Use of a novel Hill-climbing genetic algorithm in protein folding simulations

We have developed a novel Hill-climbing genetic algorithm (GA) for simulation of protein folding. The program (written in C) builds a set of Cartesian points to represent an unfolded polypeptide's backbone. The dihedral angles determining the chain's configuration are stored in an array of chromosome structures that is copied and then mutated. The fitness of the mutated chain's configuration is determined by its radius of gyration. A four-helix bundle was used to optimise simulation conditions, and the program was compared with other, larger, genetic algorithms on a variety of structures. The program ran 50% faster than other GA programs. Overall, tests on 100 non-redundant structures gave comparable results to other genetic algorithms, with the Hill-climbing program running from between 20 and 50% faster. Examples including crambin, cytochrome c, cytochrome B and hemerythrin gave good secondary structure fits with overall alpha carbon atom rms deviations of between 5 and 5.6 Angstrom with an optimised hydrophobic term in the fitness function. (C) 2003 Elsevier Ltd. All rights reserved.

Interaction of 2-(arylazo)phenols with rhodium. Usual coordination vs. C-H and C-C activation

Reaction of 2-(2'-hydroxyphenylazo)phenol with [Rh(PPh3)(3)Cl] in refluxing benzene in presence of triethylamine afforded a red complex in which the ligand is coordinated to rhodium as a tridentate O,N,O-donor. However, similar reaction of [Rh(PPh3)(3)Cl] with 2-(2'carboxyphenylazo)-4-methylphenol yielded two complexes, viz. a blue one and a green one. In both the complexes the ligand is coordinated as C,N,O-donor. However, in the blue complex orthometallation takes place from the ortho-carbon atom, which bears -COOH group via decarboxylation and in green one orthometallation occurs from the other ortho-carbon. Structures of all the three complexes were determined by X-ray crystallography. In all the three complexes rhodium is sharing the equatorial plane with the tridentate ligand and a chloride, and the two triphenylphosphines are axially disposed. All of the complexes show intense MLCT transitions in the visible region. Cyclic voltammetry on these complexes shows a Rh(III)-Rh(IV) oxidation on the positive side of SCE and a reduction of the coordinated azophenolate ligand on the negative side. (c) 2006 Elsevier B.V. All rights reserved.

Equilibrium studies on mixed ligand complex formation of Co(II), Ni(II), Cu(II) and Zn(II) with N-(2-hydroxybenzyl)-L-histidine (H(2)hb-L-his) and typical N,N donor ligands: Crystal structure of [Ni(hb-L-his)(bipyridine)]center dot H2O complex

Equilibrium study on complex formation of Co(II), Ni(II), Cu(II) and Zn(II), hereafter M(II), with the quadridentate (O-, N, O-, N) donor ligand, N-(2-hydroxybenzyl)-L-histidine (H(2)hb-L-his, hereafter H2L), in the absence and in the presence of typical (N, N) donor bidentate ligands, 1,10 phenanthroline(phen), 2, 2'-bipyridine(bipy), ethylenediamine(en), hereafter B, in aqueous solution at 25 +/- 1 degrees C was done at a fixed ionic strength, I = 0.1 mol dm(-3) (NaNO3) by combined pH-metric, UV-Vis and EPR measurements provide evidence for the formation of mononuclear and dinuclear binary and mixed ligand complexes of the types: M(L), M(L)(2)(2-), M-2(L)(2+), M-2(H-1L)(+), M(L)(B), (B)M(H-1L)M(B)(+). The imidazole moiety of the ligand is found to act as a bridging bidentate ligand in the dinuclear M-2(L)(2+), M-2(H-1L)(+) and (B)M(H-1L)M(B)(+) complexes, using its N-3 atom and N1-H deprotonated moiety. Stability constants of the complexes provide evidence of discrimination of Cu(II) from the other M(II) ions by this ligand. Solid complexes: [Ni(L)(H2O)(2)] (1), [Cu(L)(H2O)] (2), and [Ni(L)(bipy)] (.) H2O (3) have been isolated and characterized by various physicochemical studies. Single crystal X-ray diffraction of the ternary complex, 3, shows an octahedral [(O-,N,N,O-)(N,N)] geometry with extensive pi-pi stacking of the aromatic rings and H-bonding with imidazole (N1-H), secondary amino N-atom, the lattice H2O molecule, and the carboxylate and phenolate O-atoms. (c) 2006 Elsevier B.V. All rights reserved.

Construction of coordination polymers of cadmium(II) with mixed hexamethylenetetramine and terephthalate or thiocyanate ligands

Three new polymeric complexes [Cd(hmt)(SCN)(2)(H2O)(2)](n) (1), [Cd-3(mu(2)-hmt)(2)(SCN)(6)(H2O)(2)](n) (2), and [Cd-2(hmt)(2)(tP)(2)(H2O)(6)](n) (3) [hmt = hexamethylenetetramine, tp = terephthalate] have been synthesized and characterized by single crystal X-ray diffraction. Both the compounds 1 and 2 are 1-D polymers where Cd units are linked by double end-to-end thiocyanate bridges but in 2 the chain is wider containing three cadmium atoms instead of one as found in 1. In both compounds the coordination environment around cadmium atom is distorted octahedral. Compound 3 is a three-dimensional polymer having water-filled microporous channels. Both tp and brut are mu(2)-bridged. One of the acid groups of tp is coordinated in chelating bidentate and the other in monodentate fashion. Half of its Cd atoms are hexa-coordinated and the rest are hepta-coordinated. Thermogravimetric analysis and X-ray diffraction study of 3 show that its framework remains intact upon removal of water molecules. The flexibility of coordination number around cadmium atoms (six or seven) probably plays an important role in establishing the rigidity of the framework. (C) 2003 Elsevier Ltd. All rights reserved.

Dinuclear complexes of M-II thiocyanate (M = Ni and Cu) containing a tridentate Schiff-base ligand: synthesis, structural diversity and magnetic properties

A dinuclear Ni-II complex, [Ni-2(L)(2)(H2O)(NCS)(2)]center dot 3H(2)O (1) in which the metal atoms are bridged by one water molecule and two mu(2)-phenolate ions, and a thiocyanato-bridged dimeric Cull complex, [Cu(L)NCS](2) (2) [L = tridentate Schiff-base ligand, N-(3-aminopropyl)salicylaldimine, derived from 1:1 condensation of salicylaldehyde and 1,3-diaminopropane], have been synthesized and characterized by IR and UV/Vis spectroscopy, cyclic voltammetry and single-crystal X-ray diffraction studies. The structure of 1 consists of dinuclear units with crystallographic C-2 symmetry in which each Ni-II atom is in a distorted octahedral environment. The Ni-O distance and the Ni-O-Ni angle, through the bridged water molecule, are 2.240(11) angstrom and 82.5(5)degrees, respectively. The structure of 2 consists of dinuclear units bridged asymmetrically by di-mu(1,3)-NCS ions; each Cull ion is in a square-pyramidal environment with tau = 0.25. Variable-temperature magnetic susceptibility studies indicate the presence of dominant ferromagnetic exchange coupling in complex 1 with J = 3.1 cm(-1), whereas complex 2 exhibits weak antiferromagnetic coupling between the Cu-II centers with J = -1.7 cm(-1). ((c) Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005)

Investigation of the prototype silylene reaction, SiH2+H2O(and D2O): time-resolved gas-phase kinetic studies, isotope effects, RRKM calculations, and quantum chemical calculations of the reaction energy surface

Time-resolved kinetic studies of the reaction of silylene, SiH2, with H2O and with D2O have been carried out in the gas phase at 296 and at 339 K, using laser flash photolysis to generate and monitor SiH2. The reaction was studied over the pressure range 10-200 Torr with SF6 as bath gas. The second-order rate constants obtained were pressure dependent, indicating that the reaction is a third-body assisted association process. Rate constants at 339 K were about half those at 296 K. Isotope effects, k(H)/k(D), were small averaging 1.076 0.080, suggesting no involvement of H- (or D-) atom transfer in the rate determining step. RRKM modeling was undertaken based on a transition state appropriate to formation of the expected zwitterionic donoracceptor complex, H2Si...OH2. Because the reaction is close to the low pressure (third order) region, it is difficult to be definitive about the activated complex structure. Various structures were tried, both with and without the incorporation of rotational modes, leading to values for the high-pressure limiting (i.e., true secondorder) rate constant in the range 9.5 x 10(-11) to 5 x 10(-10) cm(3) molecule' s(-1). The RRKM modeling and mechanistic interpretation is supported by ab initio quantum calculations carried out at the G2 and G3 levels. The results are compared and contrasted with the previous studies.

Synthesis, crystal structure and hydrolysis of a dinuclear copper(II) complex constructed by N2O donor Schiff base and 4,4 '-bipyridine: discrete supra-molecular ensembles vs. oligomers

The tridentate Schiff base ligand, 7-amino-4-methyl-5-aza-3-hepten-2-one (HAMAH), prepared by the mono-condensation of 1,2diaminoethane and acetylacetone, reacts with Cu(BF4)(2) center dot 6H(2)O to produce initially a dinuclear Cu(II) complex, [{Cu(AMAH)}(2) (mu-4,4'-bipyJ](BF4)(2) (1) which undergoes hydrolysis in the reaction mixture and finally produces a linear polymeric chain compound, [Cu(acac)(2)(mu-4,4'-bipy)](n) (2). The geometry around the copper atom in compound 1 is distorted square planar while that in compound 2 is essentially an elongated octahedron. On the other hand, the ligand HAMAH reacts with Cu(ClO4)(2) center dot 6H(2)O to yield a polymeric zigzag chain, [{Cu(acac)(CH3OH)(mu-4,4'-bipy)}(ClO4)](n) (3). The geometry of the copper atom in 3 is square pyramidal with the two bipyridine molecules in the cis equatorial positions. All three complexes have been characterized by elemental analysis, IR and UV-Vis spectroscopy and single crystal X-ray diffraction studies. A probable explanation for the different size and shape of the reported polynuclear complexes formed by copper(II) and 4,4'-bipyridine has been put forward by taking into account the denticity and crystal field strength of the blocking ligand as well as the Jahn-Teller effect in copper(II). (c) 2007 Elsevier Ltd. All rights reserved.

Anion-pi, Lone-Pair-pi, pi-pi and Hydrogen-Bonding Interactions in a Cu-II Complex of 2-Picolinate and Protonated 4,4 '-Bipyridine: Crystal Structure and Theoretical Studies

A Cu-II complex of protonated 4,4'-bipyridine (Hbyp) and 2-picolinate (pic), [Cu-2(pic)(3)(Hbyp)(H2O)(ClO4)(2)], has been synthesised and characterised by single-crystal X-ray analysis. The structure consists of two copper atoms that have different environments, bridged by a carboxylate group. The equatorial plane is formed by the two bidentate picolinate groups in one Cu-II, and one picolinate, one monodentate 4,4'-bipyridyl ligand and a water molecule in the other. Each copper atom is also weakly bonded to a perchlorate anion in an axial position. One of the coordinated perchlorate groups displays anion-pi interaction with the coordinated pyridine ring. The noncoordinated carboxylate oxygen is involved in lone-pair (l.p.)-pi interaction with the protonated pyridine ring. In addition there are pi-pi and H-bonding interactions in the structure. Bader's theory of "atoms in molecules" (AIM) is used to characterise the anion-pi and l.p.-pi interactions observed in the solid state. A high-level ab initio study (RI-MP2/aug-cc-pVTZ level of theory) has been performed to analyse the anion-pi binding affinity of the pyridine ring when it is coordinated to a transition metal and also when the other pyridine ring of the 4,4'-bipyridine moiety is protonated. Theoretical investigations support the experimental findings of an intricate network of intermolecular interactions, which is characterised in the studied complex, and also indicate that protonation as well as coordination to the transition metal have important roles in influencing the pi-binding properties of the aromatic ring. ((C) Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009)

Copper(II) complexes of mono-anionic glutamate: anionic influence in the variations of molecular and supramolecular structures

Three new polynuclear copper(II) complexes of singly deprotonated L-glutamic acid (L-glu), {[Cu(bipy)(2)][Cu(bipy)(L-glu)H2O](2)(BF4)(4)center dot(H2O)(3)}(n) (1), {[Cu(bipy)(L-glu)H2O][Cu(bipy)(L-glu)(ClO4)]( ClO4)center dot(H2O)(2)}(n) ((2)) and [Cu(phen)(L-glu)H2O](2)(NO3)(2)center dot(H2O)(4) (3) (bipy = 2,2-bipyridine, phen = 1,10-phenanthroline), were synthesized in acidic pH (ca. 2.5) and characterized structurally. In all the complexes, L-glutamic acid acts as a bidentate chelating ligand, leaving the protonated carboxylic acid free. Both in 1 and 2, two different types of species [Cu(bipy)(2)](BF4)(2) and [Cu(bipy)(L-glu)H2O] BF4 for 1 and [Cu(bipy)(L-glu)H2O]ClO4 and [Cu(bipy)(L-glu)(ClO4)] for 2 coexist in the solid state. In complex 1, the [C( bipy)(L-glu)H2O]+ units are joined together by syn-anti carboxylate bridges to form an enantiopure (M) helical chain and the [Cu(bipy)(2)](2+) presents a very rare example of the four-coordinate distorted tetrahedral geometry of Cu(II). In complex 2, the [Cu(bipy)(L gluClO(4))] units are joined together by weakly coordinating perchlorate ions to form a 1D polymeric chain while the [Cu(bipy)(L-glu)H2O]+ units remain as mononuclear species. The different coordinating ability of the two counter anions along with their involvement in the H-bonding network seems likely to be responsible for the difference in the final polymeric structures in the two compounds. Variable-temperature (2-300 K) magnetic susceptibility measurements show negligible coupling for both the complexes. The structure of 3 consists of two independent monomeric [Cu(phen)(L-glu)H2O]+ cations, two nitrate anions and four water molecules. The copper atom occupies a five-coordinate square pyramidal environment with a water molecule in the axial position.

Synthesis, characterization, and anion selectivity of copper(II) complexes with a tetradentate Schiff base ligand

A new mononuclear Cu(II) complex, [CuL(ClO4)(2)] (1) has been derived from symmetrical tetradentate di-Schiff base, N,N'-bis-(1-pyridin-2-yl-ethylidene)-propane-1,3-diamine (L) and characterized by X-ray crystallography. The copper atom assumes a tetragonally distorted octahedral geometry with two perchlorate oxygens coordinated very weakly in the axial positions. Reactions of I with sodium azide, ammonium thiocyanate or sodium nitrite solution yielded compounds [CuL(N-3)]ClO4 (2), [CuL(SCN)ClO4 (3) or [CuL(NO2)]-ClO4 (4), respectively, all of which have been characterized by X-ray analysis. The geometries of the penta-coordinated copper(H) in complexes 2-4 are intermediate between square pyramid and trigonal bipyramid (tbp) having the Addition parameters (tau) 0.47, 0.45 and 0.58, respectively. In complex 4, the nitrite ion is coordinated as a chelating ligand and essentially both the 0 atoms of the nitrite occupy one axial site. Complex 1 shows distinct preference for the anion in the order SCN- > N-3(-) > NO2- in forming the complexes 24 when treated with a SCN-/N-3(-)/NO2- mixture. Electrochemical electron transfer study reveals (CuCuI)-Cu-II reduction in acetonitrile solution. (c) 2006 Elsevier B.V.. All rights reserved.

Potassium nickel(II) gallium phosphate hydrate, K[NiGa2(PO4)(3)(H2O)(2)]

The title compound, potassium nickel(II) digallium tris-( phosphate) dihydrate, K[NiGa2(PO4)(3)(H2O)(2)], was synthesized hydrothermally. The structure is constructed from distorted trans-NiO4(H2O)2 octahedra linked through vertices and edges to GaO5 trigonal bipyramids and PO4 tetrahedra, forming a three-dimensional framework of formula [NiGa2(PO4)(3)(H2O)(2)](-). The K, Ni and one P atom lie on special positions (Wyckoff position 4e, site symmetry 2). There are two sets of channels within the framework, one running parallel to the [10 (1) over bar] direction and the other parallel to [001]. These intersect, forming a three-dimensional pore network in which the water molecules coordinated to the Ni atoms and the K+ ions required to charge balance the framework reside. The K+ ions lie in a highly distorted environment surrounded by ten O atoms, six of which are closer than 3.1 angstrom. The coordinated water molecules are within hydrogen-bonding distance to O atoms of bridging Ga-O-P groups.

Protonation of phenylboronic acid: comparison of G3B3 and G2MP2 methods

G3B3 and G2MP2 calculations using Gaussian 03 have been carried out to investigate the protonation preferences for phenylboronic acid. All nine heavy atoms have been protonated in turn. With both methodologies, the two lowest protonation energies are obtained with the proton located either at the ipso carbon atom or at a hydroxyl oxygen atom. Within the G3B3 formalism, the lowest-energy configuration by 4.3 kcal . mol(-1) is found when the proton is located at the ipso carbon, rather than at the electronegative oxygen atom. In the resulting structure, the phenyl ring has lost a significant amount of aromaticity. By contrast, calculations with G2MP2 show that protonation at the hydroxyl oxygen atom is favored by 7.7 kcal . mol(-1). Calculations using the polarizable continuum model (PCM) solvent method also give preference to protonation at the oxygen atom when water is used as the solvent. The preference for protonation at the ipso carbon found by the more accurate G3B3 method is unexpected and its implications in Suzuki coupling are discussed. (C) 2006 Wiley Periodicals, Inc.

Effect of H-bonding on the ambivalence of SCN- towards copper(II)

Condensations of 2-(2-aminoethyl)pyridine with 4-methylimidazole-5-carboxaldehyde and 1-methyl-2-imidazolecarboxaldehyde generate the tridentate N donor ligands L and L' respectively. Reactions of Cu(NCS)(2) with L and L' yield respectively CuL(SCN)(NCS) (1) containing a CuN4S core and CuL'(NCS)(2) (2) having a CuN5 core. Both the cores are square pyramidal with SCN bound in 1 at the axial position through the S end. This differential behaviour of SCN in the two complexes despite the ligands being very similar, is investigated by DFT calculations at the B3LYP/TZV level. It is found that DFT calculations predict isolation of the Cu(ligand)(NCS)(2) species for both the ligands L and L'. Presence of an offsetting intermolecular H-bonding between the N atom of the thiocyanate and the N-H proton of the ligand L of an adjacent molecule makes the binding of SCN via the S end feasible in 1 resulting in the H-bonded-dimer Cu2L2(SCN)(2)(NCS)(2). The strength of the H-bond is estimated as 27.1 kJ mol (1) from the DFT calculations. The question of such H-bonding does not arise with L' as it lacks in a similar H atom. Dimeric 1 represents a case of two non-interacting spins. (C) 2008 Elsevier B. V. All rights reserved.

Solid state annular tautomerism in a molecule containing two imidazole moieties

The X-ray crystal structure of the 1:2 condensate (1) of hydrazine hydrate and 4-methyl-imidazole-5-carboxaldehyde has been determined. The molecule is centrosymmetric crystallising in the space group Fddd with cell dimensions: a = 10.557(14), b = 17.062(22), c = 24.759(27) angstrom. Fourier map shows that the NH hydrogen atom of each imidazole moiety has equal possibility of occupying any of its two ring N atoms. This poses the possibility of finding three tautomers in 1 in the solid state. Consideration of the H-bonding pattern observed in 1 and related B3LYP/6-311+G(2d, p) calculations show that only two tautomers are present in the solid state. The situation is compared with that in the structure of 4(5)-nitro-5(4)-methoxy-imidazole reported previously by Kubicki.

Use of HNO3 as the source of NO to prepare a nitric oxide complex of ruthenium

Reaction of cis-Ru(bisox)(2)Cl-2, where bisox is 4,4,4',4'-tetramethyl-2,2'-bisoxazoline, with HNO3 in 1 : 4 molar proportion in boiling water under N-2 atmosphere and subsequent addition of an excess of NaClO4 center dot H2O yields [Ru(bisox)(HL)(NO)](ClO4)(NO3) (1). HL is a hydrolysed form of bisox where one of the oxazoline rings opens up. X-Ray crystallography shows that 1 contains an octahedral RuN5O core. HL binds the metal through an imino N, an amide N and an alcoholic O atom. Reaction of cis-Ru(bisox)(2)Cl-2 with an excess of NaNO2 in water gives cis-Ru(bisox)(2)(NO2)(2) (2). On acidification by HClO4 in methanol, 2 is smoothly converted to cis-[Ru(bisox)(2)(NO2)(NO)](ClO4)(2) (3) due to equilibrium (1).