Complex formation of boric acids with DI- and TRI- carboxylic acids and poly(vinyl alcohol) in aqueous solutions

Complexation of dihydroxyboryl compounds such as dihydroxyboryl phenylalanine and boric acid with polycarboxylic acids as well as polyols was studied by infrared spectroscopy and zone electrophoresis. By consulting the results obtained, gel formation of poly(vinyl alcohol) (PVA) in aqueous solutions of boric acids (BA) and borax was studied. The IR spectra of aqueous PVA-BA gels indicate that BA mainly assumes a planar triangle form, while the local conformation of PVA in the gel is different from that in aqueous solutions.     

Encapsulation of small base molecules and tetrahedral/cubane-like clusters of group V atoms in the boron buckyball: a density functional theory study

A density functional theory study of small base molecules and tetrahedral and cubane-like group V clusters encapsulated in B(80) shows that the boron buckyball is a hard acid and prefers hard bases like NH(3) or N(2)H(4) to form stable off-centered complexes. In contrast, tetrahedral and cubane-like clusters of this family are metastable in the cage. The most favorable clusters are the mixed tetrahedral and cubane clusters formed by nitrogen and phosphorus atoms such as P(2)N(2)@B(80), P(3)N@B(80), and P(4)N(4)@B(80). The boron cap atoms are electrophilic centers, and prefer mainly to react with electron rich nucleophilic sites. The stability of the complexes will be governed by the size and electron donating character of the encapsulated clusters. B(80) forms stable complexes with hard materials where a bidentate interaction of the encapsulated molecule with two boron cap atoms is preferred over a single direct complex toward a single endohedral boron.     

Geometric and magnetic properties of Pt clusters supported on graphene: relativistic density-functional calculations

The geometric and magnetic structures of small Pt(n) clusters (n = 1 - 5) supported on a graphene layer have been investigated using ab initio density functional calculations including spin-orbit coupling. Pt-Pt interactions were found to be much stronger than the Pt-C interactions promoting the binding to the support. As a consequence, the equilibrium structure of the gas-phase clusters is preserved if they are deposited on graphene. However, the clusters bind to graphene only via at most two Pt-C bonds: A Pt(2) dumbbell prefers an upright position, the larger clusters are bound to graphene only via one edge of the planar cluster (Pt(3) and Pt(5)) or via two terminal Pt atoms of a bent Pt(4) rhombus. Evidently, the strong buckling of the graphene layer induced by the Pt-C bonds prevents the formation of a larger number of cluster-support bonds. As the local spin and orbital magnetic moments are quenched on the Pt atoms forming Pt-C bonds, the magnetic structure of the supported clusters is much more inhomogeneous as in the gas-phase. This leads to noncollinear magnetic structures and a strongly reduced magnetic anisotropy energy.     

Supramolecular parallel β-sheet and amyloid-like fibril forming peptides using δ-aminovaleric acid residue

Four terminally blocked tripeptides containing δ-aminovaleric acid residue self-assemble to form supramolecular β-sheet structures as are revealed from their FT-IR data. Single crystal X-ray diffraction studies of two representative peptides also show that they form parallel β-sheet structures. Self-aggregation of these β-sheet forming peptides leads to the formation of fibrillar structures, as is evident from scanning electron microscopic (SEM) and transmission electron microscopic (TEM) images. These peptide fibrils bind to a physiological dye, Congo red and exhibit a typical green-gold birefringence under polarized light, showing close resemblance to neurodegenerative disease causing amyloid fibrils.     

Reinvestigation of the reactions of camphorketene: structural evidence for pseudopericyclic pathways

The stereochemistry of the dimers (3 and 4) of camphorketene (2) have been determined. The crystal structures of 3, 20 and of related compounds show ground-state distortions that are interpreted as prefiguring planar, pseudopericyclic transition states for retro-cycloadditions to form alpha-oxoketenes. The B3LYP/6-31G* optimized geometry for the transition structure (10) for the dimerization of s-Z-formylketene (8) is consistent with this mechanism. Trapping of 2 with alcohols shows selectivity comparable to other alpha-oxoketenes. The lack of reaction of 2 with benzaldehyde and the lack of enol tautomers in camphoric acid derivatives is attributed to angle strain in the bicyclic camphor moiety.     

Effect of Co doping on catalytic activity of small Pt clusters

Platinum is the most widely used catalyst in fuel cell electrodes. Designing improved catalysts with low or no platinum content is one of the grand challenges in fuel cell research. Here, we investigate electronic structures of Pt(4) and Pt(3)Co clusters and report a comparative study of adsorption of H(2), O(2), and CO molecules on the two clusters using density functional theory. The adsorption studies show that H(2) undergoes dissociative chemisorption on the tetrahedral clusters in head on and side on approaches at Pt centers. O(2) dissociation occurs primarily in three and four center coordinations and CO prefers to adsorb on Pt or Co atop atoms. The adsorption energy of O(2) is found to be higher for the Co doped cluster. For CO, the Pt atop orientation is preferred for both Pt(4) and Pt(3)Co tetrahedral clusters. Adsorption of CO molecule on tetrahedral Pt(3)Co in side on approach leads to isomerization to planar rhombus geometry. An analysis of Hirshfeld charge distribution shows that the clusters become more polarized after adsorption of the molecules.     

The electronic origin of the dual fluorescence in donor-acceptor substituted benzene derivatives

The origin of the dual fluorescence of DMABN (dimethylaminobenzonitrile) and other benzene derivatives is explained by a charge transfer model based on the properties of the benzene anion radical. It is shown that, in general, three low-lying electronically excited states are expected for these molecules, two of which are of charge transfer (CT) character, whereas the third is a locally excited (LE) state. Dual fluorescence may arise from any two of these states, as each has a different geometry at which it attains a minimum. The Jahn-Teller induced distortion of the benzene anion radical ground state helps to classify the CT states as having quinoid (Q) and antiquinoid (AQ) forms. The intramolecular charge transfer (ICT) state is formed by the transfer of an electron from a covalently linked donor group to an anti-bonding orbital of the pi-electron system of benzene. The change in charge distribution of the molecule in the CT states leads to the most significant geometry change undergone by the molecule which is the distortion of the benzene ring to a Q or AQ structure. As the dipole moment is larger in the perpendicular geometry than in the planar one, this geometry is preferred in polar solvents, supporting the twisted intramolecular charge transfer (TICT) model. However, in many cases the planar conformation of CT excited states is lower in energy than that of the LE state, and dual fluorescence can be observed also from planar structures.     

Duplex formation and the onset of helicity in poly d(CG)n oligonucleotides in a solvent-free environment

The gas-phase conformations of a series of cytosine/guanine DNA duplexes were examined by ion mobility and molecular dynamics methods. Deprotonated duplex ions were formed by electrospray ionization, and their collision cross sections measured in helium were compared to calculated cross sections of theoretical models generated by molecular dynamics. The 4-mer (dCGCG) and 6-mer (dCGCGCG) duplexes were found to have globular conformations. Globular and helical structures were observed for the 8-mer (dCGCGCGCG) duplex, with the globular form being the more favored conformer. For the 10-mer (dCGCGCGCGCG), 14-mer (dCGCGCGCGCGCGCG), and 18-mer (dCGCGCGCGCGCGCGCGCG) duplexes, only helical structures were observed in the ion mobility measurements. Theory predicts that the helical structures are less stable than the globular forms in the gas phase and should collapse into the globular form given enough time. However, molecular dynamics simulations at 300 K indicate the helical structures are stable in aqueous solution and will retain their conformations for a limited time in the gas phase. The presence of helical structures in the ion mobility experiments indicates that the duplexes retain "solution structures" in the gas phase on the millisecond time scale.     

Fabrication of complex three-dimensional microchannel systems in PDMS

This paper describes a method for fabricating three-dimensional (3D) microfluidic channel systems in poly(dimethylsiloxane) (PDMS) with complex topologies and geometries that include a knot, a spiral channel, a "basketweave" of channels, a chaotic advective mixer, a system with "braided" channels, and a 3D grid of channels. Pseudo-3D channels, which are topologically equivalent to planar channels, are generated by bending corresponding planar channels in PDMS out of the plane into 3D shapes. True 3D channel systems are formed on the basis of the strategy of decomposing these complex networks into substructures that are planar or pseudo-3D. A methodology is developed that connects these planar and/or pseudo-3D structures to generate PDMS channel systems with the original 3D geometry. This technique of joining separate channel structures can also be used to create channel systems in PDMS over large areas by connecting features on different substrates. The channels can be used as templates to form 3D structures in other materials.     

Structures of carbohydrate-boronic acid complexes determined by NMR and molecular modelling in aqueous alkaline media

The structures of thermodynamically stable aromatic boronic acid : cyclic carbohydrate chelates in aqueous alkaline media have been studied using 1H NMR spectroscopy and molecular modelling. It is found that interacting saccharides must necessarily possess a synperiplanar diol functionality for complexation to occur. While this is possible for furanose structures which tend to have a puckered planar geometry, for pyranose forms it is postulated that bis-complexation occurs with twist conformers of the pyranose ring, providing the ring has the requisite 1,2 : 3,4 polyol stereochemistry; specifically axial,equatorial : equatorial,axial or equatorial,axial : axial,equatorial orientations. In this respect it is possible to be predictive with regard to individual carbohydrate boronic acid interactions and to give reasonably comprehensive structural assignments to complexed components. In this paper twenty four polyhydroxy compounds have been screened using 1H NMR to monitor complexation along with computational techniques on a model system to substantiate proposed structures. It has been found that all of these materials interact with aromatic mono boronic acids as expected and structures for the resulting chelates are proposed.     

Role of hydrogen bonds in protein-DNA recognition: effect of nonplanar amino groups

Amino groups are one of the various types of hydrogen bond donors, abundantly found in protein main chains, protein side chains, and DNA bases. The polar hydrogen atoms of these groups exhibit short ranged, specific, and directional hydrogen bonds, which play a decisive role in the specificity and stability of protein-DNA complexes. To date, planar amino groups are only considered for the analysis of protein-DNA interfacial hydrogen bonds. This assumption regarding hydrogen atom positions possibly failed to establish the expected role of hydrogen bonds in protein-DNA recognition. We have performed ab initio quantum chemical studies on amino acid side chains and DNA bases containing amino groups as well as on specific hydrogen bonded residue pairs selected from high-resolution protein-DNA complex crystal structures. Our results suggest that occurrences of pyramidal amino groups are more probable in comparison with the usually adopted planar geometry. This increases the quality of the existing hydrogen bonds in almost all cases. Further, detailed analysis of protein-DNA interfacial hydrogen bonds in 107 crystal structures using the in-house program "pyrHBfind" indicates that consideration of energetically more preferred nonplanar amino groups improves the geometry of hydrogen bonds and also gives rise to new contacts amounting to nearly 14.5% of the existing interactions. Large improvements have been observed specifically for the amino groups of guanine, which faces the DNA minor groove and thus helps to resolve the problem of insufficient directional contacts observed in many minor groove binding complexes. Apart from guanine, improvement observed for asparagine, glutamine, adenine, or cytosine also indicates that the consideration of nonplanar amino groups leads to a more realistic scenario of hydrogen bonds occurring between protein and DNA residues.     

Ultrathin layer convolution

Ultrathin layers are defined as thin layers which are sufficiently thin that no concentration gradients are established within the layer on the time scale of a voltammetric measurement. Mathematically, ultrathin layers are characterized by ordinary differential equations in time. These equations are simpler to solve than the space and time dependent partial differential equations which describe all other electrode geometries. In this paper, a method is presented which capitalizes on the mathematical simplicity of the ultrathin layer to model any arbitrary, parameterizable electrode geometry. Laplace transforms are used to find an integral relationship between the current response of the modeled geometry and the ultrathin layer current. The integral relationship can be evaluated either analytically or numerically. Any voltammetric perturbation, under either Nernstian or mass transport-controlled conditions, can be modeled. The method is demonstrated for both planar and spherical electrodes. Cyclic voltammetric responses are modeled numerically and potential step responses are modeled analytically. It is also shown that for cyclic voltammetric perturbations, the current-voltage curves for the following systems have the same functional form. That is, the curves are identical within known multiplicative constants. The functionally equivalent responses are for (1) radial diffusion to a point electrode (the polarographic curve), (2) convective transport to a rotating disk, (3) the integral of the ultrathin layer response, and (4) the convolution or semi-integration of the response for linear diffusion to a planar electrode.     

Vibrational analysis of amino acids and short peptides in hydrated media. II. Role of KLLL repeats to induce helical conformations in minimalist LK-peptides

Aqueous solution secondary structures of minimalist LK-peptides, with the generic sequence defined as KLL(KLLL)nKLLK, have been analyzed by means of circular dichroism (CD) and Raman scattering techniques. Our discussion in the present paper is mainly focused on four synthetic peptides (from 5 to 19 amino acids), KLLLK, KLLKLLLKLLK, KLLKLLLKLLLKLLK, and KLLKLLLKLLLKLLLKLLK, corresponding to the repeat unit, and to the peptide chains with the values of n = 1-3, respectively. CD and Raman spectra were analyzed in order to study both structural features of the peptide chains and their capability to form aggregates. On the basis of the obtained results it was concluded that the conformational flexibility of the shortest peptides (5-mer and 11-mer) is high enough to adopt random, beta-type, and helical chains in aqueous solution. However, the 11-mer shows a clear tendency to form beta-strands in phosphate buffer. The conformational equilibrium can be completely shifted to beta-type structures upon increasing ionic strength, i.e., in PBS and tris buffers. This equilibrium can also be shifted toward helical chains in the presence of methanol. Finally, the longest peptides (15-mer and 19-mer) are shown to form alpha-helical chains with an amphipathic character in aqueous solution. The possibility of bundle formation between helical chains is discussed over the temperature-dependent H-D exchange on labile hydrogens and particularly by considering the particular behavior of an intense Raman mode at 1127 cm-1 originating from the leucine residue side chain. The conformational dependence of this mode observed upon selective deuteration has never been documented up to now.     

茜素红S-硼酸体系对单糖的双光谱识别

利用硼酸与茜素红S和糖中的邻二羟基可逆结合的特点,以硼酸为中介运用竞争结合作用机理构建单糖分析法.在pH7.4的KH2PO4-NaOH缓冲溶液中,茜素红S作为指示剂与硼酸结合生成ARS-BA配合物,其结合常数为5.09×102L/mol.糖与指示剂ARS竞争结合硼酸使指示剂游离出来,产生明显的颜色变化,据此建立糖的识别方法.考察了D-葡萄糖、D-山梨醇、D-半乳糖、D-甘露糖、D-果糖、D-阿拉伯糖和L-阿拉伯糖对上述ARS-BA体系光谱的影响.结果显示:该体系对D-山梨醇和D-果糖有较好的光谱响应,其光谱变化灵敏度依D-山梨醇＞D-果糖＞D-阿拉伯糖～D-半乳糖＞D-葡萄糖＞D-甘露糖＞L-阿拉伯糖之序.     

In silico analysis of metal coordination geometry in arsenic,beryllium, and lead bound structures

Metal toxicity is a potential hazard to health and toxic effects of metals have been implicated in many diseases. Understanding the interaction of toxic metals becomes vital to prevent hazards following its association in living systems. Coordination chemistry helps in predicting the metal environments like coordinating residues, coordination space, metal coordination geometry, etc. Our work aimed at predicting the coordination of toxic metals arsenic, lead, and beryllium. In this work, we analyzed coordination for each metal from a set of arsenic, beryllium and lead bound structures which were retrieved from the Protein Data Bank. The structures were validated using B-factor and occupancy of the coordinating residues towards the metals. Coordination patterns such as chelate residues, chelate length, geometry, coordination number and structural architecture were predicted. Coordination geometry of the metals was exposed beyond the coordination space with their coordination number ranging from 2 to 11. Analysis of metal environment revealed the acidic amino acids aspartic acid, glutamic acid, and the basic amino acids lysine, histidine, and cysteine to be predominant in coordinating with the metals. Chelate patterns like DDVMITAK, DWNVTVK, ESGKNSS for beryllium, CCCSK, DSDWD for lead and FLICVI and LKHHKEE for arsenic were predicted to be common through extended coordination space. The distinct molecular geometries such as pentagonal bipyramid and square planar were observed only in lead bound structures but not in beryllium and arsenic bound structures. Beryllium had a larger influence than arsenic and lead, based on conformational changes owing to the presence of the metals. Our coordination study puts forth several propositions based on the metal environment that would help in designing chelation strategies.     

Structure, energetics, and reactivity of boric acid nanotubes: a molecular tailoring approach

Cardinality guided molecular tailoring approach (CG-MTA) [Ganesh et al. J. Chem. Phys. 2006, 125, 104019] has been effectively employed to perform ab initio calculations for large molecular clusters of boric acid. It is evident from the results that boric acid forms nanotubes, structurally similar to carbon nanotubes, with the help of an extensive hydrogen-bonding (H-bonding) network. Planar rosette-shaped hexamer of boric acid is the smallest repeating unit in such nanotubes. The stability of these tubes increases due to enhancement in the number of H-bonding interactions as the diameter increases. An analysis of molecular electrostatic potential (MESP) of these systems provides interesting features regarding the reactivity of these tubes. It is predicted that due to alternate negative and positive potentials on O and B atoms, respectively, boric acid nanotubes will interact favorably with polar systems such as water and can also form multiwalled tubes.     

单糖和硼酸形成络合物的讨论

本文用平均络合平衡常数的测定及~(13)C NMR两种方法对一些单糖、糖苷和硼酸生成的络合物进行了研究。研究结果表明醛戊糖、醛己糖虽在溶液中主要以吡喃环存在,但当它们与硼酸络合时即由吡喃转变成呋喃。     

Synthesis, characterization, and X-ray crystal structures of copper(II) and nickel(II) complexes with Schiff base

New copper(II) complexes, [Cu₂L¹L²] · ClO₄ (I) and [Ni(L³)₂] (II), where L¹ is the monoanionic form of 2-[1-(2-emthylaminoethylimino)ethyl]phenol, L² is the dianionic form of N,N′-ethylene-bis(2-hydroxyacetophenonylideneimine), L³ is the mono-anionic form of 2-(1-iminoethyl)phenol, were prepared and characterized using elemental analysis, FT-IR spectroscopy, and X-ray single-crystal diffraction. In complex I, the Cu(1) atom is coordinated by the NNO tridentate ligand L¹ and the two phenolate O atoms of L², forming a square pyramidal geometry. The Cu(2) atom in complex I is coordinated by the NNOO tetradenate ligand L², forming a square planar geometry. The Ni atom in complex II is coordinated by two phenolate O and two imine N atoms from two ligands L³, forming a square planar geometry. In the crystal structure of I, the perchlorate anions are linked to the dinuclear copper(II) complex cations through intermolecular N-H...O hydrogen bonds. In the crystal structure of II, the mononuclear nickel complex molecules are linked through intermolecular N-H...O hydrogen bonds, forming a trimer.     

Zur Bildung isomerer Trihydroxy-octadecensäuren bei der enzymatischen Oxydation von Linolsäure durch Gerstenmehl

Incubation of linoleic acid with barley flour at pH 6.8 leads to the formation of three isomeric trihydroxy octadecenoic acids, namely: 9,12,13-trihydroxy-10-trans-octadecenoic acid, 9,10,13-trihydroxy-11-trans-octadecenoic acid and 9,10,11-trihydroxy-12-trans-octadecenoic acid. The acids were isolated by column chromatography using silicic acid and boric acid impregnated silicic acid and their structures were ascertained by means of IR, NMR and mass spectroscopy.

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Synthesis and solid state structures of two new copper(II) complexes of Schiff bases derived from furfuryl and tetrahydrofurfurylamine

Two Schiff base copper(II) complexes, bis(N-furfurylsalicylaldiminato)copper(II) (I) and bis(N-tetrahydrofurfurylsalicylaldiminato)copper(II) (II), were synthesized and their solid state structures were determined by X-ray crystallography. Complex I has a square planar geometry. In contrast, complex II displays a distorted square planar geometry. Thus, the geometry around copper in the solid state structures of I and II is determined by a combination of steric and electronic effects, as well as by crystal packing forces.