Prediction of molecular crystal structures

International Nuclear Information System (INIS)

Beyer, Theresa

2001-01-01

The ab initio prediction of molecular crystal structures is a scientific challenge. Reliability of first-principle prediction calculations would show a fundamental understanding of crystallisation. Crystal structure prediction is also of considerable practical importance as different crystalline arrangements of the same molecule in the solid state (polymorphs)are likely to have different physical properties. A method of crystal structure prediction based on lattice energy minimisation has been developed in this work. The choice of the intermolecular potential and of the molecular model is crucial for the results of such studies and both of these criteria have been investigated. An empirical atom-atom repulsion-dispersion potential for carboxylic acids has been derived and applied in a crystal structure prediction study of formic, benzoic and the polymorphic system of tetrolic acid. As many experimental crystal structure determinations at different temperatures are available for the polymorphic system of paracetamol (acetaminophen), the influence of the variations of the molecular model on the crystal structure lattice energy minima, has also been studied. The general problem of prediction methods based on the assumption that the experimental thermodynamically stable polymorph corresponds to the global lattice energy minimum, is that more hypothetical low lattice energy structures are found within a few kJ mol -1 of the global minimum than are likely to be experimentally observed polymorphs. This is illustrated by the results for molecule I, 3-oxabicyclo(3.2.0)hepta-1,4-diene, studied for the first international blindtest for small organic crystal structures organised by the Cambridge Crystallographic Data Centre (CCDC) in May 1999. To reduce the number of predicted polymorphs, additional factors to thermodynamic criteria have to be considered. Therefore the elastic constants and vapour growth morphologies have been calculated for the lowest lattice energy

Prediction of molecular crystal structures

Energy Technology Data Exchange (ETDEWEB)

Beyer, Theresa

2001-07-01

The ab initio prediction of molecular crystal structures is a scientific challenge. Reliability of first-principle prediction calculations would show a fundamental understanding of crystallisation. Crystal structure prediction is also of considerable practical importance as different crystalline arrangements of the same molecule in the solid state (polymorphs)are likely to have different physical properties. A method of crystal structure prediction based on lattice energy minimisation has been developed in this work. The choice of the intermolecular potential and of the molecular model is crucial for the results of such studies and both of these criteria have been investigated. An empirical atom-atom repulsion-dispersion potential for carboxylic acids has been derived and applied in a crystal structure prediction study of formic, benzoic and the polymorphic system of tetrolic acid. As many experimental crystal structure determinations at different temperatures are available for the polymorphic system of paracetamol (acetaminophen), the influence of the variations of the molecular model on the crystal structure lattice energy minima, has also been studied. The general problem of prediction methods based on the assumption that the experimental thermodynamically stable polymorph corresponds to the global lattice energy minimum, is that more hypothetical low lattice energy structures are found within a few kJ mol{sup -1} of the global minimum than are likely to be experimentally observed polymorphs. This is illustrated by the results for molecule I, 3-oxabicyclo(3.2.0)hepta-1,4-diene, studied for the first international blindtest for small organic crystal structures organised by the Cambridge Crystallographic Data Centre (CCDC) in May 1999. To reduce the number of predicted polymorphs, additional factors to thermodynamic criteria have to be considered. Therefore the elastic constants and vapour growth morphologies have been calculated for the lowest lattice energy

Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center

Energy Technology Data Exchange (ETDEWEB)

Kim, Sung-Hou; Shin, Dong Hae; Hou, Jingtong; Chandonia, John-Marc; Das, Debanu; Choi, In-Geol; Kim, Rosalind; Kim, Sung-Hou

2007-09-02

Advances in sequence genomics have resulted in an accumulation of a huge number of protein sequences derived from genome sequences. However, the functions of a large portion of them cannot be inferred based on the current methods of sequence homology detection to proteins of known functions. Three-dimensional structure can have an important impact in providing inference of molecular function (physical and chemical function) of a protein of unknown function. Structural genomics centers worldwide have been determining many 3-D structures of the proteins of unknown functions, and possible molecular functions of them have been inferred based on their structures. Combined with bioinformatics and enzymatic assay tools, the successful acceleration of the process of protein structure determination through high throughput pipelines enables the rapid functional annotation of a large fraction of hypothetical proteins. We present a brief summary of the process we used at the Berkeley Structural Genomics Center to infer molecular functions of proteins of unknown function.

In situ structure and dynamics of DNA origami determined through molecular dynamics simulations.

Science.gov (United States)

Yoo, Jejoong; Aksimentiev, Aleksei

2013-12-10

The DNA origami method permits folding of long single-stranded DNA into complex 3D structures with subnanometer precision. Transmission electron microscopy, atomic force microscopy, and recently cryo-EM tomography have been used to characterize the properties of such DNA origami objects, however their microscopic structures and dynamics have remained unknown. Here, we report the results of all-atom molecular dynamics simulations that characterized the structural and mechanical properties of DNA origami objects in unprecedented microscopic detail. When simulated in an aqueous environment, the structures of DNA origami objects depart from their idealized targets as a result of steric, electrostatic, and solvent-mediated forces. Whereas the global structural features of such relaxed conformations conform to the target designs, local deformations are abundant and vary in magnitude along the structures. In contrast to their free-solution conformation, the Holliday junctions in the DNA origami structures adopt a left-handed antiparallel conformation. We find the DNA origami structures undergo considerable temporal fluctuations on both local and global scales. Analysis of such structural fluctuations reveals the local mechanical properties of the DNA origami objects. The lattice type of the structures considerably affects global mechanical properties such as bending rigidity. Our study demonstrates the potential of all-atom molecular dynamics simulations to play a considerable role in future development of the DNA origami field by providing accurate, quantitative assessment of local and global structural and mechanical properties of DNA origami objects.

Experimental determination of the structure of H3+

International Nuclear Information System (INIS)

Gaillard, M.J.; Gemmell, D.S.; Goldring, G.; Levine, I.; Pietsch, W.J.; Poizat, J.C.; Ratkowski, A.J.; Remillieux, J.; Vager, Z.; Zabransky, B.J.

1978-01-01

Three different measurements on the structure of the H 3 + molecular ion are reported. The measurements all make use of a new technique: the foil-induced dissociation of a fast molecular-ion beam. It is shown that the structure is equilaterally triangular in shape. The most probable length of side of the triangle is determined by the three measurements to be 0.97 +- 0.03 A, 0.95 +- 0.06 A, and 1.2 +- 0.2 A, respectively

Geometric and electronic structures of molecular ions from high energy collisions

International Nuclear Information System (INIS)

Groeneveld, K.O.

1983-01-01

This chapter examines the characteristics of heavy ion collision and of beam foil spectroscopy. It discusses the kinematic consequences of the high energies and presents results from ''Coulomb explosion'' and structure determination of molecular ions. It demonstrates that studies of molecular ions with accelerators can provide electronic and geometric structure information of molecules or molecular ions and points out that the understanding of the microscopic processes at such high energies is incomplete and needs further experimental and theoretical efforts

Targeting acetylcholinesterase: identification of chemical leads by high throughput screening, structure determination and molecular modeling.

Directory of Open Access Journals (Sweden)

Lotta Berg

Full Text Available Acetylcholinesterase (AChE is an essential enzyme that terminates cholinergic transmission by rapid hydrolysis of the neurotransmitter acetylcholine. Compounds inhibiting this enzyme can be used (inter alia to treat cholinergic deficiencies (e.g. in Alzheimer's disease, but may also act as dangerous toxins (e.g. nerve agents such as sarin. Treatment of nerve agent poisoning involves use of antidotes, small molecules capable of reactivating AChE. We have screened a collection of organic molecules to assess their ability to inhibit the enzymatic activity of AChE, aiming to find lead compounds for further optimization leading to drugs with increased efficacy and/or decreased side effects. 124 inhibitors were discovered, with considerable chemical diversity regarding size, polarity, flexibility and charge distribution. An extensive structure determination campaign resulted in a set of crystal structures of protein-ligand complexes. Overall, the ligands have substantial interactions with the peripheral anionic site of AChE, and the majority form additional interactions with the catalytic site (CAS. Reproduction of the bioactive conformation of six of the ligands using molecular docking simulations required modification of the default parameter settings of the docking software. The results show that docking-assisted structure-based design of AChE inhibitors is challenging and requires crystallographic support to obtain reliable results, at least with currently available software. The complex formed between C5685 and Mus musculus AChE (C5685•mAChE is a representative structure for the general binding mode of the determined structures. The CAS binding part of C5685 could not be structurally determined due to a disordered electron density map and the developed docking protocol was used to predict the binding modes of this part of the molecule. We believe that chemical modifications of our discovered inhibitors, biochemical and biophysical

Macromolecular structure determination in the post-genome era

International Nuclear Information System (INIS)

Kuhn, P.; Soltis, S.M.

2001-01-01

Recent advances in genetics, molecular biology and crystallographic instrumentation and methodology have led to a revolution in the field of Structural Molecular Biology (SMB). These combined advances have paved the way to a more complete and detailed understanding of the biological macromolecules that make up an organism, both in terms of their individual functions and also the interactions between them. In this paper we describe a large-scale, genomic approach to the three-dimensional structure determination of macromolecules and their complexes, using high-throughput methodology to streamline all aspects of the process. This task requires the development of automated high-intensity synchrotron beam lines for X-ray diffraction data collection from single crystal samples. Furthermore, these beam lines must be operated within a sophisticated software and hardware environment, which is capable of delivering a completely automated structure determination pipeline. The SMB resource at SSRL is developing a system for the structure determination steps of this process, starting with the initial characterization of the frozen sample, followed by data collection, data reduction, phase determination, and model building. This paper focuses on the data collection elements of this high-throughput system

Structural Molecular Biology 2017 | SSRL

Science.gov (United States)

Highlights Training Workshops & Summer Schools Summer Students Structural Molecular Biology Illuminating experimental driver for structural biology research, serving the needs of a large number of academic and — Our Mission The SSRL Structural Molecular Biology program operates as an integrated resource and has

Molecular Structure of Nucleic Acids

Indian Academy of Sciences (India)

Molecular Structure of Nucleic Acids. A Structure for Deoxyribose Nucleic Acid. J. D. Watson and F. H. C. Crick. Medical Research Council Unit for the Study of the Molecular Structure of Biological. Systems, Cavendish Laboratory, Cambridge. April 2. We wish to suggest a structure for the salt of deoxyribose nucleic acid ...

Characteristics studies of molecular structures in drugs

Directory of Open Access Journals (Sweden)

Wei Gao

2017-05-01

Full Text Available In theoretical medicine, topological indices are defined to test the medicine and pharmacy characteristics, such as melting point, boiling point, toxicity and other biological activities. As basic molecular structures, hexagonal jagged-rectangle and distance-regular structure are widely appeared in medicine, pharmacy and biology engineering. In this paper, we study the chemical properties of hexagonal jagged-rectangle from the mathematical point of view. Several vertex distance-based indices are determined. Furthermore, the Wiener related indices of distance-regular structure are also considered.

Valency and molecular structure

CERN Document Server

Cartmell, E

1977-01-01

Valency and Molecular Structure, Fourth Edition provides a comprehensive historical background and experimental foundations of theories and methods relating to valency and molecular structures. In this edition, the chapter on Bohr theory has been removed while some sections, such as structures of crystalline solids, have been expanded. Details of structures have also been revised and extended using the best available values for bond lengths and bond angles. Recent developments are mostly noted in the chapter on complex compounds, while a new chapter has been added to serve as an introduction t

The structure of molecular liquids. Neutron diffraction and molecular dynamics simulations

International Nuclear Information System (INIS)

Bianchi, L.

2000-05-01

Neutron diffraction (ND) measurements on liquid methanol (CD 3 OD, CD 3 O(H/D), CD 3 OH) under ambient conditions were performed to obtain the distinct (intra- + inter-molecular), G dist (r) and inter-molecular, G inter (r) radial distribution functions (rdfs) for the three samples. The H/D substitution on hydroxyl-hydrogen (Ho) has been used to extract the partial distribution functions, G XHo (r) (X=C, O, and H - a methyl hydrogen) and G XX (r) at both the distinct and inter-molecular levels from the difference techniques of ND. The O-Ho bond length, which has been the subject of controversy in the past, is found purely from the distinct partial distribution function, G XHo (r) to be 0.98 ± 0.01 A. The C-H distance obtained from the distinct G XX (r) partial is 1.08 ± 0.01 A. These distances determined by fitting an intra-molecular model to the total distinct structure functions are 0.961 ± 0.001 A and 1.096 ± 0.001 A, respectively. The inter-molecular G XX (r) function, dominated by contributions from the methyl groups, apart from showing broad oscillations extending up to ∼14 A is featureless, mainly because of cancellation effects from six contributing pairs. The Ho-Ho partial pair distribution function (pdf), g HoHo (r), determined from the second order difference, shows that only one other Ho atom can be found within a mean Ho-Ho separation of 2.36 A. The average position of the O-Ho hydrogen bond determined for the first time purely from experimental inter-molecular G XHo (r) partial distribution function is found to be at 1.75 ± 0.03 A. The experimental structural results at the partial distribution level are compared with those obtained from molecular dynamics (MD) simulations performed in NVE ensemble by using both 3- and 6-site force field models for the first time in this study. The MD simulations with both the models reproduce the ND rdfs rather well. However, discrepancies begin to appear between the simulated and the experimental partial

Electronic structure of molecular Rydberg states of some small molecules and molecular ion

International Nuclear Information System (INIS)

Sun Biao; Li Jiaming

1993-01-01

Based on an independent-particle-approximation (i.e. the multiple scattering self-consistent-field theory), the electronic structures of Rydberg states of the small diatomic molecules H 2 , He 2 and the He 2 + molecular ion were studied. The principal quantum number of the first state of the Rydberg series is determined from a convention of the limit of the molecular electronic configuration. The dynamics of the excited molecules and molecular ion has been elucidated. The theoretical results are in fair agreement with the existing experimental measurements, thus they can serve as a reliable basis for future refined treatment such as the configuration interaction calculation

Quantitative Determination of Organic Semiconductor Microstructure from the Molecular to Device Scale

KAUST Repository

Rivnay, Jonathan

2012-10-10

A study was conducted to demonstrate quantitative determination of organic semiconductor microstructure from the molecular to device scale. The quantitative determination of organic semiconductor microstructure from the molecular to device scale was key to obtaining precise description of the molecular structure and microstructure of the materials of interest. This information combined with electrical characterization and modeling allowed for the establishment of general design rules to guide future rational design of materials and devices. Investigations revealed that a number and variety of defects were the largest contributors to the existence of disorder within a lattice, as organic semiconductor crystals were dominated by weak van der Waals bonding. Crystallite size, texture, and variations in structure due to spatial confinement and interfaces were also found to be relevant for transport of free charge carriers and bound excitonic species over distances that were important for device operation.

Structural determination of organic compounds

International Nuclear Information System (INIS)

Kintzinger, J.P.

1991-01-01

This paper reports that the current methods available in high-field NMR spectroscopy are such that the tridimensional structure determination of any rigid molecule containing only carbon and hydrogen atoms may be achieved. The connectivities between carbon-carbon, carbon-hydrogen, and hydrogen-hydrogen atoms are determined by multipulse and two-dimensional (2D) experiments. These connectivity patterns or maps allow a step-by-step reconstruction of the molecular structures. From the carbon-carbon connectivity map, the carbon framework of the molecule is obtained, whereas the carbon-hydrogen pattern allows determination of the positions of the hydrogen atoms on their corresponding carbon atoms. High-field spectrometers are then necessary to remove fortuitous degeneracy and to reduce the proton spectra to a nearly first-order one, allowing an easy measurement of the chemical shifts and the coupling constants

Macromolecular structure determination in the post-genome era

CERN Document Server

Kuhn, P

2001-01-01

Recent advances in genetics, molecular biology and crystallographic instrumentation and methodology have led to a revolution in the field of Structural Molecular Biology (SMB). These combined advances have paved the way to a more complete and detailed understanding of the biological macromolecules that make up an organism, both in terms of their individual functions and also the interactions between them. In this paper we describe a large-scale, genomic approach to the three-dimensional structure determination of macromolecules and their complexes, using high-throughput methodology to streamline all aspects of the process. This task requires the development of automated high-intensity synchrotron beam lines for X-ray diffraction data collection from single crystal samples. Furthermore, these beam lines must be operated within a sophisticated software and hardware environment, which is capable of delivering a completely automated structure determination pipeline. The SMB resource at SSRL is developing a system...

Density functional study of molecular interactions in secondary structures of proteins.

Science.gov (United States)

Takano, Yu; Kusaka, Ayumi; Nakamura, Haruki

2016-01-01

Proteins play diverse and vital roles in biology, which are dominated by their three-dimensional structures. The three-dimensional structure of a protein determines its functions and chemical properties. Protein secondary structures, including α-helices and β-sheets, are key components of the protein architecture. Molecular interactions, in particular hydrogen bonds, play significant roles in the formation of protein secondary structures. Precise and quantitative estimations of these interactions are required to understand the principles underlying the formation of three-dimensional protein structures. In the present study, we have investigated the molecular interactions in α-helices and β-sheets, using ab initio wave function-based methods, the Hartree-Fock method (HF) and the second-order Møller-Plesset perturbation theory (MP2), density functional theory, and molecular mechanics. The characteristic interactions essential for forming the secondary structures are discussed quantitatively.

Determination and Quantification of Molecular Interactions in Protein Films: A Review

Directory of Open Access Journals (Sweden)

Felicia Hammann

2014-12-01

Full Text Available Protein based films are nowadays also prepared with the aim of replacing expensive, crude oil-based polymers as environmentally friendly and renewable alternatives. The protein structure determines the ability of protein chains to form intra- and intermolecular bonds, whereas the degree of cross-linking depends on the amino acid composition and molecular weight of the protein, besides the conditions used in film preparation and processing. The functionality varies significantly depending on the type of protein and affects the resulting film quality and properties. This paper reviews the methods used in examination of molecular interactions in protein films and discusses how these intermolecular interactions can be quantified. The qualitative determination methods can be distinguished by structural analysis of solutions (electrophoretic analysis, size exclusion chromatography and analysis of solid films (spectroscopy techniques, X-ray scattering methods. To quantify molecular interactions involved, two methods were found to be the most suitable: protein film swelling and solubility. The importance of non-covalent and covalent interactions in protein films can be investigated using different solvents. The research was focused on whey protein, whereas soy protein and wheat gluten were included as further examples of proteins.

Determination and Quantification of Molecular Interactions in Protein Films: A Review.

Science.gov (United States)

Hammann, Felicia; Schmid, Markus

2014-12-10

Protein based films are nowadays also prepared with the aim of replacing expensive, crude oil-based polymers as environmentally friendly and renewable alternatives. The protein structure determines the ability of protein chains to form intra- and intermolecular bonds, whereas the degree of cross-linking depends on the amino acid composition and molecular weight of the protein, besides the conditions used in film preparation and processing. The functionality varies significantly depending on the type of protein and affects the resulting film quality and properties. This paper reviews the methods used in examination of molecular interactions in protein films and discusses how these intermolecular interactions can be quantified. The qualitative determination methods can be distinguished by structural analysis of solutions (electrophoretic analysis, size exclusion chromatography) and analysis of solid films (spectroscopy techniques, X-ray scattering methods). To quantify molecular interactions involved, two methods were found to be the most suitable: protein film swelling and solubility. The importance of non-covalent and covalent interactions in protein films can be investigated using different solvents. The research was focused on whey protein, whereas soy protein and wheat gluten were included as further examples of proteins.

Comparative sequence and structural analyses of G-protein-coupled receptor crystal structures and implications for molecular models.

Directory of Open Access Journals (Sweden)

Catherine L Worth

Full Text Available BACKGROUND: Up until recently the only available experimental (high resolution structure of a G-protein-coupled receptor (GPCR was that of bovine rhodopsin. In the past few years the determination of GPCR structures has accelerated with three new receptors, as well as squid rhodopsin, being successfully crystallized. All share a common molecular architecture of seven transmembrane helices and can therefore serve as templates for building molecular models of homologous GPCRs. However, despite the common general architecture of these structures key differences do exist between them. The choice of which experimental GPCR structure(s to use for building a comparative model of a particular GPCR is unclear and without detailed structural and sequence analyses, could be arbitrary. The aim of this study is therefore to perform a systematic and detailed analysis of sequence-structure relationships of known GPCR structures. METHODOLOGY: We analyzed in detail conserved and unique sequence motifs and structural features in experimentally-determined GPCR structures. Deeper insight into specific and important structural features of GPCRs as well as valuable information for template selection has been gained. Using key features a workflow has been formulated for identifying the most appropriate template(s for building homology models of GPCRs of unknown structure. This workflow was applied to a set of 14 human family A GPCRs suggesting for each the most appropriate template(s for building a comparative molecular model. CONCLUSIONS: The available crystal structures represent only a subset of all possible structural variation in family A GPCRs. Some GPCRs have structural features that are distributed over different crystal structures or which are not present in the templates suggesting that homology models should be built using multiple templates. This study provides a systematic analysis of GPCR crystal structures and a consistent method for identifying

Comparative sequence and structural analyses of G-protein-coupled receptor crystal structures and implications for molecular models.

Science.gov (United States)

Worth, Catherine L; Kleinau, Gunnar; Krause, Gerd

2009-09-16

Up until recently the only available experimental (high resolution) structure of a G-protein-coupled receptor (GPCR) was that of bovine rhodopsin. In the past few years the determination of GPCR structures has accelerated with three new receptors, as well as squid rhodopsin, being successfully crystallized. All share a common molecular architecture of seven transmembrane helices and can therefore serve as templates for building molecular models of homologous GPCRs. However, despite the common general architecture of these structures key differences do exist between them. The choice of which experimental GPCR structure(s) to use for building a comparative model of a particular GPCR is unclear and without detailed structural and sequence analyses, could be arbitrary. The aim of this study is therefore to perform a systematic and detailed analysis of sequence-structure relationships of known GPCR structures. We analyzed in detail conserved and unique sequence motifs and structural features in experimentally-determined GPCR structures. Deeper insight into specific and important structural features of GPCRs as well as valuable information for template selection has been gained. Using key features a workflow has been formulated for identifying the most appropriate template(s) for building homology models of GPCRs of unknown structure. This workflow was applied to a set of 14 human family A GPCRs suggesting for each the most appropriate template(s) for building a comparative molecular model. The available crystal structures represent only a subset of all possible structural variation in family A GPCRs. Some GPCRs have structural features that are distributed over different crystal structures or which are not present in the templates suggesting that homology models should be built using multiple templates. This study provides a systematic analysis of GPCR crystal structures and a consistent method for identifying suitable templates for GPCR homology modelling that will

From bacterial to human dihydrouridine synthase: automated structure determination

Energy Technology Data Exchange (ETDEWEB)

Whelan, Fiona, E-mail: fiona.whelan@york.ac.uk; Jenkins, Huw T., E-mail: fiona.whelan@york.ac.uk [The University of York, Heslington, York YO10 5DD (United Kingdom); Griffiths, Samuel C. [University of Oxford, Headington, Oxford OX3 7BN (United Kingdom); Byrne, Robert T. [Ludwig-Maximilians-University Munich, Feodor-Lynen-Strasse 25, 81377 Munich (Germany); Dodson, Eleanor J.; Antson, Alfred A., E-mail: fiona.whelan@york.ac.uk [The University of York, Heslington, York YO10 5DD (United Kingdom)

2015-06-30

The crystal structure of a human dihydrouridine synthase, an enzyme associated with lung cancer, with 18% sequence identity to a T. maritima enzyme, has been determined at 1.9 Å resolution by molecular replacement after extensive molecular remodelling of the template. The reduction of uridine to dihydrouridine at specific positions in tRNA is catalysed by dihydrouridine synthase (Dus) enzymes. Increased expression of human dihydrouridine synthase 2 (hDus2) has been linked to pulmonary carcinogenesis, while its knockdown decreased cancer cell line viability, suggesting that it may serve as a valuable target for therapeutic intervention. Here, the X-ray crystal structure of a construct of hDus2 encompassing the catalytic and tRNA-recognition domains (residues 1–340) determined at 1.9 Å resolution is presented. It is shown that the structure can be determined automatically by phenix.mr-rosetta starting from a bacterial Dus enzyme with only 18% sequence identity and a significantly divergent structure. The overall fold of the human Dus2 is similar to that of bacterial enzymes, but has a larger recognition domain and a unique three-stranded antiparallel β-sheet insertion into the catalytic domain that packs next to the recognition domain, contributing to domain–domain interactions. The structure may inform the development of novel therapeutic approaches in the fight against lung cancer.

From bacterial to human dihydrouridine synthase: automated structure determination

International Nuclear Information System (INIS)

Whelan, Fiona; Jenkins, Huw T.; Griffiths, Samuel C.; Byrne, Robert T.; Dodson, Eleanor J.; Antson, Alfred A.

2015-01-01

The crystal structure of a human dihydrouridine synthase, an enzyme associated with lung cancer, with 18% sequence identity to a T. maritima enzyme, has been determined at 1.9 Å resolution by molecular replacement after extensive molecular remodelling of the template. The reduction of uridine to dihydrouridine at specific positions in tRNA is catalysed by dihydrouridine synthase (Dus) enzymes. Increased expression of human dihydrouridine synthase 2 (hDus2) has been linked to pulmonary carcinogenesis, while its knockdown decreased cancer cell line viability, suggesting that it may serve as a valuable target for therapeutic intervention. Here, the X-ray crystal structure of a construct of hDus2 encompassing the catalytic and tRNA-recognition domains (residues 1–340) determined at 1.9 Å resolution is presented. It is shown that the structure can be determined automatically by phenix.mr-rosetta starting from a bacterial Dus enzyme with only 18% sequence identity and a significantly divergent structure. The overall fold of the human Dus2 is similar to that of bacterial enzymes, but has a larger recognition domain and a unique three-stranded antiparallel β-sheet insertion into the catalytic domain that packs next to the recognition domain, contributing to domain–domain interactions. The structure may inform the development of novel therapeutic approaches in the fight against lung cancer

Photoionization and molecular structure

International Nuclear Information System (INIS)

Palma, A.

1983-01-01

A presentation is here given of the theoretical work on photoionization and molecular structure carried out by the author and coworkers. The implications of the photoionization process on the molecular geometry are emphasized. In particular, the ionization effect on deep orbitals is considered and it is shown that, contrary to traditional thinking, these orbitals have relevant effects on the molecular geometry. The problem of calculating photoionization relative intensities for the full spectrum is also considered, and the results of the present model are compared with experimental and other theoretical results. (author)

Study of the molecular structure and dynamics of bakelite with neutron cross section measurements

International Nuclear Information System (INIS)

Voi, D.L.

1990-06-01

The molecular structure and dynamics of calcined bakelite were studied with neutron transmission and scattering cross section measurements. The total cross sections determined were correlated with data obtained with infra-red spectroscopy, elemental analysis and other techniques to get the probable molecular formulae of bakelite. The total cross section determined showed a deviation smaller than 5% from the literature values. The frequency distribution as well as overall experimental results allowed to suggest a structural model like polycyclic hydrocarbons for bakelite calcined at 800 0 C. (F.E.). 65 refs, 31 figs, 5 tabs

Molecular dynamical and structural studies for the bakelite by neutron cross section measurements

International Nuclear Information System (INIS)

Voi, D.L.

1992-05-01

Neutron reaction cross sections were determined by transmission and scattering measurements, to study the dynamics and molecular structure of calcined bakelites. Total cross sections were determined, with a deviation smaller than 5%, from the literature values, by neutron transmission method and a specially devised approximation. These cross sections were then correlated with data obtained with infra-red spectroscopy, elemental analysis and other techniques to get the probable molecular formulae of bakelite. Double differential scattering cross sections, scattering law values and frequency distributions were determined with 15% error using the neutron inelastic scattering method. The frequency distributions as well as the overall results from all experimental techniques used in this work allowed to suggest a structural model like polycyclic hydrocarbons, for calcined bakelite at 800 0 C. (author)

Molecular Structure of Human-Liver Glycogen.

Directory of Open Access Journals (Sweden)

Bin Deng

Full Text Available 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.

STRUCTURED MOLECULAR GAS REVEALS GALACTIC SPIRAL ARMS

Energy Technology Data Exchange (ETDEWEB)

Sawada, Tsuyoshi [Joint ALMA Office, Alonso de Cordova 3107, Vitacura, Santiago 763-0355 (Chile); Hasegawa, Tetsuo [NAOJ Chile Observatory, Joaquin Montero 3000 Oficina 702, Vitacura, Santiago 763-0409 (Chile); Koda, Jin, E-mail: sawada.tsuyoshi@nao.ac.jp [Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY 11794-3800 (United States)

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.

Ab initio molecular crystal structures, spectra, and phase diagrams.

Science.gov (United States)

Hirata, So; Gilliard, Kandis; He, Xiao; Li, Jinjin; Sode, Olaseni

2014-09-16

Conspectus Molecular crystals are chemists' solids in the sense that their structures and properties can be understood in terms of those of the constituent molecules merely perturbed by a crystalline environment. They form a large and important class of solids including ices of atmospheric species, drugs, explosives, and even some organic optoelectronic materials and supramolecular assemblies. Recently, surprisingly simple yet extremely efficient, versatile, easily implemented, and systematically accurate electronic structure methods for molecular crystals have been developed. The methods, collectively referred to as the embedded-fragment scheme, divide a crystal into monomers and overlapping dimers and apply modern molecular electronic structure methods and software to these fragments of the crystal that are embedded in a self-consistently determined crystalline electrostatic field. They enable facile applications of accurate but otherwise prohibitively expensive ab initio molecular orbital theories such as Møller-Plesset perturbation and coupled-cluster theories to a broad range of properties of solids such as internal energies, enthalpies, structures, equation of state, phonon dispersion curves and density of states, infrared and Raman spectra (including band intensities and sometimes anharmonic effects), inelastic neutron scattering spectra, heat capacities, Gibbs energies, and phase diagrams, while accounting for many-body electrostatic (namely, induction or polarization) effects as well as two-body exchange and dispersion interactions from first principles. They can fundamentally alter the role of computing in the studies of molecular crystals in the same way ab initio molecular orbital theories have transformed research practices in gas-phase physical chemistry and synthetic chemistry in the last half century. In this Account, after a brief summary of formalisms and algorithms, we discuss applications of these methods performed in our group as compelling

Molecular Structural Transformation of 2:1 Clay Minerals by a Constant-Pressure Molecular Dynamics Simulation Method

International Nuclear Information System (INIS)

Wang, J.; Gutierre, M.S.

2010-01-01

This paper presents results of a molecular dynamics simulation study of dehydrated 2:1 clay minerals using the Parrinello-Rahman constant-pressure molecular dynamics method. The method is capable of simulating a system under the most general applied stress conditions by considering the changes of MD cell size and shape. Given the advantage of the method, it is the major goal of the paper to investigate the influence of imposed cell boundary conditions on the molecular structural transformation of 2:1 clay minerals under different normal pressures. Simulation results show that the degrees of freedom of the simulation cell (i.e., whether the cell size or shape change is allowed) determines the final equilibrated crystal structure of clay minerals. Both the MD method and the static method have successfully revealed unforeseen structural transformations of clay minerals upon relaxation under different normal pressures. It is found that large shear distortions of clay minerals occur when full allowance is given to the cell size and shape change. A complete elimination of the interlayer spacing is observed in a static simulation. However, when only the cell size change is allowed, interlayer spacing is retained, but large internal shear stresses also exist.

Quantitative structure-activity relationship (QSAR) models for polycyclic aromatic hydrocarbons (PAHs) dissipation in rhizosphere based on molecular structure and effect size

International Nuclear Information System (INIS)

Ma Bin; Chen Huaihai; Xu Minmin; Hayat, Tahir; He Yan; Xu Jianming

2010-01-01

Rhizoremediation is a significant form of bioremediation for polycyclic aromatic hydrocarbons (PAHs). This study examined the role of molecular structure in determining the rhizosphere effect on PAHs dissipation. Effect size in meta-analysis was employed as activity dataset for building quantitative structure-activity relationship (QSAR) models and accumulative effect sizes of 16 PAHs were used for validation of these models. Based on the genetic algorithm combined with partial least square regression, models for comprehensive dataset, Poaceae dataset, and Fabaceae dataset were built. The results showed that information indices, calculated as information content of molecules based on the calculation of equivalence classes from the molecular graph, were the most important molecular structural indices for QSAR models of rhizosphere effect on PAHs dissipation. The QSAR model, based on the molecular structure indices and effect size, has potential to be used in studying and predicting the rhizosphere effect of PAHs dissipation. - Effect size based on meta-analysis was used for building PAHs dissipation quantitative structure-activity relationship (QSAR) models.

Quantitative structure-activity relationship (QSAR) models for polycyclic aromatic hydrocarbons (PAHs) dissipation in rhizosphere based on molecular structure and effect size

Energy Technology Data Exchange (ETDEWEB)

Ma Bin; Chen Huaihai; Xu Minmin; Hayat, Tahir [Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, College of Environmental and Natural Resource Sciences, Zhejiang University, Hangzhou 310029 (China); He Yan, E-mail: yhe2006@zju.edu.c [Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, College of Environmental and Natural Resource Sciences, Zhejiang University, Hangzhou 310029 (China); Xu Jianming, E-mail: jmxu@zju.edu.c [Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, College of Environmental and Natural Resource Sciences, Zhejiang University, Hangzhou 310029 (China)

2010-08-15

Rhizoremediation is a significant form of bioremediation for polycyclic aromatic hydrocarbons (PAHs). This study examined the role of molecular structure in determining the rhizosphere effect on PAHs dissipation. Effect size in meta-analysis was employed as activity dataset for building quantitative structure-activity relationship (QSAR) models and accumulative effect sizes of 16 PAHs were used for validation of these models. Based on the genetic algorithm combined with partial least square regression, models for comprehensive dataset, Poaceae dataset, and Fabaceae dataset were built. The results showed that information indices, calculated as information content of molecules based on the calculation of equivalence classes from the molecular graph, were the most important molecular structural indices for QSAR models of rhizosphere effect on PAHs dissipation. The QSAR model, based on the molecular structure indices and effect size, has potential to be used in studying and predicting the rhizosphere effect of PAHs dissipation. - Effect size based on meta-analysis was used for building PAHs dissipation quantitative structure-activity relationship (QSAR) models.

Structure of HI-6*sarin-acetylcholinesterase determined by X-ray crystallography and molecular dynamics simulation: reactivator mechanism and design.

Directory of Open Access Journals (Sweden)

Fredrik Ekström

2009-06-01

Full Text Available Organophosphonates such as isopropyl metylphosphonofluoridate (sarin are extremely toxic as they phosphonylate the catalytic serine residue of acetylcholinesterase (AChE, an enzyme essential to humans and other species. Design of effective AChE reactivators as antidotes to various organophosphonates requires information on how the reactivators interact with the phosphonylated AChEs. However, such information has not been available hitherto because of three main challenges. First, reactivators are generally flexible in order to change from the ground state to the transition state for reactivation; this flexibility discourages determination of crystal structures of AChE in complex with effective reactivators that are intrinsically disordered. Second, reactivation occurs upon binding of a reactivator to the phosphonylated AChE. Third, the phosphorous conjugate can develop resistance to reactivation. We have identified crystallographic conditions that led to the determination of a crystal structure of the sarin(nonaged-conjugated mouse AChE in complex with [(E-[1-[(4-carbamoylpyridin-1-ium-1-ylmethoxymethyl]pyridin-2-ylidene]methyl]-oxoazanium dichloride (HI-6 at a resolution of 2.2 A. In this structure, the carboxyamino-pyridinium ring of HI-6 is sandwiched by Tyr124 and Trp286, however, the oxime-pyridinium ring is disordered. By combining crystallography with microsecond molecular dynamics simulation, we determined the oxime-pyridinium ring structure, which shows that the oxime group of HI-6 can form a hydrogen-bond network to the sarin isopropyl ether oxygen, and a water molecule is able to form a hydrogen bond to the catalytic histidine residue and subsequently deprotonates the oxime for reactivation. These results offer insights into the reactivation mechanism of HI-6 and design of better reactivators.

Molecular determinants of epidermal growth factor binding: a molecular dynamics study.

Directory of Open Access Journals (Sweden)

Jeffrey M Sanders

Full Text Available The epidermal growth factor receptor (EGFR is a member of the receptor tyrosine kinase family that plays a role in multiple cellular processes. Activation of EGFR requires binding of a ligand on the extracellular domain to promote conformational changes leading to dimerization and transphosphorylation of intracellular kinase domains. Seven ligands are known to bind EGFR with affinities ranging from sub-nanomolar to near micromolar dissociation constants. In the case of EGFR, distinct conformational states assumed upon binding a ligand is thought to be a determining factor in activation of a downstream signaling network. Previous biochemical studies suggest the existence of both low affinity and high affinity EGFR ligands. While these studies have identified functional effects of ligand binding, high-resolution structural data are lacking. To gain a better understanding of the molecular basis of EGFR binding affinities, we docked each EGFR ligand to the putative active state extracellular domain dimer and 25.0 ns molecular dynamics simulations were performed. MM-PBSA/GBSA are efficient computational approaches to approximate free energies of protein-protein interactions and decompose the free energy at the amino acid level. We applied these methods to the last 6.0 ns of each ligand-receptor simulation. MM-PBSA calculations were able to successfully rank all seven of the EGFR ligands based on the two affinity classes: EGF>HB-EGF>TGF-α>BTC>EPR>EPG>AR. Results from energy decomposition identified several interactions that are common among binding ligands. These findings reveal that while several residues are conserved among the EGFR ligand family, no single set of residues determines the affinity class. Instead we found heterogeneous sets of interactions that were driven primarily by electrostatic and Van der Waals forces. These results not only illustrate the complexity of EGFR dynamics but also pave the way for structure-based design of

Well-ordered monolayers of alkali-doped coronene and picene: Molecular arrangements and electronic structures

Energy Technology Data Exchange (ETDEWEB)

Yano, M.; Endo, M.; Hasegawa, Y.; Okada, R.; Yamada, Y., E-mail: yamada@bk.tsukuba.ac.jp; Sasaki, M. [Institute of Applied Physics, University of Tsukuba, Tsukuba, Ibaraki 305-8573 (Japan)

2014-07-21

Adsorptions of alkali metals (such as K and Li) on monolayers of coronene and picene realize the formation of ordered phases, which serve as well-defined model systems for metal-intercalated aromatic superconductors. Upon alkali-doping of the monolayers of coronene and picene, scanning tunneling microscopy and X-ray absorption spectroscopy revealed the rearrangement of the entire molecular layer. The K-induced reconstruction of both monolayers resulted in the formation of a structure with a herringbone-like arrangement of molecules, suggesting the intercalation of alkali metals between molecular planes. Upon reconstruction, a shift in both the vacuum level and core levels of coronene was observed as a result of a charge transfer from alkali metals to coronene. In addition, a new density of states near the Fermi level was formed in both the doped coronene and the doped picene monolayers. This characteristic electronic feature of the ordered monolayer has been also reported in the multilayer picene films, ensuring that the present monolayer can model the properties of the metal-intercalated aromatic hydrocarbons. It is suggested that the electronic structure near the Fermi level is sensitive to the molecular arrangement, and that both the strict control and determinations of the molecular structure in the doped phase should be important for the determination of the electronic structure of these materials.

Studying the molecular determinants of potassium channel structure and function in membranes by solid-state NMR

NARCIS (Netherlands)

van der Cruijsen, Elwin

2014-01-01

Solid-state Nuclear Magnetic Resonance (ssNMR) has made remarkable progress in the structural characterization of membrane proteins systems at atomic resolution. Such studies can be further aided by the use of molecular dynamic simulations. Moreover, ssNMR data can be directly compared to functional

Structure determination of enterovirus 71

Energy Technology Data Exchange (ETDEWEB)

Plevka, Pavel; Perera, Rushika; Cardosa, Jane; Kuhn, Richard J.; Rossmann, Michael G. (Purdue); (Sentinext)

2013-02-20

Enterovirus 71 is a picornavirus that causes hand, foot and mouth disease but may induce fatal neurological illness in infants and young children. Enterovirus 71 crystallized in a body-centered orthorhombic space group with two particles in general orientations in the crystallographic asymmetric unit. Determination of the particle orientations required that the locked rotation function excluded the twofold symmetry axes from the set of icosahedral symmetry operators. This avoided the occurrence of misleading high rotation-function values produced by the alignment of icosahedral and crystallographic twofold axes. Once the orientations and positions of the particles had been established, the structure was solved by molecular replacement and phase extension.

a Chiral Tagging Strategy for Determining Absolute Configuration and Enantiomeric Excess by Molecular Rotational Spectroscopy

Science.gov (United States)

Evangelisti, Luca; Caminati, Walther; Patterson, David; Thomas, Javix; Xu, Yunjie; West, Channing; Pate, Brooks

2017-06-01

The introduction of three wave mixing rotational spectroscopy by Patterson, Schnell, and Doyle [1,2] has expanded applications of molecular rotational spectroscopy into the field of chiral analysis. Chiral analysis of a molecule is the quantitative measurement of the relative abundances of all stereoisomers of the molecule and these include both diastereomers (with distinct molecular rotational spectra) and enantiomers (with equivalent molecular rotational spectra). This work adapts a common strategy in chiral analysis of enantiomers to molecular rotational spectroscopy. A "chiral tag" is attached to the molecule of interest by making a weakly bound complex in a pulsed jet expansion. When this tag molecule is enantiopure, it will create diastereomeric complexes with the two enantiomers of the molecule being analyzed and these can be differentiated by molecule rotational spectroscopy. Identifying the structure of this complex, with knowledge of the absolute configuration of the tag, establishes the absolute configuration of the molecule of interest. Furthermore, the diastereomer complex spectra can be used to determine the enantiomeric excess of the sample. The ability to perform chiral analysis will be illustrated by a study of solketal using propylene oxide as the tag. The possibility of using current methods of quantum chemistry to assign a specific structure to the chiral tag complex will be discussed. Finally, chiral tag rotational spectroscopy offers a "gold standard" method for determining the absolute configuration of the molecule through determination of the substitution structure of the complex. When this measurement is possible, rotational spectroscopy can deliver a quantitative three dimensional structure of the molecule with correct stereochemistry as the analysis output. [1] David Patterson, Melanie Schnell, John M. Doyle, Nature 497, 475 (2013). [2] David Patterson, John M. Doyle, Phys. Rev. Lett. 111, 023008 (2013).

A COMPARISON OF METHODS FOR DETERMINING THE MOLECULAR CONTENT OF MODEL GALAXIES

International Nuclear Information System (INIS)

Krumholz, Mark R.; Gnedin, Nickolay Y.

2011-01-01

Recent observations indicate that star formation occurs only in the molecular phase of a galaxy's interstellar medium. A realistic treatment of star formation in simulations and analytic models of galaxies therefore requires that one determine where the transition from the atomic to molecular gas occurs. In this paper, we compare two methods for making this determination in cosmological simulations where the internal structures of molecular clouds are unresolved: a complex time-dependent chemistry network coupled to a radiative transfer calculation of the dissociating ultraviolet (UV) radiation field and a simple time-independent analytic approximation. We show that these two methods produce excellent agreement at all metallicities ∼>10 -2 of the Milky Way value across a very wide range of UV fields. At lower metallicities the agreement is worse, likely because time-dependent effects become important; however, there are no observational calibrations of molecular gas content at such low metallicities, so it is unclear if either method is accurate. The comparison suggests that, in many but not all applications, the analytic approximation provides a viable and nearly cost-free alternative to full time-dependent chemistry and radiative transfer.

Exploring RNA structure by integrative molecular modelling

DEFF Research Database (Denmark)

Masquida, Benoît; Beckert, Bertrand; Jossinet, Fabrice

2010-01-01

RNA molecular modelling is adequate to rapidly tackle the structure of RNA molecules. With new structured RNAs constituting a central class of cellular regulators discovered every year, the need for swift and reliable modelling methods is more crucial than ever. The pragmatic method based...... on interactive all-atom molecular modelling relies on the observation that specific structural motifs are recurrently found in RNA sequences. Once identified by a combination of comparative sequence analysis and biochemical data, the motifs composing the secondary structure of a given RNA can be extruded...

Structure of a molecular liquid GeI4

International Nuclear Information System (INIS)

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

2016-01-01

A molecular liquid GeI 4 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. (paper)

Structural features of lipoarabinomannan from Mycobacterium bovis BCG. Determination of molecular mass by laser desorption mass spectrometry.

Science.gov (United States)

Venisse, A; Berjeaud, J M; Chaurand, P; Gilleron, M; Puzo, G

1993-06-15

It was recently shown that mycobacterial lipoarabinomannan (LAM) can be classified into two types (Chatterjee, D., Lowell, K., Rivoire B., McNeil M. R., and Brennan, P. J. (1992) J. Biol. Chem. 267, 6234-6239) according to the presence or absence of mannosyl residues (Manp) located at the nonreducing end of the oligoarabinosyl side chains. These two types of LAM were found in a pathogenic Mycobacterium tuberculosis strain and in an avirulent M. tuberculosis strain, respectively, suggesting that LAM with Manp characterizes virulent and "disease-inducing strains." We now report the structure of the LAM from Mycobacterium bovis Bacille Calmette-Guérin (BCG) strain Pasteur, largely used throughout the world as vaccine against tuberculosis. Using an up-to-date analytical approach, we found that the LAM of M. bovis BCG belongs to the class of LAMs capped with Manp. By means of two-dimensional homonuclear and heteronuclear scalar coupling NMR analysis and methylation data, the sugar spin system assignments were partially established, revealing that the LAM contained two types of terminal Manp and 2-O-linked Manp. From the following four-step process: (i) partial hydrolysis of deacylated LAM (dLAM), (ii) oligosaccharide derivatization with aminobenzoic ethyl ester, (iii) HPLC purification, (iv) FAB/MS-MS analysis; it was shown that the dimannosyl unit alpha-D-Manp-(1-->2)-alpha-D-Manp is the major residue capping the termini of the arabinan of the LAM. In this report, LAM molecular mass determination was established using matrix-assisted UV-laser desorption/ionization mass spectrometry which reveals that the LAM molecular mass is around 17.4 kDa. The similarity of the LAM structures between M. bovis BCG and M. tuberculosis H37Rv is discussed in regard to their function in the immunopathology of mycobacterial infection.

Molecular determinants of enzyme cold adaptation: comparative structural and computational studies of cold- and warm-adapted enzymes.

Science.gov (United States)

Papaleo, Elena; Tiberti, Matteo; Invernizzi, Gaetano; Pasi, Marco; Ranzani, Valeria

2011-11-01

The identification of molecular mechanisms underlying enzyme cold adaptation is a hot-topic both for fundamental research and industrial applications. In the present contribution, we review the last decades of structural computational investigations on cold-adapted enzymes in comparison to their warm-adapted counterparts. Comparative sequence and structural studies allow the definition of a multitude of adaptation strategies. Different enzymes carried out diverse mechanisms to adapt to low temperatures, so that a general theory for enzyme cold adaptation cannot be formulated. However, some common features can be traced in dynamic and flexibility properties of these enzymes, as well as in their intra- and inter-molecular interaction networks. Interestingly, the current data suggest that a family-centered point of view is necessary in the comparative analyses of cold- and warm-adapted enzymes. In fact, enzymes belonging to the same family or superfamily, thus sharing at least the three-dimensional fold and common features of the functional sites, have evolved similar structural and dynamic patterns to overcome the detrimental effects of low temperatures.

Simultaneous determination of protein structure and dynamics

DEFF Research Database (Denmark)

Lindorff-Larsen, Kresten; Best, Robert B.; DePristo, M. A.

2005-01-01

at the atomic level about the structural and dynamical features of proteins-with the ability of molecular dynamics simulations to explore a wide range of protein conformations. We illustrate the method for human ubiquitin in solution and find that there is considerable conformational heterogeneity throughout......We present a protocol for the experimental determination of ensembles of protein conformations that represent simultaneously the native structure and its associated dynamics. The procedure combines the strengths of nuclear magnetic resonance spectroscopy-for obtaining experimental information...... the protein structure. The interior atoms of the protein are tightly packed in each individual conformation that contributes to the ensemble but their overall behaviour can be described as having a significant degree of liquid-like character. The protocol is completely general and should lead to significant...

Structure and orientation of interfacial proteins determined by sum frequency generation vibrational spectroscopy: method and application.

Science.gov (United States)

Ye, Shuji; Wei, Feng; Li, Hongchun; Tian, Kangzhen; Luo, Yi

2013-01-01

In situ and real-time characterization of molecular structures and orientation of proteins at interfaces is essential to understand the nature of interfacial protein interaction. Such work will undoubtedly provide important clues to control biointerface in a desired manner. Sum frequency generation vibrational spectroscopy (SFG-VS) has been demonstrated to be a powerful technique to study the interfacial structures and interactions at the molecular level. This paper first systematically introduced the methods for the calculation of the Raman polarizability tensor, infrared transition dipole moment, and SFG molecular hyperpolarizability tensor elements of proteins/peptides with the secondary structures of α-helix, 310-helix, antiparallel β-sheet, and parallel β-sheet, as well as the methodology to determine the orientation of interfacial protein secondary structures using SFG amide I spectra. After that, recent progresses on the determination of protein structure and orientation at different interfaces by SFG-VS were then reviewed, which provides a molecular-level understanding of the structures and interactions of interfacial proteins, specially understanding the nature of driving force behind such interactions. Although this review has focused on analysis of amide I spectra, it will be expected to offer a basic idea for the spectral analysis of amide III SFG signals and other complicated molecular systems such as RNA and DNA. Copyright © 2013 Elsevier Inc. All rights reserved.

Atomic-scale structure of dislocations revealed by scanning tunneling microscopy and molecular dynamics

DEFF Research Database (Denmark)

Christiansen, Jesper; Morgenstern, K.; Schiøtz, Jakob

2002-01-01

The intersection between dislocations and a Ag(111) surface has been studied using an interplay of scanning tunneling microscopy (STM) and molecular dynamics. Whereas the STM provides atomically resolved information about the surface structure and Burgers vectors of the dislocations, the simulati......The intersection between dislocations and a Ag(111) surface has been studied using an interplay of scanning tunneling microscopy (STM) and molecular dynamics. Whereas the STM provides atomically resolved information about the surface structure and Burgers vectors of the dislocations......, the simulations can be used to determine dislocation structure and orientation in the near-surface region. In a similar way, the subsurface structure of other extended defects can be studied. The simulations show dislocations to reorient the partials in the surface region leading to an increased splitting width...

Structure of a 13-fold superhelix (almost determined from first principles

Directory of Open Access Journals (Sweden)

Guillaume A. Schoch

2015-03-01

Full Text Available Nuclear hormone receptors are cytoplasm-based transcription factors that bind a ligand, translate to the nucleus and initiate gene transcription in complex with a co-activator such as TIF2 (transcriptional intermediary factor 2. For structural studies the co-activator is usually mimicked by a peptide of circa 13 residues, which for the largest part forms an α-helix when bound to the receptor. The aim was to co-crystallize the glucocorticoid receptor in complex with a ligand and the TIF2 co-activator peptide. The 1.82 Å resolution diffraction data obtained from the crystal could not be phased by molecular replacement using the known receptor structures. HPLC analysis of the crystals revealed the absence of the receptor and indicated that only the co-activator peptide was present. The self-rotation function displayed 13-fold rotational symmetry, which initiated an exhaustive but unsuccessful molecular-replacement approach using motifs of 13-fold symmetry such as α- and β-barrels in various geometries. The structure was ultimately determined by using a single α-helix and the software ARCIMBOLDO, which assembles fragments placed by PHASER before using them as seeds for density modification model building in SHELXE. Systematic variation of the helix length revealed upper and lower size limits for successful structure determination. A beautiful but unanticipated structure was obtained that forms superhelices with left-handed twist throughout the crystal, stabilized by ligand interactions. Together with the increasing diversity of structural elements in the Protein Data Bank the results from TIF2 confirm the potential of fragment-based molecular replacement to significantly accelerate the phasing step for native diffraction data at around 2 Å resolution.

Photoionization-regulated star formation and the structure of molecular clouds

Science.gov (United States)

Mckee, Christopher F.

1989-01-01

A model for the rate of low-mass star formation in Galactic molecular clouds and for the influence of this star formation on the structure and evolution of the clouds is presented. The rate of energy injection by newly formed stars is estimated, and the effect of this energy injection on the size of the cloud is determined. It is shown that the observed rate of star formation appears adequate to support the observed clouds against gravitational collapse. The rate of photoionization-regulated star formation is estimated and it is shown to be in agreement with estimates of the observed rate of star formation if the observed molecular cloud parameters are used. The mean cloud extinction and the Galactic star formation rate per unit mass of molecular gas are predicted theoretically from the condition that photionization-regulated star formation be in equilibrium. A simple model for the evolution of isolated molecular clouds is developed.

Computer aided molecular design with combined molecular modeling and group contribution

DEFF Research Database (Denmark)

Harper, Peter Mathias; Gani, Rafiqul; Kolar, Petr

1999-01-01

Computer-aided molecular design (CAMD) provides a means for determining molecules or mixtures of molecules (CAMMD) having a desirable set of physicochemical properties. The application range of CAMD is restricted due to limitations on the complexity of the generated molecular structures and on th......Computer-aided molecular design (CAMD) provides a means for determining molecules or mixtures of molecules (CAMMD) having a desirable set of physicochemical properties. The application range of CAMD is restricted due to limitations on the complexity of the generated molecular structures...

Learning surface molecular structures via machine vision

Science.gov (United States)

Ziatdinov, Maxim; Maksov, Artem; Kalinin, Sergei V.

2017-08-01

Recent advances in high resolution scanning transmission electron and scanning probe microscopies have allowed researchers to perform measurements of materials structural parameters and functional properties in real space with a picometre precision. In many technologically relevant atomic and/or molecular systems, however, the information of interest is distributed spatially in a non-uniform manner and may have a complex multi-dimensional nature. One of the critical issues, therefore, lies in being able to accurately identify (`read out') all the individual building blocks in different atomic/molecular architectures, as well as more complex patterns that these blocks may form, on a scale of hundreds and thousands of individual atomic/molecular units. Here we employ machine vision to read and recognize complex molecular assemblies on surfaces. Specifically, we combine Markov random field model and convolutional neural networks to classify structural and rotational states of all individual building blocks in molecular assembly on the metallic surface visualized in high-resolution scanning tunneling microscopy measurements. We show how the obtained full decoding of the system allows us to directly construct a pair density function—a centerpiece in analysis of disorder-property relationship paradigm—as well as to analyze spatial correlations between multiple order parameters at the nanoscale, and elucidate reaction pathway involving molecular conformation changes. The method represents a significant shift in our way of analyzing atomic and/or molecular resolved microscopic images and can be applied to variety of other microscopic measurements of structural, electronic, and magnetic orders in different condensed matter systems.

Rotational structure in molecular infrared spectra

CERN Document Server

di Lauro, Carlo

2013-01-01

Recent advances in infrared molecular spectroscopy have resulted in sophisticated theoretical and laboratory methods that are difficult to grasp without a solid understanding of the basic principles and underlying theory of vibration-rotation absorption spectroscopy. Rotational Structure in Molecular Infrared Spectra fills the gap between these recent, complex topics and the most elementary methods in the field of rotational structure in the infrared spectra of gaseous molecules. There is an increasing need for people with the skills and knowledge to interpret vibration-rotation spectra in many scientific disciplines, including applications in atmospheric and planetary research. Consequently, the basic principles of vibration-rotation absorption spectroscopy are addressed for contemporary applications. In addition to covering operational quantum mechanical methods, spherical tensor algebra, and group theoretical methods applied to molecular symmetry, attention is also given to phase conventions and their effe...

Machine learning for the structure-energy-property landscapes of molecular crystals.

Science.gov (United States)

Musil, Félix; De, Sandip; Yang, Jack; Campbell, Joshua E; Day, Graeme M; Ceriotti, Michele

2018-02-07

Molecular crystals play an important role in several fields of science and technology. They frequently crystallize in different polymorphs with substantially different physical properties. To help guide the synthesis of candidate materials, atomic-scale modelling can be used to enumerate the stable polymorphs and to predict their properties, as well as to propose heuristic rules to rationalize the correlations between crystal structure and materials properties. Here we show how a recently-developed machine-learning (ML) framework can be used to achieve inexpensive and accurate predictions of the stability and properties of polymorphs, and a data-driven classification that is less biased and more flexible than typical heuristic rules. We discuss, as examples, the lattice energy and property landscapes of pentacene and two azapentacene isomers that are of interest as organic semiconductor materials. We show that we can estimate force field or DFT lattice energies with sub-kJ mol -1 accuracy, using only a few hundred reference configurations, and reduce by a factor of ten the computational effort needed to predict charge mobility in the crystal structures. The automatic structural classification of the polymorphs reveals a more detailed picture of molecular packing than that provided by conventional heuristics, and helps disentangle the role of hydrogen bonded and π-stacking interactions in determining molecular self-assembly. This observation demonstrates that ML is not just a black-box scheme to interpolate between reference calculations, but can also be used as a tool to gain intuitive insights into structure-property relations in molecular crystal engineering.

Contributions to advances in blend pellet products (BPP) research on molecular structure and molecular nutrition interaction by advanced synchrotron and globar molecular (Micro)spectroscopy.

Science.gov (United States)

Guevara-Oquendo, Víctor H; Zhang, Huihua; Yu, Peiqiang

2018-04-13

To date, advanced synchrotron-based and globar-sourced techniques are almost unknown to food and feed scientists. There has been little application of these advanced techniques to study blend pellet products at a molecular level. This article aims to provide recent research on advanced synchrotron and globar vibrational molecular spectroscopy contributions to advances in blend pellet products research on molecular structure and molecular nutrition interaction. How processing induced molecular structure changes in relation to nutrient availability and utilization of the blend pellet products. The study reviews Utilization of co-product components for blend pellet product in North America; Utilization and benefits of inclusion of pulse screenings; Utilization of additives in blend pellet products; Application of pellet processing in blend pellet products; Conventional evaluation techniques and methods for blend pellet products. The study focus on recent applications of cutting-edge vibrational molecular spectroscopy for molecular structure and molecular structure association with nutrient utilization in blend pellet products. The information described in this article gives better insight on how advanced molecular (micro)spectroscopy contributions to advances in blend pellet products research on molecular structure and molecular nutrition interaction.

X-ray structure determination and deuteration of nattokinase

International Nuclear Information System (INIS)

Yanagisawa, Yasuhide; Chatake, Toshiyuki; Naito, Sawa; Ohsugi, Tadanori; Yatagai, Chieko; Sumi, Hiroyuki; Kawaguchi, Akio; Chiba-Kamosida, Kaori; Ogawa, Megumi; Adachi, Tatsumi; Morimoto, Yukio

2013-01-01

X-ray structure determination and deuteration of nattokinase were performed to facilitate neutron crystallographic analysis. Nattokinase (NK) is a strong fibrinolytic enzyme, which is produced in abundance by Bacillus subtilis natto. Although NK is a member of the subtilisin family, it displays different substrate specificity when compared with other subtilisins. The results of molecular simulations predict that hydrogen arrangements around Ser221 at the active site probably account for the substrate specificity of NK. Therefore, neutron crystallographic analysis should provide valuable information that reveals the enzymatic mechanism of NK. In this report, the X-ray structure of the non-hydrogen form of undeuterated NK was determined, and the preparation of deuterated NK was successfully achieved. The non-hydrogen NK structure was determined at 1.74 Å resolution. The three-dimensional structures of NK and subtilisin E from Bacillus subtilis DB104 are near identical. Deuteration of NK was carried out by cultivating Bacillus subtilis natto in deuterated medium. The D 2 O resistant strain of Bacillus subtilis natto was obtained by successive cultivation rounds, in which the concentration of D 2 O in the medium was gradually increased. NK was purified from the culture medium and its activity was confirmed by the fibrin plate method. The results lay the framework for neutron protein crystallography analysis

Automated determination of fibrillar structures by simultaneous model building and fiber diffraction refinement.

Science.gov (United States)

Potrzebowski, Wojciech; André, Ingemar

2015-07-01

For highly oriented fibrillar molecules, three-dimensional structures can often be determined from X-ray fiber diffraction data. However, because of limited information content, structure determination and validation can be challenging. We demonstrate that automated structure determination of protein fibers can be achieved by guiding the building of macromolecular models with fiber diffraction data. We illustrate the power of our approach by determining the structures of six bacteriophage viruses de novo using fiber diffraction data alone and together with solid-state NMR data. Furthermore, we demonstrate the feasibility of molecular replacement from monomeric and fibrillar templates by solving the structure of a plant virus using homology modeling and protein-protein docking. The generated models explain the experimental data to the same degree as deposited reference structures but with improved structural quality. We also developed a cross-validation method for model selection. The results highlight the power of fiber diffraction data as structural constraints.

Molecular Models of Genetic and Organismic Structures

CERN Document Server

Baianu, I C

2004-01-01

In recent studies we showed that the earlier relational theories of organismic sets (Rashevsky,1967), Metabolic-Replication (M,R)-systems (Rosen,1958)and molecular sets (Bartholomay,1968) share a joint foundation that can be studied within a unified categorical framework of functional organismic structures (Baianu,1980. This is possible because all relational theories have a biomolecular basis, that is, complex structures such as genomes, cells,organs and biological organisms are mathematically represented in terms of biomolecular properties and entities,(that are often implicit in their representation axioms. The definition of organismic sets, for example, requires that certain essential quantities be determined from experiment: these are specified by special sets of values of general observables that are derived from physicochemical measurements(Baianu,1970; Baianu,1980; Baianu et al, 2004a.)Such observables are context-dependent and lead directly to natural transformations in categories and Topoi, that are...

Molecular weight determination of bisbenzyl-isoquinoline alkaloids by 252Cf-plasma desorption mass spectrometer

International Nuclear Information System (INIS)

Kohno, Hiroyuki; Tatsunami, Shinobu; Hiroi, Tomoko; Kouyama, Hiroshi; Taniguchi, Masashi; Yago, Nagasumi; Nakamura, Iwao

1995-01-01

Bisbenzylisoquinoline alkaloids of Stephania cepharantha have been used for various clinical purposes and recently reevaluated as stimulators of interleukin secretion in tissues. We analyzed molecular stuctures of bisbenzylisoquinoline alkaloids by determining their molecular weights using the 252 Cf-plasma desorption mass spectrometry (PDMS). The spectra were accumulated for 500 000 fission events. The acceleration voltage used here was 15 kV. Samples were analyzed using nitrocellulose-coated sample targets. Of the 5 alkaloids studied here, cepharanthine gave a main peak of molecular weight of 606.1 for the theoretical molecular weight of 606.7. The other minor peaks were considered to be demethylated fragment ions. 252 Cf-PDMS should be quite useful in studying structure, metabolism and pharmacokinetics of various drugs with extremely low coefficients of variation. (author)

The general atomic and molecular electronic structure system HONDO: Version 7.0

International Nuclear Information System (INIS)

Dupuis, M.; Watts, J.D.; Villar, H.O.; Hurst, G.J.B.

1989-01-01

We describe a computer program for ab initio quantum mechanical calculations of atomic and molecular wavefunctions and energies. Capabilities for the calculation of energy gradients and second derivatives with respect to nuclear coordinates are provided for several types of wavefunctions. Calculations of many molecular properties based on the electron density are possible. The program contains automated algorithms for the determination of equilibrium structures, saddle points, reaction pathways, vibrational spectra including infrared and Raman intensities. We illustrate the capabilities of the program by highlighting research problems recently investigated with the present program. (orig.)

Uncertainties of Molecular Structural Parameters

International Nuclear Information System (INIS)

Császár, Attila G.

2014-01-01

performed. Simply, there are significant disagreements between the same bond lengths measured by different techniques. These disagreements are, however, systematic and can be computed via techniques of quantum chemistry which deal not only with the motions of the electrons (electronic structure theory) but also with the often large amplitude motions of the nuclei. As to the relevant quantum chemical computations, since about 1970 electronic structure theory has become able to make quantitative predictions and thus challenge (or even overrule) many experiments. Nevertheless, quantitative agreement of quantum chemical results with experiment can only be expected when the motions of the atoms are also considered. In the fourth age of quantum chemistry we are living in an era where one can bridge quantitatively the gap between ‘effective’, experimental and ‘equilibrium’, computed structures at even elevated temperatures of interest thus minimizing any real uncertainties of structural parameters. The connections mentioned are extremely important as they help to understand the true uncertainty of measured structural parameters. Traditionally it is microwave (MW) and millimeterwave (MMW) spectroscopy, as well as gas-phase electron diffraction (GED), which yielded the most accurate structural parameters of molecules. The accuracy of the MW and GED experiments approached about 0.001Å and 0.1º under ideal circumstances, worse, sometimes considerably worse, in less than ideal and much more often encountered situations. Quantum chemistry can define both highly accurate equilibrium (so-called Born-Oppenheimer, r_e"B"O, and semiexperimental, r_e"S"E) structures and, via detailed investigation of molecular motions, accurate temperature-dependent rovibrationally averaged structures. Determining structures is still a rich field for research, understanding the measured or computed uncertainties of structures and structural parameters is still a challenge but there are firm and well

Adsorption and double layer charging in molecular sieve carbons in relation to molecular dimensions and pore structures

International Nuclear Information System (INIS)

Koresh, J.

1982-09-01

The pore structure of a fibrous carbon molecular sieve was studied by adsorption of molecular probes. Mild activation steps enabled the graduated opening of critical pore dimensions in the range 3.1-5.0 A, which keeps adsorption selectivity between molecules differing by 0.2 A in cross section diameter, to be considerably greater than 100/1. High adsorption stereospecificity over a wide pore dimension range enabled the studied adsorbates to be ordered in a sequence of increasing critical molecular dimension. Estimation of molecular dimensions by various experimental methods was discussed and their relevance to nonspherical molecules was evaluated. Polar molecules assume different dimensions depending on whether the carbon surface was polar (oxidized) or not. Hydrogen acquires, surprisingly, large width in accordance with its high liquid molar volume. Adsorbent-adsorbate interactions play a crucial role in determining molecular dimensions. Adsorption of ions from aqueous solutions into the developed ultramicropores of fibrous carbon electrodes was also studied. The dependence of the double layer capacitance and the charging rate on the pore critical dimension and on surface oxidation was studied using linear potential sweep voltametry. (Author)

Structures and physicochemical properties of molecular aggregates of lipids

International Nuclear Information System (INIS)

Iwahashi, Makio

2005-01-01

Structures and physicochemical properties of lipids such as fatty acids, alcohols, acylglycerols and steroids in their two- or three-dimensional states were studied through the measurements of surface pressure (π), surface-molecular area (A), vapor-pressure osmosis, radioactivity (R), self-diffusion coefficient (D), density, viscosity, near-infrared spectroscopy (NIR), 13 C-NMR spin-lattice relaxation time (T 1 ), ESR, SEM, DSC, X-ray diffraction and small-angle neutron scattering (SANS). Following results are obtained: (1) π-A and R-A relationships indicate that the explanation, being widely believed, of the reaction occurred in the oleic acid or the trioleylglycerol monolayer on the aqueous KMnO 4 solution is incorrect. (2) By using the LB film of 3 H-labelled fatty acid, the upper limit of the neutrino mass was determined. In addition, by using the LB film of 14 C-labelled fatty acid, a new type of crystal-transformation process was found, in which fatty-acid crystal transforms from its unstable state to its stable one by the transfer of the fatty acid molecules through the vapor phase. (3) Fatty acids always exist as their dimers in their liquid state and mostly in non-polar solvents; the dimers are the units of the molecular movements in the molten liquid and in solvents. T 1 results clearly showed the internal molecular movements of the dimers. In addition, D and SANS results indicated that two different kinds of fatty acids in their binary mixture make only each homodimers. (4) Furthermore, the study on the liquid structure of fatty acids such as cis-6-, cis-9-, cis-11-, trans-9-octadecenoic acids and stearic acid indicated that these fatty-acid dimers construct the clusters resemble to the smectic-liquid crystal in the liquid state. The clusters determine the physicochemical properties of the liquid of the fatty acid. (author)

The interface of protein structure, protein biophysics, and molecular evolution

Science.gov (United States)

Liberles, David A; Teichmann, Sarah A; Bahar, Ivet; Bastolla, Ugo; Bloom, Jesse; Bornberg-Bauer, Erich; Colwell, Lucy J; de Koning, A P Jason; Dokholyan, Nikolay V; Echave, Julian; Elofsson, Arne; Gerloff, Dietlind L; Goldstein, Richard A; Grahnen, Johan A; Holder, Mark T; Lakner, Clemens; Lartillot, Nicholas; Lovell, Simon C; Naylor, Gavin; Perica, Tina; Pollock, David D; Pupko, Tal; Regan, Lynne; Roger, Andrew; Rubinstein, Nimrod; Shakhnovich, Eugene; Sjölander, Kimmen; Sunyaev, Shamil; Teufel, Ashley I; Thorne, Jeffrey L; Thornton, Joseph W; Weinreich, Daniel M; Whelan, Simon

2012-01-01

Abstract The interface of protein structural biology, protein biophysics, molecular evolution, and molecular population genetics forms the foundations for a mechanistic understanding of many aspects of protein biochemistry. Current efforts in interdisciplinary protein modeling are in their infancy and the state-of-the art of such models is described. Beyond the relationship between amino acid substitution and static protein structure, protein function, and corresponding organismal fitness, other considerations are also discussed. More complex mutational processes such as insertion and deletion and domain rearrangements and even circular permutations should be evaluated. The role of intrinsically disordered proteins is still controversial, but may be increasingly important to consider. Protein geometry and protein dynamics as a deviation from static considerations of protein structure are also important. Protein expression level is known to be a major determinant of evolutionary rate and several considerations including selection at the mRNA level and the role of interaction specificity are discussed. Lastly, the relationship between modeling and needed high-throughput experimental data as well as experimental examination of protein evolution using ancestral sequence resurrection and in vitro biochemistry are presented, towards an aim of ultimately generating better models for biological inference and prediction. PMID:22528593

Structural insights of Staphylococcus aureus FtsZ inhibitors through molecular docking, 3D-QSAR and molecular dynamics simulations.

Science.gov (United States)

Ballu, Srilata; Itteboina, Ramesh; Sivan, Sree Kanth; Manga, Vijjulatha

2018-02-01

Filamentous temperature-sensitive protein Z (FtsZ) is a protein encoded by the FtsZ gene that assembles into a Z-ring at the future site of the septum of bacterial cell division. Structurally, FtsZ is a homolog of eukaryotic tubulin but has low sequence similarity; this makes it possible to obtain FtsZ inhibitors without affecting the eukaryotic cell division. Computational studies were performed on a series of substituted 3-arylalkoxybenzamide derivatives reported as inhibitors of FtsZ activity in Staphylococcus aureus. Quantitative structure-activity relationship models (QSAR) models generated showed good statistical reliability, which is evident from r 2 ncv and r 2 loo values. The predictive ability of these models was determined and an acceptable predictive correlation (r 2 Pred ) values were obtained. Finally, we performed molecular dynamics simulations in order to examine the stability of protein-ligand interactions. This facilitated us to compare free binding energies of cocrystal ligand and newly designed molecule B1. The good concordance between the docking results and comparative molecular field analysis (CoMFA)/comparative molecular similarity indices analysis (CoMSIA) contour maps afforded obliging clues for the rational modification of molecules to design more potent FtsZ inhibitors.

Large Molecule Structures by Broadband Fourier Transform Molecular Rotational Spectroscopy

Science.gov (United States)

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.

X-ray structure determination and deuteration of nattokinase

Energy Technology Data Exchange (ETDEWEB)

Yanagisawa, Yasuhide [Chiba Institute of Science, 15-8 Shiomi-cho, Cho-shi, Chiba 288-025 (Japan); Chatake, Toshiyuki [Kyoto University, Asashironishi 2, Kumatori, Osaka 590-0494 (Japan); Naito, Sawa; Ohsugi, Tadanori; Yatagai, Chieko; Sumi, Hiroyuki [Kurashiki University of Science and the Arts, 2640 Nishinoura, Tsurajima-cho, Kurashiki, Okayama 712-8505 (Japan); Kawaguchi, Akio [Kyoto University, Asashironishi 2, Kumatori, Osaka 590-0494 (Japan); Chiba-Kamosida, Kaori [Nippon Advanced Technology Co. Ltd, J-PARC, 2-4 Shirane Shirakata, Tokai, Ibaraki 319-1195 (Japan); Ogawa, Megumi; Adachi, Tatsumi [Chiba Institute of Science, 15-8 Shiomi-cho, Cho-shi, Chiba 288-025 (Japan); Morimoto, Yukio [Kyoto University, Asashironishi 2, Kumatori, Osaka 590-0494 (Japan)

2013-11-01

X-ray structure determination and deuteration of nattokinase were performed to facilitate neutron crystallographic analysis. Nattokinase (NK) is a strong fibrinolytic enzyme, which is produced in abundance by Bacillus subtilis natto. Although NK is a member of the subtilisin family, it displays different substrate specificity when compared with other subtilisins. The results of molecular simulations predict that hydrogen arrangements around Ser221 at the active site probably account for the substrate specificity of NK. Therefore, neutron crystallographic analysis should provide valuable information that reveals the enzymatic mechanism of NK. In this report, the X-ray structure of the non-hydrogen form of undeuterated NK was determined, and the preparation of deuterated NK was successfully achieved. The non-hydrogen NK structure was determined at 1.74 Å resolution. The three-dimensional structures of NK and subtilisin E from Bacillus subtilis DB104 are near identical. Deuteration of NK was carried out by cultivating Bacillus subtilis natto in deuterated medium. The D{sub 2}O resistant strain of Bacillus subtilis natto was obtained by successive cultivation rounds, in which the concentration of D{sub 2}O in the medium was gradually increased. NK was purified from the culture medium and its activity was confirmed by the fibrin plate method. The results lay the framework for neutron protein crystallography analysis.

Molecular Structure of Membrane Tethers

NARCIS (Netherlands)

Baoukina, Svetlana; Marrink, Siewert J.; Tieleman, D. Peter

2012-01-01

Membrane tethers are nanotubes formed by a lipid bilayer. They play important functional roles in cell biology and provide an experimental window on lipid properties. Tethers have been studied extensively in experiments and described by theoretical models, but their molecular structure remains

Structures of Life: The Role of Molecular Structures in Scientists' Work

NARCIS (Netherlands)

Vyas, Dhaval; Kulyk, Olga Anatoliyivna; van der Vet, P.E.; Nijholt, Antinus; van der Veer, Gerrit C.; Jorge, J

2008-01-01

The visual and multidimensional representations like images and graphical structures related to biology provide great insights into understanding the complexities of different organisms. Especially, life scientists use different representations of molecular structures to answer biological questions

Structural determinants and mechanism of HIV-1 genome packaging.

Science.gov (United States)

Lu, Kun; Heng, Xiao; Summers, Michael F

2011-07-22

Like all retroviruses, the human immunodeficiency virus selectively packages two copies of its unspliced RNA genome, both of which are utilized for strand-transfer-mediated recombination during reverse transcription-a process that enables rapid evolution under environmental and chemotherapeutic pressures. The viral RNA appears to be selected for packaging as a dimer, and there is evidence that dimerization and packaging are mechanistically coupled. Both processes are mediated by interactions between the nucleocapsid domains of a small number of assembling viral Gag polyproteins and RNA elements within the 5'-untranslated region of the genome. A number of secondary structures have been predicted for regions of the genome that are responsible for packaging, and high-resolution structures have been determined for a few small RNA fragments and protein-RNA complexes. However, major questions regarding the RNA structures (and potentially the structural changes) that are responsible for dimeric genome selection remain unanswered. Here, we review efforts that have been made to identify the molecular determinants and mechanism of human immunodeficiency virus type 1 genome packaging. Copyright © 2011 Elsevier Ltd. All rights reserved.

Advances in Rosetta structure prediction for difficult molecular-replacement problems

International Nuclear Information System (INIS)

DiMaio, Frank

2013-01-01

Modeling advances using Rosetta structure prediction to aid in solving difficult molecular-replacement problems are discussed. Recent work has shown the effectiveness of structure-prediction methods in solving difficult molecular-replacement problems. The Rosetta protein structure modeling suite can aid in the solution of difficult molecular-replacement problems using templates from 15 to 25% sequence identity; Rosetta refinement guided by noisy density has consistently led to solved structures where other methods fail. In this paper, an overview of the use of Rosetta for these difficult molecular-replacement problems is provided and new modeling developments that further improve model quality are described. Several variations to the method are introduced that significantly reduce the time needed to generate a model and the sampling required to improve the starting template. The improvements are benchmarked on a set of nine difficult cases and it is shown that this improved method obtains consistently better models in less running time. Finally, strategies for best using Rosetta to solve difficult molecular-replacement problems are presented and future directions for the role of structure-prediction methods in crystallography are discussed

Determination of the molecular structure via the medium energy electrons (500 eV-1,5 KeV) Ar, N2, Co e HCl

International Nuclear Information System (INIS)

Nogueira, J.C.

1977-01-01

Elastic Differential and Total Differential Cross Sections are measured for electron collision in medium-energy range (500 eV - 1,5 KeV) with argon, nitrogen, carbon monoxide and hydrogen chloride, all in their electronic ground state. Theoretical calculation for the Elastic Differential Cross Sections by atoms were done employing Hartree-Fock-Clementy wave function, and making use of Partial Wave and WKBJ Methods. Exchange effect is included in the case of argon. Independent Atom Model, Half Molecule Model and a new model, the Ionic Model were utilized for the molecular calculations. The Ionic Model is suggested for the interaction between HCl and electrons. Inelastic Differential Cross Section were also computed, making use of the First Born Approximation and Hartree-Fock-Clementi wave function. It is also demonstrated, for the first time, that medium energy electrons (500 eV - 1,5 Kev) can be used to determine molecular structure parameters, in gas phase [pt

Molecular determinants of magnolol targeting both RXRα and PPARγ.

Directory of Open Access Journals (Sweden)

Haitao Zhang

Full Text Available Nuclear receptors retinoic X receptor α (RXRα and peroxisome proliferator activated receptor γ (PPARγ function potently in metabolic diseases, and are both important targets for anti-diabetic drugs. Coactivation of RXRα and PPARγ is believed to synergize their effects on glucose and lipid metabolism. Here we identify the natural product magnolol as a dual agonist targeting both RXRα and PPARγ. Magnolol was previously reported to enhance adipocyte differentiation and glucose uptake, ameliorate blood glucose level and prevent development of diabetic nephropathy. Although magnolol can bind and activate both of these two nuclear receptors, the transactivation assays indicate that magnolol exhibits biased agonism on the transcription of PPAR-response element (PPRE mediated by RXRα:PPARγ heterodimer, instead of RXR-response element (RXRE mediated by RXRα:RXRα homodimer. To further elucidate the molecular basis for magnolol agonism, we determine both the co-crystal structures of RXRα and PPARγ ligand-binding domains (LBDs with magnolol. Structural analyses reveal that magnolol adopts its two 5-allyl-2-hydroxyphenyl moieties occupying the acidic and hydrophobic cavities of RXRα L-shaped ligand-binding pocket, respectively. While, two magnolol molecules cooperatively accommodate into PPARγ Y-shaped ligand-binding pocket. Based on these two complex structures, the key interactions for magnolol activating RXRα and PPARγ are determined. As the first report on the dual agonist targeting RXRα and PPARγ with receptor-ligand complex structures, our results are thus expected to help inspect the potential pharmacological mechanism for magnolol functions, and supply useful hits for nuclear receptor multi-target ligand design.

Pathways to Structure-Property Relationships of Peptide-Materials Interfaces: Challenges in Predicting Molecular Structures.

Science.gov (United States)

Walsh, Tiffany R

2017-07-18

An in-depth appreciation of how to manipulate the molecular-level recognition between peptides and aqueous materials interfaces, including nanoparticles, will advance technologies based on self-organized metamaterials for photonics and plasmonics, biosensing, catalysis, energy generation and harvesting, and nanomedicine. Exploitation of the materials-selective binding of biomolecules is pivotal to success in these areas and may be particularly key to producing new hierarchically structured biobased materials. These applications could be accomplished by realizing preferential adsorption of a given biomolecule onto one materials composition over another, one surface facet over another, or one crystalline polymorph over another. Deeper knowledge of the aqueous abiotic-biotic interface, to establish clear structure-property relationships in these systems, is needed to meet this goal. In particular, a thorough structural characterization of the surface-adsorbed peptides is essential for establishing these relationships but can often be challenging to accomplish via experimental approaches alone. In addition to myriad existing challenges associated with determining the detailed molecular structure of any molecule adsorbed at an aqueous interface, experimental characterization of materials-binding peptides brings new, complex challenges because many materials-binding peptides are thought to be intrinsically disordered. This means that these peptides are not amenable to experimental techniques that rely on the presence of well-defined secondary structure in the peptide when in the adsorbed state. To address this challenge, and in partnership with experiment, molecular simulations at the atomistic level can bring complementary and critical insights into the origins of this abiotic/biotic recognition and suggest routes for manipulating this phenomenon to realize new types of hybrid materials. For the reasons outlined above, molecular simulation approaches also face

Molecular structure of dextran sulphate sodium in aqueous environment

Science.gov (United States)

Yu, Miao; Every, Hayley A.; Jiskoot, Wim; Witkamp, Geert-Jan; Buijs, Wim

2018-03-01

Here we propose a 3D-molecular structural model for dextran sulphate sodium (DSS) in a neutral aqueous environment based on the results of a molecular modelling study. The DSS structure is dominated by the stereochemistry of the 1,6-linked α-glucose units and the presence of two sulphate groups on each α-glucose unit. The structure of DSS can be best described as a helix with various patterns of di-sulphate substitution on the glucose rings. The presence of a side chain does not alter the 3D-structure of the linear main chain much, but affects the overall spatial dimension of the polymer. The simulated polymers have a diameter similar to or in some cases even larger than model α-hemolysin nano-pores for macromolecule transport in many biological processes, indicating a size-limited translocation through such pores. All results of the molecular modelling study are in line with previously reported experimental data. This study establishes the three-dimensional structure of DSS and summarizes the spatial dimension of the polymer, serving as the basis for a better understanding on the molecular level of DSS-involved electrostatic interaction processes with biological components like proteins and cell pores.

Electronic structure and molecular orbital study of hole-transport material triphenylamine derivatives

International Nuclear Information System (INIS)

Wang, B.-C.; Liao, H.-R.; Chang, J.-C.; Chen Likey; Yeh, J.-T.

2007-01-01

Recently, triphenylamine (TPA), 4,4'-bis(phenyl-m-tolylamino)biphenyl (TPD), 4,4'-bis(1-naphthylphenylamino)biphenyl (NPB) and their derivatives are widely used in the organic light-emitting diode (OLED) devices as a hole-transporting material (HTM) layer. We have optimized twenty different structures of HTM materials by using density functional theory (DFT), B3LYP/6-31G method. All these different structures contain mono-amine and diamine TPA derivatives. The energies of highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) along with molecular orbitals for these HTMs are also determined. We have found that the central amine nitrogen atom and the phenyl ring, which is next to the central amine nitrogen atom, show significant contribution to the HOMO and LUMO, respectively. The sum of the calculated bond angles (α+β+γ) of the central amine nitrogen atom has been applied to describe the bonding and the energy difference for HOMO and LUMO in these TPA derivatives. Electronic structure calculations have been performed for these TPA derivatives. Again, the LCAO-MO patterns of HOMO and LUMO levels of these derivatives are used to investigate their electron density. A series of electron-transporting steps are predicted for these compounds employing these calculated results

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

Science.gov (United States)

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

2015-06-01

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

Microwave measurements of the spectra and molecular structure for phthalic anhydride

Science.gov (United States)

Pejlovas, Aaron M.; Sun, Ming; Kukolich, Stephen G.

2014-05-01

The microwave rotational spectrum for phthalic anhydride (PhA) has been measured in the 4-14 GHz microwave region using a pulsed-beam Fourier transform (PBFT) Flygare-Balle type microwave spectrometer. Initially, the molecular structure was calculated using Gaussian 09 suite with mp2/6-311++G** basis and the calculations were used in predicting spectra for the measured isotopologues. The experimental rotational transition frequencies were measured and used to calculate the rotational and centrifugal distortion constants. The rotational constants for the normal isotopologue, four unique 13C substituted isotopologues and two 18O isotologues, were used in a least squares fit to determine nearly all structural parameters for this molecule. Since no substitutions were made at hydrogen sites, the calculated positions of the hydrogen atoms relative to the bonded carbon atoms were used in the structure determination. The rotational constants for the parent isotopologue were determined to be A = 1801.7622(9) MHz, B = 1191.71816(26) MHz, C = 717.44614(28) MHz. Small values for the centrifugal distortion constants were obtained; DJ = 0.0127 kHz, DJK = 0.0652 kHz, and DK = -0.099 kHz, indicating a fairly rigid structure. The structure of PhA is planar with a negative inertial defect of Δ = -0.154 amu Å2. Structural parameters from the mp2 and DFT calculations are in quite good agreement with measured parameters.

xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures

International Nuclear Information System (INIS)

McGreevy, Ryan; Singharoy, Abhishek; Li, Qufei; Zhang, Jingfen; Xu, Dong; Perozo, Eduardo; Schulten, Klaus

2014-01-01

A new real-space refinement method for low-resolution X-ray crystallography is presented. The method is based on the molecular dynamics flexible fitting protocol targeted at addressing large-scale deformations of the search model to achieve refinement with minimal manual intervention. An explanation of the method is provided, augmented by results from the refinement of both synthetic and experimental low-resolution data, including an independent electrophysiological verification of the xMDFF-refined crystal structure of a voltage-sensor protein. X-ray crystallography remains the most dominant method for solving atomic structures. However, for relatively large systems, the availability of only medium-to-low-resolution diffraction data often limits the determination of all-atom details. A new molecular dynamics flexible fitting (MDFF)-based approach, xMDFF, for determining structures from such low-resolution crystallographic data is reported. xMDFF employs a real-space refinement scheme that flexibly fits atomic models into an iteratively updating electron-density map. It addresses significant large-scale deformations of the initial model to fit the low-resolution density, as tested with synthetic low-resolution maps of d-ribose-binding protein. xMDFF has been successfully applied to re-refine six low-resolution protein structures of varying sizes that had already been submitted to the Protein Data Bank. Finally, via systematic refinement of a series of data from 3.6 to 7 Å resolution, xMDFF refinements together with electrophysiology experiments were used to validate the first all-atom structure of the voltage-sensing protein Ci-VSP

xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures

Energy Technology Data Exchange (ETDEWEB)

McGreevy, Ryan; Singharoy, Abhishek [University of Illinois at Urbana-Champaign, Urbana, IL 61801 (United States); Li, Qufei [The University of Chicago, Chicago, IL 60637 (United States); Zhang, Jingfen; Xu, Dong [University of Missouri, Columbia, MO 65211 (United States); Perozo, Eduardo [The University of Chicago, Chicago, IL 60637 (United States); Schulten, Klaus, E-mail: kschulte@ks.uiuc.edu [University of Illinois at Urbana-Champaign, Urbana, IL 61801 (United States); University of Illinois at Urbana-Champaign, Urbana, IL 61801 (United States)

2014-09-01

A new real-space refinement method for low-resolution X-ray crystallography is presented. The method is based on the molecular dynamics flexible fitting protocol targeted at addressing large-scale deformations of the search model to achieve refinement with minimal manual intervention. An explanation of the method is provided, augmented by results from the refinement of both synthetic and experimental low-resolution data, including an independent electrophysiological verification of the xMDFF-refined crystal structure of a voltage-sensor protein. X-ray crystallography remains the most dominant method for solving atomic structures. However, for relatively large systems, the availability of only medium-to-low-resolution diffraction data often limits the determination of all-atom details. A new molecular dynamics flexible fitting (MDFF)-based approach, xMDFF, for determining structures from such low-resolution crystallographic data is reported. xMDFF employs a real-space refinement scheme that flexibly fits atomic models into an iteratively updating electron-density map. It addresses significant large-scale deformations of the initial model to fit the low-resolution density, as tested with synthetic low-resolution maps of d-ribose-binding protein. xMDFF has been successfully applied to re-refine six low-resolution protein structures of varying sizes that had already been submitted to the Protein Data Bank. Finally, via systematic refinement of a series of data from 3.6 to 7 Å resolution, xMDFF refinements together with electrophysiology experiments were used to validate the first all-atom structure of the voltage-sensing protein Ci-VSP.

Structure and molecular motion in three modifications of a binary C23H48-C24H50 paraffin

International Nuclear Information System (INIS)

Craievich, A.F.; Denicolo, I.; Doucet, J.

1983-01-01

The temperature dependence of the intensities of the (00l) X-ray reflections from a binary paraffin (C 23 H 48 -25% C 24 H 50 ) was determined, in order to obtain structure parameters related to the molecular motion and intramolecular defects. The long lattice spacing was also determined as a function of the temperature. All of these results are compared with the temperature dependence of the ratio of the two short lattice parameters. The clear correlation of all of these experimental results provides a close characterization of the molecular structures and their changes at the several solid state phase transitions. (Author) [pt

Study of the molecular structure and dynamics of bakelite with neutron cross section measurements; Estudo da estrutura e da dinamica moleculares da baquelite atraves de medidas de secoes de choque para neutrons

Energy Technology Data Exchange (ETDEWEB)

Voi, D L

1990-06-01

The molecular structure and dynamics of calcined bakelite were studied with neutron transmission and scattering cross section measurements. The total cross sections determined were correlated with data obtained with infra-red spectroscopy, elemental analysis and other techniques to get the probable molecular formulae of bakelite. The total cross section determined showed a deviation smaller than 5% from the literature values. The frequency distribution as well as overall experimental results allowed to suggest a structural model like polycyclic hydrocarbons for bakelite calcined at 800{sup 0} C. (F.E.). 65 refs, 31 figs, 5 tabs.

Nanohashtag structures based on carbon nanotubes and molecular linkers

Science.gov (United States)

Frye, Connor W.; Rybolt, Thomas R.

2018-03-01

Molecular mechanics was used to study the noncovalent interactions between single-walled carbon nanotubes and molecular linkers. Groups of nanotubes have the tendency to form tight, parallel bundles (||||). Molecular linkers were introduced into our models to stabilize nanostructures with carbon nanotubes held in perpendicular orientations. Molecular mechanics makes it possible to estimate the strength of noncovalent interactions holding these structures together and to calculate the overall binding energy of the structures. A set of linkers were designed and built around a 1,3,5,7-cyclooctatetraene tether with two corannulene containing pincers that extend in opposite directions from the central cyclooctatetraene portion. Each pincer consists of a pairs of "arms." These molecular linkers were modified so that the "hand" portions of each pair of "arms" could close together to grab and hold two carbon nanotubes in a perpendicular arrangement. To illustrate the possibility of more complicated and open perpendicular CNTs structures, our primary goal was to create a model of a nanohashtag (#) CNT conformation that is more stable than any parallel CNT arrangements with bound linker molecules forming clumps of CNTs and linkers in non-hashtag arrangements. This goal was achieved using a molecular linker (C280H96) that utilizes van der Waals interactions to two perpendicular oriented CNTs. Hydrogen bonding was then added between linker molecules to augment the stability of the hashtag structure. In the hashtag structure with hydrogen bonding, four (5,5) CNTs of length 4.46 nm (18 rings) and four linkers (C276H92N8O8) stabilized the hashtag so that the average binding energy per pincer was 118 kcal/mol.

Molecular structure of tetramethylgermane from gas electron diffraction

Science.gov (United States)

Csákvári, Éva; Rozsondai, Béla; Hargittai, István

1991-05-01

The molecular structure of Ge(CH 3) 4 has been determined from gas-phase electron diffraction augmented by a normal coordinate analysis. Assuming tetrahedral symmetry for the germanium bond configuration, the following structural parameters are found: rg(GeC) = 1.958 ± 0.004 Å, rg(CH) = 1.111 ± 0.003 Å and ∠(GeCH) = 110.7 ± 0.2° ( R=4.0%). The methyl torsional barrier V 0 is estimated to be 1.3 kJ mol -1 on the basis of an effective angle of torsion 23.0 ± 1.5°, from the staggered form, yielded directly by the analysis. The GeC bond length of Ge(CH 3) 4 is the same, within experimental error, as that of Ge(C 6H 5) 4 and is in agreement with the prediction of a modified Schomaker-Stevenson relationship.

Bio-functions and molecular carbohydrate structure association study in forage with different source origins revealed using non-destructive vibrational molecular spectroscopy techniques.

Science.gov (United States)

Ji, Cuiying; Zhang, Xuewei; Yan, Xiaogang; Mostafizar Rahman, M; Prates, Luciana L; Yu, Peiqiang

2017-08-05

The objectives of this study were to: 1) investigate forage carbohydrate molecular structure profiles; 2) bio-functions in terms of CHO rumen degradation characteristics and hourly effective degradation ratio of N to OM (HED N/OM ), and 3) quantify interactive association between molecular structures, bio-functions and nutrient availability. The vibrational molecular spectroscopy was applied to investigate the structure feature on a molecular basis. Two sourced-origin alfalfa forages were used as modeled forages. The results showed that the carbohydrate molecular structure profiles were highly linked to the bio-functions in terms of rumen degradation characteristics and hourly effective degradation ratio. The molecular spectroscopic technique can be used to detect forage carbohydrate structure features on a molecular basis and can be used to study interactive association between forage molecular structure and bio-functions. Copyright © 2017 Elsevier B.V. All rights reserved.

Molecular and crystal structure of 3,4-dihydroxy-2-oxo-1-methyl-4-phenylpiperidine

International Nuclear Information System (INIS)

Kuleshova, L.N.; Khrustalev, V.N.; Struchkov, Yu.T.; Soldatenkov, A.T.; Bekro, I.A.; Mamyrbekova, Zh.A.; Soldatova, S.A.

1996-01-01

The molecular and crystal structure of 3,4-dihydroxy-2-oxo-1-methyl-4-phenylpiperidine was determined. The crystal is orthorhombic: sp. gr. Pca21; a=15.764, b=5.635, and c=25.536 A; and Z=8. The structure was solved by direct methods; R1=0.051, for 2643 unique refections. Symmetry-independent molecules are related by a pseudocenter of symmetry. The piperidine cycle has an asymmetric half-chair conformation. The orientation of substituents is determined. In the crystal, intermolecular OH...O hydrogen bonds link the molecules into chains parallel to the Y-axis

Determination of the three-dimensional structure for weakly aligned biomolecules by NMR spectroscopy

International Nuclear Information System (INIS)

Shahkhatuni, Astghik A; Shahkhatuni, Aleksan G

2002-01-01

The key achievements and the potential of NMR spectroscopy for weakly aligned biomolecules are considered. Due to weak alignment, it becomes possible to determine a number of NMR parameters dependent on the orientation of biomolecules, which are averaged to zero in usual isotropic media. The addition of new orientational constraints to standard procedures of 3D structure determination markedly increases the achievable accuracy. The possibility of structure determination for biomolecules using only orientation-dependent parameters without invoking other NMR data is discussed. The methods of orientation, experimental techniques, and calculation methods are systematised. The main results obtained and the prospects of using NMR spectroscopy of weakly aligned systems to study different classes of biomolecules and to solve various problems of molecular biology are analysed. Examples of biomolecules whose structures have been determined using orientation-dependent parameters are given. The bibliography includes 508 references.

9Å structure of the COPI coat reveals that the Arf1 GTPase occupies two contrasting molecular environments.

Science.gov (United States)

Dodonova, Svetlana O; Aderhold, Patrick; Kopp, Juergen; Ganeva, Iva; Röhling, Simone; Hagen, Wim J H; Sinning, Irmgard; Wieland, Felix; Briggs, John A G

2017-06-16

COPI coated vesicles mediate trafficking within the Golgi apparatus and between the Golgi and the endoplasmic reticulum. Assembly of a COPI coated vesicle is initiated by the small GTPase Arf1 that recruits the coatomer complex to the membrane, triggering polymerization and budding. The vesicle uncoats before fusion with a target membrane. Coat components are structurally conserved between COPI and clathrin/adaptor proteins. Using cryo-electron tomography and subtomogram averaging, we determined the structure of the COPI coat assembled on membranes in vitro at 9 Å resolution. We also obtained a 2.57 Å resolution crystal structure of βδ-COP. By combining these structures we built a molecular model of the coat. We additionally determined the coat structure in the presence of ArfGAP proteins that regulate coat dissociation. We found that Arf1 occupies contrasting molecular environments within the coat, leading us to hypothesize that some Arf1 molecules may regulate vesicle assembly while others regulate coat disassembly.

Using vibrational molecular spectroscopy to reveal association of steam-flaking induced carbohydrates molecular structural changes with grain fractionation, biodigestion and biodegradation

Science.gov (United States)

Xu, Ningning; Liu, Jianxin; Yu, Peiqiang

2018-04-01

Advanced vibrational molecular spectroscopy has been developed as a rapid and non-destructive tool to reveal intrinsic molecular structure conformation of biological tissues. However, this technique has not been used to systematically study flaking induced structure changes at a molecular level. The objective of this study was to use vibrational molecular spectroscopy to reveal association between steam flaking induced CHO molecular structural changes in relation to grain CHO fractionation, predicted CHO biodegradation and biodigestion in ruminant system. The Attenuate Total Reflectance Fourier-transform Vibrational Molecular Spectroscopy (ATR-Ft/VMS) at SRP Key Lab of Molecular Structure and Molecular Nutrition, Ministry of Agriculture Strategic Research Chair Program (SRP, University of Saskatchewan) was applied in this study. The fractionation, predicted biodegradation and biodigestion were evaluated using the Cornell Net Carbohydrate Protein System. The results show that: (1) The steam flaking induced significant changes in CHO subfractions, CHO biodegradation and biodigestion in ruminant system. There were significant differences between non-processed (raw) and steam flaked grain corn (P R2 = 0.87, RSD = 0.74, P R2 = 0.87, RSD = 0.24, P < .01). In summary, the processing induced molecular CHO structure changes in grain corn could be revealed by the ATR-Ft/VMS vibrational molecular spectroscopy. These molecular structure changes in grain were potentially associated with CHO biodegradation and biodigestion.

Introductory group theory and its application to molecular structure

CERN Document Server

Ferraro, John R

1975-01-01

The success of the first edition of this book has encouraged us to revise and update it. In the second edition we have attempted to further clarify por­ tions of the text in reference to point symmetry, keeping certain sections and removing others. The ever-expanding interest in solids necessitates some discussion on space symmetry. In this edition we have expanded the discus­ sion on point symmetry to include space symmetry. The selection rules in­ clude space group selection rules (for k = 0). Numerous examples are pro­ vided to acquaint the reader with the procedure necessary to accomplish this. Recent examples from the literature are given to illustrate the use of group theory in the interpretation of molecular spectra and in the determination of molecular structure. The text is intended for scientists and students with only a limited theoretical background in spectroscopy. For this reason we have presented detailed procedures for carrying out the selection rules and normal coor­ dinate treatment of ...

Modeling the intermolecular interactions: molecular structure of N-3-hydroxyphenyl-4-methoxybenzamide.

Science.gov (United States)

Karabulut, Sedat; Namli, Hilmi; Kurtaran, Raif; Yildirim, Leyla Tatar; Leszczynski, Jerzy

2014-03-01

The title compound, N-3-hydroxyphenyl-4-methoxybenzamide (3) was prepared by the acylation reaction of 3-aminophenol (1) and 4-metoxybenzoylchloride (2) in THF and characterized by ¹H NMR, ¹³C NMR and elemental analysis. Molecular structure of the crystal was determined by single crystal X-ray diffraction and DFT calculations. 3 crystallizes in monoclinic P2₁/c space group. The influence of intermolecular interactions (dimerization and crystal packing) on molecular geometry has been evaluated by calculations performed for three different models; monomer (3), dimer (4) and dimer with added unit cell contacts (5). Molecular structure of 3, 4 and 5 was optimized by applying B3LYP method with 6-31G+(d,p) basis set in gas phase and compared with X-ray crystallographic data including bond lengths, bond angles and selected dihedral angles. It has been concluded that although the crystal packing and dimerization have a minor effect on bond lengths and angles, however, these interactions are important for the dihedral angles and the rotational conformation of aromatic rings. Copyright © 2013 Elsevier Inc. All rights reserved.

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

Directory of Open Access Journals (Sweden)

Natalie Heffernan

2015-01-01

Full Text Available 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.

Protein structure determination by exhaustive search of Protein Data Bank derived databases.

Science.gov (United States)

Stokes-Rees, Ian; Sliz, Piotr

2010-12-14

Parallel sequence and structure alignment tools have become ubiquitous and invaluable at all levels in the study of biological systems. We demonstrate the application and utility of this same parallel search paradigm to the process of protein structure determination, benefitting from the large and growing corpus of known structures. Such searches were previously computationally intractable. Through the method of Wide Search Molecular Replacement, developed here, they can be completed in a few hours with the aide of national-scale federated cyberinfrastructure. By dramatically expanding the range of models considered for structure determination, we show that small (less than 12% structural coverage) and low sequence identity (less than 20% identity) template structures can be identified through multidimensional template scoring metrics and used for structure determination. Many new macromolecular complexes can benefit significantly from such a technique due to the lack of known homologous protein folds or sequences. We demonstrate the effectiveness of the method by determining the structure of a full-length p97 homologue from Trichoplusia ni. Example cases with the MHC/T-cell receptor complex and the EmoB protein provide systematic estimates of minimum sequence identity, structure coverage, and structural similarity required for this method to succeed. We describe how this structure-search approach and other novel computationally intensive workflows are made tractable through integration with the US national computational cyberinfrastructure, allowing, for example, rapid processing of the entire Structural Classification of Proteins protein fragment database.

Quantitative Determination of Organic Semiconductor Microstructure from the Molecular to Device Scale

KAUST Repository

Rivnay, Jonathan; Mannsfeld, Stefan C. B.; Miller, Chad E.; Salleo, Alberto; Toney, Michael F.

2012-01-01

A study was conducted to demonstrate quantitative determination of organic semiconductor microstructure from the molecular to device scale. The quantitative determination of organic semiconductor microstructure from the molecular to device scale

Molecular, crystal, and electronic structure of the cobalt(II) complex with 10-(2-benzothiazolylazo)-9-phenanthrol

Energy Technology Data Exchange (ETDEWEB)

Linko, R. V., E-mail: rlinko@mail.ru [Peoples' Friendship University of Russia (Russian Federation); Sokol, V. I. [Russian Academy of Sciences, Kurnakov Institute of General and Inorganic Chemistry (Russian Federation); Polyanskaya, N. A.; Ryabov, M. A.; Strashnov, P. V.; Davydov, V. V. [Peoples' Friendship University of Russia (Russian Federation); Sergienko, V. S. [Russian Academy of Sciences, Kurnakov Institute of General and Inorganic Chemistry (Russian Federation)

2013-05-15

The reaction of 10-(2-benzothiazolylazo)-9-phenanthrol (HL) with cobalt(II) acetate gives the coordination compound [CoL{sub 2}] {center_dot} CHCl{sub 3} (I). The molecular and crystal structure of I is determined by X-ray diffraction. The coordination polyhedron of the Co atom in complex I is an octahedron. The anion L acts as a tridentate chelating ligand and is coordinated to the Co atom through the phenanthrenequinone O1 atom and the benzothiazole N1 atom of the moieties L and the N3 atom of the azo group to form two five-membered metallocycles. The molecular and electronic structures of the compounds HL, L, and CoL{sub 2} are studied at the density functional theory level. The results of the quantum-chemical calculations are in good agreement with the values determined by X-ray diffraction.

Molecular, crystal, and electronic structure of the cobalt(II) complex with 10-(2-benzothiazolylazo)-9-phenanthrol

International Nuclear Information System (INIS)

Linko, R. V.; Sokol, V. I.; Polyanskaya, N. A.; Ryabov, M. A.; Strashnov, P. V.; Davydov, V. V.; Sergienko, V. S.

2013-01-01

The reaction of 10-(2-benzothiazolylazo)-9-phenanthrol (HL) with cobalt(II) acetate gives the coordination compound [CoL 2 ] · CHCl 3 (I). The molecular and crystal structure of I is determined by X-ray diffraction. The coordination polyhedron of the Co atom in complex I is an octahedron. The anion L acts as a tridentate chelating ligand and is coordinated to the Co atom through the phenanthrenequinone O1 atom and the benzothiazole N1 atom of the moieties L and the N3 atom of the azo group to form two five-membered metallocycles. The molecular and electronic structures of the compounds HL, L, and CoL 2 are studied at the density functional theory level. The results of the quantum-chemical calculations are in good agreement with the values determined by X-ray diffraction.

Molecular structure descriptors in the computer-aided design of biologically active compounds

International Nuclear Information System (INIS)

Raevsky, Oleg A

1999-01-01

The current state of description of molecular structure in computer-aided molecular design of biologically active compounds by means of descriptors is analysed. The information contents of descriptors increases in the following sequence: element-level descriptors-structural formulae descriptors-electronic structure descriptors-molecular shape descriptors-intermolecular interaction descriptors. Each subsequent class of descriptors normally covers information contained in the previous-level ones. It is emphasised that it is practically impossible to describe all the features of a molecular structure in terms of any single class of descriptors. It is recommended to optimise the number of descriptors used by means of appropriate statistical procedures and characteristics of structure-property models based on these descriptors. The bibliography includes 371 references.

On a Molecular Basis, Investigate Association of Molecular Structure with Bioactive Compounds, Anti-Nutritional Factors and Chemical and Nutrient Profiles of Canola Seeds and Co-Products from Canola Processing: Comparison Crusher Plants within Canada and within China as well as between Canada and China.

Science.gov (United States)

Gomaa, Walaa M S; Mosaad, Gamal M; Yu, Peiqiang

2018-04-21

The objectives of this study were to: (1) Use molecular spectroscopy as a novel technique to quantify protein molecular structures in relation to its chemical profiles and bioenergy values in oil-seeds and co-products from bio-oil processing. (2) Determine and compare: (a) protein molecular structure using Fourier transform infrared (FT/IR-ATR) molecular spectroscopy technique; (b) bioactive compounds, anti-nutritional factors, and chemical composition; and (c) bioenergy values in oil seeds (canola seeds), co-products (meal or pellets) from bio-oil processing plants in Canada in comparison with China. (3) Determine the relationship between protein molecular structural features and nutrient profiles in oil-seeds and co-products from bio-oil processing. Our results showed the possibility to characterize protein molecular structure using FT/IR molecular spectroscopy. Processing induced changes between oil seeds and co-products were found in the chemical, bioenergy profiles and protein molecular structure. However, no strong correlation was found between the chemical and nutrient profiles of oil seeds (canola seeds) and their protein molecular structure. On the other hand, co-products were strongly correlated with protein molecular structure in the chemical profile and bioenergy values. Generally, comparisons of oil seeds (canola seeds) and co-products (meal or pellets) in Canada, in China, and between Canada and China indicated the presence of variations among different crusher plants and bio-oil processing products.

Structural determinants in the bulk heterojunction.

Science.gov (United States)

Acocella, Angela; Höfinger, Siegfried; Haunschmid, Ernst; Pop, Sergiu C; Narumi, Tetsu; Yasuoka, Kenji; Yasui, Masato; Zerbetto, Francesco

2018-02-21

Photovoltaics is one of the key areas in renewable energy research with remarkable progress made every year. Here we consider the case of a photoactive material and study its structural composition and the resulting consequences for the fundamental processes driving solar energy conversion. A multiscale approach is used to characterize essential molecular properties of the light-absorbing layer. A selection of bulk-representative pairs of donor/acceptor molecules is extracted from the molecular dynamics simulation of the bulk heterojunction and analyzed at increasing levels of detail. Significantly increased ground state energies together with an array of additional structural characteristics are identified that all point towards an auxiliary role of the material's structural organization in mediating charge-transfer and -separation. Mechanistic studies of the type presented here can provide important insights into fundamental principles governing solar energy conversion in next-generation photovoltaic devices.

In-situ Mass Spectrometric Determination of Molecular Structural Evolution at the Solid Electrolyte Interphase in Lithium-Ion Batteries

Energy Technology Data Exchange (ETDEWEB)

Zhu, Zihua; Zhou, Yufan; Yan, Pengfei; Vemuri, Venkata Rama Ses; Xu, Wu; Zhao, Rui; Wang, Xuelin; Thevuthasan, Suntharampillai; Baer, Donald R.; Wang, Chong M.

2015-08-19

Dynamic molecular evolution at solid/liquid electrolyte interface is always a mystery for a rechargeable battery due to the challenge to directly probe/observe the solid/liquid interface under reaction conditions, which in essence appears to be similarly true for all the fields involving solid/liquid phases, such as electrocatalysis, electrodeposition, biofuel conversion, biofilm, and biomineralization, We use in-situ liquid secondary ion mass spectroscopy (SIMS) for the first time to directly observe the molecular structural evolution at the solid electrode/liquid electrolyte interface for a lithium (Li)-ion battery under dynamic operating conditions. We have discovered that the deposition of Li metal on copper electrode leads to the condensation of solvent molecules around the electrode. Chemically, this layer of solvent condensate tends to deplete the salt anion and with low concentration of Li+ ions, which essentially leads to the formation of a lean electrolyte layer adjacent to the electrode and therefore contributes to the overpotential of the cell. This unprecedented molecular level dynamic observation at the solid electrode/liquid electrolyte interface provides vital chemical information that is needed for designing of better battery chemistry for enhanced performance, and ultimately opens new avenues for using liquid SIMS to probe molecular evolution at solid/liquid interface in general.

X-ray structure determination and deuteration of nattokinase.

Science.gov (United States)

Yanagisawa, Yasuhide; Chatake, Toshiyuki; Naito, Sawa; Ohsugi, Tadanori; Yatagai, Chieko; Sumi, Hiroyuki; Kawaguchi, Akio; Chiba-Kamosida, Kaori; Ogawa, Megumi; Adachi, Tatsumi; Morimoto, Yukio

2013-11-01

Nattokinase (NK) is a strong fibrinolytic enzyme, which is produced in abundance by Bacillus subtilis natto. Although NK is a member of the subtilisin family, it displays different substrate specificity when compared with other subtilisins. The results of molecular simulations predict that hydrogen arrangements around Ser221 at the active site probably account for the substrate specificity of NK. Therefore, neutron crystallographic analysis should provide valuable information that reveals the enzymatic mechanism of NK. In this report, the X-ray structure of the non-hydrogen form of undeuterated NK was determined, and the preparation of deuterated NK was successfully achieved. The non-hydrogen NK structure was determined at 1.74 Å resolution. The three-dimensional structures of NK and subtilisin E from Bacillus subtilis DB104 are near identical. Deuteration of NK was carried out by cultivating Bacillus subtilis natto in deuterated medium. The D2O resistant strain of Bacillus subtilis natto was obtained by successive cultivation rounds, in which the concentration of D2O in the medium was gradually increased. NK was purified from the culture medium and its activity was confirmed by the fibrin plate method. The results lay the framework for neutron protein crystallography analysis.

Molecular and crystal structure of 2-((E)-[(4-Methylphenyl)imino]methyl)-4-nitrophenol: A redetermination

International Nuclear Information System (INIS)

Kaynar, Nihal Kan; Tanak, Hasan; Şahin, Songul; Dege, Necmi; Ağar, Erbil; Yavuz, Metin

2016-01-01

The crystal structure of the title compound, C_1_4H_1_2N_2O_3, was recently determined as a mixture of its neutral (OH containing) and zwitterionic (NH containing) forms, in a 0.60 (4): 0.40 (4) ratio using the X-ray determination. In this study, the title compound has been characterized by FT-IR and X-ray diffraction. The redetermination showed that the title compound has only enol (OH) form because of lack of the NH stretching vibration in FT-IR spectrum. In addition, the molecular structure and tautomerism of the title compound have been discussed.

Molecular and crystal structure of 2-((E)-[(4-Methylphenyl)imino]methyl)-4-nitrophenol: A redetermination

Energy Technology Data Exchange (ETDEWEB)

Kaynar, Nihal Kan, E-mail: nihal-kan84@windowslive.com [Ondokuz Mayıs University, Department of Physics, Faculty of Arts and Sciences (Turkey); Tanak, Hasan [Amasya University, Department of Physics, Faculty of Arts and Sciences (Turkey); Şahin, Songul [Ondokuz Mayıs University, Department of Chemistry, Faculty of Arts and Sciences (Turkey); Dege, Necmi [Ondokuz Mayıs University, Department of Physics, Faculty of Arts and Sciences (Turkey); Ağar, Erbil [Ondokuz Mayıs University, Department of Chemistry, Faculty of Arts and Sciences (Turkey); Yavuz, Metin [Ondokuz Mayıs University, Department of Physics, Faculty of Arts and Sciences (Turkey)

2016-03-15

The crystal structure of the title compound, C{sub 14}H{sub 12}N{sub 2}O{sub 3}, was recently determined as a mixture of its neutral (OH containing) and zwitterionic (NH containing) forms, in a 0.60 (4): 0.40 (4) ratio using the X-ray determination. In this study, the title compound has been characterized by FT-IR and X-ray diffraction. The redetermination showed that the title compound has only enol (OH) form because of lack of the NH stretching vibration in FT-IR spectrum. In addition, the molecular structure and tautomerism of the title compound have been discussed.

xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures.

Science.gov (United States)

McGreevy, Ryan; Singharoy, Abhishek; Li, Qufei; Zhang, Jingfen; Xu, Dong; Perozo, Eduardo; Schulten, Klaus

2014-09-01

X-ray crystallography remains the most dominant method for solving atomic structures. However, for relatively large systems, the availability of only medium-to-low-resolution diffraction data often limits the determination of all-atom details. A new molecular dynamics flexible fitting (MDFF)-based approach, xMDFF, for determining structures from such low-resolution crystallographic data is reported. xMDFF employs a real-space refinement scheme that flexibly fits atomic models into an iteratively updating electron-density map. It addresses significant large-scale deformations of the initial model to fit the low-resolution density, as tested with synthetic low-resolution maps of D-ribose-binding protein. xMDFF has been successfully applied to re-refine six low-resolution protein structures of varying sizes that had already been submitted to the Protein Data Bank. Finally, via systematic refinement of a series of data from 3.6 to 7 Å resolution, xMDFF refinements together with electrophysiology experiments were used to validate the first all-atom structure of the voltage-sensing protein Ci-VSP.

Conformational analysis of an acyclic tetrapeptide: ab-initio structure determination from X-ray powder diffraction, Hirshfeld surface analysis and electronic structure.

Science.gov (United States)

Das, Uday; Naskar, Jishu; Mukherjee, Alok Kumar

2015-12-01

A terminally protected acyclic tetrapeptide has been synthesized, and the crystal structure of its hydrated form, Boc-Tyr-Aib-Tyr-Ile-OMe·2H2O (1), has been determined directly from powder X-ray diffraction data. The backbone conformation of tetrapeptide (1) exhibiting two consecutive β-turns is stabilized by two 4 → 1 intramolecular N-H · · · O hydrogen bonds. In the crystalline state, the tetrapeptide molecules are assembled through water-mediated O-H · · · O hydrogen bonds to form two-dimensional molecular sheets, which are further linked by intermolecular C-H · · · O hydrogen bonds into a three-dimensional supramolecular framework. The molecular electrostatic potential (MEP) surface of (1) has been used to supplement the crystallographic observations. The nature of intermolecular interactions in (1) has been analyzed quantitatively through the Hirshfeld surface and two-dimensional fingerprint plot. The DFT optimized molecular geometry of (1) agrees closely with that obtained from the X-ray structure analysis. The present structure analysis of Boc-Tyr-Aib-Tyr-Ile-OMe·2H2 O (1) represents a case where ab-initio crystal structure of an acyclic tetrapeptide with considerable molecular flexibility has been accomplished from laboratory X-ray powder diffraction data. Copyright © 2015 European Peptide Society and John Wiley & Sons, Ltd.

Purification and primary structure determination of human lysosomal dipeptidase.

Science.gov (United States)

Dolenc, Iztok; Mihelic, Marko

2003-02-01

The lysosomal metallopeptidase is an enzyme that acts preferentially on dipeptides with unsubstituted N- and C-termini. Its activity is highest in slightly acidic pH. Here we describe the isolation and characterization of lysosomal dipeptidase from human kidney. The isolated enzyme has the amino-terminal sequence DVAKAIINLAVY and is a homodimer with a molecular mass of 100 kDa. So far no amino acid sequence has been determined for this metallopeptidase. The complete primary structure as deduced from the nucleotide sequence revealed that the isolated dipeptidase is similar to blood plasma glutamate carboxypeptidase.

Photoelectron diffraction from single oriented molecules: Towards ultrafast structure determination of molecules using x-ray free-electron lasers

Science.gov (United States)

Kazama, Misato; Fujikawa, Takashi; Kishimoto, Naoki; Mizuno, Tomoya; Adachi, Jun-ichi; Yagishita, Akira

2013-06-01

We provide a molecular structure determination method, based on multiple-scattering x-ray photoelectron diffraction (XPD) calculations. This method is applied to our XPD data on several molecules having different equilibrium geometries. Then it is confirmed that, by our method, bond lengths and bond angles can be determined with a resolution of less than 0.1 Å and 10∘, respectively. Differently from any other scenario of ultrafast structure determination, we measure the two- or three-dimensional XPD of aligned or oriented molecules in the energy range from 100 to 200 eV with a 4π detection velocity map imaging spectrometer. Thanks to the intense and ultrashort pulse properties of x-ray free-electron lasers, our approach exhibits the most probable method for obtaining ultrafast real-time structural information on small to medium-sized molecules consisting of light elements, i.e., a “molecular movie.”

Tutorial: Determination of thermal boundary resistance by molecular dynamics simulations

Science.gov (United States)

Liang, Zhi; Hu, Ming

2018-05-01

Due to the high surface-to-volume ratio of nanostructured components in microelectronics and other advanced devices, the thermal resistance at material interfaces can strongly affect the overall thermal behavior in these devices. Therefore, the thermal boundary resistance, R, must be taken into account in the thermal analysis of nanoscale structures and devices. This article is a tutorial on the determination of R and the analysis of interfacial thermal transport via molecular dynamics (MD) simulations. In addition to reviewing the commonly used equilibrium and non-equilibrium MD models for the determination of R, we also discuss several MD simulation methods which can be used to understand interfacial thermal transport behavior. To illustrate how these MD models work for various interfaces, we will show several examples of MD simulation results on thermal transport across solid-solid, solid-liquid, and solid-gas interfaces. The advantages and drawbacks of a few other MD models such as approach-to-equilibrium MD and first-principles MD are also discussed.

Molecular Docking, Molecular Dynamics, and Structure-Activity Relationship Explorations of 14-Oxygenated N-Methylmorphinan-6-ones as Potent μ-Opioid Receptor Agonists.

Science.gov (United States)

Noha, Stefan M; Schmidhammer, Helmut; Spetea, Mariana

2017-06-21

Among opioids, morphinans are of major importance as the most effective analgesic drugs acting primarily via μ-opioid receptor (μ-OR) activation. Our long-standing efforts in the field of opioid analgesics from the class of morphinans led to N-methylmorphinan-6-ones differently substituted at positions 5 and 14 as μ-OR agonists inducing potent analgesia and fewer undesirable effects. Herein we present the first thorough molecular modeling study and structure-activity relationship (SAR) explorations aided by docking and molecular dynamics (MD) simulations of 14-oxygenated N-methylmorphinan-6-ones to gain insights into their mode of binding to the μ-OR and interaction mechanisms. The structure of activated μ-OR provides an essential model for how ligand/μ-OR binding is encoded within small chemical differences in otherwise structurally similar morphinans. We reveal important molecular interactions that these μ-agonists share and distinguish them. The molecular docking outcomes indicate the crucial role of the relative orientation of the ligand in the μ-OR binding site, influencing the propensity of critical non-covalent interactions that are required to facilitate ligand/μ-OR interactions and receptor activation. The MD simulations point out minor differences in the tendency to form hydrogen bonds by the 4,5α-epoxy group, along with the tendency to affect the 3-7 lock switch. The emerged SARs reveal the subtle interplay between the substituents at positions 5 and 14 in the morphinan scaffold by enabling the identification of key structural elements that determine the distinct pharmacological profiles. This study provides a significant structural basis for understanding ligand binding and μ-OR activation by the 14-oxygenated N-methylmorphinan-6-ones, which should be useful for guiding drug design.

Methodology for studying molecular and supramolecular structures of coals and carbonaceous materials

Energy Technology Data Exchange (ETDEWEB)

G.B. Skripchenko [Russian Academy of Sciences, Moscow (Russian Federation). Russia Institute for Fossil Fuels - Science and Technology Center for Complex Processing of Solid Fossil Fuels

2009-07-01

Those studying coals have to account for petrographic nonuniformity (the optical structural level), different types of chemical bonding between structural fragments, the existence of aromatic clusters in the organic matter, the appearance of a supramolecular order between aromatic clusters, and further orientation ordering of crystallites under the action of the geological pressure. Combinations of conventional chemical strategies with advanced physicochemical methods, such as IR, NMR, EPR, and X-ray spectroscopy; X-ray diffraction; electronic and scanning microscopy; and some others, are pertinent for structure determination. The appearance of supramolecular structures is a manifestation of molecular-level structural rearrangements, which are characteristic of coals, cokes, pitches, and various pyrolytic carbons. This necessitates the use of optical, electronic, and scanning microscopy along with other chemical methods. The occurrence of mineral components in coals can appreciably limit the resolution of IR spectroscopy and X-ray crystallography.

Rosetta Structure Prediction as a Tool for Solving Difficult Molecular Replacement Problems.

Science.gov (United States)

DiMaio, Frank

2017-01-01

Molecular replacement (MR), a method for solving the crystallographic phase problem using phases derived from a model of the target structure, has proven extremely valuable, accounting for the vast majority of structures solved by X-ray crystallography. However, when the resolution of data is low, or the starting model is very dissimilar to the target protein, solving structures via molecular replacement may be very challenging. In recent years, protein structure prediction methodology has emerged as a powerful tool in model building and model refinement for difficult molecular replacement problems. This chapter describes some of the tools available in Rosetta for model building and model refinement specifically geared toward difficult molecular replacement cases.

A molecular-gap device for specific determination of mercury ions

Science.gov (United States)

Guo, Zheng; Liu, Zhong-Gang; Yao, Xian-Zhi; Zhang, Kai-Sheng; Chen, Xing; Liu, Jin-Huai; Huang, Xing-Jiu

2013-11-01

Specific determination/monitoring of trace mercury ions (Hg2+) in environmental water is of significant importance for drinking safety. Complementarily to conventional inductively coupled plasma mass spectrometry and atomic emission/absorption spectroscopy, several methods, i.e., electrochemical, fluorescent, colorimetric, and surface enhanced Raman scattering approaches, have been developed recently. Despite great success, many inevitably encounter the interferences from other metal ions besides the complicated procedures and sophisticated equipments. Here we present a molecular-gap device for specific determination of trace Hg2+ in both standardized solutions and environmental samples based on conductivity-modulated glutathione dimer. Through a self-assembling technique, a thin film of glutathione monolayer capped Au nanoparticles is introduced into 2.5 μm-gap-electrodes, forming numerous double molecular layer gaps. Notably, the fabricated molecular-gap device shows a specific response toward Hg2+ with a low detection limit actually measured down to 1 nM. Theoretical calculations demonstrate that the specific sensing mechanism greatly depends on the electron transport ability of glutathione dimer bridged by heavy metal ions, which is determined by its frontier molecular orbital, not the binding energy.

Structure determination of butylone as a new psychoactive substance using chiroptical and vibrational spectroscopies.

Science.gov (United States)

Spálovská, Dita; Králík, František; Kohout, Michal; Jurásek, Bronislav; Habartová, Lucie; Kuchař, Martin; Setnička, Vladimír

2018-05-01

Recently, there has been a worldwide substantial increase in the consumption of new psychoactive substances (NPS), compounds that mimic the structure of illicit drugs, such as amphetamines or ecstasy. The producers try to avoid the law by a slight modification of illicit structures, thereby developing dozens of temporarily legal NPS every year. The current trends in the detection and monitoring of such substances demand a fast and reliable analysis. Molecular spectroscopy represents a highly effective tool for the identification of NPS and chiroptical methods can provide further information on their 3D structure, which is the key for the determination of their biological activity. We present the first systematic study of NPS, specifically butylone, combining chiroptical and vibrational spectroscopies with ab initio calculations. According to density functional theory calculations, 6 stable lowest energy conformers of butylone were found and their molecular structure was described. For each conformer, the relative abundance based on the Boltzmann distribution was estimated, their population weighted spectra predicted and compared to the experimental results. Very good agreement between the experimental and the simulated spectra was achieved, which allowed not only the assignment of the absolute configuration, but also a precise description of the molecular structure. © 2018 Wiley Periodicals, Inc.

The utility of comparative models and the local model quality for protein crystal structure determination by Molecular Replacement

Directory of Open Access Journals (Sweden)

Pawlowski Marcin

2012-11-01

Full Text Available Abstract Background Computational models of protein structures were proved to be useful as search models in Molecular Replacement (MR, a common method to solve the phase problem faced by macromolecular crystallography. The success of MR depends on the accuracy of a search model. Unfortunately, this parameter remains unknown until the final structure of the target protein is determined. During the last few years, several Model Quality Assessment Programs (MQAPs that predict the local accuracy of theoretical models have been developed. In this article, we analyze whether the application of MQAPs improves the utility of theoretical models in MR. Results For our dataset of 615 search models, the real local accuracy of a model increases the MR success ratio by 101% compared to corresponding polyalanine templates. On the contrary, when local model quality is not utilized in MR, the computational models solved only 4.5% more MR searches than polyalanine templates. For the same dataset of the 615 models, a workflow combining MR with predicted local accuracy of a model found 45% more correct solution than polyalanine templates. To predict such accuracy MetaMQAPclust, a “clustering MQAP” was used. Conclusions Using comparative models only marginally increases the MR success ratio in comparison to polyalanine structures of templates. However, the situation changes dramatically once comparative models are used together with their predicted local accuracy. A new functionality was added to the GeneSilico Fold Prediction Metaserver in order to build models that are more useful for MR searches. Additionally, we have developed a simple method, AmIgoMR (Am I good for MR?, to predict if an MR search with a template-based model for a given template is likely to find the correct solution.

Molecular structure and thermodynamic predictions to create highly sensitive microRNA biosensors

International Nuclear Information System (INIS)

Larkey, Nicholas E.; Brucks, Corinne N.; Lansing, Shan S.; Le, Sophia D.; Smith, Natasha M.; Tran, Victoria; Zhang, Lulu; Burrows, Sean M.

2016-01-01

Many studies have established microRNAs (miRNAs) as post-transcriptional regulators in a variety of intracellular molecular processes. Abnormal changes in miRNA have been associated with several diseases. However, these changes are sometimes subtle and occur at nanomolar levels or lower. Several biosensing hurdles for in situ cellular/tissue analysis of miRNA limit detection of small amounts of miRNA. Of these limitations the most challenging are selectivity and sensor degradation creating high background signals and false signals. Recently we developed a reporter+probe biosensor for let-7a that showed potential to mitigate false signal from sensor degradation. Here we designed reporter+probe biosensors for miR-26a-2-3p and miR-27a-5p to better understand the effect of thermodynamics and molecular structures of the biosensor constituents on the analytical performance. Signal changes from interactions between Cy3 and Cy5 on the reporters were used to understand structural aspects of the reporter designs. Theoretical thermodynamic values, single stranded conformations, hetero- and homodimerization structures, and equilibrium concentrations of the reporters and probes were used to interpret the experimental observations. Studies of the sensitivity and selectivity revealed 5–9 nM detection limits in the presence and absence of interfering off-analyte miRNAs. These studies will aid in determining how to rationally design reporter+probe biosensors to overcome hurdles associated with highly sensitive miRNA biosensing. - Highlights: • Challenges facing highly sensitive miRNA biosensor designs are addressed. • Thermodynamic and molecular structure design metrics for reporter+probe biosensors are proposed. • The influence of ideal and non-ideal reporter hairpin structures on reporter+probe formation and signal change are discussed. • 5–9 nM limits of detection were observed with no interference from off-analytes.

Molecular structure and thermodynamic predictions to create highly sensitive microRNA biosensors

Energy Technology Data Exchange (ETDEWEB)

Larkey, Nicholas E.; Brucks, Corinne N.; Lansing, Shan S.; Le, Sophia D.; Smith, Natasha M.; Tran, Victoria; Zhang, Lulu; Burrows, Sean M., E-mail: sean.burrows@oregonstate.edu

2016-02-25

Many studies have established microRNAs (miRNAs) as post-transcriptional regulators in a variety of intracellular molecular processes. Abnormal changes in miRNA have been associated with several diseases. However, these changes are sometimes subtle and occur at nanomolar levels or lower. Several biosensing hurdles for in situ cellular/tissue analysis of miRNA limit detection of small amounts of miRNA. Of these limitations the most challenging are selectivity and sensor degradation creating high background signals and false signals. Recently we developed a reporter+probe biosensor for let-7a that showed potential to mitigate false signal from sensor degradation. Here we designed reporter+probe biosensors for miR-26a-2-3p and miR-27a-5p to better understand the effect of thermodynamics and molecular structures of the biosensor constituents on the analytical performance. Signal changes from interactions between Cy3 and Cy5 on the reporters were used to understand structural aspects of the reporter designs. Theoretical thermodynamic values, single stranded conformations, hetero- and homodimerization structures, and equilibrium concentrations of the reporters and probes were used to interpret the experimental observations. Studies of the sensitivity and selectivity revealed 5–9 nM detection limits in the presence and absence of interfering off-analyte miRNAs. These studies will aid in determining how to rationally design reporter+probe biosensors to overcome hurdles associated with highly sensitive miRNA biosensing. - Highlights: • Challenges facing highly sensitive miRNA biosensor designs are addressed. • Thermodynamic and molecular structure design metrics for reporter+probe biosensors are proposed. • The influence of ideal and non-ideal reporter hairpin structures on reporter+probe formation and signal change are discussed. • 5–9 nM limits of detection were observed with no interference from off-analytes.

Synthesis, molecular modeling and structural characterization of vanillin derivatives as antimicrobial agents

Science.gov (United States)

Sun, Juan; Yin, Yong; Sheng, Gui-Hua; Yang, Zhi-Bo; Zhu, Hai-Liang

2013-05-01

Two vanillin derivatives have been designed and synthesized and their biological activities were also evaluated for antimicrobial activity. Their chemical structures are characterized by single crystal X-ray diffraction studies, 1H NMR, MS, and elemental analysis. Structural stabilization of them followed by intramolecular as well as intermolecular H-bonds makes these molecules as perfect examples in molecular recognition with self-complementary donor and acceptor units within a single molecule. Docking simulations have been performed to position compounds into the FtsZ active site to determine their probable binding model. Compound 3a shows the most potent biological activity, which may be a promising antimicrobial leading compound for the further research.

Determining Complex Structures using Docking Method with Single Particle Scattering Data

Directory of Open Access Journals (Sweden)

Haiguang Liu

2017-04-01

Full Text Available Protein complexes are critical for many molecular functions. Due to intrinsic flexibility and dynamics of complexes, their structures are more difficult to determine using conventional experimental methods, in contrast to individual subunits. One of the major challenges is the crystallization of protein complexes. Using X-ray free electron lasers (XFELs, it is possible to collect scattering signals from non-crystalline protein complexes, but data interpretation is more difficult because of unknown orientations. Here, we propose a hybrid approach to determine protein complex structures by combining XFEL single particle scattering data with computational docking methods. Using simulations data, we demonstrate that a small set of single particle scattering data collected at random orientations can be used to distinguish the native complex structure from the decoys generated using docking algorithms. The results also indicate that a small set of single particle scattering data is superior to spherically averaged intensity profile in distinguishing complex structures. Given the fact that XFEL experimental data are difficult to acquire and at low abundance, this hybrid approach should find wide applications in data interpretations.

The impact of chemical structure and molecular packing on the electronic polarisation of fullerene arrays.

Science.gov (United States)

Few, Sheridan; Chia, Cleaven; Teo, Daniel; Kirkpatrick, James; Nelson, Jenny

2017-07-19

Electronic polarisation contributes to the electronic landscape as seen by separating charges in organic materials. The nature of electronic polarisation depends on the polarisability, density, and arrangement of polarisable molecules. In this paper, we introduce a microscopic, coarse-grained model in which we treat each molecule as a polarisable site, and use an array of such polarisable dipoles to calculate the electric field and associated energy of any arrangement of charges in the medium. The model incorporates chemical structure via the molecular polarisability and molecular packing patterns via the structure of the array. We use this model to calculate energies of charge pairs undergoing separation in finite fullerene lattices of different chemical and crystal structures. The effective dielectric constants that we estimate from this approach are in good quantitative agreement with those measured experimentally in C 60 and phenyl-C 61 -butyric acid methyl ester (PCBM) films, but we find significant differences in dielectric constant depending on packing and on direction of separation, which we rationalise in terms of density of polarisable fullerene cages in regions of high field. In general, we find lattices containing molecules of more isotropic polarisability tensors exhibit higher dielectric constants. By exploring several model systems we conclude that differences in molecular polarisability (and therefore, chemical structure) appear to be less important than differences in molecular packing and separation direction in determining the energetic landscape for charge separation. We note that the results are relevant for finite lattices, but not necessarily for infinite systems. We propose that the model could be used to design molecular systems for effective electronic screening.

Using polarized Raman spectroscopy and the pseudospectral method to characterize molecular structure and function

Science.gov (United States)

Weisman, Andrew L.

Electronic structure calculation is an essential approach for determining the structure and function of molecules and is therefore of critical interest to physics, chemistry, and materials science. Of the various algorithms for calculating electronic structure, the pseudospectral method is among the fastest. However, the trade-off for its speed is more up-front programming and testing, and as a result, applications using the pseudospectral method currently lag behind those using other methods. In Part I of this dissertation, we first advance the pseudospectral method by optimizing it for an important application, polarized Raman spectroscopy, which is a well-established tool used to characterize molecular properties. This is an application of particular importance because often the easiest and most economical way to obtain the polarized Raman spectrum of a material is to simulate it; thus, utilization of the pseudospectral method for this purpose will accelerate progress in the determination of molecular properties. We demonstrate that our implementation of Raman spectroscopy using the pseudospectral method results in spectra that are just as accurate as those calculated using the traditional analytic method, and in the process, we derive the most comprehensive formulation to date of polarized Raman intensity formulas, applicable to both crystalline and isotropic systems. Next, we apply our implementation to determine the orientations of crystalline oligothiophenes -- a class of materials important in the field of organic electronics -- achieving excellent agreement with experiment and demonstrating the general utility of polarized Raman spectroscopy for the determination of crystal orientation. In addition, we derive from first-principles a method for using polarized Raman spectra to establish unambiguously whether a uniform region of a material is crystalline or isotropic. Finally, we introduce free, open-source software that allows a user to determine any of a

Process and apparatus for determining molecular spectra

International Nuclear Information System (INIS)

Boesl, U.; Neusser, H.J.; Schlag, E.W.

1984-01-01

A process for determining molecular spectra in unseparated mixtures, in particular unseparated isotopic mixtures, which comprises allowing said mixture to successively flow through a photoreactor which is irradiated by an adjustable-wavelength laser and then through a mass spectrometer wherein the concentration of particles of specified mass is determined by variation of the wavelength of the laser or variation of the mass setting of the mass spectrometer in such a manner that a two-dimensional spectrum results having the parameters of wavelength and mass

Molecular dynamic analysis of the structure of dendrimers

Energy Technology Data Exchange (ETDEWEB)

Canetta, E.; Maino, G. E-mail: maino@bologna.enea.it

2004-01-01

We present main results of molecular dynamics simulations that we have carried out in order to investigate structural properties of polyamidoamine (PAMAM) dendrimers. Obtained data confirm the PAMAM dendrimer structure proposed by experiments, performed by means of X-ray scattering (SAXS) and quasi-elastic light scattering (QELS) techniques.

Molecular dynamic analysis of the structure of dendrimers

International Nuclear Information System (INIS)

Canetta, E.; Maino, G.

2004-01-01

We present main results of molecular dynamics simulations that we have carried out in order to investigate structural properties of polyamidoamine (PAMAM) dendrimers. Obtained data confirm the PAMAM dendrimer structure proposed by experiments, performed by means of X-ray scattering (SAXS) and quasi-elastic light scattering (QELS) techniques

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

Science.gov (United States)

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'…

Effect of structure and molecular weight on properties of pressure sensitive adhesives (PSA) formulated from palm oil based urethane acrylate (POBUA)

International Nuclear Information System (INIS)

Mohd Hilmi Mahmood; Shahrol Najmin Baharom; Rida Tajau; Mek Zah Salleh; Khairul Zaman Mohd Dahlan; Rosley Che Ismail

2004-01-01

Various palm oil (RBD Palm Olein) based urethane acrylate prepolymers (UPs) having different structures and molecular weight were synthesized from palm oil based polyols, diisocyanate compounds and hydroxyl terminated acrylate monomers by following established synthesis procedures described elsewhere. The products (UPs) were compared with each other in term of their molecular weight (MW), viscosities and UV curing performances of pressure sensitive adhesives (PSA) UP based formulations. The molecular structure of diisocyanate compounds and hydroxyl acrylate monomers tend to determine the molecular weight and hence viscosities of the final products of urethane acrylate prepolymers (UP), whereas, the MW of the UP has no direct effects on the coatings and adhesive properties of UV curable UP based PSA. (Author)

RxnFinder: biochemical reaction search engines using molecular structures, molecular fragments and reaction similarity.

Science.gov (United States)

Hu, Qian-Nan; Deng, Zhe; Hu, Huanan; Cao, Dong-Sheng; Liang, Yi-Zeng

2011-09-01

Biochemical reactions play a key role to help sustain life and allow cells to grow. RxnFinder was developed to search biochemical reactions from KEGG reaction database using three search criteria: molecular structures, molecular fragments and reaction similarity. RxnFinder is helpful to get reference reactions for biosynthesis and xenobiotics metabolism. RxnFinder is freely available via: http://sdd.whu.edu.cn/rxnfinder. qnhu@whu.edu.cn.

Isolation, crystallization and crystal structure determination of bovine kidney Na(+),K(+)-ATPase.

Science.gov (United States)

Gregersen, Jonas Lindholt; Mattle, Daniel; Fedosova, Natalya U; Nissen, Poul; Reinhard, Linda

2016-04-01

Na(+),K(+)-ATPase is responsible for the transport of Na(+) and K(+) across the plasma membrane in animal cells, thereby sustaining vital electrochemical gradients that energize channels and secondary transporters. The crystal structure of Na(+),K(+)-ATPase has previously been elucidated using the enzyme from native sources such as porcine kidney and shark rectal gland. Here, the isolation, crystallization and first structure determination of bovine kidney Na(+),K(+)-ATPase in a high-affinity E2-BeF3(-)-ouabain complex with bound magnesium are described. Crystals belonging to the orthorhombic space group C2221 with one molecule in the asymmetric unit exhibited anisotropic diffraction to a resolution of 3.7 Å with full completeness to a resolution of 4.2 Å. The structure was determined by molecular replacement, revealing unbiased electron-density features for bound BeF3(-), ouabain and Mg(2+) ions.

Feasibility of one-shot-per-crystal structure determination using Laue diffraction

Energy Technology Data Exchange (ETDEWEB)

Cornaby, Sterling [School of Applied and Engineering Physics, Cornell University, Ithaca, New York (United States); CHESS (Cornell High Energy Synchrotron Source), Cornell University, Ithaca, New York (United States); Szebenyi, Doletha M. E. [MacCHESS (Macromolecular Diffraction Facilities at CHESS), Cornell University, Ithaca, New York (United States); Smilgies, Detlef-M. [CHESS (Cornell High Energy Synchrotron Source), Cornell University, Ithaca, New York (United States); Schuller, David J.; Gillilan, Richard; Hao, Quan [MacCHESS (Macromolecular Diffraction Facilities at CHESS), Cornell University, Ithaca, New York (United States); Bilderback, Donald H., E-mail: dhb2@cornell.edu [School of Applied and Engineering Physics, Cornell University, Ithaca, New York (United States); CHESS (Cornell High Energy Synchrotron Source), Cornell University, Ithaca, New York (United States)

2010-01-01

Structure determination was successfully carried out using single Laue exposures from a group of lysozyme crystals. The Laue method may be a viable option for collection of one-shot-per-crystal data from microcrystals. Crystal size is an important factor in determining the number of diffraction patterns which may be obtained from a protein crystal before severe radiation damage sets in. As crystal dimensions decrease this number is reduced, eventually falling to one, at which point a complete data set must be assembled using data from multiple crystals. When only a single exposure is to be collected from each crystal, the polychromatic Laue technique may be preferable to monochromatic methods owing to its simultaneous recording of a large number of fully recorded reflections per image. To assess the feasibility of solving structures using single Laue images from multiple crystals, data were collected using a ‘pink’ beam at the CHESS D1 station from groups of lysozyme crystals with dimensions of the order of 20–30 µm mounted on MicroMesh grids. Single-shot Laue data were used for structure determination by molecular replacement and correct solutions were obtained even when as few as five crystals were used.

Feasibility of one-shot-per-crystal structure determination using Laue diffraction

International Nuclear Information System (INIS)

Cornaby, Sterling; Szebenyi, Doletha M. E.; Smilgies, Detlef-M.; Schuller, David J.; Gillilan, Richard; Hao, Quan; Bilderback, Donald H.

2010-01-01

Structure determination was successfully carried out using single Laue exposures from a group of lysozyme crystals. The Laue method may be a viable option for collection of one-shot-per-crystal data from microcrystals. Crystal size is an important factor in determining the number of diffraction patterns which may be obtained from a protein crystal before severe radiation damage sets in. As crystal dimensions decrease this number is reduced, eventually falling to one, at which point a complete data set must be assembled using data from multiple crystals. When only a single exposure is to be collected from each crystal, the polychromatic Laue technique may be preferable to monochromatic methods owing to its simultaneous recording of a large number of fully recorded reflections per image. To assess the feasibility of solving structures using single Laue images from multiple crystals, data were collected using a ‘pink’ beam at the CHESS D1 station from groups of lysozyme crystals with dimensions of the order of 20–30 µm mounted on MicroMesh grids. Single-shot Laue data were used for structure determination by molecular replacement and correct solutions were obtained even when as few as five crystals were used

Mechanical Properties of Nanostructured Materials Determined Through Molecular Modeling Techniques

Science.gov (United States)

Clancy, Thomas C.; Gates, Thomas S.

2005-01-01

The potential for gains in material properties over conventional materials has motivated an effort to develop novel nanostructured materials for aerospace applications. These novel materials typically consist of a polymer matrix reinforced with particles on the nanometer length scale. In this study, molecular modeling is used to construct fully atomistic models of a carbon nanotube embedded in an epoxy polymer matrix. Functionalization of the nanotube which consists of the introduction of direct chemical bonding between the polymer matrix and the nanotube, hence providing a load transfer mechanism, is systematically varied. The relative effectiveness of functionalization in a nanostructured material may depend on a variety of factors related to the details of the chemical bonding and the polymer structure at the nanotube-polymer interface. The objective of this modeling is to determine what influence the details of functionalization of the carbon nanotube with the polymer matrix has on the resulting mechanical properties. By considering a range of degree of functionalization, the structure-property relationships of these materials is examined and mechanical properties of these models are calculated using standard techniques.

Relation between molecular electronic structure and nuclear spin-induced circular dichroism

DEFF Research Database (Denmark)

Štěpánek, Petr; Coriani, Sonia; Sundholm, Dage

2017-01-01

with spatially localized, high-resolution information. To survey the factors relating the molecular and electronic structure to the NSCD signal, we theoretically investigate NSCD of twenty structures of the four most common nucleic acid bases (adenine, guanine, thymine, cytosine). The NSCD signal correlates...... with the spatial distribution of the excited states and couplings between them, reflecting changes in molecular structure and conformation. This constitutes a marked difference to the nuclear magnetic resonance (NMR) chemical shift, which only reflects the local molecular structure in the ground electronic state....... The calculated NSCD spectra are rationalized by means of changes in the electronic density and by a sum-over-states approach, which allows to identify the contributions of the individual excited states. Two separate contributions to NSCD are identified and their physical origins and relative magnitudes...

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

Science.gov (United States)

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

2015-12-05

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

Simultaneous all-optical determination of molecular concentration and extinction coefficient.

Science.gov (United States)

Cho, Byungmoon; Tiwari, Vivek; Jonas, David M

2013-06-04

Absolute molecular number concentration and extinction coefficient are simultaneously determined from linear and nonlinear spectroscopic measurements. This method is based on measurements of absolute femtosecond pump-probe signals. Accounting for pulse propagation, we present a closed form expression for molecular number concentration in terms of absorbance, fluorescence, absolute pump-probe signal, and laser pulse parameters (pulse energy, spectrum, and spatial intensity profile); all quantities are measured optically. As in gravimetric and coulometric determinations of concentration, no standard samples are needed for calibration. The extinction coefficient can then be determined from the absorbance spectrum and the concentration. For fluorescein in basic methanol, the optically determined molar concentrations and extinction coefficients match gravimetric determinations to within 10% for concentrations from 0.032 to 0.540 mM, corresponding to absorbance from 0.06 to 1. In principle, this photonumeric method is extensible to transient chemical species for which other methods are not available.

Detecting Molecular Features of Spectra Mainly Associated with Structural and Non-Structural Carbohydrates in Co-Products from BioEthanol Production Using DRIFT with Uni- and Multivariate Molecular Spectral Analyses

Science.gov (United States)

Yu, Peiqiang; Damiran, Daalkhaijav; Azarfar, Arash; Niu, Zhiyuan

2011-01-01

The objective of this study was to use DRIFT spectroscopy with uni- and multivariate molecular spectral analyses as a novel approach to detect molecular features of spectra mainly associated with carbohydrate in the co-products (wheat DDGS, corn DDGS, blend DDGS) from bioethanol processing in comparison with original feedstock (wheat (Triticum), corn (Zea mays)). The carbohydrates related molecular spectral bands included: A_Cell (structural carbohydrates, peaks area region and baseline: ca. 1485–1188 cm−1), A_1240 (structural carbohydrates, peak area centered at ca. 1240 cm−1 with region and baseline: ca. 1292–1198 cm−1), A_CHO (total carbohydrates, peaks region and baseline: ca. 1187–950 cm−1), A_928 (non-structural carbohydrates, peak area centered at ca. 928 cm−1 with region and baseline: ca. 952–910 cm−1), A_860 (non-structural carbohydrates, peak area centered at ca. 860 cm−1 with region and baseline: ca. 880–827 cm−1), H_1415 (structural carbohydrate, peak height centered at ca. 1415 cm−1 with baseline: ca. 1485–1188 cm−1), H_1370 (structural carbohydrate, peak height at ca. 1370 cm−1 with a baseline: ca. 1485–1188 cm−1). The study shows that the grains had lower spectral intensity (KM Unit) of the cellulosic compounds of A_1240 (8.5 vs. 36.6, P carbohydrate of A_928 (17.3 vs. 2.0) and A_860 (20.7 vs. 7.6) than their co-products from bioethanol processing. There were no differences (P > 0.05) in the peak area intensities of A_Cell (structural CHO) at 1292–1198 cm−1 and A_CHO (total CHO) at 1187–950 cm−1 with average molecular infrared intensity KM unit of 226.8 and 508.1, respectively. There were no differences (P > 0.05) in the peak height intensities of H_1415 and H_1370 (structural CHOs) with average intensities 1.35 and 1.15, respectively. The multivariate molecular spectral analyses were able to discriminate and classify between the corn and corn DDGS molecular spectra, but not wheat and wheat DDGS. This

Noncanonical structures and their thermodynamics of DNA and RNA under molecular crowding: beyond the Watson-Crick double helix.

Science.gov (United States)

Sugimoto, Naoki

2014-01-01

How does molecular crowding affect the stability of nucleic acid structures inside cells? Water is the major solvent component in living cells, and the properties of water in the highly crowded media inside cells differ from that in buffered solution. As it is difficult to measure the thermodynamic behavior of nucleic acids in cells directly and quantitatively, we recently developed a cell-mimicking system using cosolutes as crowding reagents. The influences of molecular crowding on the structures and thermodynamics of various nucleic acid sequences have been reported. In this chapter, we discuss how the structures and thermodynamic properties of nucleic acids differ under various conditions such as highly crowded environments, compartment environments, and in the presence of ionic liquids, and the major determinants of the crowding effects on nucleic acids are discussed. The effects of molecular crowding on the activities of ribozymes and riboswitches on noncanonical structures of DNA- and RNA-like quadruplexes that play important roles in transcription and translation are also described. © 2014 Elsevier Inc. All rights reserved.

Molecular dynamics simulations of H2 adsorption in tetramethyl ammonium lithium phthalocyanine crystalline structures.

Science.gov (United States)

Lamonte, Kevin; Gómez Gualdrón, Diego A; Cabrales-Navarro, Fredy A; Scanlon, Lawrence G; Sandi, Giselle; Feld, William; Balbuena, Perla B

2008-12-11

Tetramethyl ammonium lithium phthalocyanine is explored as a potential material for storage of molecular hydrogen. Density functional theory calculations are used to investigate the molecular structure and the dimer conformation. Additional scans performed to determine the interactions of a H2 molecule located at various distances from the molecular sites are used to generate a simple force field including dipole-induced-dipole interactions. This force field is employed in molecular dynamics simulations to calculate adsorption isotherms at various pressures. The regions of strongest adsorption are quantified as functions of temperature, pressure, and separation between molecules in the adsorbent phase, and compared to the regions of strongest binding energy as given by the proposed force field. It is found that the total adsorption could not be predicted only from the spatial distribution of the strongest binding energies; the available volume is the other contributing factor even if the volume includes regions of much lower binding energy. The results suggest that the complex anion is primarily involved in the adsorption process with molecular hydrogen, whereas the cation serves to provide access for hydrogen adsorption in both sides of the anion molecular plane, and spacing between the planes.

Molecular structure and vibrational spectroscopy of isoproturon

Science.gov (United States)

Vrielynck, L.; Dupuy, N.; Kister, J.; Nowogrocki, G.

2006-05-01

The crystal structure of isoproturon [ N-(4-isopropylphenyl)- N', N'-dimethylurea] has been determined: the compound crystallizes in the space group Pbca with unit cell parameters a=10.186(2) Å, b=11.030(2) Å, c=20.981(4) Å. The structure was solved and refined down to R1=0.0508 and ωR2=0.12470 for 3056 reflections. The crystalline molecular network of this pesticide is stabilized, as for many molecules of the same family, by π-π interactions but especially by a medium-strong N-H⋯C dbnd6 O intermolecular hydrogen bond (2.14 Å). The X-ray parameters were then compared with the results of DFT quantum chemical calculation computed with the GAUSSIAN 94 package. A tentative assignment of the ATR-FT-IR and Raman spectra was proposed supported by vibrational mode calculation and spectroscopic data on benzenic and urea derivatives available in the literature. The presence of a tight band around 3300 cm -1, which can be assigned to the NH bond stretching mode as well as the low frequency position of the amide I band at 1640 cm -1, sensitive to solvent polarity, confirms the existence of a quite strong intermolecular hydrogen bond between neighboring molecules in the crystal of isoproturon.

Molecular structure and correlations in liquid D-2-propanol through neutron diffraction

International Nuclear Information System (INIS)

Sahoo, A.; Sarkar, S.; Joarder, R.N.; Krishna, P.S.R.

2003-01-01

Like t-butanol, 2-propanol molecules are quite big with substantial amount of asymmetry in the structure and so the analysis of the neutron diffraction data is tricky. A modified method of analysis, similar to one for liquid t-butanol, enables extraction of the detailed molecular conformation and intermolecular correlations through neutron diffraction. The pre-peak in the structure function, a signature of chain molecular association together with partially identified inter-molecular correlations yield some information about the nature of possible H-bonded molecular clusters in the liquid state. (author)

Determination of Viscosity-Average Molecular Weight of Chitosan using Intrinsic Viscosity Measurement

International Nuclear Information System (INIS)

Norzita Yacob; Norhashidah Talip; Maznah Mahmud

2011-01-01

Molecular weight of chitosan can be determined by different techniques such as Gel Permeation Chromatography (GPC), Static Light Scattering (SLS) and intrinsic viscosity measurement. Determination of molecular weight by intrinsic viscosity measurement is a simple method for characterization of chitosan. Different concentrations of chitosan were prepared and measurement was done at room temperature. The flow time data was used to calculate the intrinsic viscosity by extrapolating the reduced viscosity to zero concentration. The value of intrinsic viscosity was then recalculated into the viscosity-average molecular weight using Mark-Houwink equation. (author)

Advanced understanding on electronic structure of molecular semiconductors and their interfaces

Science.gov (United States)

Akaike, Kouki

2018-03-01

Understanding the electronic structure of organic semiconductors and their interfaces is critical to optimizing functionalities for electronics applications, by rational chemical design and appropriate combination of device constituents. The unique electronic structure of a molecular solid is characterized as (i) anisotropic electrostatic fields that originate from molecular quadrupoles, (ii) interfacial energy-level lineup governed by simple electrostatics, and (iii) weak intermolecular interactions that make not only structural order but also energy distributions of the frontier orbitals sensitive to atmosphere and interface growth. This article shows an overview on these features with reference to the improved understanding of the orientation-dependent electronic structure, comprehensive mechanisms of molecular doping, and energy-level alignment. Furthermore, the engineering of ionization energy by the control of the electrostatic fields and work function of practical electrodes by contact-induced doping is briefly described for the purpose of highlighting how the electronic structure impacts the performance of organic devices.

New insights into structural determinants of prion protein folding and stability.

Science.gov (United States)

Benetti, Federico; Legname, Giuseppe

2015-01-01

Prions are the etiological agent of fatal neurodegenerative diseases called prion diseases or transmissible spongiform encephalopathies. These maladies can be sporadic, genetic or infectious disorders. Prions are due to post-translational modifications of the cellular prion protein leading to the formation of a β-sheet enriched conformer with altered biochemical properties. The molecular events causing prion formation in sporadic prion diseases are still elusive. Recently, we published a research elucidating the contribution of major structural determinants and environmental factors in prion protein folding and stability. Our study highlighted the crucial role of octarepeats in stabilizing prion protein; the presence of a highly enthalpically stable intermediate state in prion-susceptible species; and the role of disulfide bridge in preserving native fold thus avoiding the misfolding to a β-sheet enriched isoform. Taking advantage from these findings, in this work we present new insights into structural determinants of prion protein folding and stability.

Crystal structure determination and analysis of 11S coconut allergen: Cocosin.

Science.gov (United States)

Vajravijayan, S; Nandhagopal, N; Gunasekaran, K

2017-12-01

Allergy is an abnormal immune response against an innocuous target. Food allergy is an adverse reaction caused by common foods most well-known being those involving peanuts. Apart from mono sensitized food allergy, cross-reactivity with other food allergens is also commonly observed. To understand the phenomenon of cross-reactivity related to immune response, three dimensional structures of the allergens and their antigenic epitopes has to be analysed in detail. The X-ray crystal structure of Cocosin, a common 11S food allergen from coconut, has been determined at 2.2Å resolution using molecular replacement technique. The monomer of 52kDa is composed of two β-jelly roll domains, one with acidic and the other with basic character. The structure shows hexameric association with two trimers facing each other. Though the overall structure of Cocosin is similar to other 11S allergens, the occurrence of experimentally determined epitopes of the peanut allergen Ara h 3 at flexible as well as variable regions could be the reason for the clinically reported result of cross-reactivity that the peanut allergic patients are not sensitized with coconut allergen. Copyright © 2017 Elsevier Ltd. All rights reserved.

Molecular dynamics of the structure and thermodynamics of dusty ...

African Journals Online (AJOL)

The static structure and thermodynamic properties of two-dimensional dusty plasma are analyzed for some typical values of coupling and screening parameters using classical molecular dynamics. Radial distribution function and static structure factor are computed. The radial distribution functions display the typical ...

NMR data-driven structure determination using NMR-I-TASSER in the CASD-NMR experiment

Energy Technology Data Exchange (ETDEWEB)

Jang, Richard [Huazhong University of Science and Technology, School of Software Engineering (China); Wang, Yan [Huazhong University of Science and Technology, School of Life Science and Technology (China); Xue, Zhidong, E-mail: zdxue@hust.edu.cn [Huazhong University of Science and Technology, School of Software Engineering (China); Zhang, Yang, E-mail: zhng@umich.edu [University of Michigan, Department of Computational Medicine and Bioinformatics (United States)

2015-08-15

NMR-I-TASSER, an adaption of the I-TASSER algorithm combining NMR data for protein structure determination, recently joined the second round of the CASD-NMR experiment. Unlike many molecular dynamics-based methods, NMR-I-TASSER takes a molecular replacement-like approach to the problem by first threading the target through the PDB to identify structural templates which are then used for iterative NOE assignments and fragment structure assembly refinements. The employment of multiple templates allows NMR-I-TASSER to sample different topologies while convergence to a single structure is not required. Retroactive and blind tests of the CASD-NMR targets from Rounds 1 and 2 demonstrate that even without using NOE peak lists I-TASSER can generate correct structure topology with 15 of 20 targets having a TM-score above 0.5. With the addition of NOE-based distance restraints, NMR-I-TASSER significantly improved the I-TASSER models with all models having the TM-score above 0.5. The average RMSD was reduced from 5.29 to 2.14 Å in Round 1 and 3.18 to 1.71 Å in Round 2. There is no obvious difference in the modeling results with using raw and refined peak lists, indicating robustness of the pipeline to the NOE assignment errors. Overall, despite the low-resolution modeling the current NMR-I-TASSER pipeline provides a coarse-grained structure folding approach complementary to traditional molecular dynamics simulations, which can produce fast near-native frameworks for atomic-level structural refinement.

Experimental and Computational Approaches to the Molecular Structure of 3-(2-Mercaptopyridine)phthalonitrile

International Nuclear Information System (INIS)

Tanak, Hasan; Koysal, Yavuz; Isik, Samil; Yaman, Hanifi; Ahsen, Vefa

2011-01-01

The compound 3-(2-Mercaptopyridine)phthalonitrile has been synthesized and characterized by IR, UV-vis, and X-ray single-crystal determination. The molecular geometry from X-ray determination of the title compound in the ground state has been compared using the Hartree-Fock (HF) and density functional theory (DFT) with the 6-31G(d) basis set. The calculated results show that the DFT and HF can well reproduce the structure of the title compound. The energetic behavior of the title compound in solvent media was examined using the B3LYP method with the 6-31G(d) basis set by applying the Onsager and polarizable continuum model. Using the TD-DFT and TD-HF methods, electronic absorption spectra of the title compound have been predicted and good agreement with the TD-DFT method and the experimental determination was found. The predicted nonlinear optical properties of the title compound are much greater than those of urea. Besides, molecular electrostatic potential of the title compound were investigated by theoretical calculations. The thermodynamic properties of the compound at different temperatures have been calculated and corresponding relations between the properties and temperature have also been obtained

Experimental and Computational Approaches to the Molecular Structure of 3-(2-Mercaptopyridine)phthalonitrile

Energy Technology Data Exchange (ETDEWEB)

Tanak, Hasan [Amasya University, Amasys (Turkmenistan); Koysal, Yavuz; Isik, Samil [Ondokuz Mayis University, Samsun (Turkmenistan); Yaman, Hanifi; Ahsen, Vefa [Gebze Institute of Technology Department of Chemistry, Gebze-Kocaeli (Turkmenistan)

2011-02-15

The compound 3-(2-Mercaptopyridine)phthalonitrile has been synthesized and characterized by IR, UV-vis, and X-ray single-crystal determination. The molecular geometry from X-ray determination of the title compound in the ground state has been compared using the Hartree-Fock (HF) and density functional theory (DFT) with the 6-31G(d) basis set. The calculated results show that the DFT and HF can well reproduce the structure of the title compound. The energetic behavior of the title compound in solvent media was examined using the B3LYP method with the 6-31G(d) basis set by applying the Onsager and polarizable continuum model. Using the TD-DFT and TD-HF methods, electronic absorption spectra of the title compound have been predicted and good agreement with the TD-DFT method and the experimental determination was found. The predicted nonlinear optical properties of the title compound are much greater than those of urea. Besides, molecular electrostatic potential of the title compound were investigated by theoretical calculations. The thermodynamic properties of the compound at different temperatures have been calculated and corresponding relations between the properties and temperature have also been obtained.

Physiochemical Characteristics and Molecular Structures for Digestible Carbohydrates of Silages.

Science.gov (United States)

Refat, Basim; Prates, Luciana L; Khan, Nazir A; Lei, Yaogeng; Christensen, David A; McKinnon, John J; Yu, Peiqiang

2017-10-18

The main objectives of this study were (1) to assess the magnitude of differences among new barley silage varieties (BS) selected for varying rates of in vitro neutral detergent fiber (NDF) digestibility (ivNDFD; Cowboy BS with higher ivNDFD, Copeland BS with intermediate ivNDFD, and Xena BS with lower ivNDFD) with regard to their carbohydrate (CHO) molecular makeup, CHO chemical fractions, and rumen degradability in dairy cows in comparison with a new corn silage hybrid (Pioneer 7213R) and (2) to quantify the strength and pattern of association between the molecular structures and digestibility of carbohydrates. The carbohydrate-related molecular structure spectral data was measured using advanced vibrational molecular spectroscopy (FT/IR). In comparison to BS, corn silage showed a significantly (P carbohydrates were significantly (P carbohydrate content of the silages. In conclusion, the univariate approach with only one-factor consideration (ivNDFD) might not be a satisfactory method for evaluating and ranking BS quality. FT/IR molecular spectroscopy can be used to evaluate silage quality rapidly, particularly the digestible fiber content.

Molecular structures from density functional calculations with simulated annealing

International Nuclear Information System (INIS)

Jones, R.O.

1991-01-01

The geometrical structure of any aggregate of atoms is one of its basic properties and, in principle, straightforward to predict. One chooses a structure, determines the total energy E of the system of electrons and ions, and repeats the calculation for all possible geometries. The ground state structure is that with the lowest energy. A quantum mechanical calculation of the exact wave function Ψ would lead to the total energy, but this is practicable only in very small molecules. Furthermore, the number of local minima in the energy surface increases dramatically with increasing molecular size. While traditional ab initio methods have had many impressive successes, the difficulties have meant that they have focused on systems with relatively few local minima, or have used experiments or experience to limit the range of geometries studied. On the other hand, calculations for much larger molecules and extended systems are often forced to use simplifying assumptions about the interatomic forces that limit their predictive capability. The approach described here avoids both of these extremes: Total energies of predictive value are calculated without using semi-empirical force laws, and the problem of multiple minima in the energy surface is addressed. The density functional formalism, with a local density approximation for the exchange-correlation energy, allows one to calculate the total energy for a given geometry in an efficient, if approximate, manner. Calculations for heavier elements are not significantly more difficult than for those in the first row and provide an ideal way to study bonding trends. When coupled with finite-temperature molecular dynamics, this formalism can avoid many of the energetically unfavorable minima in the energy surface. We show here that the method leads to surprising and exciting results. (orig.)

Computational tools for experimental determination and theoretical prediction of protein structure

Energy Technology Data Exchange (ETDEWEB)

O`Donoghue, S.; Rost, B.

1995-12-31

This tutorial was one of eight tutorials selected to be presented at the Third International Conference on Intelligent Systems for Molecular Biology which was held in the United Kingdom from July 16 to 19, 1995. The authors intend to review the state of the art in the experimental determination of protein 3D structure (focus on nuclear magnetic resonance), and in the theoretical prediction of protein function and of protein structure in 1D, 2D and 3D from sequence. All the atomic resolution structures determined so far have been derived from either X-ray crystallography (the majority so far) or Nuclear Magnetic Resonance (NMR) Spectroscopy (becoming increasingly more important). The authors briefly describe the physical methods behind both of these techniques; the major computational methods involved will be covered in some detail. They highlight parallels and differences between the methods, and also the current limitations. Special emphasis will be given to techniques which have application to ab initio structure prediction. Large scale sequencing techniques increase the gap between the number of known proteins sequences and that of known protein structures. They describe the scope and principles of methods that contribute successfully to closing that gap. Emphasis will be given on the specification of adequate testing procedures to validate such methods.

Structure determination of cyclo pentane terpene derivatives by crossed NMR and MS techniques

Energy Technology Data Exchange (ETDEWEB)

Pianet, I.; Bourgeois, G. [Bordeaux-1 Univ., 33 - Talence (France); Dolatkhani, M.; Cramail, H.; Deffieux, A. [Centre National de la Recherche Scientifique (CNRS), 33 - Talence (France)

1995-10-01

3 of the 4 stereoisomers of the 1-isopropenyl 2,3-dimethylcyclopentane, obtained from the cracking of 3,7-dimethylocta-1,6-diene, were purified and characterized. Dihedral angles, between the protons of the substituted carbons, have been determined by molecular modelling. Analysis of the NMR and mass spectra allowed us to access to the structure of the different isomers. (authors). 6 refs., 2 tabs.

The Static and Molecular Structure of Barium Dibromide: A Theoretical Study

International Nuclear Information System (INIS)

Guerbuez, H.

2004-01-01

The geometry of barium dibromide was first determined by electron diffraction by Akishin and Spiridov. That study concluded that the molecule is linear, but recent modern electron diffraction and quantum chemical studies of BaBr 2 indicated that its equilibrium geometry is bent. The geometrical parameters, namely, bond lengths and bond angles of barium dibromide were calculated from different levels of computation and experimentally. In this work we have calculated the molecular structure of the BaCl 2 using the Interionic Force model. On the other hand, we have calculated the interionic potentials with two different rigid ion model potentials (RIM) which one is the Vashista-Rahman (VR) semi-empirical potential and second one is the RIM potential with parametrization of Tatlipinar. These two model potential are compared with each other by reproducing the experimental static structure. The structure calculations have been performed by solving numerically the hypernetted chain approximate of liquids

DNA nanotubes for NMR structure determination of membrane proteins.

Science.gov (United States)

Bellot, Gaëtan; McClintock, Mark A; Chou, James J; Shih, William M

2013-04-01

Finding a way to determine the structures of integral membrane proteins using solution nuclear magnetic resonance (NMR) spectroscopy has proved to be challenging. A residual-dipolar-coupling-based refinement approach can be used to resolve the structure of membrane proteins up to 40 kDa in size, but to do this you need a weak-alignment medium that is detergent-resistant and it has thus far been difficult to obtain such a medium suitable for weak alignment of membrane proteins. We describe here a protocol for robust, large-scale synthesis of detergent-resistant DNA nanotubes that can be assembled into dilute liquid crystals for application as weak-alignment media in solution NMR structure determination of membrane proteins in detergent micelles. The DNA nanotubes are heterodimers of 400-nm-long six-helix bundles, each self-assembled from a M13-based p7308 scaffold strand and >170 short oligonucleotide staple strands. Compatibility with proteins bearing considerable positive charge as well as modulation of molecular alignment, toward collection of linearly independent restraints, can be introduced by reducing the negative charge of DNA nanotubes using counter ions and small DNA-binding molecules. This detergent-resistant liquid-crystal medium offers a number of properties conducive for membrane protein alignment, including high-yield production, thermal stability, buffer compatibility and structural programmability. Production of sufficient nanotubes for four or five NMR experiments can be completed in 1 week by a single individual.

Cooperativity in Molecular Dynamics Structural Models and the Dielectric Spectra of 1,2-Ethanediol

Science.gov (United States)

Usacheva, T. M.

2018-05-01

Linear relationships are established between the experimental equilibrium correlation factor and the molecular dynamics (MD) mean value of the O-H···O bond angle and the longitudinal component of the unit vector of the mean statistical dipole moment of the cluster in liquid 1,2-ethanediol (12ED). The achievements of modern MD models in describing the experimental dispersion of the permittivity of 12ED by both continuous and discrete relaxation time spectra are analyzed. The advantage computer MD experiments have over dielectric spectroscopy for calculating relaxation time and determining the molecular diffusion mechanisms of the rearrangement of the network 12ED structure, which is more complex than water, is demonstrated.

Fletcher-Reeves based Particle Swarm Optimization for prediction of molecular structure.

Science.gov (United States)

Agrawal, Shikha; Silakari, Sanjay

2014-04-01

The determination of the most stable conformers of a molecule can be formulated as a global optimization problem. Knowing the stable conformers of a molecule is important because it allows us to understand its properties and behavior based on its structure. The most stable conformation is that involving the global minimum of potential energy. The problem of finding this global minimum is highly complex, and is computationally difficult because of the number of local minima, which grows exponentially with molecular size. In this paper, we propose a hybrid approach combining Particle Swarm Optimization (PSO) and the Fletcher-Reeves algorithm to minimize the potential energy function. The proposed hybrid algorithm is applied to a simplified molecular potential energy function in problems with up to 100 degrees of freedom and also to a realistic potential energy function modeling a pseudoethane molecule. The computational results for both the cases show that the proposed method performs significantly better than the other algorithms. Copyright © 2014 Elsevier Inc. All rights reserved.

Integrated structural biology and molecular ecology of N-cycling enzymes from ammonia-oxidizing archaea.

Science.gov (United States)

Tolar, Bradley B; Herrmann, Jonathan; Bargar, John R; van den Bedem, Henry; Wakatsuki, Soichi; Francis, Christopher A

2017-10-01

Knowledge of the molecular ecology and environmental determinants of ammonia-oxidizing organisms is critical to understanding and predicting the global nitrogen (N) and carbon cycles, but an incomplete biochemical picture hinders in vitro studies of N-cycling enzymes. Although an integrative structural and dynamic characterization at the atomic scale would advance our understanding of function tremendously, structural knowledge of key N-cycling enzymes from ecologically relevant ammonia oxidizers is unfortunately extremely limited. Here, we discuss the challenges and opportunities for examining the ecology of ammonia-oxidizing organisms, particularly uncultivated Thaumarchaeota, through (meta)genome-driven structural biology of the enzymes ammonia monooxygenase (AMO) and nitrite reductase (NirK). © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data

Energy Technology Data Exchange (ETDEWEB)

Lee, Woonghee, E-mail: whlee@nmrfam.wisc.edu [University of Wisconsin-Madison, National Magnetic Resonance Facility at Madison and Biochemistry Department (United States); Petit, Chad M. [University of Alabama at Birmingham, Department of Biochemistry and Molecular Genetics (United States); Cornilescu, Gabriel; Stark, Jaime L.; Markley, John L., E-mail: markley@nmrfam.wisc.edu [University of Wisconsin-Madison, National Magnetic Resonance Facility at Madison and Biochemistry Department (United States)

2016-06-15

We introduce AUDANA (Automated Database-Assisted NOE Assignment), an algorithm for determining three-dimensional structures of proteins from NMR data that automates the assignment of 3D-NOE spectra, generates distance constraints, and conducts iterative high temperature molecular dynamics and simulated annealing. The protein sequence, chemical shift assignments, and NOE spectra are the only required inputs. Distance constraints generated automatically from ambiguously assigned NOE peaks are validated during the structure calculation against information from an enlarged version of the freely available PACSY database that incorporates information on protein structures deposited in the Protein Data Bank (PDB). This approach yields robust sets of distance constraints and 3D structures. We evaluated the performance of AUDANA with input data for 14 proteins ranging in size from 6 to 25 kDa that had 27–98 % sequence identity to proteins in the database. In all cases, the automatically calculated 3D structures passed stringent validation tests. Structures were determined with and without database support. In 9/14 cases, database support improved the agreement with manually determined structures in the PDB and in 11/14 cases, database support lowered the r.m.s.d. of the family of 20 structural models.

The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data

International Nuclear Information System (INIS)

Lee, Woonghee; Petit, Chad M.; Cornilescu, Gabriel; Stark, Jaime L.; Markley, John L.

2016-01-01

We introduce AUDANA (Automated Database-Assisted NOE Assignment), an algorithm for determining three-dimensional structures of proteins from NMR data that automates the assignment of 3D-NOE spectra, generates distance constraints, and conducts iterative high temperature molecular dynamics and simulated annealing. The protein sequence, chemical shift assignments, and NOE spectra are the only required inputs. Distance constraints generated automatically from ambiguously assigned NOE peaks are validated during the structure calculation against information from an enlarged version of the freely available PACSY database that incorporates information on protein structures deposited in the Protein Data Bank (PDB). This approach yields robust sets of distance constraints and 3D structures. We evaluated the performance of AUDANA with input data for 14 proteins ranging in size from 6 to 25 kDa that had 27–98 % sequence identity to proteins in the database. In all cases, the automatically calculated 3D structures passed stringent validation tests. Structures were determined with and without database support. In 9/14 cases, database support improved the agreement with manually determined structures in the PDB and in 11/14 cases, database support lowered the r.m.s.d. of the family of 20 structural models.

An Insight towards Conceptual Understanding: Looking into the Molecular Structures of Compounds

Science.gov (United States)

Uyulgan, Melis Arzu; Akkuzu, Nalan

2016-01-01

The subject of molecular structures is one of the most important and complex subject in chemistry which a majority of the undergraduate students have difficulties to understand its concepts and characteristics correctly. To comprehend the molecular structures and their characteristics the students need to understand related subjects such as Lewis…

Nanocylindrical confinement imparts highest structural order in molecular self-assembly of organophosphonates on aluminum oxide.

Science.gov (United States)

Pathak, Anshuma; Bora, Achyut; Braunschweig, Björn; Meltzer, Christian; Yan, Hongdan; Lemmens, Peter; Daum, Winfried; Schwartz, Jeffrey; Tornow, Marc

2017-05-18

We report the impact of geometrical constraint on intramolecular interactions in self-assembled monolayers (SAMs) of alkylphosphonates grown on anodically oxidized aluminum (AAO). Molecular order in these films was determined by sum frequency generation (SFG) spectroscopy, a more sensitive measure of order than infrared absorption spectroscopy. Using SFG we show that films grown on AAO are, within detection limits, nearly perfectly ordered in an all-trans alkyl chain configuration. In marked contrast, films formed on planar, plasma-oxidized aluminum oxide or α-Al 2 O 3 (0001) are replete with gauche defects. We attribute these differences to the nanocylindrical structure of AAO, which enforces molecular confinement.

Fabrication variables affecting the structure and properties of supported carbon molecular sieve membranes for hydrogen separation

KAUST Repository

Briceño, Kelly

2012-10-01

A high molecular weight polyimide (Matrimid) was used as a precursor for fabricating supported carbon molecular sieve membranes without crack formation at 550-700°C pyrolysis temperature. A one-step polymer (polyimide) coating method as precursor of carbon layer was used without needing a prior modification of a TiO 2 macroporous support. The following fabrication variables were optimized and studied to determine their effect on the carbon structure: polymeric solution concentration, solvent extraction, heating rate and pyrolysis temperature. Two techniques (Thermogravimetric analysis and Raman spectroscopy) were used to determine these effects on final carbon structure. Likewise, the effect of the support was also reported as an additional and important variable in the design of supported carbon membranes. Atomic force microscopy and differential scanning calorimetry quantified the degree of influence. Pure gas permeation tests were performed using CH 4, CO, CO 2 and H 2. The presence of a molecular sieving mechanism was confirmed after defects were plugged with PDMS solution at 12wt%. Gas selectivities higher than Knudsen theoretical values were reached with membranes obtained over 650°C, showing as best values 4.46, 4.70 and 10.62 for H 2/N 2, H 2/CO and H 2/CH 4 ratio, respectively. Permeance values were over 9.82×10 -9mol/(m 2Pas)during pure hydrogen permeation tests. © 2012 Elsevier B.V.

Fabrication variables affecting the structure and properties of supported carbon molecular sieve membranes for hydrogen separation

KAUST Repository

Briceñ o, Kelly; Montané , Daniel; Garcia-Valls, Ricard; Iulianelli, Adolfo; Basile, Angelo

2012-01-01

A high molecular weight polyimide (Matrimid) was used as a precursor for fabricating supported carbon molecular sieve membranes without crack formation at 550-700°C pyrolysis temperature. A one-step polymer (polyimide) coating method as precursor of carbon layer was used without needing a prior modification of a TiO 2 macroporous support. The following fabrication variables were optimized and studied to determine their effect on the carbon structure: polymeric solution concentration, solvent extraction, heating rate and pyrolysis temperature. Two techniques (Thermogravimetric analysis and Raman spectroscopy) were used to determine these effects on final carbon structure. Likewise, the effect of the support was also reported as an additional and important variable in the design of supported carbon membranes. Atomic force microscopy and differential scanning calorimetry quantified the degree of influence. Pure gas permeation tests were performed using CH 4, CO, CO 2 and H 2. The presence of a molecular sieving mechanism was confirmed after defects were plugged with PDMS solution at 12wt%. Gas selectivities higher than Knudsen theoretical values were reached with membranes obtained over 650°C, showing as best values 4.46, 4.70 and 10.62 for H 2/N 2, H 2/CO and H 2/CH 4 ratio, respectively. Permeance values were over 9.82×10 -9mol/(m 2Pas)during pure hydrogen permeation tests. © 2012 Elsevier B.V.

Energy-related atomic and molecular structure and scattering studies: Final report

International Nuclear Information System (INIS)

1987-01-01

The general goals of the DOE research concerned the use of molecular beams techniques in the study of atomic and molecular polarizabilities and the study of the interactions between electrons and highly polar molecules. Both of these goals are directly relevant to the general problem of the role played by long-range forces in atomic and molecular physics. Details related to this motivation can be found in the published literature. Here we will describe in general terms the work performed under DOE sponsorship in the atomic beams laboratory at NYU. Our original intent was to exploit techniques developed at NYU, mainly in the study of simple atomic systems, to the more complex atomic and molecular systems that are related to DOE interests. These included the developing understanding of the structure of molecular systems, particularly of alkali halide molecules, and the study of the interactions of electrons with such molecules. The structure experiments would serve as critical experimental benchmarks for computational techniques on molecular properties, including both molecular wave functions and derivative properties of them, such as vibrational and rotational constants, but in particular of molecular electric dipole polarizabilities. We believe that we have at least to some extent fulfilled these goals. 16 refs., 1 fig

Congruence between morphological and molecular markers inferred from the analysis of the intra-morphotype genetic diversity and the spatial structure of Oxalis tuberosa Mol.

Science.gov (United States)

Pissard, Audrey; Arbizu, Carlos; Ghislain, Marc; Faux, Anne-Michèle; Paulet, Sébastien; Bertin, Pierre

2008-01-01

Oxalis tuberosa is an important crop cultivated in the highest Andean zones. A germplasm collection is maintained ex situ by CIP, which has developed a morphological markers system to classify the accessions into morphotypes, i.e. groups of morphologically identical accessions. However, their genetic uniformity is currently unknown. The ISSR technique was used in two experiments to determine the relationships between both morphological and molecular markers systems. The intra-morphotype genetic diversity, the spatial structures of the diversity and the congruence between both markers systems were determined. In the first experience, 44 accessions representing five morphotypes, clearly distinct from each other, were analyzed. At the molecular level, the accessions exactly clustered according to their morphotypes. However, a genetic variability was observed inside each morphotype. In the second experiment, 34 accessions gradually differing from each other on morphological base were analyzed. The morphological clustering showed no geographical structure. On the opposite, the molecular analysis showed that the genetic structure was slightly related to the collection site. The correlation between both markers systems was weak but significant. The lack of perfect congruence between morphological and molecular data suggests that the morphological system may be useful for the morphotypes management but is not appropriate to study the genetic structure of the oca. The spatial structure of the genetic diversity can be related to the evolution of the species and the discordance between the morphological and molecular structures may result from similar selection pressures at different places leading to similar forms with a different genetic background.

Electrochemical sensor based on magnetic molecularly imprinted nanoparticles modified magnetic electrode for determination of Hb.

Science.gov (United States)

Sun, Binghua; Ni, Xinjiong; Cao, Yuhua; Cao, Guangqun

2017-05-15

A fast and selective electrochemical sensor for determination of hemoglobin (Hb) was developed based on magnetic molecularly imprinted nanoparticles modified on the magnetic glassy carbon electrode. The nanoparticles Fe 3 O 4 @SiO 2 with a magnetic core and a molecularly imprinted shell had regular structures and good monodispersity. Hb could be determined directly by electrochemical oxidization with the modified electrode. A magnetic field increased electrochemical response to Hb by two times. Imprinting Hb on the surface of Fe 3 O 4 @SiO 2 shortened the response time within 7min. Under optimum conditions, the imprinting factor toward the non-imprinted sensor was 2.8, and the separation factor of Hb to horseradish peroxidase was 2.6. The oxidation peak current had a linear relationship with Hb concentration ranged from 0.005mg/ml to 0.1mg/ml with a detection limit (S/N =3) of 0.0010mg/ml. The sensors were successfully applied to analysis of Hb in whole blood samples with recoveries between 95.7% and 105%. Copyright © 2016 Elsevier B.V. All rights reserved.

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

Science.gov (United States)

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) 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 is needed to quantify the relationship between lipid molecular structure changes and functionality/availability.

Structural investigation of water-acetonitrile mixtures: An ab initio, molecular dynamics and X-ray diffraction study

International Nuclear Information System (INIS)

Bako, Imre; Megyes, Tuende; Palinkas, Gabor

2005-01-01

In this work, we present a study on water-acetonitrile (AN) mixtures by molecular dynamics ab initio and X-ray diffraction techniques. Comparison of the experimental total G(r) functions of the mixtures with the results of molecular dynamics simulation shows an overall good agreement. The properties of hydrogen bonded clusters (water clusters, and water-AN clusters) in these mixtures have been determined. Two different types of AN-water dimers were identified by ab initio quantum chemical calculation. One of these structures proved to be a true H-bonded dimer and the other a dipole bound dimer

Molecular orientation and electronic structure at organic heterojunction interfaces

Energy Technology Data Exchange (ETDEWEB)

Zhong, Shu [Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543 Singapore (Singapore); Zhong, Jian Qiang; Wee, Andrew T.S. [Department of Physics, National University of Singapore, 2 Science Drive 3, 117542 Singapore (Singapore); Chen, Wei, E-mail: phycw@nus.edu.sg [Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543 Singapore (Singapore); Department of Physics, National University of Singapore, 2 Science Drive 3, 117542 Singapore (Singapore); National University of Singapore (Suzhou) Research Institute, Suzhou (China)

2015-10-01

Highlights: • Molecular orientation at the organic heterojunction interfaces. • Energy level alignments at the organic heterojunction interfaces. • Gap-states mediated interfacial energy level alignment. - Abstract: Due to the highly anisotropic nature of π-conjugated molecules, the molecular orientation in organic thin films can significantly affect light absorption, charge transport, energy level alignment (ELA) and hence device performance. Synchrotron-based near-edge X-ray absorption fine structure (NEXAFS) spectroscopy represents a powerful technique for probing molecular orientation. The aim of this review paper is to provide a balanced assessment on the investigation of molecular orientation at the organic–organic heterojunction (OOH) interface by NEXAFS, as well as the gap-states mediated orientation dependent energy level alignment at OOH interfaces. We highlight recent progress in elucidating molecular orientation at OOH interfaces dominated by various interfacial interactions, gap-states controlled orientation dependent energy level alignments at OOH interfaces, and the manipulations of molecular orientation and ELA in OOH.

Definition of molecular structure: by choice or by appeal to observation?

Science.gov (United States)

Bader, Richard F W

2010-07-22

There are two schools of thought in chemistry: one derived from the valence bond and molecular orbital models of bonding, the other appealing directly to the measurable electron density and the quantum mechanical theorems that determine its behavior, an approach embodied in the quantum theory of atoms in molecules, QTAIM. No one questions the validity of the former approach, and indeed molecular orbital models and QTAIM play complementary roles, the models finding expression in the principles of physics. However, some orbital proponents step beyond the models to impose their personal stamp on their use in interpretive chemistry, by denying the possible existence of a physical basis for the concepts of chemistry. This places them at odds with QTAIM, whose very existence stems from the discovery in the observable topology of the electron density, the definitions of atoms, of the bonding between atoms and hence of molecular structure. Relating these concepts to the electron density provides the necessary link for their ultimate quantum definition. This paper explores in depth the possible causes of the difficulties some have in accepting the quantum basis of structure beginning with the arguments associated with the acceptance of a "bond path" as a criterion for bonding. This identification is based on the finding that all classical structures may be mapped onto molecular graphs consisting of bond paths linking neighboring atoms, a mapping that has no known exceptions and one that is further bolstered by the finding that there are no examples of "missing bond paths". Difficulties arise when the quantum concept is applied to systems that are not amenable to the classical models of bonding. Thus one is faced with the recurring dilemma of science, of having to escape the constraints of a model that requires a change in the existing paradigm, a process that has been in operation since the discovery of new and novel structures necessitated the extension of the Lewis model

Effect of steam explosion pre-treatment on molecular structure of ...

African Journals Online (AJOL)

Purpose: To examine the effect of steam-explosion (SE) strength on the molecular ... pressure-holding time on the molecular structure of the sweet potato starch were ... overheated liquid and then their pores are filled ... expands and exerts pressure on the cell walls, ... oscillation using distilled water as the dispersing agent.

New Diethyl Ammonium Salt of Thiobarbituric Acid Derivative: Synthesis, Molecular Structure Investigations and Docking Studies

Directory of Open Access Journals (Sweden)

Assem Barakat

2015-11-01

Full Text Available The synthesis of the new diethyl ammonium salt of diethylammonium(E-5-(1,5-bis(4-fluorophenyl-3-oxopent-4-en-1-yl-1,3-diethyl-4,6-dioxo-2-thioxohexaydropyrimidin-5-ide 3 via a regioselective Michael addition of N,N-diethylthiobarbituric acid 1 to dienone 2 is described. In 3, the carboanion of the thiobarbituric moiety is stabilized by the strong intramolecular electron delocalization with the adjacent carbonyl groups and so the reaction proceeds without any cyclization. The molecular structure investigations of 3 were determined by single-crystal X-ray diffraction as well as DFT computations. The theoretically calculated (DFT/B3LYP geometry agrees well with the crystallographic data. The effect of fluorine replacement by chlorine atoms on the molecular structure aspects were investigated using DFT methods. Calculated electronic spectra showed a bathochromic shift of the π-π* transition when fluorine is replaced by chlorine. Charge decomposition analyses were performed to study possible interaction between the different fragments in the studied systems. Molecular docking simulations examining the inhibitory nature of the compound show an anti-diabetic activity with Pa (probability of activity value of 0.229.

Structure of the 30 kDa HIV-1 RNA Dimerization Signal by a Hybrid Cryo-EM, NMR, and Molecular Dynamics Approach.

Science.gov (United States)

Zhang, Kaiming; Keane, Sarah C; Su, Zhaoming; Irobalieva, Rossitza N; Chen, Muyuan; Van, Verna; Sciandra, Carly A; Marchant, Jan; Heng, Xiao; Schmid, Michael F; Case, David A; Ludtke, Steven J; Summers, Michael F; Chiu, Wah

2018-03-06

Cryoelectron microscopy (cryo-EM) and nuclear magnetic resonance (NMR) spectroscopy are routinely used to determine structures of macromolecules with molecular weights over 65 and under 25 kDa, respectively. We combined these techniques to study a 30 kDa HIV-1 dimer initiation site RNA ([DIS] 2 ; 47 nt/strand). A 9 Å cryo-EM map clearly shows major groove features of the double helix and a right-handed superhelical twist. Simulated cryo-EM maps generated from time-averaged molecular dynamics trajectories (10 ns) exhibited levels of detail similar to those in the experimental maps, suggesting internal structural flexibility limits the cryo-EM resolution. Simultaneous inclusion of the cryo-EM map and 2 H-edited NMR-derived distance restraints during structure refinement generates a structure consistent with both datasets and supporting a flipped-out base within a conserved purine-rich bulge. Our findings demonstrate the power of combining global and local structural information from these techniques for structure determination of modest-sized RNAs. Copyright © 2018 Elsevier Ltd. All rights reserved.

Prediction of retention in micellar electrokinetic chromatography based on molecular structural descriptors by using the heuristic method

International Nuclear Information System (INIS)

Liu Huanxiang; Yao Xiaojun; Liu Mancang; Hu Zhide; Fan Botao

2006-01-01

Based on calculated molecular descriptors from the solutes' structure alone, the micelle-water partition coefficients of 103 solutes in micellar electrokinetic chromatography (MEKC) were predicted using the heuristic method (HM). At the same time, in order to show the influence of different molecular descriptors on the micelle-water partition of solute and to well understand the retention mechanism in MEKC, HM was used to build several multivariable linear models using different numbers of molecular descriptors. The best 6-parameter model gave the following results: the square of correlation coefficient R 2 was 0.958 and the mean relative error was 3.98%, which proved that the predictive values were in good agreement with the experimental results. From the built model, it can be concluded that the hydrophobic, H-bond, polar interactions of solutes with the micellar and aqueous phases are the main factors that determine their partitioning behavior. In addition, this paper provided a simple, fast and effective method for predicting the retention of the solutes in MEKC from their structures and gave some insight into structural features related to the retention of the solutes

Catecholaminergic systems in stress: structural and molecular genetic approaches.

Science.gov (United States)

Kvetnansky, Richard; Sabban, Esther L; Palkovits, Miklos

2009-04-01

Stressful stimuli evoke complex endocrine, autonomic, and behavioral responses that are extremely variable and specific depending on the type and nature of the stressors. We first provide a short overview of physiology, biochemistry, and molecular genetics of sympatho-adrenomedullary, sympatho-neural, and brain catecholaminergic systems. Important processes of catecholamine biosynthesis, storage, release, secretion, uptake, reuptake, degradation, and transporters in acutely or chronically stressed organisms are described. We emphasize the structural variability of catecholamine systems and the molecular genetics of enzymes involved in biosynthesis and degradation of catecholamines and transporters. Characterization of enzyme gene promoters, transcriptional and posttranscriptional mechanisms, transcription factors, gene expression and protein translation, as well as different phases of stress-activated transcription and quantitative determination of mRNA levels in stressed organisms are discussed. Data from catecholamine enzyme gene knockout mice are shown. Interaction of catecholaminergic systems with other neurotransmitter and hormonal systems are discussed. We describe the effects of homotypic and heterotypic stressors, adaptation and maladaptation of the organism, and the specificity of stressors (physical, emotional, metabolic, etc.) on activation of catecholaminergic systems at all levels from plasma catecholamines to gene expression of catecholamine enzymes. We also discuss cross-adaptation and the effect of novel heterotypic stressors on organisms adapted to long-term monotypic stressors. The extra-adrenal nonneuronal adrenergic system is described. Stress-related central neuronal regulatory circuits and central organization of responses to various stressors are presented with selected examples of regulatory molecular mechanisms. Data summarized here indicate that catecholaminergic systems are activated in different ways following exposure to distinct

Effect of thermal processing on estimated metabolizable protein supply to dairy cattle from camelina seeds: relationship with protein molecular structural changes.

Science.gov (United States)

Peng, Quanhui; Khan, Nazir A; Wang, Zhisheng; Zhang, Xuewei; Yu, Peiqiang

2014-08-20

This study evaluated the effect of thermal processing on the estimated metabolizable protein (MP) supply to dairy cattle from camelina seeds (Camelina sativa L. Crantz) and determined the relationship between heat-induced changes in protein molecular structural characteristics and the MP supply. Seeds from two camelina varieties were sampled in two consecutive years and were either kept raw or were heated in an autoclave (moist heating) or in an air-draft oven (dry heating) at 120 °C for 1 h. The MP supply to dairy cattle was modeled by three commonly used protein evaluation systems. The protein molecular structures were analyzed by Fourier transform/infrared-attenuated total reflectance molecular spectroscopy. The results showed that both the dry and moist heating increased the contents of truly absorbable rumen-undegraded protein (ARUP) and total MP and decreased the degraded protein balance (DPB). However, the moist-heated camelina seeds had a significantly higher (P seeds. The regression equations showed that intensities of the protein molecular structural bands can be used to estimate the contents of ARUP, MP, and DPB with high accuracy (R(2) > 0.70). These results show that protein molecular structural characteristics can be used to rapidly assess the MP supply to dairy cattle from raw and heat-treated camelina seeds.

The structure of Lactococcus lactis thioredoxin reductase reveals molecular features of photo-oxidative damage

DEFF Research Database (Denmark)

Skjoldager, Nicklas; Bang, Maria Blanner; Rykær, Martin

2017-01-01

The NADPH-dependent homodimeric flavoenzyme thioredoxin reductase (TrxR) provides reducing equivalents to thioredoxin, a key regulator of various cellular redox processes. Crystal structures of photo-inactivated thioredoxin reductase (TrxR) from the Gram-positive bacterium Lactococcus lactis have...... been determined. These structures reveal novel molecular features that provide further insight into the mechanisms behind the sensitivity of this enzyme toward visible light. We propose that a pocket on the si-face of the isoalloxazine ring accommodates oxygen that reacts with photo-excited FAD...... thus be a widespread feature among bacterial TrxR with the described characteristics, which affords applications in clinical photo-therapy of drug-resistant bacteria....

Locking the Elbow: Improved Antibody Fab Fragments as Chaperones for Structure Determination.

Science.gov (United States)

Bailey, Lucas J; Sheehy, Kimberly M; Dominik, Pawel K; Liang, Wenguang G; Rui, Huan; Clark, Michael; Jaskolowski, Mateusz; Kim, Yejoon; Deneka, Dawid; Tang, Wei-Jen; Kossiakoff, Anthony A

2018-02-02

Antibody Fab fragments have been exploited with significant success to facilitate the structure determination of challenging macromolecules as crystallization chaperones and as molecular fiducial marks for single particle cryo-electron microscopy approaches. However, the inherent flexibility of the "elbow" regions, which link the constant and variable domains of the Fab, can introduce disorder and thus diminish their effectiveness. We have developed a phage display engineering strategy to generate synthetic Fab variants that significantly reduces elbow flexibility, while maintaining their high affinity and stability. This strategy was validated using previously recalcitrant Fab-antigen complexes where introduction of an engineered elbow region enhanced crystallization and diffraction resolution. Furthermore, incorporation of the mutations appears to be generally portable to other synthetic antibodies and may serve as a universal strategy to enhance the success rates of Fabs as structure determination chaperones. Copyright © 2017 Elsevier Ltd. All rights reserved.

A modified time-of-flight method for precise determination of high speed ratios in molecular beams

Energy Technology Data Exchange (ETDEWEB)

Salvador Palau, A.; Eder, S. D., E-mail: sabrina.eder@uib.no; Kaltenbacher, T.; Samelin, B.; Holst, B. [Department of Physics and Technology, University of Bergen, Allégaten 55, 5007 Bergen (Norway); Bracco, G. [Department of Physics and Technology, University of Bergen, Allégaten 55, 5007 Bergen (Norway); CNR-IMEM, Department of Physics, University of Genova, V. Dodecaneso 33, 16146 Genova (Italy)

2016-02-15

Time-of-flight (TOF) is a standard experimental technique for determining, among others, the speed ratio S (velocity spread) of a molecular beam. The speed ratio is a measure for the monochromaticity of the beam and an accurate determination of S is crucial for various applications, for example, for characterising chromatic aberrations in focussing experiments related to helium microscopy or for precise measurements of surface phonons and surface structures in molecular beam scattering experiments. For both of these applications, it is desirable to have as high a speed ratio as possible. Molecular beam TOF measurements are typically performed by chopping the beam using a rotating chopper with one or more slit openings. The TOF spectra are evaluated using a standard deconvolution method. However, for higher speed ratios, this method is very sensitive to errors related to the determination of the slit width and the beam diameter. The exact sensitivity depends on the beam diameter, the number of slits, the chopper radius, and the chopper rotation frequency. We present a modified method suitable for the evaluation of TOF measurements of high speed ratio beams. The modified method is based on a systematic variation of the chopper convolution parameters so that a set of independent measurements that can be fitted with an appropriate function are obtained. We show that with this modified method, it is possible to reduce the error by typically one order of magnitude compared to the standard method.

Building bridges between cellular and molecular structural biology.

Science.gov (United States)

Patwardhan, Ardan; Brandt, Robert; Butcher, Sarah J; Collinson, Lucy; Gault, David; Grünewald, Kay; Hecksel, Corey; Huiskonen, Juha T; Iudin, Andrii; Jones, Martin L; Korir, Paul K; Koster, Abraham J; Lagerstedt, Ingvar; Lawson, Catherine L; Mastronarde, David; McCormick, Matthew; Parkinson, Helen; Rosenthal, Peter B; Saalfeld, Stephan; Saibil, Helen R; Sarntivijai, Sirarat; Solanes Valero, Irene; Subramaniam, Sriram; Swedlow, Jason R; Tudose, Ilinca; Winn, Martyn; Kleywegt, Gerard J

2017-07-06

The integration of cellular and molecular structural data is key to understanding the function of macromolecular assemblies and complexes in their in vivo context. Here we report on the outcomes of a workshop that discussed how to integrate structural data from a range of public archives. The workshop identified two main priorities: the development of tools and file formats to support segmentation (that is, the decomposition of a three-dimensional volume into regions that can be associated with defined objects), and the development of tools to support the annotation of biological structures.

Molecular structure of the lecithin ripple phase

Science.gov (United States)

de Vries, Alex H.; Yefimov, Serge; Mark, Alan E.; Marrink, Siewert J.

2005-04-01

Molecular dynamics simulations of lecithin lipid bilayers in water as they are cooled from the liquid crystalline phase show the spontaneous formation of rippled bilayers. The ripple consists of two domains of different length and orientation, connected by a kink. The organization of the lipids in one domain of the ripple is found to be that of a splayed gel; in the other domain the lipids are gel-like and fully interdigitated. In the concave part of the kink region between the domains the lipids are disordered. The results are consistent with the experimental information available and provide an atomic-level model that may be tested by further experiments. molecular dynamics simulation | structural model

Application of molecular spectroscopy to the determination of organic structures

International Nuclear Information System (INIS)

Leicknam, J.P.

1976-01-01

Some brief accounts are presented followed by a discussion about various physico-chemical techniques: Raman spectrometry, infrared spectrometry, resonance Raman spectrometry, conformational analysis and polarized Rayleigh diffusion. Applications of the Nuclear Magnetic Resonance to nucleotide structure in aqueous solution are described as well as some applications of neutron scattering to the study of organic structures [fr

Hamiltonian flow over saddles for exploring molecular phase space structures

Science.gov (United States)

Farantos, Stavros C.

2018-03-01

Despite using potential energy surfaces, multivariable functions on molecular configuration space, to comprehend chemical dynamics for decades, the real happenings in molecules occur in phase space, in which the states of a classical dynamical system are completely determined by the coordinates and their conjugate momenta. Theoretical and numerical results are presented, employing alanine dipeptide as a model system, to support the view that geometrical structures in phase space dictate the dynamics of molecules, the fingerprints of which are traced by following the Hamiltonian flow above saddles. By properly selecting initial conditions in alanine dipeptide, we have found internally free rotor trajectories the existence of which can only be justified in a phase space perspective. This article is part of the theme issue `Modern theoretical chemistry'.

Ion-molecular equilibria and activity determination in the RbF-ZrF4 system

International Nuclear Information System (INIS)

Skokan, E.V.; Nikitin, M.I.; Sorokin, I.D.; Korenev, Yu.M.; Sidorov, L.N.

1983-01-01

Activity of zirconium tetrofluoride in 100-33.3 mol % ZrF 4 concentration range was determined during isothermal evaporation of samples of different initial composition of RbF-ZrF 4 system, using ion-molecular equilibrium method. It became possible, using the exchange ion-molecular reactions to determine ZrF 4 activity approximately 10 -10 in the region of state diagram of RbF-ZrF 4 system, adjoining to rubidium fluoride. The comparative analysis of results, obtained by the methods of isothermal evaporation, ion-molecular equilibria is given; the advantages and restrictions of ion-molecular equilibrium method are presented

Fine- and hyperfine-structure effects in molecular photoionization. II. Resonance-enhanced multiphoton ionization and hyperfine-selective generation of molecular cations

Energy Technology Data Exchange (ETDEWEB)

Germann, Matthias; Willitsch, Stefan, E-mail: stefan.willitsch@unibas.ch [Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel (Switzerland)

2016-07-28

Resonance-enhanced multiphoton ionization (REMPI) is a widely used technique for studying molecular photoionization and producing molecular cations for spectroscopy and dynamics studies. Here, we present a model for describing hyperfine-structure effects in the REMPI process and for predicting hyperfine populations in molecular ions produced by this method. This model is a generalization of our model for fine- and hyperfine-structure effects in one-photon ionization of molecules presented in Paper I [M. Germann and S. Willitsch, J. Chem. Phys. 145, 044314 (2016)]. This generalization is achieved by covering two main aspects: (1) treatment of the neutral bound-bound transition including the hyperfine structure that makes up the first step of the REMPI process and (2) modification of our ionization model to account for anisotropic populations resulting from this first excitation step. Our findings may be used for analyzing results from experiments with molecular ions produced by REMPI and may serve as a theoretical background for hyperfine-selective ionization experiments.

Molecular Bases and Phenotypic Determinants of Aromatase Excess Syndrome

Directory of Open Access Journals (Sweden)

Maki Fukami

2012-01-01

Full Text Available Aromatase excess syndrome (AEXS is a rare autosomal dominant disorder characterized by gynecomastia. This condition is caused by overexpression of CYP19A1 encoding aromatase, and three types of cryptic genomic rearrangement around CYP19A1, that is, duplications, deletions, and inversions, have been identified in AEXS. Duplications appear to have caused CYP19A1 overexpression because of an increased number of physiological promoters, whereas deletions and inversions would have induced wide CYP19A1 expression due to the formation of chimeric genes consisting of a noncoding exon(s of a neighboring gene and CYP19A1 coding exons. Genotype-phenotype analysis implies that phenotypic severity of AEXS is primarily determined by the expression pattern of CYP19A1 and the chimeric genes and by the structural property of the fused exons with a promoter function (i.e., the presence or the absence of a natural translation start codon. These results provide novel information about molecular mechanisms of human genetic disorders and biological function of estrogens.

Electronic structure of surface-supported bis(phthalocyaninato) terbium(III) single molecular magnets.

Science.gov (United States)

Vitali, Lucia; Fabris, Stefano; Conte, Adriano Mosca; Brink, Susan; Ruben, Mario; Baroni, Stefano; Kern, Klaus

2008-10-01

The electronic structure of isolated bis(phthalocyaninato) terbium(III) molecules, a novel single-molecular-magnet (SMM), supported on the Cu(111) surface has been characterized by density functional theory and scanning tunneling spectroscopy. These studies reveal that the interaction with the metal surface preserves both the molecular structure and the large spin magnetic moment of the metal center. The 4f electron states are not perturbed by the adsorption while a strong molecular/metal interaction can induce the suppression of the minor spin contribution delocalized over the molecular ligands. The calculations show that the inherent spin magnetic moment of the molecule is only weakly affected by the interaction with the surface and suggest that the SMM character might be preserved.

Production, purification, crystallization and structure determination of H-1 Parvovirus

International Nuclear Information System (INIS)

Halder, Sujata; Nam, Hyun-Joo; Govindasamy, Lakshmanan; Vogel, Michèle; Dinsart, Christiane; Salomé, Nathalie; McKenna, Robert; Agbandje-McKenna, Mavis

2012-01-01

The production, purification, crystallization and crystallographic analysis of H-1 Parvovirus, a gene-therapy vector, are reported. Crystals of H-1 Parvovirus (H-1PV), an antitumor gene-delivery vector, were obtained for DNA-containing capsids and diffracted X-rays to 2.7 Å resolution using synchrotron radiation. The crystals belonged to the monoclinic space group P2 1 , with unit-cell parameters a = 255.4, b = 350.4, c = 271.6 Å, β = 90.34°. The unit cell contained two capsids, with one capsid per crystallographic asymmetric unit. The H-1PV structure has been determined by molecular replacement and is currently being refined

Rotational temperature determinations in molecular gas lasers

International Nuclear Information System (INIS)

Weaver, L.A.; Taylor, L.H.; Denes, L.J.

1975-01-01

The small-signal gain expressions for vibrational-rotational transitions are examined in detail to determine possible methods of extracting the rotational temperature from experimental gain measurements in molecular gas lasers. Approximate values of T/subr/ can be deduced from the rotational quantum numbers for which the P- and R-branch gains are maximum. Quite accurate values of T/subr/ and the population inversion density (n/subv//sub prime/-n/subv//sub double-prime/) can be determined by fitting data to suitably linearized gain relationships, or by performing least-squares fits of the P- and R-branch experimental data to the full gain expressions. Experimental gain measurements for 15 P-branch and 12 R-branch transitions in the 10.4-μm CO 2 band have been performed for pulsed uv-preionized laser discharges in CO 2 : N 2 : He=1 : 2 : 3 mixtures at 600 Torr. These data are subjected to the several gain analyses described herein, yielding a rotational temperature of 401plus-or-minus10 degreeK and an inversion density of (3.77plus-or-minus0.07) times10 17 cm -3 for conditions of maximum gain. These techniques provide accurate values of the gas temperature in molecular gas lasers with excellent temporal and spatial resolution, and should be useful in extending the conversion efficiency and arcing limits of high-energy electrically exc []ted lasers

The fundamentals behind solving for unknown molecular structures using computer-assisted structure elucidation: a free software package at the undergraduate and graduate levels.

Science.gov (United States)

Moser, Arvin; Pautler, Brent G

2016-05-15

The successful elucidation of an unknown compound's molecular structure often requires an analyst with profound knowledge and experience of advanced spectroscopic techniques, such as Nuclear Magnetic Resonance (NMR) spectroscopy and mass spectrometry. The implementation of Computer-Assisted Structure Elucidation (CASE) software in solving for unknown structures, such as isolated natural products and/or reaction impurities, can serve both as elucidation and teaching tools. As such, the introduction of CASE software with 112 exercises to train students in conjunction with the traditional pen and paper approach will strengthen their overall understanding of solving unknowns and explore of various structural end points to determine the validity of the results quickly. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Molecular Descriptors Family on Structure Activity Relationships 1. Review of the Methodology

Directory of Open Access Journals (Sweden)

Lorentz JÄNTSCHI

2005-01-01

Full Text Available This review cumulates the knowledge about the use of Molecular Descriptors Family usage on Structure Activity Relationships. The methodology is augmented through the general Structure Activity Relationships methodology. The obtained models in a series of five papers are quantitatively analyzed by comparing with previous reported results by using of the correlated correlations tests. The scores for a series of 13 data sets unpublished yet results are presented. Two unrestricted online access portals to the Molecular Descriptors Family Structure Activity Relationship models results are given.

Protein solution structure determination using distances from two-dimensional nuclear Overhauser effect experiments: Effect of approximations on the accuracy of derived structures

International Nuclear Information System (INIS)

Thomas, P.D.; Basus, V.J.; James, T.L.

1991-01-01

Solution structures for many proteins have been determined to date utilizing interproton distance constraints estimated from two-dimensional nuclear Overhauser effect (2D NOE) spectra. Although the simple isolated spin pair approximation (ISPA) generally used can result in systematic errors in distances, the large number of constraints enables proteins structure to be defined with reasonably high resolution. Effects of these systematic errors on the resulting protein structure are examined. Iterative relaxation matrix calculations, which account for dipolar interactions between all protons in a molecule, can accurately determine internuclear distances with little or no a priori knowledge of the molecular structure. The value of this additional complexity is also addressed. To assess these distance determination methods, hypothetical experimental data, including random noise and peak overlap, are calculated for an arbitrary true protein structure. Three methods of obtaining distance constraints from 2D NOE peak intensities are examined: one entails a conservative use of ISPA, one assumes the ISPA to be fairly accurate, and on utilizes an iterative relaxation matrix method called MARDIGRAS (matrix analysis of relaxation for discerning the geometry of an aqueous structure), developed in this laboratory. An R factor for evaluating fit between experimental and calculated 2D NOE intensities is proposed

Hydrogen molecular ions for improved determination of fundamental constants

NARCIS (Netherlands)

Karr, J.-P.; Hilico, L.; Koelemeij, J.C.J.; Korobov, V.I.

2016-01-01

The possible use of high-resolution rovibrational spectroscopy of the hydrogen molecular ions H-2(+) and HD+ for an independent determination of several fundamental constants is analyzed. While these molecules had been proposed for the metrology of nuclear-to-electron mass ratios, we show that they

Solution NMR structure determination of proteins revisited

International Nuclear Information System (INIS)

Billeter, Martin; Wagner, Gerhard; Wuethrich, Kurt

2008-01-01

This 'Perspective' bears on the present state of protein structure determination by NMR in solution. The focus is on a comparison of the infrastructure available for NMR structure determination when compared to protein crystal structure determination by X-ray diffraction. The main conclusion emerges that the unique potential of NMR to generate high resolution data also on dynamics, interactions and conformational equilibria has contributed to a lack of standard procedures for structure determination which would be readily amenable to improved efficiency by automation. To spark renewed discussion on the topic of NMR structure determination of proteins, procedural steps with high potential for improvement are identified

A Molecularly Imprinted Polymer with Incorporated Graphene Oxide for Electrochemical Determination of Quercetin

Directory of Open Access Journals (Sweden)

Xiwen He

2013-04-01

Full Text Available The molecularly imprinted polymer based on polypyrrole film with incorporated graphene oxide was fabricated and used for electrochemical determination of quercetin. The electrochemical behavior of quercetin on the modified electrode was studied in detail using differential pulse voltammetry. The oxidation peak current of quercetin in B-R buffer solution (pH = 3.5 at the modified electrode was regressed with the concentration in the range from 6.0 × 10−7 to 1.5 × 10−5 mol/L (r2 = 0.997 with a detection limit of 4.8 × 10−8 mol/L (S/N = 3. This electrode showed good stability and reproducibility. In the above mentioned range, rutin or morin which has similar structures and at the same concentration as quercetin did not interfere with the determination of quercetin. The applicability of the method for complex matrix analysis was also evaluated.

VPAC receptors: structure, molecular pharmacology and interaction with accessory proteins.

Science.gov (United States)

Couvineau, Alain; Laburthe, Marc

2012-05-01

The vasoactive intestinal peptide (VIP) is a neuropeptide with wide distribution in both central and peripheral nervous systems, where it plays important regulatory role in many physiological processes. VIP displays a large biological functions including regulation of exocrine secretions, hormone release, fetal development, immune responses, etc. VIP appears to exert beneficial effect in neuro-degenerative and inflammatory diseases. The mechanism of action of VIP implicates two subtypes of receptors (VPAC1 and VPAC2), which are members of class B receptors belonging to the super-family of GPCR. This article reviews the current knowledge regarding the structure and molecular pharmacology of VPAC receptors. The structure-function relationship of VPAC1 receptor has been extensively studied, allowing to understand the molecular basis for receptor affinity, specificity, desensitization and coupling to adenylyl cyclase. Those studies have clearly demonstrated the crucial role of the N-terminal ectodomain (N-ted) of VPAC1 receptor in VIP recognition. By using different approaches including directed mutagenesis, photoaffinity labelling, NMR, molecular modelling and molecular dynamic simulation, it has been shown that the VIP molecule interacts with the N-ted of VPAC1 receptor, which is itself structured as a 'Sushi' domain. VPAC1 receptor also interacts with a few accessory proteins that play a role in cell signalling of receptors. Recent advances in the structural characterization of VPAC receptor and more generally of class B GPCRs will lead to the design of new molecules, which could have considerable interest for the treatment of inflammatory and neuro-degenerative diseases. © 2011 The Authors. British Journal of Pharmacology © 2011 The British Pharmacological Society.

NATO Advanced Study Institute on Electronic Structure of Polymers and Molecular Crystals

CERN Document Server

Ladik, János

1975-01-01

The NATO Advanced Study Institute on "Electronic Structure of Polymers and Molecular Crystals" was held at the Facultes Universi­ taires de Namur (F.U.N.) from September 1st till September 14th, 1974. We wish to express our appreciation to the NATO Scientific Affairs Division whose generous support made this Institute possible and to the Facultes Universitaires de Namur and the Societe Chimique de Belgique which provided fellowships and travel grants to a number of students. This volume contains the main lectures about the basic principles of the field and about different recent developments of the theory of the electronic structure of polymers and molecular crystals. The school started with the presentation of the basic SCF-LCAO theory of the electronic structure of periodic polymers and molecular crystals (contributions by Ladik, Andre & Delhalle) showing how a combination of quantum chemical and solid state physical methods can provide band structures for these systems. The numerical aspects of these ...

Structural determinants for protein adsorption/non-adsorption to silica surface

International Nuclear Information System (INIS)

Mathe, Christelle; Devineau, Stephanie; Aude, Jean-Christophe; Lagniel, Gilles; Chedin, Stephane; Legros, Veronique; Mathon, Marie-Helene; Renault, Jean-Philippe; Pin, Serge; Boulard, Yves; Labarre, Jean

2013-01-01

The understanding of the mechanisms involved in the interaction of proteins with inorganic surfaces is of major interest in both fundamental research and applications such as nano-technology. However, despite intense research, the mechanisms and the structural determinants of protein/surface interactions are still unclear. We developed a strategy consisting in identifying, in a mixture of hundreds of soluble proteins, those proteins that are adsorbed on the surface and those that are not. If the two protein subsets are large enough, their statistical comparative analysis must reveal the physicochemical determinants relevant for adsorption versus non-adsorption. This methodology was tested with silica nanoparticles. We found that the adsorbed proteins contain a higher number of charged amino acids, particularly arginine, which is consistent with involvement of this basic amino acid in electrostatic interactions with silica. The analysis also identified a marked bias toward low aromatic amino acid content (phenylalanine, tryptophan, tyrosine and histidine) in adsorbed proteins. Structural analyses and molecular dynamics simulations of proteins from the two groups indicate that non-adsorbed proteins have twice as many p-p interactions and higher structural rigidity. The data are consistent with the notion that adsorption is correlated with the flexibility of the protein and with its ability to spread on the surface. Our findings led us to propose a refined model of protein adsorption. (authors)

Structural determinants for protein adsorption/non-adsorption to silica surface.

Directory of Open Access Journals (Sweden)

Christelle Mathé

Full Text Available The understanding of the mechanisms involved in the interaction of proteins with inorganic surfaces is of major interest in both fundamental research and applications such as nanotechnology. However, despite intense research, the mechanisms and the structural determinants of protein/surface interactions are still unclear. We developed a strategy consisting in identifying, in a mixture of hundreds of soluble proteins, those proteins that are adsorbed on the surface and those that are not. If the two protein subsets are large enough, their statistical comparative analysis must reveal the physicochemical determinants relevant for adsorption versus non-adsorption. This methodology was tested with silica nanoparticles. We found that the adsorbed proteins contain a higher number of charged amino acids, particularly arginine, which is consistent with involvement of this basic amino acid in electrostatic interactions with silica. The analysis also identified a marked bias toward low aromatic amino acid content (phenylalanine, tryptophan, tyrosine and histidine in adsorbed proteins. Structural analyses and molecular dynamics simulations of proteins from the two groups indicate that non-adsorbed proteins have twice as many π-π interactions and higher structural rigidity. The data are consistent with the notion that adsorption is correlated with the flexibility of the protein and with its ability to spread on the surface. Our findings led us to propose a refined model of protein adsorption.

Crystal structure and pair potentials: A molecular-dynamics study

Energy Technology Data Exchange (ETDEWEB)

Parrinello, M.; Rahman, A.

1980-10-06

With use of a Lagrangian which allows for the variation of the shape and size of the periodically repeating molecular-dynamics cell, it is shown that different pair potentials lead to different crystal structures.

The Atom in a Molecule: Implications for Molecular Structure and Properties

Science.gov (United States)

2016-05-23

Briefing Charts 3. DATES COVERED (From - To) 01 February 2016 – 23 May 2016 4. TITLE AND SUBTITLE The atom in a molecule: Implications for molecular...For presentation at American Physical Society - Division of Atomic , Molecular, and Optical Physics (May 2016) PA Case Number: #16075; Clearance Date...10 Energy (eV) R C--H (au) R C--H(au) The Atom in a Molecule: Implications for Molecular Structures and Properties P. W. Langhoff, Chemistry

Effect of the molecular structure of phenolic novolac precursor resins on the properties of phenolic fibers

International Nuclear Information System (INIS)

Ying, Yong-Gang; Pan, Yan-Ping; Ren, Rui; Dang, Jiang-Min; Liu, Chun-Ling

2013-01-01

A series of phenolic resins with different weight-average molecular weights (M w ) and ortho/para (O/P) ratios were prepared. The effect of the phenolic precursor resin structure on the structure and properties of the resulting phenolic fibers was investigated. The structures of the resins and fibers were characterized by nuclear magnetic resonance spectroscopy, gel permeation chromatography, melt rheometry, dynamic mechanical analysis, and thermogravimetric analysis. The results show that the O/P ratio, unsubstituted ortho and para carbon ratio (O u /P u ), and M w of the phenolic resins play an important role in determining the properties of the phenolic fibers. The tensile strength of the phenolic fibers increases with increasing novolac precursor O u /P u ratios, corresponding to low O/P ratios, at comparable resin M w values. Also, the tensile strength of the phenolic fibers increases with increasing novolac M w values at comparable O/P ratios. Phenolic fibers with high tensile strength and good flame resistance characteristics were generated from a phenolic precursor resin, possessing a high weight-average molecular weight and a low O/P value. - Highlights: • Phenolic resins with different weight-average molecular weights and ortho/para ratios have been prepared. • The tensile strength of the phenolic fibers increases with reducing novolac O/P ratio. • The tensile strength of the phenolic fibers increases with increasing novolac M w

Molecular and vibrational structure of 2,2'-dihydroxybenzophenone

DEFF Research Database (Denmark)

Birklund Andersen, Kristine; Langgård, M.; Spanget-Larsen, Jens

1999-01-01

2,2'-dihydroxybenzophenone (DHBP) contains similar bifold intramolecular H-bonding as the psoriatic drug anthralin, but because of steric interference the phenolic rings are twisted in a propeller-like manner, resulting in a molecular structure of C2 symmetry. In contrast to the case of C2v...

Molecular and vibrational structure of 2,2'-dihydroxybenzophenone

DEFF Research Database (Denmark)

Birklund Andersen, Kristine; Langgård, M.; Spanget-Larsen, Jens

1999-01-01

2,2'-dihydroxybenzophenone (DHBP) contains similar bifold intramolecular H-bonding as the psoriatic drug anthralin, but because of steric interference the phenolic rings are twisted in a propeller-like manner, resulting in a molecular structure of C2 symmetry. In contrast to the case of C2v anthr...

Molecular structure and DFT investigations on new cobalt(II ...

Indian Academy of Sciences (India)

tion process was demonstrated.9 Late-transition metals, especially Ni, Pd ..... in table S2 (Supplementary Information). Most of the ... to molecular system because of atomic charges affect ... structure, acidity–basicity behavior and other proper-.

Coding considerations for standalone molecular dynamics simulations of atomistic structures

Science.gov (United States)

Ocaya, R. O.; Terblans, J. J.

2017-10-01

The laws of Newtonian mechanics allow ab-initio molecular dynamics to model and simulate particle trajectories in material science by defining a differentiable potential function. This paper discusses some considerations for the coding of ab-initio programs for simulation on a standalone computer and illustrates the approach by C language codes in the context of embedded metallic atoms in the face-centred cubic structure. The algorithms use velocity-time integration to determine particle parameter evolution for up to several thousands of particles in a thermodynamical ensemble. Such functions are reusable and can be placed in a redistributable header library file. While there are both commercial and free packages available, their heuristic nature prevents dissection. In addition, developing own codes has the obvious advantage of teaching techniques applicable to new problems.

Solving nucleic acid structures by molecular replacement: examples from group II intron studies

International Nuclear Information System (INIS)

Marcia, Marco; Humphris-Narayanan, Elisabeth; Keating, Kevin S.; Somarowthu, Srinivas; Rajashankar, Kanagalaghatta; Pyle, Anna Marie

2013-01-01

Strategies for phasing nucleic acid structures by molecular replacement, using both experimental and de novo designed models, are discussed. Structured RNA molecules are key players in ensuring cellular viability. It is now emerging that, like proteins, the functions of many nucleic acids are dictated by their tertiary folds. At the same time, the number of known crystal structures of nucleic acids is also increasing rapidly. In this context, molecular replacement will become an increasingly useful technique for phasing nucleic acid crystallographic data in the near future. Here, strategies to select, create and refine molecular-replacement search models for nucleic acids are discussed. Using examples taken primarily from research on group II introns, it is shown that nucleic acids are amenable to different and potentially more flexible and sophisticated molecular-replacement searches than proteins. These observations specifically aim to encourage future crystallographic studies on the newly discovered repertoire of noncoding transcripts

Human Skin Barrier Structure and Function Analyzed by Cryo-EM and Molecular Dynamics Simulation.

Science.gov (United States)

Lundborg, Magnus; Narangifard, Ali; Wennberg, Christian L; Lindahl, Erik; Daneholt, Bertil; Norlén, Lars

2018-04-24

In the present study we have analyzed the molecular structure and function of the human skin's permeability barrier using molecular dynamics simulation validated against cryo-electron microscopy data from near native skin. The skin's barrier capacity is located to an intercellular lipid structure embedding the cells of the superficial most layer of skin - the stratum corneum. According to the splayed bilayer model (Iwai et al., 2012) the lipid structure is organized as stacked bilayers of ceramides in a splayed chain conformation with cholesterol associated with the ceramide sphingoid moiety and free fatty acids associated with the ceramide fatty acid moiety. However, knowledge about the lipid structure's detailed molecular organization, and the roles of its different lipid constituents, remains circumstantial. Starting from a molecular dynamics model based on the splayed bilayer model, we have, by stepwise structural and compositional modifications, arrived at a thermodynamically stable molecular dynamics model expressing simulated electron microscopy patterns matching original cryo-electron microscopy patterns from skin extremely closely. Strikingly, the closer the individual molecular dynamics models' lipid composition was to that reported in human stratum corneum, the better was the match between the models' simulated electron microscopy patterns and the original cryo-electron microscopy patterns. Moreover, the closest-matching model's calculated water permeability and thermotropic behaviour were found compatible with that of human skin. The new model may facilitate more advanced physics-based skin permeability predictions of drugs and toxicants. The proposed procedure for molecular dynamics based analysis of cellular cryo-electron microscopy data might be applied to other biomolecular systems. Copyright © 2018. Published by Elsevier Inc.

Introduction to crystal structure determination methods using x-ray diffraction: application to some rare earth complexes

International Nuclear Information System (INIS)

Oliveira, M.A. de.

1986-01-01

This work is composed by a theoretical introduction studying crystal concept, interaction between X-ray and crystal medium, and methods for determining small molecular structures applied in solution of crystal structures of praseodymium, neodymium and europium complexes with perrhenate and trans - 1,4 - dithiane - 1,4 - dioxide, (TDTD), which general formula is [ Ln (H sub(2) O) sub(4) (η-TDTD) (η'Re O sub(4)) (μ-η sup(2)-TDTD)] sub(n) (Re O sub(4)) sub(2n). nTDTD, where, Ln = Eu, Pr, Nd and methyl-2,6-anhydrous-3-azido-4-0-benzoyl-3-deoxy-α-D-iodo pyranoside. The structure of C sub(14) H sub(15) N sub(3) O sub(5) organic complex was determined using direct methods. (M.C.K.)

Structural determinants of phenotypic diversity and replication rate of human prions.

Directory of Open Access Journals (Sweden)

Jiri G Safar

2015-04-01

Full Text Available The infectious pathogen responsible for prion diseases is the misfolded, aggregated form of the prion protein, PrPSc. In contrast to recent progress in studies of laboratory rodent-adapted prions, current understanding of the molecular basis of human prion diseases and, especially, their vast phenotypic diversity is very limited. Here, we have purified proteinase resistant PrPSc aggregates from two major phenotypes of sporadic Creutzfeldt-Jakob disease (sCJD, determined their conformational stability and replication tempo in vitro, as well as characterized structural organization using recently emerged approaches based on hydrogen/deuterium (H/D exchange coupled with mass spectrometry. Our data clearly demonstrate that these phenotypically distant prions differ in a major way with regard to their structural organization, both at the level of the polypeptide backbone (as indicated by backbone amide H/D exchange data as well as the quaternary packing arrangements (as indicated by H/D exchange kinetics for histidine side chains. Furthermore, these data indicate that, in contrast to previous observations on yeast and some murine prion strains, the replication rate of sCJD prions is primarily determined not by conformational stability but by specific structural features that control the growth rate of prion protein aggregates.

Determining the structure of Carbon-60

International Nuclear Information System (INIS)

Wif, D.

1994-01-01

Carbon-60 is the most stable and best known of the carbon cage structures known collectively as the fullerenes. It is a remarkable molecule that forms a fascinating solid. Although the molecular shape of C sub 6 sub 0 is familiar - it is simply the shape of a soccer ball with 12 pentagons and 20 hexagons - the manner in which it forms a crystal structure is by no means obvious. This talk will focus on the insights which neutron scattering at ISIS has brought to our understanding of solid C sub6 sub 0. At room temperature, the structure may be regarded as forming as essentially ideal cubic-close packed molecular b ubble-raft : each molecule is reorienting so rapidly that a time-averaged picture, over as little as a nanosecond, reveals a closely spherical shell of atomic density. At 260 K, a rather unusual structural transition occurs. The molecules order but still retain cubic symmetry. Although this may not appear to be a rather dramatic change, detailed considerations show that a profound transition has occurred that bears close similarities to a solid-liquid phase transition but in two dimensions. Below 260 K, reorientation still occurs but at a dramatically reduced rate as the temperature is lowered. Indeed at around 90 K, The reorientation is so slow that thermodynamic equilibrium cannot be achieved in a reasonable timescale an orientational glass transition occurs. Although the behaviour of solid C sub 6 sub 0 undergoes dramatic changes as a function of temperature, a coherent description has evolved in which neutron scattering plays a central role. Close analogies are to be found in the study of systems as diverse as solid H sub 2 and human-rhinovirus structures. These analogies and the central role played by neutron scattering at ISIS will be emphasised in this paper. 5 figs., 10 refs. (author)

Relationship between Molecular Structure Characteristics of Feed Proteins and Protein Digestibility and Solubility

Directory of Open Access Journals (Sweden)

Mingmei Bai

2016-08-01

Full Text Available The nutritional value of feed proteins and their utilization by livestock are related not only to the chemical composition but also to the structure of feed proteins, but few studies thus far have investigated the relationship between the structure of feed proteins and their solubility as well as digestibility in monogastric animals. To address this question we analyzed soybean meal, fish meal, corn distiller’s dried grains with solubles, corn gluten meal, and feather meal by Fourier transform infrared (FTIR spectroscopy to determine the protein molecular spectral band characteristics for amides I and II as well as α-helices and β-sheets and their ratios. Protein solubility and in vitro digestibility were measured with the Kjeldahl method using 0.2% KOH solution and the pepsin-pancreatin two-step enzymatic method, respectively. We found that all measured spectral band intensities (height and area of feed proteins were correlated with their the in vitro digestibility and solubility (p≤0.003; moreover, the relatively quantitative amounts of α-helices, random coils, and α-helix to β-sheet ratio in protein secondary structures were positively correlated with protein in vitro digestibility and solubility (p≤0.004. On the other hand, the percentage of β-sheet structures was negatively correlated with protein in vitro digestibility (p<0.001 and solubility (p = 0.002. These results demonstrate that the molecular structure characteristics of feed proteins are closely related to their in vitro digestibility at 28 h and solubility. Furthermore, the α-helix-to-β-sheet ratio can be used to predict the nutritional value of feed proteins.

Ultrafast molecular imaging by laser-induced electron diffraction

International Nuclear Information System (INIS)

Peters, M.; Nguyen-Dang, T. T.; Cornaggia, C.; Saugout, S.; Charron, E.; Keller, A.; Atabek, O.

2011-01-01

We address the feasibility of imaging geometric and orbital structures of a polyatomic molecule on an attosecond time scale using the laser-induced electron diffraction (LIED) technique. We present numerical results for the highest molecular orbitals of the CO 2 molecule excited by a near-infrared few-cycle laser pulse. The molecular geometry (bond lengths) is determined within 3% of accuracy from a diffraction pattern which also reflects the nodal properties of the initial molecular orbital. Robustness of the structure determination is discussed with respect to vibrational and rotational motions with a complete interpretation of the laser-induced mechanisms.

NMR determinations of molecular geometries in liquid crystal media

International Nuclear Information System (INIS)

Long, R.C.; Goldstein, J.H.

1983-01-01

The application of NMR spectroscopy in oriented media to the determination of molecular geometries is illustrated by results for three distinctly different molecules: naphthalene, ethylene oxide and spiropentane. The need for systematic application of vibrational corrections is emphasized and some of the effects associated with the different choices of solvent media are considered

SFG analysis of the molecular structures at the surfaces and buried interfaces of PECVD ultralow-dielectric constant pSiCOH

Science.gov (United States)

Zhang, Xiaoxian; Myers, John N.; Huang, Huai; Shobha, Hosadurga; Chen, Zhan; Grill, Alfred

2016-02-01

PECVD deposited porous SiCOH with ultralow dielectric constant has been successfully integrated as the insulator in advanced interconnects to decrease the RC delay. The effects of NH3 plasma treatment and the effectiveness of the dielectric repair on molecular structures at the surface and buried interface of a pSiCOH film deposited on top of a SiCNH film on a Si wafer were fully characterized using sum frequency generation vibrational spectroscopy (SFG), supplemented by X-ray photoelectron spectroscopy. After exposure to NH3 plasma for 18 s, about 40% of the methyl groups were removed from the pSiCOH surface, and the average orientation of surface methyl groups tilted more towards the surface. The repair method used here effectively repaired the molecular structures at the pSiCOH surface but did not totally recover the entire plasma-damaged layer. Additionally, simulated SFG spectra with various average orientations of methyl groups at the SiCNH/pSiCOH buried interface were compared with the experimental SFG spectra collected using three different laser input angles to determine the molecular structural information at the SiCNH/pSiCOH buried interface after NH3 plasma treatment and repair. The molecular structures including the coverage and the average orientation of methyl groups at the buried interface were found to be unchanged by NH3 plasma treatment and repair.

Molecular basis of structural makeup of hulless barley in relation to rumen degradation kinetics and intestinal availability in dairy cattle: A novel approach.

Science.gov (United States)

Damiran, D; Yu, P

2011-10-01

To date, no study has been done of molecular structures in relation to nutrient degradation kinetics and intestinal availability in dairy cattle. The objectives of this study were to (1) reveal molecular structures of hulless barley affected by structural alteration using molecular spectroscopy (diffuse reflectance infrared Fourier transform) as a novel approach, and (2) quantify structure features on a molecular basis in relation to digestive kinetics and nutritive value in the rumen and intestine in cattle. The modeled feeds in this study were 4 types of hulless barley (HB) cultivars modified in starch traits: (a) normal starch cultivar, (b) zero-amylose waxy, (c) waxy, and (d) high-amylose. The molecular structural features were determined using diffuse reflectance infrared Fourier transform spectroscopy in the mid-infrared region (ca. 4,000-800 cm(-1)) of the electromagnetic spectrum. The items assessed included infrared intensity attributed to protein amide I (ca. 1,715-1,575 cm(-1)), amide II (ca. 1,575-1,490 cm(-1)), α-helix (ca. 1,648-1,660 cm(-1)), β-sheet (ca. 1,625-1,640 cm(-1)), and their ratio, β-glucan (ca. 1,445-1,400 cm(-1)), total carbohydrates (CHO; ca. 1,188-820 cm(-1)) and their 3 major peaks, structural carbohydrates (ca. 1,277-1,190 cm(-1)), and ratios of amide I to II and amide I to CHO. The results show that (1) the zero-amylose waxy was the greatest in amide I and II peak areas, as well as in the ratio of protein amide I to CHO among HB; (2) α-helix-to-β-sheet ratio differed among HB: the high-amylose was the greatest, the zero-amylose waxy and waxy were the intermediate, and the normal starch was the lowest; (3) HB were similar in β-glucan and CHO molecular structural makeup; (4) altered starch HB cultivars were similar to each other, but were different from the normal starch cultivar in protein molecular makeup; and (5) the rate and extent of rumen degradation of starch and protein were highly related to the molecular structural

A stochastic phase-field model determined from molecular dynamics

KAUST Repository

von Schwerin, Erik

2010-03-17

The dynamics of dendritic growth of a crystal in an undercooled melt is determined by macroscopic diffusion-convection of heat and by capillary forces acting on the nanometer scale of the solid-liquid interface width. Its modelling is useful for instance in processing techniques based on casting. The phase-field method is widely used to study evolution of such microstructural phase transformations on a continuum level; it couples the energy equation to a phenomenological Allen-Cahn/Ginzburg-Landau equation modelling the dynamics of an order parameter determining the solid and liquid phases, including also stochastic fluctuations to obtain the qualitatively correct result of dendritic side branching. This work presents a method to determine stochastic phase-field models from atomistic formulations by coarse-graining molecular dynamics. It has three steps: (1) a precise quantitative atomistic definition of the phase-field variable, based on the local potential energy; (2) derivation of its coarse-grained dynamics model, from microscopic Smoluchowski molecular dynamics (that is Brownian or over damped Langevin dynamics); and (3) numerical computation of the coarse-grained model functions. The coarse-grained model approximates Gibbs ensemble averages of the atomistic phase-field, by choosing coarse-grained drift and diffusion functions that minimize the approximation error of observables in this ensemble average. © EDP Sciences, SMAI, 2010.

A stochastic phase-field model determined from molecular dynamics

KAUST Repository

von Schwerin, Erik; Szepessy, Anders

2010-01-01

The dynamics of dendritic growth of a crystal in an undercooled melt is determined by macroscopic diffusion-convection of heat and by capillary forces acting on the nanometer scale of the solid-liquid interface width. Its modelling is useful for instance in processing techniques based on casting. The phase-field method is widely used to study evolution of such microstructural phase transformations on a continuum level; it couples the energy equation to a phenomenological Allen-Cahn/Ginzburg-Landau equation modelling the dynamics of an order parameter determining the solid and liquid phases, including also stochastic fluctuations to obtain the qualitatively correct result of dendritic side branching. This work presents a method to determine stochastic phase-field models from atomistic formulations by coarse-graining molecular dynamics. It has three steps: (1) a precise quantitative atomistic definition of the phase-field variable, based on the local potential energy; (2) derivation of its coarse-grained dynamics model, from microscopic Smoluchowski molecular dynamics (that is Brownian or over damped Langevin dynamics); and (3) numerical computation of the coarse-grained model functions. The coarse-grained model approximates Gibbs ensemble averages of the atomistic phase-field, by choosing coarse-grained drift and diffusion functions that minimize the approximation error of observables in this ensemble average. © EDP Sciences, SMAI, 2010.

Crystal and molecular structures of 3-amino-4-hydroxy benzenesulfonamide and its hydrochloride: Quantum-chemical study of their tautomerism

Energy Technology Data Exchange (ETDEWEB)

Kovalchukova, O. V., E-mail: okovalchukova@mail.ru; Strashnova, S. B.; Romashkina, E. P.; Strashnov, P. V.; Zaitsev, B. E. [Peoples' Friendship University of Russia (Russian Federation); Sergienko, V. S. [Russian Academy of Sciences, Kurnakov Institute of General and Inorganic Chemistry (Russian Federation)

2013-03-15

3-amino-4-hydroxy benzenesulfonamide and its hydrochloride have been isolated in the crystalline state. Their crystal and molecular structures are determined by X-ray diffraction. The equilibrium between neutral tautomeric forms of the 3-amino-4-hydroxy benzenesulfonamide molecule is studied within the approximation of density functional theory (B3LYP/aug-cc-pVDZ). The constants of acid-base equilibrium of 3-amino-4-hydroxy benzenesulfonamide are deter-mined using spectrophotometry.

Ambipolar carrier transport properties and molecular packing structure of octahexyl-substituted copper phthalocyanine

Science.gov (United States)

Watanabe, Ken; Watanabe, Koichi; Tohnai, Norimitsu; Itani, Hiromichi; Shimizu, Yo; Fujii, Akihiko; Ozaki, Masanori

2018-04-01

The charge carrier mobility of a solution-processable low-molecular-weight organic semiconductor material, i.e., 1,4,8,11,15,18,22,25-octahexylphthalocyanine copper complex (C6PcCu), was investigated by the time-of-flight technique. The anomalous ambipolar carrier mobility was discussed from the viewpoint of the molecular packing structure, which was clarified by single-crystal X-ray structure analysis. In the comparison between the molecular packing structures of C6PcCu and its metal-free-type homologue, it was found that the difference in carrier mobility originates from the rotation of the molecule, which is caused by the steric hindrance due to the introduction of a center metal and the interpenetration of the nonperipheral alkyl chains.

Equilibrium simulations of proteins using molecular fragment replacement and NMR chemical shifts

DEFF Research Database (Denmark)

Boomsma, Wouter; Tian, Pengfei; Frellsen, J.

2014-01-01

recently been shown that using such information directly as input in molecular simulations based on the molecular fragment replacement strategy can help the process of protein structure determination. Here, we show how to implement this strategy to determine not only the structures of proteins but also...

Equilibrium Structures and Absorption Spectra for SixOy Molecular Clusters using Density Functional Theory

Science.gov (United States)

2017-05-05

Naval Research Laboratory Washington, DC 20375-5320 NRL/MR/6390--17-9724 Equilibrium Structures and Absorption Spectra for SixOy Molecular Clusters...TELEPHONE NUMBER (include area code) b. ABSTRACT c. THIS PAGE 18. NUMBER OF PAGES 17. LIMITATION OF ABSTRACT Equilibrium Structures and Absorption...and electronic excited-state absorption spectra for eqilibrium structures of SixOy molecular clusters using density function theory (DFT) and time

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

Science.gov (United States)

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

2017-04-04

Structural molecular biology is now becoming part of high school science curriculum thus posing a challenge for teachers who need to convey three-dimensional (3D) structures with conventional text and pictures. In many cases even interactive computer graphics does not go far enough to address these challenges. We have developed a flexible model of the polypeptide backbone using 3D printing technology. With this model we have produced a polypeptide assembly kit to create an idealized model of the Triosephosphate isomerase mutase enzyme (TIM), which forms a structure known as TIM barrel. This kit has been used in a laboratory practical where students perform a step-by-step investigation into the nature of protein folding, starting with the handedness of amino acids to the formation of secondary and tertiary structure. Based on the classroom evidence we collected, we conclude that these models are valuable and inexpensive resource for teaching structural molecular biology. Copyright © 2017 Elsevier Ltd. All rights reserved.

16O + 16O molecular structures of superdeformed states in S isotopes

Science.gov (United States)

Taniguchi, Y.

2017-06-01

Structures of excited states in S isotopes are investigated by using the antisymmetrized molecular dynamics and generator coordinate method (GCM). The GCM basis wave functions are calculated via energy variation with a constraint on the quadrupole deformation parameter β. By applying the GCM after parity and angular momentum projections, the coexistence of positive- and negative-parity superdeformed (SD) bands are predicted in 33-36S except for negative-parity states in 36S. The SD bands have structures of 16O + 16O + valence neutron(s) in molecular orbitals around the two 16O cores in a cluster picture. The configurations of the valence neutron(s) in the SD states are δ and/or π molecular orbitals.

Laser-induced blurring of molecular structure information in high harmonic spectroscopy

DEFF Research Database (Denmark)

Risoud, Francois; Leveque, Camille; Labeye, Marie

2017-01-01

High harmonic spectroscopy gives access to molecular structure with Angstrom resolution. Such information is encoded in the destructive interferences occurring between the harmonic emissions from the different parts of the molecule. By solving the time-dependent Schrodinger equation, either....... These findings have important consequences for molecular imaging and orbital tomography using high harmonic spectroscopy....

Insights into structural features of HDAC1 and its selectivity inhibition elucidated by Molecular dynamic simulation and Molecular Docking.

Science.gov (United States)

Sixto-López, Yudibeth; Bello, Martiniano; Correa-Basurto, José

2018-03-06

Histone deacetylases (HDACs) are a family of proteins whose main function is the removal of acetyl groups from lysine residues located on histone and non-histone substrates, which regulates gene transcription and other activities in cells. HDAC1 dysfunction has been implicated in cancer development and progression; thus, its inhibition has emerged as a new therapeutic strategy. Two additional metal binding sites (Site 1 and Site 2) in HDACs have been described that are primarily occupied by potassium ions, suggesting a possible structural role that affects HDAC activity. In this work, we explored the structural role of potassium ions in Site 1 and Site 2 and how they affect the interactions of compounds with high affinities for HDAC1 (AC1OCG0B, Chlamydocin, Dacinostat and Quisinostat) and SAHA (a pan-inhibitor) using molecular docking and molecular dynamics (MD) simulations in concert with a Molecular-Mechanics-Generalized-Born-Surface-Area (MMGBSA) approach. Four models were generated: one with a potassium ion (K + ) in both sites (HDAC1 k ), a second with K + only at site 1 (HDAC1 ks1 ), a third with K + only at site 2 (HDAC1 ks2 ) and a fourth with no K + (HDAC1 wk ). We found that the presence or absence of K + not only impacted the structural flexibility of HDAC1, but also its molecular recognition, consistent with experimental findings. These results could therefore be useful for further structure-based drug design studies addressing new HDAC1 inhibitors.

Grazing incidence X-ray diffraction study of the tilted phases of Langmuir films: Determination of molecular conformations using simulated annealing

International Nuclear Information System (INIS)

Pignat, J.; Daillant, J.; Cantin, S.; Perrot, F.; Konovalov, O.

2007-01-01

We have analyzed grazing incidence X-ray diffraction (GIXD) data from condensed phases of Langmuir films of long-chain fatty acids at the air-water using a new method consisting in a careful extraction of the structure factors followed by fitting of molecular parameters using simulated annealing. We show that the information contained in GIXD spectra is enough to obtain near-atomic structural information. In particular, we directly determine the orientation of the chain backbone planes and of the carboxylic headgroups, and we evaluate chain conformation defects

Grazing incidence X-ray diffraction study of the tilted phases of Langmuir films: Determination of molecular conformations using simulated annealing

Energy Technology Data Exchange (ETDEWEB)

Pignat, J. [LIONS/Service de Chimie Moleculaire, CEA-Saclay bat. 125, F-91191 Gif-sur-Yvette Cedex (France); LPPI, universite de Cergy-Pontoise, 5 mail Gay-Lussac Neuville/Oise, 95031 Cergy-Pontoise Cedex (France); Daillant, J. [LIONS/Service de Chimie Moleculaire, CEA-Saclay bat. 125, F-91191 Gif-sur-Yvette Cedex (France)]. E-mail: jean.daillant@cea.fr; Cantin, S. [LPPI, universite de Cergy-Pontoise, 5 mail Gay-Lussac Neuville/Oise, 95031 Cergy-Pontoise Cedex (France); Perrot, F. [LPPI, universite de Cergy-Pontoise, 5 mail Gay-Lussac Neuville/Oise, 95031 Cergy-Pontoise Cedex (France); Konovalov, O. [ESRF, 6 rue Jules Horowitz, BP220, 38043 Grenoble Cedex (France)

2007-05-23

We have analyzed grazing incidence X-ray diffraction (GIXD) data from condensed phases of Langmuir films of long-chain fatty acids at the air-water using a new method consisting in a careful extraction of the structure factors followed by fitting of molecular parameters using simulated annealing. We show that the information contained in GIXD spectra is enough to obtain near-atomic structural information. In particular, we directly determine the orientation of the chain backbone planes and of the carboxylic headgroups, and we evaluate chain conformation defects.

Proteomic-Biostatistic Integrated Approach for Finding the Underlying Molecular Determinants of Hypertension in Human Plasma.

Science.gov (United States)

Gajjala, Prathibha R; Jankowski, Vera; Heinze, Georg; Bilo, Grzegorz; Zanchetti, Alberto; Noels, Heidi; Liehn, Elisa; Perco, Paul; Schulz, Anna; Delles, Christian; Kork, Felix; Biessen, Erik; Narkiewicz, Krzysztof; Kawecka-Jaszcz, Kalina; Floege, Juergen; Soranna, Davide; Zidek, Walter; Jankowski, Joachim

2017-08-01

Despite advancements in lowering blood pressure, the best approach to lower it remains controversial because of the lack of information on the molecular basis of hypertension. We, therefore, performed plasma proteomics of plasma from patients with hypertension to identify molecular determinants detectable in these subjects but not in controls and vice versa. Plasma samples from hypertensive subjects (cases; n=118) and controls (n=85) from the InGenious HyperCare cohort were used for this study and performed mass spectrometric analysis. Using biostatistical methods, plasma peptides specific for hypertension were identified, and a model was developed using least absolute shrinkage and selection operator logistic regression. The underlying peptides were identified and sequenced off-line using matrix-assisted laser desorption ionization orbitrap mass spectrometry. By comparison of the molecular composition of the plasma samples, 27 molecular determinants were identified differently expressed in cases from controls. Seventy percent of the molecular determinants selected were found to occur less likely in hypertensive patients. In cross-validation, the overall R 2 was 0.434, and the area under the curve was 0.891 with 95% confidence interval 0.8482 to 0.9349, P hypertensive patients were found to be -2.007±0.3568 and 3.383±0.2643, respectively, P hypertensives and normotensives. The identified molecular determinants may be the starting point for further studies to clarify the molecular causes of hypertension. © 2017 American Heart Association, Inc.

Molecular Chemical Structure of Barley Proteins Revealed by Ultra-Spatially Resolved Synchrotron Light Sourced FTIR Microspectroscopy: Comparison of Barley Varieties

International Nuclear Information System (INIS)

Yu, P.

2007-01-01

Barley protein structure affects the barley quality, fermentation, and degradation behavior in both humans and animals among other factors such as protein matrix. Publications show various biological differences among barley varieties such as Valier and Harrington, which have significantly different degradation behaviors. The objectives of this study were to reveal the molecular structure of barley protein, comparing various varieties (Dolly, Valier, Harrington, LP955, AC Metcalfe, and Sisler), and quantify protein structure profiles using Gaussian and Lorentzian methods of multi-component peak modeling by using the ultra-spatially resolved synchrotron light sourced Fourier transform infrared microspectroscopy (SFTIRM). The items of the protein molecular structure revealed included protein structure α-helices, β-sheets, and others such as β-turns and random coils. The experiment was performed at the National Synchrotron Light Source in Brookhaven National Laboratory (BNL, US Department of Energy, NY). The results showed that with the SFTIRM, the molecular structure of barley protein could be revealed. Barley protein structures exhibited significant differences among the varieties in terms of proportion and ratio of model-fitted α-helices, β-sheets, and others. By using multi-component peaks modeling at protein amide I region of 1710-1576 cm -1 , the results show that barley protein consisted of approximately 18-34% of α-helices, 14-25% of β-sheets, and 44-69% others. AC Metcalfe, Sisler, and LP955 consisted of higher (P 0.05). The ratio of α-helices to others (0.3 to 1.0, P < 0.05) and that of β-sheets to others (0.2 to 0.8, P < 0.05) were different among the barley varieties. It needs to be pointed out that using a multi-peak modeling for protein structure analysis is only for making relative estimates and not exact determinations and only for the comparison purpose between varieties. The principal component analysis showed that protein amide I Fourier

Recent research on inherent molecular structure, physiochemical properties, and bio-functions of food and feed-type Avena sativa oats and processing-induced changes revealed with molecular microspectroscopic techniques

Energy Technology Data Exchange (ETDEWEB)

Prates, Luciana Louzada [Department of Animal and Poultry Science, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Saskatchewan, Canada; Yu, Peiqiang [Department of Animal and Poultry Science, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Saskatchewan, Canada

2017-05-16

Avena sativa oat is a cereal widely used as human food and livestock feed. However, the low metabolized energy and the rapid rumen degradations of protein and starch have limited the use of A. sativa oat grains. To overcome this disadvantage, new A. sativa oat varieties have been developed. Additionally, heat-related processing has been performed to decrease the degradation rate and improve the absorption of amino acids in the small intestine. The nutritive value is reflected by both chemical composition and inherent molecular structure conformation. However, the traditional wet chemical analysis is not able to detect the inherent molecular structures within an intact tissue. The advanced synchrotron-radiation and globar-based molecular microspectroscopy have been developed recently and applied to study internal molecular structures and the processing induced structure changes in A. sativa oats and reveal how molecular structure changes in relation to nutrient availability. This review aimed to obtain the recent information regarding physiochemical properties, molecular structures, metabolic characteristics of protein, and the heat-induced changes in new A. sativa oat varieties. The use of the advanced vibrational molecular spectroscopy was emphasized, synchrotron- and globar-based (micro)spectroscopy, to reveal the inherent structure of A. sativa oats at cellular and molecular levels and to reveal the heat processing effect on the degradation characteristics and the protein molecular structure in A. sativa oats. The relationship between nutrient availability and protein molecular inherent structure was also presented. Information described in this review gives better insight in the physiochemical properties, molecular structure, and the heat-induced changes in A. sativa oat detected with advanced molecular spectroscopic techniques in combinination with conventional nutrition study techniques.

The contribution of solid-state NMR spectroscopy to understanding biomineralization: Atomic and molecular structure of bone

Science.gov (United States)

Duer, Melinda J.

2015-04-01

Solid-state NMR spectroscopy has had a major impact on our understanding of the structure of mineralized tissues, in particular bone. Bone exemplifies the organic-inorganic composite structure inherent in mineralized tissues. The organic component of the extracellular matrix in bone is primarily composed of ordered fibrils of collagen triple-helical molecules, in which the inorganic component, calcium phosphate particles, composed of stacks of mineral platelets, are arranged around the fibrils. This perspective argues that key factors in our current structural model of bone mineral have come about through NMR spectroscopy and have yielded the primary information on how the mineral particles interface and bind with the underlying organic matrix. The structure of collagen within the organic matrix of bone or any other structural tissue has yet to be determined, but here too, this perspective shows there has been real progress made through application of solid-state NMR spectroscopy in conjunction with other techniques. In particular, NMR spectroscopy has highlighted the fact that even within these structural proteins, there is considerable dynamics, which suggests that one should be cautious when using inherently static structural models, such as those arising from X-ray diffraction analyses, to gain insight into molecular roles. It is clear that the NMR approach is still in its infancy in this area, and that we can expect many more developments in the future, particularly in understanding the molecular mechanisms of bone diseases and ageing.

Using molecular principal axes for structural comparison: determining the tertiary changes of a FAB antibody domain induced by antigenic binding

Directory of Open Access Journals (Sweden)

Silverman B David

2007-11-01

Full Text Available Abstract Background Comparison of different protein x-ray structures has previously been made in a number of different ways; for example, by visual examination, by differences in the locations of secondary structures, by explicit superposition of structural elements, e.g. α-carbon atom locations, or by procedures that utilize a common symmetry element or geometrical feature of the structures to be compared. Results A new approach is applied to determine the structural changes that an antibody protein domain experiences upon its interaction with an antigenic target. These changes are determined with the use of two different, however comparable, sets of principal axes that are obtained by diagonalizing the second-order tensors that yield the moments-of-geometry as well as an ellipsoidal characterization of domain shape, prior to and after interaction. Determination of these sets of axes for structural comparison requires no internal symmetry features of the domains, depending solely upon their representation in three-dimensional space. This representation may involve atomic, Cα, or residue centroid coordinates. The present analysis utilizes residue centroids. When the structural changes are minimal, the principal axes of the domains, prior to and after interaction, are essentially comparable and consequently may be used for structural comparison. When the differences of the axes cannot be neglected, but are nevertheless slight, a smaller relatively invariant substructure of the domains may be utilized for comparison. The procedure yields two distance metrics for structural comparison. First, the displacements of the residue centroids due to antigenic binding, referenced to the ellipsoidal principal axes, are noted. Second, changes in the ellipsoidal distances with respect to the non-interacting structure provide a direct measure of the spatial displacements of the residue centroids, towards either the interior or exterior of the domain

Molecularly Imprinted Polypyrrole Based Impedimentric Sensor for Theophylline Determination

International Nuclear Information System (INIS)

Ratautaite, Vilma; Janssens, Stoffel D.; Haenen, Ken; Nesládek, Milos; Ramanaviciene, Almira; Baleviciute, Ieva; Ramanavicius, Arunas

2014-01-01

Highlights: • Sensor based on polypyrrole imprinted by theophylline (MIP) deposited on oxygen terminated boron-doped nanocrystalline diamond was developed. • This structure was applied as impedimetric sensor sensitive for theophylline. • Optimal polymer formation conditions suitable for MIP formation were elaborated. • Some analytical parameters were determined and evaluated. - Abstract: In this study development of impedimetric sensor based on oxygen terminated boron-doped nanocrystalline diamond (B:NCD:O) modified with theophylline imprinted polypyrrole is described. Hydrogen peroxide induced chemical formation of polypyrrole molecularly imprinted by theophylline was applied for the modification of conducting silicon substrate covered by B:NCD:O film. Non-imprinted polypyrrole layer was formed on similar substrate in order to prove efficiency of imprinted polypyrrole. Electrochemical impedance spectroscopy was applied for the evaluation of analyte-induced changes in electrochemical capacitance/resistance. The impact of polymerization duration on the capacitance of impedimetric sensor was estimated. A different impedance behavior was observed at different ratio of polymerized monomer and template molecule in the polymerization media. The influence of ethanol as additive to polymerization media on registered changes in capacitance/resistance was evaluated. Degradation of sensor stored in buffer solution was evaluated

Electron Scattering Studies of Gas Phase Molecular Structure at High Temperature

Science.gov (United States)

Mawhorter, Richard J., Jr.

A high precision counting electron diffraction study of the structure of gaseous sulfur dioxide as a function of temperature from 300(DEGREES) to 1000(DEGREES)K is presented. The results agree well with current theory, and yield insight into the effects of anharmonicity on molecular structure. Another aspect of molecular structure is the molecular charge density distribution. The difference (DELTA)(sigma) is between the electron scattering cross sections for the actual molecule and independent atom model (IAM) are a sensitive measure of the change in this distribution due to bond formation. These difference cross sections have been calculated using ab initio methods, and the results for a wide range of simple polyatomic molecules are presented. Such calculations are routinely done for a single, fixed molecular geometry, an approach which neglects the effects of the vibrational motion of real molecules. The effect of vibrational averaging is studied in detail for the three normal vibrational modes of H(,2)O in the ground state. The effects are small, lending credence to the practice of comparing cross sections calculated at a fixed geometry with inherently averaged experimental data. The efficacy of the standard formula used to account for vibrational averaging in the IAM is also examined. Finally, the nature of the ionic bond is probed with an experimental study of the structure of alkali chlorides, NaCl, KCl, RbCl, and CsCl, in the gas phase. Temperatures from 840-960(DEGREES)K were required to achieve the necessary vapor pressures of approximately 0.01 torr. A planar rhombic structure for the dimer molecule is confirmed, with a fairly uniform decrease of the chlorine-alkali-chlorine angle as the alkalis increase in size. The experiment also yields information on the amount of dimer present in the vapor, and these results are compared with thermodynamic values.

The auto-orientation in high magnetic fields of oxidized cytochrome b562 as source of constraints for solution structure determination

International Nuclear Information System (INIS)

Arnesano, Fabio; Banci, Lucia; Bertini, Ivano; Wetering, Karin van der; Czisch, Michael; Kaptein, Robert

2000-01-01

15 N- 1 H 1 J couplings were measured at 500 MHz and 800 MHz for 15 N enriched oxidized cytochrome b 562 from E. coli. The magnetic field dependence of 70 1 J values, which could be measured without signal overlap, shows that there is a molecular magnetic anisotropy which provides partial molecular orientation in the magnetic field and, consequently, residual dipolar couplings (rdc). The rdc were used as further constraints to improve the existing structure [Arnesano et al. (1999) Biochemistry, 38, 8657-8670] with a protocol which uses the rhombic anisotropy [Banci et al. (1998) J. Am. Chem. Soc., 120, 12903-12909]. The overall large molecular magnetic anisotropy has been found to be determined by both the low spin iron (III) and the four helix bundle structure magnetic susceptibility anisotropy contributions

Determination of molecular species of lecithin from erythrocytes and plasma

NARCIS (Netherlands)

Golde, L.M.G. van; Tomasi, V.; Deenen, L.L.M. van

The molecular species of lecithin from erythrocyte and plasma of man and rabbit were determined after conversion of the lecithins into diglycerides by means of hydrolysis with phospholipase C. The resultant diglycerides were separated by thin-layer chromatography on silica impregnated with silver

Molecular-crystal approach to accounting of correlation corrections in the chemical bond theory in crystals: electronic structure of Ti2O3 crystal

International Nuclear Information System (INIS)

Ehvarestov, R.A.; Panin, A.I.

2000-01-01

The problem on the possibility of partial accounting for the electron correlation effects within the frames of the Hartree-Fock unlimited method (HF). The local characteristic of the electron structure of the molecular systems for the case of the multi-determinant wave functions, configurational interaction methods and multiconfigurational self-consistent field (MCSCF) are determined. The molecular-crystalline approach is applied to studies on the electron correlation effects in the Ti 2 O 3 crystal. It is shown on the basis of the [Ti 2 O 9 ] 12- cluster electron structure calculation, that the Hartree-Fock unlimited method accounts in a number of cases for an essential part of statistical correlation effects. The energy values and local characteristics of the [Ti 2 O 9 ] 12- cluster, calculated through the HF and MCSCF methods, are presented [ru

Determination of viscosity-average molecular weight of chitosan using intrinsic viscosity measurement

International Nuclear Information System (INIS)

Norzita Yacob; Norhashidah Talip; Maznah Mahmud; Nurul Aizam Idayu Mat Sani; Nor Akma Samsuddin; Norafifah Ahmad Fabillah

2013-01-01

Determination of molecular weight by intrinsic viscosity measurement is a simple method for characterization of chitosan. To study the effect of radiation on molecular weight, chitosan was first irradiated using electron beam at different doses prior to measurement. Different concentrations of chitosan were prepared and measurement was done at room temperature. The flow time data was used to calculate the intrinsic viscosity by extrapolating the reduced viscosity to zero concentration. The value of intrinsic viscosity was then recalculated into the viscosity-average molecular weight using Mark-Houwink equation. (Author)

Molecular epidemiology and population structure of bovine Streptococcus uberis

DEFF Research Database (Denmark)

Rato, M G; Bexiga, R; Nunes, S F

2008-01-01

The molecular epidemiology and population structure of 30 bovine subclinical mastitis field isolates of Streptococcus uberis, collected from 6 Portuguese herds (among 12 farms screened) during 2002 and 2003, were examined by using pulsed-field gel electrophoresis (PFGE) for clustering of the isol...

Use of X-ray diffraction, molecular simulations, and spectroscopy to determine the molecular packing in a polymer-fullerene bimolecular crystal

KAUST Repository

Miller, Nichole Cates

2012-09-05

The molecular packing in a polymer: fullerene bimolecular crystal is determined using X-ray diffraction (XRD), molecular mechanics (MM) and molecular dynamics (MD) simulations, 2D solid-state NMR spectroscopy, and IR absorption spectroscopy. The conformation of the electron-donating polymer is significantly disrupted by the incorporation of the electron-accepting fullerene molecules, which introduce twists and bends along the polymer backbone and 1D electron-conducting fullerene channels. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Use of X-ray diffraction, molecular simulations, and spectroscopy to determine the molecular packing in a polymer-fullerene bimolecular crystal

KAUST Repository

Miller, Nichole Cates; Cho, Eunkyung; Junk, Matthias J N; Gysel, Roman; Risko, Chad; Kim, Dongwook; Sweetnam, Sean; Miller, Chad E.; Richter, Lee J.; Kline, Regis Joseph; Heeney, Martin J.; McCulloch, Iain A.; Amassian, Aram; Acevedo-Feliz, Daniel; Knox, Christopher; Hansen, Michael Ryan; Dudenko, Dmytro V.; Chmelka, Bradley F.; Toney, Michael F.; Bré das, Jean Luc; McGehee, Michael D.

2012-01-01

The molecular packing in a polymer: fullerene bimolecular crystal is determined using X-ray diffraction (XRD), molecular mechanics (MM) and molecular dynamics (MD) simulations, 2D solid-state NMR spectroscopy, and IR absorption spectroscopy. The conformation of the electron-donating polymer is significantly disrupted by the incorporation of the electron-accepting fullerene molecules, which introduce twists and bends along the polymer backbone and 1D electron-conducting fullerene channels. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structure of catalase determined by MicroED

Science.gov (United States)

Nannenga, Brent L; Shi, Dan; Hattne, Johan; Reyes, Francis E; Gonen, Tamir

2014-01-01

MicroED is a recently developed method that uses electron diffraction for structure determination from very small three-dimensional crystals of biological material. Previously we used a series of still diffraction patterns to determine the structure of lysozyme at 2.9 Å resolution with MicroED (Shi et al., 2013). Here we present the structure of bovine liver catalase determined from a single crystal at 3.2 Å resolution by MicroED. The data were collected by continuous rotation of the sample under constant exposure and were processed and refined using standard programs for X-ray crystallography. The ability of MicroED to determine the structure of bovine liver catalase, a protein that has long resisted atomic analysis by traditional electron crystallography, demonstrates the potential of this method for structure determination. DOI: http://dx.doi.org/10.7554/eLife.03600.001 PMID:25303172

Structure of sulfamidase provides insight into the molecular pathology of mucopolysaccharidosis IIIA

International Nuclear Information System (INIS)

Sidhu, Navdeep S.; Schreiber, Kathrin; Pröpper, Kevin; Becker, Stefan; Usón, Isabel; Sheldrick, George M.; Gärtner, Jutta; Krätzner, Ralph; Steinfeld, Robert

2014-01-01

Mucopolysaccharidosis IIIA is a fatal neurodegenerative disease that typically manifests itself in childhood and is caused by mutations in the gene for the lysosomal enzyme sulfamidase. The first structure of this enzyme is presented, which provides insight into the molecular basis of disease-causing mutations, and the enzymatic mechanism is proposed. Mucopolysaccharidosis type IIIA (Sanfilippo A syndrome), a fatal childhood-onset neurodegenerative disease with mild facial, visceral and skeletal abnormalities, is caused by an inherited deficiency of the enzyme N-sulfoglucosamine sulfohydrolase (SGSH; sulfamidase). More than 100 mutations in the SGSH gene have been found to reduce or eliminate its enzymatic activity. However, the molecular understanding of the effect of these mutations has been confined by a lack of structural data for this enzyme. Here, the crystal structure of glycosylated SGSH is presented at 2 Å resolution. Despite the low sequence identity between this unique N-sulfatase and the group of O-sulfatases, they share a similar overall fold and active-site architecture, including a catalytic formylglycine, a divalent metal-binding site and a sulfate-binding site. However, a highly conserved lysine in O-sulfatases is replaced in SGSH by an arginine (Arg282) that is positioned to bind the N-linked sulfate substrate. The structure also provides insight into the diverse effects of pathogenic mutations on SGSH function in mucopolysaccharidosis type IIIA and convincing evidence for the molecular consequences of many missense mutations. Further, the molecular characterization of SGSH mutations will lay the groundwork for the development of structure-based drug design for this devastating neurodegenerative disorder

Structure of sulfamidase provides insight into the molecular pathology of mucopolysaccharidosis IIIA

Energy Technology Data Exchange (ETDEWEB)

Sidhu, Navdeep S. [University of Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen (Germany); University of Göttingen, Tammannstrasse 4, 37077 Göttingen (Germany); Schreiber, Kathrin [University of Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen (Germany); Pröpper, Kevin [University of Göttingen, Tammannstrasse 4, 37077 Göttingen (Germany); Becker, Stefan [Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen (Germany); Usón, Isabel [Instituto de Biologia Molecular de Barcelona (IBMB–CSIC), Barcelona Science Park, Baldiri Reixach 15, 08028 Barcelona (Spain); Institucio Catalana de Recerca i Estudis Avancats (ICREA), (Spain); Sheldrick, George M. [University of Göttingen, Tammannstrasse 4, 37077 Göttingen (Germany); Gärtner, Jutta; Krätzner, Ralph, E-mail: rkraetz@gwdg.de; Steinfeld, Robert, E-mail: rkraetz@gwdg.de [University of Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen (Germany)

2014-05-01

Mucopolysaccharidosis IIIA is a fatal neurodegenerative disease that typically manifests itself in childhood and is caused by mutations in the gene for the lysosomal enzyme sulfamidase. The first structure of this enzyme is presented, which provides insight into the molecular basis of disease-causing mutations, and the enzymatic mechanism is proposed. Mucopolysaccharidosis type IIIA (Sanfilippo A syndrome), a fatal childhood-onset neurodegenerative disease with mild facial, visceral and skeletal abnormalities, is caused by an inherited deficiency of the enzyme N-sulfoglucosamine sulfohydrolase (SGSH; sulfamidase). More than 100 mutations in the SGSH gene have been found to reduce or eliminate its enzymatic activity. However, the molecular understanding of the effect of these mutations has been confined by a lack of structural data for this enzyme. Here, the crystal structure of glycosylated SGSH is presented at 2 Å resolution. Despite the low sequence identity between this unique N-sulfatase and the group of O-sulfatases, they share a similar overall fold and active-site architecture, including a catalytic formylglycine, a divalent metal-binding site and a sulfate-binding site. However, a highly conserved lysine in O-sulfatases is replaced in SGSH by an arginine (Arg282) that is positioned to bind the N-linked sulfate substrate. The structure also provides insight into the diverse effects of pathogenic mutations on SGSH function in mucopolysaccharidosis type IIIA and convincing evidence for the molecular consequences of many missense mutations. Further, the molecular characterization of SGSH mutations will lay the groundwork for the development of structure-based drug design for this devastating neurodegenerative disorder.

Tunneling and resonant conductance in one-dimensional molecular structures

International Nuclear Information System (INIS)

Kozhushner, M.A.; Posvyanskii, V.S.; Oleynik, I.I.

2005-01-01

We present a theory of tunneling and resonant transitions in one-dimensional molecular systems which is based on Green's function theory of electron sub-barrier scattering off the structural units (or functional groups) of a molecular chain. We show that the many-electron effects are of paramount importance in electron transport and they are effectively treated using a formalism of sub-barrier scattering operators. The method which calculates the total scattering amplitude of the bridge molecule not only predicts the enhancement of the amplitude of tunneling transitions in course of tunneling electron transfer through onedimensional molecular structures but also allows us to interpret conductance mechanisms by calculating the bound energy spectrum of the tunneling electron, the energies being obtained as poles of the total scattering amplitude of the bridge molecule. We found that the resonant tunneling via bound states of the tunneling electron is the major mechanism of electron conductivity in relatively long organic molecules. The sub-barrier scattering technique naturally includes a description of tunneling in applied electric fields which allows us to calculate I-V curves at finite bias. The developed theory is applied to explain experimental findings such as bridge effect due to tunneling through organic molecules, and threshold versus Ohmic behavior of the conductance due to resonant electron transfer

The crystal structures of three pyrazine-2,5-dicarb-oxamides: three-dimensional supra-molecular structures.

Science.gov (United States)

Cati, Dilovan S; Stoeckli-Evans, Helen

2017-05-01

The complete mol-ecules of the title compounds, N 2 , N 5 -bis-(pyridin-2-ylmeth-yl)pyrazine-2,5-dicarboxamide, C 18 H 16 N 6 O 2 (I), 3,6-dimethyl- N 2 , N 5 -bis-(pyridin-2-yl-meth-yl)pyrazine-2,5-dicarboxamide, C 20 H 20 N 6 O 2 (II), and N 2 , N 5 -bis-(pyridin-4-ylmeth-yl)pyrazine-2,5-dicarboxamide, C 18 H 16 N 6 O 2 (III), are generated by inversion symmetry, with the pyrazine rings being located about centres of inversion. Each mol-ecule has an extended conformation with the pyridine rings inclined to the pyrazine ring by 89.17 (7)° in (I), 75.83 (8)° in (II) and by 82.71 (6)° in (III). In the crystal of (I), mol-ecules are linked by N-H⋯N hydrogen bonds, forming layers lying parallel to the bc plane. The layers are linked by C-H⋯O hydrogen bonds, forming a three-dimensional supra-molecular structure. In the crystal of (II), mol-ecules are also linked by N-H⋯N hydrogen bonds, forming layers lying parallel to the (10-1) plane. As in (I), the layers are linked by C-H⋯O hydrogen bonds, forming a three-dimensional supra-molecular structure. In the crystal of (III), mol-ecules are again linked by N-H⋯N hydrogen bonds, but here form corrugated sheets lying parallel to the bc plane. Within the sheets, neighbouring pyridine rings are linked by offset π-π inter-actions [inter-centroid distance = 3.739 (1) Å]. The sheets are linked by C-H⋯O hydrogen bonds, forming a three-dimensional supra-molecular structure. Compound (I) crystallizes in the monoclinic space group P 2 1 / c . Another monoclinic polymorph, space group C 2/ c , has been reported on by Cockriel et al. [ Inorg. Chem. Commun. (2008), 11 , 1-4]. The mol-ecular structures of the two polymorphs are compared.

Unambiguous Determination of Intermolecular Hydrogen Bond of NMR Structure by Molecular Dynamics Refinement Using All-Atom Force Field and Implicit Solvent Model

International Nuclear Information System (INIS)

Jee, Jun Goo

2010-01-01

It has been shown that AMD refinement is very useful for defining an intermolecular hydrogen bond in NMR structure calculation. The refined structure also provides a clue for explaining the pH dependence in Ub and UIM complexes. As reported by Choi et al., serine-mediated hydrogen bonds are the third most populated hydrogen bonds found in protein-protein intermolecular interactions, after the backbone-backbone and backbone-aspartate ones. The abundance imposes the requirement of an method to determine the interface of protein-protein complexes. The precise geometry is particularly important in the complex structures between Ub and UBDs. Ub recognizes various targets with the same surface, where both hydrophobic and hydrophobic interactions are involved. Hence, the details of the hydrophilic interactions are necessary to find the common binding modes. The structure determination of a biomolecule by NMR depends heavily on the distance restraints derived by the NOE cross peaks that are observed between two protons within 6 A through space. Therefore, the existence of the NOE peaks and their correct assignments to two corresponding protons are essential for an accurate and precise structure determination. Recent developments of NOE assignment and calculation algorithms have enabled the determination of protein 3D structures without any manual interpretation, provided chemical shifts are assigned in most atoms and sufficient NOE peaks exist. Along with these advances, the necessity of determining complicated structures such as complexes is increasing

Assessment of structural, thermal, and mechanical properties of portlandite through molecular dynamics simulations

Energy Technology Data Exchange (ETDEWEB)

Hajilar, Shahin, E-mail: shajilar@iastate.edu [Department of Civil, Construction and Environmental Engineering, Iowa State University, Ames, IA 50011-1066 (United States); Shafei, Behrouz, E-mail: shafei@iastate.edu [Department of Civil, Construction and Environmental Engineering, Department of Materials Science and Engineering, Iowa State University, Ames, IA 50011-1066 (United States)

2016-12-15

The structural, thermal, and mechanical properties of portlandite, the primary solid phase of ordinary hydrated cement paste, are investigated using the molecular dynamics method. To understand the effects of temperature on the structural properties of portlandite, the coefficients of thermal expansion of portlandite are determined in the current study and validated with what reported from the experimental tests. The atomic structure of portlandite equilibrated at various temperatures is then subjected to uniaxial tensile strains in the three orthogonal directions and the stress-strain curves are developed. Based on the obtained results, the effect of the direction of straining on the mechanical properties of portlandite is investigated in detail. Structural damage analysis is performed to reveal the failure mechanisms in different directions. The energies of the fractured surfaces are calculated in different directions and compared to those of the ideal surfaces available in the literature. The key mechanical properties, including tensile strength, Young's modulus, and fracture strain, are extracted from the stress-strain curves. The sensitivity of the obtained mechanical properties to temperature and strain rate is then explored in a systematic way. This leads to valuable information on how the structural and mechanical properties of portlandite are affected under various exposure conditions and loading rates. - Graphical abstract: Fracture mechanism of portlandite under uniaxial strain in the z-direction. - Highlights: • The structural, thermal, and mechanical properties of portlandite are investigated. • The coefficients of thermal expansion are determined. • The stress-strain relationships are studied in three orthogonal directions. • The effects of temperature and strain rate on mechanical properties are examined. • The plastic energy required for fracture in the crystalline structure is reported.

Molecular modeling of nucleic Acid structure: electrostatics and solvation.

Science.gov (United States)

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

2014-12-19

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. Copyright © 2014 John Wiley & Sons, Inc.

Design of Carborane Molecular Architectures via Electronic Structure Computations

International Nuclear Information System (INIS)

Oliva, J.M.; Serrano-Andres, L.; Klein, D.J.; Schleyer, P.V.R.; Mich, J.

2009-01-01

Quantum-mechanical electronic structure computations were employed to explore initial steps towards a comprehensive design of poly carborane architectures through assembly of molecular units. Aspects considered were (i) the striking modification of geometrical parameters through substitution, (ii) endohedral carboranes and proposed ejection mechanisms for energy/ion/atom/energy storage/transport, (iii) the excited state character in single and dimeric molecular units, and (iv) higher architectural constructs. A goal of this work is to find optimal architectures where atom/ion/energy/spin transport within carborane superclusters is feasible in order to modernize and improve future photo energy processes.

Detailed intermolecular structure of molecular liquids containing slightly distorted tetrahedral molecules with C(3v) symmetry: chloroform, bromoform, and methyl-iodide.

Science.gov (United States)

Pothoczki, Szilvia; Temleitner, László; Pusztai, László

2011-01-28

Analyses of the intermolecular structure of molecular liquids containing slightly distorted tetrahedral molecules of the CXY(3)-type are described. The process is composed of the determination of several different distance-dependent orientational correlation functions, including ones that are introduced here. As a result, a complete structure classification could be provided for CXY(3) molecular liquids, namely for liquid chloroform, bromoform, and methyl-iodide. In the present work, the calculations have been conducted on particle configurations resulting from reverse Monte Carlo computer modeling: these particle arrangements have the advantage that they are fully consistent with structure factors from neutron and x-ray diffraction measurements. It has been established that as the separation between neighboring molecules increases, the dominant mutual orientations change from face-to-face to edge-to-edge, via the edge-to-face arrangements. Depending on the actual liquid, these geometrical elements (edges and faces of the distorted tetrahedra) were found to contain different atoms. From the set of liquids studied here, the structure of methyl-iodide was found to be easiest to describe on the basis of pure steric effects (molecular shape, size, and density) and the structure of liquid chloroform seems to be the furthest away from the corresponding "flexible fused hard spheres" like reference system.

Marine Biotoxins: Laboratory Culture and Molecular Structure

Science.gov (United States)

1991-01-21

ciguateric carnivorous fishes in concentrations ranging from I to 10 ppb. Its molecular structure has been elucidated. It has been isolated from toxic...American Chemical Society, Washington, DC, 1984, pp 217-329. 6. Med. J. Australia 1986, 145 (11/12), 558; 584-5M). 7. "Toxic Plants and Animals A Guide...isolated and grown in the laboratory. Lethality of crude acetone and methanol extracts were assa~ed by ip injection into mice. In vitro cytotoxicity and

Application of the AMPLE cluster-and-truncate approach to NMR structures for molecular replacement

Energy Technology Data Exchange (ETDEWEB)

Bibby, Jaclyn [University of Liverpool, Liverpool L69 7ZB (United Kingdom); Keegan, Ronan M. [Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Didcot OX11 0FA (United Kingdom); Mayans, Olga [University of Liverpool, Liverpool L69 7ZB (United Kingdom); Winn, Martyn D. [Science and Technology Facilities Council Daresbury Laboratory, Warrington WA4 4AD (United Kingdom); Rigden, Daniel J., E-mail: drigden@liv.ac.uk [University of Liverpool, Liverpool L69 7ZB (United Kingdom)

2013-11-01

Processing of NMR structures for molecular replacement by AMPLE works well. AMPLE is a program developed for clustering and truncating ab initio protein structure predictions into search models for molecular replacement. Here, it is shown that its core cluster-and-truncate methods also work well for processing NMR ensembles into search models. Rosetta remodelling helps to extend success to NMR structures bearing low sequence identity or high structural divergence from the target protein. Potential future routes to improved performance are considered and practical, general guidelines on using AMPLE are provided.

The effect of high hydrostatic pressure treatment on the molecular structure of starches with different amylose content.

Science.gov (United States)

Szwengiel, Artur; Lewandowicz, Grażyna; Górecki, Adrian R; Błaszczak, Wioletta

2018-02-01

The effect of high hydrostatic pressure processing (650MPa/9min) on molecular mass distribution, and hydrodynamic and structural parameters of amylose (maize, sorghum, Hylon VII) and amylopectin (waxy maize, amaranth) starches was studied. The starches were characterized by high-performance size-exclusion chromatography (HPSEC) equipped with static light scattering and refractive index detectors and by Fourier Transform Infrared (FTIR) spectroscopy. Significant changes were observed in molecular mass distribution of pressurized waxy maize starch. Changes in branches/branch frequency, intrinsic viscosity, and radius of gyration were observed for all treated starches. The combination of SEC and FTIR data showed that α-1,6-glycosidic bonds are more frequently split in pressurized amaranth, Hylon VII, and waxy maize starch, while in sorghum and maize starches, the α-1,4 bonds are most commonly split. Our results show that the structural changes found for pressurized starches were more strongly determined by the starch origin than by the processing applied. Copyright © 2017 Elsevier Ltd. All rights reserved.

Electronic structure and partial charge distribution of Doxorubicin in different molecular environments.

Science.gov (United States)

Poudel, Lokendra; Wen, Amy M; French, Roger H; Parsegian, V Adrian; Podgornik, Rudolf; Steinmetz, Nicole F; Ching, Wai-Yim

2015-05-18

The electronic structure and partial charge of doxorubicin (DOX) in three different molecular environments-isolated, solvated, and intercalated in a DNA complex-are studied by first-principles density functional methods. It is shown that the addition of solvating water molecules to DOX, together with the proximity to and interaction with DNA, has a significant impact on the electronic structure as well as on the partial charge distribution. Significant improvement in estimating the DOX-DNA interaction energy is achieved. The results are further elucidated by resolving the total density of states and surface charge density into different functional groups. It is concluded that the presence of the solvent and the details of the interaction geometry matter greatly in determining the stability of DOX complexation. Ab initio calculations on realistic models are an important step toward a more accurate description of the long-range interactions in biomolecular systems. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular sieving through a graphene nanopore: non-equilibrium molecular dynamics simulation

Institute of Scientific and Technical Information of China (English)

Chengzhen Sun; Bofeng Bai

2017-01-01

Two-dimensional graphene nanopores have shown great promise as ultra-permeable molecular sieves based on their size-sieving effects.We design a nitrogen/hydrogen modified graphene nanopore and conduct a transient non-equilibrium molecular dynamics simulation on its molecular sieving effects.The distinct time-varying molecular crossing numbers show that this special nanopore can efficiently sieve CO2 and H2S molecules from CH4 molecules with high selectivity.By analyzing the molecular structure and pore functionalization-related molecular orientation and permeable zone in the nanopore,density distribution in the molecular adsorption layer on the graphene surface,as well as other features,the molecular sieving mechanisms of graphene nanopores are revealed.Finally,several implications on the design of highly-efficient graphene nanopores,especially for determining the porosity and chemical functionalization,as gas separation membranes are summarized based on the identified phenomena and mechanisms.

FlaME: Flash Molecular Editor - a 2D structure input tool for the web

Directory of Open Access Journals (Sweden)

Dallakian Pavel

2011-02-01

Full Text Available Abstract Background So far, there have been no Flash-based web tools available for chemical structure input. The authors herein present a feasibility study, aiming at the development of a compact and easy-to-use 2D structure editor, using Adobe's Flash technology and its programming language, ActionScript. As a reference model application from the Java world, we selected the Java Molecular Editor (JME. In this feasibility study, we made an attempt to realize a subset of JME's functionality in the Flash Molecular Editor (FlaME utility. These basic capabilities are: structure input, editing and depiction of single molecules, data import and export in molfile format. Implementation The result of molecular diagram sketching in FlaME is accessible in V2000 molfile format. By integrating the molecular editor into a web page, its communication with the HTML elements on this page is established using the two JavaScript functions, getMol( and setMol(. In addition, structures can be copied to the system clipboard. Conclusion A first attempt was made to create a compact single-file application for 2D molecular structure input/editing on the web, based on Flash technology. With the application examples presented in this article, it could be demonstrated that the Flash methods are principally well-suited to provide the requisite communication between the Flash object (application and the HTML elements on a web page, using JavaScript functions.

Two-dimensional dynamics of a free molecular chain with a secondary structure

DEFF Research Database (Denmark)

Zolotaryuk, Alexander; Christiansen, Peter Leth; Savin, A.V.

1996-01-01

A simple two-dimensional (2D) model of an isolated (free) molecular chain with primary and secondary structures has been suggested and investigated both analytically and numerically. This model can be considered as the simplest generalization of the well-known Fermi-Pasta-Ulam model of an anharmo......A simple two-dimensional (2D) model of an isolated (free) molecular chain with primary and secondary structures has been suggested and investigated both analytically and numerically. This model can be considered as the simplest generalization of the well-known Fermi-Pasta-Ulam model...

Effect of molecular weight on the vibronic structure of a diketopyrrolopyrrole polymer

KAUST Repository

Hayes, Sophia C.

2016-09-27

Resonance Raman Spectroscopy (RRS) is employed in this study to examine the influence of molecular weight on the optical response of a diketopyrrolopyrrole polymer (DPP-TT-T) in solution. The vibronic structure observed for the ground state absorption of this polymer is found to vary with molecular weight and solvent. Resonance Raman Intensity Analysis (RRIA) revealed that the absorption spectra can be described by at least two dipole-allowed transitions and the vibronic structure variation is due to differing contributions from linear and curved segments of the polymer.

Effect of molecular weight on the vibronic structure of a diketopyrrolopyrrole polymer

KAUST Repository

Hayes, Sophia C.; Pieridou, Galatia; Vezie, Michelle; Few, Sheridan; Bronstein, Hugo; Meager, Iain; McCulloch, Iain; Nelson, Jenny

2016-01-01

Resonance Raman Spectroscopy (RRS) is employed in this study to examine the influence of molecular weight on the optical response of a diketopyrrolopyrrole polymer (DPP-TT-T) in solution. The vibronic structure observed for the ground state absorption of this polymer is found to vary with molecular weight and solvent. Resonance Raman Intensity Analysis (RRIA) revealed that the absorption spectra can be described by at least two dipole-allowed transitions and the vibronic structure variation is due to differing contributions from linear and curved segments of the polymer.

Determination of molecular structure of succinic acid in a very complex conformational landscape: Gas-phase electron diffraction (GED) and ab initio studies

Science.gov (United States)

Vogt, Natalja; Abaev, Maxim A.; Rykov, Anatolii N.; Shishkov, Igor F.

2011-06-01

The molecular structure of succinic acid has been investigated by the gas-phase electron diffraction (GED) method for the first time. According to predictions of MP2/cc-pVTZ calculations, the molecule has 18 stable conformers with the C sbnd C sbnd C sbnd C chain in the gauche ( G) or anti ( A) configuration, and four of them, I ( G), II ( A), III ( G) and IV ( A) belonging to the C 2, C 2h, C 1 and C 1 point groups, respectively, with relative energies ΔE ZPE within 2.2 kcal/mol can be present at the experimental temperature of 445 K in noticeable amounts. The ratio of the conformers I:II:III:IV = 45(15):20(15):10(assumed):25(15) (in %) has been determined in the GED analysis guided by theoretical predictions. To take into account vibrational effects, the corrections Δ( r e - r a) to the experimental r a bond lengths were calculated from the MP2/cc-pVTZ quadratic and cubic force constants. The obtained equilibrium structural parameters of the dominant conformer I are the following (bond lengths in Å, angles in degrees): r e(C sp3sbnd C sp3) = 1.508(3), r e(C sp3sbnd C sp2) = 1.499(2), r e(C sbnd O) = 1.343(2), r e(C dbnd O) = 1.202(1), e(C sbnd C sbnd C) = 111.8(4), e(C sbnd C sbnd O) = 112.0(4), e(O sbnd C dbnd O) = 123.0(1), τ(C sbnd C sbnd C sbnd C) = 69.9(11). Yielding the best agreement with the GED structure, the MP2/cc-pVQZ approximation overestimates the C sbnd O and C dbnd O bond lengths by ca. 0.005(2) Å.

Molecular and Genetic Determinants of Glioma Cell Invasion

Directory of Open Access Journals (Sweden)

Kenta Masui

2017-12-01

Full Text Available A diffusely invasive nature is a major obstacle in treating a malignant brain tumor, “diffuse glioma”, which prevents neurooncologists from surgically removing the tumor cells even in combination with chemotherapy and radiation. Recently updated classification of diffuse gliomas based on distinct genetic and epigenetic features has culminated in a multilayered diagnostic approach to combine histologic phenotypes and molecular genotypes in an integrated diagnosis. However, it is still a work in progress to decipher how the genetic aberrations contribute to the aggressive nature of gliomas including their highly invasive capacity. Here we depict a set of recent discoveries involving molecular genetic determinants of the infiltrating nature of glioma cells, especially focusing on genetic mutations in receptor tyrosine kinase pathways and metabolic reprogramming downstream of common cancer mutations. The specific biology of glioma cell invasion provides an opportunity to explore the genotype-phenotype correlation in cancer and develop novel glioma-specific therapeutic strategies for this devastating disease.

The effect of glycosylation on the transferrin structure: A molecular dynamic simulation analysis.

Science.gov (United States)

Ghanbari, Z; Housaindokht, M R; Bozorgmehr, M R; Izadyar, M

2016-09-07

Transferrins have been defined by the highly cooperative binding of iron and a carbonate anion to form a Fe-CO3-Tf ternary complex. As such, the layout of the binding site residues affects transferrin function significantly; In contrast to N-lobe, C-lobe binding site of the transferrin structure has been less characterized and little research which surveyed the interaction of carbonate with transferrin in the C-lobe binding site has been found. In the present work, molecular dynamic simulation was employed to gain access into the molecular level understanding of carbonate binding site and their interactions in each lobe. Residues responsible for carbonate binding of transferrin structure were pointed out. In addition, native human transferrin is a glycoprotein that two N-linked complex glycan chains located in the C-lobe. Usually, in the molecular dynamic simulation for simplifying, glycan is removed from the protein structure. Here, we explore the effect of glycosylation on the transferrin structure. Glycosylation appears to have an effect on the layout of the binding site residue and transferrin structure. On the other hand, sometimes the entire transferrin formed by separated lobes that it allows the results to be interpreted in a straightforward manner rather than more parameters required for full length protein. But, it should be noted that there are differences between the separated lobe and full length transferrin, hence, a comparative analysis by the molecular dynamic simulation was performed to investigate such structural variations. Results revealed that separation in C-lobe caused a significant structural variation in comparison to N-lobe. Consequently, the separated lobes and the full length one are different, showing the importance of the interlobe communication and the impact of the lobes on each other in the transferrin structure. Copyright © 2016 Elsevier Ltd. All rights reserved.

Structural properties of iron nitride on Cu(100): An ab-initio molecular dynamics study

KAUST Repository

Heryadi, Dodi

2011-01-01

Due to their potential applications in magnetic storage devices, iron nitrides have been a subject of numerous experimental and theoretical investigations. Thin films of iron nitride have been successfully grown on different substrates. To study the structural properties of a single monolayer film of FeN we have performed an ab-initio molecular dynamics simulation of its formation on a Cu(100) substrate. The iron nitride layer formed in our simulation shows a p4gm(2x2) reconstructed surface, in agreement with experimental results. In addition to its structural properties, we are also able to determine the magnetization of this thin film. Our results show that one monolayer of iron nitride on Cu(100) is ferromagnetic with a magnetic moment of 1.67 μ B. © 2011 Materials Research Society.

Early structural development in melt-quenched polymer PTT from atomistic molecular dynamic simulations

Science.gov (United States)

Hsieh, Min-Kang; Lin, Shiang-Tai

2009-12-01

Molecular dynamics simulations are performed to study the initial structural development in poly(trimethylene terephthalate) (PTT) when quenched below its melting point. The development of local ordering has been observed in our simulations. The thermal properties, such as the glass transition temperature (Tg) and the melting temperature (Tm), determined from our simulations are in reasonable agreement with experimental values. It is found that, between these two temperatures, the number of local structures quickly increases during the thermal relaxation period soon after the system is quenched and starts to fluctuate afterwards. The formation and development of local structures is found to be driven mainly by the torsional and van der Waals forces and follows the classical nucleation-growth mechanism. The variation of local structures' fraction with temperature exhibits a maximum between Tg and Tm, resembling the temperature dependence of the crystallization rate for most polymers. In addition, the backbone torsion distribution for segments within the local structures preferentially reorganizes to the trans-gauche-gauche-trans (t-g-g-t) conformation, the same as that in the crystalline state. As a consequence, we believe that such local structural ordering could be the baby nuclei that have been suggested to form in the early stage of polymer crystallization.

Selective extraction and determination of chlorogenic acids as combined quality markers in herbal medicines using molecularly imprinted polymers based on a mimic template.

Science.gov (United States)

Ji, Wenhua; Zhang, Mingming; Yan, Huijiao; Zhao, Hengqiang; Mu, Yan; Guo, Lanping; Wang, Xiao

2017-12-01

We describe a solid-phase extraction adsorbent based on molecularly imprinted polymers (MIPs), prepared with use of a mimic template. The MIPs were used for the selective extraction and determination of three chlorogenic acids as combined quality markers for Lonicera japonica and Lianhua qingwen granules. The morphologies and surface groups of the MIPs were assessed by scanning electron microscopy, Brunauer-Emmett-Teller surface area analysis, and Fourier transform infrared spectroscopy. The adsorption isotherms, kinetics, and selectivity of the MIPs were systematically compared with those of non-molecularly imprinted polymers. The MIPs showed high selectivity toward three structurally similar chlorogenic acids (chlorogenic acid, cryptochlorogenic acid, and neochlorogenic acid). A procedure using molecularly imprinted solid-phase extraction coupled with high-performance liquid chromatography was established for the determination of three chlorogenic acids from Lonicera japonica and Lianhua qingwen granules. The recoveries of the chlorogenic acids ranged from 93.1% to 101.4%. The limits of detection and limits of quantification for the three chlorogenic acids were 0.003 mg g -1 and 0.01 mg g -1 , respectively. The newly developed method is thus a promising technique for the enrichment and determination of chlorogenic acids from herbal medicines. Graphical Abstract Mimic molecularly imprinted polymers for the selective extraction of chlorogenic acids.

The use of angle resolved electron and photon stimulated desorption for the determination of molecular structure at surfaces

International Nuclear Information System (INIS)

Madey, T.E.; Stockbauer, R.

1983-01-01

A brief review of recent data related to the use of angle-resolved electron stimulated desorption and photon stimulated desorption in determining the structures of molecules at surfaces is made. Examples include a variety of structural assignments based on ESIAD (electron stimulated desorption ion angular distributions), the observation of short-range local ordering effects induced in adsorbed molecules by surface impurities, and the application of photon stimulated desorption to both ionic and covalent adsorbate systems. (Author) [pt

The Design, Synthesis, and Study of Solid-State Molecular Rotors: Structure/Function Relationships for Condensed-Phase Anisotropic Dynamics

Science.gov (United States)

Vogelsberg, Cortnie Sue

Amphidynamic crystals are an extremely promising platform for the development of artificial molecular machines and stimuli-responsive materials. In analogy to skeletal muscle, their function will rely upon the collective operation of many densely packed molecular machines (i.e. actin-bound myosin) that are self-assembled in a highly organized anisotropic medium. By choosing lattice-forming elements and moving "parts" with specific functionalities, individual molecular machines may be synthesized and self-assembled in order to carry out desirable functions. In recent years, efforts in the design of amphidynamic materials based on molecular gyroscopes and compasses have shown that a certain amount of free volume is essential to facilitate internal rotation and reorientation within a crystal. In order to further establish structure/function relationships to advance the development of increasingly complex molecular machinery, molecular rotors and a molecular "spinning" top were synthesized and incorporated into a variety of solid-state architectures with different degrees of periodicity, dimensionality, and free volume. Specifically, lamellar molecular crystals, hierarchically ordered periodic mesoporous organosilicas, and metal-organic frameworks were targeted for the development of solid-state molecular machines. Using an array of solid-state nuclear magnetic resonance spectroscopy techniques, the dynamic properties of these novel molecular machine assemblies were determined and correlated with their corresponding structural features. It was found that architecture type has a profound influence on functional dynamics. The study of layered molecular crystals, composed of either molecular rotors or "spinning" tops, probed functional dynamics within dense, highly organized environments. From their study, it was discovered that: 1) crystallographically distinct sites may be utilized to differentiate machine function, 2) halogen bonding interactions are sufficiently

Learning Molecular Structures in a Tangible Augmented Reality Environment

Science.gov (United States)

Asai, Kikuo; Takase, Norio

2011-01-01

This article presents the characteristics of using a tangible table top environment produced by augmented reality (AR), aimed at improving the environment in which learners observe three-dimensional molecular structures. The authors perform two evaluation experiments. A performance test for a user interface demonstrates that learners with a…

Manipulation of arthropod sex determination by endosymbionts : Diversity and molecular mechanisms

NARCIS (Netherlands)

Ma, W. -J.; Vavre, F.; Beukeboom, L. W.

2014-01-01

Arthropods exhibit a large variety of sex determination systems both at the chromosomal and molecular level. Male heterogamety, female heterogamety, and haplodiploidy occur frequently, but partially different genes are involved. Endosymbionts, such as Wolbachia, Cardinium, Rickettsia, and

The Effects of Molecular Crowding on the Structure and Stability of G-Quadruplexes with an Abasic Site

Science.gov (United States)

Fujimoto, Takeshi; Nakano, Shu-ichi; Miyoshi, Daisuke; Sugimoto, Naoki

2011-01-01

Both cellular environmental factors and chemical modifications critically affect the properties of nucleic acids. However, the structure and stability of DNA containing abasic sites under cell-mimicking molecular crowding conditions remain unclear. Here, we investigated the molecular crowding effects on the structure and stability of the G-quadruplexes including a single abasic site. Structural analysis by circular dichroism showed that molecular crowding by PEG200 did not affect the topology of the G-quadruplex structure with or without an abasic site. Thermodynamic analysis further demonstrated that the degree of stabilization of the G-quadruplex by molecular crowding decreased with substitution of an abasic site for a single guanine. Notably, we found that the molecular crowding effects on the enthalpy change for G-quadruplex formation had a linear relationship with the abasic site effects depending on its position. These results are useful for predicting the structure and stability of G-quadruplexes with abasic sites in the cell-mimicking conditions. PMID:21949901

Effects of molecular structure on microscopic heat transport in chain polymer liquids

International Nuclear Information System (INIS)

Matsubara, Hiroki; Kikugawa, Gota; Ohara, Taku; Bessho, Takeshi; Yamashita, Seiji

2015-01-01

In this paper, we discuss the molecular mechanism of the heat conduction in a liquid, based on nonequilibrium molecular dynamics simulations of a systematic series of linear- and branched alkane liquids, as a continuation of our previous study on linear alkane [T. Ohara et al., J. Chem. Phys. 135, 034507 (2011)]. The thermal conductivities for these alkanes in a saturated liquid state at the same reduced temperature (0.7T c ) obtained from the simulations are compared in relation to the structural difference of the liquids. In order to connect the thermal energy transport characteristics with molecular structures, we introduce the new concept of the interatomic path of heat transfer (atomistic heat path, AHP), which is defined for each type of inter- and intramolecular interaction. It is found that the efficiency of intermolecular AHP is sensitive to the structure of the first neighbor shell, whereas that of intramolecular AHP is similar for different alkane species. The dependence of thermal conductivity on different lengths of the main and side chain can be understood from the natures of these inter- and intramolecular AHPs

Effects of molecular structure on microscopic heat transport in chain polymer liquids

Energy Technology Data Exchange (ETDEWEB)

Matsubara, Hiroki, E-mail: matsubara@microheat.ifs.tohoku.ac.jp; Kikugawa, Gota; Ohara, Taku [Institute of Fluid Science, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577 (Japan); Bessho, Takeshi; Yamashita, Seiji [Higashifuji Technical Center, Toyota Motor Corporation, 1200 Mishuku, Susono, Shizuoka 410-1193 (Japan)

2015-04-28

In this paper, we discuss the molecular mechanism of the heat conduction in a liquid, based on nonequilibrium molecular dynamics simulations of a systematic series of linear- and branched alkane liquids, as a continuation of our previous study on linear alkane [T. Ohara et al., J. Chem. Phys. 135, 034507 (2011)]. The thermal conductivities for these alkanes in a saturated liquid state at the same reduced temperature (0.7T{sub c}) obtained from the simulations are compared in relation to the structural difference of the liquids. In order to connect the thermal energy transport characteristics with molecular structures, we introduce the new concept of the interatomic path of heat transfer (atomistic heat path, AHP), which is defined for each type of inter- and intramolecular interaction. It is found that the efficiency of intermolecular AHP is sensitive to the structure of the first neighbor shell, whereas that of intramolecular AHP is similar for different alkane species. The dependence of thermal conductivity on different lengths of the main and side chain can be understood from the natures of these inter- and intramolecular AHPs.

Variable contact gap single-molecule conductance determination for a series of conjugated molecular bridges

DEFF Research Database (Denmark)

Haiss, W.; Wang, Christian; Jitchati, R.

2008-01-01

It is now becoming clear that the characteristics of the whole junction are important in determining the conductance of single molecules bound between two metal contacts. This paper shows through measurements on a series of seven conjugated molecular bridges that contact separation is an importan...... that conductance increases rather dramatically at higher tilt angle away from the normal for conformationally rigid molecular wires and that this increase in conductance arises from increased electronic coupling between the molecular bridge and the gold contacts.......It is now becoming clear that the characteristics of the whole junction are important in determining the conductance of single molecules bound between two metal contacts. This paper shows through measurements on a series of seven conjugated molecular bridges that contact separation is an important......-distance curves and knowledge of the terminal to terminal length of the molecular wire. The contact gap separation dependence is interpreted as arising from tilting of these molecules in the junction and this model is underpinned by ab initio transport computations. In this respect we make the general observation...

Electronic properties of single-molecule junction: Effect of the molecular distortion

International Nuclear Information System (INIS)

Gao, W.; Zhao, M.; Jiang, Q.

2009-01-01

For a model system consisting of a benzenedithio (BDT) molecule sandwiched between two Au plates, the electronic properties as a function of different BDT geometry are investigated using density functional theory. The distorted BDT structures are got through stretching the electrode distance. The corresponding electronic properties, including the spatial distribution of the frontier orbits, the gap between the highest occupied molecular orbital and the lowest unoccupied molecular orbital levels and density of states at the Fermi energy are determined. It reveals that the molecular distortion essentially determines electronic structures. The result should be beneficial to understand the stress-dependent or structure-dependent transport mechanism of electrons of the BDT junction.

Exponential Repulsion Improves Structural Predictability of Molecular Docking

Czech Academy of Sciences Publication Activity Database

Bazgier, Václav; Berka, K.; Otyepka, M.; Banáš, P.

2016-01-01

Roč. 37, č. 28 (2016), s. 2485-2494 ISSN 0192-8651 Institutional support: RVO:61389030 Keywords : cyclin-dependent kinases * structure-based design * scoring functions * cdk2 inhibitors * force-field * ligand interactions * drug discovery * purine * potent * protein-kinase-2 * molecular docking * dock 6.6 * drug design * cyclin-dependent kinase 2 * directory of decoys Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.229, year: 2016

Splitting of α-Helical Structure as Molecular Basis for Abolishing an Amyloid Formation by Multiple Glycosylation: A Molecular Dynamics Simulation Study

Energy Technology Data Exchange (ETDEWEB)

Choi, Youngjin [Hoseo University, Asan (Korea, Republic of); Cho, Eunae; Jung, Seunho [Konkuk University, Seoul (Korea, Republic of)

2016-07-15

Molecular details played by glycosylation are complicated by the subtle nature of variations in the glycan structure, and this complexity is one of the research barriers to establish structure-function relationship on the protein modification. This is particularly true for understanding the exact structural consequence of the glycosylation of the biological proteins. The present MD simulation revealed molecular-level mechanism of the glycosylation effect on the peptide to understand the experimentally observed phenomenon for inhibiting amyloid formation in the model peptide. The galactose residue on the Ser17 undermined the helical integrity of main protein region by enhancing sugar–amino acid interaction and perturbing natural interactions between amino acid residues.

Molecular motion and structure in plastics

International Nuclear Information System (INIS)

Doolan, K.R.; Baxter, M.

2000-01-01

Full text: When molten thermoplastics solidify, the polymeric chains form a completely amorphous structure or a mixture of crystalline and amorphous regions. Measurement of Nuclear Magnetic Resonance (NMR) relaxation times provides information about the configuration and molecular motion of polymeric chains in solid plastics. We are currently measuring the NMR relaxation times T 1 , T 2 , T 2 and T 1p as a function of temperature using a Bruker High Power pulsed NMR Spectrometer for several different classes of thermoplastics containing varying concentrations of inorganic filler materials. We present data here for T 1 , and T 2 obtained for polyethylenes, polypropylenes, polystyrenes and acrylics in the temperature range 100 K to 450 K. At temperatures below 320 K, all of the polyethylenes and polypropylenes and some of the polystyrenes and acrylics produced NMR signals after a single radio frequency (RF) pulse with rapidly and slowly decaying components corresponding to the rigid and flexible regions within the plastic. From these results we have estimated using Mathematica the amount of crystallinity within the polyethylenes and polypropylenes. For the impact modified polystyrenes and acrylics studied we have estimated the amounts of elastomeric phases present. We find that the initial rapid decay signal produced by polyethylenes and polypropylenes is Gaussian while the long tail is Lorentzian. All of the signal components from the polystyrenes and the acrylics were fitted using Lorentzian functions indicating their structures are highly amorphous. Addition of CaCO 3 filler to polypropylene resins appears to reduce the crystallinity of the material. We also present data for the activation energy of the molecular motion inducing longitudinal relaxation, from T 1 measurements

Cytoskeleton Molecular Motors: Structures and Their Functions in Neuron.

Science.gov (United States)

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.

Structure and properties of sodium aluminosilicate glasses from molecular dynamics simulations

DEFF Research Database (Denmark)

Xiang, Ye; Du, Jincheng; Smedskjær, Morten Mattrup

2013-01-01

the recent Corning® Gorilla® Glass. In this paper, the structures of sodium aluminosilicate glasses with a wide range of Al/Na ratios (from 1.5 to 0.6) have been studied using classical molecular dynamics simulations in a system containing around 3000 atoms, with the aim to understand the structural role...

Molecular characterization of composite interfaces

International Nuclear Information System (INIS)

Ishida, H.

1982-01-01

The Fourier Transform Infrared Spectroscopy was applied to elucidate the molecular structures of the glass/matrix interface. The various interfaces and interphases were studied. It is found that the structure of the silane in a treating solution is important in determining the structure of the silane on glass fibers, influences the macroscopic properties of composites. The amount of silane on glass fibers, the state of hydrogen bonding, orientation, copolymerization of the organicfunctionality with the matrix, curing of the silane, and effect of water on the interface were investigated. It is shown that the molecular approach is useful to interpret and predict physicomechanical properties of composites

Structure-Activity Relationships on the Molecular Descriptors Family Project at the End

Directory of Open Access Journals (Sweden)

Lorentz JÄNTSCHI

2007-12-01

Full Text Available Molecular Descriptors Family (MDF on the Structure-Activity Relationships (SAR, a promising approach in investigation and quantification of the link between 2D and 3D structural information and the activity, and its potential in the analysis of the biological active compounds is summarized. The approach, attempts to correlate molecular descriptors family generated and calculated on a set of biological active compounds with their observed activity. The estimation as well as prediction abilities of the approach are presented. The obtained MDF SAR models can be used to predict the biological activity of unknown substrates in a series of compounds.

The molecular structure of the insoluble organic matter isolated from Murchison carbonaceous chondrite.

Science.gov (United States)

Robert, F.; Derenne, S.

2009-04-01

During these last 10 years, our group has characterized the various molecular moieties of the insoluble organic matter (IOM) isolated from carbonaceous meteorites with the aim of reconstructing its overall molecular structure. Indeed, a precise knowledge of the structure of an organic macromolecule contains irreplaceable information that traces its mechanisms of synthesis and its conditions of formation. Such a modelled structure will be presented. Carbonaceous chondrites contain up to 3 wt % of carbon that is under the form of soluble and insoluble fractions. The IOM, which constitutes more than 75 wt% of the bulk organic matter, was isolated from the bulk rock through successive acid dissolutions. The chemical structure of the isolated IOM has been studied by both (1) destructive and (2) non destructive methods. Methods include thermal and chemical degradations followed by GC/MS, spectroscopic techniques (nuclear magnetic resonance, Fourier transform infra red spectroscopy; X-ray absorption near-edge spectroscopy, electron paramagnetic resonance) along with high resolution transmission electron microscopy. Although each technique alone cannot provide definite information on the chemical structure of such a complex material, the combination of the results can be used to reconstruct the molecular structure of the IOM. The proposed structure accounts for all these measured parameters. The details of this structure reveal information of the conditions of its formation in space and allow to discuss the mechanisms of organo-synthesis in the cosmochemical context of the formation of the solar system.

Population structure of humpback whales in the western and central South Pacific Ocean as determined by vocal exchange among populations

OpenAIRE

Garland, E.C.; Goldizen, A.W.; Lilley, M.S.; Rekdahl, M.L.; Garrigue, Claire; Constantine, R.; Hauser, N.D.; Poole, M.M.; Robbins, J.; Noad, M.J.

2015-01-01

For cetaceans, population structure is traditionally determined by molecular genetics or photographically identified individuals. Acoustic data, however, has provided information on movement and population structure with less effort and cost than traditional methods in an array of taxa. Male humpback whales (Megaptera novaeangliae) produce a continually evolving vocal sexual display, or song, that is similar among all males in a population. The rapid cultural transmission (the transfer of inf...

Capital Structure Determinants and Governance Structure Variety in Franchising

NARCIS (Netherlands)

T. Jiang (Tao)

2009-01-01

textabstractThis thesis investigates two questions: the determinants of capital structure in franchising and its subsequent impact on the franchise financing decisions; and the efficient governance structure choice in franchising. We posit that firms franchise in order to benefit from the reduced

Structural changes in polytetrafluoroethylene molecular chains upon sliding against steel

NARCIS (Netherlands)

Shen, J.T.; Pei, Y.T.; Hosson, J.Th.M. De

In this work, the influence of dry sliding between a steel counterpart ball and polytetrafluoroethylene (PTFE) plate sample on the transformation of PTFE molecular structure is investigated. With X-ray diffraction, differential scanning calorimetry, Fourier transform infrared (FT-IR) spectroscopy

The Role of Molecular Structure and Conformation in Polymer Electronics

NARCIS (Netherlands)

von Hauff, Elizabeth

2011-01-01

ABSTRACT Conjugated polymers have unique material properties that make them promising for a wide range of applications. The potential lies in the virtually infinite possibilities for creating new materials for specific applications by simply chemically tuning the molecular structure. Conjugated

ASM Inaugural Lecture 2010: Single crystal X-ray structural determination: A powerful technique for natural products research and drug discovery

International Nuclear Information System (INIS)

Fun Hoong Kun; Chantrapromma, S.; Boonnak, N.; Lee, V.S.

2010-01-01

Drug discovery from natural products resources have been extensively studied worldwide because natural products with their great structural diversity have traditionally provided most of the drugs in use. They offer major opportunities for finding novel low molecular weight leading-structures that are active against a wide range of assay targets. The most important step in the discovery process is the identification of compounds with interesting biological activity. Single crystal X-ray structure determination is a powerful technique for natural products research and drug discovery. The detailed three-dimensional structures that emerge can be co-related to the activities to these structures. In this article the following is presented: (i) co-crystal and disorder structures; (ii) determination of absolute configuration and (iii) the ability to distinguish between whether a natural product compound is a natural product or a natural product artifact. All these three properties are unique to the technique of single crystal X-ray structure determination. Case (iii) was demonstrated with a compound containing a chromene ring, namely macluraxanthone (which was isolated from Cratoxylum formosum subsp. pruniflorum, a Thai medicinal plant). (author)

Roles of water in protein structure and function studied by molecular liquid theory.

Science.gov (United States)

Imai, Takashi

2009-01-01

The roles of water in the structure and function of proteins have not been completely elucidated. Although molecular simulation has been widely used for the investigation of protein structure and function, it is not always useful for elucidating the roles of water because the effect of water ranges from atomic to thermodynamic level. The three-dimensional reference interaction site model (3D-RISM) theory, which is a statistical-mechanical theory of molecular liquids, can yield the solvation structure at the atomic level and calculate the thermodynamic quantities from the intermolecular potentials. In the last few years, the author and coworkers have succeeded in applying the 3D-RISM theory to protein aqueous solution systems and demonstrated that the theory is useful for investigating the roles of water. This article reviews some of the recent applications and findings, which are concerned with molecular recognition by protein, protein folding, and the partial molar volume of protein which is related to the pressure effect on protein.

Structural and Molecular Characterization of meso-Substituted Zinc Porphyrins: A DFT Supported Study

Directory of Open Access Journals (Sweden)

Giuseppe Mele

2011-12-01

Full Text Available Structural parameters of a range of over 100 meso-substituted zinc porphyrins were reviewed and compared to show how far the nature of the functional group may affect the interatomic distances and bond angles within the porphyrin core. It was proved that even despite evident deformations of the molecular structure, involving twisting of the porphyrin's central plane, the coupled π-bonding system remains flexible and stable. DFT calculations were applied to a number of selected porphyrins representative for the reviewed compounds to emphasize the relevance of theoretical methods in structural investigations of complex macrocyclic molecular systems. Experimental and DFT-simulated IR spectral data were reported and analyzed in context of the individual molecular features introduced by the meso substituents into the porphyrin moiety base. Raw experimental spectral data, including 1H- and 13C-NMR, UV-Vis, FTIR, XRD, and other relevant physicochemical details have been provided for a specially chosen reference zinc porphyrin functionalized by tert-butylphenyl groups.

Molecular structures of some 8-isoanalogues of steroid estrogens

International Nuclear Information System (INIS)

Starova, G.L.; Eliseev, I.I.; Abusalimov, Sh.N.; Tsogoeva, S.B.; Shavva, A.G.

2001-01-01

The molecular structures of three steroids, namely, 17β-acetoxy-3-methoxy-8-isoestra-1,3,5(10)-triene (I), 17β-acetoxy-3-methoxy-7α-methyl-8-isoestra-1,3,5(10)-triene (II), and 17β-acetoxy-3-methoxy-1-methyl-8-isoestra-1,3,5(10)-triene (III), are determined by X-ray diffraction analysis. It is shown that the substituents in the A and B rings of the compounds of the 8-iso series have a slight effect on the conformation of the steroid skeleton as a whole, which manifests itself only in insignificant distortions of the B and D rings. The methyl group in the 1-position (compound III) affects the geometric parameters of the steroid nucleus less than the same substituent in the 7-position (compound II). A sharp decrease in the uterotropic activity of compounds II and III (compared to compound I) revealed in biological studies can be attributed to unfavorable steric interactions of the substituents in the A and B rings with the estradiol receptor

Structure determination by X-ray crystallography

CERN Document Server

Ladd, M F C

1995-01-01

X-ray crystallography provides us with the most accurate picture we can get of atomic and molecular structures in crystals. It provides a hard bedrock of structural results in chemistry and in mineralogy. In biology, where the structures are not fully crystalline, it can still provide valuable results and, indeed, the impact here has been revolutionary. It is still an immense field for young workers, and no doubt will provide yet more striking develop­ ments of a major character. It does, however, require a wide range of intellectual application, and a considerable ability in many fields. This book will provide much help. It is a very straightforward and thorough guide to every aspect of the subject. The authors are experienced both as research workers themselves and as teachers of standing, and this is shown in their clarity of exposition. There are plenty of iliustrations and worked examples to aid the student to obtain a real grasp of the subject.

Invariant molecular-dynamics approach to structural phase transitions

International Nuclear Information System (INIS)

Wentzcovitch, R.M.

1991-01-01

Two fictitious Lagrangians to be used in molecular-dynamics simulations with variable cell shape and suitable to study problems like structural phase transitions are introduced. Because they are invariant with respect to the choice of the simulation cell edges and eliminate symmetry breaking associated with the fictitious part of the dynamics, they improve the physical content of numerical simulations that up to now have been done by using Parrinello-Rahman dynamics

Spatial and mass distributions of molecular clouds and spiral structure

International Nuclear Information System (INIS)

Kwan, J.; Valdes, F.; National Optical Astronomy Observatories, Tucson, AZ)

1987-01-01

The growth of molecular clouds resulting from cloud-cloud collisions and coalescence in the Galactic ring between 4 and 8 kpc are modeled, taking into account the presence of a spiral potential and the mutual cloud-cloud gravitational attraction. The mean lifetime of molecular clouds is determined to be about 200 million years. The clouds are present in both spiral arm and interarm regions, but a spiral pattern in their spatial distribution is clearly discernible, with the more massive clouds showing a stronger correlation with the spiral arms. As viewed from within the Galactic disk, however, it is very difficult to ascertain that the molecular cloud distribution in longitude-velocity space has a spiral pattern. 19 references

Isotope chemistry and molecular structure. The WINIMAX weighting factor

International Nuclear Information System (INIS)

Lee, M.W.; Bigeleisen, J.

1979-01-01

The modulating coefficients for the finite polynomial expansion of the logarithm of the reduced partition function, lnb (u), of a harmonic oscillator have been obtained for the range of 0 6 . It is shown that this weighting function is near optimum to insure minimum amplitudes of oscillation in the expansion of lnb (u) as a function of the order of the expansion and to include most of the important molecular structure information contained in the moments of the eigenvalues. Beyond Σu/sub i/ 6 , there is little new structural information

Molecular and crystal structure of the antibiotic enniatin B, a secondary microbial metabolite

International Nuclear Information System (INIS)

Zhukhlistova, N.E.; Tishchenko, G.N.; Tolstykh, I.V.; Zenkova, V.A.

1999-01-01

Single crystals of the secondary microbial metabolite C 33 H 57 N 3 O 9 ·1(2/3)H 2 O with the known molecular weight were studied by the method of X-ray diffraction analysis, where a=b=15.102(3) A, c=14.548(3) A, sp. gr.R3, R=0.057. In the course of the structure determination, it was established that the substance is a natural antibiotic, namely, enniatin B. The conformation of its molecule is similar to that of the known synthetic antibiotic. The main difference between the natural and synthesized forms reduces to the different numbers of water molecules and their arrangement in the cavity of the antibiotic molecule

Molecular imprinting-chemiluminescence determination of trimethoprim using trimethoprim-imprinted polymer as recognition material.

Science.gov (United States)

He, Yunhua; Lu, Jiuru; Liu, Mei; Du, Jianxiu

2005-07-01

A new molecular imprinting-chemiluminescence method for the determination of trimethoprim was developed, in which trimethoprim-imprinted polymer was used as the molecular recognition material and the CL reaction of trimethoprim with potassium permanganate in acidic medium was used as the detection system. The CL intensity responds linearly to the concentration of trimethoprim within the 5.0 x 10(-8)-5.0 x 10(-6) g mL(-1) range (r= 0.9983) with a detection limit of 2 x 10(-8) g mL(-1). The relative standard deviation for the determination of 1.0 x 10(-7) g mL(-1) trimethoprim solutions is 4.8% (n= 9). The method has been applied to the determination of trimethoprim in pharmaceutical preparations and body fluids, and satisfactory results were obtained.

Study of Barley Grain Molecular Structure for Ruminants Using DRIFT, FTIR-ATR and Synchrotron Radiation Infrared Microspectroscopy (SR-IMS): A Review

International Nuclear Information System (INIS)

Yu Peiqiang

2012-01-01

Barley inherent structures are highly associated with nutrient utilization and availability in both humans and animals. Barley has different degradation kinetics compared with other cereal grains. It has a relatively higher degradation rate and extent, which often cause digestive disorder in the rumen. Therefore understanding barley inherent structure at cellular and molecular levels and processing-induced structure changes is important, because we can manipulate barley inherent structures and digestive behaviors. Several molecular spectroscopy techniques can be used to detect barley inherent structures at cellular and molecular levels. This article reviews several applications of the IR molecular spectral bioanalytical techniques - DRIFT, FT/IR-ATR and SR-IMS for barley chemistry, molecular structure and molecular nutrition research

Cationic lipids: molecular structure/ transfection activity relationships and interactions with biomembranes.

Science.gov (United States)

Koynova, Rumiana; Tenchov, Boris

2010-01-01

Abstract Synthetic cationic lipids, which form complexes (lipoplexes) with polyanionic DNA, are presently the most widely used constituents of nonviral gene carriers. A large number of cationic amphiphiles have been synthesized and tested in transfection studies. However, due to the complexity of the transfection pathway, no general schemes have emerged for correlating the cationic lipid chemistry with their transfection efficacy and the approaches for optimizing their molecular structures are still largely empirical. Here we summarize data on the relationships between transfection activity and cationic lipid molecular structure and demonstrate that the transfection activity depends in a systematic way on the lipid hydrocarbon chain structure. A number of examples, including a large series of cationic phosphatidylcholine derivatives, show that optimum transfection is displayed by lipids with chain length of approximately 14 carbon atoms and that the transfection efficiency strongly increases with increase of chain unsaturation, specifically upon replacement of saturated with monounsaturated chains.

DockingShop: A Tool for Interactive Molecular Docking

Energy Technology Data Exchange (ETDEWEB)

Lu, Ting-Cheng; Max, Nelson L.; Ding, Jinhui; Bethel, E. Wes; Crivelli, Silvia N.

2005-04-24

Given two independently determined molecular structures, the molecular docking problem predicts the bound association, or best fit between them, while allowing for conformational changes of the individual molecules during construction of a molecular complex. Docking Shop is an integrated environment that permits interactive molecular docking by navigating a ligand or protein to an estimated binding site of a receptor with real-time graphical feedback of scoring factors as visual guides. Our program can be used to create initial configurations for a protein docking prediction process. Its output--the structure of aprotein-ligand or protein-protein complex--may serve as an input for aprotein docking algorithm, or an optimization process. This tool provides molecular graphics interfaces for structure modeling, interactive manipulation, navigation, optimization, and dynamic visualization to aid users steer the prediction process using their biological knowledge.

Protein Molecular Structures, Protein SubFractions, and Protein Availability Affected by Heat Processing: A Review

International Nuclear Information System (INIS)

Yu, P.

2007-01-01

The utilization and availability of protein depended on the types of protein and their specific susceptibility to enzymatic hydrolysis (inhibitory activities) in the gastrointestine and was highly associated with protein molecular structures. Studying internal protein structure and protein subfraction profiles leaded to an understanding of the components that make up a whole protein. An understanding of the molecular structure of the whole protein was often vital to understanding its digestive behavior and nutritive value in animals. In this review, recently obtained information on protein molecular structural effects of heat processing was reviewed, in relation to protein characteristics affecting digestive behavior and nutrient utilization and availability. The emphasis of this review was on (1) using the newly advanced synchrotron technology (S-FTIR) as a novel approach to reveal protein molecular chemistry affected by heat processing within intact plant tissues; (2) revealing the effects of heat processing on the profile changes of protein subfractions associated with digestive behaviors and kinetics manipulated by heat processing; (3) prediction of the changes of protein availability and supply after heat processing, using the advanced DVE/OEB and NRC-2001 models, and (4) obtaining information on optimal processing conditions of protein as intestinal protein source to achieve target values for potential high net absorbable protein in the small intestine. The information described in this article may give better insight in the mechanisms involved and the intrinsic protein molecular structural changes occurring upon processing.

Atomic Resolution Structures of Human Bufaviruses Determined by Cryo-Electron Microscopy

Directory of Open Access Journals (Sweden)

Maria Ilyas

2018-01-01

Full Text Available Bufavirus strain 1 (BuV1, a member of the Protoparvovirus genus of the Parvoviridae, was first isolated from fecal samples of children with acute diarrhea in Burkina Faso. Since this initial discovery, BuVs have been isolated in several countries, including Finland, the Netherlands, and Bhutan, in pediatric patients exhibiting similar symptoms. Towards their characterization, the structures of virus-like particles of BuV1, BuV2, and BuV3, the current known genotypes, have been determined by cryo-electron microscopy and image reconstruction to 2.84, 3.79, and 3.25 Å, respectively. The BuVs, 65–73% identical in amino acid sequence, conserve the major viral protein, VP2, structure and general capsid surface features of parvoviruses. These include a core β-barrel (βB-βI, α-helix A, and large surface loops inserted between these elements in VP2. The capsid contains depressions at the icosahedral 2-fold and around the 5-fold axes, and has three separated protrusions surrounding the 3-fold axes. Structure comparison among the BuVs and to available parvovirus structures revealed capsid surface variations and capsid 3-fold protrusions that depart from the single pinwheel arrangement of the animal protoparvoviruses. These structures provide a platform to begin the molecular characterization of these potentially pathogenic viruses.

Model of molecular structure of the insoluble organic matter isolated from Murchison meteorite

Science.gov (United States)

Derenne, Sylvie; Robert, François

2010-09-01

The molecular structure of the insoluble organic matter (IOM) from Murchison meteorite has been investigated by our group for several years using a large set of analytical methods including various spectroscopies (Fourier transform infrared spectroscopy, nuclear magnetic resonance, electron paramagnetic resonance, X-ray absorption near-edge spectroscopy), high resolution electron microscopy, and thermal (pyrolyses in the presence or not of tetramethylammonium hydroxide) and chemical (RuO4 oxidation) degradations. Taken together, these techniques provided a wealth of qualitative and quantitative information, from which we derived 11 elemental and molecular parameters on the same IOM residue. In addition to the basic elemental composition, these parameters describe the distribution of the different types of carbon, nitrogen, and sulfur atoms as well as the size of the polyaromatic units. For this molecular structure, we therefore propose a model which fits with these 11 molecular quantitative parameters. Several cosmochemical implications are derived from this structure. Based on the fact that aromatic moieties are highly substituted and aliphatic chains highly branched, it can be anticipated that the synthesis of this IOM occurred through successive additions of single carbon units in the gas-phase ending by a spontaneous cyclization for chain length ≥7 C. As a whole, these observations favor an organosynthesis in the solar T-Tauri disk.

Sensing signatures mediated by chemical structure of molecular solids in laser-induced plasmas.

Science.gov (United States)

Serrano, Jorge; Moros, Javier; Laserna, J Javier

2015-03-03

Laser ablation of organic compounds has been investigated for almost 30 years now, either in the framework of pulse laser deposition for the assembling of new materials or in the context of chemical sensing. Various monitoring techniques such as atomic and molecular fluorescence, time-of-flight mass spectrometry, and optical emission spectroscopy have been used for plasma diagnostics in an attempt to understand the spectral signature and potential origin of gas-phase ions and fragments from organic plasmas. Photochemical and photophysical processes occurring within these systems are generally much more complex than those suggested by observation of optical emission features. Together with laser ablation parameters, the structural and chemical-physical properties of molecules seem to be closely tied to the observed phenomena. The present manuscript, for the first time, discusses the role of molecular structure in the optical emission of organic plasmas. Factors altering the electronic distribution within the organic molecule have been found to have a direct impact on its ensuing optical emissions. The electron structure of an organic molecule, resulting from the presence, nature, and position of its atoms, governs the breakage of the molecule and, as a result, determines the extent of atomization and fragmentation that has proved to directly impact the emissions of CN radicals and C2 dimers. Particular properties of the molecule respond more positively depending on the laser irradiation wavelength, thereby redirecting the ablation process through photochemical or photothermal decomposition pathways. It is of paramount significance for chemical identification purposes how, despite the large energy stored and dissipated by the plasma and the considerable number of transient species formed, the emissions observed never lose sight of the original molecule.

Monte Carlo determination of heteroepitaxial misfit structures

DEFF Research Database (Denmark)

Baker, J.; Lindgård, Per-Anker

1996-01-01

We use Monte Carlo simulations to determine the structure of KBr overlayers on a NaCl(001) substrate, a system with large (17%) heteroepitaxial misfit. The equilibrium relaxation structure is determined for films of 2-6 ML, for which extensive helium-atom scattering data exist for comparison...

Molecular diversity and tools for deciphering the methanogen community structure and diversity in freshwater sediments.

Science.gov (United States)

Chaudhary, Prem Prashant; Brablcová, Lenka; Buriánková, Iva; Rulík, Martin

2013-09-01

Methanogenic archaeal communities existing in freshwater sediments are responsible for approximately 50 % of the total global emission of methane. This process contributes significantly to global warming and, hence, necessitates interventional control measures to limit its emission. Unfortunately, the diversity and functional interactions of methanogenic populations occurring in these habitats are yet to be fully characterized. Considering several disadvantages of conventional culture-based methodologies, in recent years, impetus is given to molecular biology approaches to determine the community structure of freshwater sedimentary methanogenic archaea. 16S rRNA and methyl coenzyme M reductase (mcrA) gene-based cloning techniques are the first choice for this purpose. In addition, electrophoresis-based (denaturing gradient gel electrophoresis, temperature gradient gel electrophoresis, and terminal restriction fragment length polymorphism) and quantitative real-time polymerase chain reaction techniques have also found extensive applications. These techniques are highly sensitive, rapid, and reliable as compared to traditional culture-dependent approaches. Molecular diversity studies revealed the dominance of the orders Methanomicrobiales and Methanosarcinales of methanogens in freshwater sediments. The present review discusses in detail the status of the diversity of methanogens and the molecular approaches applied in this area of research.

Cation-pi interactions stabilize the structure of the antimicrobial peptide indolicidin near membranes: molecular dynamics simulations

DEFF Research Database (Denmark)

Khandelia, Himanshu; Kaznessis, Yiannis N

2007-01-01

We implemented molecular dynamics simulations of the 13-residue antimicrobial peptide indolicidin (ILPWKWPWWPWRR-NH2) in dodecylphosphocholine (DPC) and sodium dodecyl sulfate (SDS) micelles. In DPC, a persistent cation-pi interaction between TRP11 and ARG13 defined the structure of the peptide...... near the interface. A transient cation-pi interaction was also observed between TRP4 and the choline group on DPC lipids. We also implemented simulation of a mutant of indolicidin in the DPC micelle where TRP11 was replaced by ALA11. As a result of the mutation, the boat-shaped conformation is lost...... and the structure becomes significantly less defined. On the basis of this evidence, we argue that cation-pi interactions determine the experimentally measured, well-defined boat-shaped structure of indolicidin. In SDS, the lack of such interactions and the electrostatic binding of the terminal arginine residues...

C9orf72 nucleotide repeat structures initiate molecular cascades of disease.

Science.gov (United States)

Haeusler, Aaron R; Donnelly, Christopher J; Periz, Goran; Simko, Eric A J; Shaw, Patrick G; Kim, Min-Sik; Maragakis, Nicholas J; Troncoso, Juan C; Pandey, Akhilesh; Sattler, Rita; Rothstein, Jeffrey D; Wang, Jiou

2014-03-13

A hexanucleotide repeat expansion (HRE), (GGGGCC)n, in C9orf72 is the most common genetic cause of the neurodegenerative diseases amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Here we identify a molecular mechanism by which structural polymorphism of the HRE leads to ALS/FTD pathology and defects. The HRE forms DNA and RNA G-quadruplexes with distinct structures and promotes RNA•DNA hybrids (R-loops). The structural polymorphism causes a repeat-length-dependent accumulation of transcripts aborted in the HRE region. These transcribed repeats bind to ribonucleoproteins in a conformation-dependent manner. Specifically, nucleolin, an essential nucleolar protein, preferentially binds the HRE G-quadruplex, and patient cells show evidence of nucleolar stress. Our results demonstrate that distinct C9orf72 HRE structural polymorphism at both DNA and RNA levels initiates molecular cascades leading to ALS/FTD pathologies, and provide the basis for a mechanistic model for repeat-associated neurodegenerative diseases.

Molecular structures and metabolic characteristics of protein in brown and yellow flaxseed with altered nutrient traits.

Science.gov (United States)

Khan, Nazir Ahmad; Booker, Helen; Yu, Peiqiang

2014-07-16

The objectives of this study were to investigate the chemical profiles; crude protein (CP) subfractions; ruminal CP degradation characteristics and intestinal digestibility of rumen undegraded protein (RUP); and protein molecular structures using molecular spectroscopy of newly developed yellow-seeded flax (Linum usitatissimum L.). Seeds from two yellow flaxseed breeding lines and two brown flaxseed varieties were evaluated. The yellow-seeded lines had higher (P RUP (29.2 vs 35.1% CP) than that in the brown-seeded varieties. However, the total supply of digestible RUP was not significantly different between the two seed types. Regression equations based on protein molecular structural features gave relatively good estimation for the contents of CP (R(2) = 0.87), soluble CP (R(2) = 0.92), RUP (R(2) = 0.97), and intestinal digestibility of RUP (R(2) = 0.71). In conclusion, molecular spectroscopy can be used to rapidly characterize feed protein molecular structures and predict their nutritive value.

Drug Repositioning by Kernel-Based Integration of Molecular Structure, Molecular Activity, and Phenotype Data

Science.gov (United States)

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. PMID:24244318

Applications of Cerius2, software of molecular simulation; Aplicaciones de Cerius2, software de simulacion molecular

Energy Technology Data Exchange (ETDEWEB)

Fernandez G, M E; Perez A, M; Gutierrez W, C E [ININ, 52750 La Marquesa, Estado de Mexico (Mexico)

2007-07-01

Most of the investigations have a theoretical sustenance based on molecular simulation. The area of application of molecular simulation is very wide, in the Materials Technology Department assigned to the Applied Sciences Management have been treated problems about metallic nano structures, glasses, interfaces, and molecules, to sustain and to explain some of the experimental results. Energy calculations are carried out to determine minimum energy structures, for later on to carry out calculations of some of their properties; as well as the images simulation of Electron microscopy and X-ray diffraction. (Author)

Molecular determinants for drug-receptor interactions. Part 2. An ab initio molecular orbital and dipole moment study of the novel nootropic agent piracetam (2-oxopyrrolidin-1-ylacetamide)

Science.gov (United States)

Lumbroso, H.; Liégeois, C.; Pappalardo, G. C.; Grassi, A.

From the ab initio molecular energies of the possible conformers and from a classical dipole moment analysis of 2-oxopyrrolidin-l-ylacetamide (μ = 4.02 D in dioxan at 30.0°C), the preferred conformation in solution of this novel nootropic agent has been determined. The exocyclic N-CH 2 bond is rotated in one sense by 90° and the exocyclic CH 2-C bond rotated in the same sense by 120° from the "planar" ( OO)- cis conformation. The structures of the two enantiomers in solution differ from that of the crystalline molecule.

Molecular structure input on the web

Directory of Open Access Journals (Sweden)

Ertl Peter

2010-02-01

Full Text Available Abstract 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.

From electron microscopy to X-ray crystallography: molecular-replacement case studies

International Nuclear Information System (INIS)

Xiong, Yong

2008-01-01

Test studies have been conducted on five crystal structures of large molecular assemblies, in which EM maps are used as models for structure solution by molecular replacement using various standard MR packages such as AMoRe, MOLREP and Phaser. Multi-component molecular complexes are increasingly being tackled by structural biology, bringing X-ray crystallography into the purview of electron-microscopy (EM) studies. X-ray crystallography can utilize a low-resolution EM map for structure determination followed by phase extension to high resolution. Test studies have been conducted on five crystal structures of large molecular assemblies, in which EM maps are used as models for structure solution by molecular replacement (MR) using various standard MR packages such as AMoRe, MOLREP and Phaser. The results demonstrate that EM maps are viable models for molecular replacement. Possible difficulties in data analysis, such as the effects of the EM magnification error, and the effect of MR positional/rotational errors on phase extension are discussed

ZnO: Hydroquinone superlattice structures fabricated by atomic/molecular layer deposition

International Nuclear Information System (INIS)

Tynell, Tommi; Karppinen, Maarit

2014-01-01

Here we employ atomic layer deposition in combination with molecular layer deposition to deposit crystalline thin films of ZnO interspersed with single layers of hydroquinone in an effort to create hybrid inorganic–organic superlattice structures. The ratio of the ZnO and hydroquinone deposition cycles is varied between 199:1 and 1:1, and the structure of the resultant thin films is verified with X-ray diffraction and reflectivity techniques. Clear evidence of the formation of a superlattice-type structure is observed in the X-ray reflectivity patterns and the presence of organic bonds in the films corresponding to the structure of hydroquinone is confirmed with Fourier transform infrared spectroscopy measurements. We anticipate that hybrid superlattice structures such as the ones described in this work have the potential to be of great importance for future applications where the precise control of different inorganic and organic layers in hybrid superlattice materials is required. - Highlights: • Inorganic–organic superlattices can be made by atomic/molecular layer deposition. • This is demonstrated here for ZnO and hydroquinone (HQ). • The ratio of the ZnO and HQ layers is varied between 199:1 and 14:1. • The resultant thin films are crystalline

ZnO: Hydroquinone superlattice structures fabricated by atomic/molecular layer deposition

Energy Technology Data Exchange (ETDEWEB)

Tynell, Tommi; Karppinen, Maarit, E-mail: maarit.karppinen@aalto.fi

2014-01-31

Here we employ atomic layer deposition in combination with molecular layer deposition to deposit crystalline thin films of ZnO interspersed with single layers of hydroquinone in an effort to create hybrid inorganic–organic superlattice structures. The ratio of the ZnO and hydroquinone deposition cycles is varied between 199:1 and 1:1, and the structure of the resultant thin films is verified with X-ray diffraction and reflectivity techniques. Clear evidence of the formation of a superlattice-type structure is observed in the X-ray reflectivity patterns and the presence of organic bonds in the films corresponding to the structure of hydroquinone is confirmed with Fourier transform infrared spectroscopy measurements. We anticipate that hybrid superlattice structures such as the ones described in this work have the potential to be of great importance for future applications where the precise control of different inorganic and organic layers in hybrid superlattice materials is required. - Highlights: • Inorganic–organic superlattices can be made by atomic/molecular layer deposition. • This is demonstrated here for ZnO and hydroquinone (HQ). • The ratio of the ZnO and HQ layers is varied between 199:1 and 14:1. • The resultant thin films are crystalline.

Theoretical study on molecular packing and electronic structure of bi-1,3,4-oxadiazole derivatives

KAUST Repository

Wang, Haitao; Bai, Fuquan; Jia, Xiaoshi; Cao, Di; Ravva, Mahesh Kumar; Bredas, Jean-Luc; Qu, Songnan; Bai, Binglian; Zhang, Hongxing; Li, Min

2014-01-01

The molecular aggregation structure of 5,5′-bis(naphthalen-2-yl)-2,2′-bi(1,3,4-oxadiazole) (BOXD-NP) was studied by computing the intermolecular interaction potential energy surface (PES) at density functional theory level based on a dimer model. All B3LYP, CAM-B3LYP and M062x functionals can yield a reliable isolated molecular geometry. The conformation of BOXD-NP obtained with all methods is perfectly planar, indicating good conjugation ability between oxadiazole and naphthalene rings. The vibrational frequencies of BOXD-NP were also calculated using the B3LYP/6-311+G∗∗ method, which showed great consistency with the experimental observations and makes the assignments of the IR spectra more solid. It was revealed that the lowest excited state of BOXD-NP should be assigned as a highly allowed π-π∗ state by TD-DFT calculation. Considering the non-covalent interactions in molecular aggregates, the M062x functional was applied in the construction of the PES. Besides the packing structure found in the crystals, PES also predicted several stable structures, indicating that PES has great ability in guiding molecular self-assembly. Symmetry Adapted Perturbation Theory (SAPT) analysis on these energy-minimum molecular stacking structures revealed that London dispersion forces are the strongest attractive component in the binding. This journal is

Investigation of the Influence of PLA Molecular Structure on the Crystalline Forms (α’ and α and Mechanical Properties of Wet Spinning Fibres

Directory of Open Access Journals (Sweden)

Michał Puchalski

2017-01-01

Full Text Available In this paper, the influence of the molecular structure of polylactide (PLA—characterised by its molar mass and content of d-lactide isomer—on the molecular ordering and α’–α form transition during fibre manufacturing by the wet spinning method is described. Fibres were studied by wide-angle X-ray diffraction (WAXD and differential scanning calorimetry (DSC. Additionally, the physical and mechanical properties of the fibres were determined. This study also examines the preliminary molecular ordering and crystallisation of PLA fibres at various draw ratios. The performed experiments clearly show the dependence of the molecular ordering of PLA on the molar mass and d-lactide content during the wet spinning process. The fibres manufactured from PLA with the lowest content of d-lactide and the lowest molar mass were characterised by a higher tendency for crystallisation and a higher possibility to undergo the disorder-to-order phase transition (α’ to α form. The structural changes in PLA explain the observed changes in the physical and mechanical properties of the obtained fibres.

Structural modeling of the distamycin A-d(CGCGAATTCGCG)2 complex using 2D NMR and molecular mechanics

International Nuclear Information System (INIS)

Pelton, J.G.; Wemmer, D.E.

1988-01-01

The structure of the distamycin A-d(CGCGAATTCGCG) 2 complex has been determined through a combination of SKEWSY and NOESY 2D NMR experiments and molecular mechanics calculations. NMR data provided upper bounds on many proton-proton pairs. The advantage of the SKEWSY/NOESY method is that small groups of strongly coupled spins can be treated accurately as isolated systems. The AMBER molecular mechanics package, modified to include the NMR constraints, was used in energy refinements. Distamycin A fits snugly into the 5'-AATT-3' minor-groove binding site. Structural analysis revealed van der Waals contacts between A5, A6, and A18 C2H and drug H3 protons, potential three-center hydrogen bonding between drug amide protons and adenine N3 and thymine O2 atoms analogous to the spine of hydration in the crystal structure of the free DNA, and stacking of the sugar O1' atoms of A6-C21, T7-T20, and T8-T19, over drug pyrrole rings 1, 2, and 3, respectively. In addition to hydrophobic effects, hydrogen bonding, and electrostatic interactions proposed by others, it is suggested that stacking interactions between DNA sugar O ' atoms and the three drug pyrrole rings contribute to the stability of the complex

Electronic Rydberg wavepacket effects on molecular vibration

International Nuclear Information System (INIS)

Hughes, I.G.; Meacher, D.R.

1994-01-01

Electronic wavepacket states of molecular hydrogen are considered which represent the situation of a spectator electron orbiting a molecular core. A quantum defect theory approach is used to determine the energy level structure, wavefunctions and molecular potentials, which is valid in regions where the quantum defects approach zero. In such a region the orbital motion of the wavepacket leads to a periodic variation in the molecular vibration frequency of the order of 100 cm -1 . Possible detection schemes are discussed. (author)

Molecular and electronic structure of osmium complexes confined to Au(111) surfaces using a self-assembled molecular bridge

Energy Technology Data Exchange (ETDEWEB)

Llave, Ezequiel de la; Herrera, Santiago E.; Adam, Catherine; Méndez De Leo, Lucila P.; Calvo, Ernesto J.; Williams, Federico J., E-mail: fwilliams@qi.fcen.uba.ar [INQUIMAE-CONICET, Departamento de Química Inorgánica, Analítica y Química-Física, Facultad Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires C1428EHA (Argentina)

2015-11-14

The molecular and electronic structure of Os(II) complexes covalently bonded to self-assembled monolayers (SAMs) on Au(111) surfaces was studied by means of polarization modulation infrared reflection absorption spectroscopy, photoelectron spectroscopies, scanning tunneling microscopy, scanning tunneling spectroscopy, and density functional theory calculations. Attachment of the Os complex to the SAM proceeds via an amide covalent bond with the SAM alkyl chain 40° tilted with respect to the surface normal and a total thickness of 26 Å. The highest occupied molecular orbital of the Os complex is mainly based on the Os(II) center located 2.2 eV below the Fermi edge and the LUMO molecular orbital is mainly based on the bipyridine ligands located 1.5 eV above the Fermi edge.

NMR determination of solvent dependent behavior and XRD structural properties of 4-carboxy phenylboronic acid: A DFT supported study

Science.gov (United States)

Dikmen, Gökhan; Alver, Özgür; Parlak, Cemal

2018-04-01

Solvent dependent structural properties of 4-carboxy phenylboronic acid (4-cpba) were investigated by X-ray diffraction (XRD) and nuclear magnetic resonance (NMR) spectroscopic methods. The molecular structure and geometric parameters were determined by some computational methods such as B3LYP/6-31 + G(3df,p), HF/aug-cc-pvtz and MP2/6-31G(d). Detailed elucidation of the structural and spectroscopic properties of 4-cpba was carried out with 1H, HETCOR and DOSY NMR experiments. Solvent effects on the structural properties were monitored on the changes of 1H NMR spectra by using various solvents and it was observed that 4-cpba shows serious structural preferences depending on the solvent used.

The diverse and expanding role of mass spectrometry in structural and molecular biology.

Science.gov (United States)

Lössl, Philip; van de Waterbeemd, Michiel; Heck, Albert Jr

2016-12-15

The emergence of proteomics has led to major technological advances in mass spectrometry (MS). These advancements not only benefitted MS-based high-throughput proteomics but also increased the impact of mass spectrometry on the field of structural and molecular biology. Here, we review how state-of-the-art MS methods, including native MS, top-down protein sequencing, cross-linking-MS, and hydrogen-deuterium exchange-MS, nowadays enable the characterization of biomolecular structures, functions, and interactions. In particular, we focus on the role of mass spectrometry in integrated structural and molecular biology investigations of biological macromolecular complexes and cellular machineries, highlighting work on CRISPR-Cas systems and eukaryotic transcription complexes. © 2016 The Authors. Published under the terms of the CC BY NC ND 4.0 license.

Determinants of capital structure.

Science.gov (United States)

McCue, M J; Ozcan, Y A

1992-01-01

This study analyzes the determinants of hospital capital structure in a new market setting that are created by the financial pressures of prospective payment and the intense price competition among hospitals. Using California data, the study found hospital system affiliation, bed size, growth rate in revenues, operating risk, and asset structure affected both short- and long-term debt borrowings. In addition, percentage of uncompensated care, profitability, and payer mix influenced short-term borrowings while market conditions and ownership affected long-term borrowings. Most significant of all is the finding that smaller hospitals tend to borrow more, possibly because they cannot generate funds internally.

Structure of thallium and lead calculated from Shaw local pseudopotential and molecular dynamics

Directory of Open Access Journals (Sweden)

Gasser J. G.

2011-05-01

Full Text Available Recently, we (Es Sbihi Phil. Mag 2010 have successfully calculated, by molecular dynamics, the static structure factor of liquid bismuth at different temperatures. Our results were in very good agreement with the Waseda experimental data. Our assumption was to consider the true density of states which presents a gap as measured by Indlekofer (J. Non-Cryst. Solids 1989 and calculated by Hafner-Jank (Phys. Rev. B 1990 for liquid bismuth. The number of electrons at the Fermi energy has been calculated with three conduction electrons for bismuth (number of p electrons. With this assumption, the structures were determined with an effective ion-ion potential constructed from the Shaw local Optimised Model Potential (OMP and the Ichimaru-Utsumi dielectric function. In the present paper, we generalize our assumptions to liquid thallium and lead which also present such a gap. Their calculated structures are also very close to the experimental ones. This confirms that the number of conduction electrons on the Fermi sphere is consistent with the number of p electrons as has been even shown for our electronic transport properties of liquid lead (A. Ben Abdellah, Phys. Rev. B 2003.

Membrane re-modelling by BAR domain superfamily proteins via molecular and non-molecular factors.

Science.gov (United States)

Nishimura, Tamako; Morone, Nobuhiro; Suetsugu, Shiro

2018-04-17

Lipid membranes are structural components of cell surfaces and intracellular organelles. Alterations in lipid membrane shape are accompanied by numerous cellular functions, including endocytosis, intracellular transport, and cell migration. Proteins containing Bin-Amphiphysin-Rvs (BAR) domains (BAR proteins) are unique, because their structures correspond to the membrane curvature, that is, the shape of the lipid membrane. BAR proteins present at high concentration determine the shape of the membrane, because BAR domain oligomers function as scaffolds that mould the membrane. BAR proteins co-operate with various molecular and non-molecular factors. The molecular factors include cytoskeletal proteins such as the regulators of actin filaments and the membrane scission protein dynamin. Lipid composition, including saturated or unsaturated fatty acid tails of phospholipids, also affects the ability of BAR proteins to mould the membrane. Non-molecular factors include the external physical forces applied to the membrane, such as tension and friction. In this mini-review, we will discuss how the BAR proteins orchestrate membrane dynamics together with various molecular and non-molecular factors. © 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

Molecular structure of tris(cyclopropylsilyl)amine as determined by gas electron diffraction and quantum-chemical calculations

Science.gov (United States)

Vishnevskiy, Yuri V.; Abaev, Maxim A.; Ivanov, Arkadii A.; Vilkov, Lev V.; Dakkouri, Marwan

2008-10-01

The molecular structure and conformation of tris(cyclopropylsilyl)amine (TCPSA) has been studied by means of gas-phase electron diffraction at 338 K and quantum-chemical calculations. A total of 12 relatively stable conformations of TCPSA molecule were considered. According to the experimental results and the DFT calculations the most stable conformer corresponds to a configuration (according to the Prelog-Klyne notation) of the type (-ac)(-ac)(+ac)-(-ac)(-ac)(+ac), where the first three parentheses describe the three different Si-N-Si-C torsional angles and the latter ones depict the rotation of the three cyclopropyl groups about the C ring-Si axes, respectively. The quantum-mechanical calculations were performed using various density functional (B3LYP, X3LYP and O3LYP) and perturbation MP2 methods in combination with double- and triple- ζ basis sets plus polarization and diffuse functions. The most important experimental geometrical parameters of TCPSA ( ra Å, ∠ h1 degrees) are: (Si-N) av = 1.741(3), (Si-C) av = 1.866(4), (C-C) av = 1.510(3), (C-C(Si)) av = 1.535(3), (N-Si-C) av = 115.1(18)°. For the purpose of comparison and searching for reasons leading to the planarity of the Si 3N moiety in trisilylated amines we carried out NBO analysis and optimized the geometries of numerous silylamines. Among these compounds was tris(allylsilyl)amine (TASA), which is isovalent and isoelectronic to TCPSA. Utilizing the structural results we obtained we could show that Si +⋯Si + electrostatic repulsive interaction is predominantly responsible for the planarity of the Si 3N skeleton in TCPSA and in all other trisilylamines we considered. We also found that regardless the size and partial charges of the substituents the Si-N-Si bond angle in various disilylamines amounts to 130 ± 2°.

Effects of surface proteins and lipids on molecular structure, thermal properties, and enzymatic hydrolysis of rice starch

Directory of Open Access Journals (Sweden)

Pan HU

Full Text Available Abstract Rice starches with different amylose contents were treated with sodium dodecyl sulfate (SDS to deplete surface proteins and lipids, and the changes in molecular structure, thermal properties, and enzymatic hydrolysis were evaluated. SDS treatment did not significantly change the molecular weight distribution, crystalline structure, short-range ordered degree, and gelatinization properties of starch, but significantly altered the pasting properties and increased the swelling power of starch. The removal of surface proteins and lipids increased the enzymatic hydrolysis and in vitro digestion of starch. The influences of removing surface proteins and lipids from starch on swelling power, pasting properties, and enzymatic hydrolysis were different among the various starches because of the differences in molecular structures of different starch styles. The aforementioned results indicated that removing the surface proteins and lipids from starch did not change the molecular structure but had significant effects on some functional properties.

Sex determination of Pohnpei Micronesian kingfishers using morphological and molecular genetic techniques

Science.gov (United States)

Kesler, Dylan C.; Lopes, I.F.; Haig, Susan M.

2006-01-01

Conservation-oriented studies of Micronesian Kingfishers (Todiramphus cinnamominus) have been hindered by a lack of basic natural history information, despite the status of the Guam subspecies (T. c. cinnamominus) as one of the most endangered species in the world. We used tissue samples and morphometric measures from museum specimens and wild-captured Pohnpei Micronesian Kingfishers (T. c. reichenbachii) to develop methods for sex determination. We present a modified molecular protocol and a discriminant function that yields the probability that a particular individual is male or female. Our results revealed that females were significantly larger than males, and the discriminant function correctly predicted sex in 73% (30/41) of the individuals. The sex of 86% (18/21) of individuals was correctly assigned when a moderate reliability threshold was set. Sex determination using molecular genetic techniques was more reliable than methods based on morphology. Our results will facilitate recovery efforts for the critically endangered Guam Micronesian Kingfisher and provide a basis for sex determination in the 11 other endangered congeners in the Pacific Basin.

Algorithm based on the Thomson problem for determination of equilibrium structures of metal nanoclusters

Science.gov (United States)

Arias, E.; Florez, E.; Pérez-Torres, J. F.

2017-06-01

A new algorithm for the determination of equilibrium structures suitable for metal nanoclusters is proposed. The algorithm performs a stochastic search of the minima associated with the nuclear potential energy function restricted to a sphere (similar to the Thomson problem), in order to guess configurations of the nuclear positions. Subsequently, the guessed configurations are further optimized driven by the total energy function using the conventional gradient descent method. This methodology is equivalent to using the valence shell electron pair repulsion model in guessing initial configurations in the traditional molecular quantum chemistry. The framework is illustrated in several clusters of increasing complexity: Cu7, Cu9, and Cu11 as benchmark systems, and Cu38 and Ni9 as novel systems. New equilibrium structures for Cu9, Cu11, Cu38, and Ni9 are reported.

Relationship of carbohydrates and lignin molecular structure spectral profiles to nutrient profile in newly developed oats cultivars and barley grain

Science.gov (United States)

Prates, Luciana Louzada; Refat, Basim; Lei, Yaogeng; Louzada-Prates, Mariana; Yu, Peiqiang

2018-01-01

The objectives of this study were to quantify the chemical profile and the magnitude of differences in the oat and barley grain varieties developed by Crop Development Centre (CDC) in terms of Cornell Net Carbohydrate Protein System (CNCPS) carbohydrate sub-fractions: CA4 (sugars), CB1 (starch), CB2 (soluble fibre), CB3 (available neutral detergent fibre - NDF), and CC (unavailable carbohydrate); to estimate the energy values; to detect the lignin and carbohydrate (CHO) molecular structure profiles in CDC Nasser and CDC Seabiscuit oat and CDC Meredith barley grains by using Fourier transform infrared attenuated total reflectance (FTIR-ATR); to develop a model to predict nutrient supply based on CHO molecular profile. Results showed that NDF, ADF and CHO were greater (P 0.05) for oat and barley grains as well as non-structural CHO. However, cellulosic compounds peak area and height were greater (P < 0.05) in oat than barley grains. Multiple regressions were determined to predict nutrient supply by using lignin and CHO molecular profiles. It was concluded that although there were some differences between oat and barley grains, CDC Nasser and CDC Meredith presented similarities related to chemical and molecular profiles, indicating that CDC Meredith barley could be replaced for CDC Nasser as ruminant feed. The FTIR was able to identify functional groups related to CHO molecular spectral in oat and barley grains and FTIR-ATR results could be used to predict nutrient supply in ruminant livestock systems.

Variational cellular model of the molecular and crystal electronic structure

International Nuclear Information System (INIS)

Ferreira, L.G.; Leite, J.R.

1977-12-01

A variational version of the cellular method is developed to calculate the electronic structure of molecules and crystals. Due to the simplicity of the secular equation, the method is easy to be implemented. Preliminary calculations on the hydrogen molecular ion suggest that it is also accurate and of fast convergence [pt

Molecular structure and diversity of PBAN/Pyrokinin family peptides in ants

Directory of Open Access Journals (Sweden)

Man-Yeon eChoi

2012-02-01

Full Text Available Neuropeptides are the largest group of insect hormones. They are produced in the central and peripheral nervous systems and affect insect development, reproduction, feeding and behavior. A variety of neuropeptide families have been identified in insects. One of these families is the PBAN/pyrokinin family defined by a common FXPRLamide or similar amino acid fragment at the C-terminal end. These peptides, found in all insects studied thus far, have been conserved throughout evolution. The most well studied physiological function is regulation of moth sex pheromone biosynthesis through the Pheromone Biosynthesis Activating Neurohormone (PBAN, although several developmental functions have also been reported. Over the past years we have extended knowledge of the PBAN/pyrokinin family of peptides to ants, focusing mainly on the fire ant, Solenopsis invicta. The fire ant is one of the most studied social insects and over the last 60 years a great deal has been learned about many aspects of this ant, including the behaviors and chemistry of pheromone communication. However, virtually nothing is known about the regulation of these pheromone systems. Recently, we demonstrated the presence of PBAN/pyrokinin immunoreactive neurons in the fire ant, and identified and characterized PBAN and additional neuropeptides. We have mapped the fire ant PBAN gene structure and determined the tissue expression level in the central nervous system of the ant. We review here our research to date on the molecular structure and diversity of ant PBAN/pyrokinin peptides in preparation for determining the function of the neuropeptides in ants and other social insects.

Molecular structure of self-assembled chiral nanoribbons and nanotubules revealed in the hydrated state.

Science.gov (United States)

Oda, Reiko; Artzner, Franck; Laguerre, Michel; Huc, Ivan

2008-11-05

A detailed molecular organization of racemic 16-2-16 tartrate self-assembled multi-bilayer ribbons in the hydrated state is proposed where 16-2-16 amphiphiles, tartrate ions, and water molecules are all accurately positioned by comparing experimental X-ray powder diffraction and diffraction patterns derived from modeling studies. X-ray diffuse scattering studies show that molecular organization is not fundamentally altered when comparing the flat ribbons of the racemate to chirally twisted or helical ribbons of the pure tartrate enantiomer. Essential features of the three-dimensional molecular organizations of these structures include interdigitation of alkyl chains within each bilayer and well-defined networks of ionic and hydrogen bonds between cations, anions, and water molecules between bilayers. The detailed study of diffraction patterns also indicated that the gemini headgroups are oriented parallel to the long edge of the ribbons. The structure thus possesses a high cohesion and good crystallinity, and for the first time, we could relate the packing of the chiral molecules to the expression of the chirality at a mesoscopic scale. The organization of the ribbons at the molecular level sheds light on a number of their macroscopic features. Among these are the reason why enantiomerically pure 16-2-16 tartrate forms ribbons that consist of exactly two bilayers, and a plausible mechanism by which a chirally twisted or helical shape may emerge from the packing of chiral tartrate ions. Importantly, the distinction between commonly observed helical and twisted morphologies could be related to a subtle symmetry breaking. These results demonstrate that accurately solving the molecular structure of self-assembled soft materials--a process rarely achieved--is within reach, that it is a valid approach to correlate molecular parameters to macroscopic properties, and thus that it offers opportunities to modulate properties through molecular design.

Adhesives, fillers & potting compounds: Special report molecular weight determinations of dimethypolysiloxane polymers

Energy Technology Data Exchange (ETDEWEB)

Luthey, Z.A.

1968-09-03

Using a Mechrolab Vapor Phase Osmometer and a Hallikainen Automatic Membrane Osmometer the number-average molecular weight of two samples of dimethylpolysiloxane - 2300 and 8000 cstk - as well as samples made by mixing the two previously mentioned materials were determined.

Structural Determinants of Specific Lipid Binding to Potassium Channels

NARCIS (Netherlands)

Weingarth, M.H.|info:eu-repo/dai/nl/330985655; Prokofyev, A.; van der Cruijsen, E.A.W.|info:eu-repo/dai/nl/330826743; Nand, D.|info:eu-repo/dai/nl/337731403; Bonvin, A.M.J.J.|info:eu-repo/dai/nl/113691238; Pongs, O.; Baldus, M.|info:eu-repo/dai/nl/314410864

2013-01-01

We have investigated specific lipid binding to the pore domain of potassium channels KcsA and chimeric KcsAKv1.3 on the structural and functional level using extensive coarse-grained and atomistic molecular dynamics simulations, solid-state NMR, and single channel measurements. We show that, while

Chemistry and structure of giant molecular clouds in energetic environments

Science.gov (United States)

Anderson, Crystal Nicole

2016-09-01

Throughout the years many studies on Galactic star formation have been conducted. This resulted in the idea that giant molecular clouds (GMCs) are hierarchical in nature with substructures spanning a large range of sizes. The physical processes that determine how molecular clouds fragment, form clumps/cores and then stars depends strongly on both recent radiative and mechanical feed- back from massive stars and, on longer term, from enhanced cooling due to the buildup of metals. Radiative and mechanical energy input from stellar populations can alter subsequent star formation over a large part of a galaxy and hence is relevant to the evolution of galaxies. Much of our knowledge of star formation on galaxy wide scales is based on scaling laws and other parametric descriptions. But to understand the overall evolution of star formation in galaxies we need to watch the feedback processes at work on giant molecular cloud (GMC) scales. By doing this we can begin to answer how strong feedback environments change the properties of the substructure in GMCs. Tests of Galactic star formation theory to other galaxies has been a challenging process due to the lack of resolution with current instruments. Thus, only the nearest galaxies allow us to resolve GMCs and their substructures. The Large Magellanic Cloud (LMC), is one of the closest low metallicity dwarf galaxies (D˜ 50 kpc) and is close enough that current instruments can resolve the sub- structure of its GMCs to molecular gas tracers (e.g. HCO+, HCN, HNC, CS, C2H, N2H+) detected in the LMC at 1.5-40 pc scales and in NGC 5253 at 40 pc scales. I then compare the molecular gas detections to the Central Molecular Zone in our Galaxy. Dense molecular gas was detected in all of the sources. For the regions in the LMC, molecular lines of CS, N2H+, C 2H, HNC, HCO+ and HCN were all detected in N159W and N113 while only HCN, HCO+, HNC, and C2H were detected in 30Dor-10. Toward NGC 5253 only HCO+, HCN, C2H and CS were detected. I

Molecularly imprinted electrochemical sensor based on nickel nanoparticle-modified electrodes for phenobarbital determination

International Nuclear Information System (INIS)

Yu, Hui Cheng; Huang, Xue Yi; Lei, Fu Hou; Tan, Xue Cai; Wei, Yi Chun; Li, Hao

2014-01-01

Highlights: • Uniform Ni nanoparticles were synthesized. • A Ni nanoparticle-modified imprinted sensor was developed to detect phenobarbital. • The modified sensor exhibited high sensitivity for phenobarbital. • The electrochemical properties of the modified sensor were investigated. • The prepared sensor was applied to detect phenobarbital in fish samples. - Abstract: Uniform nickel nanoparticles were applied to improve the sensitivity of sensors for phenobarbital (PB) determination. A Ni nanoparticle-modified imprinted electrochemical sensor was developed by thermal polymerization with the use of methacrylic acid as the functional monomer and ethylene glycol maleic rosinate acrylate as the crosslinking agent. The chemical structures and morphologies of the imprinted films were characterized using Fourier transform infrared spectroscopy and scanning electron microscopy. The success of the fabrication of Ni nanoparticles, as well as the Ni nanoparticle-modified imprinted electrochemical sensor, was confirmed by the analytical results. The electrochemical properties of the modified molecularly imprinted and non-imprinted polymer sensors were investigated by cyclic voltammetry, differential pulse voltammetry, electrochemical impedance spectroscopy, and chronoamperometry. Results showed that the electrochemical properties of the molecularly imprinted sensor were remarkably different from those of the non-imprinted sensor. Linear responses of the imprinted sensor to PB were observed for concentrations ranging from 1.4 × 10 −7 mol L −1 to 1.3 × 10 −4 mol L −1 (r 2 = 0.9976), with a detection limit of 8.2 × 10 −9 mol L −1 (S/N = 3). The imprinted electrochemical sensor was used to determine PB in actual fish samples, in which average recoveries between 95.60% and 104.67% were achieved. The developed Ni nanoparticle-modified electrochemical sensor exhibited high sensitivity, high selectivity, and good recovery

Molecular dynamics simulations of structural transformation of perfluorooctane sulfonate (PFOS) at water/rutile interfaces.

Science.gov (United States)

He, Guangzhi; Zhang, Meiyi; Zhou, Qin; Pan, Gang

2015-09-01

Concentration and salinity conditions are the dominant environmental factors affecting the behavior of perfluorinated compounds (PFCs) on the surfaces of a variety of solid matrices (suspended particles, sediments, and natural minerals). However, the mechanism has not yet been examined at molecular scales. Here, the structural transformation of perfluorooctane sulfonate (PFOS) at water/rutile interfaces induced by changes of the concentration level of PFOS and salt condition was investigated using molecular dynamics (MD) simulations. At low and intermediate concentrations all PFOS molecules directly interacted with the rutile (110) surface mainly by the sulfonate headgroups through electrostatic attraction, yielding a typical monolayer structure. As the concentration of PFOS increased, the molecules aggregated in a complex multi-layered structure, where an irregular assembling configuration was adsorbed on the monolayer structure by the van der Waals interactions between the perfluoroalkyl chains. When adding CaCl2 to the system, the multi-layered structure changed to a monolayer again, indicating that the addition of CaCl2 enhanced the critical concentration value to yield PFOS multilayer assemblies. The divalent Ca(2+) substituted for monovalent K(+) as the bridging counterion in PFOS adsorption. MD simulation may trigger wide applications in study of perfluorinated compounds (PFCs) from atomic/molecular scale. Copyright © 2015 Elsevier Ltd. All rights reserved.

Integral membrane protein structure determination using pseudocontact shifts

Energy Technology Data Exchange (ETDEWEB)

Crick, Duncan J.; Wang, Jue X. [University of Cambridge, Department of Biochemistry (United Kingdom); Graham, Bim; Swarbrick, James D. [Monash University, Monash Institute of Pharmaceutical Sciences (Australia); Mott, Helen R.; Nietlispach, Daniel, E-mail: dn206@cam.ac.uk [University of Cambridge, Department of Biochemistry (United Kingdom)

2015-04-15

Obtaining enough experimental restraints can be a limiting factor in the NMR structure determination of larger proteins. This is particularly the case for large assemblies such as membrane proteins that have been solubilized in a membrane-mimicking environment. Whilst in such cases extensive deuteration strategies are regularly utilised with the aim to improve the spectral quality, these schemes often limit the number of NOEs obtainable, making complementary strategies highly beneficial for successful structure elucidation. Recently, lanthanide-induced pseudocontact shifts (PCSs) have been established as a structural tool for globular proteins. Here, we demonstrate that a PCS-based approach can be successfully applied for the structure determination of integral membrane proteins. Using the 7TM α-helical microbial receptor pSRII, we show that PCS-derived restraints from lanthanide binding tags attached to four different positions of the protein facilitate the backbone structure determination when combined with a limited set of NOEs. In contrast, the same set of NOEs fails to determine the correct 3D fold. The latter situation is frequently encountered in polytopical α-helical membrane proteins and a PCS approach is thus suitable even for this particularly challenging class of membrane proteins. The ease of measuring PCSs makes this an attractive route for structure determination of large membrane proteins in general.

Fluid bilayer structure determination: Joint refinement in composition space using X-ray and neutron diffraction data

Energy Technology Data Exchange (ETDEWEB)

White, S.H. [Univ. of California, Irvine, CA (United States); Wiener, M.C. [Univ. of California, San Francisco, CA (United States)

1994-12-31

Experimentally-determined structural models of fluid lipid bilayers are essential for verifying molecular dynamics simulations of bilayers and for understanding the structural consequences of peptide interactions. The extreme thermal motion of bilayers precludes the possibility of atomic-level structural models. Defining {open_quote}the structure{close_quote} of a bilayer as the time-averaged transbilayer distribution of the water and the principal lipid structural groups such as the carbonyls and double-bonds (quasimolecular fragments), one can represent the bilayer structure as a sum of Gaussian functions referred to collectively as the quasimolecular structure. One method of determining the structure is by neutron diffraction combined with exhaustive specific deuteration. This method is impractical because of the expense of the chemical syntheses and the limited amount of neutron beam time currently available. We have therefore developed the composition space refinement method for combining X-ray and minimal neutron diffraction data to arrive at remarkably detailed and accurate structures of fluid bilayers. The composition space representation of the bilayer describes the probability of occupancy per unit length across the width of the bilayer of each quasimolecular component and permits the joint refinement of X-ray and neutron lamellar diffraction data by means of a single quasimolecular structure that is fitted simultaneously to both data sets. Scaling of each component by the appropriate neutron or X-ray scattering length maps the composition-space profile to the appropriate scattering length space for comparison to experimental data. The difficulty with the method is that fluid bilayer structures are generally only marginally determined by the experimental data. This means that the space of possible solutions must be extensively explored in conjunction with a thorough analysis of errors.

Fluid bilayer structure determination: Joint refinement in composition space using X-ray and neutron diffraction data

International Nuclear Information System (INIS)

White, S.H.; Wiener, M.C.

1994-01-01

Experimentally-determined structural models of fluid lipid bilayers are essential for verifying molecular dynamics simulations of bilayers and for understanding the structural consequences of peptide interactions. The extreme thermal motion of bilayers precludes the possibility of atomic-level structural models. Defining open-quote the structure close-quote of a bilayer as the time-averaged transbilayer distribution of the water and the principal lipid structural groups such as the carbonyls and double-bonds (quasimolecular fragments), one can represent the bilayer structure as a sum of Gaussian functions referred to collectively as the quasimolecular structure. One method of determining the structure is by neutron diffraction combined with exhaustive specific deuteration. This method is impractical because of the expense of the chemical syntheses and the limited amount of neutron beam time currently available. We have therefore developed the composition space refinement method for combining X-ray and minimal neutron diffraction data to arrive at remarkably detailed and accurate structures of fluid bilayers. The composition space representation of the bilayer describes the probability of occupancy per unit length across the width of the bilayer of each quasimolecular component and permits the joint refinement of X-ray and neutron lamellar diffraction data by means of a single quasimolecular structure that is fitted simultaneously to both data sets. Scaling of each component by the appropriate neutron or X-ray scattering length maps the composition-space profile to the appropriate scattering length space for comparison to experimental data. The difficulty with the method is that fluid bilayer structures are generally only marginally determined by the experimental data. This means that the space of possible solutions must be extensively explored in conjunction with a thorough analysis of errors

Multiscale modeling of complex molecular structure and dynamics with MBN Explorer

CERN Document Server

Solov’yov, Ilia A; Solov’yov, Andrey V

2017-01-01

This book introduces readers to MesoBioNano (MBN) Explorer – a multi-purpose software package designed to model molecular systems at various levels of size and complexity. In addition, it presents a specially designed multi-task toolkit and interface – the MBN Studio – which enables the set-up of input files, controls the simulations, and supports the subsequent visualization and analysis of the results obtained. The book subsequently provides a systematic description of the capabilities of this universal and powerful software package within the framework of computational molecular science, and guides readers through its applications in numerous areas of research in bio- and chemical physics and material science – ranging from the nano- to the meso-scale. MBN Explorer is particularly suited to computing the system’s energy, to optimizing molecular structure, and to exploring the various facets of molecular and random walk dynamics. The package allows the use of a broad variety of interatomic potenti...

Structure determination of the functional domain interaction of a chimeric nonribosomal peptide synthetase from a challenging crystal with noncrystallographic translational symmetry

Energy Technology Data Exchange (ETDEWEB)

Sundlov, Jesse A.; Gulick, Andrew M., E-mail: gulick@hwi.buffalo.edu [University at Buffalo, 700 Ellicott Street, Buffalo, NY 14203 (United States)

2013-08-01

The structure of the functional interaction of NRPS adenylation and carrier protein domains, trapped with a mechanism-based inhibitor, is described. Crystals exhibit translational non-crystallographic symmetry, which challenged structure determination and refinement. The nonribosomal peptide synthetases (NRPSs) are a family of modular proteins that contain multiple catalytic domains joined in a single protein. Together, these domains work to produce chemically diverse peptides, including compounds with antibiotic activity or that play a role in iron acquisition. Understanding the structural mechanisms that govern the domain interactions has been a long-standing goal. During NRPS synthesis, amino-acid substrates are loaded onto integrated carrier protein domains through the activity of NRPS adenylation domains. The structures of two adenylation domain–carrier protein domain complexes have recently been determined in an effort that required the use of a mechanism-based inhibitor to trap the domain interaction. Here, the continued analysis of these proteins is presented, including a higher resolution structure of an engineered di-domain protein containing the EntE adenylation domain fused with the carrier protein domain of its partner EntB. The protein crystallized in a novel space group in which molecular replacement and refinement were challenged by noncrystallographic pseudo-translational symmetry. The structure determination and how the molecular packing impacted the diffraction intensities are reported. Importantly, the structure illustrates that in this new crystal form the functional interface between the adenylation domain and the carrier protein domain remains the same as that observed previously. At a resolution that allows inclusion of water molecules, additional interactions are observed between the two protein domains and between the protein and its ligands. In particular, a highly solvated region that surrounds the carrier protein cofactor is described.

Structure determination of the functional domain interaction of a chimeric nonribosomal peptide synthetase from a challenging crystal with noncrystallographic translational symmetry

International Nuclear Information System (INIS)

Sundlov, Jesse A.; Gulick, Andrew M.

2013-01-01

The structure of the functional interaction of NRPS adenylation and carrier protein domains, trapped with a mechanism-based inhibitor, is described. Crystals exhibit translational non-crystallographic symmetry, which challenged structure determination and refinement. The nonribosomal peptide synthetases (NRPSs) are a family of modular proteins that contain multiple catalytic domains joined in a single protein. Together, these domains work to produce chemically diverse peptides, including compounds with antibiotic activity or that play a role in iron acquisition. Understanding the structural mechanisms that govern the domain interactions has been a long-standing goal. During NRPS synthesis, amino-acid substrates are loaded onto integrated carrier protein domains through the activity of NRPS adenylation domains. The structures of two adenylation domain–carrier protein domain complexes have recently been determined in an effort that required the use of a mechanism-based inhibitor to trap the domain interaction. Here, the continued analysis of these proteins is presented, including a higher resolution structure of an engineered di-domain protein containing the EntE adenylation domain fused with the carrier protein domain of its partner EntB. The protein crystallized in a novel space group in which molecular replacement and refinement were challenged by noncrystallographic pseudo-translational symmetry. The structure determination and how the molecular packing impacted the diffraction intensities are reported. Importantly, the structure illustrates that in this new crystal form the functional interface between the adenylation domain and the carrier protein domain remains the same as that observed previously. At a resolution that allows inclusion of water molecules, additional interactions are observed between the two protein domains and between the protein and its ligands. In particular, a highly solvated region that surrounds the carrier protein cofactor is described

Molecular Dynamic Simulation of Space and Earth-Grown Crystal Structures of Thermostable T1 Lipase Geobacillus zalihae Revealed a Better Structure.

Science.gov (United States)

Ishak, Siti Nor Hasmah; Aris, Sayangku Nor Ariati Mohamad; Halim, Khairul Bariyyah Abd; Ali, Mohd Shukuri Mohamad; Leow, Thean Chor; Kamarudin, Nor Hafizah Ahmad; Masomian, Malihe; Rahman, Raja Noor Zaliha Raja Abd

2017-09-25

Less sedimentation and convection in a microgravity environment has become a well-suited condition for growing high quality protein crystals. Thermostable T1 lipase derived from bacterium Geobacillus zalihae has been crystallized using the counter diffusion method under space and earth conditions. Preliminary study using YASARA molecular modeling structure program for both structures showed differences in number of hydrogen bond, ionic interaction, and conformation. The space-grown crystal structure contains more hydrogen bonds as compared with the earth-grown crystal structure. A molecular dynamics simulation study was used to provide insight on the fluctuations and conformational changes of both T1 lipase structures. The analysis of root mean square deviation (RMSD), radius of gyration, and root mean square fluctuation (RMSF) showed that space-grown structure is more stable than the earth-grown structure. Space-structure also showed more hydrogen bonds and ion interactions compared to the earth-grown structure. Further analysis also revealed that the space-grown structure has long-lived interactions, hence it is considered as the more stable structure. This study provides the conformational dynamics of T1 lipase crystal structure grown in space and earth condition.

Molecules and Models The molecular structures of main group element compounds

CERN Document Server

Haaland, Arne

2008-01-01

This book provides a systematic description of the molecular structures and bonding in simple compounds of the main group elements with particular emphasis on bond distances, bond energies and coordination geometries. The description includes the structures of hydrogen, halogen and methyl derivatives of the elements in each group, some of these molecules are ionic, some polar covalent. The survey of molecules whose structures conform to well-established trends is followed byrepresentative examples of molecules that do not conform. We also describe electron donor-acceptor and hydrogen bonded co

Protein Structure Determination Using Chemical Shifts

DEFF Research Database (Denmark)

Christensen, Anders Steen

is determined using only chemical shifts recorded and assigned through automated processes. The CARMSD to the experimental X-ray for this structure is 1.1. Å. Additionally, the method is combined with very sparse NOE-restraints and evolutionary distance restraints and tested on several protein structures >100...

Chirality induction and protonation-induced molecular motions in helical molecular strands.

Science.gov (United States)

Kolomiets, Elena; Berl, Volker; Lehn, Jean-Marie

2007-01-01

The long oligopyridinedicarboxamide strand 9, containing 15 heterocyclic rings has been synthesized and its helical structure determined by X-ray crystallography. It was shown that the shorter analogue 6 displays induced circular dichroism and amplification of induced chirality upon dissolution in an optically active solvent, diethyl-L-tartrate. A novel class of helical foldamers was prepared, strands 14-16, based on two oligopyridine carboxamide segments linked through a L-tartaric acid derived spacer. These tartro strands display internal chirality induction as well as chirality amplification. NMR spectroscopy (on 8 and 9) and circular dichroism (on 16) studies show that the oligopyridine carboxamide strands undergo reversible unfolding/folding upon protonation. The protonation-induced unfolding has been confirmed by X-ray crystallographic determination of the molecular structure of the extended protonated heptameric form 8(+). The molecular-scale mechano-chemical motions of the protonation-induced structural switching consist of a change of the length of the molecule, from 6 angstroms (6, coiled form) to 29 angstroms (8(+), uncoiled form) for the heptamer and from 12.5 angstroms (9, coiled form, X-ray structure) to 57 angstroms (9(+), uncoiled form, from modeling) for the pentadecamer. Similar unfolding/folding motional processes take place in the L-tartro strands 15 and 16 upon protonation/deprotonation, with loss of helicity-induced circular dichroism on unfolding as shown for the protonated form 16(+).

Multi-scale calculation of the electric properties of organic-based devices from the molecular structure

KAUST Repository

Li, Haoyuan; Qiu, Yong; Duan, Lian

2016-01-01

A method is proposed to calculate the electric properties of organic-based devices from the molecular structure. The charge transfer rate is obtained using non-adiabatic molecular dynamics. The organic film in the device is modeled using

Determination of the threshold of nanoparticle behavior: Structural and electronic properties study of nano-sized copper

International Nuclear Information System (INIS)

Torres-Vega, Juan J.; Medrano, L.R.; Landauro, C.V.; Rojas-Tapia, J.

2014-01-01

In the present work we determine the threshold of the nanoparticle behavior of copper nanoparticles by studying their structural and electronic properties. The studied nanoparticles contain from 13 to 8217 atoms and were obtained by molecular dynamics simulations using the Johnson potential for copper based on the embedded atom method. The results indicate that for small copper nanoparticles ( 2000atoms, ∼3.5 nm), with spherical-like external shape and large percentage of fcc-like local structure, this effect is negligible and their electronic character are similar to such expected in solid copper. Finally, it has also been shown that copper nanoparticles change their electronic character, from metallic to insulating, after increasing the strength of the chemical disorder

Studies of the surface structures of molecular crystals and of adsorbed molecular monolayers on the (111) crystal faces of platinum and silver by low-energy electron diffraction

International Nuclear Information System (INIS)

Firment, L.E.

1977-01-01

The structures of molecular crystal surfaces were investigated for the first time by the use of low-energy electron diffraction (LEED). The experimental results from a variety of molecular crystals were examined and compared as a first step towards understanding the properties of these surfaces on a microscopic level. The method of sample preparation employed, vapor deposition onto metal single-crystal substrates at low temperatures in ultrahigh vacuum, allowed concurrent study of the structures of adsorbed monolayers on metal surfaces and of the growth processes of molecular films on metal substrates. The systems investigated were ice, ammonia, naphthalene, benzene, the n-paraffins (C 3 to C 8 ), cyclohexane, trioxane, acetic acid, propionic acid, methanol, and methylamine adsorbed and condensed on both Pt(111) and Ag(111) surfaces. Electron-beam-induced damage of the molecular surfaces was observed after electron exposures of 10 -4 A sec cm -2 at 20 eV. Aromatic molecular crystal samples were more resistant to damage than samples of saturated molecules. The quality and orientation of the grown molecular crystal films were influenced by substrate preparation and growth conditions. Forty ordered monolayer structures were observed. 110 figures, 22 tables, 162 references

Molecular imprinted polypyrrole modified glassy carbon electrode for the determination of tobramycin

International Nuclear Information System (INIS)

Gupta, Vinod Kumar; Yola, Mehmet Lütfi; Özaltın, Nuran; Atar, Necip; Üstündağ, Zafer; Uzun, Lokman

2013-01-01

Graphical abstract: Atomic force microscopic images of (A) bare GCE and (B) TOB imprinted PPy/GCE surface. - Highlights: • Glassy carbon electrode based on molecularly imprinted polypyrrole was prepared. • The developed surfaces were characterized by AFM, FTIR, EIS and CV. • The developed nanosensor was applied to egg and milk samples. - Abstract: Over the past two decades, molecular imprinted polymers have attracted a broad interest from scientists in sensor development. In the preparation of molecular imprinted polymers the desired molecule (template) induces the creation of specific recognition sites in the polymer. In this study, the glassy carbon electrode (GCE) based on molecularly imprinted polypyrrole (PPy) was fabricated for the determination of tobramycin (TOB). The developed electrode was prepared by incorporation of a template molecule (TOB) during the electropolymerization of pyrrole on GCE in aqueous solution using cyclic voltammetry (CV) method. The performance of the imprinted and non-imprinted electrodes was evaluated by square wave voltammetry (SWV). The effect of pH, monomer and template concentrations, electropolymerization cycles on the performance of the imprinted and non-imprinted electrodes was investigated and optimized. The non-modified and TOB-imprinted surfaces were characterized by using atomic force microscopy (AFM), Fourier transform infrared spectroscopy (FTIR), electrochemical impedance spectroscopy (EIS) and CV. The linearity range of TOB was 5.0 × 10 −10 –1.0 × 10 −8 M with the detection limit of 1.4 × 10 −10 M. The developed nanosensor was applied successfully for the determination of TOB in egg and milk

Micro structure processing on plastics by accelerated hydrogen molecular ions

Science.gov (United States)

Hayashi, H.; Hayakawa, S.; Nishikawa, H.

2017-08-01

A proton has 1836 times the mass of an electron and is the lightest nucleus to be used for accelerator in material modification. We can setup accelerator with the lowest acceleration voltage. It is preferable characteristics of Proton Beam Writer (PBW) for industrial applications. On the contrary ;proton; has the lowest charge among all nuclei and the potential impact to material is lowest. The object of this research is to improve productivity of the PBW for industry application focusing on hydrogen molecular ions. These ions are generated in the same ion source by ionizing hydrogen molecule. There is no specific ion source requested and it is suitable for industrial use. We demonstrated three dimensional (3D) multilevel micro structures on polyester base FPC (Flexible Printed Circuits) using proton, H2+ and H3+. The reactivity of hydrogen molecular ions is much higher than that of proton and coincident with the level of expectation. We can apply this result to make micro devices of 3D multilevel structures on FPC.

Structural insights into the molecular mechanisms of myasthenia gravis and their therapeutic implications

Energy Technology Data Exchange (ETDEWEB)

Noridomi, Kaori; Watanabe, Go; Hansen, Melissa N.; Han, Gye Won; Chen, Lin (USC)

2017-04-25

The nicotinic acetylcholine receptor (nAChR) is a major target of autoantibodies in myasthenia gravis (MG), an autoimmune disease that causes neuromuscular transmission dysfunction. Despite decades of research, the molecular mechanisms underlying MG have not been fully elucidated. Here, we present the crystal structure of the nAChR α1 subunit bound by the Fab fragment of mAb35, a reference monoclonal antibody that causes experimental MG and competes with ~65% of antibodies from MG patients. Our structures reveal for the first time the detailed molecular interactions between MG antibodies and a core region on nAChR α1. These structures suggest a major nAChR-binding mechanism shared by a large number of MG antibodies and the possibility to treat MG by blocking this binding mechanism. Structure-based modeling also provides insights into antibody-mediated nAChR cross-linking known to cause receptor degradation. Our studies establish a structural basis for further mechanistic studies and therapeutic development of MG.

Amino Acid Molecular Units: Building Primary and Secondary Protein Structures

Directory of Open Access Journals (Sweden)

Aparecido R. Silva

2008-05-01

Full Text Available In order to guarantee the learning quality and suitable knowledge  use  about structural biology, it is fundamental to  exist, since the beginning of  students’ formation, the possibility of clear visualization of biomolecule structures. Nevertheless, the didactic books can only bring  schematic  drawings; even more elaborated figures and graphic computation  do not permit the necessary interaction.  The representation of three-dimensional molecular structures with ludic models, built with representative units, have supplied to the students and teachers a successfully experience to  visualize such structures and correlate them to the real molecules.  The design and applicability of the representative units were discussed with researchers and teachers before mould implementation.  In this stage  it  will be presented the  developed  kit  containing the  representative  plastic parts of the main amino acids.  The kit can demonstrate the interaction among the amino acids  functional groups  (represented by colors, shapes,  sizes and  the peptidic bonds between them  facilitating the assembly and visuali zation of the primary and secondary protein structure.  The models were designed for  Ca,  amino,  carboxyl groups  and  hydrogen. The  lateral chains have  well defined models that represent their geometrical shape.  The completed kit set  will be presented in this meeting (patent requested.  In the last phase of the project will be realized  an effective evaluation  of the kit  as a facilitative didactic tool of the teaching/learning process in the Structural Molecular Biology area.

Quantum level structure of molecular magnets, Fe12 and V15

Energy Technology Data Exchange (ETDEWEB)

Ajiro, Y.; Inagaki, Y.; Itoh, H.; Asano, T.; Narumi, Y.; Kindo, K.; Sakon, T.; Nojiri, H.; Motokawa, M.; Cornia, A.; Gatteschi, D.; Mueller, A.; Barbara, B

2003-05-01

We review our recent work on molecular magnets, Fe12 and V15 with focus on the determination of low-lying quantum energy levels which have permanent importance in understanding their unique quantum magnetism.

Quantum level structure of molecular magnets, Fe12 and V15

International Nuclear Information System (INIS)

Ajiro, Y.; Inagaki, Y.; Itoh, H.; Asano, T.; Narumi, Y.; Kindo, K.; Sakon, T.; Nojiri, H.; Motokawa, M.; Cornia, A.; Gatteschi, D.; Mueller, A.; Barbara, B.

2003-01-01

We review our recent work on molecular magnets, Fe12 and V15 with focus on the determination of low-lying quantum energy levels which have permanent importance in understanding their unique quantum magnetism

Synchrotron-Based Microspectroscopic Analysis of Molecular and Biopolymer Structures Using Multivariate Techniques and Advanced Multi-Components Modeling

International Nuclear Information System (INIS)

Yu, P.

2008-01-01

More recently, advanced synchrotron radiation-based bioanalytical technique (SRFTIRM) has been applied as a novel non-invasive analysis tool to study molecular, functional group and biopolymer chemistry, nutrient make-up and structural conformation in biomaterials. This novel synchrotron technique, taking advantage of bright synchrotron light (which is million times brighter than sunlight), is capable of exploring the biomaterials at molecular and cellular levels. However, with the synchrotron RFTIRM technique, a large number of molecular spectral data are usually collected. The objective of this article was to illustrate how to use two multivariate statistical techniques: (1) agglomerative hierarchical cluster analysis (AHCA) and (2) principal component analysis (PCA) and two advanced multicomponent modeling methods: (1) Gaussian and (2) Lorentzian multi-component peak modeling for molecular spectrum analysis of bio-tissues. The studies indicated that the two multivariate analyses (AHCA, PCA) are able to create molecular spectral corrections by including not just one intensity or frequency point of a molecular spectrum, but by utilizing the entire spectral information. Gaussian and Lorentzian modeling techniques are able to quantify spectral omponent peaks of molecular structure, functional group and biopolymer. By application of these four statistical methods of the multivariate techniques and Gaussian and Lorentzian modeling, inherent molecular structures, functional group and biopolymer onformation between and among biological samples can be quantified, discriminated and classified with great efficiency.

New experimental possibilities for the study of the molecular structure and the dynamics of liquids

International Nuclear Information System (INIS)

Versmold, H.

1981-01-01

The general space-time-pair distribution function G(Rsub(A)(0), Ωsub(A)(0), Rsub(B)(t), Ωsub(B)(t) plays an important role for the theoretical description of liquids. In this report first the relationship between the space-time-pair distribution function and static pair distribution functions, which characterize the liquid structure, and time correlation functions, which can be used to comprehend the dynamics of liquids, will be introduced. As an experimental method, which is particularly suited to determine the static pair distribution function, coherent neutron scattering is discussed. The power of this method for the determination of the liquid structure is demonstrated by considering the examples of a fused salt and a molecular liquid. For investigations of the dynamics of liquids incoherent neutron scattering and several spectroscopic experiments have been in use during the last few years. The relationship between these experiments and time correlation functions is presented. A discussion concerning the possibility to study translational and rotational dynamics by incoherent neutron scattering follows. Finally, by referring to a depolarized Rayleigh experiment, the relationship between spectroscopic experiments and orientational correlation functions, which describe the reorientational dynamics in liquids, is illustrated. (orig.)

Molecular assays for determining Mycobacterium leprae viability in tissues of experimentally infected mice.

Science.gov (United States)

Davis, Grace L; Ray, Nashone A; Lahiri, Ramanuj; Gillis, Thomas P; Krahenbuhl, James L; Williams, Diana L; Adams, Linda B

2013-01-01

The inability of Mycobacterium leprae to grow on axenic media has necessitated specialized techniques in order to determine viability of this organism. The purpose of this study was to develop a simple and sensitive molecular assay for determining M. leprae viability directly from infected tissues. Two M. leprae-specific quantitative reverse transcription PCR (qRT-PCR) assays based on the expression levels of esxA, encoding the ESAT-6 protein, and hsp18, encoding the heat shock 18 kDa protein, were developed and tested using infected footpad (FP) tissues of both immunocompetent and immunocompromised (athymic nu/nu) mice. In addition, the ability of these assays to detect the effects of anti-leprosy drug treatment on M. leprae viability was determined using rifampin and rifapentine, each at 10 mg/kg for 1, 5, or 20 daily doses, in the athymic nu/nu FP model. Molecular enumeration (RLEP PCR) and viability determinations (qRT-PCR) were performed via Taqman methodology on DNA and RNA, respectively, purified from ethanol-fixed FP tissue and compared with conventional enumeration (microscopic counting of acid fast bacilli) and viability assays (radiorespirometry, viability staining) which utilized bacilli freshly harvested from the contralateral FP. Both molecular and conventional assays demonstrated growth and high viability of M. leprae in nu/nu FPs over a 4 month infection period. In contrast, viability was markedly decreased by 8 weeks in immunocompetent mice. Rifapentine significantly reduced bacterial viability after 5 treatments, whereas rifampin required up to 20 treatments for the same efficacy. Neither drug was effective after a single treatment. In addition, host gene expression was monitored with the same RNA preparations. hsp18 and esxA qRT-PCR are sensitive molecular indicators, reliably detecting viability of M. leprae in tissues without the need for bacterial isolation or immediate processing, making these assays applicable for in vivo drug screening and

Cryo-EM Structure Determination Using Segmented Helical Image Reconstruction.

Science.gov (United States)

Fromm, S A; Sachse, C

2016-01-01

Treating helices as single-particle-like segments followed by helical image reconstruction has become the method of choice for high-resolution structure determination of well-ordered helical viruses as well as flexible filaments. In this review, we will illustrate how the combination of latest hardware developments with optimized image processing routines have led to a series of near-atomic resolution structures of helical assemblies. Originally, the treatment of helices as a sequence of segments followed by Fourier-Bessel reconstruction revealed the potential to determine near-atomic resolution structures from helical specimens. In the meantime, real-space image processing of helices in a stack of single particles was developed and enabled the structure determination of specimens that resisted classical Fourier helical reconstruction and also facilitated high-resolution structure determination. Despite the progress in real-space analysis, the combination of Fourier and real-space processing is still commonly used to better estimate the symmetry parameters as the imposition of the correct helical symmetry is essential for high-resolution structure determination. Recent hardware advancement by the introduction of direct electron detectors has significantly enhanced the image quality and together with improved image processing procedures has made segmented helical reconstruction a very productive cryo-EM structure determination method. © 2016 Elsevier Inc. All rights reserved.

Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D)

International Nuclear Information System (INIS)

Streek, Jacco van de; Neumann, Marcus A.

2014-01-01

The accuracy of 215 experimental organic crystal structures from powder diffraction data is validated against a dispersion-corrected density functional theory method. In 2010 we energy-minimized 225 high-quality single-crystal (SX) structures with dispersion-corrected density functional theory (DFT-D) to establish a quantitative benchmark. For the current paper, 215 organic crystal structures determined from X-ray powder diffraction (XRPD) data and published in an IUCr journal were energy-minimized with DFT-D and compared to the SX benchmark. The on average slightly less accurate atomic coordinates of XRPD structures do lead to systematically higher root mean square Cartesian displacement (RMSCD) values upon energy minimization than for SX structures, but the RMSCD value is still a good indicator for the detection of structures that deserve a closer look. The upper RMSCD limit for a correct structure must be increased from 0.25 Å for SX structures to 0.35 Å for XRPD structures; the grey area must be extended from 0.30 to 0.40 Å. Based on the energy minimizations, three structures are re-refined to give more precise atomic coordinates. For six structures our calculations provide the missing positions for the H atoms, for five structures they provide corrected positions for some H atoms. Seven crystal structures showed a minor error for a non-H atom. For five structures the energy minimizations suggest a higher space-group symmetry. For the 225 SX structures, the only deviations observed upon energy minimization were three minor H-atom related issues. Preferred orientation is the most important cause of problems. A preferred-orientation correction is the only correction where the experimental data are modified to fit the model. We conclude that molecular crystal structures determined from powder diffraction data that are published in IUCr journals are of high quality, with less than 4% containing an error in a non-H atom

Crystal structure determination of Efavirenz

International Nuclear Information System (INIS)

Popeneciu, Horea; Dumitru, Ristoiu; Tripon, Carmen; Borodi, Gheorghe; Pop, Mihaela Maria

2015-01-01

Needle-shaped single crystals of the title compound, C 14 H 9 ClF 3 NO 2 , were obtained from a co-crystallization experiment of Efavirenz with maleic acid in a (1:1) ratio, using methanol as solvent. Crystal structure determination at room temperature revealed a significant anisotropy of the lattice expansion compared to the previously reported low-temperature structure. In both low- and room temperature structures the cyclopropylethynyl fragment in one of the asymmetric unit molecules is disordered. While at low-temperature only one C atom exhibits positional disorder, at room temperature the disorder is present for two C atoms of the cyclopropane ring

Molecular equilibrium structures from experimental rotational constants and calculated vibration-rotation interaction constants

DEFF Research Database (Denmark)

Pawlowski, F; Jorgensen, P; Olsen, Jeppe

2002-01-01

A detailed study is carried out of the accuracy of molecular equilibrium geometries obtained from least-squares fits involving experimental rotational constants B(0) and sums of ab initio vibration-rotation interaction constants alpha(r)(B). The vibration-rotation interaction constants have been...... calculated for 18 single-configuration dominated molecules containing hydrogen and first-row atoms at various standard levels of ab initio theory. Comparisons with the experimental data and tests for the internal consistency of the calculations show that the equilibrium structures generated using Hartree......-Fock vibration-rotation interaction constants have an accuracy similar to that obtained by a direct minimization of the CCSD(T) energy. The most accurate vibration-rotation interaction constants are those calculated at the CCSD(T)/cc-pVQZ level. The equilibrium bond distances determined from these interaction...

Molecular mechanics of DNA bricks: in situ structure, mechanical properties and ionic conductivity

International Nuclear Information System (INIS)

Slone, Scott Michael; Li, Chen-Yu; Aksimentiev, Aleksei; Yoo, Jejoong

2016-01-01

The DNA bricks method exploits self-assembly of short DNA fragments to produce custom three-dimensional objects with subnanometer precision. In contrast to DNA origami, the DNA brick method permits a variety of different structures to be realized using the same library of DNA strands. As a consequence of their design, however, assembled DNA brick structures have fewer interhelical connections in comparison to equivalent DNA origami structures. Although the overall shape of the DNA brick objects has been characterized and found to conform to the features of the target designs, the microscopic properties of DNA brick objects remain yet to be determined. Here, we use the all-atom molecular dynamics method to directly compare the structure, mechanical properties and ionic conductivity of DNA brick and DNA origami structures different only by internal connectivity of their consistituent DNA strands. In comparison to equivalent DNA origami structures, the DNA brick structures are found to be less rigid and less dense and have a larger cross-section area normal to the DNA helix direction. At the microscopic level, the junction in the DNA brick structures are found to be right-handed, similar to the structure of individual Holliday junctions (HJ) in solution, which contrasts with the left-handed structure of HJ in DNA origami. Subject to external electric field, a DNA brick plate is more leaky to ions than an equivalent DNA origami plate because of its lower density and larger cross-section area. Overall, our results indicate that the structures produced by the DNA brick method are fairly similar in their overall appearance to those created by the DNA origami method but are more compliant when subject to external forces, which likely is a consequence of their single crossover design. (paper)

Structure of hydrogenated amorphous silicon from ab initio molecular dynamics

Energy Technology Data Exchange (ETDEWEB)

Buda, F. (Department of Physics, The Ohio State University, 174 West 18th Avenue, Columbus, Ohio (USA)); Chiarotti, G.L. (International School for Advanced Studies, Strada Costiera 11, I-34014 Trieste (Italy) Laboratorio Tecnologie Avanzate Superfici e Catalisi del Consorzio Interuniversitario Nazionale di Fisica della Materia, Padriciano 99, I-34012 Trieste (Italy)); Car, R. (International School for Advanced Studies, Strada Costiera 11, I-34014 Trieste (Italy) Institut Romard de Recherche Numerique en Physique des Materiaux, CH-1015 Lausanne, Switzerland Department of Condensed Matter Physics, University of Geneva, CH-1211 Geneva (Switzerland)); Parrinello, M. (IBM Research Division, Zurich Research Laboratory, CH-8803 Rueschlikon (Switzerland))

1991-09-15

We have generated a model of hydrogenated amorphous silicon by first-principles molecular dynamics. Our results are in good agreement with the available experimental data and provide new insight into the microscopic structure of this material. The calculation lends support to models in which monohydride complexes are prevalent, and indicates a strong tendency of hydrogen to form small clusters.

Molecular Structures and Dynamics of the Stepwise Activation Mechanism of a Matrix Metalloproteinase Zymogen: Challenging the Cysteine Switch Dogma

International Nuclear Information System (INIS)

Rosenblum, G.; Meroueh, S.; Toth, M.; Fisher, J.; Fridman, R.; Mobashery, S.; Sagi, I.

2007-01-01

Activation of matrix metalloproteinase zymogen (pro-MMP) is a vital homeostatic process, yet its molecular basis remains unresolved. Using stopped-flow X-ray spectroscopy of the active site zinc ion, we determined the temporal sequence of pro-MMP-9 activation catalyzed by tissue kallikrein protease in milliseconds to several minutes. The identity of three intermediates seen by X-ray spectroscopy was corroborated by molecular dynamics simulations and quantum mechanics/molecular mechanics calculations. The cysteine-zinc interaction that maintains enzyme latency is disrupted via active-site proton transfers that mediate transient metal-protein coordination events and eventual binding of water. Unexpectedly, these events ensue as a direct result of complexation of pro-MMP-9 and kallikrein and occur before proteolysis and eventual dissociation of the pro-peptide from the catalytic site. Here we demonstrate the synergism among long-range protein conformational transitions, local structural rearrangements, and fine atomic events in the process of zymogen activation.

NATO Advanced Research Workshop on Vectorization of Advanced Methods for Molecular Electronic Structure

CERN Document Server

1984-01-01

That there have been remarkable advances in the field of molecular electronic structure during the last decade is clear not only to those working in the field but also to anyone else who has used quantum chemical results to guide their own investiga­ tions. The progress in calculating the electronic structures of molecules has occurred through the truly ingenious theoretical and methodological developments that have made computationally tractable the underlying physics of electron distributions around a collection of nuclei. At the same time there has been consider­ able benefit from the great advances in computer technology. The growing sophistication, declining costs and increasing accessibi­ lity of computers have let theorists apply their methods to prob­ lems in virtually all areas of molecular science. Consequently, each year witnesses calculations on larger molecules than in the year before and calculations with greater accuracy and more com­ plete information on molecular properties. We can surel...

16O+16O molecular nature of the superdeformed band of 32S and the evolution of the molecular structure

International Nuclear Information System (INIS)

Kimura, Masaaki; Horiuchi, Hisashi

2004-01-01

The relation between the superdeformed band of 32 S and 16 O+ 16 O molecular bands is studied by the deformed-basis antisymmetrized molecular dynamics with the Gogny D1S force. It is found that the obtained superdeformed band members of S have a considerable amount of the 16 O+ 16 O component. Above the superdeformed band, we have obtained two excited rotational bands which have more prominent character of the 16 O+ 16 O molecular band. These three rotational bands are regarded as a series of 16 O+ 16 O molecular bands which were predicted by using the unique 16 O- 16 O optical potential. As the excitation energy and principal quantum number of the relative motion increase, the 16 O+ 16 O cluster structure becomes more prominent but at the same time, the band members are fragmented into several states

Plant-based food and feed protein structure changes induced by gene-transformation, heating and bio-ethanol processing: a synchrotron-based molecular structure and nutrition research program.

Science.gov (United States)

Yu, Peiqiang

2010-11-01

Unlike traditional "wet" analytical methods which during processing for analysis often result in destruction or alteration of the intrinsic protein structures, advanced synchrotron radiation-based Fourier transform infrared microspectroscopy has been developed as a rapid and nondestructive and bioanalytical technique. This cutting-edge synchrotron-based bioanalytical technology, taking advantages of synchrotron light brightness (million times brighter than sun), is capable of exploring the molecular chemistry or structure of a biological tissue without destruction inherent structures at ultra-spatial resolutions. In this article, a novel approach is introduced to show the potential of the advanced synchrotron-based analytical technology, which can be used to study plant-based food or feed protein molecular structure in relation to nutrient utilization and availability. Recent progress was reported on using synchrotron-based bioanalytical technique synchrotron radiation-based Fourier transform infrared microspectroscopy and diffused reflectance infrared Fourier transform spectroscopy to detect the effects of gene-transformation (Application 1), autoclaving (Application 2), and bio-ethanol processing (Application 3) on plant-based food and feed protein structure changes on a molecular basis. The synchrotron-based technology provides a new approach for plant-based protein structure research at ultra-spatial resolutions at cellular and molecular levels.

The effect of structural changes on charge transfer states in a light-harvesting carotenoid-diaryl-porphyrin-C{sub 60} molecular triad

Energy Technology Data Exchange (ETDEWEB)

Olguin, Marco [Computational Science Program, University of Texas at El Paso, El Paso, Texas 79968 (United States); Basurto, Luis; Zope, Rajendra R. [Department of Physics, The University of Texas at El Paso, El Paso, Texas 79968 (United States); Baruah, Tunna, E-mail: tbaruah@utep.edu [Computational Science Program, University of Texas at El Paso, El Paso, Texas 79968 (United States); Department of Physics, The University of Texas at El Paso, El Paso, Texas 79968 (United States)

2014-05-28

We present a detailed study of charge transfer (CT) excited states for a large number of configurations in a light-harvesting Carotenoid-diaryl-Porphyrin-C{sub 60} (CPC{sub 60}) molecular triad. The chain-like molecular triad undergoes photoinduced charge transfer process exhibiting a large excited state dipole moment, making it suitable for application to molecular-scale opto-electronic devices. An important consideration is that the structural flexibility of the CPC{sub 60} triad impacts its dynamics in solvents. Since experimentally measured dipole moments for the triad of ∼110 D and ∼160 D strongly indicate a range in structural variability in the excited state, studying the effect of structural changes on the CT excited state energetics furthers the understanding of its charge transfer states. We have calculated the variation in the lowest CT excited state energies by performing a scan of possible variation in the structure of the triad. Some of these configurations were generated by incrementally scanning a 360° torsional (dihedral) twist at the C{sub 60}-porhyrin linkage and the porphyrin-carotenoid linkage. Additionally, five different CPC{sub 60} conformations were studied to determine the effect of pi-conjugation and particle-hole Coulombic attraction on the CT excitation energies. Our calculations show that configurational changes in the triad induces a variation of ∼0.6 eV in CT excited state energies in the gas-phase. The corresponding calculated excited state dipoles show a range of 47 D–188 D. The absorption spectra and density of states of these structures show little variation except for the structures where the porphyrin and aryl conjugation is changed.

Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D).

Science.gov (United States)

van de Streek, Jacco; Neumann, Marcus A

2014-12-01

In 2010 we energy-minimized 225 high-quality single-crystal (SX) structures with dispersion-corrected density functional theory (DFT-D) to establish a quantitative benchmark. For the current paper, 215 organic crystal structures determined from X-ray powder diffraction (XRPD) data and published in an IUCr journal were energy-minimized with DFT-D and compared to the SX benchmark. The on average slightly less accurate atomic coordinates of XRPD structures do lead to systematically higher root mean square Cartesian displacement (RMSCD) values upon energy minimization than for SX structures, but the RMSCD value is still a good indicator for the detection of structures that deserve a closer look. The upper RMSCD limit for a correct structure must be increased from 0.25 Å for SX structures to 0.35 Å for XRPD structures; the grey area must be extended from 0.30 to 0.40 Å. Based on the energy minimizations, three structures are re-refined to give more precise atomic coordinates. For six structures our calculations provide the missing positions for the H atoms, for five structures they provide corrected positions for some H atoms. Seven crystal structures showed a minor error for a non-H atom. For five structures the energy minimizations suggest a higher space-group symmetry. For the 225 SX structures, the only deviations observed upon energy minimization were three minor H-atom related issues. Preferred orientation is the most important cause of problems. A preferred-orientation correction is the only correction where the experimental data are modified to fit the model. We conclude that molecular crystal structures determined from powder diffraction data that are published in IUCr journals are of high quality, with less than 4% containing an error in a non-H atom.

Genarris: Random generation of molecular crystal structures and fast screening with a Harris approximation

Science.gov (United States)

Li, Xiayue; Curtis, Farren S.; Rose, Timothy; Schober, Christoph; Vazquez-Mayagoitia, Alvaro; Reuter, Karsten; Oberhofer, Harald; Marom, Noa

2018-06-01

We present Genarris, a Python package that performs configuration space screening for molecular crystals of rigid molecules by random sampling with physical constraints. For fast energy evaluations, Genarris employs a Harris approximation, whereby the total density of a molecular crystal is constructed via superposition of single molecule densities. Dispersion-inclusive density functional theory is then used for the Harris density without performing a self-consistency cycle. Genarris uses machine learning for clustering, based on a relative coordinate descriptor developed specifically for molecular crystals, which is shown to be robust in identifying packing motif similarity. In addition to random structure generation, Genarris offers three workflows based on different sequences of successive clustering and selection steps: the "Rigorous" workflow is an exhaustive exploration of the potential energy landscape, the "Energy" workflow produces a set of low energy structures, and the "Diverse" workflow produces a maximally diverse set of structures. The latter is recommended for generating initial populations for genetic algorithms. Here, the implementation of Genarris is reported and its application is demonstrated for three test cases.

Molecular Dynamics Simulation of the Structure and Properties of Lithium Phosphate Glasses

Energy Technology Data Exchange (ETDEWEB)

Liang, J-J; Cygan, R.T.; Alam, T.M.

1999-07-09

A new forcefield model was developed for the computer simulation of phosphate materials that have many important applications in the electronics and biomedical industries. The model provides a fundamental basis for the evaluation of phosphate glass structure and thermodynamics. Molecular dynamics simulations of a series of lithium phosphate glass compositions were performed using the forcefield model. A high concentration of three-membered rings (P{sub 3}O{sub 3}) occurs in the glass of intermediate composition (0.2 Li{sub 2}O {center_dot} 0.8P{sub 2}O{sub 5}) that corresponds to the minimum in the glass transition temperature curve for the compositional series. Molecular orbital calculations of various phosphate ring clusters indicate an increasing stabilization of the phosphate ring structure going from two- to four-membered rings.

III - V semiconductor structures for biosensor and molecular electronics applications

Energy Technology Data Exchange (ETDEWEB)

Luber, S M

2007-01-15

The present work reports on the employment of III-V semiconductor structures to biosensor and molecular electronics applications. In the first part a sensor based on a surface-near two dimensional electron gas for a use in biological environment is studied. Such a two dimensional electron gas inherently forms in a molecular beam epitaxy (MBE) grown, doped aluminum gallium arsenide - gallium arsenide (AlGaAs-GaAs) heterostructure. Due to the intrinsic instability of GaAs in aqueous solutions the device is passivated by deposition of a monolayer of 4'-substituted mercaptobiphenyl molecules. The influence of these molecules which bind to the GaAs via a sulfur group is investigated by Kelvin probe measurements in air. They reveal a dependence of GaAs electron affinity on the intrinsic molecular dipole moment of the mercaptobiphenyls. Furthermore, transient surface photovoltage measurements are presented which demonstrate an additional influence of mercaptobiphenyl chemisorption on surface carrier recombination rates. As a next step, the influence of pH-value and salt concentration upon the sensor device is discussed based on the results obtained from sensor conductance measurements in physiological solutions. A dependence of the device surface potential on both parameters due to surface charging is deduced. Model calculations applying Poisson-Boltzmann theory reveal as possible surface charging mechanisms either the adsorption of OH- ions on the surface, or the dissociation of OH groups in surface oxides. A comparison between simulation settings and physical device properties indicate the OH- adsorption as the most probable mechanism. In the second part of the present study the suitability of MBE grown III-V semiconductor structures for molecular electronics applications is examined. In doing so, a method to fabricate nanometer separated, coplanar, metallic electrodes based on the cleavage of a supporting AlGaAs-GaAs heterostructure is presented. This is followed by a

III - V semiconductor structures for biosensor and molecular electronics applications

Energy Technology Data Exchange (ETDEWEB)

Luber, S.M.

2007-01-15

The present work reports on the employment of III-V semiconductor structures to biosensor and molecular electronics applications. In the first part a sensor based on a surface-near two dimensional electron gas for a use in biological environment is studied. Such a two dimensional electron gas inherently forms in a molecular beam epitaxy (MBE) grown, doped aluminum gallium arsenide - gallium arsenide (AlGaAs-GaAs) heterostructure. Due to the intrinsic instability of GaAs in aqueous solutions the device is passivated by deposition of a monolayer of 4'-substituted mercaptobiphenyl molecules. The influence of these molecules which bind to the GaAs via a sulfur group is investigated by Kelvin probe measurements in air. They reveal a dependence of GaAs electron affinity on the intrinsic molecular dipole moment of the mercaptobiphenyls. Furthermore, transient surface photovoltage measurements are presented which demonstrate an additional influence of mercaptobiphenyl chemisorption on surface carrier recombination rates. As a next step, the influence of pH-value and salt concentration upon the sensor device is discussed based on the results obtained from sensor conductance measurements in physiological solutions. A dependence of the device surface potential on both parameters due to surface charging is deduced. Model calculations applying Poisson-Boltzmann theory reveal as possible surface charging mechanisms either the adsorption of OH- ions on the surface, or the dissociation of OH groups in surface oxides. A comparison between simulation settings and physical device properties indicate the OH- adsorption as the most probable mechanism. In the second part of the present study the suitability of MBE grown III-V semiconductor structures for molecular electronics applications is examined. In doing so, a method to fabricate nanometer separated, coplanar, metallic electrodes based on the cleavage of a supporting AlGaAs-GaAs heterostructure is presented. This is followed

Molecular Cloud Structures and Massive Star Formation in N159

Science.gov (United States)

Nayak, O.; Meixner, M.; Fukui, Y.; Tachihara, K.; Onishi, T.; Saigo, K.; Tokuda, K.; Harada, R.

2018-02-01

The N159 star-forming region is one of the most massive giant molecular clouds (GMCs) in the Large Magellanic Cloud (LMC). We show the 12CO, 13CO, CS molecular gas lines observed with ALMA in N159 west (N159W) and N159 east (N159E). We relate the structure of the gas clumps to the properties of 24 massive young stellar objects (YSOs) that include 10 newly identified YSOs based on our search. We use dendrogram analysis to identify properties of the molecular clumps, such as flux, mass, linewidth, size, and virial parameter. We relate the YSO properties to the molecular gas properties. We find that the CS gas clumps have a steeper size–linewidth relation than the 12CO or 13CO gas clumps. This larger slope could potentially occur if the CS gas is tracing shocks. The virial parameters of the 13CO gas clumps in N159W and N159E are low (<1). The threshold for massive star formation in N159W is 501 M ⊙ pc‑2, and the threshold for massive star formation in N159E is 794 M ⊙ pc‑2. We find that 13CO is more photodissociated in N159E than N159W. The most massive YSO in N159E has cleared out a molecular gas hole in its vicinity. All the massive YSO candidates in N159E have a more evolved spectral energy distribution type in comparison to the YSO candidates in N159W. These differences lead us to conclude that the giant molecular cloud complex in N159E is more evolved than the giant molecular cloud complex in N159W.

A circumstellar molecular gas structure associated with the massive young star Cepheus A-HW 2

Science.gov (United States)

Torrelles, Jose M.; Rodriguez, Luis F.; Canto, Jorge; Ho, Paul T. P.

1993-01-01

We report the detection via VLA-D observations of ammonia of a circumstellar high-density molecular gas structure toward the massive young star related to the object Cepheus A-HW 2, a firm candidate for the powering source of the high-velocity molecular outflow in the region. We suggest that the circumstellar molecular gas structure could be related to the circumstellar disk previously suggested from infrared, H2O, and OH maser observations. We consider as a plausible scenario that the double radio continuum source of HW 2 could represent the ionized inner part of the circumstellar disk, in the same way as proposed to explain the double radio source in L1551. The observed motions in the circumstellar molecular gas can be produced by bound motions (e.g., infall or rotation) around a central mass of about 10-20 solar masses (B0.5 V star or earlier).

CRYSTAL AND MOLECULAR STRUCTURE OF 5-NITROPIRIDINE PIPERIDINE-SULFENAMIDE

OpenAIRE

Brito, Iván; León, Yasna; Arias, Mauricio; Vargas, Danitza; Carmona, Francisco; Ramírez, Eduardo; Restovic, Ambrosio; Cárdenas, Alejandro; Wittke, Oscar; López-Rodríguez, Matías

2002-01-01

The crystal and molecular structure of 5-nitropiridine piperidine-sulfenamide, C10H13N3O2 S is described and compared with other sulfenamides and with other similar compounds. This structure belongs to a type of divalent sulphur compound and crystallizes in the orthorhombic space group Pnma with a= 27.810(4), b=6.797(1), c=6.110(1)Å, and Dx =1.376 g cm-3 with Z=4. The S-N bond distance of 1.699(4) Å is shorter than a single S-N bond [1.74 Å]. The NO2-(C6H3N)-S-N(C 5H10) molecule lies on a cry...

Structure determination of disease associated peak AAA from l-Tryptophan implicated in the eosinophilia-myalgia syndrome.

Science.gov (United States)

Klarskov, Klaus; Gagnon, Hugo; Boudreault, Pierre-Luc; Normandin, Chad; Plancq, Baptiste; Marsault, Eric; Gleich, Gerald J; Naylor, Stephen

2018-01-05

The eosinophilia-myalgia syndrome (EMS) outbreak of 1989 that occurred in the USA and elsewhere was caused by the ingestion of l-Tryptophan (L-Trp) solely manufactured by the Japanese company Showa Denko K.K. (SD). Six compounds present in the SD L-Trp were reported to be case-associated contaminants. However, "one" of these compounds, Peak AAA has remained structurally uncharacterized, despite the fact that it was described as "the only statistically significant (p=0.0014) contaminant". Here, we employ on-line microcapillary-high performance liquid chromatography-electrospray ionization mass spectrometry (LC-MS), and tandem mass spectrometry (MS/MS) to determine that Peak AAA is in fact two structurally related isomers. Peak AAA 1 and Peak AAA 2 differed in LC retention times, and were determined by accurate mass-LC-MS to both have a protonated molecular ion (MH +) of mass 343.239Da (Da), corresponding to a molecular formula of C 21 H 30 N 2 O 2, and possessing eight degrees of unsaturation (DoU) for the non-protonated molecule. By comparing the LC-MS and LC-MS-MS retention times and spectra with authentic synthetic standards, Peak AAA 1 was identified as the intermolecular condensation product of L-Trp with anteiso 7-methylnonanoic acid, to afford (S)-2-amino-3-(2-((S,E)-7-methylnon-1-en-1-yl)-1H-indol-3-yl)propanoic acid. Peak AAA 2 was determined to be a condensation product of L-Trp with decanoic acid, which produced (S)-2-amino-3-(2-((E)-dec-1-en-1-yl)-1H-indol-3-yl)propanoic acid. Copyright © 2017 Elsevier B.V. All rights reserved.

Energy group structure determination using particle swarm optimization