Solid state structure of p-bromo phenyl 4,5,7-tri-O-benzyl-beta-D-glycero-D-talo-septanoside and an analysis of non-covalent interactions

The solid state structure of a new seven-membered sugar oxepane derivative, namely, p-bromo phenyl 4,5,7-tri-O-benzyl-beta-D-glycero-D-talo-septanoside is discussed, as determined through single crystal X-ray structural determination and in relation to their conformational features. The molecule adopts twist-chair as the preferred conformation, with conformational descriptor (TC2,3)-T-0,1. The solid state packing of molecules is governed by a rich network of non-covalent bonding originating from O-H center dot center dot center dot O, C-H center dot center dot center dot pi, C-H center dot center dot center dot Br and aromatic pi center dot center dot center dot pi interactions that stabilize the packing of molecules in the crystal. (C) 2015 Elsevier Ltd. All rights reserved.

Do we see what we should see? Describing non-covalent interactions in protein structures including precision

The power of X-ray crystal structure analysis as a technique is to `see where the atoms are'. The results are extensively used by a wide variety of research communities. However, this `seeing where the atoms are' can give a false sense of security unless the precision of the placement of the atoms has been taken into account. Indeed, the presentation of bond distances and angles to a false precision (i.e. to too many decimal places) is commonplace. This article has three themes. Firstly, a basis for a proper representation of protein crystal structure results is detailed and demonstrated with respect to analyses of Protein Data Bank entries. The basis for establishing the precision of placement of each atom in a protein crystal structure is non-trivial. Secondly, a knowledge base harnessing such a descriptor of precision is presented. It is applied here to the case of salt bridges, i.e. ion pairs, in protein structures; this is the most fundamental place to start with such structure-precision representations since salt bridges are one of the tenets of protein structure stability. Ion pairs also play a central role in protein oligomerization, molecular recognition of ligands and substrates, allosteric regulation, domain motion and alpha-helix capping. A new knowledge base, SBPS (Salt Bridges in Protein Structures), takes these structural precisions into account and is the first of its kind. The third theme of the article is to indicate natural extensions of the need for such a description of precision, such as those involving metalloproteins and the determination of the protonation states of ionizable amino acids. Overall, it is also noted that this work and these examples are also relevant to protein three-dimensional structure molecular graphics software.

Structural diversity in supramolecular architectures of Mn(II) through non-covalent interactions

Two mononuclear complexes of manganese(II), [Mn(OCN)(2)(phen)(2)] 1 and [Mn(NCO)(2)(bpy)(2)] 2 [1,10-phenanthroline (phen); 2,2'-bipyridine (bpy)], have been synthesized and characterized by single crystal X-ray analysis, infra-red spectroscopy and magnetic studies. The coordination structure of complex 2 is already reported. The cyanate anions are pendent in both the complexes. In 1, cyanate anion links manganese(II) through O-atom, whereas in 2 it coordinates through N-atom. The mononuclear fragments of 1 are built up to a supramolecular lamellar 3D architecture by pi-pi interactions only. On the other hand, mononuclear fragments of 2 are assembled to a 2D supramolecular brick-wall architecture by C-H-... pi interactions.

Contribution of Non-Covalent Interactions and Electronic Effects on the Conformational Landscape and Tautomeric Equilibria of Molecules and Molecular Complexes: Structural and Dynamical Data from Rotational Spectroscopy

This thesis concerns the study of complex conformational surfaces and tautomeric equilibria of molecules and molecular complexes by quantum chemical methods and rotational spectroscopy techniques. In particular, the focus of this research is on the effects of substitution and noncovalent interactions in determining the energies and geometries of different conformers, tautomers or molecular complexes. The Free-Jet Absorption Millimeter Wave spectroscopy and the Pulsed-Jet Fourier Transform Microwave spectroscopy have been applied to perform these studies and the obtained results showcase the suitability of these techniques for the study of conformational surfaces and intermolecular interactions. The series of investigations of selected medium-size molecules and complexes have shown how different instrumental setups can be used to obtain a variety of results on molecular properties. The systems studied, include molecules of biological interest such as anethole and molecules of astrophysical interest such as N-methylaminoethanol. Moreover halogenation effects have been investigated on halogen substituted tautomeric systems (5-chlorohydroxypyridine and 6-chlorohydroxypyridine), where it has shown that the position of the inserted halogen atom affects the prototropic equilibrium. As for fluorination effects, interesting results have been achieved investigating some small complexes where a molecule of water is used as a probe to reveal the changes on the electrostatic potential of different fluorinated compounds: 2-fluoropyridine, 3-fluoropyridine and penta-fluoropyridine. While in the case of the molecular complex between water and 2-fluoropyridine and 3-fluoropyridine the geometry of the complex with one water molecule is analogous to that of pyridine with the water molecule linked to the pyridine nitrogen, the case of pentafluoropyridine reveals the effect of perfluorination and the water oxygen points towards the positive center of the pyridine ring. Additional molecular adducts with a molecule of water have been analyzed (benzylamine-water and acrylic acid-water) in order to reveal the stabilizing driving forces that characterize these complexes.

Non-covalent surface modification of boron nitride nanotubes for enhanced catalysis

Boron nitride nanotubes were functionalized by microperoxidase-11 in aqueous media, showing improved catalytic performance due to a strong electron coupling 10 between the active centre of microperoxidase-11 and boron nitride nanotubes. One main application challenge of enzymes as biocatalysts is molecular aggregation in the aqueous solution. This issue is addressed by immobilization of enzymes on solid supports which 15 can enhance enzyme stability and facilitate separation, and recovery for reuse while maintaining catalytic activity and selectivity. The protein-nanoparticle interactions play a key role in bio-nanotechnology and emerge with the development of nanoparticle-protein “corona”. Bio-molecular coronas provide a 20 unique biological identity of nanosized materials.1, 2 As a structural analogue to carbon nanotubes (CNTs), Boron nitride nanotubes have boron and nitrogen atoms distributed equally in hexagonal rings and exhibit excellent mechanical strength, unique physical properties, and chemical stability at high-temperatures. 25 The chemical inertness of BN materials suits to work in hazardous environments, making them an optimal candidate in practical applications in biological and medical field.3, 4

Non-covalent C-Cl center dot center dot center dot pi interaction in acetylene-carbon tetrachloride adducts: Matrix isolation infrared and ab initio computational studies

Non-covalent halogen-bonding interactions between n cloud of acetylene (C2H2) and chlorine atom of carbon tetrachloride (CCl4) have been investigated using matrix isolation infrared spectroscopy and quantum chemical computations. The structure and the energies of the 1:1 C2H2-CCl4 adducts were computed at the B3LYP, MP2 and M05-2X levels of theory using 6-311++G(d,p) basis set. The computations indicated two minima for the 1:1 C2H2-CCl4 adducts; with the C-Cl center dot center dot center dot pi adduct being the global minimum, where pi cloud of C2H2 is the electron donor. The second minimum corresponded to a C-H...Cl adduct, in which C2H2 is the proton donor. The interaction energies for the adducts A and B were found to be nearly identical. Experimentally, both C-Cl center dot center dot center dot pi and C-H center dot center dot center dot Cl adducts were generated in Ar and N2 matrixes and characterized using infrared spectroscopy. This is the first report on halogen bonded adduct, stabilized through C-Cl center dot center dot center dot pi interaction being identified at low temperatures using matrix isolation infrared spectroscopy. Atoms in Molecules (AIM) and Natural Bond Orbital (NBO) analyses were performed to support the experimental results. The structures of 2:1 ((C2H2)(2)-CCl4) and 1:2 (C2H2-(CCl4)(2)) multimers and their identification in the low temperature matrixes were also discussed. (C) 2015 Elsevier B.V. All rights reserved.

A study of the non-covalent interaction between flavonoids and DNA triplexes by electrospray ionization mass spectrometry

The binding interactions of 22 flavonoids (9 aglycones and 13 glycosides) with DNA triplexes were investigated using electrospray ionization mass spectrometry (ESI-MS). The results revealed that the hydroxyl positions of aglycones. the locations and numbers of saccharide, as well as the aglycone skeletons play roles in the triplex-binding properties of flavonoids. The presence of 3-OH, or 3'-OH, or replacement of 4'-OH with methoxy group in aglycones decreased the fraction of bound DNA sharply. Flavonoid glycosides exhibit higher binding affinities towards the DNA triplexes than their aglycone counterparts. Glycosylations of flavones at the 8-C position and isoflavones at the 7-O position show higher binding affinities than those on the other positions of ring A of aglycones. Glycosylation with a disaccharide on 0 position of flavonol results in higher binding affinity than that with monosaccharide. Flexibility of the ring B is favorable for its interaction with DNA triplex. According to sustained off-resonance irradiation collision-induced dissociation (SORI-CID) experiments, glycosylation and non-planarity of flavonoid aglycones lead to different dissociation pathways of the flavonoid/triplex complexes.

Non-covalent hydrogels of cyclodextrins and poloxamines for the controlled release of proteins

Different types of gels were prepared by combining poloxamines (Tetronic), i.e. poly(ethylene oxide)/poly(propylene oxide) (PEO/PPO) octablock star copolymers, and cyclodextrins (CD). Two different poloxamines with the same molecular weight (ca. 7000) but different molecular architectures were used. For each of their four diblock arms, direct Tetronic 904 presents PEO outer blocks while in reverse Tetronic 90R4 the hydrophilic PEO blocks are the inner ones. These gels were prepared by combining alpha-CD and poloxamine aqueous solutions. The physicochemical properties of these systems depend on several factors such as the structure of the block copolymers and the Tetronic/alpha-CD ratio. These gels were characterized using differential scanning calorimetry (DSC), viscometry and X-ray diffraction measurements. The 90R4 gels present a consistency that makes them suitable for sustained drug delivery. The resulting gels were easily eroded: these complexes were dismantled when placed in a large amount of water, so controlled release of entrapped large molecules such as proteins (Bovine Serum Albumin, BSA) is feasible and can be tuned by varying the copolymer/CD ratio. 

Non-Covalent Interaction: Revealed by Rotational Spectroscopy

The pulsed jet Fourier transform microwave spectroscopy have been applied to several molecular complexes involving H2O, freons, methane, carboxylic acids, and rare gas. The obtained results showcase the suitability of this technique for studying the intermolecular interactions. The rotational spectra of three water adducts of halogenated organic molecules, i.e. chlorotrifluoroethylene, isoflurane and alfa,alfa,alfa,-trifluoroanisole, have been investigated. It has been found that, the halogenation of the partner molecules definitely changes the way in which water will link to the partner molecule. Quadrupole hyperfine structures and/or the tunneling splittings have been observed in the rotational spectra of difluoromethane-dichloromethane, chlorotrifluorometane-fluoromethane, difluoromethane-formaldehyde and trifluoromethane-benzene. These features have been useful to describe their intermolecular interactions (weak hydrogen bonds or halogen bonds), and to size the potential energy surfaces of their internal motions. The rotational spectrum of pyridine-methane pointed out that methane prefers to locate above the ring and link to pyridine through a C-H•••π weak hydrogen bond, rather than the C-H•••n interaction. This behavior, typical of complexes of pyridine with rare gases, suggests classifying CH4, in relation to its ability to form molecular complexes with aromatic molecules, as a pseudo rare gas. The conformational equilibria of three bi-molecules of carboxylic acids, acrylic acid-trifluoroacetic acid, difluoroacetic acid-formic acid and acrylic acid-fluoroacetic acid have been studied. The increase of the hydrogen bond length upon H→D isotopic substitution (Ubbelohde effect) has been deduced from the elongation of the carboxylic carbons C•••C distance. The van der Waals complex tetrahydrofuran-krypton shows that the systematic doubling of the rotational lines has been attributed to the residual pseudo-rotation of tetrahydrofuran in the complex, based on the values of the Coriolis coupling constants, and on the type (mu_b) of the interstate transitions.

EPR spectroscopy as a tool for the elucidation of non-covalent structuring principles in complex soft matter

This thesis aims at connecting structural and functional changes of complex soft matter systems due to external stimuli with non-covalent molecular interaction profiles. It addresses the problem of elucidating non-covalent forces as structuring principle of mainly polymer-based systems in solution. The structuring principles of a wide variety of complex soft matter types are analyzed. In many cases this is done by exploring conformational changes upon the exertion of external stimuli. The central question throughout this thesis is how a certain non-covalent interaction profile leads to solution condition-dependent structuring of a polymeric system.rnTo answer this question, electron paramagnetic resonance (EPR) spectroscopy is chosen as the main experimental method for the investigation of the structure principles of polymers. With EPR one detects only the local surroundings or environments of molecules that carry an unpaired electron. Non-covalent forces are normally effective on length scales of a few nanometers and below. Thus, EPR is excellently suited for their investigations. It allows for detection of interactions on length scales ranging from approx. 0.1 nm up to 10 nm. However, restriction to only one experimental technique likely leads to only incomplete pictures of complex systems. Therefore, the presented studies are frequently augmented with further experimental and computational methods in order to yield more comprehensive descriptions of the systems chosen for investigation.rnElectrostatic correlation effects in non-covalent interaction profiles as structuring principles in colloid-like ionic clusters and DNA condensation are investigated first. Building on this it is shown how electrostatic structuring principles can be combined with hydrophobic ones, at the example of host-guest interactions in so-called dendronized polymers (denpols).rnSubsequently, the focus is shifted from electrostatics in dendronized polymers to thermoresponsive alkylene oxide-based materials, whose structuring principles are based on hydrogen bonds and counteracting hydrophobic interactions. The collapse mechanism in dependence of hydrophilic-hydrophobic balance and topology of these polymers is elucidated. Complementarily the temperature-dependent phase behavior of elastin-like polypeptides (ELPs) is investigated. ELPs are the first (and so far only) class of compounds that is shown to feature a first-order inverse phase transition on nanoscopic length scales.rnFinally, this thesis addresses complex biological systems, namely intrinsically disordered proteins (IDPs). It is shown that the conformational space of the IDPs Osteopontin (OPN), a cytokine involved in metastasis of several kinds of cancer, and BASP1 (brain acid soluble protein one), a protein associated with neurite outgrowth, is governed by a subtle interplay between electrostatic forces, hydrophobic interaction, system entropy and hydrogen bonds. Such, IDPs can even sample cooperatively folded structures, which have so far only been associated with globular proteins.

Non-covalent immobilization of RhDuphos on carbon nanotubes and carbon xerogels

The immobilization of the chiral complex RhDuphos, by electrostatic or π–π (adsorption) interactions, on carbon nanotubes and carbon xerogels is investigated. To promote such interactions, the supports were either oxidized or heat treated to create carboxylic type surface groups or an apolar surface, respectively. The catalysts were tested in the hydrogenation of methyl 2-acetamidoacrylate. The prepared hybrid catalysts are less active than the homogeneous RhDuphos, but most of them show a high enantioselectivity and the one prepared with the oxidized carbon xerogel is also reusable, being able to give a high substrate conversion, keeping as well a high enantioselectivity. The anchorage by electrostatic interactions is more interesting than the anchorage by π–π interactions, as the π–π adsorption method produces a modification of the metal complex structure leading to an active hybrid catalyst but without enantioselectivity. The creation of carboxylic groups on the support surface has led to some hindering of the complex leaching.

Structure and interactions of aspirin-like drugs

A pre-requisite for the elucidation of the mechanism of action of aspirin-like drugs, which are believed to exert their pharmacological effects through the inhibition of prostaglandin biosynthesis, is an understanding of their molecular geometry, the non-covalent interactions they are likely to be involved in, and the geometrical and the electronic consequences of such interactions. This has been sought to be achieved through the x-ray analysis of these drug molecules and their crystalline complexes with other suitable molecules. The results obtained from such studies have been discussed in terms of specific typical examples. For instance, antipyrine can form metal and hydrogen-bonded complexes; phenylbutazone can form ionic complexes with basic molecules. Complex formation is accompanied by characteristic changes in the molecular geometry and the electronic structure in both the cases. The results obtained so far appear to indicate that the important common invariant structural features of the fenamates, deduced from crystal structures, are retained even when complexation takes place.

Non-bonded interactions in 2,2,4,4-tetramethyl-1,3-cyclobutanedithione and 2,2,4,4-tetramethyl-3-thio-1,3-cyclobutanedione

Electronic absorption and emission spectra as well as He(I) photoelectron spectra of 2,2,4,4-tetramethyl-,3-cyclobutanedithione and 2,2,4,4-tetramethyl-1-3-thio-1,3-cyclobutanedione have been interpreted on the basis of molecular orbital calculations. The results show that the non-bonded orbital of the dithione is split owing to through-bond interaction, the magnitude of splitting being 0.4 eV. The π* orbital of the dithione appears to be split by about 0.2 eV. Electronic absorption spectra show evidence for the existence of four n—π* transitions, arising out of the splitting of the orbitals referred to above, just as in the case of 2,2,4,4-tetramethyl-1,3-cyclobutanedione. Electronic and photoelectron spectra of the thio-dione show evidence for weak interaction between the C=S and C&.zdbnd;O groups, probably via π* orbitals. Infrared spectra of both the dithione and the thio-dione are consistent with the planar cyclobutane ring; the ring-puckering frequency responsible for non-bonded interactions is around 67 cm−1 in both the dithione and the thio-dione, the value not being very different from that in the dione. The 1,3-transannular distance is also similar in the three molecules.

Non-bonded interactions in cyclobutane-thiones

Using UVPES and electronic spectral data the presence of an interaction between thd 1,3-thiocarbonyl groups in Image has been identified. EHT calculations also predict such an interaction. Presence of weak interaction between 1,3-carbonyl and thiocarbonyl groups in Image has been inferred from electronic absorption and emission spectra.

Effect of density variation and non-covalent functionalization on the compressive behavior of carbon nanotube arrays

Arrays of aligned carbon nanotubes (CNTs) have been proposed for different applications, including electrochemical energy storage and shock-absorbing materials. Understanding their mechanical response, in relation to their structural characteristics, is important for tailoring the synthesis method to the different operational conditions of the material. In this paper, we grow vertically aligned CNT arrays using a thermal chemical vapor deposition system, and we study the effects of precursor flow on the structural and mechanical properties of the CNT arrays. We show that the CNT growth process is inhomogeneous along the direction of the precursor flow, resulting in varying bulk density at different points on the growth substrate. We also study the effects of non-covalent functionalization of the CNTs after growth, using surfactant and nanoparticles, to vary the effective bulk density and structural arrangement of the arrays. We find that the stiffness and peak stress of the materials increase approximately linearly with increasing bulk density.