of Molecular Structure and Thermodynamic Properties

    SciTech Connect

    Kim, Taejin; Assary, Rajeev A.; Marshall, Christopher L.; Gosztola, David J.; Curtiss, Larry A.; Stair, Peter C.

    2011-07-22

    The liquid-phase polymerization of furfuryl alcohol catalyzed by sulfuric acid catalysts and the identities of molecular intermediates were investigated by using Raman spectroscopy and density functional theory calculation. At room temperature, with an acid catalyst, a vigorous furfuryl alcohol polymerization reaction was observed, whereas even at a high water concentration, furfuryl alcohol was very stable in the absence of an acid catalyst. Theoretical studies were carried out to investigate the thermodynamics of protonation of furfuryl alcohol, initiation of polymerization, and formation of conjugated dienes and diketonic species by using the B3LYP level of theory. A strong aliphatic C=C band observed in the calculated and measured Raman spectra provided crucial evidence to understand the polymerization reaction mechanism. It is confirmed that the formation of a conjugated diene structure rather than a diketone structure is involved in the furfuryl alcohol polymerization reaction.

  20. Gas-phase reactions in extraterrestrial environments: laboratory investigations by crossed molecular beams.

    PubMed

    Balucani, Nadia; Casavecchia, Piergiorgio

    2006-12-01

    We have investigated gas-phase reactions of N((2)D) with the most abundant hydrocarbons in the atmosphere of Titan by the crossed molecular beam technique. In all cases, molecular products containing a novel CN bond are formed, thus suggesting possible routes of formation of gas-phase nitriles in the atmosphere of Titan and primordial Earth. The same approach has been recently extended to the study of radical-radical reactions, such as the reaction of atomic oxygen with the CH(3) and C(3)H(5) radicals. Products other than those already considered in the modeling of planetary atmospheres and interstellar medium have been identified.

  1. Biodegradation of starch films: the roles of molecular and crystalline structure.

    PubMed

    Li, Ming; Witt, Torsten; Xie, Fengwei; Warren, Frederick J; Halley, Peter J; Gilbert, Robert G

    2015-05-20

    The influences of molecular, crystalline and granular structures on the biodegradability of compression-molded starch films were investigated. Fungal α-amylase was used as model degradation agent. The substrates comprised varied starch structures obtained by different degrees of acid hydrolysis, different granular sizes using size fractionation, and different degrees of crystallinity by aging for different times (up to 14 days). Two stages are identified for unretrograded films by fitting degradation data using first-order kinetics. Starch films containing larger molecules were degraded faster, but the rate coefficient was independent of the granule size. Retrograded films were degraded much slower than unretrograded ones, with a similar rate coefficient to that in the second stage of unretrograded films. Although initially the smaller molecules or the easily accessible starch chains on the amorphous film surface were degraded faster, the more ordered structure (resistant starch) formed from retrogradation, either before or during enzymatic degradation, strongly inhibits film biodegradation.

  2. Effects of temperature on Cu structure deposited on Si substrate: A molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Hidayat, Aulia Fikri; Rosikhin, Ahmad; Syuhada, Ibnu; Winata, Toto

    2016-02-01

    The deposition process of copper onto silicon substrate was studied by the molecular dynamics method. Tersoff, MEAM, and Morse potentials were used to describe the interaction of Si-Si Cu-Cu, and Cu-Si, respectively. Deposition process was performed using NVE ensemble and applying Berendsen thermostat with 0,2 fs timestep for 100 ps. The effect of substrate temperature on the percentage of amorphous structure, radial distribution function (RDF), and coordination number was investigated. The result was indicated that at 300 K, the percentage of amorphous structure was relatively lower compared to another temperature. First peaks of RDF at each temperature were found at radius 3,05 Å and were still relatively wide, indicating short-range order structure.

  3. Scanning tunneling microscope investigations of organic heterostructures prepared by a combination of self-assembly and molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Staub, R.; Toerker, M.; Fritz, T.; Schmitz-Hübsch, T.; Sellam, F.; Leo, K.

    2000-01-01

    We report the realization of organic-organic heteroepitaxy by combining liquid-phase self-assembly with ultrahigh vacuum (UHV) gas-phase molecular beam epitaxy. As a model system, we have used self-assembled monolayers (SAMs) prepared by exposing an Au(111)-mica substrate to a dilute solution of decanethiol in ethanol, with subsequent evaporation of 3,4,9,10-perylene-tetracarboxylic-dianhydride (PTCDA) dye molecules. The well-known (3×3)R30° superstructure of almost upright standing molecules after chemisorption is replaced by the 11.5×3 (33.2 Å) pin-stripe phase with flat lying molecules when the samples are annealed in UHV and coverage decreases. The deposition of PTCDA induces reordering and displacement in the decanethiol SAM. Additional to the 33.2 Å periodicity, the previously reported 22 Å thiol stripe phase can be observed by scanning tunneling microscopy. Several PTCDA structures are observed: single and double rows of PTCDA that grow along decanethiol stripes on top of the flat-lying alkane chain groups, as well as densely packed PTCDA monolayer domains embedded into the thiol layer. These exhibit the well-known herringbone structure or a novel square lattice structure. We have also investigated thicker PTCDA islands and observed molecular resolution for a thickness of several monolayers. The structure of the three-dimensional islands can be identified as the α bulk modification.

  4. Theoretical studies on the molecular structure, conformational preferences, topological and vibrational analysis of allicin

    NASA Astrophysics Data System (ADS)

    Durlak, Piotr; Berski, Sławomir; Latajka, Zdzisław

    2016-01-01

    The molecular structure, conformational preferences, topological and vibrational analysis of allicin has been investigated at two different approaches. Calculations have been carried out on static (DFT and MP2) levels with an assortment of Dunning's basis sets and dynamic CPMD simulations. In this both case within the isolated molecule approximation. The results point out that at least twenty different conformers coexist on the PES as confirmed by the flexible character of this molecule. The topological analysis of ELF showed very similar nature of the Ssbnd S and Ssbnd O bonds. The infrared spectrum has been calculated, and a comparative vibrational analysis has been performed.

  5. Molecular structures and π π interactions of some flavonoids and biflavonoids

    NASA Astrophysics Data System (ADS)

    Jiang, Ren-Wang; Ye, Wen-Cai; Woo, Ka-Yan; Du, Jiang; Che, Chun-Tao; But, Paul Pui-Hay; Mak, Thomas C. W.

    2002-12-01

    The molecular structures of two flavones, wogonin ( 1) and mikanin ( 2), and two biflavonoids, cupressuflavone ( 3) and neochamaejasmin A ( 4), were determined by single-crystal X-ray analysis. The intermolecular π-π interactions in 1- 4 and the flavanones alpinetin ( 5) and naringenin ( 6) were investigated. Compounds 1- 4 feature offset face-to-face intermolecular π-π interactions with centroid-centroid distances ranging from 3.70 to 3.81 Å and displacement angles ranging from 2.7 to 9.9°.

  6. Structural and dynamical properties of hot dense matter by a Thomas-Fermi-Dirac molecular dynamics

    NASA Astrophysics Data System (ADS)

    Lambert, F.; Clérouin, J.; Mazevet, S.

    2006-09-01

    We use a model combining, in a consistent way, orbital-free density functional theory (OF-DFT) and molecular dynamics (MD), to compute the thermodynamical, structural and dynamical properties of Fe and Au plasmas at conditions relevant to astrophysics and inertial confinement fusion (ICF). The newly developed parallel numerical scheme presented here allows to propagate hundreds of particles and to obtain accurate transport properties. This allows us to investigate the validity of the commonly used one-component plasma (OCP) model in predicting the pair correlation, the diffusion and viscosity coefficients for these two high-temperature high-density plasmas.

  7. Quantitative structure-property relationships for predicting Henry's law constant from molecular structure.

    PubMed

    Dearden, John C; Schüürmann, Gerrit

    2003-08-01

    Various models are available for the prediction of Henry's law constant (H) or the air-water partition coefficient (Kaw), its dimensionless counterpart. Incremental methods are based on structural features such as atom types, bond types, and local structural environments; other regression models employ physicochemical properties, structural descriptors such as connectivity indices, and descriptors reflecting the electronic structure. There are also methods to calculate H from the ratio of vapor pressure (p(v)) and water solubility (S(w)) that in turn can be estimated from molecular structure, and quantum chemical continuum-solvation models to predict H via the solvation-free energy (deltaG(s)). This review is confined to methods that calculate H from molecular structure without experimental information and covers more than 40 methods published in the last 26 years. For a subset of eight incremental methods and four continuum-solvation models, a comparative analysis of their prediction performance is made using a test set of 700 compounds that includes a significant number of more complex and drug-like chemical structures. The results reveal substantial differences in the application range as well as in the prediction capability, a general decrease in prediction performance with decreasing H, and surprisingly large individual prediction errors, which are particularly striking for some quantum chemical schemes. The overall best-performing method appears to be the bond contribution method as implemented in the HENRYWIN software package, yielding a predictive squared correlation coefficient (q2) of 0.87 and a standard error of 1.03 log units for the test set.

  8. Electronic excitation transport in photosynthesis and crystal and molecular structures of porphyrin compounds

    SciTech Connect

    Yang, Shumei.

    1991-04-22

    The excitation energy transfer in three photosynthetic organism samples, Bacteriochlorophyll a-protein from Prosthecochloris aestuarii, and enriched photosystem I particles from spinach chloroplasts, have been investigated by pump-probe ultrafast spectroscopy. The isotropic photobleaching profiles were best described by two exponential decay components in one Bchl a-protein complex, and three exponential decay components in another. The experimental results from the three samples show that nonrandom chromophore orientations exist and Sauer's pebble mosaic'' model is an appropriate one for excitation transfer in these samples. The polarized pump-probe transients have been analyzed in terms of an exciton hopping model that incorporates the known geometry of the Bchl a-protein. The crystal and molecular structures of four metalloporphyrins have been determined by X-ray diffraction and molecular mechanics. 207 refs., 44 figs., 15 tabs.

  9. Crystal and molecular structure of the antimalarial agent enpiroline.

    PubMed Central

    Karle, J M; Karle, I L

    1989-01-01

    To identify common spatial and structural features of amino alcohol antimalarial agents with the eventual goal of designing more effective drugs and a better understanding of the mechanism of action of this class of antimalarial agents, the three-dimensional crystal and molecular structure of enpiroline, a new antimalarial agent active against chloroquine-resistant Plasmodium falciparum, was determined by X-ray crystallography and compared with the crystal structures of the cinchona alkaloids and of the new antimalarial agent WR 194,965. The aromatic rings of the phenyl-pyridine ring system of enpiroline are twisted from each other by approximately 18 degrees. The intramolecular aliphatic N-O distance in enpiroline was 2.80 A (1 A = 0.1 nm), which is close to the N-O distance found in the antimalarial cinchona alkaloids. Enpiroline contains both an intramolecular hydrogen bond between the aliphatic nitrogen and oxygen atoms and an intermolecular hydrogen bond between the aliphatic nitrogen and oxygen atoms of two neighboring molecules. One enantiomer of enpiroline superimposed best with quinine, and the other enantiomer of enpiroline superimposed best with quinidine, suggesting that both enantiomers of enpiroline possess antimalarial activity. Since a common feature of the crystal structures of the amino alcohol antimalarial agents is the formation of intermolecular hydrogen bonds, the common spatial direction of hydrogen bond formation indicates the potential ability of these antimalarial agents to bind to a common receptor site. The crystallographic parameters were as follows: C19H18F6N5O; Mr = 404.3; symmetry of unit cell, monoclinic; space group, P2(1)/a; parameters of unit cell---a = 9.454 +/- 0.004 A, b = 18.908 +/- 0.008 A, c = 10.300 +/- 0.004 A, and beta = 96.55 +/- 0.03 degrees: V (volume of unit cell) = 1829.2 A3; Z (number of molecules per unit cell) = 4; Dchi (calculated density) = 1.46 g cm-3; source of radiation, CuK alpha (lambda = 1.54178 A); mu

  10. FTIR of binary lead borate glass: Structural investigation

    NASA Astrophysics Data System (ADS)

    Othman, H. A.; Elkholy, H. S.; Hager, I. Z.

    2016-02-01

    The glass samples were prepared according to the following formula: (100-x) B2O3 - x PbO, where x = 20-80 mol% by melt quenching method. The density of the prepared samples was measured and molar volume was calculated. IR spectra were measured for the prepared samples to investigate the glass structure. The IR spectra were deconvoluted using curves of Gaussian shape at approximately the same frequencies. The deconvoluted data were used to study the effect of PbO content on all the structural borate groups. Some structural parameters such as density, packing density, bond length and bond force constant were theoretically calculated and were compared to the obtained experimental results. Deviation between the experimental and theoretically calculated parameters reflects the dual role of PbO content on the network of borate glass.

  11. Investigation of Vibrational Energy Transfer in Connected Structures

    NASA Technical Reports Server (NTRS)

    Hwang, C.; Pi, W. S.

    1973-01-01

    The results are reported of an analytical and experimental investigation on the vibrational energy transfer between connected substructures under random excitation. In the analytical area, the basic foundation and assumptions of the statistical energy analysis (SEA) method, a major tool in random response analysis of structures, were examined and reviewed. A new SEA formulation based on the strong coupling condition of the substructures was carried out and presented. Also presented were the results of vibration energy transfer study based on the wave equations applied to connected structures. In the experimental phase, three simple structural models were fabricated and tested. Additional tests were performed on selected substructures which formed parts of the test models. The test results were presented and evaluated against the analytical data.

  12. 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.

  13. 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.

  14. 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

  15. Pervasive small-scale structure in molecular clouds

    NASA Technical Reports Server (NTRS)

    Martin, B.; Lada, E.

    1986-01-01

    An unbiased CO survey of molecular cloud cores was completed, and the profiles were analyzed within the context of a model for emission from clumpy clouds. It was found that all sources observed contain a significant amount of structure that is not resolved with our 2.3-arcmin beam, and that the parameters which describe the degree of clumping span a remarkably narrow range of the possible values. We studied two separate samples of cloud cores: a large sample of warm cores from the Massachusetts-Stony Brook 12CO survey of the first galactic quadrant, and a sample of cool cores in the Taurus dark clouds chosen primarily on the basis of H2CO emission. We observed all sources in the 1-0 transition of 12CO and 13CO with the 5-m telescope of the Millimeter Wave Observatory. The 12CO/13CO ratios can be explained if there is unresolved structure giving rise to significant variations of opacity across the beam. Our model cloud consists of a large number of identical clumps distributed randomly in the beam. These clumps have velocity widths v small compared to the width of the observed profile, which is determined by the relative motion of the clumps. The entire cloud is isothermal and in local thermodynamic equilibrium. With these assumptions the intensity and linewidth ratios depend on three parameters: the abundance ratio; the peak 13CO opacity through a single clump, tau(0); and the average number of clumps on a line of sight N. Small tau(0) and large N correspond to the microturbulent limit, which is indistinguishable from a uniform gas distribution. In the other extreme, large tau(0) and snall N, at a given velocity at most one clump contributes to the profile on each line of sight. A figure is presented which shows the model parameters which reproduce the measured intensity and linewidth ratios for the sample of warm cores, assuming an abundance ratio of 75.

  16. Unraveling the Molecular Mechanisms Underlying the Nasopharyngeal Bacterial Community Structure

    PubMed Central

    de Steenhuijsen Piters, Wouter A. A.

    2016-01-01

    ABSTRACT The upper respiratory tract is colonized by a diverse array of commensal bacteria that harbor potential pathogens, such as Streptococcus pneumoniae. As long as the local microbial ecosystem—also called “microbiome”—is in balance, these potentially pathogenic bacterial residents cause no harm to the host. However, similar to macrobiological ecosystems, when the bacterial community structure gets perturbed, potential pathogens can overtake the niche and cause mild to severe infections. Recent studies using next-generation sequencing show that S. pneumoniae, as well as other potential pathogens, might be kept at bay by certain commensal bacteria, including Corynebacterium and Dolosigranulum spp. Bomar and colleagues are the first to explore a specific biological mechanism contributing to the antagonistic interaction between Corynebacterium accolens and S. pneumoniae in vitro [L. Bomar, S. D. Brugger, B. H. Yost, S. S. Davies, K. P. Lemon, mBio 7(1):e01725-15, 2016, doi:10.1128/mBio.01725-15]. The authors comprehensively show that C. accolens is capable of hydrolyzing host triacylglycerols into free fatty acids, which display antipneumococcal properties, suggesting that these bacteria might contribute to the containment of pneumococcus. This work exemplifies how molecular epidemiological findings can lay the foundation for mechanistic studies to elucidate the host-microbe and microbial interspecies interactions underlying the bacterial community structure. Next, translation of these results to an in vivo setting seems necessary to unveil the magnitude and importance of the observed effect in its natural, polymicrobial setting. PMID:26838716

  17. Development of Laser Desorption Imaging Mass Spectrometry Methods to Investigate the Molecular Composition of Latent Fingermarks

    NASA Astrophysics Data System (ADS)

    Lauzon, Nidia; Dufresne, Martin; Chauhan, Vinita; Chaurand, Pierre

    2015-06-01

    For a century, fingermark analysis has been one of the most important and common methods in forensic investigations. Modern chemical analysis technologies have added the potential to determine the molecular composition of fingermarks and possibly identify chemicals a suspect may have come into contact with. Improvements in analytical detection of the molecular composition of fingermarks is therefore of great importance. In this regard, matrix-assisted laser desorption ionization (MALDI) and laser desorption ionization (LDI) imaging mass spectrometry (IMS) have proven to be useful technologies for fingermark analysis. In these analyses, the choice of ionizing agent and its mode of deposition are critical steps for the identification of molecular markers. Here we propose two novel and complementary IMS approaches for endogenous and exogenous substance detection in fingermarks: sublimation of 2-mercaptobenzothiazol (2-MBT) matrix and silver sputtering.

  18. Comparative Investigation of Normal Modes and Molecular Dynamics of Hepatitis C NS5B Protein

    NASA Astrophysics Data System (ADS)

    Asafi, M. S.; Yildirim, A.; Tekpinar, M.

    2016-04-01

    Understanding dynamics of proteins has many practical implications in terms of finding a cure for many protein related diseases. Normal mode analysis and molecular dynamics methods are widely used physics-based computational methods for investigating dynamics of proteins. In this work, we studied dynamics of Hepatitis C NS5B protein with molecular dynamics and normal mode analysis. Principal components obtained from a 100 nanoseconds molecular dynamics simulation show good overlaps with normal modes calculated with a coarse-grained elastic network model. Coarse-grained normal mode analysis takes at least an order of magnitude shorter time. Encouraged by this good overlaps and short computation times, we analyzed further low frequency normal modes of Hepatitis C NS5B. Motion directions and average spatial fluctuations have been analyzed in detail. Finally, biological implications of these motions in drug design efforts against Hepatitis C infections have been elaborated.

  19. Fluorescence fluctuation microscopy: a diversified arsenal of methods to investigate molecular dynamics inside cells.

    PubMed

    Weidemann, Thomas; Mücksch, Jonas; Schwille, Petra

    2014-10-01

    Fluorescence microscopy provides insight into the subcellular organization of biological functions. However, images are snap shots averaging over a highly dynamic molecular system. Fluorescence fluctuation microscopy, employing similar detection technology, encompasses a powerful arsenal of analysis tools that investigate the molecular heterogeneity in space and time. Analyzing signal fluctuations from small ensembles (several hundred particles) reveals their concentration, the stoichiometry, the stochastic motion, as well as superimposed signatures of the environment such as spatial confinement and binding events. Thus, fluctuation analysis provides access to dynamic molecular properties that can be used to build physical models of cellular processes. In the last decade these methods experienced a remarkable diversification, which we revisit here with a particular focus on live cell applications.

  20. Automatic molecular structure perception for the universal force field.

    PubMed

    Artemova, Svetlana; Jaillet, Léonard; Redon, Stephane

    2016-05-15

    The Universal Force Field (UFF) is a classical force field applicable to almost all atom types of the periodic table. Such a flexibility makes this force field a potential good candidate for simulations involving a large spectrum of systems and, indeed, UFF has been applied to various families of molecules. Unfortunately, initializing UFF, that is, performing molecular structure perception to determine which parameters should be used to compute the UFF energy and forces, appears to be a difficult problem. Although many perception methods exist, they mostly focus on organic molecules, and are thus not well-adapted to the diversity of systems potentially considered with UFF. In this article, we propose an automatic perception method for initializing UFF that includes the identification of the system's connectivity, the assignment of bond orders as well as UFF atom types. This perception scheme is proposed as a self-contained UFF implementation integrated in a new module for the SAMSON software platform for computational nanoscience (http://www.samson-connect.net). We validate both the automatic perception method and the UFF implementation on a series of benchmarks.

  1. Modeling Carbon and Hydrocarbon Molecular Structures in EZTB

    NASA Technical Reports Server (NTRS)

    Lee, Seungwon; vonAllmen, Paul

    2007-01-01

    A software module that models the electronic and mechanical aspects of hydrocarbon molecules and carbon molecular structures on the basis of first principles has been written for incorporation into, and execution within, the Easy (Modular) Tight-Binding (EZTB) software infrastructure, which is summarized briefly in the immediately preceding article. Of particular interest, this module can model carbon crystals and nanotubes characterized by various coordinates and containing defects, without need to adjust parameters of the physical model. The module has been used to study the changes in electronic properties of carbon nanotubes, caused by bending of the nanotubes, for potential utility as the basis of a nonvolatile, electriccharge- free memory devices. For example, in one application of the module, it was found that an initially 50-nmlong carbon, (10,10)-chirality nanotube, which is a metallic conductor when straight, becomes a semiconductor with an energy gap of .3 meV when bent to a lateral displacement of 4 nm at the middle.

  2. Death Associated Protein Kinases: Molecular Structure and Brain Injury

    PubMed Central

    Nair, Syam; Hagberg, Henrik; Krishnamurthy, Rajanikant; Thornton, Claire; Mallard, Carina

    2013-01-01

    Perinatal brain damage underlies an important share of motor and neurodevelopmental disabilities, such as cerebral palsy, cognitive impairment, visual dysfunction and epilepsy. Clinical, epidemiological, and experimental studies have revealed that factors such as inflammation, excitotoxicity and oxidative stress contribute considerably to both white and grey matter injury in the immature brain. A member of the death associated protein kinase (DAPk) family, DAPk1, has been implicated in cerebral ischemic damage, whereby DAPk1 potentiates NMDA receptor-mediated excitotoxicity through interaction with the NR2BR subunit. DAPk1 also mediate a range of activities from autophagy, membrane blebbing and DNA fragmentation ultimately leading to cell death. DAPk mRNA levels are particularly highly expressed in the developing brain and thus, we hypothesize that DAPk1 may play a role in perinatal brain injury. In addition to reviewing current knowledge, we present new aspects of the molecular structure of DAPk domains, and relate these findings to interacting partners of DAPk1, DAPk-regulation in NMDA-induced cerebral injury and novel approaches to blocking the injurious effects of DAPk1. PMID:23880846

  3. Death associated protein kinases: molecular structure and brain injury.

    PubMed

    Nair, Syam; Hagberg, Henrik; Krishnamurthy, Rajanikant; Thornton, Claire; Mallard, Carina

    2013-07-04

    Perinatal brain damage underlies an important share of motor and neurodevelopmental disabilities, such as cerebral palsy, cognitive impairment, visual dysfunction and epilepsy. Clinical, epidemiological, and experimental studies have revealed that factors such as inflammation, excitotoxicity and oxidative stress contribute considerably to both white and grey matter injury in the immature brain. A member of the death associated protein kinase (DAPk) family, DAPk1, has been implicated in cerebral ischemic damage, whereby DAPk1 potentiates NMDA receptor-mediated excitotoxicity through interaction with the NR2BR subunit. DAPk1 also mediate a range of activities from autophagy, membrane blebbing and DNA fragmentation ultimately leading to cell death. DAPk mRNA levels are particularly highly expressed in the developing brain and thus, we hypothesize that DAPk1 may play a role in perinatal brain injury. In addition to reviewing current knowledge, we present new aspects of the molecular structure of DAPk domains, and relate these findings to interacting partners of DAPk1, DAPk-regulation in NMDA-induced cerebral injury and novel approaches to blocking the injurious effects of DAPk1.

  4. Molecular structures of fructans from Agave tequilana Weber var. azul.

    PubMed

    Lopez, Mercedes G; Mancilla-Margalli, Norma A; Mendoza-Diaz, Guillermo

    2003-12-31

    Agave plants utilize crassulacean acid metabolism (CAM) for CO(2) fixation. Fructans are the principal photosynthetic products generated by agave plants. These carbohydrates are fructose-bound polymers frequently with a single glucose moiety. Agave tequilana Weber var. azul is an economically important CAM species not only because it is the sole plant allowed for tequila production but because it is a potential source of prebiotics. Because of the large amounts of carbohydrates in A. tequilana, in this study the molecular structures of its fructans were determined by fructan derivatization for linkage analysis coupled with gas chromatography-mass spectrometry (GC-MS), nuclear magnetic resonance (NMR), and matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF-MS). Fructans were extracted from 8-year-old A. tequilana plants. The linkage types present in fructans from A. tequilana were determined by permethylation followed by reductive cleavage, acetylation, and finally GC-MS analysis. Analysis of the degree of polymerization (DP) estimated by (1)H NMR integration and (13)C NMR and confirmed by MALDI-TOF-MS showed a wide DP ranging from 3 to 29 units. All of the analyses performed demonstrated that fructans from A. tequilana consist of a complex mixture of fructooligosaccharides containing principally beta(2 --> 1) linkages, but also beta(2 --> 6) and branch moieties were observed. Finally, it can be stated that fructans from A. tequilana Weber var. azul are not an inulin type as previously thought.

  5. Structural basis for the antifolding activity of a molecular chaperone

    PubMed Central

    Huang, Chengdong; Rossi, Paolo; Saio, Tomohide; Kalodimos, Charalampos G.

    2016-01-01

    Molecular chaperones act on non-native proteins in the cell to prevent their aggregation, premature folding or misfolding. Different chaperones often exert distinct effects, such as acceleration or delay of folding, on client proteins via mechanisms that are poorly understood. Here we report the solution structure of SecB, a chaperone that exhibits strong antifolding activity, in complex with alkaline phosphatase (PhoA) and maltose binding protein (MBP) captured in their unfolded states. SecB uses long hydrophobic grooves that run around its disk-like shape to recognize and bind to multiple hydrophobic segments across the length of the non-native proteins. The multivalent binding mode results in proteins wrapping around SecB. This unique complex architecture alters the kinetics of protein binding to SecB and confers strong antifolding activity on the chaperone. The data show how the different architectures of chaperones result in distinct binding modes with non-native proteins that ultimately define the activity of the chaperone. PMID:27501151

  6. Characterization of Chitin and Chitosan Molecular Structure in Aqueous Solution

    SciTech Connect

    Franca, Eduardo D.; Lins, Roberto D.; Freitas, Luiz C.; Straatsma, t. P.

    2008-11-08

    Molecular dynamics simulations have been used to characterize the structure of chitin and chitosan fibers in aqueous solutions. Chitin fibers, whether isolated or in the form of a β-chitin nanoparticle, adopt the so-called 2-fold helix with Φ and φ values similar to its crystalline state. In solution, the intramolecular hydrogen bond HO3(n)•••O5(n+1) responsible for the 2-fold helical motif is stabilized by hydrogen bonds with water molecules in a well-defined orientation. On the other hand, chitosan can adopt five distinct helical motifs and its conformational equilibrium is highly dependent on pH. The hydrogen bond pattern and solvation around the O3 atom of insoluble chitosan (basic pH) are nearly identical to these quantities in chitin. Our findings suggest that the solubility and conformation of these polysaccharides are related to the stability of the intrachain HO3(n)•••O5(n+1) hydrogen bond, which is affect by the water exchange around the O3-HO3 hydroxyl group.

  7. The Influence of Molecular Cooling in Pregalactic Structure Formation

    NASA Astrophysics Data System (ADS)

    Stancil, P. C.; Abel, T.; Lepp, S.; Dalgarno, A.

    1999-12-01

    The detailed chemistry and cooling in collapsing primordial clouds will be presented for total baryonic densities up to 106 cm-3. The model consists of 160 reactions of 23 species including H2, HD, HeH+, and LiH, and accounts for 8 different cooling and heating mechanisms. The hydrodynamic evolution of the gas is modeled under the assumptions of free-fall, isothermal, and isobaric collapse as well as for the central regions of 105 M⊙ objects in hierarchical scenarios. The latter being drawn from three-dimensional cosmological hydrodynamical simulations. The dominant processes in the reaction network are identified and a minimal model that accurately predicts the full chemistry will be presented. It is found that radiative cooling due to collisional excitation of HD can lower the temperature in a primordial cloud below that reachable through H2 cooling alone. Further, the temperature evolution is influenced by the choice of the adopted H2 radiative cooling function. Implications for globular cluster and primordial star formation, as well as structure formation on small scales and the importance of molecular cooling in general will be discussed. The work of P.C.S. was supported by the DoE ORNL LDRD Seed Money Fund. T.A. acknowledges support from NSF Grant ASC--9318185. The work of S.L. and A.D. was supported by NSF Cooperative Agreement OSR-9353227 and Astronomical Sciences Grant AST-93-01099, respectively.

  8. Structural basis for the antifolding activity of a molecular chaperone

    NASA Astrophysics Data System (ADS)

    Huang, Chengdong; Rossi, Paolo; Saio, Tomohide; Kalodimos, Charalampos G.

    2016-09-01

    Molecular chaperones act on non-native proteins in the cell to prevent their aggregation, premature folding or misfolding. Different chaperones often exert distinct effects, such as acceleration or delay of folding, on client proteins via mechanisms that are poorly understood. Here we report the solution structure of SecB, a chaperone that exhibits strong antifolding activity, in complex with alkaline phosphatase and maltose-binding protein captured in their unfolded states. SecB uses long hydrophobic grooves that run around its disk-like shape to recognize and bind to multiple hydrophobic segments across the length of non-native proteins. The multivalent binding mode results in proteins wrapping around SecB. This unique complex architecture alters the kinetics of protein binding to SecB and confers strong antifolding activity on the chaperone. The data show how the different architectures of chaperones result in distinct binding modes with non-native proteins that ultimately define the activity of the chaperone.

  9. Weak links between fast mobility and local structure in molecular and atomic liquids

    SciTech Connect

    Bernini, S.; Puosi, F.; Leporini, D.

    2015-03-28

    We investigate by molecular-dynamics simulations, the fast mobility—the rattling amplitude of the particles temporarily trapped by the cage of the neighbors—in mildly supercooled states of dense molecular (linear trimers) and atomic (binary mixtures) liquids. The mixture particles interact by the Lennard-Jones potential. The non-bonded particles of the molecular system are coupled by the more general Mie potential with variable repulsive and attractive exponents in a range which is a characteristic of small n-alkanes and n-alcohols. Possible links between the fast mobility and the geometry of the cage (size and shape) are searched. The correlations on a per-particle basis are rather weak. Instead, if one groups either the particles in fast-mobility subsets or the cages in geometric subsets, the increase of the fast mobility with both the size and the asphericity of the cage is revealed. The observed correlations are weak and differ in states with equal relaxation time. Local forces between a tagged particle and the first-neighbour shell do not correlate with the fast mobility in the molecular liquid. It is concluded that the cage geometry alone is unable to provide a microscopic interpretation of the known, universal link between the fast mobility and the slow structural relaxation. We suggest that the particle fast dynamics is affected by regions beyond the first neighbours, thus supporting the presence of collective, extended fast modes.

  10. Resolving Intra- and Inter-Molecular Structure with Non-Contact Atomic Force Microscopy.

    PubMed

    Jarvis, Samuel Paul

    2015-08-21

    A major challenge in molecular investigations at surfaces has been to image individual molecules, and the assemblies they form, with single-bond resolution. Scanning probe microscopy, with its exceptionally high resolution, is ideally suited to this goal. With the introduction of methods exploiting molecularly-terminated tips, where the apex of the probe is, for example, terminated with a single CO, Xe or H2 molecule, scanning probe methods can now achieve higher resolution than ever before. In this review, some of the landmark results related to attaining intramolecular resolution with non-contact atomic force microscopy (NC-AFM) are summarised before focussing on recent reports probing molecular assemblies where apparent intermolecular features have been observed. Several groups have now highlighted the critical role that flexure in the tip-sample junction plays in producing the exceptionally sharp images of both intra- and apparent inter-molecular structure. In the latter case, the features have been identified as imaging artefacts, rather than real intermolecular bonds. This review discusses the potential for NC-AFM to provide exceptional resolution of supramolecular assemblies stabilised via a variety of intermolecular forces and highlights the potential challenges and pitfalls involved in interpreting bonding interactions.

  11. Resolving Intra- and Inter-Molecular Structure with Non-Contact Atomic Force Microscopy

    PubMed Central

    Jarvis, Samuel Paul

    2015-01-01

    A major challenge in molecular investigations at surfaces has been to image individual molecules, and the assemblies they form, with single-bond resolution. Scanning probe microscopy, with its exceptionally high resolution, is ideally suited to this goal. With the introduction of methods exploiting molecularly-terminated tips, where the apex of the probe is, for example, terminated with a single CO, Xe or H2 molecule, scanning probe methods can now achieve higher resolution than ever before. In this review, some of the landmark results related to attaining intramolecular resolution with non-contact atomic force microscopy (NC-AFM) are summarised before focussing on recent reports probing molecular assemblies where apparent intermolecular features have been observed. Several groups have now highlighted the critical role that flexure in the tip-sample junction plays in producing the exceptionally sharp images of both intra- and apparent inter-molecular structure. In the latter case, the features have been identified as imaging artefacts, rather than real intermolecular bonds. This review discusses the potential for NC-AFM to provide exceptional resolution of supramolecular assemblies stabilised via a variety of intermolecular forces and highlights the potential challenges and pitfalls involved in interpreting bonding interactions. PMID:26307976

  12. Animal Hairs as Water-stimulated Shape Memory Materials: Mechanism and Structural Networks in Molecular Assemblies

    NASA Astrophysics Data System (ADS)

    Xiao, Xueliang; Hu, Jinlian

    2016-05-01

    Animal hairs consisting of α-keratin biopolymers existing broadly in nature may be responsive to water for recovery to the innate shape from their fixed deformation, thus possess smart behavior, namely shape memory effect (SME). In this article, three typical animal hair fibers were first time investigated for their water-stimulated SME, and therefrom to identify the corresponding net-points and switches in their molecular and morphological structures. Experimentally, the SME manifested a good stability of high shape fixation ratio and reasonable recovery rate after many cycles of deformation programming under water stimulation. The effects of hydration on hair lateral size, recovery kinetics, dynamic mechanical behaviors and structural components (crystal, disulfide and hydrogen bonds) were then systematically studied. SME mechanisms were explored based on the variations of structural components in molecular assemblies of such smart fibers. A hybrid structural network model with single-switch and twin-net-points was thereafter proposed to interpret the water-stimulated shape memory mechanism of animal hairs. This original work is expected to provide inspiration for exploring other natural materials to reveal their smart functions and natural laws in animals including human as well as making more remarkable synthetic smart materials.

  13. Animal Hairs as Water-stimulated Shape Memory Materials: Mechanism and Structural Networks in Molecular Assemblies

    PubMed Central

    Xiao, Xueliang; Hu, Jinlian

    2016-01-01

    Animal hairs consisting of α-keratin biopolymers existing broadly in nature may be responsive to water for recovery to the innate shape from their fixed deformation, thus possess smart behavior, namely shape memory effect (SME). In this article, three typical animal hair fibers were first time investigated for their water-stimulated SME, and therefrom to identify the corresponding net-points and switches in their molecular and morphological structures. Experimentally, the SME manifested a good stability of high shape fixation ratio and reasonable recovery rate after many cycles of deformation programming under water stimulation. The effects of hydration on hair lateral size, recovery kinetics, dynamic mechanical behaviors and structural components (crystal, disulfide and hydrogen bonds) were then systematically studied. SME mechanisms were explored based on the variations of structural components in molecular assemblies of such smart fibers. A hybrid structural network model with single-switch and twin-net-points was thereafter proposed to interpret the water-stimulated shape memory mechanism of animal hairs. This original work is expected to provide inspiration for exploring other natural materials to reveal their smart functions and natural laws in animals including human as well as making more remarkable synthetic smart materials. PMID:27230823

  14. Polyoxometalate-based layered structures for charge transport control in molecular devices.

    PubMed

    Douvas, Antonios M; Makarona, Eleni; Glezos, Nikos; Argitis, Panagiotis; Mielczarski, Jerzy A; Mielczarski, Ela

    2008-04-01

    Hybrid organic-inorganic films consisted of molecular layers of a Keggin-structure polyoxometalate (POM: 12-tungstophosphoric acid, H(3)PW(12)O(40)) and 1,12-diaminododecane (DD) on 3-aminopropyl triethoxysilane (APTES)-modified silicon surface, fabricated via the layer-by-layer (LBL) self-assembly method are evaluated as molecular materials for electronic devices. The effect of the fabrication process parameters, including primarily compositions of deposition solutions, on the structural characteristics of the POM-based multilayers was studied extensively with a combination of spectroscopic methods (UV, FTIR, and XPS). Well-characterized POM-based films (both single-layers and multilayers) in a controlled and reproducible way were obtained. The conduction mechanisms in single-layered and multilayered structures were elucidated by the electrical characterization of the produced films supported by the appropriate theoretical analysis. Fowler-Nordheim (FN) tunneling and percolation mechanisms were encountered in good correlation with the structural characteristics of the films encouraging further investigation on the use of these materials in electronic and, in particular, in memory devices.

  15. Linking molecular models with ion mobility experiments. Illustration with a rigid nucleic acid structure

    PubMed Central

    D'Atri, Valentina; Porrini, Massimiliano; Rosu, Frédéric; Gabelica, Valérie

    2015-01-01

    Ion mobility spectrometry experiments allow the mass spectrometrist to determine an ion's rotationally averaged collision cross section ΩEXP. Molecular modelling is used to visualize what ion three-dimensional structure(s) is(are) compatible with the experiment. The collision cross sections of candidate molecular models have to be calculated, and the resulting ΩCALC are compared with the experimental data. Researchers who want to apply this strategy to a new type of molecule face many questions: (1) What experimental error is associated with ΩEXP determination, and how to estimate it (in particular when using a calibration for traveling wave ion guides)? (2) How to generate plausible 3D models in the gas phase? (3) Different collision cross section calculation models exist, which have been developed for other analytes than mine. Which one(s) can I apply to my systems? To apply ion mobility spectrometry to nucleic acid structural characterization, we explored each of these questions using a rigid structure which we know is preserved in the gas phase: the tetramolecular G-quadruplex [dTGGGGT]4, and we will present these detailed investigation in this tutorial. © 2015 The Authors. Journal of Mass Spectrometry published by John Wiley & Sons Ltd. PMID:26259654

  16. Effect of repeated cycled crystallization on digestibility and molecular structure of glutinous Bora rice starch.

    PubMed

    Borah, Pallab Kumar; Deka, Sankar Chandra; Duary, Raj Kumar

    2017-05-15

    The effects of repeated cycled crystallization on the digestibility and molecular structure of glutinous Bora rice starch were investigated. Temperature cycle 4/45°C; cycle duration 5d; time interval of cycles 24h; and starch to water ratio 1:2 were found to be optimum for SDS (slow digestible starch) product development. The SDS content increased from 18.01±2.11% to 82.81±2.34%. An increase in the resistance to digestion, crystallinity, molecular weight, polydispersity and molecular order was observed in the optimal SDS product. Notably, the FT-IR peak at 947cm(-1) and XRD peaks at 2θ≈13° and 20° in the optimal SDS product indicated the formation of V-type complexes even without the presence of co-polymers. Birefringence studies showed a loss of typical Maltese cross in the SDS product and revealed a reorientation of crystalline structures within starch granules, suggestive of imperfect crystallite development.

  17. 2D IR spectra of cyanide in water investigated by molecular dynamics simulations

    USGS Publications Warehouse

    Lee, Myung Won; Carr, Joshua K.; Göllner, Michael; Hamm, Peter; Meuwly, Markus

    2013-01-01

    Using classical molecular dynamics simulations, the 2D infrared (IR) spectroscopy of CN− solvated in D2O is investigated. Depending on the force field parametrizations, most of which are based on multipolar interactions for the CN− molecule, the frequency-frequency correlation function and observables computed from it differ. Most notably, models based on multipoles for CN− and TIP3P for water yield quantitatively correct results when compared with experiments. Furthermore, the recent finding that T 1 times are sensitive to the van der Waals ranges on the CN− is confirmed in the present study. For the linear IR spectrum, the best model reproduces the full widths at half maximum almost quantitatively (13.0 cm−1 vs. 14.9 cm−1) if the rotational contribution to the linewidth is included. Without the rotational contribution, the lines are too narrow by about a factor of two, which agrees with Raman and IR experiments. The computed and experimental tilt angles (or nodal slopes) α as a function of the 2D IR waiting time compare favorably with the measured ones and the frequency fluctuation correlation function is invariably found to contain three time scales: a sub-ps, 1 ps, and one on the 10-ps time scale. These time scales are discussed in terms of the structural dynamics of the surrounding solvent and it is found that the longest time scale (≈10 ps) most likely corresponds to solvent exchange between the first and second solvation shell, in agreement with interpretations from nuclear magnetic resonance measurements.

  18. Investigation of alternative organizational structures for a digitized platoon

    NASA Astrophysics Data System (ADS)

    Bossi, Linda L. M.; Tack, David W.; Angel, Harold A.; Vilhena, Paul G. S.; Frim, John

    2006-05-01

    To evaluate the effect of digitization on platoon effectiveness and investigate the suitability of different platoon structures, a twelve-day field trial was undertaken with a Company of light infantry at Fort Benning, Georgia. Test missions were conducted in both day and night conditions, in wooded and urban terrain environments, in each of three organizational structures, with and without digitization. The three different organizational structures included our current in-service 8-man Section, a 13-man USMC squad, and a distributed model comprising six four-man teams. Results of this study confirmed that the effectiveness of a dismounted platoon is significantly enhanced by the use of select digital enhancements in the areas of navigation, situation awareness, communications, and command. During night operations, digitally-enabled capabilities were the difference between mission success and failure. None of the organizational structures tested proved to be universally better than the others at optimizing the benefits of digitally-enhanced capabilities, although each had their strengths and weaknesses. However, considerable insights were gained in the organizational structure issues of distributed small unit command and control, swarming formation tactics, and the tactics, techniques, and procedures necessary to employ small units effectively in a NCW environment.

  19. Latest Results from the Mars Pathfinder Atmospheric Structure Investigation

    NASA Technical Reports Server (NTRS)

    Magalhaes, J. A.

    1999-01-01

    The Mars Pathfinder Atmospheric Structure Investigation (ASI) obtained information on Martian atmospheric structure from three science accelerometers, which measured the deceleration of the probe at all levels in the atmosphere. Entry, descent, and landing occurred within 850 km of the Viking 1 landing site and somewhat later in northern summer. Pathfinder entered at 3 AME Local Mars Time (LMT), which provided the first opportunity to study Mars' nighttime atmospheric structure, and Viking 1 entered at 4:15 PME LMT. Magalhaes et al and Schofield et al have previously reported on the analysis of accelerometer measurements from the entry phase, which ended at about 8.5 km. The derived temperature profile extends from 140 km altitude down to 8.9 km, with a vertical resolution ranging from 250 meters to 50 meters, respectively. Here we report on a refined analysis of the Pathfinder entry phase ASIE data in which the effects of the small angular motions of the entry vehicle have been removed, thus enabling a search for small amplitude and small vertical wavelength structures. In addition, we will report on the atmospheric structure at altitudes below 8 km which is being derived from the accelerometer data acquired during the parachute descent phase. Additional information is contained in the original extended abstract.

  20. How Molecular Structure Affects Mechanical Properties of an Advanced Polymer

    NASA Technical Reports Server (NTRS)

    Nicholson, Lee M.; Whitley, Karen S.; Gates, Thomas S.; Hinkley, Jeffrey A.

    2000-01-01

    density was performed over a range of temperatures below the glass transition temperature. The physical characterization, elastic properties and notched tensile strength all as a function of molecular weight and test temperature were determined. For the uncrosslinked SI material, it was shown that notched tensile strength is a strong function of both temperature and molecular weight, whereas stiffness is only a strong function of temperature. For the crosslinked PETI-SI material, it was shown that the effect of crosslinking significantly enhances the mechanical performance of the low molecular weight material; comparable to that exhibited by the high molecular weight material.

  1. Quantitative structure-hydrophobicity relationships of molecular fragments and beyond.

    PubMed

    Zou, Jian-Wei; Huang, Meilan; Huang, Jian-Xiang; Hu, Gui-Xiang; Jiang, Yong-Jun

    2016-03-01

    Quantitative structure-property relationship (QSPR) models were firstly established for the hydrophobic substituent constant (πX) using the theoretical descriptors derived solely from electrostatic potentials (EPSs) at the substituent atoms. The descriptors introduced are found to be related to hydrogen-bond basicity, hydrogen-bond acidity, cavity, or dipolarity/polarizability terms in linear solvation energy relationship, which endows the models good interpretability. The predictive capabilities of the models constructed were also verified by rigorous Monte Carlo cross-validation. Then, eight groups of meta- or para-disubstituted benzenes and one group of substituted pyridines were investigated. QSPR models for individual systems were achieved with the ESP-derived descriptors. Additionally, two QSPR models were also established for Rekker's fragment constants (foct), which is a secondary-treatment quantity and reflects average contribution of the fragment to logP. It has been demonstrated that the descriptors derived from ESPs at the fragments, can be well used to quantitatively express the relationship between fragment structures and their hydrophobic properties, regardless of the attached parent structure or the valence state. Finally, the relations of Hammett σ constant and ESP quantities were explored. It implies that σ and π, which are essential in classic QSAR and represent different type of contributions to biological activities, are also complementary in interaction site.

  2. Structure and dynamics of Ni2+ in liquid ammonia: A quantum mechanical charge field molecular dynamics (QMCF-MD) study

    NASA Astrophysics Data System (ADS)

    Saleh, Muhammad; Hofer, Thomas S.

    2016-09-01

    An investigation of structural and dynamical properties of Ni2+ in liquid ammonia has been carried out via Quantum Mechanical Charge Field Molecular Dynamics. By extending the quantum mechanical region to include first and second solvation shell, a more realistic representation of the system was achieved yielding improved results on present computational facilities. The structural results obtained from the 16 ps trajectory agree well with experimental investigations for various nitrogen-containing Ni2+ systems. Detailed analysis of mean residence time and vibrational properties highlights a rather flexible structure of the first and second shells compared to Ni2+ in aqueous solution.

  3. A coupled Car-Parrinello molecular dynamics and EXAFS data analysis investigation of aqueous Co(2+).

    PubMed

    Spezia, Riccardo; Duvail, Magali; Vitorge, Pierre; Cartailler, Thierry; Tortajada, Jeanine; Chillemi, Giovanni; D'Angelo, Paola; Gaigeot, Marie-Pierre

    2006-12-07

    We have studied the microscopic solvation structure of Co(2+) in liquid water by means of density functional theory (DFT)-based Car-Parrinello molecular dynamics (CPMD) simulations and extended X-ray absorption fine structure (EXAFS) data analysis. The effect of the number of explicit water molecules in the simulation box on the first and second hydration shell structures has been considered. Classical molecular dynamics simulations, using an effective two-body potential for Co(2+)-water interactions, were also performed to show box size effects in a larger range. We have found that the number of explicit solvent molecules has a marginal role on the first solvation shell structural parameters, whereas larger boxes may be necessary to provide a better description of the second solvation shell. Car-Parrinello simulations were determined to provide a reliable description of structural and dynamical properties of Co(2+) in liquid water. In particular, they seem to describe both the first and second hydration shells correctly. The EXAFS signal was reconstructed from Car-Parrinello simulations. Good agreement between the theoretical and experimental signals was observed, thus strengthening the microscopic picture of the Co(2+) solvation properties obtained using first-principle simulations.

  4. Computational molecular technology towards macroscopic chemical phenomena-molecular control of complex chemical reactions, stereospecificity and aggregate structures

    SciTech Connect

    Nagaoka, Masataka

    2015-12-31

    A new efficient hybrid Monte Carlo (MC)/molecular dynamics (MD) reaction method with a rare event-driving mechanism is introduced as a practical ‘atomistic’ molecular simulation of large-scale chemically reactive systems. Starting its demonstrative application to the racemization reaction of (R)-2-chlorobutane in N,N-dimethylformamide solution, several other applications are shown from the practical viewpoint of molecular controlling of complex chemical reactions, stereochemistry and aggregate structures. Finally, I would like to mention the future applications of the hybrid MC/MD reaction method.

  5. Computational molecular technology towards macroscopic chemical phenomena-molecular control of complex chemical reactions, stereospecificity and aggregate structures

    NASA Astrophysics Data System (ADS)

    Nagaoka, Masataka

    2015-12-01

    A new efficient hybrid Monte Carlo (MC)/molecular dynamics (MD) reaction method with a rare event-driving mechanism is introduced as a practical `atomistic' molecular simulation of large-scale chemically reactive systems. Starting its demonstrative application to the racemization reaction of (R)-2-chlorobutane in N,N-dimethylformamide solution, several other applications are shown from the practical viewpoint of molecular controlling of complex chemical reactions, stereochemistry and aggregate structures. Finally, I would like to mention the future applications of the hybrid MC/MD reaction method.

  6. Molecular and Electronic Structure of Cyclic Trinuclear Gold(I) Carbeniate Complexes: Insights for Structure/Luminescence/Conductivity Relationships

    SciTech Connect

    McDougaldJr, Roy N; Chilukuri, Bhaskar; Jia, Huiping; Perez, Michael R; Rabaa, Hassan; Wang, Xiaoping; Nesterov, Vladimir; Cundari, Thomas R.; Gnade, Bruce E; Omary, Mohammad A

    2014-01-01

    An experimental and computational study of correlations between solid-state structure and optical/electronic properties of cyclotrimeric gold(I) carbeniates, [Au-3(RN=COR')(3)] (R, R' = H, Me, Bu-n, or (c)Pe), is reported. Synthesis and structural and photophysical characterization of novel complexes [Au-3(MeN=(COBu)-Bu-n)(3)], [Au-3((BuN)-Bu-n=COMe)(3)], [Au-3((BuN)-Bu-n=(COBu)-Bu-n)(3)], and [Au-3((c)PeN=COMe)(3)] are presented. Changes in R and R' lead to distinctive variations in solid-state stacking, luminescence spectra, and conductive properties. Solid-state emission and excitation spectra for each complex display a remarkable dependence on the solid-state packing of the cyclotrimers. The electronic structure of [Au-3(RN=COR')(3)] was investigated via molecular and solid-state simulations. Calculations on [Au-3(HN=COH)(3)] models indicate that the infinitely extended chain of eclipsed structures with equidistant Au-Au intertrimer aurophilic bonding can have lower band gaps, smaller Stokes shifts, and reduced reorganization energies (lambda). The action of one cyclotrimer as a molecular nanowire is demonstrated via fabrication of an organic field effect transistor and shown to produce a p-type field effect. Hole transport for the same cyclotrimer-doped within a poly(9-vinylcarbazole) host-produced a colossal increase in current density from similar to 1 to similar to 1000 mA/cm(2). Computations and experiments thus delineate the complex relationships between solid-state morphologies, electronic structures, and optoelectronic properties of gold(I) carbeniates.

  7. 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.

  8. Early molecular investigations of lichen-forming symbionts: 1986-2001*.

    PubMed

    DePriest, Paula T

    2004-01-01

    From the mid-1980s the symbionts in lichen associations, heterotrophic fungi and photosynthetic algae or cyanobacteria, were the subject of increasing numbers of molecular investigations. Many of the studies examined the phylogenetic placement of the individual symbiotic partners with their free-living relatives, refining their nomenclature and classification. Resulting phylogenies permitted the mapping of transitions to and from lichenization and stimulated discussion of the relative ease of gaining and losing symbiotic lifestyles. Comparing symbiont phylogenies both rejected strict cospeciation and mirrored phylogenies and hinted at more complex forces of coevolution, including symbiont switching and selection. Studies at the species and population levels examined patterns of species delimitation and geographic dispersion and processes such as gene flow, self-fertilization, and founder effect. Significant genetic variation often was associated with mobile elements, group I and spliceosomal introns. This review examines the influence of molecular investigation on lichenology during this first 15 years.

  9. Molecular identification of blow flies recovered from human cadavers during crime scene investigations in Malaysia.

    PubMed

    Kavitha, Rajagopal; Nazni, Wasi Ahmad; Tan, Tian Chye; Lee, Han Lim; Isa, Mohd Noor Mat; Azirun, Mohd Sofian

    2012-12-01

    Forensic entomology applies knowledge about insects associated with decedent in crime scene investigation. It is possible to calculate a minimum postmortem interval (PMI) by determining the age and species of the oldest blow fly larvae feeding on decedent. This study was conducted in Malaysia to identify maggot specimens collected during crime scene investigations. The usefulness of the molecular and morphological approach in species identifications was evaluated in 10 morphologically identified blow fly larvae sampled from 10 different crime scenes in Malaysia. The molecular identification method involved the sequencing of a total length of 2.2 kilo base pairs encompassing the 'barcode' fragments of the mitochondrial cytochrome oxidase I (COI), cytochrome oxidase II (COII) and t-RNA leucine genes. Phylogenetic analyses confirmed the presence of Chrysomya megacephala, Chrysomya rufifacies and Chrysomya nigripes. In addition, one unidentified blow fly species was found based on phylogenetic tree analysis.

  10. Assessment of structural, thermal, and mechanical properties of portlandite through molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Hajilar, Shahin; Shafei, Behrouz

    2016-12-01

    The structural, thermal, and mechanical properties of portlandite, the primary solid phase of ordinary hydrated cement paste, are investigated using the molecular dynamics method. To understand the effects of temperature on the structural properties of portlandite, the coefficients of thermal expansion of portlandite are determined in the current study and validated with what reported from the experimental tests. The atomic structure of portlandite equilibrated at various temperatures is then subjected to uniaxial tensile strains in the three orthogonal directions and the stress-strain curves are developed. Based on the obtained results, the effect of the direction of straining on the mechanical properties of portlandite is investigated in detail. Structural damage analysis is performed to reveal the failure mechanisms in different directions. The energies of the fractured surfaces are calculated in different directions and compared to those of the ideal surfaces available in the literature. The key mechanical properties, including tensile strength, Young's modulus, and fracture strain, are extracted from the stress-strain curves. The sensitivity of the obtained mechanical properties to temperature and strain rate is then explored in a systematic way. This leads to valuable information on how the structural and mechanical properties of portlandite are affected under various exposure conditions and loading rates.

  11. Molecular Dynamics Investigations of the alpha-helix to Beta-barrel Conformational Transformation in RfaH

    NASA Astrophysics Data System (ADS)

    Gc, Jeevan; Bhandari, Yuba; Gerstman, Bernard; Chapagain, Prem

    2015-03-01

    We used combination of replica exchange molecular dynamics simulations with implicit solvent and detailed all-atom simulations with explicit solvent to investigate the α-helix to β-structure transformation of RfaH-CTD. While interacting with the N-terminal domain (NTD), the C-terminal domain (CTD) of RfaH folds to a α-helix bundle but it undergoes an all- α to all- β conformational transformation when it does not interact with the NTD. The RfaH-CTD in the all- α topology is involved in regulating transcription whereas in the all- β topology it is involved in stimulating translation by recruiting a ribosome to an mRNA. Calculations of free-energy landscape and transfer entropy elucidate the details of the RfaH-CTD transformation process. The importance of interfacial interactions between the two domains of RfaH is highlighted by the compromised structural integrity of the helical form of the CTD in the absence NTD. We also studied interdomain and intradomain interactions in RfaH using Steered Molecular Dynamics Simulations. We investigated the role of the interdomain salt-bridge interaction in the domain stability Potential mean force was calculated to obtain free energy profile using Jarzynski Equality.

  12. First-Principles Molecular Dynamics Simulation for Calcium under High-Pressure: Thermodynamic Effect on Simple Cubic Structure

    NASA Astrophysics Data System (ADS)

    Ishikawa, Takahiro; Nagara, Hitose; Suzuki, Naoshi; Shimizu, Katsuya

    2012-12-01

    The crystal structure of the simple cubic phase in calcium is investigated by first-principles molecular dynamics simulations at pressure of 40 GPa and at temperatures of 300 and 10 K. For the k-point sampling over the Brillouin zone, at least 3 × 3 × 3 k-points are required to achieve reliable dynamic behavior of the simulation cell consisting of 4 × 4 × 4 simple cubic primitive cells. As a result of the simulation, a dynamically fluctuating simple cubic lattice emerges at 300 K. The dynamic structure is distorted slightly from the cubic lattice at 10 K, which is consistent with previous experimental observations. A static crystal structure obtained by reducing the particle velocities in the course of the simulation becomes an orthorhombic structure, which is far from the simple cubic structure. Our molecular dynamics study indicates that thermal contribution is crucial for a discussion about the emergence of the simple cubic calcium.

  13. 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.

  14. Photodissociation Structural Dynamics of TrirutheniumDodecacarbonyl Investigated by X-ray Transient Absorption Spectroscopy

    NASA Astrophysics Data System (ADS)

    Harpham, Michael R.; Stickrath, Andrew, B.; Zhang, Xiaoyi,; Huang, Jier; Mara, Michael W.; Chen, Lin X.; Liu, Di-Jia

    2013-10-01

    The molecular and electronic structures of the transient intermediates generated from the photolysis of trirutheniumdodecacarbonyl, Ru3(CO)12, by ultrafast UV (351 nm) laser excitation were investigated using X-ray transient absorption (XTA) spectroscopy. The electronic configuration change and nuclear rearrangement after the dissociation of carbonyls were observed at ruthenium K-edge X-ray absorption near edge structure and X-ray absorption fine structure spectra. Analysis of XTA data, acquired after 100, 200, and 400 ps and 300 ns time delay following the photoexcitation, identified the presence of three intermediate species with Ru3(CO)10 being the most dominating one. The results set an example of applying XTA in capturing both transient electronic and nuclear configurations in metal clusters simulating catalysts in chemical reactions.

  15. Admittance Investigation of MIS Structures with HgTe-Based Single Quantum Wells.

    PubMed

    Izhnin, Ihor I; Nesmelov, Sergey N; Dzyadukh, Stanislav M; Voitsekhovskii, Alexander V; Gorn, Dmitry I; Dvoretsky, Sergey A; Mikhailov, Nikolaj N

    2016-12-01

    This work presents results of the investigation of admittance of metal-insulator-semiconductor structure based on Hg1 - x Cd x Te grown by molecular beam epitaxy. The structure contains a single quantum well Hg0.35Cd0.65Te/HgTe/Hg0.35Cd0.65Te with thickness of 5.6 nm in the sub-surface layer of the semiconductor. Both the conductance-voltage and capacitance-voltage characteristics show strong oscillations when the metal-insulator-semiconductor (MIS) structure with a single quantum well based on HgTe is biased into the strong inversion mode. Also, oscillations on the voltage dependencies of differential resistance of the space charge region were observed. These oscillations were related to the recharging of quantum levels in HgTe.

  16. Molecular Dynamics Simulation and NMR Investigation of the Association of the β-Blockers Atenolol and Propranolol with a Chiral Molecular Micelle

    PubMed Central

    Morris, Kevin F.; Billiot, Eugene J.; Billiot, Fereshteh H.; Hoffman, Charlene B.; Gladis, Ashley A.; Lipkowitz, Kenny B.; Southerland, William M.; Fang, Yayin

    2015-01-01

    Molecular dynamics simulations and NMR spectroscopy were used to compare the binding of two β-blocker drugs to the chiral molecular micelle poly-(sodium undecyl-(L)-leucine-valine). The molecular micelle is used as a chiral selector in capillary electrophoresis. This study is part of a larger effort to understand the mechanism of chiral recognition in capillary electrophoresis by characterizing the molecular micelle binding of chiral compounds with different geometries and charges. Propranolol and atenolol were chosen because their structures are similar, but their chiral interactions with the molecular micelle are different. Molecular dynamics simulations showed both propranolol enantiomers inserted their aromatic rings into the molecular micelle core and that (S)-propranolol associated more strongly with the molecular micelle than (R)-propranolol. This difference was attributed to stronger molecular micelle hydrogen bonding interactions experienced by (S)-propranolol. Atenolol enantiomers were found to bind near the molecular micelle surface and to have similar molecular micelle binding free energies. PMID:26257464

  17. Population age structure and asset returns: an empirical investigation.