Interaction of metal ions with 6-oxopurine nucleotides. Part 2. X-Ray structures of ternary nickel(II) complexes with 2'-deoxyguanosine 5'-monophosphate or guanosine 5'-monophosphate

The ternary metal nucleotide complexes [Ni(en)1.3(H2O)1.4(H2O)2][Ni(5?-dGMP)2(en)0.7-(H2O)0.6(H2O)2]·7H2O (1) and [Ni(en)2(H2O)2][Ni(5?-GMP)2(H2O)4]·6H2O (2)(en = ethylenediamine, 5?-dGMP = 2?-deoxyguanosine 5?-monophosphate, 5?-GMP = guanosine 5?-monophosphate) have been prepared and their structures analyzed by X-ray diffraction methods. Both compounds crystallise in the space group C2221 with a= 8.810(1), b= 25.090(4), c= 21.084(1)Å, and Z= 4 for (1) and a= 8.730(1), b= 25.691(4), c= 21.313(5)Å, and Z= 4 for (2). The structures were deduced from the analogous CoIII complexes and refined by full-matrix least-squares methods to final R values of 0.087 and 0.131 for 1 211 and 954 reflections for (1) and (2) respectively. An interesting feature of the deoxyribonucleotide complex (1) is that en is not totally labilized from the metal centre on nucleotide co-ordination, as observed in corresponding ribonucleotide complexes. Apart from extensive intra- and inter-molecular hydrogen bonding, the structures are stabilized by significant intracomplex base�base and base�sugar interactions. The nucleotides in both complexes have an anti base, C(2?)-endo sugar pucker, and gauche�gauche conformation about the C(4?)�C(5?) bond.

Inter And Intramolecular Interactions Of Porphyrins With 5,5′-Dithiobis(2-Nitrobenzoic Acid)

meso-Tetraphenylporphyrin and its metal [zinc(II) and copper(II)] derivatives form both inter and intramolecular complexes with 5,5′-dithiobis(2-nitrobenzoic acid) (DTNB). The nature of interaction is predominantly charge transfer (CT) in origin, with the porphyrin functioning as a II-donor and DTNB as an acceptor. Among the covalently linked intramolecular systems, the magnitude of CT interaction varies with the position (of one of the aryl groups of the porphyrin) to which DTNB is attached as ortho meta > para. Steady-state and time-resolved fluorescence studies revealed electron transfer to be the dominant pathway for the fluorescence quenching in these systems. Steady-state photolysis experiments probed using EPR and optical absorption studies have shown that electron transfer (from the excited singlet state of the porphyrin) to DTNB results in the formation of thiyl radical and production of free thiolate anion. It is found that the products of electrochemical reduction of covalently linked porphyrin-DTNB systems are different from those observed for the photochemical studies.

Weak molecular complexes as studied by NMR spectroscopy of oriented molecules

Weak molecular interactions such as those in pyridine-iodine, benzene-iodine and benzene-chloroform systems oriented in thermotropic liquid crystals have been studied from the changes of the order parameters as a result of complex formation. The results indicate the formation of at least two types of charge transfer complexes in pyridine-iodine solutions. The pi-complexes in benzene-chloroform and benzene-iodine mixtures have also been detected. No detectable changes in the inter-proton distances in these systems were observed.

Hydrogen bonding, halogen bonding and lithium bonding: an atoms in molecules and natural bond orbital perspective towards conservation of total bond order, inter- and intra-molecular bonding

One hundred complexes have been investigated exhibiting D-X center dot center dot center dot A interactions, where X = H, Cl or Li and DX is the `X bond' donor and A is the acceptor. The optimized structures of all these complexes have been used to propose a generalized `Legon-Millen rule' for the angular geometry in all these interactions. A detailed Atoms in Molecules (AIM) theoretical analysis confirms an important conclusion, known in the literature: there is a strong correlation between the electron density at the X center dot center dot center dot A bond critical point (BCP) and the interaction energy for all these interactions. In addition, we show that extrapolation of the fitted line leads to the ionic bond for Li-bonding (electrostatic) while for hydrogen and chlorine bonding, it leads to the covalent bond. Further, we observe a strong correlation between the change in electron density at the D-X BCP and that at the X center dot center dot center dot A BCP, suggesting conservation of the bond order. The correlation found between penetration and electron density at BCP can be very useful for crystal structure analysis, which relies on arbitrary van der Waals radii for estimating penetration. Various criteria proposed for shared-and closed-shell interactions based on electron density topology have been tested for H/Cl/Li bonded complexes. Finally, using the natural bond orbital (NBO) analysis it is shown that the D-X bond weakens upon X bond formation, whether it is ionic (DLi) or covalent (DH/DCl) and the respective indices such as ionicity or covalent bond order decrease. Clearly, one can think of conservation of bond order that includes ionic and covalent contributions to both D-X and X center dot center dot center dot A bonds, for not only X = H/Cl/Li investigated here but also any atom involved in intermolecular bonding.

Dynamics of the chemical bond: inter- and intra-molecular hydrogen bond

In this discussion, we show that a static definition of a `bond' is not viable by looking at a few examples for both inter-and intra-molecular hydrogen bonding. This follows from our earlier work (Goswami and Arunan, Phys. Chem. Chem. Phys. 2009, 11, 8974) which showed a practical way to differentiate `hydrogen bonding' from `van der Waals interaction'. We report results from ab initio and atoms in molecules theoretical calculations for a series of Rg center dot center dot center dot HX complexes (Rg = He/Ne/Ar and X = F/Cl/Br) and ethane-1,2-diol. Results for the Rg center dot center dot center dot HX/DX complexes show that Rg center dot center dot center dot DX could have a `deuterium bond' even when Rg center dot center dot center dot HX is not `hydrogen bonded', according to the practical criterion given by Goswami and Arunan. Results for ethane-1,2-diol show that an `intra-molecular hydrogen bond' can appear during a normal mode vibration which is dominated by the O center dot center dot center dot O stretching, though a `bond' is not found in the equilibrium structure. This dynamical `bond' formation may nevertheless be important in ensuring the continuity of electron density across a molecule. In the former case, a vibration `breaks' an existing bond and in the later case, a vibration leads to `bond' formation. In both cases, the molecule/complex stays bound irrespective of what happens to this `hydrogen bond'. Both these cases push the borders on the recent IUPAC recommendation on hydrogen bonding (Arunan et al. Pure. Appl. Chem. 2011, 83 1637) and justify the inclusive nature of the definition.

Weak conservation of structural features in the interfaces of homologous transient protein-protein complexes

Residue types at the interface of protein-protein complexes (PPCs) are known to be reasonably well conserved. However, we show, using a dataset of known 3-D structures of homologous transient PPCs, that the 3-D location of interfacial residues and their interaction patterns are only moderately and poorly conserved, respectively. Another surprising observation is that a residue at the interface that is conserved is not necessarily in the interface in the homolog. Such differences in homologous complexes are manifested by substitution of the residues that are spatially proximal to the conserved residue and structural differences at the interfaces as well as differences in spatial orientations of the interacting proteins. Conservation of interface location and the interaction pattern at the core of the interfaces is higher than at the periphery of the interface patch. Extents of variability of various structural features reported here for homologous transient PPCs are higher than the variation in homologous permanent homomers. Our findings suggest that straightforward extrapolation of interfacial nature and inter-residue interaction patterns from template to target could lead to serious errors in the modeled complex structure. Understanding the evolution of interfaces provides insights to improve comparative modeling of PPC structures.

Crystal Coulomb energies: I. Organic donor-acceptor complexes--a review. II. Classical Ewald calculations of the Coulomb binding energy of four donor-acceptor crystals and Wurster's blue perchlorate. III. A rapid-convergence quantum-mechanical formalism for crystal electronic energies

Chapter I

Theories for organic donor-acceptor (DA) complexes in solution and in the solid state are reviewed, and compared with the available experimental data. As shown by McConnell et al. (Proc. Natl. Acad. Sci. U.S., 53, 46-50 (1965)), the DA crystals fall into two classes, the holoionic class with a fully or almost fully ionic ground state, and the nonionic class with little or no ionic character. If the total lattice binding energy 2ε₁ (per DA pair) gained in ionizing a DA lattice exceeds the cost 2ε_o of ionizing each DA pair, ε₁ + ε_o less than 0, then the lattice is holoionic. The charge-transfer (CT) band in crystals and in solution can be explained, following Mulliken, by a second-order mixing of states, or by any theory that makes the CT transition strongly allowed, and yet due to a small change in the ground state of the non-interacting components D and A (or D⁺ and A^-). The magnetic properties of the DA crystals are discussed.

Chapter II

A computer program, EWALD, was written to calculate by the Ewald fast-convergence method the crystal Coulomb binding energy E_C due to classical monopole-monopole interactions for crystals of any symmetry. The precision of E_C values obtained is high: the uncertainties, estimated by the effect on E_C of changing the Ewald convergence parameter η, ranged from ± 0.00002 eV to ± 0.01 eV in the worst case. The charge distribution for organic ions was idealized as fractional point charges localized at the crystallographic atomic positions: these charges were chosen from available theoretical and experimental estimates. The uncertainty in E_C due to different charge distribution models is typically ± 0.1 eV (± 3%): thus, even the simple Hückel model can give decent results.

E_C for Wurster's Blue Perchl orate is -4.1 eV/molecule: the crystal is stable under the binding provided by direct Coulomb interactions. E_C for N-Methylphenazinium Tetracyanoquino- dimethanide is 0.1 eV: exchange Coulomb interactions, which cannot be estimated classically, must provide the necessary binding.

EWALD was also used to test the McConnell classification of DA crystals. For the holoionic (1:1)-(N,N,N',N'-Tetramethyl-para- phenylenediamine: 7,7,8,8-Tetracyanoquinodimethan) E_C = -4.0 eV while 2ε_o = 4.6₅ eV: clearly, exchange forces must provide the balance. For the holoionic (1:1)-(N,N,N',N'-Tetramethyl-para- phenylenediamine:para-Chloranil) E_C = -4.4 eV, while 2ε_o = 5.0 eV: again EC falls short of 2ε₁. As a Gedankenexperiment, two nonionic crystals were assumed to be ionized: for (1:1)-(Hexamethyl- benzene:para-Chloranil) E_C = -4.5 eV, 2ε_o = 6.6 eV; for (1:1)- (Napthalene:Tetracyanoethylene) E_C = -4.3 eV, 2ε_o = 6.5 eV. Thus, exchange energies in these nonionic crystals must not exceed 1 eV.

Chapter III

A rapid-convergence quantum-mechanical formalism is derived to calculate the electronic energy of an arbitrary molecular (or molecular-ion) crystal: this provides estimates of crystal binding energies which include the exchange Coulomb inter- actions. Previously obtained LCAO-MO wavefunctions for the isolated molecule(s) ("unit cell spin-orbitals") provide the starting-point. Bloch's theorem is used to construct "crystal spin-orbitals". Overlap between the unit cell orbitals localized in different unit cells is neglected, or is eliminated by Löwdin orthogonalization. Then simple formulas for the total kinetic energy Q^(XT)_λ, nuclear attraction [λ/λ]^XT, direct Coulomb [λλ/λ'λ']^XT and exchange Coulomb [λλ'/λ'λ]^XT integrals are obtained, and direct-space brute-force expansions in atomic wavefunctions are given. Fourier series are obtained for [λ/λ]^XT, [λλ/λ'λ']^XT, and [λλ/λ'λ]^XT with the help of the convolution theorem; the Fourier coefficients require the evaluation of Silverstone's two-center Fourier transform integrals. If the short-range interactions are calculated by brute-force integrations in direct space, and the long-range effects are summed in Fourier space, then rapid convergence is possible for [λ/λ]^XT, [λλ/λ'λ']^XT and [λλ'/λ'λ]^XT. This is achieved, as in the Ewald method, by modifying each atomic wavefunction by a "Gaussian convergence acceleration factor", and evaluating separately in direct and in Fourier space appropriate portions of [λ/λ]^XT, etc., where some of the portions contain the Gaussian factor.

Influence of Polyelectrolyte on DNA-RecA Nucleoprotein Filaments: Poly-L-Lysine Used as a Model

RecA of Escherichia coli and its active nucleoprotein filaments with DNA are important for the genomic integrity and the genetic diversity. The formation of the DNA-RecA nucleoprotein filaments is a complex multiple-step process and can be affected by many factors. In this work, the effects of poly-L-lysine (PLL) on the DNA-RecA nucleoprotein filaments are investigated in vitro by agarose gel electrophoresis and atomic force microscopy (AFM). The observed morphologies vary with the concentration, the length, and the addition order of PLL. These distinctions provide information for the conformation change of DNA and the binding sites of RecA protein in the formation process of nucleoprotein filaments.

A method to construct polyelectrolyte multilayers film containing gold nanoparticles

Gold nanoparticles in polyelectrolyte multilayers film can be easily prepared by repeating immersion of a substrate in poly(diallyl dimethylammonium) chloride (PDDA)-AuCl4- complexes solution followed by reduction Au3+ through heating. UV-vis spectroscopy, cyclic voltammetry (CV) and tapping-mode atomic force microscopy (AFM) are used to confirm the successful construction of the polyelectrolyte multilayers film and the formation of gold nanoparticles. The multilayers film shows electrocatalytic activity to dioxygen reduction.

Syntheses and crystal structures of mononuclear rhodium hydrido complexes from the reactions of [Rh(H)(2)(PPh3)(2)(EtOH)(2)]ClO4 with various nitrogen ligands

Reactions of the Rh hydrido complex [Rh(H)(2)(PPh3)(2)(EtOH)(2)]ClO4 (1) With nitrogen ligands such as 2-(4-thiazolyl)benzimidazole (tbz). pyridazine (pdz), imidazole (im) and pyrimidine (pmd) in CH,Cl, afforded Various mononuclear Rh hydrido complexes, [Rh(H)(2)(PPh3)(2)(tbz)]CIO4 (2), [Rh(H)(2)(PPh3)(2)(pdZ)(2)]ClO(4)(.)2CH(2)Cl(2) (3). [Rh(H)Cl(PPh3)(2)(pdz)(2)](ClO4CH2Cl2)-C-. (4). [Rh(H)(2)(PPh3)(2)(im)(2)]ClO(4)(.)2CH(2)Cl(2) (5). [Rh(H)Cl(PPh3)(2)(im)(2)](ClO4CH2Cl2)-C-. (6). [Rh(H)(2)(PPh3)(2)(pmd)(2)](ClO4CH2Cl2)-C-. (7) and the Rh non-hydrido complex [RhCl2(pmd)(4)]ClO4 (8). The Rh complexes 2. 3, 5 and 6 were crystallographically characterized. The formation process was monitored by H-1 NMR and UV-Vis spectra. In all the Rh hydrido complexes, the Rh atom is coordinated by two PPh3. ligands in trans-positions and two nitrogen ligands in the cis-positions. The remaining sites Lire occupied by one or two hydride atoms to form a saturated 18-electron framework in a slightly distorted octahedral geometry. For complex 2 an appreciable inter-molecular pi interaction is observed between planes of tbz and PPh3 ligands, while an intra-molecular hydrogen bonding interaction between C-H and Cl atoms is found in complex 6.

Electrochemiluminescence of tris(2,2 '-bipyridyl)ruthenium (II) ion-exchanged in polyelectrolyte-silica composite thin-films

The organic-inorganic hybrid, PSS-silica composite material was developed for the immobilization of tris(2,2'-bipyridyl)ruthenium(II) (Ru(bpy)(3)(2+)) on glassy carbon electrode via ion-exchange (PSS stands for poly(sodium 4-styrene-sulfonate)). The electrochemiluminescence (ECL) and electrochemistry of Ru(bpy)(3)(2-) immobilized in the composite thin films have been investigated with tripropylamine (TPA) as the coreactant. The immobilized Ru(bpy)(3)(2-) underwent a surface process. The modified electrode was used for the ECL detection of TPA and showed high sensitivity. Detection limit was 0,1 mumol L-1 for TPA (S/N = 3) with a linear range from 0.5 mumol L-1 to 5 mmol L-1 (R = 0.998), Moreover, the resulting modified electrode was stable over six months and the good stability may be due to the strong interaction between Ru(bpy)(3)(2-) and the high ion-exchange able PSS-silica composite films on GCE. Compared with other materials. the PSS-silica composite films containing incorporated Ru(bpy)(3)(2-) showed improved sensitivity and long-term stability, Thus, such composite thin film can be a promising material for the construction of ECL sensor.

Lanthanide coordination polymers with dicarboxylate-like ligands: crystal structures of polymeric lanthanum(III) and terbium(III) complexes with flexible double betaines

Four novel polymeric lanthanide(III) complexes of two new double betaine derivatives have been synthesized and structurally determined. In [{La-2(L-1)(2)(H2O)(9)}(n)]Cl-6n. 2nH(2)O (1) and [{Tb(L-1)(H2O)(4)}(n)]Cl-3n. nH(2)O (2) (L-1 =4,4'-trimethylenedipyridinio-N,N'-diacetate), the lanthanide(III) ions form a two-dimensional layer in which each pair of lanthanide(III) ions is bridged by two syn-anti mu-carboxylato-O,O' groups. Adjacent layers are cross-linked through hydrogen bonds among aqua ligands, lattice water molecules and chloride ions, to form a three-dimensional network. Isomorphous [{Ln(L-1)(H2O)(4)}(n)]Cl-3n. 5nH(2)O (Ln=La, 3; Ln=Tb, 4; L-2=1,3 bis(pyridinio-4-carboxylato)-propane) each contain a centrosymmetric paddle-wheel-like dimeric unit in which each pair of adjacent metal atoms is bridged by four syn-syn mu-carboxylato-O,O' groups that are oriented nearly perpendicular to each other about the metal-metal axis. Neighboring dimeric subunits are bridged by a pair of flexible LL ligands into a polymeric chain. Adjacent chains are inter-linked by hydrogen bonds among aqua ligands, lattice water molecules and chloride ions into a three-dimensional network. (C) 1999 Elsevier Science Ltd. All rights reserved.

Structural characterization and luminescence studies of new lanthanide(III) complexes with nicotinic and isonicotinic acid N-oxides

Four new polymeric lanthanide(III) complexes of nicotinic acid N-oxide and isonicotinic acid N-oxide have been synthesized and structurally determined. In the isomorphous compounds [(Ln(L-1)(3) (H2O)(2))(n)]. 4nH(2)O(HL1 = nicotinic acid N-oxide; Ln = Eu, 1; Ln = Er, 2) the lanthanide(III) ions form infinite double chains along the b direction through the coordination of bridging carboxylate and N-oxide groups. The chains are cross-linked through hydrogen bonds between aqua ligands and uncoordinated N-oxide groups and between aqua ligands and lattice water molecules, to form a three-dimensional network. [(Eu(L-2)(2)-(H2O)(4))(n)](NO3)(n). nH(2)O (HL2 = isonicotinic acid N-oxide, 3) has a polymeric structure in which the europium (III) ions are connected into infinite chains by pairs of syn-syn carboxylate groups. Adjacent chains are interlinked by hydrogen bonds between aqua ligands and N-oxide groups to form a layer parallel to the (100) plane, and such layers are connected by hydrogen bonds between nitrate anions and aqua ligands, and between oxide groups and lattice water molecules, into a three-dimensional network. In [(Er-2(L-2)(4)(H2O)(10))](NO3)(2). H2O, 4, dinuclear units are inter-linked into a three-dimensional network through hydrogen bonding between aqua ligands and N-oxide groups of both bidentate bridging and unidentate L-2 ligands. Factors affecting the formation of coordination chains and dinuclear units are discussed. Luminescence properties of 1 and 3 have also been studied. (C) 1998 Elsevier Science Ltd. All rights reserved.

Collaborations complexes : modèle théorique et vérification empirique préliminaire en contexte de projets interdisciplinaires et interorganisationnels

La collaboration constitue une stratégie efficace pour aider les organisations et les individus à évoluer dans des environnements dynamiques et complexes, et génère de nombreux avantages cognitifs, affectifs et pécuniaires. De plus en plus, les équipes de travail sont impliquées dans des collaborations complexes, lesquelles requièrent de transiger à travers les frontières nationales, organisationnelles et disciplinaires. Bien que les collaborations complexes soient de plus en plus courantes en milieux organisationnels et étudiées par les scientifiques, peu d’études empiriques ont été réalisées sur le sujet et la documentation inhérente est disséminée dans divers silos parallèles de connaissances, donnant lieu à des modèles conceptuels divergents et incomplets. L’importance croissante de ces formes de collaboration crée l’impératif scientifique et pratique d’en acquérir une meilleure compréhension ainsi que d’identifier et d’évaluer les conditions et les facteurs qui favorisent leur succès et leur efficacité. Cette thèse vise à combler les lacunes susmentionnées et permettre un avancement des connaissances sur le sujet par l’entremise de deux articles répondant à divers objectifs de recherche. Le premier article avance une définition claire des collaborations complexes, en vue de réduire la confusion entourant ce construit. Il présente également la première revue de documentation sur les facteurs favorisant le succès des collaborations complexes, unifiant les résultats issus de divers contextes et disciplines scientifiques. Cette démarche a permis d’identifier 14 variables clés provenant de 26 études empiriques. À partir de ces données, un modèle conceptuel fondé sur des assises théoriques solides et reconnues en psychologie du travail et des organisations est proposé, offrant ainsi un canevas systémique et dynamique du phénomène ainsi qu’une orientation détaillée des pistes de recherches pertinentes. Le deuxième article part des résultats obtenus dans le premier article afin d’évaluer empiriquement les relations entre certains facteurs clés ayant un impact sur des extrants importants de collaborations complexes. L’étude multiphasique est réalisée auprès de 16 équipes de projets (N=93) interdisciplinaires et interorganisationnelles prenant part à des sessions de travail intensives visant la production de concepts novateurs en design intégré lié au développement durable. Les analyses corrélationnelles montrent des liens positifs entre l’ouverture à la diversité, les processus collaboratifs, la viabilité, la performance d’équipe et la performance de projet, ainsi que des liens négatifs entre les conflits et ces mêmes extrants. De plus, les analyses de médiation multiple révèlent qu’une plus grande ouverture à la diversité influence positivement la viabilité, la performance d’équipe et la performance de projet en favorisant les processus collaboratifs efficaces et en réduisant les conflits. Les implications théoriques et pratiques découlant de ces résultats sont discutées.

Inter- State Variations in Productivity trends and Technological Change in Indian industry

The present study entitled ‘Inter-State Variations in Manufacturing Productivity and Technological Changes in India’ covers a period of 38 years from l960 tol998-99. The study is mainly based on ASI data. The study starts with a discussion of the major facilitating factors of industrialization, namely, historical forces, public policy and infrastructure facilities. These are discussed in greater details in the context of our discussion on Perrox’s (1998) ‘growth pole’ and ‘development pole’, Hirschman’s (1958) ‘industrial centers’ and Myrdal’s ‘spread effect’ Most of the existing literature more or less agrees that the process of industrialization has not been unifonn in all Indian states. There has been a decline in inter-state industrial disparities over time. This aspect is dealt at some length in the third chapter. An important element that deserves detailed attention is the intra-regional differences in industrialisation. Regional industrialisation implies the emergence of a few focal points and industrial regions. Calcutta, Bombay and Madras were the initial focal points. Later other centers like Bangalore, Amritsar, Ahemedabad etc. emerged as nodal points in other states. All major states account for focal points. The analysis made in the third chapter shows that industrial activities generally converge to one or two focal points and industrial regions have emerged out of the focal points in almost all states. One of the general features of these complexes and regions is that they approximately accommodate 50 to 75 percent of the total industrial units and workers in the state. Such convergence is seen hands in glow with urbanization. It was further seen that intra-regional industrial disparity comes down in industrial states like Maharashtra, Gujarat and Uttar Pradesh.