Science.gov

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. 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

  3. 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'…

  4. Investigating the correlations among the chemical structures, bioactivity profiles and molecular targets of small molecules

    PubMed Central

    Cheng, Tiejun; Wang, Yanli; Bryant, Stephen H.

    2010-01-01

    Motivation: Most of the previous data mining studies based on the NCI-60 dataset, due to its intrinsic cell-based nature, can hardly provide insights into the molecular targets for screened compounds. On the other hand, the abundant information of the compound–target associations in PubChem can offer extensive experimental evidence of molecular targets for tested compounds. Therefore, by taking advantages of the data from both public repositories, one may investigate the correlations between the bioactivity profiles of small molecules from the NCI-60 dataset (cellular level) and their patterns of interactions with relevant protein targets from PubChem (molecular level) simultaneously. Results: We investigated a set of 37 small molecules by providing links among their bioactivity profiles, protein targets and chemical structures. Hierarchical clustering of compounds was carried out based on their bioactivity profiles. We found that compounds were clustered into groups with similar mode of actions, which strongly correlated with chemical structures. Furthermore, we observed that compounds similar in bioactivity profiles also shared similar patterns of interactions with relevant protein targets, especially when chemical structures were related. The current work presents a new strategy for combining and data mining the NCI-60 dataset and PubChem. This analysis shows that bioactivity profile comparison can provide insights into the mode of actions at the molecular level, thus will facilitate the knowledge-based discovery of novel compounds with desired pharmacological properties. Availability: The bioactivity profiling data and the target annotation information are publicly available in the PubChem BioAssay database (ftp://ftp.ncbi.nlm.nih.gov/pubchem/Bioassay/). Contact: ywang@ncbi.nlm.nih.gov; bryant@ncbi.nlm.nih.gov Supplementary information: Supplementary data are available at Bioinformatics online. PMID:20947527

  5. A classical molecular dynamics investigation of the free energy and structure of short polyproline conformers

    NASA Astrophysics Data System (ADS)

    Moradi, Mahmoud; Babin, Volodymyr; Roland, Christopher; Sagui, Celeste

    2010-09-01

    Folded polyproline peptides can exist as either left-(PPII) or right-handed (PPI) helices, depending on their environment. In this work, we have characterized the conformations and the free energy landscapes of Ace-(Pro)n-Nme, n =2,3,…,9, and 13 peptides both in vacuo and in an implicit solvent environment. In order to enhance the sampling provided by regular molecular dynamics simulations, we have used the recently developed adaptively biased molecular dynamics method—which provides an accurate description of the free energy landscapes in terms of a set of relevant collective variables—combined with Hamiltonian and temperature replica exchange molecular dynamics methods. The collective variables, which are chosen so as to reflect the stable structures and the "slow modes" of the polyproline system, were based primarily on properties of length and of the cis/trans isomerization associated with the prolyl bonds. Results indicate that the space of peptide structures is characterized not just by pure PPII and PPI structures, but rather by a broad distribution of stable minima with similar free energies. These results are in agreement with recent experimental work. In addition, we have used steered molecular dynamics methods in order to quantitatively estimate the free energy difference of PPI and PPII for peptides of the length n =2,…,5 in vacuo and implicit water and qualitatively investigate transition pathways and mechanisms for the PPII to PPI transitions. A zipper-like mechanism, starting from either the center of the peptide or the amidated end, appear to be the most likely mechanisms for the PPII→PPI transition for the longer peptides.

  6. 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

  7. Investigation of Molecular Structure of Porous Epoxy Thermosets via Swelling and Glass Transition Behavior

    NASA Astrophysics Data System (ADS)

    Sharifi, Majid; Ghorpade, Kaustubh; Raman, Vijay; Palmese, Giuseppe

    2014-05-01

    Many of the excellent properties of highly crosslinked polymers are due to their molecular structures. In this study, network structures of three epoxy systems, Epon828-PACM, Epon836-PACM, and Epon1001F-PACM were investigated via equilibrium swelling theory. Each systems separately cured in presence of an inert solvent, THF, ranging from 0 to 92% by volume fraction of solvent. Experimental results showed that the conventional swelling theory is valid for specimens polymerized in moderate dilute environments, i.e. up to around 60% solvent by vol. whereas in extremely dilute environments, i.e. above 60%, the computed Mc values are exponentially increasing. This drastic increase in Mc was investigated by Tg measurement of the polymer phase (on supercritically dried specimens). The measured Mc could not predict the corresponding Tg values according to Fox equation. Due to the highly porous nature of the resulting thermosets after supercritical drying, a modifying factor, based on the probability of finding elastic chains in a porous network, was incorporated in the conventional swelling model (Bray-Merrill equation). It was shown that the adjusted Mc values of each thermoset and the corresponding Tgs are acceptably match via the well-known Fox equation. The modified Mc values indicate that, polymer networks produced in presence of miscible inert phases have relatively uniform molecular weight between crosslinks, irrespective of the amount of that inert phase.

  8. Investigation of the structure of levan polysaccharide chains in water via molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Turgut, Deniz; Coskunkan, Binnaz; Cem, Gulcin; Rende, Deniz; Arga, K. Yalcin; Bucak, Seyda; Baysal, Nihat; Toksoy-Oner, Ebru; Ozisik, Rahmi

    2014-03-01

    Levan is a biopolymer consisting of β-D-fructofuranose units with β (2-6) linkages between fructose rings. Investigation of the structure and behavior of levan in aqeous environments is necessary to understand its biological activity and its potential use in various applications such as carbohydrate-derived drug release. The use of different in vivo and in vitro bioactivity assays fail to relate the chemical structure and conformation to the observed biological activity. Therefore, considerable research has been directed on elucidating the biological activity mechanisms of polysaccharides by structure-function analysis. To overcome the inherent difficulties of experiments, molecular dynamics (MD) simulations have been used to retrieve comprehensive information regarding the conformations of polysaccharides and their dynamic properties. In the current study, the structure of levan is investigated in aqueous medium and in saline solutions via fully atomistic MD simulations at 298 and 310 K, representing room temperature and physiological temperatures, respectively. The material is partially based upon work supported by NSF under Grant Nos. 1200270 and 1003574, and TUBITAK 111M232 and 113M265.

  9. Nanoindentation-induced phase transformation and structural deformation of monocrystalline germanium: a molecular dynamics simulation investigation

    PubMed Central

    2013-01-01

    Molecular dynamics simulations were conducted to study the nanoindentation of monocrystalline germanium. The path of phase transformation and distribution of transformed region on different crystallographic orientations were investigated. The results indicate the anisotropic behavior of monocrystalline germanium. The nanoindentation-induced phase transformation from diamond cubic structure to β-tin-Ge was found in the subsurface region beneath the tool when indented on the (010) plane, while direct amorphization was observed in the region right under the indenter when the germanium was loaded along the [101] and [111] directions. The transformed phases extend along the < 110 > slip direction of germanium. The depth and shape of the deformed layers after unloading are quite different according to the crystal orientation of the indentation plane. The study results suggest that phase transformation is the dominant mechanism of deformation of monocrystalline germanium film in nanoindentation. PMID:23947487

  10. Molecular- and nm-scale Investigation of the Structure and Compositional Heterogeneity of Naturally Occurring Ferrihydrite

    NASA Astrophysics Data System (ADS)

    Cismasu, C.; Michel, F. M.; Stebbins, J. F.; Tcaciuc, A. P.; Brown, G. E.

    2008-12-01

    Ferrihydrite is a hydrated Fe(III) nano-oxide that forms in vast quantities in contaminated acid mine drainage environments. As a result of its high surface area, ferrihydrite is an important environmental sorbent, and plays an essential role in the geochemical cycling of pollutant metal(loid)s in these settings. Despite its environmental relevance, this nanomineral remains one of the least understood environmental solids in terms of its structure (bulk and surface), compositional variations, and the factors affecting its reactivity. Under natural aqueous conditions, ferrihydrite often precipitates in the presence of several inorganic compounds such as aluminum, silica, arsenic, etc., or in the presence of organic matter. These impurities can affect the molecular-level structure of naturally occurring ferrihydrite, thus modifying fundamental properties that are directly correlated with solid-phase stability and surface reactivity. Currently there exists a significant gap in our understanding of the structure of synthetic vs. natural ferrihydrites, due to the inherent difficulties associated to the investigation of these poorly crystalline nanophases. In this study, we combined synchrotron- and laboratory-based techniques to characterize naturally occurring ferrihydrite from an acid mine drainage system situated at the New Idria mercury mine in California. We used high-energy X-ray total scattering and pair distribution function analysis to elucidate quantitative structural details of these samples. We have additionally used scanning transmission X-ray microscopy high resolution imaging (30 nm) to evaluate the spatial relationship of major elements Si, Al, and C within ferrihydrite. Al, Si and C K-edge near- edge X-ray absorption fine structure spectroscopy and 27Al nuclear magnetic resonance spectroscopy were used to obtain short-range structural information. By combining these techniques we attain the highest level of resolution permitted by current analytical

  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. Synthesis, spectroscopic and molecular structures investigations of some carboxylated schiff bases

    NASA Astrophysics Data System (ADS)

    Titinchi, Salam J. J.; Abbo, Hanna S.; Saeed, Ali A. H.

    2004-11-01

    A series of nine carboxylated Schiff bases (five of them are newly prepared viz. compounds 5- 9), are prepared and characterized by various physico-chemical techniques. The molecular structures of synthesized Schiff bases are investigated by IR, UV-Visible, molar conductivities at different concentrations in two different solvents and by their pH values in ethanolic solutions. The IR spectra show absorptions due to = N⊕H- stretching and -N-H bending vibrations, the UV-Visible spectra indicates absorptions are due to protonated species. The molar conductivities, 0.1-0.6 Ω -1 cm 2 mol -1, prove that these compounds are weak electrolytes and are even weaker than tyrosine and phenylalanine, 2.5-13 Ω -1 cm 2 mol -1. The melting points and pH values of Schiff bases are compared with those of some α-aminoacids and some related Schiff bases that have no COOH group in their structures. On the bases of these data, it was concluded that carboxylated Schiff bases exist in two forms, the ionized and the free base where the later is predominant. The ionized form is similar to the zwitterion of the α-aminoacid, in which a proton is transferred from COOH to the azomethine (-CH dbnd6 N-) group.

  13. Investigation of water structure in nafion membranes by infrared spectroscopy and molecular dynamics simulation.

    PubMed

    Hofmann, Detlef W M; Kuleshova, Liudmila; D'Aguanno, Bruno; Di Noto, Vito; Negro, Enrico; Conti, Fosca; Vittadello, Michele

    2009-01-22

    The structure and interactions of water species in hydrated Nafion membranes as a function of water content were investigated on the basis of medium-infrared spectral analysis and molecular dynamics (MD) simulations. The spectral decomposition of the FT-IR data in the stretching OH region was performed on different levels of hydration of the sulfate functional groups (lambdaH2O/RSO3- = 2-22). Quantum mechanical calculations of two model systems [perfluoroethanesulfonic acid/(H2O)6 cluster] and a [perfluorobutanesulfonic acid/(H2O)6 crystal] were carried out in order to account for the band assignments of Nafion in the stretching OH region (2500-4000 cm-1). Our findings indicated that the secondary structure of water species in Nafion can be accurately explained in terms of our reactive force field for water. The distinction between "surface" and "bulk" water contributions in Nafion membrane pores is proposed along with a quantitative estimate of the different types of OH groups present in the system. The average pore size was calculated and supported by the spectral results. PMID:19113878

  14. 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.

  15. Effects of wettability and interfacial nanobubbles on flow through structured nanochannels: an investigation of molecular dynamics

    NASA Astrophysics Data System (ADS)

    Yen, Tsu-Hsu

    2015-12-01

    Solid-fluid boundary conditions are strongly influenced by a number of factors, including the intrinsic properties of the solid/fluid materials, surface roughness, wettability, and the presence of interfacial nanobubbles (INBs). The interconnected nature of these factors means that they should be considered jointly. This paper employs molecular dynamics (MD) simulation in a series of studies aimed at elucidating the influence of wettability in boundary behaviour and the accumulation of interfacial gas. Specifically, we examined the relationship between effective slip length, the morphology of nanobubbles, and wettability. Two methods were employed for the promotion of hydrophobicity between two structured substrates with similar intrinsic contact angles. We also compared anisotropic and isotropic atomic arrangements in the form of graphite and Si(100), respectively. A physical method was employed to deal with variations in surface roughness, whereas a chemical method was used to adjust the wall-fluid interaction energy (ɛwf). We first compared the characteristic properties of wettability, including contact angle and fluid density within the cavity. We then investigated the means by which variations in solid-fluid interfacial wettability affect interfacial gas molecules. Our results reveal that the morphology of INB on a patterned substrate is determined by wettability as well as the methods employed for the promotion of hydrophobicity. The present study also illustrates the means by which the multiple effects of the atomic arrangement of solids, surface roughness, wettability and INB influence effective slip length.

  16. Structure based investigation on the binding interaction of transport proteins in leishmaniasis: insights from molecular simulation.

    PubMed

    Singh, Shailza; Mandlik, Vineetha

    2015-05-01

    Leishmania major is the causative agent of cutaneous leishmaniasis which affects over 1 million people in 88 different countries. The incidence of this disease is on the rise due to the current problems associated with the present chemotherapeutics. In addition, Leishmania confronts resistance to the traditional drugs like sodium stibogluconate and newer repurposed drugs like miltefosine. ABC transporters are involved in the development of drug resistance. Miltefosine, the drug used for the treatment of leishmaniasis, is effluxed by P4 ATPase and ABC transporter, which is the prime focus of our study in this paper. P4 ATPase (MDR1) along with an unnamed protein (cdc50) translocates miltefosine from the outer to the inner leaflet by the process of flipping which is ATP driven. In contrast, miltefosine also escapes from the cells by an energy dependent mechanism that involves the ABC transporter protein (ABC). It is known that certain genes in the parasite amplify the portions of a gene which encodes ABC transporter and P4 ATPase involved in translocating phospholipids and hence resistance to miltefosine. We observed the ABC and P4 ATPase genes, 39 T-box elements were observed in the ABC transporter protein and three elements were observed in the P4 ATPase gene suggesting its role in transcription regulation. To the best of our knowledge, there are no structural and regulatory reports on these two proteins in L. major. Computational structural biology tools may aid in understanding the interaction of miltefosine with the P4-ATPase-cdc50 complex and the ABC transporter. This can be achieved by modeling the target protein structures, studying the dynamics associated with the different domains of the protein and later using activators and inhibitors to alter the functioning of the protein. Molecular dynamics simulation with a lipid bilayer is performed to investigate the conformational changes and structure-activity relationship. As transporters are difficult to model

  17. Core structure of a dissociated edge dislocation and pipe diffusion in copper investigated by molecular dynamics

    NASA Astrophysics Data System (ADS)

    Huang, J.; Meyer, M.; Pontikis, V.

    1991-06-01

    The atomic core structure of two Schockley partial dislocations in copper has been investigated as a function of temperature using molecular dynamics. We employed a resonant model pseudopotential adapted to copper. Our results show that at increasing temperature, the core of the partials becomes increasingly extended and invades entirely the fault ribbon, yet, the separation distance between the partials remains unchanged. At high temperatures vibrational amplitudes of atoms are much larger in the core of the partials than in the bulk of the perfect crystal and the local atomic structure becomes highly disordered. Although disordered, the core structure remains solid-like up to temperatures close to the melting point. Pipe diffusion along this dissociated dislocation has also been investigated. The formation energies of a vacancy and an interstitial are obtained by quasi-dynamics relaxation at T = 0 K while the migration energies for pipe diffusion are calculated at high temperature. Contrary to current assumptions in favour of a vacancy mechanism, we found that in our model the two types of defects may contribute comparably to pipe diffusion since their activation energies are very close. The trajectories of the migrating defects involve not only the partials' cores but also the stacking fault ribbon extending between them, thus explaining why pipe diffusion is slower when the dislocations are dissociated. La structure de coeur de deux dislocations partielles de Schockley a été étudiée, par dynamique moléculaire, en fonction de la température. Nous avons utilisé un pseudopotentiel calculé pour le cuivre à l'aide d'un modèle de résonance. Nos résultats montrent que le coeur des partielles s'étend de plus en plus à mesure que la température augmente et qu'il recouvre complètement le ruban de faute. Cependant la distance de dissociation entre les partielles ne change pas. A haute température, les amplitudes de vibration atomique sont nettement plus

  18. 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.

  19. 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. PMID:27478937

  20. 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.

  1. Molecular dynamics investigation of the structure of a fully hydrated gel-phase dipalmitoylphosphatidylcholine bilayer.

    PubMed Central

    Tu, K; Tobias, D J; Blasie, J K; Klein, M L

    1996-01-01

    We report the results of a constant pressure and temperature molecular dynamics simulation of a gel-phase dipalmitoylphosphatidylcholine bilayer with nw = 11.8 water molecules/lipid at 19 degrees C. The results of the simulation were compared in detail with a variety of x-ray and neutron diffraction data. The average positions of specific carbon atoms along the bilayer normal and the interlamellar spacing and electron density profile were in very good agreement with neutron and x-ray diffraction results. The area per lipid and the details of the in-plane hydrocarbon chain structure were in excellent agreement with wide-angle x-ray diffraction results. The only significant deviation is that the chains met in a pleated arrangement at the bilayer center, although they should be parallel. Novel discoveries made in the present work include the observation of a bimodal headgroup orientational distribution. Furthermore, we found that there are a significant number of gauche conformations near the ends of the hydrocarbon chains and, in addition to verifying a previous suggestion that there is partial rotational ordering in the hydrocarbon chains, that the two chains in a given molecule are inequivalent with respect to rotations. Finally, we have investigated the lipid/water interface and found that the water penetrates beneath the headgroups, but not as far as the carbonyl groups, that the phosphates are strongly hydrated almost exclusively at the nonesterified oxygen atoms, and that the hydration of the ammonium groups is more diffuse, with some water molecules concentrated in the grooves between the methyl groups. Images FIGURE 2 FIGURE 7 FIGURE 8 FIGURE 12 FIGURE 16 PMID:8789079

  2. 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.

  3. 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

  4. Structural properties of coal metallic glasses investigated by molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Xia, J. H.; Gao, Xue-Mei; Xiao, Xu-Yang; Cheng, Zheng-Fu

    2015-01-01

    Based on using molecular dynamics simulations, the structural transitions of Co25Al75 and Co75Al25 were studied during two different quenching processes. The pair-correlation function, the Honeycutt-Andersen (HA) pair analysis technique, Voronoi indices and structural snapshot are adopted in both rapid quenching processes. The results provide direct evidence of the liquid-crystal transition and the liquid Co75Al25 crystallizes into bcc phase at 300 K during the rapid quenching process r1 = 1 K/ps. While during the rapid quenching r2 = 10 K/ps the liquid is frozen into the glass state at 300 K. Meanwhile, the liquid Co25Al75 is frozen into the glass state at 300 K during the two rapid quenching processes. Our results show that the phase formation is strongly dependent on the cooling rates and the compositions.

  5. 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

  6. 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

  7. Solution Structure of Molecular Associations Investigated Using NMR for Polysaccharides: Xanthan/Galactomannan Mixtures.

    PubMed

    Takemasa, Makoto; Nishinari, Katsuyoshi

    2016-03-31

    Although the intermolecular nuclear Overhauser effect (NOE) signal was valuable to elucidate molecular association structure, it could not always be observed for associated molecules due to the short spin-spin relaxation time T2 in NMR measurements, especially for high molar mass systems. While almost no study has been reported for high molar mass polymers (>1 × 10(6)), especially for polysaccharide-polysaccharide interactions, NOE signals were observed for the first time between two different types of polysaccharides, xanthan and galactomannan (locust bean gum), forming a synergistic gel, as a direct evidence of intermolecular binding of polysaccharides. The NOE peak was found between pyruvic acid in xanthan and anomeric proton of mannose of galactomannan. This NOE signal was observed only when mixing time >0.5 s, indicating indirect NOEs caused by spin diffusion. Therefore, this NOE could not be used to construct the molecular models. However, it is a direct evidence for the binding between two different types of polysaccharide to elucidate the synergistic gelation. This NOE signal was observed only for low molar mass galactomannans (1.4 × 10(4)). T2 of pyruvate methyl drastically decreased at low temperatures in the presence of synergistic interaction, suggesting that pyruvate group at terminal end of side chain in xanthan plays an essential role in synergistic interaction. PMID:26943259

  8. 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

  9. 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.

  10. Morphological and molecular investigations of population structure of Phlebotomus perniciosus and Phlebotomus longicuspis (Diptera: Psychodidae) in Tunisia.

    PubMed

    Boudabous, Raja; Jaouadi, Kaouther; Bounamous, Azzedine; Babba, Hamouda

    2012-07-01

    Morphological and molecular characterization of Phlebotomus (Larroussius) perniciosus Newstead and Phlebotomus (L.) longicuspis Nitzulescu in Tunisia is reported. Different localities in central and southern Tunisia were sampled. Sand flies were collected by sticky-paper traps and Center for Disease Control traps. For morphological study of males, the copulatory valves (aedeagi) were examined and the number of coxite hairs was recorded. For molecular analysis, the mitochondrial cytochrome b gene and the cytochrome c oxidase I gene were sequenced to investigate the population structure of P. perniciosus and P. longicuspis. The majority of P. perniciosus samples from southern and some specimens from central Tunisia showed single-pointed aedeagi curved at their apicies that were indistinguishable from the P. longicuspis aedeagi and appeared similar to the atypical morph of P. perniciosus, previously described in northern Morocco. The current study gives evidence of a wide distribution of atypical morphs of P. perniciosus in southern and central Tunisia.

  11. 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.

  12. In situ spectroscopic investigation of molecular structures of highly dispersed vanadium oxide on silica under various conditions

    SciTech Connect

    Gao, X.; Wachs, I.R.; Bare, S.R.; Weckhuysen, B.M.

    1998-12-24

    The molecularly dispersed V{sub 2}O{sub 5}/SiO{sub 2} supported oxides were prepared by the incipient wetness impregnation of 2-propanol solutions of V-isopropoxide. The experimental maximum dispersion of surface vanadium oxide species on SiO{sub 2} was achieved at {approximately}12 wt% v{sub 2}O{sub 5} ({approximately}2.6 V atoms/nm{sup 2}). The surface structures of the molecularly dispersed V{sub 2}O{sub 5}/SiO{sub 2} samples under various conditions were extensively investigated by in situ Raman, UV-vis-NIR DRS and XANES spectroscopies. The combined characterization techniques revealed that in the dehydrated state only isolated VO{sub 4} species are present on the silica surface up to monolayer coverage. Interestingly, the three-member siloxane rings on the silica surface appear to be the most favorable sites for anchoring the isolated, three-legged (SiO){sub 3} V{double_bond}O species. Hydration dramatically changes the molecular structure of the surface vanadium oxide species. The specific structure of the hydrated surface vanadium oxide species is dependent on the degree of hydration. The molecular structure of the fully hydrated vanadium oxide species closely resembles V{sub 2}O{sub 5}{center_dot}nH{sub 2}O gels, rather than V{sub 2}O{sub 5} crystallites. The fully hydrated surface vanadium oxide species are proposed to be chain and/or two-dimensional polymers with highly distorted square-pyramidal VO{sub 5} connected by V-OH-V bridges, which are stabilized on the silica surface by the sixth neighbor of Si-OH hydroxyls via Si-OH{hor_ellipsis}V hydrogen bonds. In analogy to the hydration process, alcoholysis occurs during methanol chemisorption, and similar molecular structures are proposed to interpret the interaction between methanol molecules and the surface vanadium oxide species on silica.

  13. An investigation of molecular structure of copolymers using positron annihilation spectroscopy

    NASA Technical Reports Server (NTRS)

    Singh, J. J.; St.clair, T. L.; Holt, W. H.; Mock, W., Jr.

    1985-01-01

    Positron lifetime measurements were made in copolyimides synthesized from linear 4,4 prime-bis(3,4-dicarboxyphenoxy) diphenylsulfide dianhydride (BDSDA)/4,4 prime-diaminodiphenyl (ODA) and BDSDA/1,3-diaminobenzene (m-phenylene diamine) homopolymers. The probability of positronium formation as well as its subsequent lifetime are lower in the BDSDA/ODA/MPD (50-50) copolyimide, indicating the presence of a transition molecular architecture characterized by higher electron density and stronger bonds which permit both chemical as well as physical entry of water molecules into it. The presence of this transition region imparts unique physical and mechanical properties to the copolyimide.

  14. 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.

  15. 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.

  16. Molecular structure and vibrational spectroscopic investigation of secnidazole using density functional theory.

    PubMed

    Mishra, Soni; Chaturvedi, Deepika; Tandon, Poonam; Gupta, V P; Ayala, A P; Honorato, S B; Siesler, H W

    2009-01-01

    Secnidazole (alpha,2-dimethyl-5-nitro-1H-imidazole-1-ethanol) is an antimicrobical drug, and it is particularly effective in the treatment of amebiasis, giardiasis, trichomoniasis, and bacterial vaginosis. Secnidazole crystallizes as a hemihydrate, which belongs to a monoclinic system having space group P2(1)/c, with a = 12.424 A, b = 12.187 A, c = 6.662 A, and beta = 100.9 degrees. The optimized geometries and total energies of different conformers of the secnidazole molecule have been determined by the method of density functional theory (DFT). For both geometry and total energy, it has been combined with B3LYP functionals having extended basis sets 4-31G, 6-31G, and 6-311++G(d,p) for each of the three stable conformers of secnidazole. Using this optimized structure, we have calculated the infrared and Raman wavenumbers and compared them with the experimental data. The calculated wavenumbers are in an excellent agreement with the experimental values. Based on these results, we have discussed the correlation between the vibrational modes and the crystalline structure of the most stable conformer of secnidazole. A complete assignment is provided for the observed Raman and IR spectra. PMID:19072620

  17. 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.

  18. From the molecular structure to spectroscopic and material properties: computational investigation of a bent-core nematic liquid crystal.

    PubMed

    Greco, Cristina; Marini, Alberto; Frezza, Elisa; Ferrarini, Alberta

    2014-05-19

    We present a computational investigation of the nematic phase of the bent-core liquid crystal A131. We use an integrated approach that bridges density functional theory calculations of molecular geometry and torsional potentials to elastic properties through the molecular conformational and orientational distribution function. This unique capability to simultaneously access different length scales enables us to consistently describe molecular and material properties. We can reassign (13)C NMR chemical shifts and analyze the dependence of phase properties on molecular shape. Focusing on the elastic constants we can draw some general conclusions on the unconventional behavior of bent-core nematics and highlight the crucial role of a properly-bent shape.

  19. 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

  20. 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.

  1. Molecular structure and conformational composition of 1,1-dichlorobutane: a gas-phase electron diffraction and ab initio investigation

    NASA Astrophysics Data System (ADS)

    Aarset, Kirsten; Hagen, Kolbjørn; Stølevik, Reidar

    1997-09-01

    Gas-phase electron diffraction data obtained at 23°C, together with results from ab initio molecular orbital calculations ( {HF}/{6-31 G(d)}). were used to determine the structure and conformational composition of 1,1-dichlorobutane. Of the five distinguishable conformers (AA, G + A, AG +, G + G + and G + G -), the G + A conformer was found to be the low-energy form, and the investigation also indicated that certain amounts of the AA and G + G - conformers might be present. The symbols describing the conformers refer to torsion about the C 1C 2 and C 2C 3 bonds, anti (A) with H 5C 1C 2C 3 and C 1C 2C 3C 4 torsion angles of 180° and gauche (G + or G -) with torsion angles of + 60° or 300° (-60°) respectively. The results for the principal distances ( rg) and angles (∠ α) from the combined electron diffraction/ab initio study for the G + A conformer, with estimated 2σ uncertainties, were as follows: r( C1 C2) = 1.521(4) Å, r( C2 C3) = 1.539(4) Å, r( C3 C4) = 1.546(4) Å, r( C Cl6) = 1.782(3) Å, r( CCl7) = 1.782(3) Å, = 1.106(6) Å, ∠C 1C 2C 3 = 114.4(13)°, ∠C 2C 3C 4 = 112.5(13)°, ∠CCCl 6 = 110.4(7)°, ∠CCCl 7 = 111.9(7)°, <∠CCH> = 108.9(47)°. Only average values for r(CC), r(CCl), r(CH), ∠CCC, ∠CCX and ∠CCH were determined in the least-square refinements; the differences between the values for these parameters in the same conformer and between the different conformers were kept constant at the values obtained from the ab initio molecular orbital calculations.

  2. Structure and Transformation of Amorphous Calcium Carbonate: A Solid-State 43Ca NMR and Computational Molecular Dynamics Investigation

    SciTech Connect

    Singer, Jared W.; Yazaydin, A. O.; Kirkpatrick, Robert J.; Bowers, Geoffrey M.

    2012-05-22

    Amorphous calcium carbonate (ACC) is a metastable precursor to crystalline CaCO{sub 3} phases that precipitates by aggregation of ion pairs and prenucleation clusters. We use {sup 43}Ca solid-state NMR spectroscopy to probe the local structure and transformation of ACC synthesized from seawater-like solutions with and without Mg{sup 2+} and computational molecular dynamics (MD) simulations to provide more detailed molecular-scale understanding of the ACC structure. The {sup 43}Ca NMR spectra of ACC collected immediately after synthesis consist of broad, featureless resonances with Gaussian line shapes (FWHH = 27.6 {+-} 1 ppm) that do not depend on Mg{sup 2+} or H{sub 2}O content. A correlation between {sup 43}Ca isotropic chemical shifts and mean Ca-O bond distances for crystalline hydrous and anhydrous calcium carbonate phases indicates indistinguishable maximum mean Ca-O bond lengths of {approx}2.45 {angstrom} for all our samples. This value is near the upper end of the published Ca-O bond distance range for biogenic and synthetic ACCs obtained by Ca-X-ray absorption spectroscopy. It is slightly smaller than the values from the structural model of Mgfree ACC by Goodwin et al. obtained from reverse Monte Carlo (RMC) modeling of X-ray scattering data and our own computational molecular dynamics (MD) simulation based on this model. An MD simulation starting with the atomic positions of the Goodwin et al. RMC model using the force field of Raiteri and Gale shows significant structural reorganization during the simulation and that the interconnected carbonate/water-rich channels in the Goodwin et al. model shrink in size over the 2 ns simulation time. The distribution of polyhedrally averaged Ca-O bond distances from the MD simulation is in good agreement with the {sup 43}Ca NMR peak shape, suggesting that local structural disorder dominates the experimental line width of ACC.

  3. 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…

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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. PMID:19368351

  9. 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.

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

    PubMed

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

    2013-10-21

    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 the accurate molecular structure and spectroscopic properties of the title molecule, but more importantly, it demonstrates a reliable approach for the accurate investigation of isolated small biomolecules.

  11. Molecular structures and conformational compositions of 2-chlorobutane and 2-bromobutane; an investigation using gas-phase electron-diffraction data and ab initio molecular orbital calculations

    NASA Astrophysics Data System (ADS)

    Aarset, Kirsten; Hagen, Kolbjørn; Stølevik, Reidar

    2001-06-01

    The structure and conformational composition of 2-chlorobutane and 2-bromobutane have been studied by gas-phase electron diffraction (GED) at 25°C, together with ab initio molecular orbital calculations (HF/6-311+G(d,p)). These molecules may exist as three distinguishable conformers (G+, A, and G-). The symbols refer to anti (A) with a torsion angle Φ2(X 8-C 2-C 3-C 4) of about 180° and gauche (G+ and G-) with torsion angles Φ2(X 8-C 2-C 3-C 4) of about +60° and 300°(-60°), respectively. It was not possible; from our GED-data alone, to accurately determine the conformational composition because the distance distributions for two of the conformers (G+ and G-) are very similar. The conformational composition for 2-chlorobutane obtained from the ab initio calculations (G+ 62%, A 25% G- 13%) was found to fit the experimental data quite well. For 2-bromobutane the ab initio calculated conformational composition (G+ 58%, A 28% G- 14%) did not, however, fit the experimental data. Here a much better fit was obtained by using only 10% of the A conformer and using the relative energy for the two gauche conformers, as obtained in the ab initio molecular orbital calculations, to calculate the relative amounts of the two gauche forms (G+ 73%, A 10% G- 17%). The results for the principal distances ( rg) and angles ∠ α for the G+ conformer of 2-chlorobutane, with estimated 2 σ uncertainties, obtained from the combined GED/ab initio study are: r( C1- C2)=1.524(3) Å, r( C2- C3)=1.528(3) Å, r( C3- C4)=1.539(3) Å, r( C- Cl)=1.812(3) Å, r( C- H) ave=1.098(4) Å, ∠C 1C 2C 3=111.5(16)°, ∠C 2C 3C 4=113.3(5)°, ∠C 1C 2C1=110.4(9)°. The results for the G+ conformer of 2-bromobutane are: r( C1- C2)=1.526(4) Å, r( C2- C3)=1.530(4) Å, r( C3- C4)=1.540(4) Å, r( C- Br)=1.982(5) Å, r( C- H) ave=1.111(8) Å, ∠C 1C 2C 3=112.5(16)°, ∠C 2C 3C 4=114.6(15)°, ∠C 1C 2Br=110.1(16)°. Only average values for r(C-C), r(C-H), ∠CCC, and ∠CCH could be determined in the

  12. 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

  13. NMR investigations of molecular dynamics

    NASA Astrophysics Data System (ADS)

    Palmer, Arthur

    2011-03-01

    NMR spectroscopy is a powerful experimental approach for characterizing protein conformational dynamics on multiple time scales. The insights obtained from NMR studies are complemented and by molecular dynamics (MD) simulations, which provide full atomistic details of protein dynamics. Homologous mesophilic (E. coli) and thermophilic (T. thermophilus) ribonuclease H (RNase H) enzymes serve to illustrate how changes in protein sequence and structure that affect conformational dynamic processes can be monitored and characterized by joint analysis of NMR spectroscopy and MD simulations. A Gly residue inserted within a putative hinge between helices B and C is conserved among thermophilic RNases H, but absent in mesophilic RNases H. Experimental spin relaxation measurements show that the dynamic properties of T. thermophilus RNase H are recapitulated in E. coli RNase H by insertion of a Gly residue between helices B and C. Additional specific intramolecular interactions that modulate backbone and sidechain dynamical properties of the Gly-rich loop and of the conserved Trp residue flanking the Gly insertion site have been identified using MD simulations and subsequently confirmed by NMR spin relaxation measurements. These results emphasize the importance of hydrogen bonds and local steric interactions in restricting conformational fluctuations, and the absence of such interactions in allowing conformational adaptation to substrate binding.

  14. Theoretical investigations on the molecular structure, vibrational spectra, HOMO-LUMO and NBO analysis of 5-chloro-2-((4-chlorophenoxy)methyl)benzimidazole

    NASA Astrophysics Data System (ADS)

    Mary, Y. Shyma; Jojo, P. J.; Panicker, C. Yohannan; Van Alsenoy, Christian; Ataei, Sanaz; Yildiz, Ilkay

    2014-03-01

    The optimized molecular structure, vibrational frequencies, corresponding vibrational assignments of 5-chloro-2-((4-chlorophenoxy)methyl)benzimidazole have been investigated experimentally and theoretically using Gaussian09 software package. The energy and oscillator strength calculated by time dependent density functional theory results almost compliments with experimental findings. Gauge-including atomic orbital 1H NMR chemical shifts calculations were carried out and compared with experimental data. The HOMO and LUMO analysis is used to determine the charge transfer within the molecule. The stability of the molecule arising from hyper-conjugative interaction and charge delocalization has been analyzed using NBO analysis. Molecular electrostatic potential was performed by the DFT method and the infrared intensities and Raman activities are reported. Mulliken's net charges have been calculated and compared with the atomic natural charges. Fist hyperpolarizability is calculated in order to find its role in non-linear optics.

  15. 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.

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

    PubMed

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

    2012-11-01

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

  17. 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.

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

    PubMed

    Banerjee, Antara; Chakraborty, Subhadip; Chakraborty, Abhijit; 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

  19. 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

  20. Investigation of torsional potentials, molecular structure, vibrational properties, molecular characteristics and NBO analysis of some bipyridines using experimental and theoretical tools

    NASA Astrophysics Data System (ADS)

    Prashanth, J.; Reddy, B. Venkatram; Rao, G. Ramana

    2016-08-01

    The Fourier Transform Infrared (FTIR) and Fourier Transform Raman (FT-Raman) spectra of 2,2‧-bipyridine (2BPE); 4,4‧-bipyridine (4BPE); and 2,4‧-bipyridine (24BPE) were measured in the range 4000-450 cm-1 and 4000-50 cm-1, respectively. Torsional potentials were evaluated at various angles of rotation around the C-C inter-ring bond for the three molecules in order to arrive at the molecular conformation of lowest energy. This conformation was further optimized to get ground state geometry. Vibrational frequencies along with infrared and Raman intensities were computed. In the above calculations, DFT employing B3LYP functional with 6311++G(d,p) basis set was used. The rms error between observed and calculated frequencies was 10.0, 10.9 and 10.2 cm-1 for 2BPE, 4BPE and 24BPE, respectively. A 54-parameter modified valence force field was derived by solving inverse vibrational problem using Wilson's GF matrix method. The force constants were refined using 117 experimental frequencies of the three molecules in overlay least-squares technique. The average error between observed and computed frequencies was 12.44 cm-1. PED and eigen vectors calculated in the process were used to make unambiguous vibrational assignments of all the fundamental vibrations. The values of dipole moment, polarizability and hyperpolarizability were computed to determine the NLO behaviour of these molecules. The HOMO and LUMO energies, thermodynamic parameters and molecular electrostatic surface potentials (MESP) were also evaluated. Stability of the molecules arising from hyper conjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis.

  1. 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.

  2. Theoretical investigations on molecular structure, vibrational spectra, HOMO, LUMO, NBO analysis and hyperpolarizability calculations of thiophene-2-carbohydrazide

    NASA Astrophysics Data System (ADS)

    Balachandran, V.; Janaki, A.; Nataraj, A.

    2014-01-01

    The Fourier-Transform infrared and Fourier-Transform Raman spectra of thiophene-2-carbohydrazide (TCH) was recorded in the region 4000-400 cm-1 and 3500-100 cm-1. Quantum chemical calculations of energies, geometrical structure and vibrational wavenumbers of TCH were carried out by DFT (B3LYP) method with 6-311++G(d,p) as basis set. The difference between the observed and scaled wavenumber values of most of the fundamentals is very small. Stability of the molecule arising from hyper conjugative interaction and charge delocalization has been analyzed using natural bond orbital (NBO) analysis. UV spectrum was measured in different solvent. The energy and oscillator strength are calculated by Time Dependant Density Functional Theory (TD-DFT) results. The calculated HOMO and LUMO energies also confirm that charge transfer occurs within the molecule. The complete assignments were performed on the basis of the potential energy distribution (PED) of vibrational modes, calculated with scaled quantum mechanics (SQM) method. Finally the theoretical FT-IR, FT-Raman, and UV spectra of the title molecule have also been constructed.

  3. Theoretical investigations on molecular structure, vibrational spectra, HOMO, LUMO, NBO analysis and hyperpolarizability calculations of thiophene-2-carbohydrazide.

    PubMed

    Balachandran, V; Janaki, A; Nataraj, A

    2014-01-24

    The Fourier-Transform infrared and Fourier-Transform Raman spectra of thiophene-2-carbohydrazide (TCH) was recorded in the region 4000-400 cm(-1) and 3500-100 cm(-1). Quantum chemical calculations of energies, geometrical structure and vibrational wavenumbers of TCH were carried out by DFT (B3LYP) method with 6-311++G(d,p) as basis set. The difference between the observed and scaled wavenumber values of most of the fundamentals is very small. Stability of the molecule arising from hyper conjugative interaction and charge delocalization has been analyzed using natural bond orbital (NBO) analysis. UV spectrum was measured in different solvent. The energy and oscillator strength are calculated by Time Dependant Density Functional Theory (TD-DFT) results. The calculated HOMO and LUMO energies also confirm that charge transfer occurs within the molecule. The complete assignments were performed on the basis of the potential energy distribution (PED) of vibrational modes, calculated with scaled quantum mechanics (SQM) method. Finally the theoretical FT-IR, FT-Raman, and UV spectra of the title molecule have also been constructed. PMID:24060478

  4. Investigation of Pseudomonas aeruginosa quorum-sensing signaling system for identifying multiple inhibitors using molecular docking and structural analysis methodology.

    PubMed

    Soheili, Vahid; Bazzaz, Bibi Sedigheh Fazly; Abdollahpour, Nooshin; Hadizadeh, Farzin

    2015-12-01

    Pseudomonas aeruginosa is an opportunistic human pathogen and a common Gram-negative bacterium in hospital-acquired infections. It causes death in many burn victims, cystic-fibrosis and neutropenic-cancer patients. It is known that P. aeruginosa biofilm maturation and production of cell-associated and extracellular virulence factors such as pyocyanin, elastase and rhamnolipids are under the control of a quorum-sensing (QS) system. Among several proteins involved in the Pseudomonas QS mechanism, LasR and PqsE play an important role in its cascade signaling system. They can cause increases in QS factors, biofilm maturation, and the production of virulence factors. Therefore, inhibition of these proteins can reduce the pathogenicity of P. aeruginosa. According to the structure of corresponding auto-inducers bound to these proteins, in silico calculations were performed with some non-steroidal anti-inflammatory drugs (NSAIDs) to estimate possible interactions and find the co-inhibitors of LasR and PqsE. The results showed that oxicams (Piroxicam and Meloxicam) can interact well with active sites of both proteins with the Ki of 119.43 nM and 4.0 μM for Meloxicam and 201.39 nM and 4.88 μM against LasR and PqsE, respectively. These findings suggested that Piroxicam and Meloxicam can be used as potential inhibitors for control of the P. aeruginosa QS signaling system and biofilm formation, and may be used in the design of multiple inhibitors.

  5. Theoretical investigation of 5-(2-acetoxyethyl)-6-methylpyrimidin-2,4-dione: conformational study, NBO and NLO analysis, molecular structure and NMR spectra.

    PubMed

    Pir, Hacer; Günay, Nergin; Tamer, Ömer; Avcı, Davut; Atalay, Yusuf

    2013-08-01

    Structural and conformational, natural bond orbital (NBO) and nonlinear optical (NLO) analysis was performed, and (1)H and (13)C NMR chemical shifts values of 5-(2-Acetoxyethyl)-6-methylpyrimidin-2,4-dione [C9H12N2O4] in the ground state were calculated by using Density Functional Theory (DFT-B3LYP/6-311++G(d,p)) and Hartree-Fock (HF/6-311++G(d,p)) methods. The NMR data were calculated by means of the GIAO, CSGT, and IGAIM methods. In addition, the molecular frontier orbital energies, thermodynamic parameters (in the range of 200-700 K), molecular surfaces, Mulliken charges and atomic polar tensor-based charges were investigated. Besides, the analysis of all possible conformational of the title compound, a detailed potential energy curve for τ1(C8O3C10O4), τ2 (C8O3C10C11) and τ3 (C5C7C8O3) dihedral angles were performed in steps of 10° from 0° to 360°, and depicted to find the most stable form. Finally, the calculated HOMO and LUMO energies show that charge transfer occurs within the title compound.

  6. 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.

  7. 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

  8. Cytochrome C on a gold surface: investigating structural relaxations and their role in protein-surface electron transfer by molecular dynamics simulations.

    PubMed

    Siwko, Magdalena E; Corni, Stefano

    2013-04-28

    Proteins immobilized on inorganic surfaces are important in technological fields such as biosensors, enzymatic biofuel cells and biomolecular electronics. In these frameworks, it has been demonstrated that some proteins are able to keep their functionality, although the latter may be somewhat modified by the interaction with the surface. Cytochrome C, an heme-based electron transfer protein, has been found to be able to exchange electrons with the gold surface on which it is immobilized, but some deviations from the expected electron transfer rates were evidenced [C. A. Bortolotti, et al., J. Phys. Chem. C 2007, 111, 12100-12105]. In this work we have used molecular dynamics simulations of (native and mutated) yeast cytochrome C supported on Au(111) to investigate the microscopic picture behind the experimental behavior of the molecule. In particular, we have focused on the structural re-arrangements due to the interactions with the surface. We found that, despite being secondary-structure preserving, they can profoundly affect protein-surface electronic coupling and, in turn, electron transfer rates, explaining experimental findings. The conformational flexibility of the protein in the region of the protein-surface bond is thus pivotal in determining the resulting ET functionality of the immobilized protein.

  9. 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. PMID:19239216

  10. Effect of water on structure and dynamics of [BMIM][PF6] ionic liquid: An all-atom molecular dynamics simulation investigation.

    PubMed

    Sharma, Anirban; Ghorai, Pradip Kr

    2016-03-21

    Composition dependent structural and dynamical properties of aqueous hydrophobic 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]) ionic liquid (IL) have been investigated by using all-atom molecular dynamics simulation. We observe that addition of water does not increase significant number of dissociated ions in the solution over the pure state. As a consequence, self-diffusion coefficient of the cation and anion is comparable to each other at all water concentration similar to that is observed for the pure state. Voronoi polyhedra analysis exhibits strong dependence on the local environment of IL concentration. Void and neck distributions in Voronoi tessellation are approximately Gaussian for pure IL but upon subsequent addition of water, we observe deviation from the Gaussian behaviour with an asymmetric broadening with long tail of exponential decay at large void radius, particularly at higher water concentrations. The increase in void space and neck size at higher water concentration facilitates ionic motion, thus, decreasing dynamical heterogeneity and IL reorientation time and increases self-diffusion coefficient significantly.

  11. Effect of water on structure and dynamics of [BMIM][PF6] ionic liquid: An all-atom molecular dynamics simulation investigation

    NASA Astrophysics Data System (ADS)

    Sharma, Anirban; Ghorai, Pradip Kr.

    2016-03-01

    Composition dependent structural and dynamical properties of aqueous hydrophobic 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]) ionic liquid (IL) have been investigated by using all-atom molecular dynamics simulation. We observe that addition of water does not increase significant number of dissociated ions in the solution over the pure state. As a consequence, self-diffusion coefficient of the cation and anion is comparable to each other at all water concentration similar to that is observed for the pure state. Voronoi polyhedra analysis exhibits strong dependence on the local environment of IL concentration. Void and neck distributions in Voronoi tessellation are approximately Gaussian for pure IL but upon subsequent addition of water, we observe deviation from the Gaussian behaviour with an asymmetric broadening with long tail of exponential decay at large void radius, particularly at higher water concentrations. The increase in void space and neck size at higher water concentration facilitates ionic motion, thus, decreasing dynamical heterogeneity and IL reorientation time and increases self-diffusion coefficient significantly.

  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. Emerging molecular methods for male infertility investigation.

    PubMed

    Benkhalifa, Moncef; Montjean, Debbie; Belloc, Stephanie; Dalleac, Alain; Ducasse, Michel; Boyer, Pierre; Merviel, Philippe; Copin, Henri

    2014-01-01

    Male factors account for approximately 50% of reproductive pathology. Different disorders, including urogenital and endocrine system development abnormalities, lead to testicular and gametogenesis defects. Parallely, studies have reported that somatic and germ cell genome decay are a major cause of male infertility. It has been shown that in somatic karyotype, there is a higher incidence of chromosomal aberrations in infertile men than neonatal population and significant chromosome Y microdeletion or specific gene alterations in affected spermatogenesis. Karyotyping and FISH application at somatic and germ cell levels are no longer sufficient to investigate the potential contribution of genome disorders on male infertility. A wide range of molecular methods are required for better understanding of male infertility causes. Molecular omes and omics techniques have become a great tool to investigate male infertility from chromosome to protein. This review reports different molecular tests and methods that can be offered for male infertility investigation.

  14. Investigation of coal structure

    SciTech Connect

    Not Available

    1993-01-01

    The method was applied to standard polymers under the same condition above. The particle size distribution with volume diameters of polyvinylpyrrolidone (average molecular mass; 10,000) was measured at sample/solvent = 0.50 g/100 ml. This polymer readily dissolve in methanol and water, while the polymer does not dissolve in n-hexane and toluene, and toluene is a slightly better solvent than n-hexane. Figure 3 shows the particle size distributions in n-hexane (a) and toluene (b-1 and -2). The distribution in toluene changed time to time, and two representative distributions are shown. The mean volume diameters-were 14 [mu]m in n-hexane and 18 and 31 [mu]m in toluene. The particle size distribution of cross-linked polyvinylpyrrolidone was further examined in methanol and n-hexane. Figure 4 compares these distributions with scanned counts at sample/solvent = 0.50 g/100 ml. As a significant portion of particles was over 250 [mu]m with volume diameters, the distributions are presented with scanned counts. Figure 4 compared the specific swelling ratio (Q') versus sample/solvent (w/w %) in the same solvents for this sample. It is seen that methanol is a good solvent than n-hexane and swells the sample. It is also seen that the swelling is dependent on the sample concentration. Therefore, the particle size in good solvent methanol is expected to be larger due to swelling. However, the particle size was smaller in methanol than in n-hexane (Figure 4). The dependence of sample concentration on solvent swelling in methanol (Figure 5) is interpreted as follows: Polymer particles disaggregated at low sample concentration and the interparticle voidage of the swollen polymer after centrifugation changed depending upon disaggregation.

  15. 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.

  16. 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.

  17. Interactive Modelling of Molecular Structures

    NASA Astrophysics Data System (ADS)

    Rustad, J. R.; Kreylos, O.; Hamann, B.

    2004-12-01

    The "Nanotech Construction Kit" (NCK) [1] is a new project aimed at improving the understanding of molecular structures at a nanometer-scale level by visualization and interactive manipulation. Our very first prototype is a virtual-reality program allowing the construction of silica and carbon structures from scratch by assembling them one atom at a time. In silica crystals or glasses, the basic building block is an SiO4 unit, with the four oxygen atoms arranged around the central silicon atom in the shape of a regular tetrahedron. Two silicate units can connect to each other by their silicon atoms covalently bonding to one shared oxygen atom. Geometrically, this means that two tetrahedra can link at their vertices. Our program is based on geometric representations and uses simple force fields to simulate the interaction of building blocks, such as forming/breaking of bonds and repulsion. Together with stereoscopic visualization and direct manipulation of building blocks using wands or data gloves, this enables users to create realistic and complex molecular models in short amounts of time. The NCK can either be used as a standalone tool, to analyze or experiment with molecular structures, or it can be used in combination with "traditional" molecular dynamics (MD) simulations. In a first step, the NCK can create initial configurations for subsequent MD simulation. In a more evolved setup, the NCK can serve as a visual front-end for an ongoing MD simulation, visualizing changes in simulation state in real time. Additionally, the NCK can be used to change simulation state on-the-fly, to experiment with different simulation conditions, or force certain events, e.g., the forming of a bond, and observe the simulation's reaction. [1] http://graphics.cs.ucdavis.edu/~okreylos/ResDev/NanoTech

  18. Investigating the molecular structural features of hulless barley (Hordeum vulgare L.) in relation to metabolic characteristics using synchrotron-based fourier transform infrared microspectroscopy.

    PubMed

    Yang, Ling; Christensen, David A; McKinnon, John J; Beattie, Aaron D; Xin, Hangshu; Yu, Peiqiang

    2013-11-27

    The synchrotron-based Fourier transform infrared microspectroscopy (SR-FTIRM) technique was used to quantify molecular structural features of the four hulless barley lines with altered carbohydrate traits [amylose, 1-40% of dry matter (DM); β-glucan, 5-10% of DM] in relation to rumen degradation kinetics, intestinal nutrient digestion, and predicted protein supply. Spectral features of β-glucan (both area and heights) in hulless barley lines showed a negative correlation with protein availability in the small intestine, including truly digested protein in the small intestine (DVE) (r = -0.76, P < 0.01; r = -0.84, P < 0.01) and total metabolizable protein (MP) (r = -0.71, P < 0.05; r = -0.84, P < 0.01). Variation in absorption intensities of total carbohydrate (CHO) was observed with negative effects on protein degradation, digestion, and potential protein supply (P < 0.05). Molecular structural features of CHO in hulless barley have negative effects on the supply of true protein to ruminants. The results clearly indicated the impact of the carbohydrate-protein structure and matrix.

  19. Molecular crime scene investigation - dusting for fingerprints.

    PubMed

    Jürgen Bajorath

    2013-12-01

    In chemoinformatics and drug design, fingerprints (FPs) are defined as string representations of molecular structure and properties and are popular descriptors for similarity searching. FPs are generally characterized by the simplicity of their design and ease of use. Despite a long history in chemoinformatics, the potential and limitations of FP searching are often not well under- stood. Standard FPs can also be subjected to engineering techniques to tune them for specific search applications.

  20. Molecular-level investigation of the structure, transformation, and bioactivity of single living fission yeast cells by time- and space-resolved Raman spectroscopy.

    PubMed

    Huang, Yu-San; Karashima, Takeshi; Yamamoto, Masayuki; Hamaguchi, Hiro-o

    2005-08-01

    The structure, transformation, and bioactivity of single living Schizosaccharomyces pombe cells at the molecular level have been studied in vivo by time- and space-resolved Raman spectroscopy. A time resolution of 100 s and a space resolution of 250 nm have been achieved with the use of a confocal Raman microspectrometer. The space-resolved Raman spectra of living S. pombe cells at different cell cycle stages were recorded in an effort to elucidate the molecular compositions of organelles, including nuclei, cytoplasm, mitochondria, and septa. The time- and space-resolved measurement of the central part of a dividing yeast cell showed continuous spectral evolution from that of the nucleus to those of the cytoplasm and mitochondria and finally to that of the septum, in accordance with the transformation during the cell cycle. A strong Raman band was observed at 1602 cm(-)(1) only when cells were under good nutrient conditions. The effect of a respiration inhibitor, KCN, on a living yeast cell was studied by measuring the Raman spectra of its mitochondria. A sudden disappearance of the 1602 cm(-)(1) band followed by the change in the shape and intensity of the phospholipid bands was observed, indicating a strong relationship between the cell activity and the intensity of this band. We therefore call this band "the Raman spectroscopic signature of life". The Raman mapping of a living yeast cell was also carried out. Not only the distributions of molecular species but also those of active mitochondria in the cell were successfully visualized in vivo.

  1. Quantum chemical investigation and statistical analysis of the relationship between corrosion inhibition efficiency and molecular structure of xanthene and its derivatives on mild steel in sulphuric acid

    NASA Astrophysics Data System (ADS)

    Obi-Egbedi, N. O.; Obot, I. B.; El-Khaiary, Mohammad I.

    2011-09-01

    A density functional theory (DFT) study of xanthene (XEN) and two of its derivatives namely xanthone (XAN) and xanthione (XION) recently used as corrosion inhibitors for mild steel in 0.5 M H 2SO 4 was undertaken at the B3LYP/631G (d) level. Inhibition efficiency obtained experimentally followed the order: XEN < XAN < XION. It was found that when the organic molecules adsorbed on the steel surface, molecular structure influences their interaction mechanism and by extension their inhibition efficiencies. The quantum chemical properties/descriptors most relevant to their potential action as corrosion inhibitors have been calculated in the neutral and protonated forms in aqueous phase for comparison. They include: Total energy (TE), EHOMO, ELUMO, energy gap (Δ E), dipole moment ( D), molecular area (MA), molecular volume (MV), hardness (η), softness ( σ˙), the fractions of electrons transferred (Δ N), electrophilicity index (ω) and total energy change (Δ ET). The quantum chemical parameters/descriptors were correlated with inhibition effect of the three inhibitors and were further used to explain the electron transfer mechanism between the inhibitors and the steel surface. Furthermore, equations were proposed using the non-linear and the multiple-linear regression analysis. The theoretical obtained results were found to be consistent with the experimental data reported.

  2. 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.

  3. Investigating the Conformational Structure and Potential Site Interactions of SOD Inhibitors on Ec-SOD in Marine Mud Crab Scylla serrata: A Molecular Modeling Approach.

    PubMed

    Paital, Biswaranjan; Sablok, Gaurav; Kumar, Sunil; Singh, Sanjeev Kumar; Chainy, G B N

    2016-09-01

    Superoxide dismutases (SODs) act as a first line of the enzymatic antioxidant defense system to control cellular superoxide anion toxicity. Previously, several inhibitors have been widely identified and catalogued for inhibition of SOD activity; however, still the information about the mechanism of interaction and points toward the inhibitor interactions in structures of SODs in general and in extracellular (Ec)-SOD in particular is still in naive. In the present research, we present an insight to elucidate the molecular basis of interactions of SOD inhibitors with Ec-SOD in mud crab Scylla serrata using molecular modeling and docking approaches. Different inhibitors of SOD such as hydrogen peroxide [Formula: see text], potassium cyanide, sodium dodecyl sulfate (SDS), [Formula: see text]-mercaptoethanol and dithiocarbamate were screened to understand the potential sites that may act as sites for cleavage or blocking in the protein. SOD-SDS and [Formula: see text] complex interactions indicate residues Pro72 and Asp102 of the predicted crab Ec-SOD as common targets. The GOLD result indicates that Pro72, Asp102 and Thr103 are commonly acting as the site of interaction in Ec-SOD of S. serrata with SOD inhibitors. For the first time, the results of this study provide an insight into the structural properties of Ec-SOD of S. serrata and define the possible involvements between the amino acids present in its active sites, i.e., in the regions from 70 to 84 and from 101 to 103 and different inhibitors.

  4. 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.

  5. 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. PMID:23978748

  6. Molecular investigations of flaxseed mucilage polysaccharides.

    PubMed

    Roulard, Romain; Petit, Emmanuel; Mesnard, François; Rhazi, Larbi

    2016-05-01

    The molecular properties of flaxseed mucilage were determined using a multi-angle laser light scattering (MALLS) detector coupled on-line to size exclusion chromatography (SEC) and asymmetric flow field-flow fractionation (AF4). Water and salt solution were tested as mobile phases. The SEC-MALLS method gave partial information and enabled molecular characterization of disaggregated mucilage molecules. Regardless of the eluent used, the observed Mw ranged from about 1.6 × 10(6) to more than 10 × 10(6) g/mol for mucilage polysaccharides. The AF4-MALLS system enabled a complete analysis of mucilage carbohydrate aggregates in water, in which two populations were satisfactorily separated. The molecular weight distribution (MWD) of molecules ranged from 1.5 × 10(6) to more than 4 × 10(8) g/mol. Experiments showed that the conformational structure of mucilage molecules was strongly influenced by ionic strength. Mucilage carbohydrates exhibited a spherical and compact structure in NaCl solution while they displayed a random-coil conformation in water. PMID:26851358

  7. Molecular investigations of flaxseed mucilage polysaccharides.

    PubMed

    Roulard, Romain; Petit, Emmanuel; Mesnard, François; Rhazi, Larbi

    2016-05-01

    The molecular properties of flaxseed mucilage were determined using a multi-angle laser light scattering (MALLS) detector coupled on-line to size exclusion chromatography (SEC) and asymmetric flow field-flow fractionation (AF4). Water and salt solution were tested as mobile phases. The SEC-MALLS method gave partial information and enabled molecular characterization of disaggregated mucilage molecules. Regardless of the eluent used, the observed Mw ranged from about 1.6 × 10(6) to more than 10 × 10(6) g/mol for mucilage polysaccharides. The AF4-MALLS system enabled a complete analysis of mucilage carbohydrate aggregates in water, in which two populations were satisfactorily separated. The molecular weight distribution (MWD) of molecules ranged from 1.5 × 10(6) to more than 4 × 10(8) g/mol. Experiments showed that the conformational structure of mucilage molecules was strongly influenced by ionic strength. Mucilage carbohydrates exhibited a spherical and compact structure in NaCl solution while they displayed a random-coil conformation in water.

  8. Conformational analysis of the antiulcer drug pirenzepine. X-ray investigations, molecular mechanics and quantum mechanical calculations and comparisons with structurally or pharmacologically related compounds.

    PubMed

    Trummlitz, G; Schmidt, G; Wagner, H U; Luger, P

    1984-01-01

    The crystal structures of the antiulcer drug 5,11-dihydro-11-[(4-methyl-1-piperazinyl) acetyl]-6H-pyrido[2,3-b] [1,4]benzodiazepin-6-one dihydrochloride (pirenzepine dihydrochloride, L-S 519 CL 2, Gastrozepin) and its monoprotonated form (pirenzepine monohydrochloride, L-S 519 CL) were determined by X-ray analysis. Molecular mechanics (MMPI) and semiempirical quantum chemical (MNDO) calculations showed that the calculated minimum energy conformations of the tricycle and of the exocyclic amide group are in agreement with the crystal structures. The conformational energies of pirenzepine as a function of four important torsional angles were calculated using different semiempirical quantum chemical methods with the CNDO/2 (complete neglect of differential overlap)-, MNDO (modified neglect of diatomic overlap)- and PCILO (perturbative configuration interaction using localized orbitals)-approximations. The conformation of one local energy minimum corresponds closely to the crystal structure of pirenzepine monohydrochloride. This conformation has a spatial arrangement which is analogous to a single consistent conformation known from the literature of 24 anticholinergic agents determined from their crystal structures by a computer graphics analysis. On the other hand there are no structural relationships of any low energy conformation of pirenzepine to conformations of other classes of tricyclic compounds which could rationalize their antidepressant, neuroleptic or antihistaminic activity. This finding explains the absence of any central effect of pirenzepine following intracerebral application. The computational elucidation of the conformational requirements for the interaction with the muscarinic receptors may be helpful for the interpretation of the selectivity of pirenzepine within the muscarinic system.

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

    PubMed

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

    2000-06-01

    , 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.

  10. 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.

  11. Band Spectra and Molecular Structure

    NASA Astrophysics Data System (ADS)

    Kronig, R. De L.

    2011-06-01

    Introduction; Part I. The Energy Levels of Diatomic Molecules and their Classification by Means of Quantum Numbers: 1. General foundations; 2. Wave mechanics of diatomic molecules; 3. Electronic levels; 4. Vibrational levels; 5. Rotational levels; 6. Stark and Zeeman effect; 7. Energy levels of polyatomic molecules; Part II. Fine Structure and Wave Mechanical Properties of the Energy Levels of Diatomic Molecules: 8. The perturbation function; 9. Rotational distortion of spin multiplets; 10. Fine structure; 11. Perturbations and predissociation; 12. Even and odd levels; 13. Symmetrical and antisymmetrical levels; Part III. Selection Rules and Intensities in Diatomic Molecules: 14. General foundations; 15. Electronic bands; 16. Vibrational bands; 17. Rotational bands; 18. Band spectra and nuclear structure; 19. Transitions in the Stark and Zeeman effect; Part IV. Macroscopic Properties of Molecular Gases: 20. Scattering; 21. Dispersion; 22. Kerr and Faraday effect; 23. Dielectric constants; 24. Magnetic susceptibilities; 25. Specific heats; Part V. Molecule Formation and Chemical Binding: 26. Heteropolar molecules; 27. Homopolar molecules. Chemical forces between two H-atoms and two He-atoms; 28. The general theory of homopolar compounds; Bibliography; Subject index.

  12. 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.

  13. 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.

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

    PubMed

    Karunakaran, V; Balachandran, V

    2014-07-15

    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 (1)H and (13)C 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.

  15. 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).

  16. The JPL Molecular Contamination Investigation Facility

    NASA Technical Reports Server (NTRS)

    Taylor, Daniel M.; Soules, David; Osborn, David

    1990-01-01

    The Molecular Contamination Investigation Facility (MCIF) is discussed in terms of its use for improving the far-UV performance of a camera and its broader applications. The MCIF incorporates two independent vacuum systems with sample isolation chambers and regulated heat exchangers as well as three quartz-crystal microbalances (QCMs) and a residual gas analyzer. One cryogenic QCM is heat sunk into an LN2 heat exchanger, while the others are thermoelectrically controlled and are heat sunk into a regulated heat exchanger. Outgas accumulation can be measured at three surface temperatures between -180 and 80 C simultaneously, and results are presented for the testing of 34 samples in a large-chambered system and 22 samples in a system with a smaller chamber. The MCIF results provide a database for fabrication processes, material selection, maximum bakeout temperatures, and the development of an ultraclean bakeout chamber.

  17. 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. PMID:21642339

  18. 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.

  19. 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. PMID:25072741

  20. 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.

  1. 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

  2. Break-junctions for investigating transport at the molecular scale

    NASA Astrophysics Data System (ADS)

    Schwarz, Florian; Lörtscher, Emanuel

    2014-11-01

    Break-junctions (BJs) enable a pair of atomic-sized electrodes to be created and the relative position between them to be controlled with sub-nanometer accuracy by mechanical means—a level of microscopic control that is not yet achievable by top-down fabrication. Locally, a BJ consists of a single-atom contact, an arrangement that is ideal not only to study various types of quantum point contacts, but also to investigate transport through an individual molecule that can bridge such a junction. In this topical review, we will provide a broad overview on the field of single-molecule electronics, in which BJs serve as the main tool of investigation. To correlate the molecular structure and transport properties to gain a fundamental understanding of the underlying transport mechanisms at the molecular scale, basic experiments that systematically cover all aspects of transport by rational chemical design and tailored experiments are needed. The variety of fascinating transport mechanisms and intrinsic molecular functionalities discovered in the past range from nonlinear transport over conductance switching to quantum interference effects observable even at room temperature. Beside discussing these results, we also look at novel directions and the most recent advances in molecular electronics investigating simultaneously electronic transport and also the mechanical and thermal properties of single-molecule junctions as well as the interaction between molecules and light. Finally, we will describe the requirements for a stepwise transition from fundamental BJ experiments towards technology-relevant architectures for future nanoelectronics applications based on ultimately-scaled molecular building blocks.

  3. Computing stoichiometric molecular composition from crystal structures

    PubMed Central

    Gražulis, Saulius; Merkys, Andrius; Vaitkus, Antanas; Okulič-Kazarinas, Mykolas

    2015-01-01

    Crystallographic investigations deliver high-accuracy information about positions of atoms in crystal unit cells. For chemists, however, the structure of a molecule is most often of interest. The structure must thus be reconstructed from crystallographic files using symmetry information and chemical properties of atoms. Most existing algorithms faithfully reconstruct separate molecules but not the overall stoichiometry of the complex present in a crystal. Here, an algorithm that can reconstruct stoichiometrically correct multimolecular ensembles is described. This algorithm uses only the crystal symmetry information for determining molecule numbers and their stoichiometric ratios. The algorithm can be used by chemists and crystallographers as a standalone implementation for investigating above-molecular ensembles or as a function implemented in graphical crystal analysis software. The greatest envisaged benefit of the algorithm, however, is for the users of large crystallographic and chemical databases, since it will permit database maintainers to generate stoichiometrically correct chemical representations of crystal structures automatically and to match them against chemical databases, enabling multidisciplinary searches across multiple databases. PMID:26089747

  4. Molecular and Supermolecular Structure of Commercial Pyrodextrins.

    PubMed

    Le Thanh-Blicharz, Joanna; Błaszczak, Wioletta; Szwengiel, Artur; Paukszta, Dominik; Lewandowicz, Grażyna

    2016-09-01

    Size exclusion chromatography with triple detection as well as infrared spectroscopy studies of commercially available pyrodextrins proved that these molecules are characterized not only by significantly lower molecular mass, in comparison to that of native starch, but also by increased branching. Therefore, pyrodextrins adopt a very compact structure in solution and show Newtonian behavior under shear in spite of their molecular masses of tens of thousands Daltons. The results also indicate that 50% reduction of digestibility of pyrodextrins is, to a minor extent, caused by formation of low-molecular color compounds containing carbonyl functional groups. The main reason is, as postulated in the literature, transglycosidation that leads to decreased occurrence of α-1,4-glycoside bonds in the molecular structure. In the process of dextrinization starch also undergoes changes in supermolecular structure, which, however, have no influence on digestibility. Likewise, the effect of formation of low-molecular colorful compounds containing carbonyl groups is not crucial.

  5. Molecular and Supermolecular Structure of Commercial Pyrodextrins.

    PubMed

    Le Thanh-Blicharz, Joanna; Błaszczak, Wioletta; Szwengiel, Artur; Paukszta, Dominik; Lewandowicz, Grażyna

    2016-09-01

    Size exclusion chromatography with triple detection as well as infrared spectroscopy studies of commercially available pyrodextrins proved that these molecules are characterized not only by significantly lower molecular mass, in comparison to that of native starch, but also by increased branching. Therefore, pyrodextrins adopt a very compact structure in solution and show Newtonian behavior under shear in spite of their molecular masses of tens of thousands Daltons. The results also indicate that 50% reduction of digestibility of pyrodextrins is, to a minor extent, caused by formation of low-molecular color compounds containing carbonyl functional groups. The main reason is, as postulated in the literature, transglycosidation that leads to decreased occurrence of α-1,4-glycoside bonds in the molecular structure. In the process of dextrinization starch also undergoes changes in supermolecular structure, which, however, have no influence on digestibility. Likewise, the effect of formation of low-molecular colorful compounds containing carbonyl groups is not crucial. PMID:27447364

  6. 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.

  7. 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

    2015-03-01

    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. PMID:25528504

  8. 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

    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

  9. 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

  10. 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

  11. Investigation of superlattice device structures

    NASA Astrophysics Data System (ADS)

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

    1985-06-01

    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

  12. Adaptive modelling of structured molecular representations for toxicity prediction

    NASA Astrophysics Data System (ADS)

    Bertinetto, Carlo; Duce, Celia; Micheli, Alessio; Solaro, Roberto; Tiné, Maria Rosaria

    2012-12-01

    We investigated the possibility of modelling structure-toxicity relationships by direct treatment of the molecular structure (without using descriptors) through an adaptive model able to retain the appropriate structural information. With respect to traditional descriptor-based approaches, this provides a more general and flexible way to tackle prediction problems that is particularly suitable when little or no background knowledge is available. Our method employs a tree-structured molecular representation, which is processed by a recursive neural network (RNN). To explore the realization of RNN modelling in toxicological problems, we employed a data set containing growth impairment concentrations (IGC50) for Tetrahymena pyriformis.

  13. 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.

  14. 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.

  15. 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.

  16. Fluorescence Titrations of Bio-relevant Complexes with DNA: Synthesis, Structural Investigation, DNA Binding/Cleavage, Antimicrobial and Molecular Docking Studies.

    PubMed

    Arun, Thesingu Rajan; Subramanian, Ramasamy; Packianathan, Seemon; Raman, Natarajan

    2015-07-01

    In the present work, we attempted to develop new metal complexes (Cu(II), Co(II), Ni(II) and Zn(II)) of the imine ligand which was synthesized from 9,10-phenanthrenequinone and para-anisidine. With an intention to make the complexes most stable, very special chelating amino acid has been coordinated to the metal centre. The resultant metal complexes have been characterized by variety of techniques including FT-IR, UV-Vis., (1)H NMR, (13)C NMR, powder XRD, EPR and mass spectral studies. The interaction of the complexes with DNA has been effectively examined and explored by fluorescence titration, UV-Vis absorption, viscometer titration, cyclic voltammetry (CV) and differential pulse voltammetry. Moreover, molecular docking analysis has been performed to understand the nature of binding of the complexes with DNA. These studies prove that CT DNA interaction of the complexes follows intercalation mode. The metal complexes exhibit effective cleavage of pUC19 DNA by an oxidative cleavage mechanism. The antimicrobial screening indicates that these complexes are good antimicrobial agents against various organisms.

  17. Investigation of the molecular structure of radical cation of s-trioxane: quantum chemical calculations and low-temperature EPR results

    NASA Astrophysics Data System (ADS)

    Janovský, I.; Naumov, S.; Knolle, W.; Mehnert, R.

    2003-06-01

    s-Trioxane radical cation was radiolytically generated in freon matrix and the changes of the EPR spectra with temperature, arising from conformational interconversion involving ring, were observed. The equilibration, leading to six equivalent protons (hfs splitting constant 5.9 mT) characteristic of the average planar geometry of the radical cation, occurs at ˜120 K in CF 3CCl 3. Supplementary experiments with 1,3-dioxane, which forms a radical cation with a similar electronic structure, were also performed. DFT quantum chemical calculations were used to support the experimental results.

  18. 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.

  19. 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

    NASA Astrophysics Data System (ADS)

    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 13C 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.

  20. Ab Initio Investigation of the Structure, Stability and Atmospheric Distribution of Molecular Clusters Containing H2O, CO2 and N2O.

    NASA Astrophysics Data System (ADS)

    Lemke, K. H.; Seward, T. M.

    2007-12-01

    We present results from ab initio calculations for the structures, energetics and atmospheric abundances of neutral clusters containing water, carbon dioxide and nitrous oxide up to 45km altitude using the complete basis set CBS-Q and G3 multi-level procedures. Gas phase hydration energies, enthalpies and entropies for the stepwise attachment of water onto clusters according to X(H2O)n + H2O = X(H2O)n+1 (where X = H2O, CO2 and N2O) are reported for up to n=5. In particular, our results demonstrate that values for the incremental hydration enthalpies and entropies of all three gases H2O, CO2 and N2O asymptotically approach values characteristic of bulk liquid water (i.e. -44.0 kJ/mol for the enthalpy and -118.8 J/Kmol for the entropy of condensation) following attachment of around 3-4 water molecules. Interestingly, our calculated number densities for the water dimer at 292Kelvin are in excellent agreement with recent values obtained from IR measurements of atmospheric media (Pfeilsticker et al., 2003, Science). Our quantum chemical calculations indicate that water attachment onto H2O, CO2 and N2O is a thermodynamically favorable process, such that hydrated clusters would form a significant atmospheric repository of these species.

  1. Ab initio investigation of the structure, stability, and atmospheric distribution of molecular clusters containing H2O, CO2, and N2O

    NASA Astrophysics Data System (ADS)

    Lemke, Kono H.; Seward, Terry M.

    2008-10-01

    We present results from ab initio calculations for the structures and energetic properties of neutral clusters containing water, carbon dioxide, and nitrous oxide using the complete basis set CBS-Q multilevel procedure. Gas phase hydration energies ΔG0, enthalpies ΔH0, and entropies ΔS0 for the stepwise attachment of water onto clusters according to X·(H2O)n + H2O ↔ X·(H2O)n+1 (X = CO2, N2O, and H2O) are reported for n ≤ 4. In particular, our results demonstrate that values for the incremental hydration enthalpies and entropies of all three gases CO2, N2O, and H2O asymptotically approach values characteristic of bulk water (i.e., -44.0 kJ mol-1 for the enthalpy and -118.8 J K-1 mol-1 for the entropy of condensation) following attachment of around three to four water molecules. Our ab initio calculations indicate that water attachment onto CO2, N2O, and H2O is a thermodynamically favorable process, such that hydrated CO2·(H2O)n, N2O·(H2O)n, and H2O·(H2O)n clusters would form a significant atmospheric repository of these species.

  2. Structures in Molecular Clouds: Modeling

    SciTech Connect

    Kane, J O; Mizuta, A; Pound, M W; Remington, B A; Ryutov, D D

    2006-04-20

    We attempt to predict the observed morphology, column density and velocity gradient of Pillar II of the Eagle Nebula, using Rayleigh Taylor (RT) models in which growth is seeded by an initial perturbation in density or in shape of the illuminated surface, and cometary models in which structure is arises from a initially spherical cloud with a dense core. Attempting to mitigate suppression of RT growth by recombination, we use a large cylindrical model volume containing the illuminating source and the self-consistently evolving ablated outflow and the photon flux field, and use initial clouds with finite lateral extent. An RT model shows no growth, while a cometary model appears to be more successful at reproducing observations.

  3. [Oligoglycine surface structures: molecular dynamics simulation].

    PubMed

    Gus'kova, O A; Khalatur, P G; Khokhlov, A R; Chinarev, A A; Tsygankova, S V; Bovin, N V

    2010-01-01

    The full-atomic molecular dynamics (MD) simulation of adsorption mode for diantennary oligoglycines [H-Gly4-NH(CH2)5]2 onto graphite and mica surface is described. The resulting structure of adsorption layers is analyzed. The peptide second structure motives have been studied by both STRIDE (structural identification) and DSSP (dictionary of secondary structure of proteins) methods. The obtained results confirm the possibility of polyglycine II (PGII) structure formation in diantennary oligoglycine (DAOG) monolayers deposited onto graphite surface, which was earlier estimated based on atomic-force microscopy measurements.

  4. Structure investigations on oxygen fluorides.

    PubMed

    Marx, Rupert; Seppelt, Konrad

    2015-12-01

    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. PMID:26351980

  5. 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 -}.

  6. 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.

  7. Molecular Structure of Human-Liver Glycogen

    PubMed Central

    Deng, Bin; Sullivan, Mitchell A.; Chen, Cheng; Li, Jialun; Powell, Prudence O.; Hu, Zhenxia; Gilbert, Robert G.

    2016-01-01

    Glycogen is a highly branched glucose polymer which is involved in maintaining blood-sugar homeostasis. Liver glycogen contains large composite α particles made up of linked β particles. Previous studies have shown that the binding which links β particles into α particles is impaired in diabetic mice. The present study reports the first molecular structural characterization of human-liver glycogen from non-diabetic patients, using transmission electron microscopy for morphology and size-exclusion chromatography for the molecular size distribution; the latter is also studied as a function of time during acid hydrolysis in vitro, which is sensitive to certain structural features, particularly glycosidic vs. proteinaceous linkages. The results are compared with those seen in mice and pigs. The molecular structural change during acid hydrolysis is similar in each case, and indicates that the linkage of β into α particles is not glycosidic. This result, and the similar morphology in each case, together imply that human liver glycogen has similar molecular structure to those of mice and pigs. This knowledge will be useful for future diabetes drug targets. PMID:26934359

  8. 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)

  9. How We Teach Molecular Structure to Freshmen.

    ERIC Educational Resources Information Center

    Hurst, Michael O.

    2002-01-01

    Currently molecular structure is taught in general chemistry using three theories, this being based more on historical development rather than logical pedagogy. Electronegativity is taught with a confusing mixture of definitions that do not correspond to modern practice. Valence bond theory and VSEPR are used together in a way that often confuses…

  10. Synthesis, molecular structure, FT-IR, Raman, XRD and theoretical investigations of (2E)-1-(5-chlorothiophen-2-yl)-3-(naphthalen-2-yl)prop-2-en-1-one.

    PubMed

    Chidan Kumar, Chandraju Sadolalu; Fun, Hoong Kun; Parlak, Cemal; Rhyman, Lydia; Ramasami, Ponnadurai; Tursun, Mahir; Chandraju, Siddegowda; Quah, Ching Kheng

    2014-11-11

    A novel (2E)-1-(5-chlorothiophen-2-yl)-3-(naphthalen-2-yl)prop-2-en-1-one [C17H11ClOS] compound has been synthesized and its structure has been characterized by FT-IR, Raman and single-crystal X-ray diffraction techniques. The isomers, optimized geometrical parameters, normal mode frequencies and corresponding vibrational assignments of the compound have been examined by means of the density functional theory method, employing, the Becke-3-Lee-Yang-Parr functional and the 6-311+G(3df,p) basis set. Reliable vibrational assignments and molecular orbitals have been investigated by the potential energy distribution and natural bonding orbital analyses, respectively. The compound crystallizes in the monoclinic space group P2₁/c with the unit cell parameters a=5.7827(8)Å, b=14.590(2)Å, c=16.138(2)Å and β=89.987 (°). The CC bond of the central enone group adopts an E configuration. There is a good agreement between the theoretically predicted structural parameters and vibrational frequencies and those obtained experimentally.

  11. Molecular and structural analysis of viscoelastic properties

    NASA Astrophysics Data System (ADS)

    Yapp, Rebecca D.; Kalyanam, Sureshkumar; Insana, Michael F.

    2007-03-01

    Elasticity imaging is emerging as an important tool for breast cancer detection and monitoring of treatment. Viscoelastic image contrast in breast lesions is generated by disease specific processes that modify the molecular structure of connective tissues. We showed previously that gelatin hydrogels exhibit mechanical behavior similar to native collagen found in breast tissue and therefore are suitable as phantoms for elasticity imaging. This paper summarizes our study of the viscoelastic properties of hydrogels designed to discover molecular-scale sources of elasticity image contrast.

  12. 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.

  13. C-C bond unsaturation degree in monosubstituted ferrocenes for molecular electronics investigated by a combined near-edge x-ray absorption fine structure, x-ray photoemission spectroscopy, and density functional theory approach

    SciTech Connect

    Boccia, A.; Lanzilotto, V.; Marrani, A. G.; Zanoni, R.; Stranges, S.; Alagia, M.; Fronzoni, G.; Decleva, P.

    2012-04-07

    We present the results of an experimental and theoretical investigation of monosubstituted ethyl-, vinyl-, and ethynyl-ferrocene (EtFC, VFC, and EFC) free molecules, obtained by means of synchrotron-radiation based C 1s photoabsorption (NEXAFS) and photoemission (C 1s XPS) spectroscopies, and density functional theory (DFT) calculations. Such a combined study is aimed at elucidating the role played by the C-C bond unsaturation degree of the substituent on the electronic structure of the ferrocene derivatives. Such substituents are required for molecular chemical anchoring onto relevant surfaces when ferrocenes are used for molecular electronics hybrid devices. The high resolution C 1s NEXAFS spectra exhibit distinctive features that depend on the degree of unsaturation of the hydrocarbon substituent. The theoretical approach to consider the NEXAFS spectrum made of three parts allowed to disentangle the specific contribution of the substituent group to the experimental spectrum as a function of its unsaturation degree. C 1s IEs were derived from the experimental data analysis based on the DFT calculated IE values for the different carbon atoms of the substituent and cyclopentadienyl (Cp) rings. Distinctive trends of chemical shifts were observed for the substituent carbon atoms and the substituted atom of the Cp ring along the series of ferrocenes. The calculated IE pattern was rationalized in terms of initial and final state effects influencing the IE value, with special regard to the different mechanism of electron conjugation between the Cp ring and the substituent, namely the {sigma}/{pi} hyperconjugation in EtFC and the {pi}-conjugation in VFC and EFC.

  14. C-C bond unsaturation degree in monosubstituted ferrocenes for molecular electronics investigated by a combined near-edge x-ray absorption fine structure, x-ray photoemission spectroscopy, and density functional theory approach

    NASA Astrophysics Data System (ADS)

    Boccia, A.; Lanzilotto, V.; Marrani, A. G.; Stranges, S.; Zanoni, R.; Alagia, M.; Fronzoni, G.; Decleva, P.

    2012-04-01

    We present the results of an experimental and theoretical investigation of monosubstituted ethyl-, vinyl-, and ethynyl-ferrocene (EtFC, VFC, and EFC) free molecules, obtained by means of synchrotron-radiation based C 1s photoabsorption (NEXAFS) and photoemission (C 1s XPS) spectroscopies, and density functional theory (DFT) calculations. Such a combined study is aimed at elucidating the role played by the C-C bond unsaturation degree of the substituent on the electronic structure of the ferrocene derivatives. Such substituents are required for molecular chemical anchoring onto relevant surfaces when ferrocenes are used for molecular electronics hybrid devices. The high resolution C 1s NEXAFS spectra exhibit distinctive features that depend on the degree of unsaturation of the hydrocarbon substituent. The theoretical approach to consider the NEXAFS spectrum made of three parts allowed to disentangle the specific contribution of the substituent group to the experimental spectrum as a function of its unsaturation degree. C 1s IEs were derived from the experimental data analysis based on the DFT calculated IE values for the different carbon atoms of the substituent and cyclopentadienyl (Cp) rings. Distinctive trends of chemical shifts were observed for the substituent carbon atoms and the substituted atom of the Cp ring along the series of ferrocenes. The calculated IE pattern was rationalized in terms of initial and final state effects influencing the IE value, with special regard to the different mechanism of electron conjugation between the Cp ring and the substituent, namely the σ/π hyperconjugation in EtFC and the π-conjugation in VFC and EFC.

  15. 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).

  16. Silylated carbodiimides in molecular and extended structures

    NASA Astrophysics Data System (ADS)

    Kroll, Peter; Riedel, Ralf; Hoffmann, Roald

    1999-08-01

    This work studies the ternary Si-C-N phases SiC2N4 and Si2CN4,exploiting an analogy between the NCN and O groups. Starting from the molecular model of N,N'-bis(trimethylsilyl)-carbodiimide and proceeding to extended models, we calculate that the energy hypersurface associated with the Si-N=C bond angle φN is very shallow, for both molecular and extended structures. We propose a crystal structure for the low-temperature modification α-SiC2N4 in space group P4322 (95), which is 40 meV (~4 kJ/mol) lower in energy than an ideal cubic arrangement in space group Pn3¯m.A second structure, β-SiC2N4 [space group P4¯n2 (118)], is slightly higher in energy than α-SiC2N4,but still more stable than the cubic structure, and may be the high-temperature structure of SiC2N4.Both variants of SiC2N4 show a small bulk modulus of about 8 GPa (~0.13 Mbar),suggesting a high compressibility of these nonoxide covalently bonded materials. For Si2CN4 we refined the crystal structure of the compound within the experimentally determined space group Aba2 (41). We also found a second candidate nearly equal in energy, with space group Cmc21,differing only in the connection pattern of the SiN2 layered sheets. Both ternary compounds appear to be thermodynamically unstable with respect to decomposition into Si3N4,C, and molecular N2.

  17. 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.

  18. Solution 1H NMR investigation of the active site molecular and electronic structures of substrate-bound, cyanide-inhibited HmuO, a bacterial heme oxygenase from Corynebacterium diphtheriae.

    PubMed

    Li, Yiming; Syvitski, Ray T; Chu, Grace C; Ikeda-Saito, Masao; Mar, Gerd N La

    2003-02-28

    The molecular structure and dynamic properties of the active site environment of HmuO, a heme oxygenase (HO) from the pathogenic bacterium Corynebacterium diphtheriae, have been investigated by (1)H NMR spectroscopy using the human HO (hHO) complex as a homology model. It is demonstrated that not only the spatial contacts among residues and between residues and heme, but the magnetic axes that can be related to the direction and magnitude of the steric tilt of the FeCN unit are strongly conserved in the two HO complexes. The results indicate that very similar contributions of steric blockage of several meso positions and steric tilt of the attacking ligand are operative. A distal H-bond network that involves numerous very strong H-bonds and immobilized water molecules is identified in HmuO that is analogous to that previously identified in hHO (Li, Y., Syvitski, R. T., Auclair, K., Wilks, A., Ortiz de Montellano, P. R., and La Mar, G. N. (2002) J. Biol. Chem. 277, 33018-33031). The NMR results are completely consistent with the very recent crystal structure of the HmuO.substrate complex. The H-bond network/ordered water molecules are proposed to orient the distal water molecule near the catalytically key Asp(136) (Asp(140) in hHO) that stabilizes the hydroperoxy intermediate. The dynamic stability of this H-bond network in HmuO is significantly greater than in hHO and may account for the slower catalytic rate in bacterial HO compared with mammalian HO.

  19. A structural investigation of ionic liquid mixtures.

    PubMed

    Matthews, Richard P; Villar-Garcia, Ignacio J; Weber, Cameron C; Griffith, Jeraime; Cameron, Fiona; Hallett, Jason P; Hunt, Patricia A; Welton, Tom

    2016-03-28

    The structures of mixtures of ionic liquids (ILs) featuring a common 1-butyl-3-methylimidazolium ([C4C1im](+)) cation but different anions have been investigated both experimentally and computationally. (1)H and (13)C NMR of the ILs and their mixtures has been performed both on the undiluted liquids and those diluted by CD2Cl2. These experiments have been complemented by quantum chemical density functional theory calculations and molecular dynamics simulations. These techniques have identified the formation of preferential interactions between H(2) of the imidazolium cation and the most strongly hydrogen bond (H-bond) accepting anion. In addition, a preference for the more weakly H-bond accepting anion to interact above the imidazolium ring through anion-π(+) interactions has been identified. The modelling of these data has identified that the magnitude of these preferences are small, of the order of only a few kJ mol(-1), for all IL mixtures. No clustering of the anions around a specific cation could be observed, indicating that these interactions arise from the reorientation of the cation within a randomly assigned network of anions. π(+)-π(+) stacking of the imidazolium cations was also studied and found to be promoted by ILs with a strong H-bond accepting anion. Stacking interactions are easily disrupted by the introduction of small proportions (<50 mol%) of a weakly coordinating anion due to their propensity to form anion-π(+) interactions. These results suggest that the formation of IL mixtures with different anions leads to subtle structural changes of much lower energy than the Coulombic ordering of ions, accounting for why most IL mixtures exhibit ideal, or nearly ideal, behaviour. PMID:26947103

  20. A structural investigation of ionic liquid mixtures.

    PubMed

    Matthews, Richard P; Villar-Garcia, Ignacio J; Weber, Cameron C; Griffith, Jeraime; Cameron, Fiona; Hallett, Jason P; Hunt, Patricia A; Welton, Tom

    2016-03-28

    The structures of mixtures of ionic liquids (ILs) featuring a common 1-butyl-3-methylimidazolium ([C4C1im](+)) cation but different anions have been investigated both experimentally and computationally. (1)H and (13)C NMR of the ILs and their mixtures has been performed both on the undiluted liquids and those diluted by CD2Cl2. These experiments have been complemented by quantum chemical density functional theory calculations and molecular dynamics simulations. These techniques have identified the formation of preferential interactions between H(2) of the imidazolium cation and the most strongly hydrogen bond (H-bond) accepting anion. In addition, a preference for the more weakly H-bond accepting anion to interact above the imidazolium ring through anion-π(+) interactions has been identified. The modelling of these data has identified that the magnitude of these preferences are small, of the order of only a few kJ mol(-1), for all IL mixtures. No clustering of the anions around a specific cation could be observed, indicating that these interactions arise from the reorientation of the cation within a randomly assigned network of anions. π(+)-π(+) stacking of the imidazolium cations was also studied and found to be promoted by ILs with a strong H-bond accepting anion. Stacking interactions are easily disrupted by the introduction of small proportions (<50 mol%) of a weakly coordinating anion due to their propensity to form anion-π(+) interactions. These results suggest that the formation of IL mixtures with different anions leads to subtle structural changes of much lower energy than the Coulombic ordering of ions, accounting for why most IL mixtures exhibit ideal, or nearly ideal, behaviour.

  1. On calculating the equilibrium structure of molecular crystals.

    SciTech Connect

    Mattsson, Ann Elisabet; Wixom, Ryan R.; Mattsson, Thomas Kjell Rene

    2010-03-01

    The difficulty of calculating the ambient properties of molecular crystals, such as the explosive PETN, has long hampered much needed computational investigations of these materials. One reason for the shortcomings is that the exchange-correlation functionals available for Density Functional Theory (DFT) based calculations do not correctly describe the weak intermolecular van der Waals' forces present in molecular crystals. However, this weak interaction also poses other challenges for the computational schemes used. We will discuss these issues in the context of calculations of lattice constants and structure of PETN with a number of different functionals, and also discuss if these limitations can be circumvented for studies at non-ambient conditions.

  2. 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. PMID:27142698

  3. [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.

  4. 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.

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

    PubMed

    Le, Minh Quy; 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. PMID:27678335

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

    PubMed

    Le, Minh Quy; 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.

  7. 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.

  8. Effects of amine molecular structure on carbon nanotubes functionalization.

    PubMed

    Jimeno, A; Goyanes, S; Eceiza, A; Kortaberria, G; Mondragon, I; Corcuera, M A

    2009-10-01

    Three amines with different molecular structure, triethylenetetramine (TETA) and two polyetheramines (Jeffamine D-230 and Jeffamine T-403) were employed to functionalize multi-walled carbon nanotubes (MWCNT) previously oxidized by acid treatment. The functionalized MWCNT were characterized by Fourier transform infrared spectroscopy (FT-IR), Raman spectroscopy, UV-vis spectroscopy and the surface modification was investigated by field emission scanning electron microscopy (FE-SEM). Thermogravimetric analysis (TGA) was employed to quantify the amount of amine groups anchored to MWCNTs. The results have shown that the efficiency of amine functionalization is in the order TETA > D-230 > T-403, thus showing that amine chemical structure and molecular weight are important parameters on functionalization of carbon nanotubes. PMID:19908518

  9. 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).

  10. First principles investigation of the structure of a bacteriochlorophyll crystal

    SciTech Connect

    Marchi, M. |; Hutter, J.; Parrinello, M.

    1996-08-21

    In this communication we present an ab initio study of the crystal of methyl bacteriophorbide (MeBPheo) a, a bacteriochlorophyll derivative, and high-precision structure of which is available. Our main purpose has been to investigate the viability of the technique toward complex molecular systems relevant to biologically important phenomena, in this particular case photosynthesis. Here we present the following results: First, we show that DFT is capable of calculating nuclear positions in excellent agreement with the experimental X-ray structure. Second, the calculated electronic density of the HOMO orbital reveals a {pi} type bond between rings I and III, consistent with the one-dimensional chain structure of the MeBPheo a molecules in the crystal. Finally, after performing the optimization of the molecular geometry with one electron in the LUMO state, we find localized bond length changes near the ring II of the MeBPheo a. 19 refs., 3 figs.

  11. Molecular composition, structure, and sensitivity of explosives

    SciTech Connect

    Storm, C.B.; Travis, J.R.

    1992-01-01

    High explosives, blasting agents, propellants, and pyrotechnics are all metastable relative to reaction products and are termed energetic materials. They are thermodynamically unstable but the kinetics of decomposition at ambient conditions are sufficiently slow that they can be handled safely under controlled conditions. The ease with which an energetic material can be caused to undergo a violent reaction or detonation is called its sensitivity. Sensitivity tests for energetic materials are aimed at defining the response of the material to a specific situation, usually prompt shock initiation or a delayed reaction in an accident. The observed response is always due to a combination of the physical state and the molecular structure of the material. Modeling of any initiation process must consider both factors. The physical state of the material determines how and where the energy is deposited in the material. The molecular structure determines the mechanism of decomposition of the material and the rate of energy release. Slower inherent reaction chemistry leads to longer reaction zones in detonation and inherently safer materials. Slower chemistry also requires hot spots involved in initiation to be hotter and to survive for longer periods of time. High thermal conductivity also leads to quenching of small hot spots and makes a material more difficult to initiate. Early endothermic decomposition chemistry also delays initiation by delaying heat release to support hot spot growth. The growth to violent reaction or detonation also depends on the nature of the early reaction products. If chemical intermediates are produced that drive further accelerating autocatalytic decomposition the initiation will grow rapidly to a violent reaction.

  12. 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.

  13. Plant sex chromosomes: molecular structure and function.

    PubMed

    Jamilena, M; Mariotti, B; Manzano, S

    2008-01-01

    Recent molecular and genomic studies carried out in a number of model dioecious plant species, including Asparagus officinalis, Carica papaya, Silene latifolia, Rumex acetosa and Marchantia polymorpha, have shed light on the molecular structure of both homomorphic and heteromorphic sex chromosomes, and also on the gene functions they have maintained since their evolution from a pair of autosomes. The molecular structure of sex chromosomes in species from different plant families represents the evolutionary pathway followed by sex chromosomes during their evolution. The degree of Y chromosome degeneration that accompanies the suppression of recombination between the Xs and Ys differs among species. The primitive Ys of A. officinalis and C. papaya have only diverged from their homomorphic Xs in a short male-specific and non-recombining region (MSY), while the heteromorphic Ys of S. latifolia, R. acetosa and M. polymorpha have diverged from their respective Xs. As in the Y chromosomes of mammals and Drosophila, the accumulation of repetitive DNA, including both transposable elements and satellite DNA, has played an important role in the divergence and size enlargement of plant Ys, and consequently in reducing gene density. Nevertheless, the degeneration process in plants does not appear to have reached the Y-linked genes. Although a low gene density has been found in the sequenced Y chromosome of M. polymorpha, most of its genes are essential and are expressed in the vegetative and reproductive organs in both male and females. Similarly, most of the Y-linked genes that have been isolated and characterized up to now in S. latifolia are housekeeping genes that have X-linked homologues, and are therefore expressed in both males and females. Only one of them seems to be degenerate with respect to its homologous region in the X. Sequence analysis of larger regions in the homomorphic X and Y chromosomes of papaya and asparagus, and also in the heteromorphic sex chromosomes

  14. A molecular investigation of adsorption onto mineral pigments

    NASA Astrophysics Data System (ADS)

    Ninness, Brian J.

    Pigment suspensions are important in several processes such as ceramics, paints, inks, and coatings. In the wet state, pigments are combined with a variety of chemical species such as polymers, surfactants, and polyelectrolytes which produce a complex colloidal system. The adsorption, desorption, and redistribution of these species at the pigment-aqueous solution interface can have an impact on the behavior in both the wet state or its final dried state. The goal of this work is to establish a molecular picture of the adsorption properties of these pigmented systems. A novel in situ infrared technique has been developed which allows the detection of adsorbed surface species on pigment particles in an aqueous environment. The technique involves the use of a polymeric binder to anchor the colloidal pigment particles to the surface of an internal reflection element (IRE). The binder only weakly perturbs about 25% of the reactive surface sites (hydroxyl groups) on silica. The reaction of succinic anhydride with an aminosilanized silica surface has been quantified using this technique. The adsorption dynamics of the cationic surfactant cetyltrimethylammonium bromide (C16TAB) at the TiO2-aqueous solution interface has been investigated using Fourier transform infrared-attenuated total reflection spectroscopy (FTIR-ATR) and electrokinetic analysis. At low bulk concentrations, C16TAB is shown to adsorb as isolated islands with a "defective" bilayer structure. Anionic probe molecules are shown to effectively "tune" the adsorbed surfactant microstructure. The results indicate that the structure of the adsorbed surfactant layer, and not the amount of adsorbed surfactant, dictates the subsequent adsorption behavior of the system. Atomic Layer Deposition is used to deposit a TiO2 layer onto the surfaces of silica and kaolin pigments. The process involves the cyclic reaction sequence of the vapors of TiCl4 and H2O. Three complete deposition cycles are needed before the surfaces

  15. Molecular structure input on the web.

    PubMed

    Ertl, Peter

    2010-02-02

    A molecule editor, that is program for input and editing of molecules, is an indispensable part of every cheminformatics or molecular processing system. This review focuses on a special type of molecule editors, namely those that are used for molecule structure input on the web. Scientific computing is now moving more and more in the direction of web services and cloud computing, with servers scattered all around the Internet. Thus a web browser has become the universal scientific user interface, and a tool to edit molecules directly within the web browser is essential.The review covers a history of web-based structure input, starting with simple text entry boxes and early molecule editors based on clickable maps, before moving to the current situation dominated by Java applets. One typical example - the popular JME Molecule Editor - will be described in more detail. Modern Ajax server-side molecule editors are also presented. And finally, the possible future direction of web-based molecule editing, based on technologies like JavaScript and Flash, is discussed.

  16. DFT charge transfer of hybrid molecular ferrocene/Si structures

    NASA Astrophysics Data System (ADS)

    Calborean, Adrian; Buimaga-Iarinca, Luiza; Graur, Florin

    2015-05-01

    The electrochemical behavior and electronic properties of redox-active ferrocenes grafted onto semiconductor Si(100) substrate were investigated theoretically by first-principles calculations. Organic molecules were attached via the formation of Si-C covalent bonds through two different linkers: vinyl (direct grafting), and N3(CH2)11 (indirect grafting). Redox energies and the electronic properties relating to different spacers in hybrid ferrocene Fc/Si and ferrocenium Fc+/Si structures were theoretically extracted and compared with experimental cyclic voltametry data. Electronic charge transfers are discussed through the alignment positions of the frontier orbitals of the molecule with respect to the Si substrate gap. Periodic boundary conditions were used to investigate the Si(100) as a slab surface and hybrid Fc/Si structures. The resulting projected density of states (PDOS) were compared with molecular results and discussed in the light of experimental data.

  17. 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...

  18. [Evolution and systematics of nematodes based on molecular investigation].

    PubMed

    Okulewicz, Anna; Perec, Agnieszka

    2004-01-01

    Evolution and systematics of nematodes based on molecular investigation. The use of molecular phylogenetics to examine the interrelationships between animal parasites, free-living nematodes, and plant parasites versus traditional classification based on morphological-ecological characters was discussed and reviewed. Distinct differences were observed between parasitic nematodes and free-living ones. Within the former group, animal parasites turned out to be distinctly different from plant parasites. Using small subunit of ribosomal RNA gene sequence from a wide range of nematodes, there is a possibility to compare animal-parasitic, plant-parasitic and free-living taxa. Nowadays the parasitic nematodes expressed sequence tag (EST) project is currently generating sequence information to provide a new source of data to examine the evolutionary history of this taxonomic group. PMID:16859012

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

    NASA Astrophysics Data System (ADS)

    Neogi, Anupam; Mitra, Nilanjan

    2016-02-01

    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.

  20. 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.)

  1. 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.

  2. 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.

  3. 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

  4. Nonlinear Optical Investigations of Vibrational Relaxation in Molecular Crystals

    NASA Astrophysics Data System (ADS)

    Decola, Philip Lawrence

    Experimental studies of four-wave mixing have been used to obtain novel spectroscopic information in molecular crystals. This work can be separated into singly resonant and multiresonant investigations. One effort was to exploit the frequency and time domain capabilities of singly resonant coherent anti-Stokes Raman spectroscopy (CARS) to study vibrational dynamics in naphthalene and benzene single crystals at liquid Helium temperatures. To a large extent vibrational energy is chemical energy, so to understand the flow of vibrational energy in molecules and molecular aggregates can enhance our understanding of chemical reaction rates and pathways. Some of the salient results are: (1) the existence of motional narrowing in molecular crystals makes it possible for lifetime (T _1) broadening to dominate the linewidth of the vibrational transition even when the intrinsic disorder width is much larger than 1/T_1, (2) relaxation in molecular crystals can be surprisingly slow, ranging from subnanosecond to nanosecond, (3) substantial mode dependent contribution to relaxation from ^{13}C impurities in benzene, and (4) evidence of mode specific energy relaxation observed in a systematic study of benzene Raman active modes. The results obtained here are applied to the problems of understanding the contributions to residual low-temperature vibron linewidths and of developing simple mechanical intuitions to explain systematically the kinetic pathways for vibrational relaxation in molecular crystals. These results are discussed in light of the current theories of excitation dynamics in condensed phases. The other area of study was multiresonant nonlinear spectroscopic investigations of mixed organic crystals. The first multiresonant CARS and its Stokes analogue (CSRS) have been obtained in a mixed crystal of pentacene in benzoic acid allowing the simultaneous observation of ground and excited state Raman spectra. These spectra contain lines that are much sharper than expected

  5. Molecular Dynamics Simulations to Investigate the Influences of Amino Acid Mutations on Protein Three-Dimensional Structures of Cytochrome P450 2D6.1, 2, 10, 14A, 51, and 62.

    PubMed

    Fukuyoshi, Shuichi; Kometani, Masaharu; Watanabe, Yurie; Hiratsuka, Masahiro; Yamaotsu, Noriyuki; Hirono, Shuichi; Manabe, Noriyoshi; Takahashi, Ohgi; Oda, Akifumi

    2016-01-01

    Many natural mutants of the drug metabolizing enzyme cytochrome P450 (CYP) 2D6 have been reported. Because the enzymatic activities of many mutants are different from that of the wild type, the genetic polymorphism of CYP2D6 plays an important role in drug metabolism. In this study, the molecular dynamics simulations of the wild type and mutants of CYP2D6, CYP2D6.1, 2, 10, 14A, 51, and 62 were performed, and the predictions of static and dynamic structures within them were conducted. In the mutant CYP2D6.10, 14A, and 61, dynamic properties of the F-G loop, which is one of the components of the active site access channel of CYP2D6, were different from that of the wild type. The F-G loop acted as the "hatch" of the channel, which was closed in those mutants. The structure of CYP2D6.51 was not converged by the simulation, which indicated that the three-dimensional structure of CYP2D6.51 was largely different from that of the wild type. In addition, the intramolecular interaction network of CYP2D6.10, 14A, and 61 was different from that of the wild type, and it is considered that these structural changes are the reason for the decrease or loss of enzymatic activities. On the other hand, the static and dynamic properties of CYP2D6.2, whose activity was normal, were not considerably different from those of the wild type.

  6. Molecular Dynamics Simulations to Investigate the Influences of Amino Acid Mutations on Protein Three-Dimensional Structures of Cytochrome P450 2D6.1, 2, 10, 14A, 51, and 62

    PubMed Central

    Watanabe, Yurie; Hiratsuka, Masahiro; Yamaotsu, Noriyuki; Hirono, Shuichi; Manabe, Noriyoshi; Takahashi, Ohgi; Oda, Akifumi

    2016-01-01

    Many natural mutants of the drug metabolizing enzyme cytochrome P450 (CYP) 2D6 have been reported. Because the enzymatic activities of many mutants are different from that of the wild type, the genetic polymorphism of CYP2D6 plays an important role in drug metabolism. In this study, the molecular dynamics simulations of the wild type and mutants of CYP2D6, CYP2D6.1, 2, 10, 14A, 51, and 62 were performed, and the predictions of static and dynamic structures within them were conducted. In the mutant CYP2D6.10, 14A, and 61, dynamic properties of the F-G loop, which is one of the components of the active site access channel of CYP2D6, were different from that of the wild type. The F-G loop acted as the “hatch” of the channel, which was closed in those mutants. The structure of CYP2D6.51 was not converged by the simulation, which indicated that the three-dimensional structure of CYP2D6.51 was largely different from that of the wild type. In addition, the intramolecular interaction network of CYP2D6.10, 14A, and 61 was different from that of the wild type, and it is considered that these structural changes are the reason for the decrease or loss of enzymatic activities. On the other hand, the static and dynamic properties of CYP2D6.2, whose activity was normal, were not considerably different from those of the wild type. PMID:27046024

  7. 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

  8. 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.

  9. Spectroscopic investigations of the electronic structure of neptunyl ions.

    SciTech Connect

    Wilkerson, M. P.; Berg, J. M.; Dewey, H. J.

    2003-01-01

    Molecular electronic structures are innately sensitive to the geometric and chemical environments around the metal center of coordination compounds . However, the interrelationships between the electronic structures and molecular geometries of actinide species, which often contain more than one electron in the Sf valence shell, are quite complex due to the large numbers of possible electronic states and high densities of vibronically enabled transitions .1'2 Investigations of the optical signatures of simple, well-defined molecular systems should provide the most straightforward approach for unharnessing these fundamental relationships, and in particular, systems with a single electron in the valence Sf shell, such as the neptunyl ion (Np0 22+), should provide the most viable means for characte rizing actinide electronic structure. Furthermore, Sf orbital-occupied actinide systems exhibit not only visible and ultraviolet ligand-to-metal charge-transfer spectral bands, but also near-infrared Sf-Sf transitions resulting from promotion of a Sf electron to an orbital of primarily Sf character .

  10. Molecular structure and motion in zero field magnetic resonance

    SciTech Connect

    Jarvie, T.P.

    1989-10-01

    Zero field magnetic resonance is well suited for the determination of molecular structure and the study of motion in disordered materials. Experiments performed in zero applied magnetic field avoid the anisotropic broadening in high field nuclear magnetic resonance (NMR) experiments. As a result, molecular structure and subtle effects of motion are more readily observed.

  11. Quantum Theory of Atomic and Molecular Structures and Interactions

    NASA Astrophysics Data System (ADS)

    Makrides, Constantinos

    This dissertation consists of topics in two related areas of research that together provide quantum mechanical descriptions of atomic and molecular interactions and reactions. The first is the ab initio electronic structure calculation that provides the atomic and molecular interaction potential, including the long-range potential. The second is the quantum theory of interactions that uses such potentials to understand scattering, long-range molecules, and reactions. In ab initio electronic structure calculations, we present results of dynamic polarizabilities for a variety of atoms and molecules, and the long-range dispersion coefficients for a number of atom-atom and atom-molecule cases. We also present results of a potential energy surface for the triatomic lithium-ytterbium-lithium system, aimed at understanding the related chemical reactions. In the quantum theory of interactions, we present a multichannel quantum-defect theory (MQDT) for atomic interactions in a magnetic field. This subject, which is complex especially for atoms with hyperfine structure, is essential for the understanding and the realization of control and tuning of atomic interactions by a magnetic field: a key feature that has popularized cold atom physics in its investigations of few-body and many-body quantum systems. Through the example of LiK, we show how MQDT provides a systematic and an efficient understanding of atomic interaction in a magnetic field, especially magnetic Feshbach resonances in nonzero partial waves.

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

    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.

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. Imaging radar investigations of the Sudbury structure

    NASA Technical Reports Server (NTRS)

    Lowman, P. D.; Singhroy, V. H.; Slaney, V. R.

    1992-01-01

    This paper reports preliminary results of airborne imaging radar studies of the Sudbury structure carried out in preparation for a CCRS European Remote Sensing Satellite (ERS-1) investigation. The data used were synthetic aperture radar (SAR) C-band (5.66 cm) images acquired from about 6 km altitude in 1987. They cover the Sudbury area in both wide and narrow swath modes, with east-west flight paths and north-south illumination directions. Narrow swath resolution is 6 m in range and azimuth; wide swath resolution is 20 m in range and 10 m in azimuth. The STAR imagery has proven highly effective for field use, providing excellent rendition of topography and topographically expressed structure. Reasons for this include the illumination geometry, notably the look azimuth normal to the long axis of the Sudbury structure and Penokean fold axes, the good spatial resolution, and the short wavelength. Forested areas in the Sudbury area tend to be uniformly rough at C-band wavelength, with backscatter dominated by local incidence angle (i.e., topography). Field work using the SAR imagery has to date been concentrated in the North Range and Superior Province as far north as the Benny greenstone belt. This area was chosen for initial investigation of the original size and shape of the Sudbury structure because the effects of the Penokean Orogeny were minimal there. Field work using SAR indicates that there has been little postimpact deformation of the North Range or adjacent Superior Province rock. There appears to be no evidence for an outer ring concentric with the North Range as indicated by early Landsat imagery. The apparent ring shown by Landsat is visible on the SAR imagery as the intersection of two regional fracture patterns not related to the Sudbury structure. There is no outer ring visible southwest of the structure. This can reasonably be explained by Penokean deformation, but there is no outer ring to the northeast cutting the relatively undeformed Huronian

  20. Molecular-dynamics investigation of the desensitization of detonable material

    NASA Astrophysics Data System (ADS)

    Rice, Betsy M.; Mattson, William; Trevino, Samuel F.

    1998-05-01

    A molecular-dynamics investigation of the effects of a diluent on the detonation of a model crystalline explosive is presented. The diluent, a heavy material that cannot exothermally react with any species of the system, is inserted into the crystalline explosive in two ways. The first series of simulations investigates the attenuation of the energy of a detonation wave in a pure explosive after it encounters a small layer of crystalline diluent that has been inserted into the lattice of the pure explosive. After the shock wave has traversed the diluent layer, it reenters the pure explosive. Unsupported detonation is not reestablished unless the energy of the detonation wave exceeds a threshold value. The second series of simulations investigates detonation of solid solutions of different concentrations of the explosive and diluent. For both types of simulations, the key to reestablishing or reaching unsupported detonation is the attainment of a critical number density behind the shock front. Once this critical density is reached, the explosive molecules make a transition to an atomic phase. This is the first step in the reaction mechanism that leads to the heat release that sustains the detonation. The reactive fragments formed from the atomization of the heteronuclear reactants subsequently combine with new partners, with homonuclear product formation exothermally favored. The results of detonation of the explosive-diluent crystals are consistent with those presented in an earlier study on detonation of pure explosive [B. M. Rice, W. Mattson, J. Grosh, and S. F. Trevino, Phys. Rev. E 53, 611 (1996)].

  1. Molecular structural order and anomalies in liquid silica.

    PubMed

    Shell, M Scott; Debenedetti, Pablo G; Panagiotopoulos, Athanassios Z

    2002-07-01

    The present investigation examines the relationship between structural order, diffusivity anomalies, and density anomalies in liquid silica by means of molecular dynamics simulations. We use previously defined orientational and translational order parameters to quantify local structural order in atomic configurations. Extensive simulations are performed at different state points to measure structural order, diffusivity, and thermodynamic properties. It is found that silica shares many trends recently reported for water [J. R. Errington and P. G. Debenedetti, Nature 409, 318 (2001)]. At intermediate densities, the distribution of local orientational order is bimodal. At fixed temperature, order parameter extrema occur upon compression: a maximum in orientational order followed by a minimum in translational order. Unlike water, however, silica's translational order parameter minimum is broad, and there is no range of thermodynamic conditions where both parameters are strictly coupled. Furthermore, the temperature-density regime where both structural order parameters decrease upon isothermal compression (the structurally anomalous regime) does not encompass the region of diffusivity anomalies, as was the case for water. PMID:12241346

  2. 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. PMID:26627128

  3. 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.

  4. Rheological and microstructural investigation of oat β-glucan isolates varying in molecular weight.

    PubMed

    Agbenorhevi, Jacob K; Kontogiorgos, Vassilis; Kirby, Andrew R; Morris, Victor J; Tosh, Susan M

    2011-10-01

    The rheological properties and microstructure of aqueous oat β-glucan solutions varying in molecular weight were investigated. The structural features and molecular weights (MW) were characterized by (13)C NMR spectroscopy and high performance size-exclusion chromatography (HPSEC), respectively. The microstructure of the β-glucans dispersions was also examined by atomic force microscopy (AFM). The samples with β-glucan content between 78 and 86% on a dry weight basis had MW, intrinsic viscosity ([η]) and critical concentration (c*) in the range of 142-2800×10(3)g/mol, 1.7-7.2dl/g and 0.25-1.10g/dl, respectively. The flow and viscoelastic behaviour was highly dependent on MW and on the concentration of the β-glucans dispersions. Pseudoplastic behaviour was exhibited at high concentrations and Newtonian behaviour was evident at low concentrations. At the same concentration, the viscosity was higher for higher MW samples. The Cox-Merz rule was applicable for the lower molecular weight samples at higher concentrations whereas the high molecular weight sample deviated at concentrations greater than 1.0%, w/v. The mechanical spectra with variation of both MW and concentration were typical of entangled biopolymer solutions. AFM images revealed the formation of clusters or aggregates linked via individual polymer chains scattered heterogeneously throughout the system. The aggregate size increased with the molecular weight of the samples investigated and has been linked to the rheological behaviour of the samples.

  5. 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.

  6. 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.

  7. The molecular structure of 1-methyl- trans-cyclooctene

    NASA Astrophysics Data System (ADS)

    Traetteberg, M.; Bakken, P.; Almenningen, A.

    1981-07-01

    The molecular structure of 1 -methyl- trans-cyclooctene has been studied by the gas electron diffraction method. A molecular mechanics calculation has been done for the title compound and for trans-cyclooctene and 1,2-dimethyl- trans-cyclooctene.

  8. Molecular Modeling and Structural Analysis of Arylesterase of Ancylostoma Duodenale

    PubMed Central

    Panda, Subhamay; Panda, Santamay; Kumari, Leena

    2016-01-01

    Parasitic worm infection of humans is one of the most commonly prevalent helminth infection that has imposed great impact on society and public health in the developing world. The two species of hookworm, namely Ancylostoma duodenale and Necator americanus may be primarily responsible for causing parasitic infections in human beings. The highly prevalent areas for Ancylostoma duodenale infections are mainly India, Middle East, Australia, northern Africa and other parts of the world. The serum arylesterases/paraoxonases are family of enzymes that is involved in the hydrolysis of a number of organophosphorus insecticides to the nontoxic products. The participation of the enzymes in the breakdown of a variety of organophosphate substrates that is generally made up of paraoxon and numerous aromatic carboxylic acid esters (e.g., phenyl acetate), and hence combats the toxic effect of organophosphates. The aim of the present investigation is to evaluate the arylesterases of Ancylostoma duodenale giving special importance to structure generation, validation of the generated models, distribution of secondary structural elements and positive charge distribution over the structure. By the implementation of comparative modeling approach we propose the first molecular model structure of arylesterases of Ancylostoma duodenale. PMID:27642240

  9. Molecular Modeling and Structural Analysis of Arylesterase of Ancylostoma Duodenale

    PubMed Central

    Panda, Subhamay; Panda, Santamay; Kumari, Leena

    2016-01-01

    Parasitic worm infection of humans is one of the most commonly prevalent helminth infection that has imposed great impact on society and public health in the developing world. The two species of hookworm, namely Ancylostoma duodenale and Necator americanus may be primarily responsible for causing parasitic infections in human beings. The highly prevalent areas for Ancylostoma duodenale infections are mainly India, Middle East, Australia, northern Africa and other parts of the world. The serum arylesterases/paraoxonases are family of enzymes that is involved in the hydrolysis of a number of organophosphorus insecticides to the nontoxic products. The participation of the enzymes in the breakdown of a variety of organophosphate substrates that is generally made up of paraoxon and numerous aromatic carboxylic acid esters (e.g., phenyl acetate), and hence combats the toxic effect of organophosphates. The aim of the present investigation is to evaluate the arylesterases of Ancylostoma duodenale giving special importance to structure generation, validation of the generated models, distribution of secondary structural elements and positive charge distribution over the structure. By the implementation of comparative modeling approach we propose the first molecular model structure of arylesterases of Ancylostoma duodenale.

  10. Molecular Dynamics of Shock Wave Interaction with Nanoscale Structured Materials

    NASA Astrophysics Data System (ADS)

    Al-Qananwah, Ahmad K.

    Typical theoretical treatments of shock wave interactions are based on a continuum approach, which cannot resolve the spatial variations in solids with nano-scale porous structure. Nano-structured materials have the potential to attenuate the strength of traveling shock waves because of their high surface-to-volume ratio. To investigate such interactions we have developed a molecular dynamics simulation model, based on Short Range Attractive interactions. A piston, modeled as a uni-directional repulsive force field translating at a prescribed velocity, impinges on a region of gas which is compressed to form a shock, which in turn is driven against an atomistic solid wall. Periodic boundary conditions are used in the directions orthogonal to the piston motion, and we have considered solids based on either embedded atom potentials (target structure) or tethered potential (rigid piston, holding wall). Velocity, temperature and stress fields are computed locally in both gas and solid regions, and displacements within the solid are interpreted in terms of its elastic constants. In this work we present results of the elastic behavior of solid structures subjected to shock wave impact and analysis of energy transport and absorption in porous materials. The results indicated that the presence of nano-porous material layers in front of a target wall reduced the stress magnitude detected inside and the energy deposited there by about 30 percent while, at the same time, its loading rate was decreased substantially.

  11. Investigation of Changes in the Microscopic Structure of Anionic Poly(N-isopropylacrylamide-co-Acrylic acid) Microgels in the Presence of Cationic Organic Dyes toward Precisely Controlled Uptake/Release of Low-Molecular-Weight Chemical Compound.

    PubMed

    Kureha, Takuma; Shibamoto, Takahisa; Matsui, Shusuke; Sato, Takaaki; Suzuki, Daisuke

    2016-05-10

    Changes in a microscopic structure of an anionic poly(N-isopropylacrylamide-co-acrylic acid) microgel were investigated using small- and wide-angle X-ray scattering (SWAXS). The scattering profiles of the microgels were analyzed in a wide scattering vector (q) range of 0.07 ≤ q/nm(-1) ≤ 20. In particular, the microscopic structure of the microgel in the presence of a cationic dye rhodamine 6G (R6G) was characterized in terms of its correlation length (ξ), which represents the length scale of the spatial correlation of the network density fluctuations, and characteristic distance (d*), which originated from the local packing of isopropyl groups of two neighboring chains. In the presence of cationic R6G, ξ exhibited a divergent-like behavior, which was not seen in the absence of R6G, and d* was decreased with decreasing the volume of the microgel upon increasing temperature. At the same time, the amount of R6G adsorbed per unit mass of the microgel increased upon heating. These results suggested that a coil-to-globule transition of the poly(N-isopropylacrylamide) chains in the present anionic microgel occurred because of efficiently screened, thus, short ranged electrostatic repulsion between the charged groups, and hydrophobic interaction between the isopropyl groups in the presence of cationic R6G. The combination of hydrophobic and electrostatic interaction between the cationic dye and the microgel affected the separation and volume transition behavior of the microgel. PMID:27101468

  12. 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)

  13. 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.

  14. 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.

  15. Crystal structural and diffusion property in titanium carbides: A molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Lv, Yanan; Gao, Weimin

    2016-09-01

    Titanium carbides were studied via molecular dynamics simulation to characterize TiCx structures with respect to the carbon diffusion properties in this study. The effect of carbon concentration on atomic structures of titanium carbides was investigated through discussing the structure variation and the radial distribution functions of carbon atoms in titanium carbides. The carbon diffusion in titanium carbides was also analyzed, focusing on the dependence on carbon concentration and carbide structure. Carbon diffusivity with different carbon concentrations was determined by molecular dynamics (MD) calculations and compared with the available experimental data. The simulation results showed an atomic exchange mechanism for carbon diffusion in titanium carbide.

  16. 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.

  17. Molecular dynamics simulation investigations of atomic-scale wear

    NASA Astrophysics Data System (ADS)

    Shao, Yuchong; Falk, Michael

    2013-03-01

    Frictional running-in and material transfer in wear take place at the micro- and nano-scale but the fundamental physics remain poorly understood. Here we intend to investigate wear and running-in phenomena in silicon based materials, which are widely utilized in micro/nano electromechanical systems(MEMS/NEMS). We use an atomic force microscopy (AFM) model composed of a crystalline silicon tip and substrate coated with native oxide layers. Molecular dynamics simulation has been performed over a range of temperatures, external loads and slip rates. Results show that adhesive wear takes place across the interface in an atom-by-atom fashion which remodels the tip leading to a final steady state. We quantify the rate of material transfer as a function of the coverage of non-bridging oxygen (NBO) atoms, which has a pronounced change of the system's tribological and wear behaviors. A constitutive rate and state model is proposed to predict the evolution of frictional strength and wear. This work is supported by the National Science Foundation under Award No. 0926111.

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

    DOE PAGES

    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 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

  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. 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)

  1. Synthesis and molecular structure of gold triarylcorroles.

    PubMed

    Thomas, Kolle E; Alemayehu, Abraham B; Conradie, Jeanet; Beavers, Christine; Ghosh, Abhik

    2011-12-19

    A number of third-row transition-metal corroles have remained elusive as synthetic targets until now, notably osmium, platinum, and gold corroles. Against this backdrop, we present a simple and general synthesis of β-unsubstituted gold(III) triarylcorroles and the first X-ray crystal structure of such a complex. Comparison with analogous copper and silver corrole structures, supplemented by extensive scalar-relativistic, dispersion-corrected density functional theory calculations, suggests that "inherent saddling" may occur for of all coinage metal corroles. The degree of saddling, however, varies considerably among the three metals, decreasing conspicuously along the series Cu > Ag > Au. The structural differences reflect significant differences in metal-corrole bonding, which are also reflected in the electrochemistry and electronic absorption spectra of the complexes. From Cu to Au, the electronic structure changes from noninnocent metal(II)-corrole(•2-) to relatively innocent metal(III)-corrole(3-). PMID:22111600

  2. 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.

  3. Iron affects the structure of cell membrane molecular models.

    PubMed

    Suwalsky, M; Martínez, F; Cárdenas, H; Grzyb, J; Strzałka, K

    2005-03-01

    The effects of Fe(3+) and Fe(2+) on molecular models of biomembranes were investigated. These consisted of bilayers of dimyristoylphosphatidylcholine (DMPC) and of dimyristoylphosphatidylethanolamine (DMPE), classes of phospholipids located in the outer and inner moieties of cell membranes, respectively. X-ray studies showed that very low concentrations of Fe(3+) affected DMPC organization and 10(-3)M induced a total loss of its multilamellar periodic stacking. Experiments carried out with Fe(2+) on DMPC showed weaker effects than those induced by Fe(3+) ions. Similar experiments were performed on DMPE bilayers. Fe(3+) from 10(-7)M up to 10(-4)M had practically no effect on DMPE structure. However, 10(-3)M Fe(3+) induced a deep perturbation of the multilamellar structure of DMPE. However, 10(-3)M Fe(2+) had no effect on DMPE organization practically. Differential scanning calorimetry measurements also revealed different effects of Fe(3+) and Fe(2+) on the phase transition and other thermal properties of the examined lipids. In conclusion, the results obtained indicate that iron ions interact with phospholipid bilayers perturbing their structures. These findings are consistent with the observation that iron ions change cell membrane fluidity and, therefore, affect its functions. PMID:15752465

  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. Molecular and cluster structures in 18O

    NASA Astrophysics Data System (ADS)

    von Oertzen, W.; Dorsch, T.; Bohlen, H. G.; Krücken, R.; Faestermann, T.; Hertenberger, R.; Kokalova, Tz.; Mahgoub, M.; Milin, M.; Wheldon, C.; Wirth, H.-F.

    2010-01-01

    We have studied the multi-nucleon transfer reaction 12C ( 7Li ,p) at E lab = 44 MeV, populating states in the oxygen isotope 18O . The experiments were performed at the Tandem accelerator of the Maier-Leibniz Laboratory in Munich using the high-resolution Q3D magnetic spectrograph. States were populated up to an excitation energy of 21.2MeV with an overall energy resolution of 45keV, and 30 new states of 18O have been identified. The structure of the rotational bands observed is discussed in terms of cluster bands with the underlying cluster structures: 14C ⊗ α and 12C ⊗ 2 n ⊗ α . Because of the broken intrinsic reflection symmetry in these structures the corresponding rotational bands appear as parity doublets.

  6. 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.

  7. 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.

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

    PubMed

    Mehere, Prajwalini; Han, Qian; Lemkul, Justin A; Vavricka, Christopher J; Robinson, Howard; Bevan, David R; Li, Jianyong

    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 α-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 Å 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.

  9. 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.

  10. Investigation of hydrogen bonded molecular solids by diffraction, spectroscopy, and computational chemistry

    NASA Astrophysics Data System (ADS)

    Hudson, Matthew R.

    The nature of hydrogen-bonding interactions in the solid state is examined through the investigation of molecular crystals by incoherent inelastic neutron scattering (INS) spectroscopy, Raman spectroscopy, X-ray and neutron diffraction, and computational chemistry. The molecular solids studied range from small organic molecules to larger inorganic acid salts. Hydrogen bonding is the primary mode of interaction in the solid state for each of the systems studied. INS spectra were collected at 25 K for each molecular solid and the motions of the hydrogen atoms assigned. Raman spectra were collected at 78 and 298 K to aid in the molecular mode assignments of the INS spectra and to examine possible phase changes as a function of temperature. Neutron diffraction was employed, when possible, to accurately locate the hydrogen atom positions, and X-ray diffraction was performed to obtain accurate unit cell dimensions and to obtain initial characterizations of the samples. The diffraction structures served as the basis for solid-state density functional theory (DFT) calculations. DFT simulations were used to aid in the vibrational normal mode assignments, to investigate possible solid-phase transitions, and as a test of the limits of basis sets and the available DFT theory. Of the six molecular solids studied, several important observations were made: (1) the determination of a structural phase transition in L-alanine alaninium nitrate by both spectroscopic and theoretical methods, (2) the structure of picolinic acid was elucidated at 25 K and room-temperature by the combination of INS and theory, (3) glycine lithium sulfate was found to be a useful test of DFT to accurately optimize the structure and calculate the normal modes of a complex 3D network of hydrogen-bonding interactions, (4) nicotinic acid was found to be a useful test of one dimensional hydrogen-bonding interactions with pi-stacking interactions dominating the orthogonal directions, and (5) parabanic acid

  11. 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

  12. 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…

  13. Molecular structure of β-amyloid fibrils in Alzheimer’s disease brain tissue

    PubMed Central

    Lu, Jun-Xia; Qiang, Wei; Yau, Wai-Ming; Schwieters, Charles D.; Meredith, Stephen C.; Tycko, Robert

    2013-01-01

    In vitro, β-amyloid (Aβ) peptides form polymorphic fibrils, with molecular structures that depend on growth conditions, plus various oligomeric and protofibrillar aggregates. Detailed structural information about Aβ assemblies in the human brain has been lacking. Here, we investigate structures of brain-derived Aβ fibrils, using seeded fibril growth from brain extract and data from solid state nuclear magnetic resonance and electron microscopy. Experiments on tissue from two Alzheimer’s disease (AD) patients with distinct clinical histories indicate a single predominant 40-residue Aβ (Aβ40) fibril structure in each patient, but different structures in the two patients. A molecular structural model developed for Aβ40 fibrils from one patient reveals features that distinguish in vivo from in vitro fibrils. The data suggest that fibrils in the brain may spread from a single nucleation site, that structural variations may correlate with variations in AD, and that structure-specific amyloid imaging agents may be an important future goal. PMID:24034249

  14. 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.

  15. 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.

  16. 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.

  17. ATOMIC AND MOLECULAR PHYSICS: Triatomic wake effect and the determination of the molecular structure of HD2+ from the Coulomb explosion

    NASA Astrophysics Data System (ADS)

    Zhu, Zhou-Sen; Miao, Jing-Wei; Liao, Xue-Hua; Miao, Lei; Yuan, Xue-Dong; Shi, Mian-Gong

    2009-11-01

    A new theoretical model of the triatomic molecular wake effect is proposed and applied to molecular ions D3+ and HD2+ while passing through a solid. The wake effects resulting from the reactions of the two similar ions with thin carbon foil are also investigated by using the Coulomb explosion technique. The experimental results are in good agreement with theoretical estimates and the molecular structure of HD2+ is determined by using the model.

  18. Linking numerical simulations of molecular cloud structure with observations.

    NASA Astrophysics Data System (ADS)

    Kainulainen, Jouni

    2015-08-01

    Understanding the physical processes that control the life-cycle of the cold interstellar medium (ISM) is one of the key themes in the astrophysics of galaxies today. This importance derives from the role of the cold ISM as the birthplace of new stars, and consequently, as an indivisible constituent of galaxy evolution. In the current paradigm of turbulence-regulated ISM, star formation is controlled by the internal structure of individual molecular clouds, which in turn is set by a complex interplay of turbulence, gravity, and magnetic fields in the clouds. It is in the very focus of the field to determine how these processes give rise to the observed structure of molecular clouds. In this talk, I will review our current efforts to confront this paradigm with the goal of observationally constraining how different processes regulate molecular cloud structure and star formation. At the heart of these efforts lies the use of numerical simulations of gravo-turbulent media to A) define physically meaningful characteristics that are sensitive to the different cloud-shaping processes, and B) determine if and how such characteristics can be recovered by observations. I will show in my talk how this approach has recently led to new constraints for some fundamental measures of the molecular cloud structure. Such constraints allow us to assess the roles of turbulence and gravity in controlling the ISM structure and star formation. I will also highlight specific recent results, focusing on the nature of filamentary structures within molecular clouds. These results may provide a novel set of observational constraints with which to challenge the turbulence-regulated ISM paradigm. Finally, I will discuss the current challenges and open questions in understanding the link between molecular cloud structure and star formation, and speculate on key directions to aim the near-future studies.

  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. Molecular structure-adsorption study on current textile dyes.

    PubMed

    Örücü, E; Tugcu, G; Saçan, M T

    2014-01-01

    This study was performed to investigate the adsorption of a diverse set of textile dyes onto granulated activated carbon (GAC). The adsorption experiments were carried out in a batch system. The Langmuir and Freundlich isotherm models were applied to experimental data and the isotherm constants were calculated for 33 anthraquinone and azo dyes. The adsorption equilibrium data fitted more adequately to the Langmuir isotherm model than the Freundlich isotherm model. Added to a qualitative analysis of experimental results, multiple linear regression (MLR), support vector regression (SVR) and back propagation neural network (BPNN) methods were used to develop quantitative structure-property relationship (QSPR) models with the novel adsorption data. The data were divided randomly into training and test sets. The predictive ability of all models was evaluated using the test set. Descriptors were selected with a genetic algorithm (GA) using QSARINS software. Results related to QSPR models on the adsorption capacity of GAC showed that molecular structure of dyes was represented by ionization potential based on two-dimensional topological distances, chromophoric features and a property filter index. Comparison of the performance of the models demonstrated the superiority of the BPNN over GA-MLR and SVR models. PMID:25529487

  1. 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.

  2. Molecular information structures in the brain.

    PubMed

    Conrad, M

    1976-01-01

    This paper presents a theory of memory and memory mediated learning based on the manipulation of macromolecular conformations. The main features of the theory are: 1) the brain contains primary and reference neurons; 2) inputs from the external environment produce particular patterns of primary firing; 3) the firing of a primary neuron sensitizes certain of its dendrites; 4) the sensitized primaries are loaded by the reference neuron active at the time and in such a way that they fire when called by this reference neuron, thus reconstructing the original pattern of primary activity. The reference neurons may also be loaded by primaries, thus making it possible for the reconstruction process to be initiated by some feature of the initial input. Each reference neuron loads and calls at most one primary pattern of activity, thereby preventing superposition of memories. If the primaries are loadable by sequences of impulses, this makes it possible to increase the connectivity among the various types of neurons by using party-line organization. The loading and calling processes themselves are mediated by call molecules. These are allosteric enzymes, located in the dendrites of primary and reference neurons, whose states are set either by an impulse or sequence of impulses and which catalyze events leading to impulse formation whenever this input recurs. The call molecules are capable of duplicating their setting (or conformation) using either intra- or interneuronal potentials, thereby ensuring stability of the memory trace. The theory allows for general powers of memory manipulation (by rememorization), for the construction of time ordered, content ordered, and associative data structures, and for computation with global representations of the environment. It makes a large number of testable predictions, provides a natural interpretation for the structure of the cerebral cortex, and accounts for: resistance to cooling, differential effects of chemical agents on short

  3. Laser pulse induced multiple exciton kinetics in molecular ring structures

    NASA Astrophysics Data System (ADS)

    Hou, Xiao; Wang, Luxia

    2016-11-01

    Multiple excitons can be formed upon strong optical excitation of molecular aggregates and complexes. Based on a theoretical approach on exciton-exciton annihilation dynamics in supramolecular systems (May et al., 2014), exciton interaction kinetics in ring aggregates of two-level molecules are investigated. Excited by the sub-picosecond laser pulse, multiple excitons keep stable in the molecular ring shaped as a regular polygon. If the symmetry is destroyed by changing the dipole of a single molecule, the excitation of different molecules becomes not identical, and the changed dipole-dipole interaction initiates subsequent energy redistribution. Depending on the molecular distance and the dipole configuration, the kinetics undergo different types of processes, but all get stable within some hundreds of femtoseconds. The study of exciton kinetics will be helpful for further investigations of the efficiency of optical devices based on molecular aggregates.

  4. 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.

  5. 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.

  6. Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments

    PubMed Central

    Shen, Rong; Han, Wei; Fiorin, Giacomo; Islam, Shahidul M.; Schulten, Klaus; Roux, Benoît

    2015-01-01

    The knowledge of multiple conformational states is a prerequisite to understand the function of membrane transport proteins. Unfortunately, the determination of detailed atomic structures for all these functionally important conformational states with conventional high-resolution approaches is often difficult and unsuccessful. In some cases, biophysical and biochemical approaches can provide important complementary structural information that can be exploited with the help of advanced computational methods to derive structural models of specific conformational states. In particular, functional and spectroscopic measurements in combination with site-directed mutations constitute one important source of information to obtain these mixed-resolution structural models. A very common problem with this strategy, however, is the difficulty to simultaneously integrate all the information from multiple independent experiments involving different mutations or chemical labels to derive a unique structural model consistent with the data. To resolve this issue, a novel restrained molecular dynamics structural refinement method is developed to simultaneously incorporate multiple experimentally determined constraints (e.g., engineered metal bridges or spin-labels), each treated as an individual molecular fragment with all atomic details. The internal structure of each of the molecular fragments is treated realistically, while there is no interaction between different molecular fragments to avoid unphysical steric clashes. The information from all the molecular fragments is exploited simultaneously to constrain the backbone to refine a three-dimensional model of the conformational state of the protein. The method is illustrated by refining the structure of the voltage-sensing domain (VSD) of the Kv1.2 potassium channel in the resting state and by exploring the distance histograms between spin-labels attached to T4 lysozyme. The resulting VSD structures are in good agreement with

  7. Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments.

    PubMed

    Shen, Rong; Han, Wei; Fiorin, Giacomo; Islam, Shahidul M; Schulten, Klaus; Roux, Benoît

    2015-10-01

    The knowledge of multiple conformational states is a prerequisite to understand the function of membrane transport proteins. Unfortunately, the determination of detailed atomic structures for all these functionally important conformational states with conventional high-resolution approaches is often difficult and unsuccessful. In some cases, biophysical and biochemical approaches can provide important complementary structural information that can be exploited with the help of advanced computational methods to derive structural models of specific conformational states. In particular, functional and spectroscopic measurements in combination with site-directed mutations constitute one important source of information to obtain these mixed-resolution structural models. A very common problem with this strategy, however, is the difficulty to simultaneously integrate all the information from multiple independent experiments involving different mutations or chemical labels to derive a unique structural model consistent with the data. To resolve this issue, a novel restrained molecular dynamics structural refinement method is developed to simultaneously incorporate multiple experimentally determined constraints (e.g., engineered metal bridges or spin-labels), each treated as an individual molecular fragment with all atomic details. The internal structure of each of the molecular fragments is treated realistically, while there is no interaction between different molecular fragments to avoid unphysical steric clashes. The information from all the molecular fragments is exploited simultaneously to constrain the backbone to refine a three-dimensional model of the conformational state of the protein. The method is illustrated by refining the structure of the voltage-sensing domain (VSD) of the Kv1.2 potassium channel in the resting state and by exploring the distance histograms between spin-labels attached to T4 lysozyme. The resulting VSD structures are in good agreement with

  8. 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.

  9. 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.

  10. 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). PMID:25116151

  11. Investigation of aircraft vortex wake structure

    NASA Astrophysics Data System (ADS)

    Baranov, N. A.; Turchak, L. I.

    2014-11-01

    In this work we analyze the mechanisms of formation of the vortex wake structure of aircraft with different wing shape in the plan flying close to or away from the underlying surface cleaned or released mechanization wing.

  12. 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.

  13. 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.

  14. 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.

  15. Investigating the Structure of Discourse Completion Tests.

    ERIC Educational Resources Information Center

    Varghese, Manka; Billmyer, Kristine

    1996-01-01

    A study examined internal structure of the Discourse Completion Test (DCT), a technique used to elicit data in sociolinguistic research, and effects of systematic modification to its situational prompt on subject response. The DCT is a questionnaire containing situations, briefly described, designed to elicit a particular speech act. Subjects read…

  16. Molecular dynamics simulation study on the molecular structures of the amylin fibril models.

    PubMed

    Xu, Weixin; Su, Haibin; Zhang, John Z H; Mu, Yuguang

    2012-12-01

    The structural characterization of amyloid fibers is one of the most investigated areas in structural biology. Recently, protofibril models for amylin, i.e., the 37-residue human islet amyloid polypeptide or hIAPP were suggested by two groups based on NMR (Biochemistry 2007, 46, 13505-13522) and X-ray (Protein Sci. 2008, 17, 1467-1474) techniques. However, there are significant differences in the two models which maybe originate from the polymorphic nature of amylin fibrils. To obtain further insights into the packing and stability features of the different models, we performed a series of molecular dynamics simulations on them. Our analysis showed that even pairs of β-sheets composed of a limited number of β-strands are stable in the 100-ns simulations, which suggests that steric zipper interactions at a β-sheet-β-sheet interface strongly contribute to the stability of these amyloid aggregates. For both models, outer strands are more flexible, which might coincide with the dynamical requirement that outer strands act as growing sites facilitating conformational changes of new incoming chains. Moreover, simulation results showed that the X-ray models are structurally more compact than the NMR models and have more intimate patterns, which lead to more rigid amyloid models. As a result, the X-ray models are energetically more stable than the NMR models. Further modeling analyses verify the most likely amylin fibril model among both NMR and X-ray models. Upon further study of the force-induced dissociation of a single chain from the protofibrils, the binding energy and the mechanical stability of the fibril models are revealed. On these bases, it is possible to reconcile the crystallographic and the NMR data on the basic amylin fiber unit. PMID:23145779

  17. Investigating Molecular Hydrogen in Active Regions with IRIS

    NASA Astrophysics Data System (ADS)

    Jaeggli, Sarah A.; Saar, Steven H.; Daw, Adrian N.; Innes, Davina

    2014-06-01

    Molecular hydrogen should be the most abundant molecular species in sunspots, but recent observations with IRIS show that its florescent signature is absent from above the sunspot umbra, but appears brightly during flares. In this poster we continue the analysis of FUV observations of H2 in active regions, examining the correlation between the intensity of the H2 lines and the lines of C II and Si IV which are responsible for their excitation. We particularly focus on differentiating places where H2 is abundant, holes in the chromospheric opacity where FUV photons can enter more deeply into the solar atmosphere, and places where the FUV radiation field is intense, as in flares.

  18. Investigating Molecular Kinetics by Variationally Optimized Diffusion Maps.

    PubMed

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

    2015-12-01

    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.

  19. Investigation of the hybrid molecular probe for intracellular studies

    PubMed Central

    Martinez, Karen; Medley, Colin D.; Yang, Chaoyong James; Tan, Weihong

    2009-01-01

    Monitoring gene expression in vivo is essential to the advancement of biological studies, medical diagnostics, and drug discovery. Adding to major efforts in developing molecular probes for mRNA monitoring, we have recently developed an alternative tool, the hybrid molecular probe (HMP). To optimize the probe, a series of experiments were performed to study the properties of HMP hybridization kinetics and stability. The results demonstrated the potential of the HMP as a prospective tool for use in both hybridization studies and in vitro and in vivo analyses. The HMP has shown no tendency to produce false positive signals, which is a major concern for living cell studies. Moreover, HMP has shown the ability to detect the mRNA expression of different genes inside single cells from both basal and stimulated genes. As an effective alternative to conventional molecular probes, the proven sensitivity, simplicity, and stability of HMPs show promise for their use in monitoring mRNA expression in living cells. PMID:18421445

  20. 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. PMID:23754475

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

    PubMed

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

    2015-01-01

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

  2. 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

  3. The theoretical investigation of one of the derivatives of 1, 2-dithienylcyclopentene as a molecular switch.

    PubMed

    Safarpour, Mohammad Ali; Hashemianzadeh, Seyed Majid; Kasaeian, Azam

    2008-04-01

    The structural and electronic properties of a three-state molecular switch-an active device in a nano-electronic circuit-were studied using the B3LYP/6-31G* method. Due to its chemical stability, high conductivity upon doping, and non-linear optical properties, polythiophene is among the most widely studied conjugated organic polymers, both experimentally and theoretically. The aim of the present work was to theoretically study a very complex case: a three-state switch synthesized and experimentally investigated by Nishida et al. (Org Lett 6:2523-2526, 2004). An initial set of test calculations showed B3LYP level of theory and 6-31G* basis set to be the most appropriate for our purpose, i.e., the study of the structure, charge and spin distributions, as well as electrical characteristics such as electric polarizability, HOMO-LUMO gap (HLG) and electric dipole moment, for one of the 1,2-dithienylcyclopentene derivatives. Also, natural bond orbital analyses were performed to calculate local charges and charge transfers in order to study the capability of the molecule as a molecular switch. The results reported here are of general significance, and demonstrate that it is possible to use certain structural and electrical properties to understand and design electro-photochromic compounds showing a switching function in cases where stable forms can be exchanged by light or electron transfer. Figure Model of a thiophene wire incorporating a redox active unit.

  4. Investigate the binding of catechins to trypsin using docking and molecular dynamics simulation.

    PubMed

    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

  5. 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. PMID:26752623

  6. 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. PMID:23892116

  7. 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

    NASA Astrophysics Data System (ADS)

    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 4000-400 cm-1 and 4000-10 cm-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 1H and 13C 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. 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

  13. 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).

  14. 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).

  15. Molecular structures and protonation state of 2-Mercaptopyridine in aqueous solution

    NASA Astrophysics Data System (ADS)

    Eckert, S.; Miedema, P. S.; Quevedo, W.; O'Cinneide, B.; Fondell, M.; Beye, M.; Pietzsch, A.; Ross, M.; Khalil, M.; Föhlisch, A.

    2016-03-01

    The speciation of 2-Mercaptopyridine in aqueous solution has been investigated with nitrogen 1s Near Edge X-ray Absorption Fine Structure spectroscopy and time dependent Density Functional Theory. The prevalence of distinct species as a function of the solvent basicity is established. No indications of dimerization towards high concentrations are found. The determination of different molecular structures of 2-Mercaptopyridine in aqueous solution is put into the context of proton-transfer in keto-enol and thione-thiol tautomerisms.

  16. 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

  17. 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. PMID:12725967

  18. Investigation of lunar crustal structure and isostasy

    NASA Technical Reports Server (NTRS)

    Thurber, Clifford H.

    1987-01-01

    The lunar mascon basins have strongly free air gravity anomalies, generally exceeding 100 milligals at an elevation of 100 km. The source of the anomalies is a combination of mantle uplift beneath the impact basins and subsequent infilling by high-density mare basalts. The relative contribution of these two components is still somewhat uncertain, although it is generally accepted that the amount of mantle uplift greatly exceeds the thickness of the basalts. Extensive studies have been carried out of the crustal structure of mare basins, based on gravity data, and their tectonic evolution, based on compressive and extensional tectonic features. The present study endeavored to develop a unified, self-consistent model of the lunar crust and lithosphere incorporating both gravity and tectonic constraints.

  19. 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.

  20. Semifluorinated Alkanes at the Air-Water Interface: Tailoring Structure and Rheology at the Molecular Scale.

    PubMed

    Theodoratou, Antigoni; Jonas, Ulrich; Loppinet, Benoit; Geue, Thomas; Stangenberg, Rene; Keller, Rabea; Li, Dan; Berger, Rüdiger; Vermant, Jan; Vlassopoulos, Dimitris

    2016-04-01

    Semifluorinated alkanes form monolayers with interesting properties at the air-water interface due to their pronounced amphi-solvophobic nature and the stiffness of the fluorocarbons. In the present work, using a combination of structural and dynamic probes, we investigated how small molecular changes can be used to control the properties of such an interface, in particular its organization, rheology, and reversibility during compression-expansion cycles. Starting from a reference system perfluor(dodecyl)dodecane, we first retained the linear structure but changed the linkage groups between the alkyl chains and the fluorocarbons, by introducing either a phenyl group or two oxygens. Next, the molecular structure was changed from linear to branched, with four side chains (two fluorocarbons and two hydrocarbons) connected to extended aromatic cores. Neutron reflectivity at the air-water interface and scanning force microscopy on deposited films show how the changes in the molecular structure affect molecular arrangement relative to the interface. Rheological and compression-expansion measurements demonstrate the significant consequences of these changes in molecular structure and interactions on the interfacial properties. Remarkably, even with these simple molecules, a wide range of surface rheological behaviors can be engineered, from viscous over viscoelastic to brittle solids, for very similar values of the surface pressure.

  1. 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.

  2. Investigation of the molecular similarity in closely related protein systems: The PrP case study.

    PubMed

    Storchi, Loriano; Paciotti, Roberto; Re, Nazzareno; Marrone, Alessandro

    2015-10-01

    The amyloid conversion is a massive detrimental modification affecting several proteins upon specific physical or chemical stimuli characterizing a plethora of diseases. In many cases, the amyloidogenic stimuli induce specific structural features to the protein conferring the propensity to misfold and form amyloid deposits. The investigation of mutants, structurally similar to their native isoform but inherently prone to amyloid conversion, may be a viable strategy to elucidate the structural features connected with amyloidogenesis. In this article, we present a computational protocol based on the combination of molecular dynamics (MD) and grid-based approaches suited for the pairwise comparison of closely related protein structures. This method was applied on the cellular prion protein (PrP(C)) as a case study and, in particular, addressed to the quali/quantification of the structural features conferred by either E200K mutations and treatment with CaCl(2), both able to induce the scrapie conversion of PrP. Several schemes of comparison were developed and applied to this case study, and made up suitable of application to other protein systems. At this purpose an in-house python codes has been implemented that, together with the parallelization of the GRID force fields program, will spread the applicability of the proposed computational procedure. PMID:26018750

  3. 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

  4. 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

  5. Molecular investigation into outbreak of HIV in a Scottish prison.

    PubMed Central

    Yirrell, D. L.; Robertson, P.; Goldberg, D. J.; McMenamin, J.; Cameron, S.; Leigh Brown, A. J.

    1997-01-01

    OBJECTIVES: To support already established epidemiological links between inmates of Glenochil prison positive for HIV infection by using molecular techniques and thus provide evidence of the extent of acquisition during a recent outbreak of the disease resulting from needle sharing. To identify possible sources of the outbreak, and to demonstrate the ability of the methodology to make further links beyond the original outbreak. DESIGN: Viral sequences obtained from the blood of HIV positive prisoners previously identified by standard epidemiological methods were compared with each other and with sequences from other Scottish patients. SETTING: Glenochil prison for men, central Scotland. SUBJECTS: Adult inmates and their possible contacts. RESULTS: Phylogenetic analysis of viral sequences in two different genomic regions showed that 13 of the 14 HIV positive prisoners had been infected from a common source. Previous research had shown that six of these had acquired their infection in Glenochil; molecular evidence suggests that more than double this number were infected while incarcerated. Virus from two long term HIV positive patients who were in the prison at the time of the outbreak but who were not identified in the original or subsequent surveys was sufficiently different to make it unlikely that they were the source. A viral sequence from heterosexual transmission from one inmate showed the ability of these techniques to follow the infection through different routes of infection. CONCLUSION: The number of prisoners infected with HIV during the 1993 outbreak within Glenochil prison was more than twice that previously shown. This shows the potential for the spread of bloodborne diseases within prisons by injecting drugs. PMID:9167560

  6. 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

  7. Molecular spectroscopy and molecular structure - Selected communications presented at the 1st International Turkish Congress on Molecular Spectroscopy (TURCMOS 2013)

    NASA Astrophysics Data System (ADS)

    Durig, James R.; Fausto, Rui; Ünsalan, Ozan; Bayarı, Sevgi; Kuş, Nihal; Ildız, Gülce Ö.

    2016-01-01

    The First International Turkish Congress on Molecular Spectroscopy (TURCMOS 2013) took place at the Harbiye Cultural Center & Museum, Istanbul, Turkey, September 15-20, 2013. The main aim of the congress was to encourage the exchange of scientific ideas and collaborations all around the world, introduce new techniques and instruments, and discuss recent developments in the field of molecular spectroscopy. Among the different subjects covered, particular emphasis was given to the relevance of spectroscopy to elucidate details of the molecular structure and the chemical and physical behavior of systems ranging from simple molecules to complex biochemical molecules. Besides experimental spectroscopic approaches, related computational and theoretical methods were also considered. In this volume, selected contributions presented at the congress were put together.

  8. Molecular docking and structure-based drug design strategies.

    PubMed

    Ferreira, Leonardo G; Dos Santos, Ricardo N; Oliva, Glaucius; Andricopulo, Adriano D

    2015-07-22

    Pharmaceutical research has successfully incorporated a wealth of molecular modeling methods, within a variety of drug discovery programs, to study complex biological and chemical systems. The integration of computational and experimental strategies has been of great value in the identification and development of novel promising compounds. Broadly used in modern drug design, molecular docking methods explore the ligand conformations adopted within the binding sites of macromolecular targets. This approach also estimates the ligand-receptor binding free energy by evaluating critical phenomena involved in the intermolecular recognition process. Today, as a variety of docking algorithms are available, an understanding of the advantages and limitations of each method is of fundamental importance in the development of effective strategies and the generation of relevant results. The purpose of this review is to examine current molecular docking strategies used in drug discovery and medicinal chemistry, exploring the advances in the field and the role played by the integration of structure- and ligand-based methods.

  9. 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.

  10. First-principles investigation of electronic structures and properties of impurities in molecular solids and semiconductors: I. Muon and muonium in organic ferromagnets. II. Erbium in silicon-optoelectronic system

    NASA Astrophysics Data System (ADS)

    Jeong, Junho

    The first-principles Hartree-Fock theory is used to obtain the electronic structures and properties of three different systems. For the TEMPO system, the trapping sites were obtained near NO group site for muonium singlet and near chlorine and bridge nitrogen for muon. The calculated hyperfine interactions including relaxation and vibrational effect were used to compare the observed zero field muSR frequency 3.2 MHz. It has been concluded that the two trapping centers that can best explain the observed muSR frequency is trapped singlet muonium near the radical oxygen and a trapped muon site near the chlorine. The direction for the easy axis is determined to be the b-axis of the monoclinic lattice and also is obtained using the magnetic moment distributions in the ferromagnetic state in the absence of muon and muonium. The nuclear quadrupole coupling constants and asymmetry parameters (eta) have studied for the 35Cl, 17O, and 14N nuclei in the TEMPO system for the bare system and systems with trapped muon and muonium. Substantial influence of the muon and muonium on the coupling constants and eta for the nuclei close to the trapping sites have been observed for the systems with trapped muon and muonium. For the beta-NPNN, the observed muSR signal at zero field with frequency 2.1 MHz is assigned to the singlet muonium sites near the two oxygens of the two NO groups and the high frequency signal ascribed to an isotropic hyperfine constant of 400MHz is assigned to the trapped muon sites near the oxygen atoms of the NO groups. Er3+-Si material which emits 1.54 mum wavelength has led to interest in optoelectronic system. Using first-principles HF procedure, the locations of Er3+ in silicon cluster without codopant were determined. Since covalent radius of Er3+ is bigger than that of silicon, the first nearest and second nearest silicon of Er3+ for Hi (Er3+Si14H18), Ti (Er3+ Si10H16, Er3+Si26H 48), and Substitutional site (Er3+Si18H 36) applied relaxation effect. The

  11. 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.

  12. Psychometric precision in phenotype definition is a useful step in molecular genetic investigation of psychiatric disorders

    PubMed Central

    Xu, M K; Gaysina, D; Barnett, J H; Scoriels, L; van de Lagemaat, L N; Wong, A; Richards, M; Croudace, T J; Jones, P B

    2015-01-01

    Affective disorders are highly heritable, but few genetic risk variants have been consistently replicated in molecular genetic association studies. The common method of defining psychiatric phenotypes in molecular genetic research is either a summation of symptom scores or binary threshold score representing the risk of diagnosis. Psychometric latent variable methods can improve the precision of psychiatric phenotypes, especially when the data structure is not straightforward. Using data from the British 1946 birth cohort, we compared summary scores with psychometric modeling based on the General Health Questionnaire (GHQ-28) scale for affective symptoms in an association analysis of 27 candidate genes (249 single-nucleotide polymorphisms (SNPs)). The psychometric method utilized a bi-factor model that partitioned the phenotype variances into five orthogonal latent variable factors, in accordance with the multidimensional data structure of the GHQ-28 involving somatic, social, anxiety and depression domains. Results showed that, compared with the summation approach, the affective symptoms defined by the bi-factor psychometric model had a higher number of associated SNPs of larger effect sizes. These results suggest that psychometrically defined mental health phenotypes can reflect the dimensions of complex phenotypes better than summation scores, and therefore offer a useful approach in genetic association investigations. PMID:26125156

  13. 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

  14. 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

  15. Detection of internal molecular structural motions using anisotropic spectroscopy

    NASA Astrophysics Data System (ADS)

    Singh, Rohit; George, Deepu; Korter, Timothy; Markelz, Andrea

    2012-02-01

    The far infrared spectroscopy of molecular crystals reveals both intra and inter molecular vibrational modes [1,2]. With the significant increase in complexity of structures, one finds increasing overlap in the internal modes. As an overall strategy to measure the correlated structural motions in protein, we use anisotropic and birefringent behavior of molecular crystals to develop a new technique called MOSTS (Modulated Orientation Sensitive THz Spectroscopy). We achieve high sensitivity and mode separation by using single molecular crystal such as sucrose and rapid modulation of the relative alignment of the terahertz polarization and the crystal axes by rotating the sample. By locking into the signal at the rotation frequency we determine the polarization sensitive signal and map out the optically active vibrational resonances. To illustrate the technique we compare our measured spectra with the calculated and find a close agreement. [4pt] [1] D.G. Allis, J.A. Zeitler, P.F.Taday and T.M.Korter, Chem. Phys. Lett., 463, 84 (2008).[0pt] [2] P.U. Jepsen and J.C. Stewart, Chem. Phys. Lett., 442, 275 (2007).

  16. Molecular modeling of nucleic Acid structure: electrostatics and solvation.

    PubMed

    Bergonzo, Christina; Galindo-Murillo, Rodrigo; Cheatham, Thomas E

    2014-01-01

    This unit presents an overview of computer simulation techniques as applied to nucleic acid systems, ranging from simple in vacuo molecular modeling techniques to more complete all-atom molecular dynamics treatments that include an explicit representation of the environment. The third in a series of four units, this unit focuses on critical issues in solvation and the treatment of electrostatics. UNITS 7.5 & 7.8 introduced the modeling of nucleic acid structure at the molecular level. This included a discussion of how to generate an initial model, how to evaluate the utility or reliability of a given model, and ultimately how to manipulate this model to better understand its structure, dynamics, and interactions. Subject to an appropriate representation of the energy, such as a specifically parameterized empirical force field, the techniques of minimization and Monte Carlo simulation, as well as molecular dynamics (MD) methods, were introduced as a way of sampling conformational space for a better understanding of the relevance of a given model. This discussion highlighted the major limitations with modeling in general. When sampling conformational space effectively, difficult issues are encountered, such as multiple minima or conformational sampling problems, and accurately representing the underlying energy of interaction. In order to provide a realistic model of the underlying energetics for nucleic acids in their native environments, it is crucial to include some representation of solvation (by water) and also to properly treat the electrostatic interactions. These subjects are discussed in detail in this unit. PMID:25631536

  17. Structure, subunit composition, and molecular weight of RD-114 RNA.

    PubMed Central

    Kung, H J; Bailey, J M; Davidson, N; Nicolson, M O; McAllister, R M

    1975-01-01

    The properties and subunit composition of the RNA extracted from RD-114 virions have been studied. The RNA extracted from the virion has a sedimentation coefficient of 52S in a nondenaturing aqueous electrolyte. The estimated molecular weight by sedimentation in nondenaturing and weakly denaturing media is in the range 5.7 X 10(6) to 7.0 X 10(6). By electron microscopy, under moderately denaturing conditions, the 52S molecule is seen to be an extended single strand with a contour length of about 4.0 mum corresponding to a molecular weight of 5.74 X 10(6). It contains two characteristic secondary structure features: (i) a central Y- or T-shaped structure (the rabbit ears) with a molecular weight of 0.3 X 10(6), (ii) two symmetreically disposed loops on each side of and at equal distance from the center. The 52S molecule consists of two half-size molecules, with molecular weight 2.8 X 10(6), joined together within the central rabbit ears feature. Melting of the rabbit ears with concomitant dissociation of the 52S molecule into subunits, has been caused by either one of two strongly denaturing treatments: incubation in a mixture of CH3HgOH and glyoxal at room temperature, or thermal dissociation in a urea-formamide solvent. When half-size molecules are quenched from denaturing temperatures, a new off-center secondary structure feature termed the branch-like structure is seen. The dissociation behavior of the 52S complex and the molecular weight of the subunits have been confirmed by gel electrophoresis studies. The loop structures melt at fairly low temperatures; the dissociation of the 52S molecule into its two subunits occurs at a higher temperature corresponding to a base composition of about 63% guanosine plus cytosine. Polyadenylic acid mapping by electron microscopy shows that the 52S molecule contains two polyadenylic acid segments, one at each end. It thus appears that 52S RD-114 RNA consists of two 2.8 X 10(6) dalton subunits, each with a characteristic

  18. 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

  19. Polymer brushes with nanoinclusions under shear: A molecular dynamics investigation

    PubMed Central

    Milchev, A.; Dimitrov, D. I.; Binder, K.

    2010-01-01

    We use molecular dynamics simulations with a dissipative particle dynamics thermostat to study the behavior of nanosized inclusions (colloids) in a polymer brush under shear whereby the solvent is explicitly included in the simulation. The brush is described by a bead-spring model for flexible polymer chains, grafted on a solid substrate, while the polymer-soluble nanoparticles in the solution are taken as soft spheres whose diameter is about three times larger than that of the chain segments and the solvent. We find that the brush number density profile, as well as the density profiles of the nanoinclusions and the solvent, remains insensitive to strong shear although the grafted chains tilt in direction of the flow. The thickness of the penetration layer of nanoinclusions, as well as their average concentration in the brush, stays largely unaffected even at the strongest shear. Our result manifests the remarkable robustness of polymer brushes with embedded nanoparticles under high shear which could be of importance for technological applications. PMID:21045924

  20. 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. PMID:18158914

  1. 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.

  2. 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

  3. 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

  4. Copromicroscopic and molecular investigations on intestinal parasites in kenneled dogs.

    PubMed

    Simonato, Giulia; Frangipane di Regalbono, Antonio; Cassini, Rudi; Traversa, Donato; Beraldo, Paola; Tessarin, Cinzia; Pietrobelli, Mario

    2015-05-01

    Intestinal parasites are common in dogs worldwide, and their importance has recently increased for a renewed awareness on the public health relevance that some of them have. In this study, the prevalence of helminths and protozoa was evaluated by microscopy in 318 canine faecal samples collected from eight rescue shelters in the North-eastern Italy; 285 of them were also submitted to the molecular characterization of Giardia duodenalis and Cryptosporidium spp. isolates. An analysis was performed to evaluate the prevalence rates in relation to canine individual data, shelter provenance and anthelmintic treatments. Overall, 52.5% (167/318) of faecal samples were positive for at least one parasite. Trichuris vulpis showed the highest overall prevalence rate (29.2%), followed by G. duodenalis (15.1%), Toxocara canis (9.7%), ancylostomatids (8.2%) and Cystoisospora (5.7%). The prevalence of G. duodenalis, evaluated by real-time PCR, was 57.9% (165/285), and 79 isolates were characterized by nested PCR on the β-giardin gene. The assemblages found were mainly the host-specific genotypes C and D, while only one assemblage was identified as the human-specific genotype B1. Isolates of Cryptosporidium spp., recorded in 3/285 (1.1%) stool samples, were Cryptosporidium parvum based on the characterization of the Cryptosporidium oocyst wall protein (COWP) gene. Although the results describe a relatively limited risk of dog-originating zoonoses, there is the need to improve the quality of shelter practices towards better health managements for safe pet-adoption campaigns and a minimization of the environmental faecal pollution with canine intestinal parasites. PMID:25687526

  5. 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.

  6. Optimization techniques in molecular structure and function elucidation.

    PubMed

    Sahinidis, Nikolaos V

    2009-12-01

    This paper discusses recent optimization approaches to the protein side-chain prediction problem, protein structural alignment, and molecular structure determination from X-ray diffraction measurements. The machinery employed to solve these problems has included algorithms from linear programming, dynamic programming, combinatorial optimization, and mixed-integer nonlinear programming. Many of these problems are purely continuous in nature. Yet, to this date, they have been approached mostly via combinatorial optimization algorithms that are applied to discrete approximations. The main purpose of the paper is to offer an introduction and motivate further systems approaches to these problems. PMID:20160866

  7. 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

  8. Structural Changes of a Doubly Spin-Labeled Chemically Driven Molecular Shuttle Probed by PELDOR Spectroscopy.

    PubMed

    Franchi, Paola; Bleve, Valentina; Mezzina, Elisabetta; Schäfer, Christian; Ragazzon, Giulio; Albertini, Marco; Carbonera, Donatella; Credi, Alberto; Di Valentin, Marilena; Lucarini, Marco

    2016-06-20

    Gaining detailed information on the structural rearrangements associated with stimuli-induced molecular movements is of utmost importance for understanding the operation of molecular machines. Pulsed electron-electron double resonance (PELDOR) was employed to monitor the geometrical changes arising upon chemical switching of a [2]rotaxane that behaves as an acid-base-controlled molecular shuttle. To this aim, the rotaxane was endowed with stable nitroxide radical units in both the ring and axle components. The combination of PELDOR data and molecular dynamic calculations indicates that in the investigated rotaxane, the ring displacement along the axle, caused by the addition of a base, does not alter significantly the distance between the nitroxide labels, but it is accompanied by a profound change in the geometry adopted by the macrocycle. PMID:27123774

  9. Hybrid Molecular Structure of the Giant Protease Tripeptidyl Peptidase II

    PubMed Central

    Chuang, Crystal K.; Rockel, Beate; Seyit, Gönül; Walian, Peter J.; Schönegge, Anne–Marie; Peters, Jürgen; Zwart, Petrus H.; Baumeister, Wolfgang; Jap, Bing K.

    2010-01-01

    Tripeptidyl peptidase II (TPP II) is the largest known eukaryotic protease (6MDa). It is believed to act downstream of the 26S proteasome cleaving tripeptides from the N– termini of longer peptides and it is implicated in numerous cellular processes. Here we report the structure of Drosophila TPP II determined by a hybrid approach: The structure of the dimer was solved by x–ray crystallography and docked into the three– dimensional map of the holocomplex obtained by single-particle cryo-electron microscopy. The resulting structure reveals the compartmentalization of the active sites inside a system of chambers and suggests the existence of a molecular ruler determining the size of the cleavage products. Furthermore, the structure suggests a model for activation of TPP II involving the relocation of a flexible loop and a repositioning of the active–site serine, coupling it to holocomplex assembly and active site sequestration. PMID:20676100

  10. Structural Modeling and Molecular Dynamics Simulation of the Actin Filament

    SciTech Connect

    Splettstoesser, Thomas; Holmes, Kenneth; Noe, Frank; Smith, Jeremy C

    2011-01-01

    Actin is a major structural protein of the eukaryotic cytoskeleton and enables cell motility. Here, we present a model of the actin filament (F-actin) that not only incorporates the global structure of the recently published model by Oda et al. but also conserves internal stereochemistry. A comparison is made using molecular dynamics simulation of the model with other recent F-actin models. A number of structural determents such as the protomer propeller angle, the number of hydrogen bonds, and the structural variation among the protomers are analyzed. The MD comparison is found to reflect the evolution in quality of actin models over the last 6 years. In addition, simulations of the model are carried out in states with both ADP or ATP bound and local hydrogen-bonding differences characterized.

  11. Structure and dynamics of complex liquid water: Molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    S, Indrajith V.; Natesan, Baskaran

    2015-06-01

    We have carried out detailed structure and dynamical studies of complex liquid water using molecular dynamics simulations. Three different model potentials, namely, TIP3P, TIP4P and SPC-E have been used in the simulations, in order to arrive at the best possible potential function that could reproduce the structure of experimental bulk water. All the simulations were performed in the NVE micro canonical ensemble using LAMMPS. The radial distribution functions, gOO, gOH and gHH and the self diffusion coefficient, Ds, were calculated for all three models. We conclude from our results that the structure and dynamical parameters obtained for SPC-E model matched well with the experimental values, suggesting that among the models studied here, the SPC-E model gives the best structure and dynamics of bulk water.

  12. 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.

  13. 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

  14. Metal nanoelectrodes for molecular transistor and investigation of electron transport in molecular systems

    NASA Astrophysics Data System (ADS)

    Suyatin, D. B.; Soldatov, E. S.; Maximov, Ivan; Montelius, Lars; Samuelson, Lars; Khomutov, G. B.; Gubin, S. P.; Sergeev-Cherenkov, A. N.

    2002-06-01

    Gold nanoelectrodes with gaps of less than 10 nm were formed by conventional E-beam lithography on silicon substrates covered by Al2O3. Molecular films were deposited on the electrodes by Langmuir-Shaefer technique. The I-V curves of such systems show a suppressed conductance indicating a correlated electron tunnelling through the system. All measurements were made at room temperature.

  15. Metal nanoelectrodes for molecular transistor and investigation of electron transport in molecular systems

    NASA Astrophysics Data System (ADS)

    Suyatin, D. B.; Soldatov, E. S.; Maximov, Ivan; Montelius, Lars; Samuelson, Lars; Khomutov, G. B.; Gubin, S. P.; Sergeev-Cherenkov, A. N.

    2003-06-01

    Gold nanoelectrodes with gaps of less than 10 nm were formed by conventional E-beam lithography on silicon substrates covered by Al2O3. Molecular films were deposited on the electrodes by Langmuir-Shaefer technique. The I-V curves of such systems show a suppressed conductance indicating a correlated electron tunnelling through the system. All measurements were made at room temperature.

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

    PubMed

    Karthick, T; Balachandran, V; Perumal, S

    2015-04-15

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

  17. 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.

  18. 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…

  19. Probing the molecular structure of interfacial films and crystals

    NASA Astrophysics Data System (ADS)

    Wang, Anfeng

    The properties of outside surfaces were found to play an important role in the nucleation and crystallization processes. Thus controlling the surface properties would provide an effective means for crystal engineering. Hydrophobic surface is prepared by self-assembled monolayer (SAM) formation of octadecyltrichlorosilane (OTS) on silicon surface, with the hydrophobicity adjusted by the monolayer coverage. Silicon wafer treated by RCA method is hydrophilic, so are SAMs formed by two amine-terminated organosilanes on silicon. However these three hydrophilic surfaces are unstable, due to contamination of the amine-terminated SAMs and hydrolysis of RCA treated silicon. Polymethine dyes, BDH+Cl- and BDH +ClO4-, are synthesized and characterized by UV spectra and crystal morphology. They have identical UV spectrum in dilute solutions due to the same chromophore, and J-aggregation happens at much higher concentrations. IR spectra are analyzed to monitor the crystallization process of BDH+Cl- OTS SAM surface and the crystallization process of BDH+Cl- on substrates with varying hydrophobicity was monitored by optical microscopy and compared. Due to the extreme flexibility of polysiloxane, silicone surfactants can arrange themselves at the interfaces quickly to adopt configurations with minimum free energy. Polysiloxane is hydrophobic but not oleophilic, which makes them effective emulsifiers and stabilizers in aqueous and nonaqueous media. The interaction between an AFM Si3N4 tip and a hydrophobic surface in silicone polyether (SPE) solution in the presence of ethanol was investigated by Atomic Force Microscopy (AFM) force measurement. ABA triblock type and comb-type SPE surfactants, adsorbed at the liquid-solid interface, provide steric barriers, even with significant addition of ethanol. On the contrary, conventional low-molecular weight and polymeric alkyl surfactants display no steric barrier even in the presence of moderate amount of ethanol. This unique property makes

  20. Aggregation-Induced Emission Mechanism of Dimethoxy-Tetraphenylethylene in Water Solution: Molecular Dynamics and QM/MM Investigations.

    PubMed

    Sun, Guangxu; Zhao, Yi; Liang, WanZhen

    2015-05-12

    Molecular dynamics simulations and combined quantum mechanics and molecular mechanics calculations are employed to investigate dimethoxy-tetraphenylethylene (DMO-TPE) molecules in water solution for their detailed aggregation process and the mechanism of aggregation-induced emission. The molecular dynamics simulations show that the aggregates start to appear in the nanosecond time scale, and small molecular aggregates appear at low concentration; whereas the large aggregates with a chain-type structure appear at high concentration, and the intramolecular rotation is largely restricted by a molecular aggregated environment. The average radical distribution demonstrates that the waters join the aggregation process and that two types of hydrogen bonds between DMO-TPE and water molecules are built with the peaks at about 0.5 and 0.7 nm, respectively. The spectral features further reveal that the aggregates dominantly present J-type aggregation although they fluctuate between J-type and H-type at a given temperature. The statistical absorption, emission spectra, and the aggregation-induced emission enhancement with respect to the solution concentration agree well with the experimental measurements, indicating the significant effect of molecular environments on the molecular properties. PMID:26574424

  1. Profiling of the Molecular Weight and Structural Isomer Abundance of Macroalgae-Derived Phlorotannins

    PubMed Central

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

    2015-01-01

    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. PMID:25603345

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. Energy-weighted sum rules and the analysis of vibrational structure in molecular spectra

    NASA Astrophysics Data System (ADS)

    Smith, W. L.

    2015-10-01

    The energy-weighted sum SV = Σn (E‧n - E″m)|<ψ″m|ψ‧n>|2 = <ψ″m|ΔV|ψ″m> for the vibrational potential functions V‧, V″ associated with transitions between two electronic states of diatomic molecular species is investigated and specific formulae are given using Morse functions for V‧ and V″. It is found that these formulae are useful approximations which provide a convenient way to analyse the vibrational structure of real spectra to give estimates of molecular parameters such as the change in internuclear distance accompanying a transition.

  7. 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.

  8. 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

  9. Investigation of molecular interaction between cefpodoxime acid and human mixtard insulin by ultrasonic and spectral methods.

    PubMed

    Ganesh, T; Kannappan, V; Mohamed Kamil, M G; Kumar, R

    2016-09-10

    This paper deals with the extensive investigation of molecular interaction between third generation cephalosporin antibiotic, Cefpodoxime Acid (CA) and Human Mixtard Insulin (HMI) in an aqueous medium through ultrasonic, dilute solution viscometric (DSV) and spectral [UV-vis, Attenuated total reflection (ATR)-FT IR] methods at various blend compositions of the drug and insulin at three different (303K, 310K and 313K) temperatures. This is an attempt to unravel the possibility of drug induced hypoglycemic effect. The existence of solute-solute interaction in aqueous solutions of CA and HMI is established from the variation of ultrasonic velocity and other acoustical parameters with blend composition. DSV method is used to confirm the range of blend composition at which the molecular interaction is significant. The conclusions drawn from ultrasonic and DSV methods are further established by the UV-vis and ATR- FT IR spectral studies of ternary mixtures at different blend compositions. Further, the existing interactions suggest the possibility of cefpodoxime acid induced hypoglycemia which is discussed based on the structural aspects of the two components.

  10. Conformational Changes in Acetylcholine Binding Protein Investigated by Temperature Accelerated Molecular Dynamics

    PubMed Central

    Mohammad Hosseini Naveh, Zeynab; Malliavin, Therese E.; Maragliano, Luca; Cottone, Grazia; Ciccotti, Giovanni

    2014-01-01

    Despite the large number of studies available on nicotinic acetylcholine receptors, a complete account of the mechanistic aspects of their gating transition in response to ligand binding still remains elusive. As a first step toward dissecting the transition mechanism by accelerated sampling techniques, we study the ligand-induced conformational changes of the acetylcholine binding protein (AChBP), a widely accepted model for the full receptor extracellular domain. Using unbiased Molecular Dynamics (MD) and Temperature Accelerated Molecular Dynamics (TAMD) simulations we investigate the AChBP transition between the apo and the agonist-bound state. In long standard MD simulations, both conformations of the native protein are stable, while the agonist-bound structure evolves toward the apo one if the orientation of few key sidechains in the orthosteric cavity is modified. Conversely, TAMD simulations initiated from the native conformations are able to produce the spontaneous transition. With respect to the modified conformations, TAMD accelerates the transition by at least a factor 10. The analysis of some specific residue-residue interactions points out that the transition mechanism is based on the disruption/formation of few key hydrogen bonds. Finally, while early events of ligand dissociation are observed already in standard MD, TAMD accelerates the ligand detachment and, at the highest TAMD effective temperature, it is able to produce a complete dissociation path in one AChBP subunit. PMID:24551117

  11. Biophysical Investigations with MARCKS-ED: Dissecting the Molecular Mechanism of Its Curvature Sensing Behaviors

    PubMed Central

    de Jesus, Armando J.; Espinoza, Arianna; Yin, Hang

    2014-01-01

    Curved membranes are a common and important attribute in cells. Protein and peptide curvature sensors are known to activate signaling pathways, initiate vesicle budding, trigger membrane fusion, and facilitate molecular transport across cell membranes. Nonetheless, there is little understanding how these proteins and peptides achieve preferential binding of different membrane curvatures. The current study is to elucidate specific factors required for curvature sensing. As a model system, we employed a recently identified peptide curvature sensor, MARCKS-ED, derived from the effector domain of the myristoylated alanine-rich C-kinase substrate protein, for these biophysical investigations. An atomistic molecular dynamics (MD) simulation suggested an important role played by the insertion of the Phe residues within MARCKS-ED. To test these observations from our computational simulations, we performed electron paramagnetic resonance (EPR) studies to determine the insertion depth of MARCKS-ED into differently curved membrane bilayers. Next, studies with varied lipid compositions revealed their influence on curvature sensing by MARCKS-ED, suggesting contributions from membrane fluidity, rigidity, as well as various lipid structures. Finally, we demonstrated that the curvature sensing by MARCKS-ED is configuration independent. In summary, our studies have shed further light to the understanding of how MARCKS-ED differentiates between membrane curvatures, which may be generally applicable to protein curvature sensing behavior. PMID:25195712

  12. Supramolecular structure formation of molecular copper(II)methylsalicylate complexes with nicotinamide or methylnicotinamide - Crystal structure and spectral properties

    NASA Astrophysics Data System (ADS)

    Puchoňová, Miroslava; Repická, Zuzana; Moncol, Jan; Růžičková, Zdeňka; Mazúr, Milan; Valigura, Dušan

    2015-07-01

    As the systematic investigation of salicylatocopper complexes with nicotinamide derivatives the preparation, characterization and X-ray structure determination of four new molecular copper(II) complexes with x-methylsalicylate anion (x-Mesal-) and nicotinamide (nia) or N-methylnicotinamide (mna) are reported. The molecular complexes [Cu(5-Mesal)2(nia)2] (1), [Cu(3-Mesal)2(nia)2] (2) build up 2-D supramolecular structures of different character. The ladder-type supramolecular structure of (1) is formed by the head-to-head H-bonds of neighbouring carboxamide groups, while the supramolecular structure of (2) is formed by Nsbnd H⋯O H-bonds of carboxamide groups into 1-D chain that are by the additional Hsbnd H⋯O H-bonds of Nsbnd H carboxamide and the carboxylate group oxygen atoms linked to 2-D layers. The centrosymmetrical crystal molecular structure of [Cu(4-Mesal)2(mna)2(H2O)2]ṡ2EtOH (3) or [Cu(5-Mesal)2(mna)2(H2O)2]ṡ2MeOH (4) are forming 1-D supramolecular chains that involve the methylcarboxamide Nsbnd H group, the crystalosolvate alcohol Osbnd H group, the coordinated water molecule Osbnd H bond and oxygen atom of neighbouring complex molecule. The coordination polyhedron symmetry corresponds with the isotropic character of EPR spectra of (1) and (2) while the EPR spectrum of (4) is of axial symmetry.

  13. Investigating the deformation of nanocrystalline copper with microscale kinematic metrics and molecular dynamics

    NASA Astrophysics Data System (ADS)

    Tucker, Garritt J.; Tiwari, Shreevant; Zimmerman, Jonathan A.; McDowell, David L.

    2012-03-01

    Atomistic simulations are employed to investigate the deformation of nanocrystalline copper and the associated strain accommodation mechanisms at 10 K as a function of grain size. Volume-averaged kinematic metrics based on continuum mechanics theory are formulated to analyze the results of molecular dynamics simulations. The metrics rely on both reference and current configurations, along with nearest neighbor lists to estimate nanoscale behavior of atomic deformation fields in nanocrystalline copper. Various deformation mechanisms are activated in the structures, and shown to depend on average grain size of the nanocrystalline structure. Furthermore, grain boundaries, along with dislocation glide, become an important source of strain accommodation as grain size is reduced. It is demonstrated that the metrics capture the contributions of various mechanisms, and provide a sense of the history of atomic regions undergoing both elastic and plastic deformation. The significance of this research is that unique kinematic signatures of the mechanisms are uncovered using certain metrics, and we are able to resolve the contributions of the deformation mechanisms to the overall strain of the structure using Green strain.

  14. 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.

  15. 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.

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

    PubMed

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

    2014-11-07

    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.

  17. Solid state structural and theoretical investigations of a biologically active chalcone

    NASA Astrophysics Data System (ADS)

    Abbas, Asghar; Gökce, Halil; Bahceli, Semiha; Bolte, Michael; Naseer, Muhammad Moazzam

    2016-05-01

    The computational methods are presently emerging as an efficient and reliable tool for predicting structural properties of biologically important compounds. In the present manuscript, the solid state structural and theoretical investigations of a biologically active chalcone i-e (E)-3-(4-(hexyloxy)phenyl)-1-phenylprop-2-en-1-one (6c) have been reported. The solid state structure of 6c was measured by X-ray crystallographic technique whereas the optimized molecular geometry, vibrational frequencies, the simulated UV-vis spectra (in gas and in methanol solvent), 1H and 13C NMR chemical shift (in gas and in chloroform solvent) values, HOMO-LUMO analysis, the molecular electrostatic potential (MEP) surface and thermodynamic parameters were calculated by using DFT/B3LYP method with 6-311++G(d,p) basis set in ground state. The results of the theoretical investigations were found to be in good agreement with experimental data.

  18. 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.

  19. Structure of a molecular liquid GeI4.

    PubMed

    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. PMID:27605016

  20. 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

  1. Investigation into the molecular and thermodynamic basis of protein interactions in multimodal chromatography using functionalized nanoparticles.

    PubMed

    Srinivasan, Kartik; Parimal, Siddharth; Lopez, Maria M; McCallum, Scott A; Cramer, Steven M

    2014-11-11

    Although multimodal chromatography offers significant potential for bioseparations, there is a lack of molecular level understanding of the nature of protein binding in these systems. In this study a nanoparticle system is employed that can simulate a chromatographic resin surface while also being amenable to isothermal titration calorimetry (ITC) and solution NMR. ITC and NMR titration experiments are carried out with (15)N-labeled ubiquitin to investigate the interactions of ubiquitin with nanoparticles functionalized with two industrially important multimodal ligands. The ITC results suggest that binding to both multimodal ligand surfaces is entropically driven over a range of temperatures and that this is due primarily to the release of surface bound waters. In order to reveal structural details of the interaction process, binding-induced chemical shift changes obtained from the NMR experiments are employed to obtain dissociation constants of individual amino acid residues on the protein surface. The residue level information obtained from NMR is then used to identify a preferred binding face on ubiquitin for interaction to both multimodal ligand surfaces. In addition, electrostatic potential and spatial aggregation propensity maps are used to determine important protein surface property data that are shown to correlate well with the molecular level information obtained from NMR. Importantly, the data demonstrate that the cluster of interacting residues on the protein surface act co-operatively to give rise to multimodal binding affinities several orders of magnitude greater than those obtained previously for interactions with free solution ligands. The use of NMR and ITC to study protein interactions with functionalized nanoparticles offers a new tool for obtaining important molecular and thermodynamic insights into protein affinity in multimodal chromatographic systems. PMID:25310519

  2. Investigation of polarization effects in the gramicidin A channel from ab initio molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Timko, Jeff; Kuyucak, Serdar

    2012-11-01

    Polarization is an important component of molecular interactions and is expected to play a particularly significant role in inhomogeneous environments such as pores and interfaces. Here we investigate the effects of polarization in the gramicidin A ion channel by performing quantum mechanics/molecular mechanics molecular dynamics (MD) simulations and comparing the results with those obtained from classical MD simulations with non-polarizable force fields. We consider the dipole moments of backbone carbonyl groups and channel water molecules as well as a number of structural quantities of interest. The ab initio results show that the dipole moments of the carbonyl groups and water molecules are highly sensitive to the hydrogen bonds (H-bonds) they participate in. In the absence of a K+ ion, water molecules in the channel are quite mobile, making the H-bond network highly dynamic. A central K+ ion acts as an anchor for the channel waters, stabilizing the H-bond network and thereby increasing their average dipole moments. In contrast, the K+ ion has little effect on the dipole moments of the neighboring carbonyl groups. The weakness of the ion-peptide interactions helps to explain the near diffusion-rate conductance of K+ ions through the channel. We also address the sampling issue in relatively short ab initio MD simulations. Results obtained from a continuous 20 ps ab initio MD simulation are compared with those generated by sampling ten windows from a much longer classical MD simulation and running each window for 2 ps with ab initio MD. Both methods yield similar results for a number of quantities of interest, indicating that fluctuations are fast enough to justify the short ab initio MD simulations.

  3. Investigation of polarization effects in the gramicidin A channel from ab initio molecular dynamics simulations.

    PubMed

    Timko, Jeff; Kuyucak, Serdar

    2012-11-28

    Polarization is an important component of molecular interactions and is expected to play a particularly significant role in inhomogeneous environments such as pores and interfaces. Here we investigate the effects of polarization in the gramicidin A ion channel by performing quantum mechanics/molecular mechanics molecular dynamics (MD) simulations and comparing the results with those obtained from classical MD simulations with non-polarizable force fields. We consider the dipole moments of backbone carbonyl groups and channel water molecules as well as a number of structural quantities of interest. The ab initio results show that the dipole moments of the carbonyl groups and water molecules are highly sensitive to the hydrogen bonds (H-bonds) they participate in. In the absence of a K(+) ion, water molecules in the channel are quite mobile, making the H-bond network highly dynamic. A central K(+) ion acts as an anchor for the channel waters, stabilizing the H-bond network and thereby increasing their average dipole moments. In contrast, the K(+) ion has little effect on the dipole moments of the neighboring carbonyl groups. The weakness of the ion-peptide interactions helps to explain the near diffusion-rate conductance of K(+) ions through the channel. We also address the sampling issue in relatively short ab initio MD simulations. Results obtained from a continuous 20 ps ab initio MD simulation are compared with those generated by sampling ten windows from a much longer classical MD simulation and running each window for 2 ps with ab initio MD. Both methods yield similar results for a number of quantities of interest, indicating that fluctuations are fast enough to justify the short ab initio MD simulations.

  4. Roles in Modulation of Molecular Structures on Metal Surfaces

    NASA Astrophysics Data System (ADS)

    Gao, H.-J.

    2007-03-01

    We studied the adsorption of organic molecules, their growth behavior, and their physical properties on silver and gold surfaces at the single molecule or sub-molecular scale by using low-temperature scanning tunneling microscopes. Combined with low energy electron diffraction and first-principles density functional theory calculations, the key parameters in modulating molecular structures on metals are analyzed. It is found that the alkyl chains of quinacridone derivatives (QA) determine the orientation of molecular overlayers on an Ag(110) substrate. The interaction of QA and the Ag substrate is primarily due to chemical bonding of oxygen to specific positions at the silver substrate, determining the molecular orientation and preferred adsorption site. However, the intermolecular arrangement can be adjusted via the length of attached alkyl chains. We are thus able to fabricate uniform QA films with very well controlled physical properties. Furthermore, by thermal and chemical control, we are able to self-assemble three dimensional molecular nanostructures, e.g. ordered PTCDA structures exclusively on flat Ag(111) facets, or DMe-DCNQI structures exclusively on stepped Ag(221) facets. It is demonstrated that bonding, the key factor for selectivity, occurs via the end-atoms, while the molecule's mid-region arches away from the substrate. Theoretical results, obtained by high-level theory, are consistent with the experimental observations, which have previously been interpreted in terms of bonding through the mid-region. In collaboration with D.X. Shi, S.X. Du, W. Ji, Z.T. Deng, L. Gao, Institute of Physics, and X. Lin, Chinese Academy of Sciences, China; C. Seidel and H. Fuchs, Universit"at M"unster, Germany; W.A. Hofer, The University of Liverpool, Britain; and S. T. Pantelides, Vanderbilt University, USA. [1] D.X. Shi et al., Phys. Rev. Lett. 96, 226101(2006). [2] S.X. Du et al., Phys. Rev. Lett. 96, 226101(2006). [3] L. Gao et al., Phys. Rev. B 73, 075424(2006).

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

    PubMed

    Napoleon, Raeanne L; Moore, Preston B

    2006-03-01

    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. 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.

  10. 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.

  11. Single molecule switches and molecular self-assembly: Low temperature STM investigations and manipulations

    NASA Astrophysics Data System (ADS)

    Iancu, Violeta

    This dissertation is devoted to single molecule investigations and manipulations of two porphyrin-based molecules, chlorophyll-a and Co-porphyrin. The molecules are adsorbed 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 detailed underlying switching mechanisms are uncovered from the statistical analyses conducted over 1200 switching events together with the support of geometrically relaxed parametric calculations. The second switch, a spintronic switch, uses Co-porphyrin conformational changes to tune the spin-electron interaction between the Co atom and Cu(111) electrons. A change in the molecular conformation, from saddle to planar, leads to enhanced spin-electron coupling strength, and consequently, elevated Kondo temperatures. Self-assembly process is exploited for both the molecules and the analyses reveal important information regarding the layer growth and the electronic differences that appear due to the modified molecule-substrate environment.

  12. 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. PMID:26969524

  13. Investigating Protein Structure and Evolution with SCOP2.

    PubMed

    Andreeva, Antonina; Howorth, Dave; Chothia, Cyrus; Kulesha, Eugene; Murzin, Alexey G

    2015-03-09

    SCOP2 is a successor to the Structural Classification of Proteins (SCOP) database that organizes proteins of known structure according to their structural and evolutionary relationships. It was designed to provide a more advanced framework for the classification of proteins. The SCOP2 classification is described in terms of a directed acyclic graph in which each node defines a relationship of particular type that is represented by a region of protein structure and sequence. The SCOP2 data are accessible via SCOP2-Browser and SCOP2-Graph. This protocol unit describes different ways to explore and investigate the SCOP2 evolutionary and structural groupings.

  14. Structure-Directed Exciton Dynamics in Templated Molecular Nanorings

    PubMed Central

    2015-01-01

    Conjugated polymers with cyclic structures are interesting because their symmetry leads to unique electronic properties. Recent advances in Vernier templating now allow large shape-persistent fully conjugated porphyrin nanorings to be synthesized, exhibiting unique electronic properties. We examine the impact of different conformations on exciton delocalization and emission depolarization in a range of different porphyrin nanoring topologies with comparable spatial extent. Low photoluminescence anisotropy values are found to occur within the first few hundred femtoseconds after pulsed excitation, suggesting ultrafast delocalization of excitons across the nanoring structures. Molecular dynamics simulations show that further polarization memory loss is caused by out-of-plane distortions associated with twisting and bending of the templated nanoring topologies. PMID:25960822

  15. Surfaces of Microparticles in Colloids: Structure and Molecular Adsorption Kinetics

    NASA Astrophysics Data System (ADS)

    Dai, Hai-Lung

    2002-03-01

    Surfaces of micron and sub-micron size particles in liquid solution are probed by second harmonic generation (SHG) facilitated with femtosecond laser pulses. The particles probed include inorganic objects such as carbon black and color pigments, polymeric species like polystyrene beads, and biological systems such as blood cells and ecoli. In the experiments, dye molecules are first adsorbed onto the particle surface to allow generation of second harmonics upon light irradiation. Competition for adsorption between these surface dye molecules and the molecules of interest in the solution is then monitored by the SHG signal to reveal the molecular adsorption kinetics and surface structure. Specifically, surfactant adsorption on polymer surfaces, the structure of carbon black surface, and protein adsorption on biological surfaces, monitored by this technique, will be discussed.

  16. 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.

  17. Physics-based protein structure refinement through multiple molecular dynamics trajectories and structure averaging.

    PubMed

    Mirjalili, Vahid; Noyes, Keenan; Feig, Michael

    2014-02-01

    We used molecular dynamics (MD) simulations for structure refinement of Critical Assessment of Techniques for Protein Structure Prediction 10 (CASP10) targets. Refinement was achieved by selecting structures from the MD-based ensembles followed by structural averaging. The overall performance of this method in CASP10 is described, and specific aspects are analyzed in detail to provide insight into key components. In particular, the use of different restraint types, sampling from multiple short simulations versus a single long simulation, the success of a quality assessment criterion, the application of scoring versus averaging, and the impact of a final refinement step are discussed in detail.

  18. PCR hot start using primers with the structure of molecular beacons (hairpin-like structure).

    PubMed

    Kaboev, O K; Luchkina, L A; Tret'iakov, A N; Bahrmand, A R

    2000-11-01

    A new technique of PCR hot start using oligonucleotide primers with a stem-loop structure is developed here. The molecular beacon oligonucleotide structure without any chromophore addition to the ends was used. The 3'-end sequence of the primers was complementary to the target and five or six nucleotides complementary to the 3'-end were added to the 5'-end. During preparation of the reaction mixture and initial heating, the oligonucleotide has a stem-loop structure and cannot serve as an effective primer for DNA polymerase. After heating to the annealing temperature it acquires a linear structure and primer extension can begin.

  19. 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.

  20. Protein Structure Refinement through Structure Selection and Averaging from Molecular Dynamics Ensembles.

    PubMed

    Mirjalili, Vahid; Feig, Michael

    2013-02-12

    A molecular dynamics (MD) simulation based protocol for structure refinement of template-based model predictions is described. The protocol involves the application of restraints, ensemble averaging of selected subsets, interpolation between initial and refined structures, and assessment of refinement success. It is found that sub-microsecond MD-based sampling when combined with ensemble averaging can produce moderate but consistent refinement for most systems in the CASP targets considered here.

  1. 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

    2015-03-01

    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. PMID:25498634

  2. Drug repositioning by kernel-based integration of molecular structure, molecular activity, and phenotype data.

    PubMed

    Wang, Yongcui; Chen, Shilong; Deng, Naiyang; Wang, Yong

    2013-01-01

    Computational inference of novel therapeutic values for existing drugs, i.e., drug repositioning, offers the great prospect for faster and low-risk drug development. Previous researches have indicated that chemical structures, target proteins, and side-effects could provide rich information in drug similarity assessment and further disease similarity. However, each single data source is important in its own way and data integration holds the great promise to reposition drug more accurately. Here, we propose a new method for drug repositioning, PreDR (Predict Drug Repositioning), to integrate molecular structure, molecular activity, and phenotype data. Specifically, we characterize drug by profiling in chemical structure, target protein, and side-effects space, and define a kernel function to correlate drugs with diseases. Then we train a support vector machine (SVM) to computationally predict novel drug-disease interactions. PreDR is validated on a well-established drug-disease network with 1,933 interactions among 593 drugs and 313 diseases. By cross-validation, we find that chemical structure, drug target, and side-effects information are all predictive for drug-disease relationships. More experimentally observed drug-disease interactions can be revealed by integrating these three data sources. Comparison with existing methods demonstrates that PreDR is competitive both in accuracy and coverage. Follow-up database search and pathway analysis indicate that our new predictions are worthy of further experimental validation. Particularly several novel predictions are supported by clinical trials databases and this shows the significant prospects of PreDR in future drug treatment. In conclusion, our new method, PreDR, can serve as a useful tool in drug discovery to efficiently identify novel drug-disease interactions. In addition, our heterogeneous data integration framework can be applied to other problems.

  3. 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).

  4. 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.

  5. 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.

  6. 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.

  7. Atomic and electronic structures of carbon nanotube covalent connecting with graphene by oxygen molecular

    NASA Astrophysics Data System (ADS)

    Wei, Jianwei; Wei, Qiang; Ma, Zengwei; Zeng, Hui

    2016-02-01

    Based on density functional theories, we have investigated the nanostructure in which boron and nitrogen co-doped carbon nanotube (CNT)/graphene (GR) were connected by an oxygen molecular. The geometry structure and electronic properties of the system were calculated carefully. The band structures indicate that the impurity state of oxygen transfer the semiconducting co-doped carbon nanotube/graphene into a semimetallic composite material. The results show that the connection can be achieved with energy release under a wider range of distance between the nanotube and graphene. It indicates that the connection between the nanotube and the graphene might be a self-assemble process.

  8. Mesoscopic superposition and sub-Planck-scale structure in molecular wave packets

    SciTech Connect

    Ghosh, Suranjana; Banerji, J.; Panigrahi, P. K.; Chiruvelli, Aravind

    2006-01-15

    We demonstrate the possibility of realizing sub-Planck-scale structures in the mesoscopic superposition of molecular wave packets involving vibrational levels. The time evolution of the wave packet, taken here as the SU(2) coherent state of the Morse potential describing hydrogen iodide molecules, produces macroscopic-quantum-superposition-like states, responsible for the above phenomenon. We investigate the phase-space dynamics of the coherent state through the Wigner function approach and identify the interference phenomena behind the sub-Planck-scale structures. The optimal parameter ranges are specified for observing these features.

  9. 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.

  10. 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.

  11. 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.

  12. Unveiling the molecular mechanism of brassinosteroids: Insights from structure-based molecular modeling studies.

    PubMed

    Lei, Beilei; Liu, Jiyuan; Yao, Xiaojun

    2015-12-01

    Brassinosteroid (BR) phytohormones play indispensable roles in plant growth and development. Brassinolide (BL) and 24-epibrassinolide (24-epiBL) are the most active ones among the BRs reported thus far. Unfortunately, the extremely low natural content and intricate synthesis process limit their popularization in agricultural production. Earlier reports to discover alternative compounds have resulted in molecules with nearly same scaffold structure and without diversity in chemical space. In the present study, receptors structure based BRs regulation mechanism was analyzed. First, we examined the detailed binding interactions and their dynamic stability between BL and its receptor BRI1 and co-receptor BAK1. Then, the binding modes and binding free energies for 24-epiBL and a series of representative BRs binding with BRI1 and BRI1-BAK1 were carried out by molecular docking, energy minimization and MM-PBSA free energy calculation. The obtained binding structures and energetic results provided vital insights into the structural factors affecting the activity from both receptors and BRs aspects. Subsequently, the obtained knowledge will serve as valuable guidance to build pharmacophore models for rational screening of new scaffold alternative BRs.

  13. The Structure and Evolution of Self-Gravitating Molecular Clouds

    NASA Astrophysics Data System (ADS)

    Holliman, John Herbert, II

    1995-01-01

    We present a theoretical formalism to evaluate the structure of molecular clouds and to determine precollapse conditions in star-forming regions. Models consist of pressure-bounded, self-gravitating spheres of a single -fluid ideal gas. We treat the case without rotation. The analysis is generalized to consider states in hydrostatic equilibrium maintained by multiple pressure components. Individual pressures vary with density as P_i(r) ~ rho^{gamma {rm p},i}(r), where gamma_{rm p},i is the polytropic index. Evolution depends additionally on whether conduction occurs on a dynamical time scale and on the adiabatic index gammai of each component, which is modified to account for the effects of any thermal coupling to the environment of the cloud. Special attention is given to properly representing the major contributors to dynamical support in molecular clouds: the pressures due to static magnetic fields, Alfven waves, and thermal motions. Straightforward adjustments to the model allow us to treat the intrinsically anisotropic support provided by the static fields. We derive structure equations, as well as perturbation equations for performing a linear stability analysis. The analysis provides insight on the nature of dynamical motions due to collapse from an equilibrium state and estimates the mass of condensed objects that form in such a process. After presenting a set of general results, we describe models of star-forming regions that include the major pressure components. We parameterize the extent of ambipolar diffusion. The analysis contributes to the physical understanding of several key results from observations of these regions. Commonly observed quantities are explicitly cross-referenced with model results. We theoretically determine density and linewidth profiles on scales ranging from that of molecular cloud cores to that of giant molecular clouds (GMCs). The model offers an explanation of the mean pressures in GMCs, which are observed to be high relative

  14. Molecular Structures of Polymer/Sulfur Composites for Lithium-Sulfur Batteries with Long Cycle Life

    SciTech Connect

    Xiao, Lifen; Cao, Yuliang; Xiao, Jie; Schwenzer, Birgit; Engelhard, Mark H.; Saraf, Laxmikant V.; Nie, Zimin; Exarhos, Gregory J.; Liu, Jun

    2013-04-26

    Vulcanizedpolyaniline/sulfur (SPANI/S) nanostructures were investigated for Li-S battery applications, but the detailed molecular structures of such composites have not been fully illustrated. In this paper, we synthesize SPANI/S composites with different S content in a nanorod configuration. FTIR, Raman, XPS, XRD, SEM and elemental analysis methods are used to characterize the molecular structure of the materials. We provide clear evidence that a portion of S was grafted on PANI during heating and connected the PANI chains with disulfide bonds to form a crosslinked network and the rest of S was encapsulated within it.. Polysulfides and elementary sulfur nanoparticles are physically trapped inside the polymer network and are not chemically bound to the polymer. The performance of the composites is further improved by reducing the particle size. Even after 500 cycles a capacity retention rate of 68.8% is observed in the SPANI/S composite with 55% S content.

  15. Molecular structure and vibrational spectra of Irinotecan: A density functional theoretical study

    NASA Astrophysics Data System (ADS)

    Chinna Babu, P.; Sundaraganesan, N.; Sudha, S.; Aroulmoji, V.; Murano, E.

    2012-12-01

    The solid phase FTIR and FT-Raman spectra of Irinotecan have been recorded in the regions 400-4000 and 50-4000 cm-1, respectively. The spectra were interpreted in terms of fundamentals modes, combination and overtone bands. The structure of the molecule was optimized and the structural characteristics were determined by density functional theory (DFT) using B3LYP method with 6-31G(d) as basis set. The vibrational frequencies were calculated for Irinotecan by DFT method and were compared with the experimental frequencies, which yield good agreement between observed and calculated frequencies. The infrared spectrum was also simulated from the calculated intensities. Besides, molecular electrostatic potential (MEP), frontier molecular orbitals (FMO) analysis were investigated using theoretical calculations.

  16. 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.

  17. Structural surface investigations with low-energy backscattered electrons

    NASA Astrophysics Data System (ADS)

    De Crescenzi, Maurizio

    The development of electron spectroscopies based on inelastic scattering fine structure is driven mainly by the need for structural methods which allow the investigation of the geometrical environment of different atomic species of the surface region of the sample. The EELFS (Extended Energy Loss Fine Structure) technique, using low-kinetic-energy electrons (1000-2000 eV) in reflection geometry, has been proven a useful tool for local structural investigation of clean surfaces, thin films and chemisorbed species. The main appeal of this technique, besides its experimental accessibility, is that the data analysis follows the procedure used for EXAFS (Extended X-ray Absorption Fine Structure) spectroscopy to obtain the atomic selectivity, the radial distribution function, the coordination number and the thermal and anisotropic effects. The near-edge energy-loss feature has been used to investigate the density of empty states close to EF and it appeeal particularly sensitive for following the structural changes and for discriminating among various phases and compound formations which occur in the surface region. In this work I review some recent developments, applications and theoretical considerations of the EELFS technique to give local structural parameters and to assess the basic mechanisms which dominate the low-energy electron-surface interaction.

  18. Stochastic Molecular Transport on Microtubule Bundles with Structural Defects

    NASA Astrophysics Data System (ADS)

    Gramlich, M. W.; Tabei, S. M. Ali

    Intracellular transport involves complex coordination of multiple components such as: the cytoskeletal network and molecular motors. Perturbations in this process can amplify over time and space, thereby affecting transport. One little studied component of transport are structural defects in the cytoskeletal network. In this talk we will present a stochastic model of the interaction of the molecular motor, kinesin-1, and a bundled cystoskeletal network of microtubules, and explicitly explore the role of microtubule ends (a type of defect) on long-range transport. We will show how different types of end distributions can ultimately result in the same observed transport behavior for bundles. We compare transport on completely uniform bundles, found in the axon, to completely random bundles, found in dendrites. Because of the un-biased random bundle nature, defects affect transport on dendrite bundles more than on uniform bundles in the axon. Further, defects act as large spatial-scale traps that result in random wait-times which have been assumed in previous models.

  19. How does the molecular network structure influence PDMS elastomer wettability?

    NASA Astrophysics Data System (ADS)

    Melillo, Matthew; Genzer, Jan

    Poly(dimethylsiloxane) (PDMS) is one of the most common elastomers, with applications ranging from medical devices to absorbents for water treatment. Fundamental understanding of how liquids spread on the surface of and absorb into PDMS networks is of critical importance for the design and use of another application - microfluidic devices. We have systematically studied the effects of polymer molecular weight, loading of tetra-functional crosslinker, end-group chemical functionality, and the extent of dilution of the curing mixture on the mechanical and surface properties of end-linked PDMS networks. The gel and sol fractions, storage and loss moduli, liquid swelling ratios, and water contact angles have all been shown to vary greatly based on the aforementioned variables. Similar trends were observed for the commercial PDMS material, Sylgard-184. Our results have confirmed theories predicting the relationships between modulus and swelling. Furthermore, we have provided new evidence for the strong influence that substrate modulus and molecular network structure have on the wettability of PDMS elastomers. These findings will aid in the design and implementation of efficient microfluidics and other PDMS-based materials that involve the transport of liquids.

  20. Electronic Structure and Molecular Dynamics Calculations for KBH4

    NASA Astrophysics Data System (ADS)

    Papaconstantopoulos, Dimitrios; Shabaev, Andrew; Hoang, Khang; Mehl, Michael; Kioussis, Nicholas

    2012-02-01

    In the search for hydrogen storage materials, alkali borohydrides MBH4 (M=Li, Na, K) are especially interesting because of their light weight and the high number of hydrogen atoms per metal atom. Electronic structure calculations can give insights into the properties of these complex hydrides and provide understanding of the structural properties and of the bonding of hydrogen. We have performed first-principles density-functional theory (DFT) and tight-binding (TB) calculations for KBH4 in both the high temperature (HT) and low temperature (LT) phases to understand its electronic and structural properties. Our DFT calculations were carried out using the VASP code. The results were then used as a database to develop a tight-binding Hamiltonian using the NRL-TB method. This approach allowed for computationally efficient calculations of phonon frequencies and elastic constants using the static module of the NRL-TB, and also using the molecular dynamics module to calculate mean-square displacements and formation energies of hydrogen vacancies.

  1. Towards a molecular description of intermediate filament structure and assembly

    SciTech Connect

    Parry, David A.D.; Strelkov, Sergei V.; Burkhard, Peter; Aebi, Ueli; Herrmann, Harald . E-mail: h.herrmann@dkfz.de

    2007-06-10

    Intermediate filaments (IFs) represent one of the prominent cytoskeletal elements of metazoan cells. Their constituent proteins are coded by a multigene family, whose members are expressed in complex patterns that are controlled by developmental programs of differentiation. Hence, IF proteins found in epidermis differ significantly from those in muscle or neuronal tissues. Due to their fibrous nature, which stems from a fairly conserved central {alpha}-helical coiled-coil rod domain, IF proteins have long resisted crystallization and thus determination of their atomic structure. Since they represent the primary structural elements that determine the shape of the nucleus and the cell more generally, a major challenge is to arrive at a more rational understanding of how their nanomechanical properties effect the stability and plasticity of cells and tissues. Here, we review recent structural results of the coiled-coil dimer, assembly intermediates and growing filaments that have been obtained by a hybrid methods approach involving a rigorous combination of X-ray crystallography, small angle X-ray scattering, cryo-electron tomography, computational analysis and molecular modeling.

  2. 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.

  3. 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. PMID:25475529

  4. 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.

  5. Studies of the correlation of electrode kinetics with molecular structure

    NASA Astrophysics Data System (ADS)

    Weaver, M. J.

    1983-06-01

    The overall objective is to develop our understanding of the connections between the kinetics and mechanisms of heterogeneous electron-transfer reactions at metal-electrolyte interfaces and the molecular structure of the reactant and the interfacial region. We have chiefly focussed attention on transition-metal redox couples, especially Co(III)/(II), Cr(III)/(II), and Ru(III)/(II) containing adsorbing inorganic and organic ligands at a number of electrocatalytic solid surfaces, especially silver, platinum, and gold, as well as at mercury electrodes. By combining electrochemical kinetic and reactant adsorption thermodynamic measurements, along with in situ vibrational spectroscopic studies using Surface-Enhanced Raman Scattering (SERS), the various catalytic influences exerted by the metal interface upon the energetics of electrode reactions have been probed in detail.

  6. Molecular structures and crystal packings of 2-styrylquinoxaline derivatives

    NASA Astrophysics Data System (ADS)

    Kuz'mina, L. G.; Sitin, A. G.; Gulakova, E. N.; Fedorova, O. A.; Lermontova, E. Kh.; Churakov, A. V.

    2012-01-01

    The crystal and molecular structures of 2-styrylquinoxaline derivatives with different substituents in the styryl fragment are determined. The degree of planarity of the molecules studied varies in a very wide range, from 1.7° to 33.5°. In the ethylene fragment, the double bond is essentially localized. The bicycle-pedal disordering of the ethylene fragment is found in the crystals of the methoxy and oxyacetyl derivatives of 2-styrylquinoxaline. None of the packings contains packing motifs favorable for the photocycloaddition (PCA) reaction with single crystal retention. The crystal packings of these compounds and that of 2-(4-methylstyryl)quinoxaline are characterized by a stacking motif of the head-to-head type, which eliminates the possibility of PCA taking place with single crystal retention but is suitable for this reaction in polycrystalline films. The crystal packing of 2-(3,4-dimethoxystyryl)quinoxaline does not contain elements with stacking interactions.

  7. 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.

  8. 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.

  9. Molecular Modeling of Mechanosensory Ion Channel Structural and Functional Features

    PubMed Central

    Gessmann, Renate; Kourtis, Nikos; Petratos, Kyriacos; Tavernarakis, Nektarios

    2010-01-01

    The DEG/ENaC (Degenerin/Epithelial Sodium Channel) protein family comprises related ion channel subunits from all metazoans, including humans. Members of this protein family play roles in several important biological processes such as transduction of mechanical stimuli, sodium re-absorption and blood pressure regulation. Several blocks of amino acid sequence are conserved in DEG/ENaC proteins, but structure/function relations in this channel class are poorly understood. Given the considerable experimental limitations associated with the crystallization of integral membrane proteins, knowledge-based modeling is often the only route towards obtaining reliable structural information. To gain insight into the structural characteristics of DEG/ENaC ion channels, we derived three-dimensional models of MEC-4 and UNC-8, based on the available crystal structures of ASIC1 (Acid Sensing Ion Channel 1). MEC-4 and UNC-8 are two DEG/ENaC family members involved in mechanosensation and proprioception respectively, in the nematode Caenorhabditis elegans. We used these models to examine the structural effects of specific mutations that alter channel function in vivo. The trimeric MEC-4 model provides insight into the mechanism by which gain-of-function mutations cause structural alterations that result in increased channel permeability, which trigger cell degeneration. Our analysis provides an introductory framework to further investigate the multimeric organization of the DEG/ENaC ion channel complex. PMID:20877470

  10. Molecular modeling of mechanosensory ion channel structural and functional features.

    PubMed

    Gessmann, Renate; Kourtis, Nikos; Petratos, Kyriacos; Tavernarakis, Nektarios

    2010-09-16

    The DEG/ENaC (Degenerin/Epithelial Sodium Channel) protein family comprises related ion channel subunits from all metazoans, including humans. Members of this protein family play roles in several important biological processes such as transduction of mechanical stimuli, sodium re-absorption and blood pressure regulation. Several blocks of amino acid sequence are conserved in DEG/ENaC proteins, but structure/function relations in this channel class are poorly understood. Given the considerable experimental limitations associated with the crystallization of integral membrane proteins, knowledge-based modeling is often the only route towards obtaining reliable structural information. To gain insight into the structural characteristics of DEG/ENaC ion channels, we derived three-dimensional models of MEC-4 and UNC-8, based on the available crystal structures of ASIC1 (Acid Sensing Ion Channel 1). MEC-4 and UNC-8 are two DEG/ENaC family members involved in mechanosensation and proprioception respectively, in the nematode Caenorhabditis elegans. We used these models to examine the structural effects of specific mutations that alter channel function in vivo. The trimeric MEC-4 model provides insight into the mechanism by which gain-of-function mutations cause structural alterations that result in increased channel permeability, which trigger cell degeneration. Our analysis provides an introductory framework to further investigate the multimeric organization of the DEG/ENaC ion channel complex.

  11. Investigation of Mixed Surfactant Films at Water Surface Using Molecular Dynamics Simulations.

    PubMed

    Habartová, Alena; Roeselová, Martina; Cwiklik, Lukasz

    2015-10-27

    Multicomponent Langmuir monolayers are important models of organic coatings of naturally occurring water-vapor interfaces such as the surfaces of oceans or aerosol particles. We investigated mixed monolayers comprised of palmitic acid, C15H31COOH (PA) and 1-bromoalkanes of different chain length (C5, C10, and C16) at the air-water interface employing classical molecular dynamics simulations. Different composition ratios and lateral compression of the monolayers were considered. The structural parameters, such as density profiles, and deuterium order parameter, evaluated as functions of composition and the lateral film packing, provide microscopic information about organization and dynamics of the mixed monolayers. Simulations demonstrate that stable and well mixed monolayers are formed by the mixtures of PA and BrC16H33 (BrCl6), whereas the two considered shorter bromoalkanes, BrC5H11 (BrC5) and BrC10H21 (BrC10), do not form stable films. This is in accord with earlier experimental studies. Under high lateral pressures, in PA/BrC10 mixed systems molecules of the bromoalkane readily flip in the monolayer and subsequently leave the film, while the molecules of the longer BrC16 are expelled from the PA film but no flipping occurs. These results suggest that the film collapse under pressure is preceded by squeezing-out of bromoalkanes from the PA monolayer. PMID:26439598

  12. 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.

  13. 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.

  14. Investigations of protostellar outflow launching and gas entrainment: Hydrodynamic simulations and molecular emission

    SciTech Connect

    Offner, Stella S. R.; Arce, Héctor G.

    2014-03-20

    We investigate protostellar outflow evolution, gas entrainment, and star formation efficiency using radiation-hydrodynamic simulations of isolated, turbulent low-mass cores. We adopt an X-wind launching model, in which the outflow rate is coupled to the instantaneous protostellar accretion rate and evolution. We vary the outflow collimation angle from θ = 0.01-0.1 and find that even well-collimated outflows effectively sweep up and entrain significant core mass. The Stage 0 lifetime ranges from 0.14-0.19 Myr, which is similar to the observed Class 0 lifetime. The star formation efficiency of the cores spans 0.41-0.51. In all cases, the outflows drive strong turbulence in the surrounding material. Although the initial core turbulence is purely solenoidal by construction, the simulations converge to approximate equipartition between solenoidal and compressive motions due to a combination of outflow driving and collapse. When compared to simulation of a cluster of protostars, which is not gravitationally centrally condensed, we find that the outflows drive motions that are mainly solenoidal. The final turbulent velocity dispersion is about twice the initial value of the cores, indicating that an individual outflow is easily able to replenish turbulent motions on sub-parsec scales. We post-process the simulations to produce synthetic molecular line emission maps of {sup 12}CO, {sup 13}CO, and C{sup 18}O and evaluate how well these tracers reproduce the underlying mass and velocity structure.

  15. Investigations of drug-DNA interactions using molecular docking, cyclic voltammetry and UV-Vis spectroscopy

    NASA Astrophysics Data System (ADS)

    Perveen, Fouzia; Qureshi, Rumana; Ansari, Farzana Latif; Kalsoom, Saima; Ahmed, Safeer

    2011-10-01

    Molecular docking and QSAR studies were carried out for the investigation of interactions between 11 antitumor drugs and double stranded DNA. Quantitative structure activity relationship was established using MOE software package showing good correlation of binding strength with various physicochemical parameters e.g., hydrophobic surface area ( Vsurf), EHOMO, EHUMO, partition coefficient (log P) and molar refractivity ( M R) of the drugs . The most important parameter obtained from the docking studies was the formation constant ( K f) which is an indicative of the binding strength of the drug with DNA. This parameter was also calculated using the experimental techniques namely cyclic voltammetry (CV) and UV-Vis spectrophotometry. Variation in electrochemical characteristics (shift in peak potential and peak current decrease) and spectral profile of these drugs on the addition of DNA were used to determine the values of formation constant. The docking studies were used to predict the mode of interaction of the drug with DNA. It was observed that as far as binding strength was concerned the computational results complemented the experimental results. The order of magnitude of experimental and theoretical K f was same. The high value of K f implied that the respective drugs bind to DNA most efficiently.

  16. 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.

  17. The E-state as the basis for molecular structure space definition and structure similarity

    PubMed

    Hall; Kier

    2000-05-01

    The electrotopological state (E-state) is presented as a representation of molecular structure useful for definition of a space for chemical structures. This E-state representation provides the basis for chemical database management. The E-state formalism is presented along with its extension to the atom-type E-state. An approach to database organization, using polychlorobiphenyls (PCBs) as examples, reveals the descriptive power of the E-state paradigm. A well-organized chemical database, as described here, may be searched to find structures similar to a target structure with the expectation that such structures may exhibit properties similar to the target. Searches using the atom-type E-state indices are demonstrated with two example drug molecules.

  18. 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

  19. 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.

  20. Investigating the Counteracting Effect of Trehalose on Urea-Induced Protein Denaturation Using Molecular Dynamics Simulation.

    PubMed

    Paul, Subrata; Paul, Sandip

    2015-08-27

    Molecular dynamics simulations are performed to investigate the counteracting effect of trehalose against urea-induced denaturation of S-peptide analogue. The calculations of Cα root-mean-square deviation, radius of gyration, and solvent-accessible surface area reveal that the peptide loses its native structure in aqueous 8 M urea solution at 310 K and that this unfolding process is prevented in the presence of trehalose. Interestingly, the native structure of the peptide in ternary mixed urea/trehalose solution is similar to that in the pure water system. The estimation of helical percentage of peptide residues as well as peptide-peptide intramolecular hydrogen bond number for different systems also support the above findings. Decomposition of protein-urea total interaction energy into electrostatic and van der Waals contributions shows that the presence of trehalose molecules makes the latter contribution unfavorable without affecting the former. These observations are further supported by preferential interaction calculations. Furthermore, the hydrogen bond analyses show that with the addition of urea molecules to the peptide-water system, the formation of peptide-urea hydrogen bonds takes place at the expense of peptide-water hydrogen bonds. In ternary mixed osmolytes system, because of formation of a considerable amount of peptide-trehalose hydrogen bonds, some urea molecules are excluded from the peptide surface. This essentially reduces the interaction between peptide and urea molecules, and because of this, we notice a reduction in the number of peptide-urea hydrogen bonds. Interestingly, the total number of peptide-solution species hydrogen bonds in the pure water system is very similar to that for the mixed osmolytes system. From these observations we infer that in the ternary solution, peptide-solution species hydrogen bonds are shared by water, urea, and trehalose molecules. The presence of trehalose in the mixed osmolyte system causes a significant

  1. 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.

  2. Bonding and structure in dense multi-component molecular mixtures

    DOE PAGES

    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 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. 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.

  4. Fast electronic structure methods for strongly correlated molecular systems

    NASA Astrophysics Data System (ADS)

    Head-Gordon, Martin; Beran, Gregory J. O.; Sodt, Alex; Jung, Yousung

    2005-01-01

    A short review is given of newly developed fast electronic structure methods that are designed to treat molecular systems with strong electron correlations, such as diradicaloid molecules, for which standard electronic structure methods such as density functional theory are inadequate. These new local correlation methods are based on coupled cluster theory within a perfect pairing active space, containing either a linear or quadratic number of pair correlation amplitudes, to yield the perfect pairing (PP) and imperfect pairing (IP) models. This reduces the scaling of the coupled cluster iterations to no worse than cubic, relative to the sixth power dependence of the usual (untruncated) coupled cluster doubles model. A second order perturbation correction, PP(2), to treat the neglected (weaker) correlations is formulated for the PP model. To ensure minimal prefactors, in addition to favorable size-scaling, highly efficient implementations of PP, IP and PP(2) have been completed, using auxiliary basis expansions. This yields speedups of almost an order of magnitude over the best alternatives using 4-center 2-electron integrals. A short discussion of the scope of accessible chemical applications is given.

  5. 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.

  6. Molecular structure and absolute configuration of the diterpene lactone, praelolide.

    PubMed

    Dai, J B; Wan, Z L; Rao, Z H; Liang, D C; Fang, Z; Luo, Y K; Long, K H

    1985-11-01

    Praelolide is a new compound which was isolated out from the gorgonian, Menella praelonga (Ridley), collected from the South Sea of China at Zhanjiang, Guangdong. The molecular formula is C28H35O12Cl. The research result by X-ray diffraction method on the crystal structure is presented. The compound is orthorhombic with space group P2(1)2(1)2, cell dimensions a = 16.936, b = 16.709, c = 10.333 A, and Z = 4. The structure has been solved by direct method and refined to R = 0.055 for 2257 unique observable reflexions by least-squares. The molecule is composed of the major conformational isomer in which the three main rings (a six-membered ring, an eight-membered ring, a six-membered ring) take separately the form of chair-chairboat-chair, a five-membered actone ring, a C1 substitution, 4 acetate groups, and a three-membered epoxide ring. The absolute configuration of the molecule has also been determined by statistics (R factor ratio R = 1.012) and Bijvoet pairs observation. For 30 pairs of the greatest anomalous contributions the residuals are R'(+) = 0.057 for the first enantiomorph and R'(-) = 0.005 for the second one, so the latter should unambiguously correspond to the absolute configuration of the molecule.

  7. 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.

  8. Molecular investigations of food-borne Cladosporium and Fusarium species from Nigeria

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A sampling of contaminated foodstuffs throughout southwest Nigeria yielded three fungal isolates belonging to the genus Fusarium and two fungal isolates belonging to the genus Cladosporium. In this study we subjected these isolates to various molecular investigations. We were able to confirm or refi...

  9. The molecular clock of neutral evolution can be accelerated or slowed by asymmetric spatial structure.

    PubMed

    Allen, Benjamin; Sample, Christine; Dementieva, Yulia; Medeiros, Ruben C; Paoletti, Christopher; Nowak, Martin A

    2015-02-01

    Over time, a population acquires neutral genetic substitutions as a consequence of random drift. A famous result in population genetics asserts that the rate, K, at which these substitutions accumulate in the population coincides with the mutation rate, u, at which they arise in individuals: K = u. This identity enables genetic sequence data to be used as a "molecular clock" to estimate the timing of evolutionary events. While the molecular clock is known to be perturbed by selection, it is thought that K = u holds very generally for neutral evolution. Here we show that asymmetric spatial population structure can alter the molecular clock rate for neutral mutations, leading to either Ku. Our results apply to a general class of haploid, asexually reproducing, spatially structured populations. Deviations from K = u occur because mutations arise unequally at different sites and have different probabilities of fixation depending on where they arise. If birth rates are uniform across sites, then K ≤ u. In general, K can take any value between 0 and Nu. Our model can be applied to a variety of population structures. In one example, we investigate the accumulation of genetic mutations in the small intestine. In another application, we analyze over 900 Twitter networks to study the effect of network topology on the fixation of neutral innovations in social evolution.

  10. 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…

  11. Application of terahertz spectroscopy and molecular modeling in isomers investigation: Glucose and fructose

    NASA Astrophysics Data System (ADS)

    Zheng, Zhuan-Ping; Fan, Wen-Hui; Liang, Yu-Qing; Yan, Hui

    2012-04-01

    Terahertz spectra of glucose and fructose have been measured by terahertz time-domain spectroscopy (THz-TDS) at room temperature. Because they have the same molecular formula, the differences of the THz spectra can be attributed to their molecular structures and the arrangement of molecules in unit cell. In this paper, gaseous-state theory has been employed to simulate the isolated molecule of these two isomers. The results indicate that experimental THz spectral features (0.5 - 4.0 THz) of glucose and fructose arise from the mixture of intramolecular and intermolecular modes, involving hydrogen bonds and covalent bonds, and with the intermolecular modes dominating.

  12. Molecular and Supramolecular Structural Studies on Human Tropoelastin Sequences

    PubMed Central

    Ostuni, Angela; Bochicchio, Brigida; Armentano, Maria F.; Bisaccia, Faustino; Tamburro, Antonio M.

    2007-01-01

    One of the unusual properties of elastin is its ability to coacervate, which has been proposed to play an important role in the alignment of monomeric elastin for cross-linking into the polymeric elastin matrix. The temperature at which this transition takes place depends on several factors including protein concentration, ionic strength, and pH. Previously, polypeptide sequences encoded by different exons of the human tropoelastin gene have been analyzed for their ability to coacervate and to self-assemble. Few of them were indeed able to coacervate and only one, that encoded by exon 30 (EX30), gave amyloid fibers. In this article, we report on two chemically synthesized peptides—a decapeptide and an octadecapeptide—whose sequences are contained in the longer EX30 peptide and on a polypeptide (EX1–7) of 125 amino-acid residues corresponding to the sequence coded by the exons 1–7 and on a polypeptide (EX2–7) of 99 amino-acid residues encoded by exons 2–7 of human tropoelastin obtained by recombinant DNA techniques. Molecular and supramolecular structural characterization of these peptides showed that a minimum sequence of ∼20 amino acids is needed to form amyloid fibers in the exon 30-derived peptides. The N-terminal region of mature tropoelastin (EX2–7) gives rise to a coacervate and forms elastinlike fibers, whereas the polypeptide sequence containing the signal peptide (EX1–7) forms mainly amyloid fibers. Circular dichroism spectra show that β-structure is ubiquitous in all the sequences studied, suggesting that the presence of a β-structure is a necessary, although not sufficient, requirement for the appearance of amyloid fibers. PMID:17693470

  13. Structure of liquid phosphorus: A liquid-liquid phase transition via constant-pressure first-principles molecular dynamics

    NASA Astrophysics Data System (ADS)

    Morishita, Tetsuya

    2001-12-01

    Constant-pressure first-principles molecular dynamics simulations have been carried out to study structural phase transitions of liquid black phosphorus. By compressing the tetrahedral molecular liquid (a low-pressure phase), a structural phase transition from the molecular to polymeric liquid (a high-pressure phase) was successfully realized just as observed in the recent experiment by Katayama et al. [Nature 170 (2000) 403]. Structural properties in the polymeric liquid were investigated and it is found that the covalent p-state bonds are dominant within the first nearest neighbors of each atom. However, further compression of the polymeric liquid shows that the covalent bonding is weakened as pressure is increased. As a result, liquid phosphorus becomes similar to the simple liquid in which atoms form a close-packed structure at very high pressure.

  14. 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

  15. Structure of DPPC-hyaluronan interfacial layers - effects of molecular weight and ion composition.

    PubMed

    Wieland, D C Florian; Degen, Patrick; Zander, Thomas; Gayer, Sören; Raj, Akanksha; An, Junxue; Dėdinaitė, Andra; Claesson, Per; Willumeit-Römer, Regine

    2016-01-21

    Hyaluronan and phospholipids play an important role in lubrication in articular joints and provide in combination with glycoproteins exceptionally low friction coefficients. We have investigated the structural organization of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) Langmuir layers at the solution-air interface at different length scales with respect to the adsorption of hyaluronan (HA). This allows us to assemble a comprehensive picture of the adsorption and the resulting structures, and how they are affected by the molecular weight of HA and the presence of calcium ions. Brewster angle microscopy and grazing incident diffraction were used to determine the lateral structure at the micro- and macro scale. The data reveals an influence of HA on both the macro and micro structure of the DPPC Langmuir layer, and that the strength of this effect increases with decreasing molecular weight of HA and in presence of calcium ions. Furthermore, from X-ray reflectivity measurements we conclude that HA adsorbs to the hydrophilic part of DPPC, but data also suggest that two types of interfacial structures are formed at the interface. We argue that hydrophobic forces and electrostatic interactions play important rules for the association between DPPC and HA. Surface pressure area isotherms were used to determine the influence of HA on the phase behavior of DPPC while electrophoretic mobility measurements were used to gain insight into the binding of calcium ions to DPPC vesicles and hyaluronan.

  16. Structure, dynamics, and electronic structure of liquid Ag-Se alloys investigated by ab initio simulation

    NASA Astrophysics Data System (ADS)

    Kirchhoff, F.; Holender, J. M.; Gillan, M. J.

    1996-07-01

    Ab initio molecular-dynamics simulations have been used to investigate the structure, dynamics, and electronic properties of the liquid alloy Ag1-xSex at 1350 K and at the three compositions x=0.33, 0.42, and 0.65. To provide a point of reference, calculations are also presented for the equilibrium structure and the electronic structure of the α-Ag2Se crystal. The calculations are based on density-functional theory in the local-density approximation and on the pseudopotential plane-wave method. For the solid, we find excellent agreement with experiment for the equilibrium lattice parameters and the atomic coordinates of the 12-atom orthorhombic unit cell, and we present an analysis of the electronic density of states and density distribution. The reliability of the liquid simulations is confirmed by detailed comparisons with very recent neutron-diffraction results for the partial structure factors and radial distribution functions (RDF) of the stoichiometric liquid Ag2Se. Comparison with the predictions of an empirical interaction model due to Rino et al. is also given for l-Ag2Se. The ab initio simulations show a dramatic change of the Se-Se RDF with increasing Se content. This change is due to the formation of Se clusters bound by covalent bonds, the Se-Se bond length being almost the same as in pure c-Se and l-Se. The clusters are predominantly chainlike, but for higher x there is a significant fraction of threefold coordinated Se atoms. It is shown that the equilibrium fractions of Se present as isolated atoms and in clusters can be understood on a simple charge-balance model based on an ionic interpretation. The Ag diffusion coefficient in the simulated stoichiometric liquid is consistent with experimental values measured in the high-temperature superionic solid. The Ag and Se diffusion coefficients both increase with Se content, in spite of the Se clustering. An analysis of the Se-Se bond dynamics reveals surprisingly short bond lifetimes of less than 1 ps

  17. 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.

  18. NMR studies of molecular structure in fruit cuticle polyesters.

    PubMed

    Fang, X; Qiu, F; Yan, B; Wang, H; Mort, A J; Stark, R E

    2001-07-01

    The cuticle of higher plants functions primarily as a protective barrier for the leaves and fruits, controlling microbial attack as well as the diffusion of water and chemicals from the outside environment. Its major chemical constituents are waxes (for waterproofing) and cutin (a structural support polymer). However, the insolubility of cutin has hampered investigations of its covalent structure and domain architecture, which are viewed as essential for the design of crop protection strategies and the development of improved synthetic waterproofing materials. Recently developed strategies designed to meet these investigative challenges include partial depolymerization using enzymatic or chemical reagents and spectroscopic examination of the intact polyesters in a solvent-swelled form. The soluble oligomers from degradative treatments of lime fruit cutin are composed primarily of the expected 10,16-dihydroxyhexadecanoic and 16-hydroxy-10-oxo-hexadecanoic acids; low-temperature HF treatments also reveal sugar units that are covalently attached to the hydroxyfatty acids. Parallel investigations of solvent-swollen cutin using 2D NMR spectroscopy assisted by magic-angle spinning yield well-resolved spectra that permit detailed comparisons to be made among chemical moieties present in the intact biopolymer, the soluble degradation products, and the unreacted solid residue. PMID:11423150

  19. 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

  20. Light-operated machines based on threaded molecular structures.

    PubMed

    Credi, Alberto; Silvi, Serena; Venturi, Margherita

    2014-01-01

    Rotaxanes and related species represent the most common implementation of the concept of artificial molecular machines, because the supramolecular nature of the interactions between the components and their interlocked architecture allow a precise control on the position and movement of the molecular units. The use of light to power artificial molecular machines is particularly valuable because it can play the dual role of "writing" and "reading" the system. Moreover, light-driven machines can operate without accumulation of waste products, and photons are the ideal inputs to enable autonomous operation mechanisms. In appropriately designed molecular machines, light can be used to control not only the stability of the system, which affects the relative position of the molecular components but also the kinetics of the mechanical processes, thereby enabling control on the direction of the movements. This step forward is necessary in order to make a leap from molecular machines to molecular motors.

  1. Molecular histology of arteries: mass spectrometry imaging as a novel ex vivo tool to investigate atherosclerosis.

    PubMed

    Martin-Lorenzo, Marta; Alvarez-Llamas, Gloria; McDonnell, Liam A; Vivanco, Fernando

    2016-01-01

    Atherosclerosis is usually the underlying cause of a fatal event such as myocardial infarction or ictus. The atherome plaque develops silently and asymptomatically within the arterial intima layer. In this context, the possibility to analyze the molecular content of arterial tissue while preserving each molecule's specific localization is of great interest as it may reveal further insights into the physiopathological changes taking place. Mass spectrometry imaging (MSI) enables the spatially resolved molecular analysis of proteins, peptides, metabolites, lipids and drugs directly in tissue, with a resolution sufficient to reveal molecular features specific to distinct arterial structures. MSI represents a novel ex vivo imaging tool still underexplored in cardiovascular diseases. This review focuses on the MSI technique applied to cardiovascular disease and covers the main contributions to date, ongoing efforts, the main challenges and current limitations of MSI.

  2. 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.

  3. 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.

  4. Hybrid inorganic–organic superlattice structures with atomic layer deposition/molecular layer deposition

    SciTech Connect

    Tynell, Tommi; Yamauchi, Hisao; Karppinen, Maarit

    2014-01-15

    A combination of the atomic layer deposition (ALD) and molecular layer deposition (MLD) techniques is successfully employed to fabricate thin films incorporating superlattice structures that consist of single layers of organic molecules between thicker layers of ZnO. Diethyl zinc and water are used as precursors for the deposition of ZnO by ALD, while three different organic precursors are investigated for the MLD part: hydroquinone, 4-aminophenol and 4,4′-oxydianiline. The successful superlattice formation with all the organic precursors is verified through x-ray reflectivity studies. The effects of the interspersed organic layers/superlattice structure on the electrical and thermoelectric properties of ZnO are investigated through resistivity and Seebeck coefficient measurements at room temperature. The results suggest an increase in carrier concentration for small concentrations of organic layers, while higher concentrations seem to lead to rather large reductions in carrier concentration.

  5. Correlation of molecular structure with fluorescence spectra in rare earth chelates. I.

    NASA Technical Reports Server (NTRS)

    Bjorklund, S.; Degnan, J.; Filipescu, N.; Mcavoy, N.

    1968-01-01

    Rare earth chelates fluorescence spectra correlation with molecular structure, analyzing emission spectrum internal Stark splitting of tetramethylammonium tetrakis /dibenzoylmethido/europate microcrystals

  6. 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.

  7. 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.

  8. 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. PMID:25817650

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. Unraveling the Molecular Mechanisms Underlying the Nasopharyngeal Bacterial Community Structure.

    PubMed

    de Steenhuijsen Piters, Wouter A A; Bogaert, Debby

    2016-01-01

    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

  15. 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. PMID:26963729

  16. 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.

  17. 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. PMID:26927616

  18. 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.

  19. Mineral-Biochar Composites: Molecular Structure and Porosity.

    PubMed

    Rawal, Aditya; Joseph, Stephen D; Hook, James M; Chia, Chee H; Munroe, Paul R; Donne, Scott; Lin, Yun; Phelan, David; Mitchell, David R G; Pace, Ben; Horvat, Joseph; Webber, J Beau W

    2016-07-19

    Dramatic changes in molecular structure, degradation pathway, and porosity of biochar are observed at pyrolysis temperatures ranging from 250 to 550 °C when bamboo biomass is pretreated by iron-sulfate-clay slurries (iron-clay biochar), as compared to untreated bamboo biochar. Electron microscopy analysis of the biochar reveals the infusion of mineral species into the pores of the biochar and the formation of mineral nanostructures. Quantitative (13)C nuclear magnetic resonance (NMR) spectroscopy shows that the presence of the iron clay prevents degradation of the cellulosic fraction at pyrolysis temperatures of 250 °C, whereas at higher temperatures (350-550 °C), the clay promotes biomass degradation, resulting in an increase in both the concentrations of condensed aromatic, acidic, and phenolic carbon species. The porosity of the biochar, as measured by NMR cryoporosimetry, is altered by the iron-clay pretreatment. In the presence of the clay, at lower pyrolysis temperatures, the biochar develops a higher pore volume, while at higher temperature, the presence of clay causes a reduction in the biochar pore volume. The most dramatic reduction in pore volume is observed in the kaolinite-infiltrated biochar at 550 °C, which is attributed to the blocking of the mesopores (2-50 nm pore) by the nonporous metakaolinite formed from kaolinite. PMID:27284608

  20. Molecular advances in understanding social insect population structure.

    PubMed

    Crozier, R H; Oldroyd, B P; Tay, W T; Kaufmann, B E; Johnson, R N; Carew, M E; Jennings, K M

    1997-08-01

    Social insects present many phenomena seen in all organisms but in more extreme forms and with larger sample sizes than those observable in most natural populations of vertebrates. Microsatellites are proving very much more informative than allozymes for the analysis of population biological problems, and prolifically polymorphic markers are fairly readily developed. In addition, the male-haploid genetic system of many social insects facilitates genetic analysis. The ability to amplify DNA from sperm stored in a female's sperm storage device enables the determination of mating types long after the death of the short-lived males, in addition to information on the degree of mixing of sperm from different males. Mitochondrial (mt) DNA sequences are also proving important, not only in phylogenetic studies but also in molecular population genetics, as a tracer of female movements. Mitochondrial markers have definitively shown the movement of females between colonies, challenging models giving exclusive primacy to kin selection as the explanation for multiqueen colonies, in Australian meat ants, Iridomyrmex purpureus, and the aridzone queenless ant Rhytidoponera sp. 12. Microsatellite and mtDNA variation are being studied in Camponotus consobrinus sugar ants, showing an unexpected diversity of complexity in colony structure, and microsatellites have shown that transfer of ants between nests of the weaver ant Polyrhachis doddi must be slight, despite an apparent lack of hostility.

  1. Molecular structure from a single NMR sequence (fast-PANACEA)

    NASA Astrophysics Data System (ADS)

    Kupče, Ēriks; Freeman, Ray

    2010-09-01

    The PANACEA experiment combines three standard NMR pulse sequences (INADEQUATE, HSQC and HMBC) into a single entity, and is designed for spectrometers with two or more receivers operating in parallel. For small molecules it offers a direct route to molecular structure. Often the INADEQUATE feature is the rate-determining step, being limited by the low natural abundance of directly coupled 13C sbnd 13C pairs. This new version, fast-PANACEA, speeds up this measurement by two alternative schemes. In the first, the individual 13C sites are excited by selective radiofrequency pulses acting on double-quantum coherence, and encoded according to the rows of a Hadamard matrix. The columns of this matrix are used to decode the experimental data into separate F 2 spectra. This reduction in the number of required scans secures a faster result than the conventional stepwise exploration of the evolution dimension where the Nyquist condition and the resolution requirements must both be satisfied. The second scheme makes use of multiple aliasing in the evolution dimension. Significant speed improvements are achieved by either technique, illustrated by measurements made on samples of menthol and cholesterol. A new stabilization scheme (i-lock) is introduced. This is a software program that corrects the final NMR frequencies based on the observed frequency of a strong X-spin signal. It replaces the conventional deuterium lock, permitting measurements on neat liquids such as peanut oil and silicone oil, and offering advantages where deuterated solvents are undesirable.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. Investigation of the Binding Profiles of AZD2184 and Thioflavin T with Amyloid-β(1-42) Fibril by Molecular Docking and Molecular Dynamics Methods.

    PubMed

    Kuang, Guanglin; Murugan, N Arul; Tu, Yaoquan; Nordberg, Agneta; Ågren, Hans

    2015-09-01

    Detecting deposits of amyloid β fibrils in the brain is of paramount importance for an early diagnosis of Alzheimer's disease. A number of PET tracers have been developed for amyloid imaging, but many suffer from poor specificity and large signal to background ratio. Design of tracers with specificity and improved binding affinity requires knowledge about various potential binding sites in the amyloid β fibril available for the tracers and the nature of the local microenvironment of these sites. In this study we investigate the local structure of fibrils using two important probes, namely, thioflavin T (a fluorescent probe) and AZD2184 (a PET tracer). The target structures for amyloid-β(1-42) fibril are based on reported NMR solution models. By explicitly considering the effect of fibril flexibility on the available binding sites for all these models, the binding affinity of these probes has been investigated. The binding profiles of AZD2184 and thioflavin T were studied by molecular docking and molecular dynamics simulation methods. The two compounds were found to bind at the same sites of the fibril: three of which are within the fibril, and one is on the two sides of the Met35 residue on the surface. The binding affinity of AZD2184 and thioflavin T is found to be higher at the core sites than on the surface due to more contact residues. The binding affinity of AZD2184 is much higher than that of thioflavin T at every site due to electrostatic interaction and spatial restriction, which is in good agreement with experimental observation. However, the structural change of thioflavin T is much more significant than that of AZD2184, which is the chemical basis for its usage as a fluorescent probe. The ramifications of these results for the design and optimization of PET radioligands and fluorescent probes are briefly discussed.

  9. 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

  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. 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.

  12. In vivo investigation of cilia structure and function using Xenopus

    PubMed Central

    Brooks, Eric R.; Wallingford, John B.

    2015-01-01

    Cilia are key organelles in development and homeostasis. The ever-expanding complement of cilia associated proteins necessitates rapid and tractable models for in vivo functional investigation. Xenopus laevis provides an attractive model for such studies, having multiple ciliated populations, including primary and multiciliated tissues. The rapid external development of Xenopus and the large cells make it an especially excellent platform for imaging studies. Here we present embryological and cell-biological methods for the investigation of cilia structure and function in Xenopus laevis, with a focus on quantitative live and fixed imaging. PMID:25837389

  13. A DFT analyses for molecular structure, electronic state and spectroscopic property of a dithiolene tungsten carbonyl complex.

    PubMed

    Arifin, Khuzaimah; Daud, Wan Ramli Wan; Kassim, Mohammad B

    2014-04-24

    Bis(dithiolene) tungsten carbonyl complex, W(S2C2Ph2)2(CO)2 was successfully synthesized and the structure, frontier molecular orbital and optical properties of the complex were investigated theoretically using density functional theory calculations. The investigation started with a molecular structure construction, followed by an optimization of the structural geometry using generalized-gradient approximation (GGA) in a double numeric plus polarization (DNP) basis set at three different functional calculation approaches. Vibrational frequency analysis was used to confirm the optimized geometry of two possible conformations of [W(S2C2Ph2)2(CO)2], which showed distorted octahedral geometry. Electronic structure and optical characterization were done on the ground states. Metal to ligand and ligand to metal charge transfer were dominant in this system.

  14. 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.

  15. 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

  16. Animal Hairs as Water-stimulated Shape Memory Materials: Mechanism and Structural Networks in Molecular Assemblies.

    PubMed

    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.

  17. Animal Hairs as Water-stimulated Shape Memory Materials: Mechanism and Structural Networks in Molecular Assemblies.

    PubMed

    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

  18. Structural specifics of light-induced metastable states in copper(II)-nitroxide molecular magnets.

    PubMed

    Barskaya, I Yu; Veber, S L; Fokin, S V; Tretyakov, E V; Bagryanskaya, E G; Ovcharenko, V I; Fedin, M V

    2015-12-28

    Although light-induced magnetostructural switching in copper(II)-nitroxide molecular magnets Cu(hfac)2L(R) has been known for several years, structural characterization of metastable photoinduced states has not yet been accomplished due to significant technical demands. In this work we apply, for the first time, variable-temperature FTIR spectroscopy with photoexcitation to investigate the structural specifics of light-induced states in the Cu(hfac)2L(R) family represented by (i) Cu(hfac)2L(Me) comprising two-spin copper(II)-nitroxide clusters, and (ii) Cu(hfac)2L(Pr) comprising three-spin nitroxide-copper(II)-nitroxide clusters. The light-induced state of Cu(hfac)2L(Me) manifests the same set of vibrational bands as the corresponding thermally-induced state, implying their similar structures. For the second compound Cu(hfac)2L(Pr), the coordination environment of copper(II) is similar in light- and thermally-induced states, but distinct differences are found for packing of the peripheral n-propyl substituent of nitroxide. Thus, generally the structures of the corresponding thermally- and light-induced states in molecular magnets Cu(hfac)2L(R) might differ, and FTIR spectroscopy provides a useful approach for revealing and elucidating such differences.

  19. 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

  20. Compact structure and proteins of pasta retard in vitro digestive evolution of branched starch molecular structure.

    PubMed

    Zou, Wei; Sissons, Mike; Warren, Frederick J; Gidley, Michael J; Gilbert, Robert G

    2016-11-01

    The roles that the compact structure and proteins in pasta play in retarding evolution of starch molecular structure during in vitro digestion are explored, using four types of cooked samples: whole pasta, pasta powder, semolina (with proteins) and extracted starch without proteins. These were subjected to in vitro digestion with porcine α-amylase, collecting samples at different times and characterizing the weight distribution of branched starch molecules using size-exclusion chromatography. Measurement of α-amylase activity showed that a protein (or proteins) from semolina or pasta powder interacted with α-amylase, causing reduced enzymatic activity and retarding digestion of branched starch molecules with hydrodynamic radius (Rh)<100nm; this protein(s) was susceptible to proteolysis. Thus the compact structure of pasta protects the starch and proteins in the interior of the whole pasta, reducing the enzymatic degradation of starch molecules, especially for molecules with Rh>100nm. PMID:27516291

  1. Structural investigations on iron containing natural Zincblende using EBSD

    NASA Astrophysics Data System (ADS)

    Zscheckel, Tilman; Kreher-Hartmann, Birgit; Rüssel, Christian

    2016-05-01

    A sample of natural zinc sulfide containing iron (from Portugal, Albergaria, Velha) was systematically investigated with respect to its microstructure using XRD (X-ray diffraction) and EBSD (electron back scatter diffraction). The habitus of the black sample suggests a hexagonal crystal structure, i.e. the occurrence of the Wurtzite phase. Nevertheless, using XRD and EBSD allowed only detecting and localizing the cubic Zincblende structure within the sample with the fibrous habitus while the expected hexagonal Wurtzite structure and possibly a hexagonal FeS structure were missed. The macroscopic fibrous structures consist of non-uniform and elongated grain structures which possess a preferred orientation with the <224>-direction parallel to the fiber direction. Inside the grains, twinning occurs (Σ3-Twinning) as well as grain fragmentation. Iron is not distributed homogeneously; instead areas with unique iron concentrations occurred. They were arranged like twins with iron concentrations from 4.1 up to 5.1 at% as detected and localized using energy dispersive x-ray spectroscopy (EDS). Fe2+ is incorporated in lattice sites of Zn2+. Although the phase diagram FeS-Zn-S is not yet completely determined in all composition ranges of interest, coexisting phases (zincblende and FeS) should be expected at room temperatures. The results may contribute to further insights into the growth mechanisms of natural zinc sulfide, respectively to the discussion about. Furthermore, it was shown, that the crystal habitus not always allows concluding on the crystals symmetry with certainty.

  2. 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.

  3. The dependence of star formation on initial conditions and molecular cloud structure

    NASA Astrophysics Data System (ADS)

    Bate, Matthew R.

    2009-07-01

    We investigate the dependence of stellar properties on the initial kinematic structure of the gas in star-forming molecular clouds. We compare the results from two large-scale hydrodynamical simulations of star cluster formation that resolve the fragmentation process down to the opacity limit, the first of which was reported by Bate, Bonnell & Bromm. The initial conditions of the two calculations are identical, but in the new simulation the power spectrum of the velocity field imposed on the cloud initially and allowed to decay is biased in favour of large-scale motions. Whereas the calculation of Bate et al. began with a power spectrum P(k) ~ k-4 to match the Larson scaling relations for the turbulent motions observed in molecular clouds, the new calculation begins with a power spectrum P(k) ~ k-6. Despite this change to the initial motions in the cloud and the resulting density structure of the molecular cloud, the stellar properties resulting from the two calculations are indistinguishable. This demonstrates that the results of such hydrodynamical calculations of star cluster formation are relatively insensitive to the initial conditions. It is also consistent with the fact that the statistical properties of stars and brown dwarfs (e.g. the stellar initial mass function) are observed to be relatively invariant within our Galaxy and do not appear to depend on environment.

  4. Investigation of possible structures of hybrid neutron stars

    SciTech Connect

    Paoli, M. G.; Menezes, D. P.

    2010-11-12

    This work investigates the structure of hybrid stars built in two different ways. The first one considers the existence of a mixed phase at intermediate stellar densities. The second implies the inexistence of this mixed phase. In this case, the hadron phase and the quark phase are in direct contact. We use the non-linear Walecka model (NLWM) to describe the hadron phase and the Nambu-Jona-Lasinio model (NJL) for the quark phase.

  5. Development and evaluation of double locus sequence typing for molecular epidemiological investigations of Clostridium difficile.

    PubMed

    Stojanov, M; Magalhaes, B; Terletsky, V; Basset, P; Prod'hom, G; Greub, G; Senn, L; Blanc, D S

    2016-02-01

    Despite the development of novel typing methods based on whole genome sequencing, most laboratories still rely on classical molecular methods for outbreak investigation or surveillance. Reference methods for Clostridium difficile include ribotyping and pulsed-field gel electrophoresis, which are band-comparing methods often difficult to establish and which require reference strain collections. Here, we present the double locus sequence typing (DLST) scheme as a tool to analyse C. difficile isolates. Using a collection of clinical C. difficile isolates recovered during a 1-year period, we evaluated the performance of DLST and compared the results to multilocus sequence typing (MLST), a sequence-based method that has been used to study the structure of bacterial populations and highlight major clones. DLST had a higher discriminatory power compared to MLST (Simpson's index of diversity of 0.979 versus 0.965) and successfully identified all isolates of the study (100 % typeability). Previous studies showed that the discriminatory power of ribotyping was comparable to that of MLST; thus, DLST might be more discriminatory than ribotyping. DLST is easy to establish and provides several advantages, including absence of DNA extraction [polymerase chain reaction (PCR) is performed on colonies], no specific instrumentation, low cost and unambiguous definition of types. Moreover, the implementation of a DLST typing scheme on an Internet database, such as that previously done for Staphylococcus aureus and Pseudomonas aeruginosa ( http://www.dlst.org ), will allow users to easily obtain the DLST type by submitting directly sequencing files and will avoid problems associated with multiple databases. PMID:26581425

  6. 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.

  7. Phase sensitive molecular dynamics of self-assembly glycolipid thin films: A dielectric spectroscopy investigation

    NASA Astrophysics Data System (ADS)

    Velayutham, T. S.; Ng, B. K.; Gan, W. C.; Majid, W. H. Abd.; Hashim, R.; Zahid, N. I.; Chaiprapa, Jitrin

    2014-08-01

    Glycolipid, found commonly in membranes, is also a liquid crystal material which can self-assemble without the presence of a solvent. Here, the dielectric and conductivity properties of three synthetic glycolipid thin films in different thermotropic liquid crystal phases were investigated over a frequency and temperature range of (10-2-106 Hz) and (303-463 K), respectively. The observed relaxation processes distinguish between the different phases (smectic A, columnar/hexagonal, and bicontinuous cubic Q) and the glycolipid molecular structures. Large dielectric responses were observed in the columnar and bicontinuous cubic phases of the longer branched alkyl chain glycolipids. Glycolipids with the shortest branched alkyl chain experience the most restricted self-assembly dynamic process over the broad temperature range studied compared to the longer ones. A high frequency dielectric absorption (Process I) was observed in all samples. This is related to the dynamics of the hydrogen bond network from the sugar group. An additional low-frequency mechanism (Process II) with a large dielectric strength was observed due to the internal dynamics of the self-assembly organization. Phase sensitive domain heterogeneity in the bicontinuous cubic phase was related to the diffusion of charge carriers. The microscopic features of charge hopping were modelled using the random walk scheme, and two charge carrier hopping lengths were estimated for two glycolipid systems. For Process I, the hopping length is comparable to the hydrogen bond and is related to the dynamics of the hydrogen bond network. Additionally, that for Process II is comparable to the bilayer spacing, hence confirming that this low-frequency mechanism is associated with the internal dynamics within the phase.

  8. [Investigation of molecular machine that integrates microtubules depolymerization and chromosomes movement in mitosis].

    PubMed

    Volkov, V A; Ataullakhanov, F I

    2013-02-01

    The main goal of a dividing cell is to distribute its genetic material equally between two daughter cells. Each of the two sister chromatids comprising each chromosome should go into one of the daughter cells. This is possible thanks to polar protein polymers called microtubules, which form a structure called "spindle" during mitosis. Microtubules are one of the basic elements of the cytoskeleton, but at the same time they are highly dynamic. Minus ends of the microtubules attach to the two poles of the spindle, while their plus ends are constantly growing or shrinking, and are also able to attach to the chromosomes and to move them. Chromosomes attach to the microtubule ends with a special protein super-complex called kinetochore. Each sister chromatid in a pair attaches to the microtubules emanating from a corresponding spindle pole. Kinetochores are attached to the dynamic plus ends of the microtubules, but tubulin subunits are still able to attach and detach to these attached ends. One of the most important questions in mitosis is understanding of the mechanism that allows such attachment to be stable (since unstable attachments lead to chromosome loss and aneuploidy) yet dynamic (arrest of the microtubule dynamics stops mitosis). More than 100 proteins comprising the kinetochore are known today, but there is no clear mechanical view on the molecular machine that forms kinetochore-microtubule attachment. The difficulties in understanding this mechanism are due to the variety of theoretical views on the principle of such machine, as well as limited number of biochemically isolated candidates to test these hypotheses experimentally. Therefore, investigation of the properties of putative couplers of microtubule depolymerization and chromosome movement is an important task.

  9. Optical investigation of functional structures in isolated perfused pig heart

    NASA Astrophysics Data System (ADS)

    Rauh, Robert; Boehnert, Markus; Mahlke, Christine; Kessler, Manfred D.

    2000-11-01

    Light scattering in tissue of mammals and humans is affected by subcellular structures. Since these structures correlate well with the status of cells and tissue, light scattering seems to be ideal for monitoring of functional tissue state. By use of EMPHO SSK Oxyscan we investigated functional parameters in a novel kind of isolated perfused pig heart model. In this perfusion model we use organs obtained by the local slaughterhouse that are reanimated at our institute by application of a heart-lung machine. By creating 3D-images of tissue scattering we found an interesting relation between anatomical structures of myocardium and the 3D-images. Additionally, we detected coherence between backscattered light intensity and functional tissue status. Furthermore, we got a sight into the redox state of cytochrome aa3, b and c by creating difference spectra. We believe that this new kind of tissue imaging method will give us the opportunity to get new insights into myocardial function.

  10. 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.

  11. Structural and Electrical Investigation of C60-Graphene Vertical Heterostructures.

    PubMed

    Kim, Kwanpyo; Lee, Tae Hoon; Santos, Elton J G; Jo, Pil Sung; Salleo, Alberto; Nishi, Yoshio; Bao, Zhenan

    2015-06-23

    Graphene, with its unique electronic and structural qualities, has become an important playground for studying adsorption and assembly of various materials including organic molecules. Moreover, organic/graphene vertical structures assembled by van der Waals interaction have potential for multifunctional device applications. Here, we investigate structural and electrical properties of vertical heterostructures composed of C60 thin film on graphene. The assembled film structure of C60 on graphene is investigated using transmission electron microscopy, which reveals a uniform morphology of C60 film on graphene with a grain size as large as 500 nm. The strong epitaxial relations between C60 crystal and graphene lattice directions are found, and van der Waals ab initio calculations support the observed phenomena. Moreover, using C60-graphene heterostructures, we fabricate vertical graphene transistors incorporating n-type organic semiconducting materials with an on/off ratio above 3 × 10(3). Our work demonstrates that graphene can serve as an excellent substrate for assembly of molecules, and attained organic/graphene heterostructures have great potential for electronics applications.

  12. Structure-function investigations of bacterial photosynthetic reaction centers.

    PubMed

    Leonova, M M; Fufina, T Yu; Vasilieva, L G; Shuvalov, V A

    2011-12-01

    During photosynthesis light energy is converted into energy of chemical bonds through a series of electron and proton transfer reactions. Over the first ultrafast steps of photosynthesis that take place in the reaction center (RC) the quantum efficiency of the light energy transduction is nearly 100%. Compared to the plant and cyanobacterial photosystems, bacterial RCs are well studied and have relatively simple structure. Therefore they represent a useful model system both for manipulating of the electron transfer parameters to study detailed mechanisms of its separate steps as well as to investigate the common principles of the photosynthetic RC structure, function, and evolution. This review is focused on the research papers devoted to chemical and genetic modifications of the RCs of purple bacteria in order to study principles and mechanisms of their functioning. Investigations of the last two decades show that the maximal rates of the electron transfer reactions in the RC depend on a number of parameters. Chemical structure of the cofactors, distances between them, their relative orientation, and interactions to each other are of great importance for this process. By means of genetic and spectral methods, it was demonstrated that RC protein is also an essential factor affecting the efficiency of the photochemical charge separation. Finally, some of conservative water molecules found in RC not only contribute to stability of the protein structure, but are directly involved in the functioning of the complex.

  13. Structural investigation of the titanium/diamond film interface

    NASA Astrophysics Data System (ADS)

    Terranova, M. L.; Rossi, M.; Vitali, G.

    1996-09-01

    Reflection high-energy electron diffraction (RHEED) technique, with the possibility to shift, rotate, and tilt the sample with respect to the electron beam, has been used to investigate the structure of the transition layers formed at the interface between titanium substrate and diamond films. The diamond films were deposited on partially masked titanium sheets by means of the chemical vapor deposition technique, using CH4/H2 mixtures activated by hot filament. Deposition experiments have been performed at 650 and 730 °C. The RHEED analysis has been carried out in selected area conditions on the boundary between coated and uncoated regions; it enabled us to detect and characterise the inhomogeneous and complex structural configuration of the diamond/titanium interface. For the samples deposited at 650 °C we identified, starting from the titanium surface: a mixed phase constituted by titanium hydride and carbide precipitates, graphitic clusters embedded into a titanium hydride/carbide phase, TiC layers, and finally diamond films. At 730 °C both growth location and formation sequence of the various structures were found to be similar to those detected at 650 °C, resulting, however, in the complete absence of the Ti hydride phase. A first indication about the time scale of the process has been determined from structural investigations of deposits grown by runs lasting from 3 up to 20 min. A schematic model is presented which describes the growth sequence of the various species inside the intermediate reaction layers.

  14. Structurally-modified subphthalocyanines: molecular design towards realization of expected properties from the electronic structure and structural features of subphthalocyanine.

    PubMed

    Shimizu, Soji; Kobayashi, Nagao

    2014-07-01

    This feature article summarizes recent contributions of the authors in the synthesis of structurally-modified subphthalocyanines. The structural modification covers (1) modification of the conjugated system of subphthalocyanines to create novel conjugated systems comprising three pyrroles or pyrrole-like subunits, (2) core-modification by expansion of the inner pyrrolic five-membered ring to larger six- and seven-membered ring units, and (3) exterior-modification by annulation of functional units to subphthalocyanines. These modifications in the structure of subphthalocyanines have been performed with the aim of demonstrating unique properties originating from the bowl-shaped C3v-symmetric structure as well as the electronic structure delineated by the 14π-electron conjugated system on the curved molecular surface. The possible structural modifications surveyed in this feature article and their concomitant properties will provide important future guidelines to the design of subphthalocyanine-based functional molecules, considering the fact that subphthalocyanines have recently been attracting considerable attention as potential candidates in the field of optoelectronics and molecular electronics. PMID:24710280

  15. A molecular picture of the problems in ensuring structural purity of tazofelone

    NASA Astrophysics Data System (ADS)

    Price, Louise S.; McMahon, Jennifer A.; Lingireddy, Sreenivas R.; Lau, Suk-Fai; Diseroad, Benjamin A.; Price, Sarah L.; Reutzel-Edens, Susan M.

    2014-12-01

    Almost twenty years after the crystal polymorphism of tazofelone was first studied at Lilly, the compound was revisited by calculating the crystal energy landscape and complementing the calculations with experimental work for calibration purposes. The crystal structure prediction study confirmed the stability of racemic form II (RCII) and showed that the racemic compound had greater potential for polymorphism than the single enantiomer. The seeding experiment that has previously been shown to produce a racemic solid solution (SS) correlates with the isostructurality between some low energy racemic structures and the enantiopure form. Other low energy structures have the same layer structure as both racemic polymorphs and the newly-discovered, but closely related, polymorph RCIII, which accounts for the difficulty in obtaining phase pure samples of the metastable RCI and RCIII and the problems of structural purity evidenced by streaked diffraction spots for RCI-III in the single crystal diffraction. This molecular picture of the problems in ensuring structural purity in the layer structure polymorphs of tazofelone not only explains the crystal dependent thermochemistry measurements of tazofelone, but also shows the value of combining a range of experimental and computational techniques to investigate the organic solid state.

  16. Investigating the Structure of Multicomponent Gel-Phase Lipid Bilayers.

    PubMed

    Hartkamp, Remco; Moore, Timothy C; Iacovella, Christopher R; Thompson, Michael A; Bulsara, Pallav A; Moore, David J; McCabe, Clare

    2016-08-23

    Single- and multicomponent lipid bilayers of 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC), 1,2-distearoyl-sn-glycero-3-phosphatidylcholine (DSPC), isostearyl isostearate, and heptadecanoyl heptadecanoate in the gel phase are studied via molecular dynamics simulations. It is shown that the structural properties of multicomponent bilayers can deviate strongly from the structures of their single-component counterparts. Specifically, the lipid mixtures are shown to adopt a compact packing by offsetting the positioning depths at which different lipid species are located in the bilayer. This packing mechanism affects the area per lipid, the bilayer height, and the chain tilt angles and has important consequences for other bilayer properties, such as interfacial hydrogen bonding and bilayer permeability. In particular, the simulations suggest that bilayers containing isostearyl isostearate or heptadecanoyl heptadecanoate are less permeable than pure 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine or DSPC bilayers. Furthermore, hydrogen-bond analysis shows that the residence times of lipid-water hydrogen bonds depend strongly on the bilayer composition, with longer residence times for bilayers that have a higher DSPC content. The findings illustrate and explain the fundamental differences between the properties of single- and multicomponent bilayers. PMID:27558724

  17. 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.

  18. Ligands Binding and Molecular Simulation: the Potential Investigation of a Biosensor Based on an Insect Odorant Binding Protein

    PubMed Central

    Yi, Xin; Zhang, Yanbo; Wang, Peidan; Qi, Jiangwei; Hu, Meiying; Zhong, Guohua

    2015-01-01

    Based on mimicking biological olfaction, biosensors have been applied for the detection of various ligands in complex environment, which could represent one of the most promising research fields. In this study, the basic characters of one insect odorant binding protein (OBP) as a biosensor were explored. To explore the molecular recognition process, the tertiary structure of the protein was modeled and the protein-ligand interactions with 1,536,550 chemicals were investigated by the molecular docking. The availability of large amount of recombinant SlitOBP1 overcame the difficulty to obtain biological sensing material. After obtained the purified recombinant protein, the result of fluorescence binding assays proved the candidate protein has good affinities with the majority of the tested chemicals. With the aid of simulation docking, the key conserved amino acids within the binding site were identified and then mutated to alanine. After mutation, the protein-ligand binding characteristics were recorded, and the competitive binding assays were carried out to provide experimental verification. The detailed information on its structure and affinities investigated in this study could allow the design of specific mutants with desired characteristics, which provides a solid base for tailoring OBP for biosensor and provides a role model for screening the other elements in olfactory system for different applications. PMID:25552932

  19. Ligands binding and molecular simulation: the potential investigation of a biosensor based on an insect odorant binding protein.

    PubMed

    Yi, Xin; Zhang, Yanbo; Wang, Peidan; Qi, Jiangwei; Hu, Meiying; Zhong, Guohua

    2015-01-01

    Based on mimicking biological olfaction, biosensors have been applied for the detection of various ligands in complex environment, which could represent one of the most promising research fields. In this study, the basic characters of one insect odorant binding protein (OBP) as a biosensor were explored. To explore the molecular recognition process, the tertiary structure of the protein was modeled and the protein-ligand interactions with 1,536,550 chemicals were investigated by the molecular docking. The availability of large amount of recombinant SlitOBP1 overcame the difficulty to obtain biological sensing material. After obtained the purified recombinant protein, the result of fluorescence binding assays proved the candidate protein has good affinities with the majority of the tested chemicals. With the aid of simulation docking, the key conserved amino acids within the binding site were identified and then mutated to alanine. After mutation, the protein-ligand binding characteristics were recorded, and the competitive binding assays were carried out to provide experimental verification. The detailed information on its structure and affinities investigated in this study could allow the design of specific mutants with desired characteristics, which provides a solid base for tailoring OBP for biosensor and provides a role model for screening the other elements in olfactory system for different applications. PMID:25552932

  20. The investigation of molecular mixing and segregation in opv materials and devices

    NASA Astrophysics Data System (ADS)

    Rochester, Christopher W.

    With the growing energy demand and the threat of global warming caused by our excessive use of fossil fuels, it is imperative that we search for and develop alternative ways to generate energy. Using photovoltaic technologies to produce energy is a good way to supplement our current energy supplies. The problem with conventional PV technology is that it is too expensive to compete with cheap fossil fuels. Polymer solar cells have the potential to be a much cheaper alternative to conventional PV technology, as they can easily be manufactured using simple roll-to-roll printing methods, are light-weight, and are flexible. Polymer solar cells consist of layered organic materials that are deposited using solution deposition methods. The organic layers often consist of mixtures of organic molecules, that may be composed of polymer and small molecules. The behavior of these organic materials are not always predictable as they have been found to often diffuse, causing material segregation and mixing within layers and at interfaces. These processes are measured and observed using a combination of experimental techniques. P3HT/PCBM bilayer samples were fabricated by spin coating PCBM dissolved in CH2Cl 2 onto P3HT films. We show using steady-state spectroscopy, neutron reflectometry, and current-voltage measurements that substantial mixing occurs between the P3HT and PCBM during the PCBM deposition. We conclude that the PCBM mixes with amorphous P3HT and does not disrupt the existing crystalline domains. A PCBM loading of 25-30 wt% into the P3HT layer was determined, which explains why reported photovoltaic performances of these solution processed bilayer structures are comparable to that of bulk-heterojunctions. The use of F4-TCNQ as a molecular dopant for the polymeric hole transport layer, S-P3MEET, for use in organic photovoltaic devices was investigated. It is shown that F4-TCNQ effectively oxidized the S-P3MEET polymer, and that even for low doping concentrations

  1. 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.

  2. Investigation of the disc-and-washer structure

    SciTech Connect

    Mavrogenes, G.; Gallagher, W.J.

    1981-01-01

    About 1971 a proposed accelerating structure was described by the radiotechnical Institute, Moscow, which was intended for proton acceleration in a planned meson factory linac. The structure has several quite useful features and has been subsequently investigated by AECL (Chalk River, Canada), LASL (UC Los Alamos, NM) and Argonne National Laboratory. A sketch of the structure is shown which reveals the origin of the name disc-and-washer structure (DAW). The origin and development of the concept upon which the structure is founded is provided from considerations of a chain of individual TM-01 cavities designed to produce kinetic energy gain to a bunched beam transiting their common axis. It is assumed the cavities are individually excited without inter-coupling; so that for maximum energy gain there is a specific phasing requirement based on the transit time from the previous cavity. Such a system would be very complex to operate and would only be considered in the special case of a few cavities as, for example, the LASL PHERMEX.

  3. 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.

  4. 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

  5. The influence of molecular structure of fatty acid monoalkyl esters on diesel combustion

    SciTech Connect

    Schoenborn, Alessandro; Ladommatos, Nicos; Williams, John; Allan, Robert; Rogerson, John

    2009-07-15

    The subject of this paper is a series of experiments conducted on a single-cylinder research engine investigating the influence of molecular structure on the combustion behaviour of fatty acid alcohol ester (biodiesel) molecules under diesel engine conditions. The fuels employed in these experiments comprised various samples of pure individual fatty acid alcohol ester molecules of different structure, as well as several mixtures of such molecules. The latter consisted in biodiesel fuels produced by the transesterification of naturally occurring plant oils or animal fat with a monohydric alcohol. It was observed that the molecular structure of the fuel significantly influenced the formation of NO{sub x} and particulate matter and their respective concentration in the exhaust gas. The influence on the formation of NO{sub x} in particular, appeared to be exerted first through the effect which the molecular structure had on the auto-ignition delay occurring after the fuel was injected into the combustion chamber, and second through the flame temperature at which the various molecules burned. The emission of particulates on the other hand showed correlation with the number of double bonds in the fuel molecules for the case of larger accumulation mode particles, and with the boiling point of the fuel samples for the case of the smaller, nucleation mode particles. The effect of ignition delay on the exhaust emissions of these pollutants was isolated by adding the ignition promoting molecule 2-ethylhexyl nitrate to some of the fuel samples in closely specified concentrations, so as to equalise the ignition delay for the relevant fuel samples. The removal of the ignition delay as a main influence on the combustion process enabled the observation of the lesser effects of adiabatic flame temperature. (author)

  6. Molecular Structure and Reactivity in the Pyrolysis of Aldehydes

    NASA Astrophysics Data System (ADS)

    Sias, Eric; Cole, Sarah; Sowards, John; Warner, Brian; Wright, Emily; McCunn, Laura R.

    2016-06-01

    The effect of alkyl chain structure on pyrolysis mechanisms has been investigated in a series of aldehydes. Isovaleraldehyde, CH_3CH(CH_3)CH_2CHO, and pivaldehyde, (CH_3)_3CCHO, were subject to thermal decomposition in a resistively heated SiC tubular reactor at 800-1200 °C. Matrix-isolation FTIR spectroscopy was used to identify pyrolysis products. Carbon monoxide and isobutene were major products from each of the aldehydes, which is consistent with what is known from previous studies of unbranched alkyl-chain aldehydes. Other products observed include vinyl alcohol, propene, acetylene, and ethylene, revealing complexities to be considered in the pyrolysis of large, branched-chain aldehydes.

  7. Prediction of water-phosphatidylcholine membrane partition coefficient of some drugs from their molecular structures.

    PubMed

    Fatemi, Mohammad Hossein; Moghaddam, Masoomeh Raei

    2012-10-01

    In this work, the phosphatidylcholine membrane-water partition coefficients (MA) of some drugs were estimated from their theoretical derived molecular descriptors by applying quantitative structure-activity relationship (QSAR) methodology. The data set consisted of 46 drugs where their log MA were determined experimentally. Descriptors used in this work were calculated by DRAGON (version 1) package, on the basis of optimized molecular structures, and the most relevant descriptors were selected by stepwise multilinear regressions (MLRs). These descriptors were used to developing linear and nonlinear models by using MLR and artificial neural networks (ANNs), respectively. During this investigation, the best QSAR model was identified when using the ANN model that produced a reasonable level of correlation coefficients (R(train) = 0.995, R(test) = 0.948) and low standard error (SE(train) = 0.099, SE(test) = 0.326). The built model was fully assessed by various validation methods, including internal and external validation test, Y-randomization test, and cross-validation (Q(2) = 0.805). The results of this investigation revealed the applicability of QSAR approaches in the estimation of phosphatidylcholine membrane-water partition coefficients.

  8. Investigation of Laser Induced Structure formation and resultant fluorescence

    NASA Astrophysics Data System (ADS)

    Kandpal, Sanjeev Kumar; Otterson, Samantha L.; Bousfield, Douglas W.; Neivandt, David J.; Mason, Michael D.

    2015-04-01

    The formation mechanism of 3D micron-sized fluorescent structures generated in silver nanoparticle containing sodium citrate dihydrate films, during exposure to focused laser radiation, was investigated. Microscopic and thermochemical data indicate that heat accumulates at the nanoparticle surface. The heat causes local melting and an increase in temperature beyond the decomposition point of the immediate surrounding layer. In turn this leads to the rapid release of volatile gases (H2O and CO2). These expanding gases push the melted liquid pool outward, from the center of the focal volume, leaving behind a trough-like structure with elevated edges. It was observed that the edges of the structures were fluorescent. The fluorescence mechanism was investigated using atomic force, scanning electron and Confocal Fluorescence Microscopy. The observed fluorescence was attributed to the decomposition of sodium citrate dihydrate to sodium citrate. The presence of water acts to quench fluorescence in the bulk film, but near regions that experienced heat, the water is driven off.

  9. Adsorption mechanisms of microcystin variant conformations at water-mineral interfaces: A molecular modeling investigation.

    PubMed

    Pochodylo, Amy L; Aoki, Thalia G; Aristilde, Ludmilla

    2016-10-15

    Microcystins (MCs) are potent toxins released during cyanobacterial blooms. Clay minerals are implicated in trapping MCs within soil particles in surface waters and sediments. In the absence of molecular characterization, the relevance of previously proposed adsorption mechanisms is lacking. Towards obtaining this characterization, we conducted Monte Carlo simulations combined with molecular dynamics relaxation of two MC variants, MC-leucine-arginine (MC-LR) and MC-leucine-alanine (MC-LA), adsorbed on hydrated montmorillonite with different electrolytes. The resulting adsorbate structures revealed how MC conformations and aqueous conditions dictate binding interactions at the mineral surface. Electrostatic coupling between the arginine residue and a carboxylate in MC-LR excluded the participation of arginine in mediating adsorption on montmorillonite in a NaCl solution. However, in a CaCl2 solution, the complexation of Ca by two carboxylate moieties in MC-LR changed the MC conformation, which allowed arginine to mediate electrostatic interaction with the mineral. By contrast, due to the lack of arginine in MC-LA, complexation of Ca by only one carboxylate in MC-LA was required to favor Ca-bridging interaction with the mineral. Multiple water-bridged H-bonding interactions were also important in anchoring MCs at the mineral surface. Our modeling results offer molecular insights into the structural and chemical factors that can control the fate of MCs at water-mineral interfaces.

  10. Adsorption mechanisms of microcystin variant conformations at water-mineral interfaces: A molecular modeling investigation.

    PubMed

    Pochodylo, Amy L; Aoki, Thalia G; Aristilde, Ludmilla

    2016-10-15

    Microcystins (MCs) are potent toxins released during cyanobacterial blooms. Clay minerals are implicated in trapping MCs within soil particles in surface waters and sediments. In the absence of molecular characterization, the relevance of previously proposed adsorption mechanisms is lacking. Towards obtaining this characterization, we conducted Monte Carlo simulations combined with molecular dynamics relaxation of two MC variants, MC-leucine-arginine (MC-LR) and MC-leucine-alanine (MC-LA), adsorbed on hydrated montmorillonite with different electrolytes. The resulting adsorbate structures revealed how MC conformations and aqueous conditions dictate binding interactions at the mineral surface. Electrostatic coupling between the arginine residue and a carboxylate in MC-LR excluded the participation of arginine in mediating adsorption on montmorillonite in a NaCl solution. However, in a CaCl2 solution, the complexation of Ca by two carboxylate moieties in MC-LR changed the MC conformation, which allowed arginine to mediate electrostatic interaction with the mineral. By contrast, due to the lack of arginine in MC-LA, complexation of Ca by only one carboxylate in MC-LA was required to favor Ca-bridging interaction with the mineral. Multiple water-bridged H-bonding interactions were also important in anchoring MCs at the mineral surface. Our modeling results offer molecular insights into the structural and chemical factors that can control the fate of MCs at water-mineral interfaces. PMID:27433998

  11. Admittance Investigation of MIS Structures with HgTe-Based Single Quantum Wells

    NASA Astrophysics Data System (ADS)

    Izhnin, Ihor I.; Nesmelov, Sergey N.; Dzyadukh, Stanislav M.; Voitsekhovskii, Alexander V.; Gorn, Dmitry I.; Dvoretsky, Sergey A.; Mikhailov, Nikolaj N.

    2016-02-01

    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.

  12. Molecular structures of two tetrodotoxin analogs containing a monooxa-hydrocarbon cage: A computational study

    NASA Astrophysics Data System (ADS)

    Pichierri, Fabio

    2016-02-01

    Using quantum chemical calculations we investigate the molecular structures of two tetrodotoxin (TTX) analogs recently isolated from the Japanese toxic newt Cynops ensicauda popei. These novel analogs are characterized by a monooxa-hydrocarbon cage with a direct C5-C10 bond that replaces one of the ether bridges in the canonical dioxa-adamantane cage of TTX. The computed change in the 13C NMR chemical shifts is in good agreement with the change in the corresponding experimental values that results from the above chemical modification. This confirms the chemical structure assigned to the TTX analogs. A topological analysis of the theoretical electronic charge density indicates that the removal of the oxygen bridge in TTX increases the magnitude of the charge density at the cage critical point. A database search indicates that the monooxa-hydrocarbon cage is also present in other natural products such as cinnzeylanine and platensimycin whose molecular structures have been characterized by single-crystal X-ray diffraction analyses.

  13. Effects of ultrasound on molecular properties, structure, chain conformation and degradation kinetics of carboxylic curdlan.

    PubMed

    Yan, Jing-Kun; Pei, Juan-Juan; Ma, Hai-Le; Wang, Zhen-Bin

    2015-05-01

    In this study, high-intensity ultrasound (20 kHz), a simple, effective and without any additive method, was used to the degradation of carboxylic curdlan (Cc) produced by 4-acetamido-TEMPO-mediated oxidation. The effects of ultrasound on molecular properties, structure and chain conformations of Cc were investigated by viscometry, size-exclusion chromatography with multiangle laser-light scattering (SEC-MALLS) analysis, as well as FTIR and NMR spectroscopies. The results indicated that the intrinsic viscosity [η] and the weight-average molecular weight (Mw) of Cc decreased obviously after ultrasound, and a uniform and narrow distribution of degradation product was obtained. The z-average radius of gyrations (Rg) firstly increased and then decreased as the sonication time prolonged. Ultrasound destroyed the hydrogen bonds resulting in the transition from compact random coil conformation to more flexible and even shorter extended chains. Ultrasonic treatment could not alter the primary chemical structure of Cc molecules according to the structural analysis by FTIR and NMR spectroscopies. Degradation kinetics based on Schmid model was applied to estimate the degradation rate constant k. It was found that the k value of Cc decreased with increasing the polymer concentration from 0.05 to 0.2% (w/v). PMID:25659672

  14. The molecular interfacial structure and plasticizer migration behavior of "green" plasticized poly(vinyl chloride).

    PubMed

    Zhang, Xiaoxian; Li, Yaoxin; Hankett, Jeanne M; Chen, Zhan

    2015-02-14

    Tributyl acetyl citrate (TBAC), a widely-used "green" plasticizer, has been extensively applied in products for daily use. In this paper, a variety of analytical tools including sum frequency generation vibrational spectroscopy (SFG), coherent anti-Stokes Raman spectroscopy (CARS), contact angle goniometry (CA), and Fourier transform infrared spectroscopy (FTIR) were applied together to investigate the molecular structures of TBAC plasticized poly(vinyl chloride) (PVC) and the migration behavior of TBAC from PVC-TBAC mixtures into water. We comprehensively examine the effects of oxygen and argon plasma treatments on the surface structures of PVC-TBAC thin films containing various bulk percentages of plasticizers and the leaching behavior of TBAC into water. It was found that TBAC is a relatively stable PVC plasticizer compared to traditional non-covalent plasticizers but is also surface active. Oxygen plasma treatment increased the hydrophilicity of TBAC-PVC surfaces, but did not enhance TBAC leaching. However, argon plasma treatment greatly enhanced the leaching of TBAC molecules from PVC plastics to water. Based on our observations, we believe that oxygen plasma treatment could be applied to TBAC plasticized PVC products to enhance surface hydrophilicity for improving the biocompatibility and antibacterial properties of PVC products. The structural information obtained in this study will ultimately facilitate a molecular level understanding of plasticized polymers, aiding in the design of PVC materials with improved properties. PMID:25579625

  15. Investigation of multiaxial molecular dynamics by 2H MAS NMR spectroscopy.

    PubMed

    Kristensen, J H; Hoatson, G L; Vold, R L

    1998-11-01

    The technique of 2H MAS NMR spectroscopy is presented for the investigation of multiaxial molecular dynamics. To evaluate the effects of discrete random reorientation a Lie algebraic formalism based on the stochastic Liouville-von Neumann equation is developed. The solution to the stochastic Liouville-von Neumann equation is obtained both in the presence and absence of rf irradiation. This allows effects of molecular dynamics to be evaluated during rf pulses and extends the applicability of the formalism to arbitrary multiple pulse experiments. Theoretical methods are presented for the description of multiaxial dynamics with particular emphasis on the application of vector parameters to represent molecular rotations. Numerical time and powder integration algorithms are presented that are both efficient and easy to implement computationally. The applicability of 2H MAS NMR spectroscopy for investigating molecular dynamics is evaluated from theoretical spectra. To demonstrate the potential of the technique the dynamics of thiourea-2H4 is investigated experimentally. From a series of variable temperature MAS and quadrupole echo spectra it has been found that the dynamics can be described by composite rotation about the CS and CN bonds. Both experiments are sensitive to the fast CS rotation which is shown to be described by the Arrhenius parameters E(CS) = 46.4 +/- 2.3 kJ mol(-1) and ln(A(CS))= 32.6 +/- 0.9. The MAS experiment represents a significant improvement by simultaneously allowing the dynamics of the slow CN rotation to be fully characterized in terms of E(CN) = 56.3 +/- 3.4 kJ mol(-1) and ln(A(CN)) = 25.3 +/- 1.1. PMID:9875600

  16. Computational investigation of locked nucleic acid (LNA) nucleotides in the active sites of DNA polymerases by molecular docking simulations.

    PubMed

    Poongavanam, Vasanthanathan; Madala, Praveen K; Højland, Torben; Veedu, Rakesh N

    2014-01-01

    Aptamers constitute a potential class of therapeutic molecules typically selected from a large pool of oligonucleotides against a specific target. With a scope of developing unique shorter aptamers with very high biostability and affinity, locked nucleic acid (LNA) nucleotides have been investigated as a substrate for various polymerases. Various reports showed that some thermophilic B-family DNA polymerases, particularly KOD and Phusion DNA polymerases, accepted LNA-nucleoside 5'-triphosphates as substrates. In this study, we investigated the docking of LNA nucleotides in the active sites of RB69 and KOD DNA polymerases by molecular docking simulations. The study revealed that the incoming LNA-TTP is bound in the active site of the RB69 and KOD DNA polymerases in a manner similar to that seen in the case of dTTP, and with LNA structure, there is no other option than the locked C3'-endo conformation which in fact helps better orienting within the active site. PMID:25036012

  17. Molecular docking, molecular dynamics simulation, and structure-based 3D-QSAR studies on estrogenic activity of hydroxylated polychlorinated biphenyls.

    PubMed

    Li, Xiaolin; Ye, Li; Wang, Xiaoxiang; Wang, Xinzhou; Liu, Hongling; Qian, Xiangping; Zhu, Yongliang; Yu, Hongxia

    2012-12-15

    Hydroxylated polychlorinated biphenyls (HO-PCBs), major metabolites of PCBs, have been reported to present agonist or antagonist interactions with estrogen receptor α (ERα) and induce ER-mediated responses. In this work, a multistep framework combining molecular docking, molecular dynamics (MD) simulations, and structure-based three-dimensional quantitative structure-activity relationship (3D-QSAR) studies were performed to explore the influence of structural features on the estrogenic activities of HO-PCBs, and to investigate the molecular mechanism of ERα-ligand interactions. The CoMSIA (comparative molecular similarity indices analysis) model was developed from the conformations obtained from molecular docking. The model exhibited statistically significant results as the cross-validated correlation coefficient q² was 0.648, the non-cross-validated correlation coefficient r² was 0.968, and the external predictive correlation coefficient r(pred)² was 0.625. The key amino acid residues were identified by molecular docking, and the detailed binding modes of the compounds with different activities were determined by MD simulations. The binding free energies correlated well with the experimental activity. An energetic analysis, MM-GBSA energy decomposition, revealed that the van der Waals interaction was the major driving force for the binding of compounds to ERα. The hydrogen bond interactions between the ligands and residue His524 help to stabilize the conformation of ligands at the binding pocket. These results are expected to be beneficial to predict estrogenic activities of other HO-PCB congeners and helpful for understanding the binding mechanism of HO-PCBs and ERα. PMID:23137989

  18. Ligand binding to anti-cancer target CD44 investigated by molecular simulations.

    PubMed

    Nguyen, Tin Trung; Tran, Duy Phuoc; Pham Dinh Quoc Huy; Hoang, Zung; Carloni, Paolo; Van Pham, Phuc; Nguyen, Chuong; Li, Mai Suan

    2016-07-01

    CD44 is a cell-surface glycoprotein and receptor for hyaluronan, one of the major components of the tumor extracellular matrix. There is evidence that the interaction between CD44 and hyaluronan promotes breast cancer metastasis. Recently, the molecule F-19848A was shown to inhibit hyaluronan binding to receptor CD44 in a cell-based assay. In this study, we investigated the mechanism and energetics of F-19848A binding to CD44 using molecular simulation. Using the molecular mechanics/Poisson Boltzmann surface area (MM-PBSA) method, we obtained the binding free energy and inhibition constant of the complex. The van der Waals (vdW) interaction and the extended portion of F-19848A play key roles in the binding affinity. We screened natural products from a traditional Chinese medicine database to search for CD44 inhibitors. From combining pharmaceutical requirements with docking and molecular dynamics simulations, we found ten compounds that are potentially better or equal to the F-19848A ligand at binding to CD44 receptor. Therefore, we have identified new candidates of CD44 inhibitors, based on molecular simulation, which may be effective small molecules for the therapy of breast cancer. PMID:27342250

  19. Molecular dynamics simulation of atomic-scale frictional behavior of corrugated nano-structured surfaces.

    PubMed

    Kim, Hyun-Joon; Kim, Dae-Eun

    2012-07-01

    Surface morphology is one of the critical parameters that affect the frictional behavior of two contacting bodies in relative motion. It is important because the real contact area as well as the contact stiffness is dictated by the micro- and nano-scale geometry of the surface. In this regard, the frictional behavior may be controlled by varying the surface morphology through nano-structuring. In this study, molecular dynamics simulations were conducted to investigate the effects of contact area and structural stiffness of corrugated nano-structures on the fundamental frictional behavior at the atomic-scale. The nano-structured surface was modeled as an array of corrugated carbon atoms with a given periodicity. It was found that the friction coefficient of the nano-structured surface was lower than that of a smooth surface under specific contact conditions. The effect of applied load on the friction coefficient was dependent on the size of the corrugation. Furthermore, stiffness of the nano-structure was identified to be an important variable in dictating the frictional behavior.

  20. Structural and spectral investigation of terbium molybdate nanophosphor

    NASA Astrophysics Data System (ADS)

    Mani, Kamal P.; Vimal, G.; Biju, P. R.; Joseph, Cyriac; Unnikrishnan, N. V.; Ittyachen, M. A.

    2015-09-01

    Terbium molybdate nanophosphors were synthesized through a facile sol-gel route. The structure of the phosphors was characterized by X-ray diffraction, Raman spectra and Fourier transform infrared spectroscopy analysis. The X-ray diffraction studies revealed that the structure of the nanophosphor gradually changes from monoclinic to orthorhombic phase as heated from 700 to 900 °C. High resolution transmission electron microscopy, SAED and EDS were also employed to characterize the size, crystallinity and composition of the samples. Detailed spectroscopic investigations were carried out by Judd-Ofelt analysis based on UV-Visible-NIR absorption and emission spectra. The luminescence spectra suggest that phosphors with orthorhombic structure have better luminescence properties than the monoclinic structure. The phosphors showed intense green emission under near-UV excitation due to the energy transfer from the host lattice to Tb3+ ions. The CIE coordinates suggest enhanced color purity for green emission and short fluorescence decay values proposes the suitability for LED applications. These phosphors can be applied as promising candidates for blue and near-UV excited WLEDs.

  1. Structural Investigations of Complex Oxides using Synchrotron Radiation

    SciTech Connect

    Hans-Conrad zur Loye

    2007-03-24

    The work is a collaborative effort between Prof. Hanno zur Loye at the University of South Carolina and Dr. Tom Vogt at Brookhaven National Laboratory. The collaborative research focuses on the synthesis and the structural characterization of perovskites and perovskite related oxides and will target new oxide systems where we have demonstrated expertise in synthesis, yet lack the experimental capabilities to answer important structural issues. Synthetically, we will focus on two subgroups of perovskite structures, the double and triple perovskites, and the 2H-perovskite related oxides belonging to the A3n+3mA’nB3m+nO9m+6n family. In the first part of the proposal, our goal of synthesizing and structurally characterizing new ruthenium, iridium, rhodium and ruthenium containing double and triple perovskites, with the emphasis on exercising control over the oxidation state(s) of the metals, is described. These oxides will be of interest for their electronic and magnetic properties that will be investigated as well.

  2. Investigations of coherent structures in free turbulent shear flows

    NASA Technical Reports Server (NTRS)

    Hussain, A. K. M. F.

    1979-01-01

    The dynamics of large-scale coherent structures in general, and studies based on flow-visualization and phase-locked hot-wire measurements of the structures in the near fields of circular jets are considered. A study involving the nature of coherent structures under conditions of stable vortex pairing induced by controlled axisymmetric acoustic excitation reveals that azimuthal coherence initially enhanced by the excitation is lost before the end of the potential core through evolution of azimuthal lobe structures and turbulent breakdown. The evolution of a spark-induced spot in an axisymmetric turbulent mixing layer is also investigated, and the coherent Reynolds stress associated with the spot is found to be much higher than the background turbulence Reynolds stress. In addition, the state of organization in a high Reynolds number unperturbed axisymmetric mixing layer is examined, and it is shown that the shear layer is infrequently organized and the motions are intensely three-dimensional, while tearing and fractional pairing occur as frequently as complete pairing.

  3. Thermodynamic and Structural Investigation of Synthetic Actinide-Peptide Scaffolds.

    PubMed

    Safi, Samir; Jeanson, Aurélie; Roques, Jérome; Solari, Pier Lorenzo; Charnay-Pouget, Florence; Den Auwer, Christophe; Creff, Gaëlle; Aitken, David J; Simoni, Eric

    2016-01-19

    The complexation of uranium and europium, in oxidation states +VI and +III, respectively, was investigated with pertinent bio-inorganic systems. Three aspartate-rich pentapeptides with different structural properties were selected for study to rationalize the structure-affinity relationships. Thermodynamic results, crosschecked by both isothermal titration calorimetry and time-resolved laser fluorescence spectroscopy, showed different affinity depending on the peptide for both Eu(III) and U(VI). The thermodynamic aspects were correlated to structural predictions, which were acquired by density functional theory quantum chemical calculations and from IR and extended X-ray absorption fine structure experiments. The combination of these microscopic properties revealed that carbonyl-metal interactions affected the entropy in the case of europium, while the larger uranyl cation was mostly affected by preorganization and steric effects, so that the affinity was enhanced through enthalpy. The approach described here revealed various microscopic aspects governing peptide actinide affinity. Highlighting these mechanisms should certainly contribute to the rational synthesis of higher affinity biomimetic aspartic ligands.

  4. Investigation of upper crustal structure beneath eastern Java

    NASA Astrophysics Data System (ADS)

    Martha, Agustya Adi; Widiyantoro, Sri; Cummnins, Phil; Saygin, Erdinc; Masturyono

    2016-05-01

    The complexity of geology structure in eastern Java causes this region has many potential resources as much as the disasters. Therefore, the East Java province represents an interesting area to be explored, especially regarding its upper crustal structure. To investigate this structure, we employ the Ambient Noise Tomography (ANT) method. We have used seismic waveform data from 25 Meteorological, Climatological and Geophysical Agency (BMKG) stationary seismographic stations and 26 portable seismographs installed for 2 to 8 weeks. Inter-station cross-correlation produces more than 800 Rayleigh wave components, which depict the structure beneath eastern Java. Based on the checkerboard resolution test, we found that the optimal grid size is 0.25ox0.25o. Our inversion results for the periods of 1 to 10 s indicate a good agreement with geological and Bouguer anomaly maps. Rembang high depression, most of the southern mountains zone, the northern part of Rembang zone and the central part of the Madura Island, the area of high gravity anomaly and areas dominated with igneous rocks are associated with high velocity zones. On the other hand, Kendeng zone and most of the basin in the Rembang zone are associated with low velocity zones.

  5. Improvement in Aqueous Solubility of Retinoic Acid Receptor (RAR) Agonists by Bending the Molecular Structure.

    PubMed

    Hiramatsu, Michiaki; Ichikawa, Yuki; Tomoshige, Shusuke; Makishima, Makoto; Muranaka, Atsuya; Uchiyama, Masanobu; Yamaguchi, Takao; Hashimoto, Yuichi; Ishikawa, Minoru

    2016-08-01

    Aqueous solubility is a key requirement for many functional molecules, e. g., drug candidates. Decrease of the partition coefficient (log P) by chemical modification, i.e., introduction of hydrophilic group(s) into molecules, is a classical strategy for improving aqueous solubility. We have been investigating alternative strategies for improving the aqueous solubility of pharmaceutical compounds by disrupting intermolecular interactions. Here, we show that introducing a bend into the molecular structure of retinoic acid receptor (RAR) agonists by changing the substitution pattern from para to meta or ortho dramatically enhances aqueous solubility by up to 890-fold. We found that meta analogs exhibit similar hydrophobicity to the parent para compound, and have lower melting points, supporting the idea that the increase of aqueous solubility was due to decreased intermolecular interactions in the solid state as a result of the structural changes.

  6. Molecular structure and conformations of caramboxin, a natural neurotoxin from the star fruit: A computational study

    NASA Astrophysics Data System (ADS)

    Pichierri, Fabio

    2015-01-01

    Using density functional theory calculations we investigate the molecular structure and conformations of caramboxin, a neurotoxin recently isolated from the star fruit Averroha carambola. Among the seven conformers that exist within an energy window of ∼16.0 kcal/mol, two of them are the most favored ones with an energy difference of less than 2.0 kcal/mol. The computed chemical shifts of these two low-energy conformers are in good agreement with the experimental values determined in deuterated dimethylsulfoxide thus confirming the 2D chemical structure assigned to the neurotoxin. A topological analysis of the theoretical electronic charge density of four caramboxin conformers reveals the existence of intramolecular CH⋯O/N interactions which, in addition to the classical OH⋯O/N H-bonding interactions, contribute to decrease the conformational freedom of the neurotoxin.

  7. Improvement in Aqueous Solubility of Retinoic Acid Receptor (RAR) Agonists by Bending the Molecular Structure.

    PubMed

    Hiramatsu, Michiaki; Ichikawa, Yuki; Tomoshige, Shusuke; Makishima, Makoto; Muranaka, Atsuya; Uchiyama, Masanobu; Yamaguchi, Takao; Hashimoto, Yuichi; Ishikawa, Minoru

    2016-08-01

    Aqueous solubility is a key requirement for many functional molecules, e. g., drug candidates. Decrease of the partition coefficient (log P) by chemical modification, i.e., introduction of hydrophilic group(s) into molecules, is a classical strategy for improving aqueous solubility. We have been investigating alternative strategies for improving the aqueous solubility of pharmaceutical compounds by disrupting intermolecular interactions. Here, we show that introducing a bend into the molecular structure of retinoic acid receptor (RAR) agonists by changing the substitution pattern from para to meta or ortho dramatically enhances aqueous solubility by up to 890-fold. We found that meta analogs exhibit similar hydrophobicity to the parent para compound, and have lower melting points, supporting the idea that the increase of aqueous solubility was due to decreased intermolecular interactions in the solid state as a result of the structural changes. PMID:27378357

  8. Theoretical studies of molecular structures and properties of platinum (II) antitumor drugs

    NASA Astrophysics Data System (ADS)

    Gao, Hongwei

    2011-08-01

    The molecular structure and vibration spectra of carboplatin were investigated by the different density functional models (mPW1PW, BPV86, HCTH, PBEPBE, LSDA and PBE1PBE) using several basis sets including LANL2DZ, SDD, LANL2MB, CEP-4G, CEP-31G and CEP-121G. The results indicate that LSDA/SDD and LSDA/LANL2DZ levels are clearly superior to all the remaining density functional methods in predicting the structures of carboplatin. Mean absolute deviation between the calculated harmonic and observed fundamental vibration frequencies for each method indicates that PBE1PBE/CEP-121G and PBE1PBE/SDD methods are sufficient to predict vibration spectrum of carboplatin comparing with other DFT methods.

  9. Sulfation effect on levan polysaccharide chains structure with molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Coskunkan, Binnaz; Turgut, Deniz; Rende, Deniz; Malta, Seyda; Baysal, Nihat; Ozisik, Rahmi; Toksoy-Oner, Ebru

    Diversity in conformations and structural heterogeneity make polysaccharides the most challenging biopolymer type for experimental and theoretical characterization studies. Levan is a biopolymer chain that consists of fructose rings with β(2-6) linkages. It is a glycan that has great potential as a functional biopolymer in foods, feeds, cosmetics, pharmaceutical and chemical industries. Sulfated polysaccharides are group of macromolecules with sulfated groups in their hydroxyl parts with a range of important biological properties. Sulfate groups and their positions have a major effect on anticoagulant activity. It is reported that sulfate modified levan has anticoagulant activity such as heparin. In the current study, the effect of sulfation on the structure and dynamics of unmodified and sulfate modified levan are investigated via fully atomistic Molecular Dynamics simulations in aqueous media and varying salt concentrations at 310 K. This material is based upon work supported by the National Science Foundation under Grant No. CMMI-1538730.

  10. Molecular Dynamics Studies of Structure and Functions of Water-Membrane Interfaces

    NASA Technical Reports Server (NTRS)

    Pohorille, Andrew; Wilson, Michael A.; DeVincenzi, Donald L. (Technical Monitor)

    2001-01-01

    A large number of essential cellular processes occur at the interfaces between water and membranes. The selectivity and dynamics of these processes are largely determined by the structural and electrical properties of the water-membrane interface. We investigate these properties by the molecular dynamics method. Over the time scales of the simulations, the membrane undergoes fluctuations described by the capillary wave model. These fluctuations produce occasional thinning defects in the membrane which provide effective pathways for passive transport of ions and small molecules across the membrane. Ions moving through the membrane markedly disrupt its structure and allow for significant water penetration into the membrane interior. Selectivity of transport, with respect to ionic charge, is determined by the interfacial electrostatic potential. Many small molecules. of potential significance in catalysis, bioenergetics and pharmacology, are shown to bind to the interface. The energetics and dynamics of this process will be discussed.

  11. Synthesis, structural and spectroscopic investigations of nanostructured samarium oxalate crystals.

    PubMed

    Vimal, G; Mani, Kamal P; Biju, P R; Joseph, Cyriac; Unnikrishnan, N V; Ittyachen, M A

    2014-03-25

    Nanostructured samarium oxalate crystals were prepared via microwave assisted co-precipitation method. The crystal structure and morphology of the sample were analyzed using X-ray powder diffraction, Scanning electron microscopy and Transmission electron microscopy. The presence of functional groups is ascertained by Fourier transform infrared spectroscopy. Samarium oxalate nanocrystals of average size 20 nm were aggregated together to form nano-plate structure in sub-microrange. Detailed spectroscopic investigation of the prepared phosphor material was carried out by Judd-Ofelt analysis based on the UV-Visible-NIR absorption spectra and photoluminescence emission spectra. The analysis reveals that the transition from energy level (4)G5/2 to (6)H7/2 of Sm(3+) ion has maximum branching ratio and the corresponding orange emission can be used for display applications.

  12. Investigating cell membrane structure and dynamics with TCSPC-FLIM

    NASA Astrophysics Data System (ADS)

    Le Marois, Alix; Owen, Dylan M.; Suhling, Klaus

    2015-03-01

    We report the use of Time-Correlated Single Photon Counting (TCSPC) in a polarization-resolved Fluorescence Lifetime Imaging (FLIM) setup for the investigation of cell membrane structural and dynamic properties. This technique allows us to study the orientation and mobility of fluorescent membrane dyes, namely di-4-ANEPPDHQ and DiO, in model bilayers of different lipid compositions. Dipole alignment and extent of rotational motion can be linked to membrane order and fluidity. Comparison of the time-resolved anisotropy decays of the two fluorescent dyes suggests that rotational motion of membrane constituents is restricted in liquid-ordered phases, and appears to be limited to the region of aliphatic tails in liquid-disordered phases. In living cells, understanding the membrane structure provides crucial information on its functional properties, such as exo- and endocytosis, cell mobility and signal transduction.

  13. Structure-property-glass transition relationships in non-isocyanate polyurethanes investigated by dynamic nanoindentation

    NASA Astrophysics Data System (ADS)

    Weyand, Stephan; Blattmann, Hannes; Schimpf, Vitalij; Mülhaupt, Rolf; Schwaiger, Ruth

    2016-07-01

    Newly developed green-chemistry approaches towards the synthesis of non-isocyanate polyurethane (NIPU) systems represent a promising alternative to polyurethanes (PU) eliminating the need for harmful ingredients. A series of NIPU systems were studied using different nanoindentation techniques in order to understand the influence of molecular parameters on the mechanical behavior. Nanoindentation revealed a unique characteristic feature of those materials, i.e. stiffening with increasing deformation. It is argued that the origin of this observed stiffening is a consequence of the thermodynamic state of the polymer network, the molecular characteristics of the chemical building blocks and resulting anisotropic elastic response of the network structure. Flat-punch nanoindentation was applied in order to characterize the constitutive viscoelastic nature of the materials. The complex modulus shows distinct changes as a function of the NIPU network topology illustrating the influence of the chemical building blocks. The reproducibility of the data indicates that the materials are homogeneous over the volumes sampled by nanoindentation. Our study demonstrates that nanoindentation is very well-suited to investigate the molecular characteristics of NIPU materials that cannot be quantified in conventional experiments. Moreover, the technique provides insight into the functional significance of complex molecular architectures thereby supporting the development of NIPU materials with tailored properties.

  14. A chromogenic molecular capsule attributable to dipolar amide resonance structure.

    PubMed

    Park, Yeon Sil; Park, Juwan; Paek, Kyungsoo

    2015-04-01

    A new chromogenic, self-assembled molecular capsule G@22 is developed by introducing four (N,N-dimethyl-4-aminophenyl) azobenzyl moieties on the upper rim of a resorcin[4]arene-based amidoimino-cavitand. The tuning of conjugation between amido and (N,N-dimethyl-4-aminophenyl)azobenzyl groups by acid-base titration allows naked-eye detection of molecular capsule formation. PMID:25740710

  15. Investigations of pressure induced structural phase transformations in pentaerythritol

    NASA Astrophysics Data System (ADS)

    Garg, Nandini; Sharma, Surinder M.; Sikka, S. K.

    2005-10-01

    We have investigated the pressure induced structural changes in pentaerythritol {2,2-bis-(hydroxymethyl)-1,3-propanediol} with the help of X-ray diffraction studies. Our results show that this compound undergoes transformations to a lower symmetry phase between 5.2-5.9 GPa. It further undergoes phase transformations at ˜8.5 and ˜11 GPa; eventually evolving to a disordered phase beyond 14-15 GPa in agreement with our earlier Raman studies. On release of pressure from 18.5 GPa, the compound transforms back to the initial tetragonal phase.

  16. Conductometric investigations of multicharged ion track structure in various polymers

    NASA Astrophysics Data System (ADS)

    Apel, P. Yu.

    The radial structure of etchable tracks of multicharged ions in polyethylene terephtalate, polycarbonate, polyarylate, and polypropylene is investigated using conductometric method. The doses of gel formation under irradiation of these polymers by accelerated xenon ions with approximately 1 MeV/nucleon energy are estimated. It is found that the track of highly ionizing particles in a polymer consists of a core where intensive destruction occurs and a halo where, as a rule, the crosslinking of macromolecules predominates. Recombination of the interior radicals provides the crosslinking formation. The radius of the crosslinking region depends on the relation between the hydrogen atom diffusion speed and the rate of their chemical interaction with macromolecules.

  17. Track-structure investigations: A supplement to microdosimetry

    SciTech Connect

    Conte, V.; Colautti, P.; Grosswendt, B.; Moro, D.; De Nardo, L.

    2013-07-18

    We conceived and developed an experimental apparatus able to measure the track structure (the spatial distribution of the points of ionizing collisions) of light ions, allowing the investigation of the track-core and penumbra regions separately. The device is based on single-electron counting technique, and simulates a target volume V of about 20 nm in diameter that can be moved with respect to a narrow primary particle beam, allowing the measurement of the ionization-cluster-size distribution as a function of the impact parameter. The experimental set up is mounted at the Tandem-Alpi LNL particle accelerator complex. The goal of the experiment is to investigate the formation of ionization-cluster-size distributions caused in a nanometre-sized volume by different light ions of medical interest (protons, lithium ions and carbon ions), when penetrating through or passing by the target volume at a specified distance.

  18. Investigation of the impact of annealing on global molecular mobility in glasses: optimization for stabilization of amorphous pharmaceuticals.

    PubMed

    Luthra, Suman A; Hodge, Ian M; Pikal, Michael J

    2008-09-01

    The purpose of this research was to investigate the effect of annealing on the molecular mobility in lyophilized glasses using differential scanning calorimetry (DSC) and isothermal microcalorimetry (IMC) techniques. A second objective that emerged was a systematic study of the unusual pre-T(g) thermal events that were observed during DSC warming scans after annealing. Aspartame lyophilized with three different excipients; sucrose, trehalose and poly vinyl pyrrolidone (PVP) was studied. The aim of this work was to quantify the decrease in mobility in amorphous lyophilized aspartame formulations upon systematic postlyophilization annealing. DSC scans of aspartame:sucrose formulation (T(g) = 73 degrees C) showed the presence of a pre-T(g) endotherm which disappeared upon annealing. Aspartame:trehalose (T(g) = 112 degrees C) and aspartame:PVP (T(g) = 100 degrees C) showed a broad exotherm before T(g) and annealing caused appearance of endothermic peaks before T(g). This work also employed IMC to measure the global molecular mobility represented by structural relaxation time (tau(beta)) in both un-annealed and annealed formulations. The effect of annealing on the enthalpy relaxation of lyophilized glasses, as measured by DSC and IMC, was consistent with the behavior predicted using the Tool-Narayanaswamy-Moynihan (TNM) phenomenology (Luthra et al., 2007, in press). The results show that the systems annealed at T(g) -15 degrees C to T(g) -20 degrees C have the lowest molecular mobility.

  19. Structural heterogeneity and dynamics in liquid PbSiO3: insight from analysis and visualization of molecular dynamics data

    NASA Astrophysics Data System (ADS)

    Yen, N. V.; Hong, N. V.; Hung, P. K.; Huy, N. V.

    2015-06-01

    The structure and dynamics of liquid lead silicate (PbSiO3) are investigated by molecular dynamics simulation with the pair potentials. The models of PbSiO3 consisting of 5000 atoms (1000 Pb, 1000 Si, and 3000 O atoms) are constructed at 3200 K and in a 0-35 GPa pressure range. The local structure, polymorphism, and dynamics in liquid PbSiO3 are investigated through pair radial distribution function, coordination distribution, topology structure of basic structural units, and mean square displacement. Short-range order (SRO) and intermediate-range order (IRO) are clarified by visualization of simulated data. The local environment around Pb+2 and Si+4 ions, the network structure of SiOx (x = 4, 5, 6) and PbOn (n = 3 - 9) polyhedra, and the correlation between structure and dynamics, as well as their change under compression, are also discussed in detail.

  20. Understanding the structure of hydrophobic surfactants at the air/water interface from molecular level.

    PubMed

    Zhang, Li; Liu, Zhipei; Ren, Tao; Wu, Pan; Shen, Jia-Wei; Zhang, Wei; Wang, Xinping

    2014-11-25

    Understanding the behavior of fluorocarbon surfactants at the air/water interface is crucial for many applications, such as lubricants, paints, cosmetics, and fire-fighting foams. In this study, molecular dynamics (MD) simulations were employed to investigate the microscopic properties of non-ionic fluorocarbon surfactants at the air/water interface. Several properties, including the distribution of head groups, the distribution probability of the tilt angle between hydrophobic tails with respect to the xy plane, and the order parameter of surfactants, were computed to probe the structure of hydrophobic surfactants at the air/water interface. The effects of the monomer structure on interfacial phenomena of non-ionic surfactants were investigated as well. It is observed that the structure of fluorocarbon surfactants at the air/water interface is more ordered than that of hydrocarbons, which is dominated by the van der Waals interaction between surfactants and water molecules. However, replacing one or two CF2 with one or two CH2 group does not significantly influence the interfacial structure, suggesting that hydrocarbons may be promising alternatives to perfluorinated surfactants.