Molecular chains in the structure of a Zinc(Ii) Complex with Pyrazine-2,6-Dicarboxylate and Water Ligands

Crystals of catena-[diaqua-(μ-pyrazine-2,6-dicarboxylato-N,O,O′-μ-N′)]zinc(II) contain molecular chains in which the Zn(II) ions are bridged by pyrazine-2,6-dicarboxylate ligands via two symmetry-related oxygen atoms, each donated by a different carboxylic group [Zn–O(1) and O(1) ^I : 2.182(2)?Å] and the hetero-ring nitrogen atom [Zn–N(1): 2.049(3)?Å] situated between them on one side and the second hetero-ring nitrogen atom [Zn–N(2) ^II 2.118(3)?Å] from the adjacent ligand on the other. The Zn(II) ion and four coordinating atoms are coplanar. Two symmetry related water molecules [Zn–O3 and O: 2.116(2)?Å] situated above and below this plane complete the coordination around the Zn(II) ion to six atoms forming a distorted octahedron.     

K2[HCr2AsO10]: redetermination of phase II and the predicted structure of phase I

Our prediction that phase II of dipotassium hydrogen chromatoarsenate, K₂[HCr₂AsO₁₀], is ferroelectric, based on the analysis of the atomic coordinates by Averbuch‐Pouchot, Durif & Guitel [Acta Cryst. (1978), B 34 , 3725–3727], led to an independent redetermination of the structure using two separate crystals. The resulting improved accuracy allows the inference that the H atom is located in the hydrogen bonds of length 2.555 (5) Å which form between the terminal O atoms of shared AsO₃OH tetrahedra in adjacent HCr₂AsO₁₀²⁻ ions. The largest atomic displacement of 0.586 Å between phase II and the predicted paraelectric phase I is by these two O atoms. The H atoms form helices of radius ∼0.60 Å about the 3₁ or 3₂ axes. Normal probability analysis reveals systematic error in seven or more of the earlier atomic coordinates.     

Rapid approximation to molecular surface area via the use of Boolean logic and look-up tables

We report the development of a new approximate method of calculating molecular surface areas. Our technique is based upon the method of Sharake and Rupley but incorporates several major advances. First, we represent the state of surface points as bits in a bit string so we can utilize Boolean operations to simultaneously turn off multiple test points in one Boolean AND operation. Second, we use a series of Boolean mask look-up tables to reduce the time complexity of the calculation of molecular surface area down to the same magnitude as doing a potential energy evaluation. When we use a 256 surface point sphere for all of the atoms in BPTI, a 454 nonhydrogen atom protein, and a 1.4-Å solvent probe, we in general underestimate the total solvent-accessible surface area (SASA) by approximately 1.25% with a correlation coefficient of 0.9990 over a wide range of conformations. The average CPU time required to calculate the SASA of a BPTI conformer is 0.58 s on an SGI 4D/220 workstation. We also describe a method by which we can calculate an approximate finite difference SASA gradient for BPTI in 0.79 of CPU time. © 1993 John Wiley & Sons, Inc.     

Crystal structures of two Ca(II) complexes with imidazole-4,5-dicarboxylate and water ligands

The structure of compound I: poly-diaqua(μ-imidazole-4,5-dicarboxylato-N,O; -O′; -O′′, -O′′′) calcium(II) monohydrate [Ca(C₅H₂N₂O₄)(H₂O)₂·H₂O] is built of molecular sheets in which imidazole-4,5-dicarboxylate ligands bridge the metal ions using both carboxylate groups, each bidentate. Ca(II) is coordinated by six oxygen atoms and one hetero-ring nitrogen atom distributed at the apices of a capped tetragonal bipyramid. The basal plane of the pyramid is formed by two carboxylate oxygen atoms [d(Ca–O2?=?2.374(1)?Å, d(Ca–O4)?=?2.412(1)?Å] and two water oxygen atoms [d(Ca–O5)?=?2.384(1)?Å, d(Ca–O6)?=?2.455(1)?Å], the capped position is occupied by the carboxylate oxygen atom O3 [d(Ca–O3)?=?2.325(1)?Å], the hetero-ring nitrogen atom [d(Ca–N2)?=?2.523(1)?Å] and the carboxylate oxygen atom O4 [d(Ca–O2)?= 2.412(1)?Å] form the apices of the prism. The solvation water molecule plays a significant role in a framework of hydrogen bonds responsible for the stability of the crystal. The structure of compound II: trans-tetraquadi(H-imidazole-4,5-dicarboxylato-N,O) calcium(II) monohydrate, [Ca(C₅H₃N₂O₄)₂(H₂O)₄·H₂O] consists of monomers in which the Ca(II) ion is located on a centre of symmetry. The coordination around the Ca(II) is a strongly deformed pentagonal bipyramidal with the imidazole-4,5-dicarboxylate (4,5-IDA) ligands in the trans arrangement forming a dihedral angle of 68.3°. An imidazole-ring nitrogen atom [d(Ca–N)?=?2.632(2)?Å] and one carboxylate O atom [d(Ca–O)?=?2.531(2)?Å] from each ligand coordinate to the metal ion. The coordination is completed by four water oxygen atoms [d(Ca–O)?=?2.393(2)?Å] and [d(Ca–O)?=?2.367(2)?Å]. The coordinated water molecules act as hydrogen bond donors and acceptors to the unbonded carboxylate oxygen atoms in adjacent monomers giving rise to a three-dimensional molecular network.     

Efficient approximate all-atom solvent accessible surface area method parameterized for folded and denatured protein conformations

Continuing advances in computer hardware and software are permitting atomic-resolution molecular simulations for longer time scales and on larger systems. Despite these advances, routinely performing atomistic simulations with explicit water for even small proteins, which reach the folding time of such proteins, remains intractable for the foreseeable future. An implicit approximation of the solvent environment using a solvent accessible surface area (SASA) term in a molecular mechanics potential function allows exclusion of the explicit water molecules in protein simulations. This reduces the number of particles by approximately an order of magnitude. We present a fast and acceptably accurate approximate all-atom SASA method parameterized using a set of folded and heat-denatured conformations of globular proteins. The parameters are shown to be transferable to folded and heat-denatured conformations for another set of proteins. Calculation of the approximate SASA and the associated derivatives with respect to atomic positions for a 4644 atom protein requires only 1/11th the CPU time required for calculation of the nonbonded interactions for this system. On a per atom basis, this algorithm is three times faster than the fastest previously published approximate SASA method and achieves the same level of accuracy.     

Geometrical,spectroscopic, and magnetic properties of an oxygen atom adsorbed on the Ni(100) surface

Spin-polarized linear combinations of Gaussian-type orbital–model core potential–local spin density (LCGTO –MCP –LSD ) computations have been performed for oxygen chemisorption on a Ni(100) surface simulated by four different clusters. Results show that the oxygen atom chemisorbs preferentially on the fourfold hollow site with an equilibrium distance of 1.931 Å and a vertical vibrational frequency of 401 cm^?1. The corresponding experimental values are 1.960 Å and 423 or 430 cm^?1. A satisfactory agreement with experiment is also found for the adsorption energy (6.7 vs. 5.6 eV). The bridge position lies at only 0.4 eV above the fourfold hollow one. It is found that oxygen adsorption leaves the bare cluster total spin magnetic moment unchanged, but induces appreciable reductions of the local atomic moment on the surface nickel atoms. © 1993 John Wiley & Sons, Inc.     

The crystal structure of Thorium(IV)tetrakis(trifluoroacetylacetonate)

The crystal structure of the compound thorium(IV)tetrakis(trifluoro-acetylacetonate) was determined by means of a threedimensional X-ray analysis. The space group is C2/c and the cell dimensions are a = 25,05 Å, b = 6.43 Å, c = 21.3 Å, β = 125.4°, with Z = 4. The thorium atom is coordinated by 8 oxygen atoms in the form of an 1111 (D₄–422) antiprism. The mean of the Th–O distances is 2.39 Å with a standard deviation ± 0.04 Å. The trifluoroacetylacetonate rings are approximately planar, except for the CH₃ and CF₃ groups which show significant deviations. The Th–O bonds form angles of approximately 72° and 50° with the theoretical 8 -axis of the antiprism. The structure is stabilized by VAN DER WAALS contacts between neighbouring molecules. The refinement of the atomic positions, the anisotropic temperature parameter of thorium and isotropic temperature parameters of all the other atoms by the least squares method, has given a reliability index of 0.148.     

Synthese und Eigenschaften von cis-Diacidophthalocyaninato(2–)thallaten(III); Kristallstruktur von Tetra(n-butyl)ammonium-cisdinitrito(O,O′)- und -cis-dichlorophthalocyaninato(2–)thallat(III)

Syntheses and Properties of cis -Diacidophthalocyaninato(2–)thallates(III); Crystal Structure of Tetra(n-butyl)ammonium cis -dinitrito(O,O ′)- and cis -dichlorophthalocyaninato(2–)thallate(III) Blue green cis-diacidophthalocyaninato(2–)thallate(III), ^cis[Tl(X)₂pc^2–]^– (X = Cl, ONO′, NCO) is prepared from iodophthalocyaninato(2–)thallium(III) and the corresponding tetra(n-butyl)ammonium salt, (ⁿBu₄N)X in dichloromethane, and isolated as (ⁿBu₄N)^cis[Tl(X)₂pc^2–]. (ⁿBu₄N)^cis[Tl(ONO′)₂pc^2–] ( 1 ) and (ⁿBu₄N)^cis[Tl(X)₂pc^2–] · 0,5 (C₂H₅)₂O ( 2 ) crystallize in the monoclinic space group P2₁/n with cell parameters for 1: a = 14.496(2) Å, b = 17.293(5) Å, c = 18.293(2) Å, β = 98.76(1)° resp. for 2 : a = 13.146(1) Å, b = 14.204(5) Å, c = 24.900(3) Å, β = 93.88(1)°; Z = 4. In 1 , the octa-coordinated Tl atom is surrounded by four isoindole-N atoms (N_iso) and four O atoms of the bidental nitrito(O,O′) ligands in a distorted antiprism. The Tl–N_iso distances vary between 2.257(3) and 2.312(3) Å, the Tl–O distances between 2.408(3) and 2.562(3) Å. In 2 , the hexa-coordinated Tl atom ligates four N_iso atoms and two Cl atoms in a typical cis-arrangement. The average Tl–N_iso distance is 2.276 Å, the average Tl–Cl distance is 2.550 Å. In 1 and 2 , the Tl atom is directed out of the centre of the (N_iso)₄ plane (Ct_N) towards the acido ligands (d(Tl–Ct_N) = 1.144(1) Å in 1 , 1.116(2) Å in 2 ), and the phthalocyaninato ligand is concavely distorted. The vertical displacements of the periphereal C atoms amounts up to 0.82 Å. The optical and vibrational spectra as well as the electrochemical properties are discussed.     

2,6‐Bis[bis(2‐pyridiniomethyl)aminomethyl]‐4‐tert‐butylphenol dichloride diperchlorate hydrate

The title compound, C₃₆H₄₄N₆O⁴⁺·2Cl^?·2ClO₄^?·0.132H₂O, is shown to be protonated at all the pyridine N atoms; the two chloride ions are hydrogen bonded to three pyridine N atoms and to the phenolic O atom of the same cation [Cl?N = 3.045 (2)–3.131 (2) Å and Cl?O = 2.938 (2) Å], and the remaining pyridine N atom is hydrogen bonded to the phenolic O atom [N?O = 2.861 (2) Å]. The mean value of the C—N—C angle of the protonated pyridine rings is 123.4 (1)°, which is significantly larger than that found for unprotonated pyridine rings.     

Synthesis and Crystal Structure of α‐ThTe3

The binary thorium tritelluride, α‐ThTe₃, was synthesized by solid‐state methods at 1223 K. From a single‐crystal X‐ray diffraction study the material crystallizes in the TiS₃ structure type with two formula units in space group C²_2h–P2₁/m of the monoclinic system in a cell with lattice constants a = 6.1730 (4) Å, b = 4.3625(3) Å, c = 10.4161(6) Å, and β = 97.756(3)° (at 100 K). The asymmetric unit of this compound comprises one Th atom and three Te atoms each with site symmetry m. Each Th atom is coordinated to eight Te atoms in a bicapped trigonal‐pyramidal arrangement. Th–Te distances range from 3.1708(4) Å to 3.2496(6) Å. The structure features a Te–Te interaction 2.7631(8) Å in length, which is typical for a Te–Te single bond. Thus α‐ThTe₃ may be charge balanced and formulated as Th⁴⁺Te^2–Te₂^2–.     

VESPA: A new,fast approach to electrostatic potential-derived atomic charges from semiempirical methods

An improved semiempirical method for computing electrostatic potential-derived atomic charges is described. It includes a very fast algorithm for the generation of the grid points around the molecule and the calculation of the electrostatic potential at these points. The dependency of the atomic point charges obtained on the number of grid points used in the fitting procedure is examined. For “buried” atoms a high density grid is necessary. It is possible to obtain 6–31G*-quality atom-centered point charges, even for phosphorus compounds, using AM1 or PM3. This approach can therefore be recommended for general use in QSAR or molecular mechanics for any organic and bioorganic system up to about 200 atoms. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 744–756, 1997     

3He NMR studies on helium–pyrrole,helium–indole,and helium–carbazole systems: a new tool for following chemistry of heterocyclic compounds

The ³He nuclear magnetic shieldings were calculated for free helium atom and He–pyrrole, He–indole, and He–carbazole complexes. Several levels of theory, including Hartree–Fock (HF), Second‐order Møller‐Plesset Perturbation Theory (MP2), and Density Functional Theory (DFT) (VSXC, M062X, APFD, BHandHLYP, and mPW1PW91), combined with polarization‐consistent pcS‐2 and aug‐pcS‐2 basis sets were employed. Gauge‐including atomic orbital (GIAO) calculated ³He nuclear magnetic shieldings reproduced accurately previously reported theoretical values for helium gas. ³He nuclear magnetic shieldings and energy changes as result of single helium atom approaching to the five‐membered ring of pyrrole, indole, and carbazole were tested. It was observed that ³He NMR parameters of single helium atom, calculated at various levels of theory (HF, MP2, and DFT) are sensitive to the presence of heteroatomic rings. The helium atom was insensitive to the studied molecules at distances above 5 Å. Our results, obtained with BHandHLYP method, predicted fairly accurately the He–pyrrole plane separation of 3.15 Å (close to 3.24 Å, calculated by MP2) and yielded a sizable ³He NMR chemical shift (about ?1.5 ppm). The changes of calculated nucleus‐independent chemical shifts (NICS) with the distance above the rings showed a very similar pattern to helium‐3 NMR chemical shift. The ring currents above the five‐membered rings were seen by helium magnetic probe to about 5 Å above the ring planes verified by the calculated NICS index. Copyright © 2014 John Wiley & Sons, Ltd.     

Iodophthalocyaninato(2–)thallium(III) – Synthese und Kristallstruktur

Iodophthalocyaninato(2–)thallium(III) – Synthesis and Crystal Structure Oxidation of dithalliumphthalocyaninate(2–) with excess iodine yields crystalline, blue-green iodophthalocyaninato(2–)thallium(III). It crystallizes in the orthorhombic space group Pnma (no. 62) with lattice parameters: a = 13.778(3) Å, b = 14.649(2) Å, c = 14.907(1) Å, Z = 4. The Tl atom coordinates four N_iso atoms (isoindole N atoms) and one I atom in a tetragonal pyramidal arrangement. The Tl atom is located out of the centre of the (N_iso)₄ plane towards the iodine atom by 0.959(3) Å. The Tl–I distance is 2.674(1) Å, the Tl–N_iso distances range from 2.20(1) to 2.23(1) Å (average 2.22(1) Å). The phthalocyaninate(2–) is severely distorted from planarity (concave distortion).     

Hexa‐μ2‐chloro‐μ4‐oxo‐tetrakis[(2‐ethyl­tetrazole‐κN4)copper(II)]

In the title molecular complex, [Cu₄Cl₆O(2‐EtTz)₄], where 2‐EtTz is 2‐ethyl­tetrazole (C₃H₆N₄), the central O atom is located on the symmetry site and is tetrahedrally coordinated to four Cu atoms, with Cu—O distances of 1.8966 (4) Å. A very slight distortion of Cu₄O from a regular tetrahedron is observed [two Cu—O—Cu angles are 108.76 (3)° and four others are 109.828 (13)°]. Each Cu atom is connected to three others via the Cl atoms, forming a slightly distorted Cl octahedron around the O atom, with O⋯Cl distances of 2.9265 (7) Å for Cl atoms lying on the twofold axis and 2.9441 (13) Å for those in general positions. The Cu atom has a distorted trigonal–bipyramidal environment, with three Cl atoms in the equatorial plane, and with the N atom of the 2‐ethyl­tetrazole ligand and the μ₄‐O atom in axial positions. The Cu atom is displaced out of the equatorial plane by ca 0.91 Å towards the coordinated N atom of the 2‐­ethyl­tetrazole ligand.     

Atomic transferability within the exchange‐correlation density

Starting from either the exchange or the exchange‐correlation density together with Bader's definition of an atom in a molecule, an atomic hole density function can be defined. Contour maps of atomic hole density functions are able to show how the electron density of each atom in a molecule is partially delocalized into the rest of atoms in the molecule. The degree of delocalization of the atomic density ultimately depends on the nature of the atom studied and its environment. Atomic hole density functions are also used to define an atomic similarity measure, which allows for the quantitative assessment of the degree of atomic transferability in different molecular environments. In this article, contour maps for the N atom in the (N₂, CN⁻, NO⁺) series and the O atom in the (CO, H₂CO, and HCOOH) series are presented at the Hartree–Fock and CISD levels of theory. Moreover, the transferability of N and O within the two series is studied by means of atomic similarity measures. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 1361–1374, 2000     

ADME evaluation in drug discovery. 2. Prediction of partition coefficient by atom-additive approach based on atom-weighted solvent accessible surface areas

A novel method for the calculations of 1-octanol/water partition coefficient (log P) of organic molecules has been presented here. The method, SLOGP v1.0, estimates the log P values by summing the contribution of atom-weighted solvent accessible surface areas (SASA) and correction factors. Altogether 100 atom/group types were used to classify atoms with different chemical environments, and two correlation factors were used to consider the intermolecular hydrophobic interactions and intramolecular hydrogen bonds. Coefficient values for 100 atom/group and two correction factors have been derived from a training set of 1850 compounds. The parametrization procedure for different kinds of atoms was performed as follows: first, the atoms in a molecule were defined to different atom/group types based on SMARTS language, and the correction factors were determined by substructure searching; then, SASA for each atom/group type was calculated and added; finally, multivariate linear regression analysis was applied to optimize the hydrophobic parameters for different atom/group types and correction factors in order to reproduce the experimental log P. The correlation based on the training set gives a model with the correlation coefficient (r) of 0.988, the standard deviation (SD) of 0.368 log units, and the absolute unsigned mean error of 0.261. Comparison of various procedures of log P calculations for the external test set of 138 organic compounds demonstrates that our method bears very good accuracy and is comparable or even better than the fragment-based approaches. Moreover, the atom-additive approach based on SASA was compared with the simple atom-additive approach based on the number of atoms. The calculated results show that the atom-additive approach based on SASA gives better predictions than the simple atom-additive one. Due to the connection between the molecular conformation and the molecular surface areas, the atom-additive model based on SASA may be a more universal model for log P estimation especially for large molecules.     

Molecular Chains in the Crystals of a Calcium(II) Complex with Pyridine-3,5-Dicarboxylate (Dinicotinate) and Water Ligands

The crystal of pentaqua (catena-pyridine-3,5-dicarboxylato-O,O) calcium(II) contain zigzag molecular chains composed of Ca ions linked by two bridging oxygen atoms, each donated by one carboxylate group [Ca-O1 2.353(2) Å, Ca-O3^III 2.334(1) Å]. The Ca ions, the ligand molecules and one water oxygen atom coordinated by each metal ion [Ca-O5 2.410(2) Å] are coplanar. The coordination of the Ca ion is completed by four other water oxygen atoms situated above and below the plane of the chain [Ca-O6 2.475(1) Å, Ca-O7 2.371(2) Å]. The coordination number of the calcium(II) ion is seven. The water molecules act as donors in a system of hydrogen bonds.     

Crystal and Molecular Structure of Bis(1-Vinylimidazole)diacetatozinc

The crystal and molecular structure of bis(1-vinylimidazole)diacetatozinc (C₁₄H₁₈N₄O₄Zn), a highly effective antidote and antihypoxic drug, was determined [R₁ 0.0335 for 8902 unique reflections with I > 2σ(I) and wR₂ 0.0931 for all 10 752 unique reflections]. The triclinic unit cell contains two independent molecules of the complex, A and B. These molecules have short contacts O?H-C. The zinc atoms in molecules A and B have distorted tetrahedral coordination with the coordination sites occupied by the imidazole nitrogen atoms and acetate oxygen atoms. The lengths of the Zn-N bonds (2.019–2.050 Å) and Zn-O bonds with three acetate groups (1.956–1.958 Å) are typical for zinc complexes, whereas the Zn-O³ bond with one of the acetate groups in molecule A is somewhat longer, 2.009(1) Å; also, there is an additional contact of the zinc atom with the carbonyl oxygen atom of this group (Zn-O⁴ 2.498 Å).     

Spectral characteristics and structures of metal complexes with 3-Hydroxy-4,6-dinitro-2-ethoxypyridine: Crystal and molecular structures of di(3-hydroxy-4,6-dinitro-2-ethoxypyridinato)diaquacopper(II)

Seven complexes of manganese(II), copper(II), cadmium, silver(I), samarium(III), and praseodymium( III) with 3-hydroxy-4,6-dinitro-2-ethoxypyridine (HL) were isolated in the crystalline state and studied by IR and UV spectroscopy. The molecular and crystal structures of di(3-hydroxy-4,6-dinitro-2-ethoxypyridinato) diaquacopper(II) [CuL₂(H₂O)₂] were determined. The coordination mode of the organic ligand L^? is bidentate chelating through the O(2) oxygen atoms of the hydroxy group and the O(1) atom of the ethoxy group. The coordination polyhedron of the copper atom is a prolate tetragonal bipyramid (4 + 2) with two O(1) atoms in the axial positions (Cu-O(1) 2.413 Å) and two O(2) atoms of the two L^?ligands and the O(7) atoms of the water molecules in the equatorial plane (Cu-O(2), 1.912 Å; Cu-O(7), 1.972 Å).     

Crystal Structure of Mixed Crystals of the Tetra(n-butyl)ammonium Salts of cis-Tetrafluorophthalocyaninato(2−)tantalate(V) and cis-Trifluorophthalocyaninato(2−)tantalate(IV)

cis-Trichlorophthalocyaninato(2?)tantalate(V) reacts with excess tetra(n-butyl)ammonium fluoride trihydrate yielding mixed crystals of the tetra(n-butyl)ammonium salts of cis-tetrafluorophthalocyaninato(2?)tantalate(V) and cis-trifluorophthalocyaninato(2?)tantalate(IV) in the ratio five to four. These crystallize in the monoclinic space group P2₁/ n with cell parameters: a = 13.368(2) Å, b = 13.787(2) Å, c = 23.069(3) Å, β = 93.35(1)°, Z = 4. Ta^v is octacoordinated with four F atoms and four N_iso atoms in an antiprismatic cis-arrangement. The Ta^v-F distance varies from 1.919(7) to 1.966(4) Å. Ta^IV is heptacoordinated with three F atoms in a cis-arrangement. The Ta^IV-F distance varies from 1.74(1) to 1.966(4) Å. The Ta atom is located out of the centre of the N₄ plane towards the F atoms by 1.234(3) Å. The Ta–N distances range from 2.261(6) to 2.310(6) Å.