Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Structure”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 451 records · Page 25Linked to original sources

Emergence of non-random structure in local food webs generated from randomly structured regional webs.

Previous studies have shown that high-resolution, empirical food webs possess a non-random network structure, typically characterized by uniform or exponential degree distributions. However, the empirical food webs that have been investigated for their structural properties represent local communities that are only a subset of a larger pool of regionally coexisting species. Here, we use a simple model to investigate the effects of regional food web structure on local food webs that are assembled by two simple processes: random immigration of species from a source web (regional food web), and random extinction of species within the local web. The model shows that local webs with non-random degree distributions can arise from randomly structured source webs. A comparison of local webs assembled from randomly structured source webs with local webs assembled from source webs generated by the niche model shows that the former have higher species richness at equilibrium, but have a nonlinear response to changing extinction rates. These results imply that the network structure of regional food webs can play a significant role in the assembly and dynamics of local webs in natural ecosystems. With natural landscapes becoming increasingly fragmented, understanding such structure may be a necessary key to understanding the maintenance and stability of local species diversity.

Animals↗

Production of a D-glycero-D-manno-heptosyltransferase mutant of Mannheimia haemolytica displaying a veterinary pathogen specific conserved LPS structure; development and functionality of antibodies to this LPS structure.

Previous structural studies of the lipopolysaccharides from the veterinary pathogens Mannheimia haemolytica (Mh), Actinobacillus pleuropneumoniae (Ap) and Pasteurella multocida (Pm) had identified a conserved inner core oligosaccharide structure that was present in all strains investigated. In order to examine the potential of this inner core structure as a vaccine, a mutagenesis strategy was adopted to interrupt a D-glycero-D-manno-heptosyltransferase gene (losB) of Mh. This gene encodes the enzyme responsible for the addition of a D-glycero-D-manno-heptose residue, the first residue beyond the conserved inner core, and its inactivation exposed the conserved inner core structure as a terminal unit on the mutant LPS molecule. Subsequent analyses confirmed the targeted structure of the mutant LPS had been obtained, and complementation with losB in trans confirmed that the losB gene encodes an alpha-1,6-D-glycero-D-manno-heptosyltransferase. Monoclonal antibodies raised in mice to this LPS structure were found to recognise LPS and whole-cells of the truncated mutant and wild-type Mh. The antibodies were bactericidal against a wild-type Mh strain and were able to passively protect mice in a model of Mh disease. This illustrates that it is possible to raise functional antibodies against the conserved inner core LPS structure.

Animals↗

Preparation of steroid structural data for the consideration of possible structural-functional relationships.

A format has been established for the presentation of steroid structural data which may prove to be useful in the consideration of the possible structural-functional relationships of steroids in biological systems. In preparing this format the detailed structural information for all steroids with known crystallographic structures has been computed and summarized, including bond lengths and angles, non-planarity coefficients, dihedral angles, length of the steroid nucleus, and side group inclinations. From the structural point of view it is interesting to note that (a) bond lengths do not differ significantly from the theoretical values, (b) bond angles do differ significantly from the theoretical values, (c) the non-planarity coefficient of the steroid molecule seems to be a function of the number of angular methyl groups but is unaffected by the presence of one heavy atom, (d) except where aromatic bonds are present the non-planarity coefficients of the two-ring and one-ring subdivisions of the steroid nucleus is 0.25 A, (e) the average non-planarity coefficient of the ring joins and "seat" portions of the chairs is 0.03 A, (f) dihedral angles deviate from the theoretically expected values and also show wide variation in the steroids studied, (g) the length of the steroid nucleus is variable, (h) analysis of side group inclination data must be deferred until more steroid structural information is available. From the biological point of view it is currently impossible to estimate the importance of each steroid structural feature in determining physiological function.

Androsterone↗

How the lipid-free structure of the N-terminal truncated human apoA-I converts to the lipid-bound form: new insights from NMR and X-ray structural comparison.

The X-ray structure of the N-terminal truncated human apoA-I [Borhani et al., Proc. Natl. Acad. Sci. USA 94 (1997) 12291] and the NMR structure of intact human apoA-I [Okon et al., FEBS Lett. 517 (2002) 139] found similar repeating helices. The crystal structure is a twisted circular four-helix bundle, consisting of four molecules of apoA-I(44-243), where four copies of the lecithin:cholesterol acyltransferase (LCAT)-activating domains are located outside the ring structure, while the aromatic-rich strong lipid-binding domains are inside. This architecture suggests a lipid-binding mechanism that lipids directly enter the hole of the crystal structure. Indeed, four copies of Trp50 and Trp72 are exposed and oriented toward the center of the ring, initiating lipid binding. This is followed by the inside-out rotations of the terminal helices to make a belt with all the hydrophobic faces of the helices facing inward. Such lipid-binding induced rotations have an impact on the conformation of the lipid-free form. Indeed, the structure of residues 78-81 changes from helical (free) to disordered (bound) while the structure of residues 221-227 changes from extended to helical.

Apolipoprotein A-I↗

Crystal structure of plakalbumin, a proteolytically nicked form of ovalbumin. Its relationship to the structure of cleaved alpha-1-proteinase inhibitor.

The crystal structure of plakalbumin, a proteolytically nicked form of ovalbumin, has been determined to a resolution of 2.8 A by the isomorphous replacement method and preliminary refinement. The structure closely resembles that of the cleaved form of alpha-1-proteinase inhibitor, with some important exceptions. The disposition of the new carboxyl chain terminus liberated by proteolysis is different with respect to the central beta-sheet A in the structures of these two molecules. In alpha-1-proteinase inhibitor, the new chain terminus inserts in beta-sheet A to add a middle strand to the sheet. In plakalbumin, this strand remains free near the site at which the cleavage occurs. A structural basis for this difference in behavior is proposed from the structures and sequences of these two molecules and other members of the serpin family. The structures and positions of the putative signal peptide of ovalbumin, the several post-translational modifications, and the relationship of the intron-exon patterns of plakalbumin and alpha-1-proteinase inhibitor to their protein structures are also described.

Amino Acid Sequence↗

Direct structural evidence for formation of a stem-loop structure involved in ribosomal frameshifting in human immunodeficiency virus type 1.

Programmed ribosomal frameshifting in viral messenger RNA occurs in response to neighboring sequence elements consisting of: a frameshift site, a spacer, and a downstream enhancer sequence. In human immunodeficiency virus type 1 (HIV-1) mRNA, this sequence element has a potential to form either a stem-loop or a pseudoknot structure. Based on many mutational studies, the stem-loop structure has been proposed for the downstream enhancer region of the HIV-1 mRNA. This stimulatory stem-loop structure is separated from the shift site by a spacer of seven nucleotides. In contrast, a recent report has proposed an alternative model in which the bases in the spacer sequence form a pseudoknot structure as the downstream enhancer sequence [Du et al., Biochemistry 35 (1996) 4187-4198.]. Using UV melting and enzymatic mapping analyses, we have investigated the conformation of the sequence region involved in ribosomal frameshifting in HIV-1. Our S1, V1, and T1 endonuclease mappings, together with UV melting analysis, clearly indicate that this sequence element of the HIV-1 mRNA frameshift site forms a stem-loop structure, not a pseudoknot structure. This finding further supports the stem-loop structure proposed by many mutational studies for the downstream enhancer sequence of the HIV-1 mRNA.

Endoribonucleases↗

Neuronal BC1 RNA structure: evolutionary conversion of a tRNA(Ala) domain into an extended stem-loop structure.

By chemical and enzymatic probing, we have analyzed the secondary structure of rodent BC1 RNA, a small brain-specific non-messenger RNA. BC1 RNA is specifically transported into dendrites of neuronal cells, where it is proposed to play a role in regulation of translation near synapses. In this study we demonstrate that the 5' domain of BC1 RNA, derived from tRNA(Ala), does not fold into the predicted canonical tRNA cloverleaf structure. We present evidence that by changing bases within the tRNA(Ala) domain during the course of evolution, an extended stem-loop structure has been created in BC1 RNA. The new structural domain might function, in part, as a putative binding site for protein(s) involved in dendritic transport of BC1 RNA within neurons. Furthermore, BC1 RNA contains, in addition to the extended stem-loop structure, an internal poly(A)-rich region that is supposedly single stranded, followed by a second smaller stem-loop structure at the 3' end of the RNA. The three distinct structural domains reflect evolutionary legacies of BC1 RNA.

Aldehydes↗

Crystal structure of glycosomal glyceraldehyde-3-phosphate dehydrogenase from Leishmania mexicana: implications for structure-based drug design and a new position for the inorganic phosphate binding site.

The structure of glycosomal glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from the trypanosomatid parasite Leishmania mexicana has been determined by X-ray crystallography. The protein crystallizes in space group P2(1)2(1)2(1) with unit cell parameters a = 99.0 A, b = 126.5 A, and c = 138.9 A. There is one 156,000 Da protein tetramer per asymmetric unit. The model of the protein with bound NAD+s and phosphates has been refined against 86% complete data from 10.0 to 2.8 A to a crystallographic Rfactor of 0.198. Density modification by noncrystallographic symmetry averaging was used during model building. The final model of the L. mexicana GAPDH tetramer shows small deviations of less than 0.5 degrees from ideal 222 molecular symmetry. The structure of L. mexicana GAPDH is very similar to that of glycosomal GAPDH from the related trypanosomatid Trypanosoma brucei. A significant structural difference between L. mexicana GAPDH and most previously determined GAPDH structures occurs in a loop region located at the active site. This unusual loop conformation in L. mexicana GAPDH occludes the inorganic phosphate binding site which has been seen in previous GAPDH structures. A new inorganic phosphate position is observed in the L. mexicana GAPDH structure. Model building studies indicate that this new anion binding site is well situated for nucleophilic attack of the inorganic phosphate on the thioester intermediate in the GAPDH-catalyzed reaction. Since crystals of L. mexicana GAPDH can be grown reproducibly and diffract much better than those of T. brucei GAPDH, L. mexicana GAPDH will be used as a basis for structure-based drug design targeted against trypanosomatid GAPDHs.

Animals↗

Secondary structure prediction of 52 membrane-bound cytochromes P450 shows a strong structural similarity to P450cam.

The secondary structure of 52 aligned cytochrome P450 sequences, all of which are membrane bound, is predicted and collectively compared with the crystal structure of the soluble cytochrome P450cam. Ten of 13 helical regions, 6 of 7 beta-pair regions, and beta-structure corresponding to a known beta-bulge near the active site of P450cam are predicted to exist in the membrane-bound P450s. Three turns associated with beta-structure in the soluble enzyme are also predicted for the membrane-bound forms. A strong structural similarity is evident between membrane P450s and the soluble P450cam. Consequently, a multitransmembrane structure involving much of P450 seems highly unlikely. A structure with two N-terminal transmembrane segments is compatible with these observations.

Animals↗

Internal transcribed spacer 1 of the yeast precursor ribosomal RNA. Higher order structure and common structural motifs.

The higher order structure of the first internal transcribed spacer between the 18S and the 5.8S rRNA sequences in the Saccharomyces cerevisiae precursor ribosomal RNA has been investigated. Sites of potential base pairing in the RNA region have been determined by using a combination of enzymatic and chemical structure sensitive probes. Data generated have been used to evaluate secondary structure models predicted by minimum free energy calculations. Several alternative suboptimal structures were also evaluated. The derived model contains several stable hairpins. Theoretical secondary structural models for the corresponding RNA region from S. carlsbergensis, S. pombe, N. crassa, X. laevis, and mung bean have also been derived from identical calculations and assumptions. Certain structural motifs appear to be conserved despite extensive divergence in the base sequence. The yeast model should be a useful prototype for investigation of structure and function of precursor ribosomal RNA molecules.

Alkylating Agents↗

Structure and function of S-adenosylmethionine synthetase: crystal structures of S-adenosylmethionine synthetase with ADP, BrADP, and PPi at 28 angstroms resolution.

S-Adenosylmethionine synthetase (MAT,ATP:L-methionine S-adenosltransferase, EC 2.5.1.6) plays a central metabolic role in all organisms. MAT catalyzes the two-step reaction which synthesizes S-adenosylmethionine (AdoMet), pyrophosphate (PPi), and orthophosphate (Pi) from ATP and L-methionine. AdoMet is the primary methyl group donor in biological systems. The first crystal structure of MAT from Escherichia coli has recently been determined [Takusagawa et al. (1995) J. Biol. Chem. 271, 136-147]. In order to elucidate the active site and possible catalytic reaction mechanism, the MAT structures in the crystals grown with the substrate ATP (and BrATP) and the product PPi have been determined (space group P6(2)22; unit cell a = b = 128.9 Angstroms, c= 139.8 Angstroms, resolution limit 2.8 Angstroms; R O.19; Rfree 0.26). The enzyme consists of four identical subunits; two subunits form a spherical dimer, and pairs of these tightly bound dimers form a tetrameric enzyme. Each dimer has two active sites which are located between the subunits. Each subunit consists of three domains related to each other by a pseudo 3-fold symmetry. The crystal structures showed that the ATP molecules were hydrolyzed to ADP and Pi by the enzyme. Those products were found at the active site along with the essential metal ions (K+ and Mg2+). This rather unexpected finding was first confirmed by the structure of the complex with PPi and later by an HPLC analysis. The enzyme hydrolyzed ATP to ADP and Pi in 72 h under the same conditions as the crystallization of the enzyme. In the active site, the diphosphate moiety of ADP and Pi interacts extensively with amino acid residues from the two subunits of the enzyme, whereas the adenine and ribose moieties have little interaction with the enzyme. The enzyme structure is little changed upon binding ADP. All amino acid residues involved in the active site are found to be conserved in the 14 reported sequences of MAT from a wide range of organisms. Thus the structure determined in this study can be utilized as a model for other members of the MAT family. On the basis of the crystal structures, the catalytic reaction mechanisms of AdoMet formation and hydrolysis of tripolyphosphate are proposed.

Adenosine Diphosphate↗

Structural variation among retroviral primer-DNA junctions: solution structure of the HIV-1 (-)-strand Okazaki fragment r(gcca)d(CTGC).d(GCAGTGGC).

The three-dimensional solution structure of the hybrid-chimeric duplex r(gcca)d(CTGC).d(GCAGTGGC) has been determined by two-dimensional NMR, restrained molecular dynamics (rMD), and NOE back-calculation methods. This chimera, consisting of a chimeric RNA-DNA strand and its complementary DNA strand, is formed after priming (-)-strand DNA synthesis by tRNA(Lys3) and subsequent (+)-strand DNA synthesis by reverse transcriptase and is an obligatory intermediate in the formation of double-stranded DNA prior to HIV-1 retrovirus integration. The duplex consists of two different types of double helix: a hybrid form (H-form) and a B-form structure connected by a junction. It is chemically similar to several other Okazaki fragments whose structures have been previously determined in our laboratory. However, some structural parameters are not the same and were found to be sequence dependent. In particular, the sugar conformations at the DNA base pair proximal to the hybrid segment vary from O4'-endo to C2'-endo depending on the base composition. The position of the transition from the relatively wide groove of H-form to the narrow groove of B-form is also sequence dependent, occurring either exactly at the RNA-DNA junction or within the purely DNA segment of the chimera-as is the case in the structure of the present HIV-1 (-)-strand primer. This structural change produces a kink at the DNA-DNA step adjacent to the RNA-DNA junction in the HIV-1 (-)-strand primer. The sequence dependence of structures of RNA-DNA chimeric duplexes may be responsible for the variable cleavage pattern of different Okazaki fragments by reverse transcriptase RNase H.

Base Composition↗

Ternary lanthanoid ruthenium gallides with a high gallium content: Ln(2)Ru(3)Ga(10) (Ln = Yb, Lu) with a new structure type and LnRu(2)Ga(8) (Ln = La-Nd) with CaCo(2)Al(8)-type structure.

The title compounds were prepared by reaction of the elemental components at high temperatures. The compounds Yb(2)Ru(3)Ga(10) and Lu(2)Ru(3)Ga(10) crystallize with a new structure type, which has been determined from the single-crystal X-ray data of Yb(2)Ru(3)Ga(10): P4/mbm, Z = 2, a = 881.9(1) pm, c = 632.5(1) pm. In this structure the gallium atoms form two-dimensionally infinite double layers that extend perpendicular to the tetragonal axis. They contain two-thirds of the ruthenium atoms. The other ruthenium and the ytterbium atoms are situated between the gallium double layers. The structure is closely related to that of Mn(2)Hg(5). The latter compound may be written with the formula Mn(2)Mn(2)(square)Hg(10), thus indicating that its structure may be regarded as a defect-variant of the presently reported structure of Yb(2)Ru(3)Ga(10). The four gallides of the series LnRu(2)Ga(8) (Ln = La-Nd) crystallize with the orthorhombic CaCo(2)Al(8)-type structure (Pbam, Z = 4). This structure has been refined from single-crystal X-ray data of the cerium and neodymium compounds. Slight deviations from the ideal composition for one of the two ruthenium sites resulted in the formulas CeRu(1.913(4))Ga(8) and NdRu(1.858(4))Ga(8). Magnetic susceptibility measurements with a SQUID magnetometer indicate diamagnetism for LaRu(2)Ga(8), which is partially compensated by the expected Pauli paramagnetism. The cerium atoms in CeRu(2)Ga(8) show mixed or intermediate valent behavior, and PrRu(2)Ga(8) follows the Curie-Weiss law with no magnetic order down to 4 K.

Journal Article↗

Evolution of the structural chemistry of vanadium organodiphosphonate networks and frameworks: structural consequences of fluoride incorporation in the development of stable phases with void channels.

Hydrothermal reactions of solutions containing a vanadate source, an organodiphosphonate, an organonitrogen component, and HF (V/P/O/F) yield a series of oxyfluorovanadium-diphosphonates with charge-compensation provided by organoammonium cations or hydronium cations. While V/P/O/F networks provide the recurrent structural motif, the linkage between the layers and the details of the polyhedral connectivities within the layers are quite distinct for the five structures of this study. [H2pip][V4F4O2(H2O)2{O3P(CH2)3PO3}2] (1) (pip = piperazine) is a conventional three-dimensional (3D) "pillared" layer structure, whose V/P/O/F networks are buttressed by the propylene chains of the diphosphonate ligands. In contrast, [H2en][V2O2F2(H2O)2{O3P(CH2)4PO3}] (2) and [H2en]2[V6F12(H2O)2{O3P(CH2)5PO3}2 {HO3P(CH2)5PO3H}] (3) are two-dimensional (2D) slablike structures constructed of pairs of V/P/O/F networks sandwiching the pillaring organic tethers of the diphosphonate ligands. Despite the common overall topology, the layer substructures are quite different: isolated {VO5F} octahedra in 2 and chains of corner-sharing {VO(3)F(3)} octahedra in 3. The 3D structure of [H2en]2[V7O6F4(H2O)2{O3P(CH2)2PO3}4].7H2O (4.7H2O) exhibits a layer substructure that contains the ethylene bridges of the diphosphonate ligands and are linked through corner-sharing octahedral {VO6} sites. The connectivity requirements provide large channels that enclose readily removed water of crystallization. The structure of [H3O][V3F2(H2O)2{O3P(CH2)2PO3}2].3.5H2O (5.3.5H2O) is also 3D. Because of the similiarity with 4.7H2O, it exhibits V/P/O/F layers that include the organic tethers of the diphosphonates and are linked through corner-sharing {VO6} octahedra. In contrast to the network substructure of 4.7H2O, which contains binuclear and trinuclear vanadium clusters, the layers of 5.3.5 H2O are constructed from chains of corner-sharing {VO4F2} octahedra. Thermal studies of the open framework materials 4 and 5 reveal that incorporation of fluoride into the inorganic substructures provides robust scaffoldings that retain their crystallinity to 450 degrees C and above. In the case of 4, dehydration does not change the powder X-ray diffraction pattern of the material, which remains substantially unchanged to 450 degrees C. In the case of 5, there are two dehydration steps, that is, the higher temperature process associated with loss of coordinated water. This second dehydration results in structural changes as monitored by powder X-ray diffraction, but this new phase is retained to ca. 450 degrees C. The materials of this study exhibit a range of reduced oxidation states: 1 is mixed valence V(IV)/V(III) while 2 and 4.7H(2)O are exclusively V(IV) and 3 and 5.3.5H2O are exclusively V(III). These oxidation states are reflected in the magnetic properties of the materials. The paramagnetism of 1 arises from the presence of V(III) and V(IV) sites and conforms to the Curie-Weiss law with C = 2.38 em K/(Oe mol) and = -66 K with mu(eff) (300 K) = 4.33 mu(B). Compounds 3-5 exhibit Curie-Weiss law dependence of magnetism on temperature with mu(eff) (300 K) = 5.45 mu(B) for 3 (six V(III) sites), mu(eff) = 4.60 mu(B) for 4 (seven V(IV) sites) and mu(eff) = 4.13 mu(B) for 5 (two V(III) sites). Compound 2 exhibits antiferromagnetic interactions, and the magnetism may be described in terms of the Heisenberg linear antiferromagnetic chain model for V(IV). The effective magnetic moment at 300 K is 2.77 mu(B) (two V(IV) sites).

Journal Article↗

Lanthanoid Rhenium Aluminides with a High Content of Aluminum: LnRe(2)Al(10) (Ln = Ho-Lu) with a New Structure Type and NdRe(2)Al(10) with CaCr(2)Al(10)-Type Structure.

The title compounds were obtained by reaction of the elemental components with an excess of aluminum after dissolving the matrix in hydrochloric acid. The compounds LnRe(2)Al(10) (Ln = Ho-Lu) crystallize with a new structure type, which was determined from single-crystal X-ray data of LuRe(2)Al(10): Cmcm, a = 929.1(1) pm, b = 1027.7(2) pm, c = 2684.1(5) pm, Z = 12. The two different lutetium atoms of the structure are coordinated by four rhenium and 16 aluminum atoms, while the two rhenium positions are in distorted icosahedral coordination of two lutetium and 10 aluminum atoms. The 12 different aluminum atoms have between 12 and 14 neighbors, of which two are rhenium and one or two are lutetium atoms. The structure may be considered as a stacking variant of the recently determined structure of YbFe(2)Al(10). Both structures are related to that of ThMn(12). They contain hexagonally close-packed, puckered sheets similar to those known from the close-packed TiAl(3)-type structure. In LuRe(2)Al(10) and YbFe(2)Al(10) these sheets of the compositions Re(2)Al(6) and Fe(2)Al(6), respectively, alternate with less densely packed layers of the composition LnAl(4). The crystal structures of YbRe(2)Al(10) (LuRe(2)Al(10) type, a = 930.7(2) pm, b = 1029.3(2) pm, c = 2687.9(5) pm) and NdRe(2)Al(10) (CaCr(2)Al(10) type, a = 1293.7(1) pm, c = 517.4(1) pm) were also refined from single-crystal X-ray data. The refinements of the occupancy factors of these as well as those of 20 other intermetallic compounds with high aluminum content indicate a seemingly slightly lower (on average 2-3%) scattering power for the aluminum positions in all cases. This is ascribed to the differing electron distributions in the free and in the bonded aluminum atoms. The cell volume of YbRe(2)Al(10) indicates a mixed or intermediate +II/+III valence of the ytterbium atoms.

Journal Article↗

Construction by molecular dynamics modeling and simulations of the porous structures formed by dextran polymer chains attached on the surface of the pores of a base matrix: characterization of porous structures.

Significant increases in the separation of bioactive molecules by using ion-exchange chromatography are realized by utilizing porous adsorbent particles in which the affinity group/ligand is linked to the base matrix of the porous particle via a polymeric extender. To study and understand the behavior of such systems, the M3B model is modified and used in molecular dynamics (MD) simulation studies to construct porous dextran layers on the surface of a base matrix, where the dextran polymer chains and the surface are covered by water. Two different porous polymer layers having 25 and 40 monomers per main polymer chain of dextran, respectively, are constructed, and their three-dimensional (3D) porous structures are characterized with respect to porosity, pore size distribution, and number of conducting pathways along the direction of net transport. It is found that the more desirable practical implications with respect to structural properties exhibited by the porous polymer layer having 40 monomers per main polymer chain, are mainly due to the higher flexibility of the polymer chains of this system, especially in the upper region of the porous structure. The characterization and analysis of the porous structures have suggested a useful definition for the physical meaning and implications of the pore connectivity of a real porous medium that is significantly different than the artificial physical meaning associated with the pore connectivity parameter employed in pore network models and whose physical limitations are discussed; furthermore, the methodology developed for the characterization of the three-dimensional structures of real porous media could be used to analyze the experimental data obtained from high-resolution noninvasive three-dimensional methods like high-resolution optical microscopy. The MD modeling and simulations methodology presented here could be used, considering that the type and size of affinity group/ligand as well as the size of the biomolecule to be adsorbed onto the affinity group/ligand are known, to construct different porous dextran layers by varying the length of the polymeric chain of dextran, the number of attachment points to the base matrix, the degree of side branching, and the number of main polymeric chains immobilized per unit surface area of base matrix. After the characterization of the porous structures of the different porous dextran layers is performed, then only a few promising structures would be selected for studying the immobilization of adsorption sites on the pore surfaces and the subsequent adsorption of the bioactive molecules onto the immobilized affinity groups/ligands.

Adsorption↗

Semispectroscopic and quantitative structure-property relationship estimates of the equilibrium and vibrationally averaged structure and dipole moment of 1-buten-3-yne.

Systematic quantum chemical calculations have been performed to obtain precise estimates of the equilibrium and vibrationally averaged molecular structure and electric dipole moment of vinylacetylene (VA, 1-buten-3-yne). Anharmonic (cubic and semi-diagonal quartic) MP2/cc-pVTZ force fields in normal coordinates were computed to account for anharmonic vibrational effects, including zero-point contributions to the rotational constants and the electric dipole moment. A simultaneous weighted least-squares structural refinement was performed, resulting in the best semispectroscopic estimate of the re structure of VA. The refinement was based on experimentally measured ground-state rotational constants of two isotopologs of VA corrected to equilibrium values using MP2/cc-pVTZ vibration-rotation interaction constants and all-electron CCSD(T)/aug-cc-pVTZ structural constraints. The semispectroscopic re structure of VA agrees excellently with the high-level CCSD(T)/aug-cc-pVTZ ab initio structure. The most dependable, CCSD(T)/cc-pVQZ//CCSD(T)/aug-cc-pVTZ equilibrium electric dipole moment of VA, in D, is mua= 0.4088, mub= 0.0004, and muc= 0. The vibrationally corrected a-component of 0.4214 D is in excellent agreement with one of the available experimental values. The present analysis shows that mub is negligible even after vibrational correction. A simple quantitative structure-property relationship (QSPR) model resulted in a highly similar estimate, 0.45 D, for the electric dipole moment of VA.

Journal Article↗

Methane hydrate formation and decomposition: structural studies via neutron diffraction and empirical potential structure refinement.

Neutron diffraction studies with hydrogen/deuterium isotope substitution measurements are performed to investigate the water structure at the early, medium, and late periods of methane clathrate hydrate formation and decomposition. These measurements are coupled with simultaneous gas consumption measurements to track the formation of methane hydrate from a gas/water mixture, and then the complete decomposition of hydrate. Empirical potential structure refinement computer simulations are used to analyze the neutron diffraction data and extract from the data the water structure in the bulk methane hydrate solution. The results highlight the significant changes in the water structure of the remaining liquid at various stages of hydrate formation and decomposition, and give further insight into the way in which hydrates form. The results also have important implications on the memory effect, suggesting that the water structure in the presence of hydrate crystallites is significantly different at equivalent stages of forming compared to decomposing. These results are in sharp contrast to the previously reported cases when all remaining hydrate crystallites are absent from the solution. For these systems there is no detectable change in the water structure or the methane hydration shell before hydrate formation and after decomposition. Based on the new results presented in this paper, it is clear that the local water structure is affected by the presence of hydrate crystallites, which may in turn be responsible for the "history" or "memory" effect where the production of hydrate from a solution of formed and then subsequently melted hydrate is reportedly much quicker than producing hydrate from a fresh water/gas mixture.

Journal Article↗