Density functional finite cluster method for polarizability of large BeN three‐dimensional systems

The structures and the properties of small clusters are known to be quite different from those of the bulk material. Consequently, the focus of most studies is towards understanding the changes in electronic properties with increasing cluster size. Linear static electronic dipole polarizabilities of the Be_N (N→∞) solid are obtained at the DFT(PWB91) level by extrapolation of ab initio calculations on Be_N (N=1,…,132) clusters. For the mean polarizability, a [5s3p] basis set is shown to give accurate values if the tri‐periodic clusters are big enough. No calculation has yet been carried out on Be_N (N→∞), but it is clear that these linear properties converge relatively slowly with cluster size. For Be_N, cluster size up to N=90 atoms are sufficient to give limiting infinite solid polarizabilities with relatively small uncertainties. For N=132, the mean polarizability result is probably very accurate. These results suggest that DFT is a good method for the determination of these properties. © 2000 John Wiley & Sons, Inc. J Comput Chem 22: 230–240, 2001     

A fluorophore‐labelled copper complex: crystal structure,hybrid cyclic water–perchlorate cluster and biological properties

A fluorophore‐labelled copper(II) complex, aquabis(dimethylformamide‐κO )(perchlorato‐κO )[2‐(quinolin‐2‐yl)‐1,3‐oxazolo[4,5‐f ][1,10]phenanthroline]copper(II) perchlorate monohydrate, [Cu(ClO₄)(C₂₂H₁₂N₄O)(C₃H₇NO)₂(H₂O)]ClO₄·H₂O, has been synthesized and characterized. A cyclic hydrogen‐bonded water–perchlorate anionic cluster, i.e. [(ClO₄)₂(H₂O)₂]²⁻, has been identified within the structure. Each cyclic anionic cluster unit is interconnected by hydrogen bonding to the cation. The cations join into an infinite hydrogen‐bonded chain running in the [010] direction. Furthermore, interaction of the complex with calf‐thymus DNA (CT‐DNA) and cellular localization within the cells was explored. Spectroscopic studies indicate that the compound has a good affinity for DNA and stains the nucleus of the cells.     

Determination of Band Structure Parameters and the Quasi‐Particle Gap of CdSe Quantum Dots by Cyclic Voltammetry

Band structure parameters such as the conduction band edge, the valence band edge and the quasi‐particle gap of diffusing CdSe quantum dots (Q‐dots) of various sizes were determined using cyclic voltammetry. These parameters are strongly dependent on the size of the Q‐dots. The results obtained from voltammetric measurements are compared to spectroscopic and theoretical data. The fit obtained to the reported calculations based on the semi‐empirical pseudopotential method (SEPM)—especially in the strong size‐confinement region, is the best reported so far, according to our knowledge. For the smallest CdSe Q‐dots, the difference between the quasi‐particle gap and the optical band gap gives the electron–hole Coulombic interaction energy (J_e1,h1). Interband states seen in the photoluminescence spectra were verified with cyclic voltammetry measurements.     

The influence of peripheral ligand bulk on nitrogen activation by three‐coordinate molybdenum complexes—A theoretical study using the ONIOM method

Electronic structure methods have been combined with the ONIOM approach to carry out a comprehensive study of the effect of ligand bulk on the activation of dinitrogen with three‐coordinate molybdenum complexes. Calculations were performed with both density functional and CCSD(T) methods. Our results show that not only is there expected destabilization of the intermediate on the pathway due to direct steric interactions of the bulky groups, but also there is significant electronic destabilization as the size of the ligand increases. This latter destabilization is due to the inability of the molecule to accommodate a rotated amide group bound to the molybdenum once the amide reaches a certain size. This destabilization also leads to a clear preference for the triplet intermediate (rather than the singlet intermediate) for bulky substituents which is in agreement with experiment. Overall, the calculated reaction profile for the bulky substituents shows a good correlation with the available experimental data. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009     

Structural and spectropscopic studies of a three‐dimensional hydrogen‐bonded copper(II) complex: aqua[bis(pyridin‐2‐ylcarbonyl)amidato]cyanidocopper(II)

The preparation and X‐ray and spectroscopic studies of the title copper(II) complex, [Cu(C₁₂H₈N₃O₂)(CN)(H₂O)], are reported. The Cu^II cation is five‐coordinated, forming a distorted square‐planar pyramid with an Addison τ parameter of 0.14. The UV–vis spectrum shows a d–d transition of the Cu^II centre at 638 nm, and the electron paramagnetic resonance (EPR) spectrum confirms that the Cu^II cation has an axial symmetry coordination and that the unpaired electrons occupy the d_x2–y2 orbital. Cyclic voltammetric studies show two irreversible oxidation and reduction peaks.     

Hydrogen‐bonded two‐ and three‐dimensional polymeric structures in the ammonium salts of 3,5‐dinitrobenzoic acid, 4‐nitrobenzoic acid and 2,4‐dichlorobenzoic acid

The structures of ammonium 3,5‐dinitrobenzoate, NH₄⁺·C₇H₃N₂O₆⁻, (I), ammonium 4‐nitrobenzoate dihydrate, NH₄⁺·C₇H₄NO₄⁻·2H₂O, (II), and ammonium 2,4‐dichlorobenzoate hemihydrate, NH₄⁺·C₇H₃Cl₂O₂⁻·0.5H₂O, (III), have been determined and their hydrogen‐bonded structures are described. All three salts form hydrogen‐bonded polymeric structures, viz. three‐dimensional in (I) and two‐dimensional in (II) and (III). With (I), a primary cation–anion cyclic association is formed [graph set R₄³(10)] through N—H...O hydrogen bonds, involving a carboxylate group with both O atoms contributing to the hydrogen bonds (denoted O,O′‐carboxylate) on one side and a carboxylate group with one O atom involved in two hydrogen bonds (denoted O‐carboxylate) on the other. Structure extension involves N—H...O hydrogen bonds to both carboxylate and nitro O‐atom acceptors. With structure (II), the primary inter‐species interactions and structure extension into layers lying parallel to (001) are through conjoined cyclic hydrogen‐bonding motifs, viz.R₄³(10) (one cation, an O,O′‐carboxylate group and two water molecules) and centrosymmetric R₄²(8) (two cations and two water molecules). The structure of (III) also has conjoined R₄³(10) and centrosymmetric R₄²(8) motifs in the layered structure but these differ in that the first motif involves one cation, an O,O′‐carboxylate group, an O‐carboxylate group and one water molecule, and the second motif involves two cations and two O‐carboxylate groups. The layers lie parallel to (100). The structures of salt hydrates (II) and (III), displaying two‐dimensional layered arrays through conjoined hydrogen‐bonded nets, provide further illustration of a previously indicated trend among ammonium salts of carboxylic acids, but the anhydrous three‐dimensional structure of (I) is inconsistent with that trend.     

Reactivation pathway of the hydrogenase H‐cluster: Density functional theory study

This work puts forth a reaction pathway for the reactivation of exogenous ligand inhibited H‐cluster, the active site of Fe‐only hydrogenases. The H‐cluster is a dimetal complex, Fe–Fe, with the metal centers bridged by di(thiomethyl)amine. Exogenous ligands, H₂O, and OH^?, are bound to the distal iron (Fe_d). Density functional theory (DFT) calculations on the native and ruthenium‐modified H‐cluster have been performed using the B3LYP functional with 6‐31+G** and 6‐311+G** basis sets. We have ascertained that there is a thermodynamically favorable pathway for the reactivation of the OH^? inhibited H‐cluster, which proceeds by an initial protonation of the Fe_d–OH^? complex. The proposed reaction pathway has all its intermediate reactions ensue exothermically. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Model reaction for the synthesis of polyhydroxyurethanes from cyclic carbonates with amines: Substituent effect on the reactivity and selectivity of ring‐opening direction in the reaction of five‐membered cyclic carbonates with amine

This article focuses on the substituent effect on the reactivity and selectivity of the ring‐opening direction in the reaction of five‐membered cyclic carbonates with n‐hexylamine. The reactivity of the cyclic carbonate and the formation selectivity of the adduct with a secondary hydroxyl group increased as a stronger electron‐withdrawing group was introduced at the α‐methylene of the cyclic carbonate. These results are discussed on the basis of the stability of intermediates, primary and secondary alcoholate anions, Mulliken charges on carbonyl carbon, and the bond lengths and orders of the O? C?O single bond. © 2001 John Wiley & Sons, Inc. J Polym Sci Part A: Polym Chem 39: 3678–3685, 2001     

2,3‐bis(5‐Hexylthiophen‐2‐yl)‐6,7‐bis(octyloxy)‐5,8‐di(thiophen‐2‐yl) quinoxaline: A good construction block with adjustable role in the donor‐π‐acceptor system for bulk‐heterojunction solar cells

Three 2,3‐bis(5‐hexylthiophen‐2‐yl)‐6,7‐bis(octyloxy)‐5,8‐di(thiophen‐2‐yl)‐quinoxaline ( BTTQ )‐based conjugated polymers, namely, PF‐BTTQ ( P1 ), PP‐BTTQ ( P2 ), and PDCP‐BTTQ ( P3 ), were successfully synthesized for efficient polymer solar cells (PSCs) with electron‐rich units of fluorene and dialkoxybenzene and electron‐deficient unit dicyanobenzene, respectively. All the polymers exhibited good solubility in common organic solvents and good thermal stability. Their deep‐lying HOMO energy levels enabled them good stability in the air and the relatively low HOMO energy level assured a higher open circuit potential when used in PSCs. Bulk‐heterojunction solar cells were fabricated using these copolymers blended with a fullerene derivative as an acceptor. All of them exhibited promising performance, and the best device performance with power conversion efficiency up to 3.30% was achieved under one sun of AM 1.5 solar simulator illumination (100 mW/cm²). © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012     

A fast polygon inflation algorithm to compute the area of feasible solutions for three‐component systems. I: concepts and applications

The multicomponent factorization of multivariate data often results in nonunique solutions. The so‐called rotational ambiguity paraphrases the existence of multiple solutions that can be represented by the area of feasible solutions (AFS). The AFS is a bounded set that may consist of isolated subsets. The numerical computation of the AFS is well understood for two‐component systems and is an expensive numerical process for three‐component systems. In this paper, a new fast and accurate algorithm is suggested that is based on the inflation of polygons. Starting with an initial triangle located in a topologically connected subset of the AFS, an automatic extrusion algorithm is used to form a sequence of growing polygons that approximate the AFS from the interior. The polygon inflation algorithm can be generalized to systems with more than three components. The efficiency of this algorithm is demonstrated for a model problem including noise and a multicomponent chemical reaction system. Further, the method is compared with the recent triangle‐boundary‐enclosing scheme of Golshan, Abdollahi, and Maeder (Anal. Chem. 2011, 83, 836–841). Copyright © 2013 John Wiley & Sons, Ltd.     

OBGMX: A web‐based generator of GROMACS topologies for molecular and periodic systems using the universal force field

OBGMX is a web service providing topologies for the GROMACS molecular dynamics software package according to the Universal Force Field, as implemented in the Open Babel package. OBGMX can deal with molecular and periodic systems. The geometrical parameters appearing in the potential energy functions for the bonded interactions can be set to those measured in the input configuration. The performance of OBGMX in reproducing the structure of periodic systems is analyzed by calculating the root mean‐squared displacements of optimized configurations of a large set of metal–organic frameworks. OBGMX is available at http://software‐lisc.fbk.eu/obgmx/ . © 2012 Wiley Periodicals, Inc.     

Purine 3′:5′‐cyclic nucleotides with the nucleobase in a syn orientation: cAMP,cGMP and cIMP

Purine 3′:5′‐cyclic nucleotides are very well known for their role as the secondary messengers in hormone action and cellular signal transduction. Nonetheless, their solid‐state conformational details still require investigation. Five crystals containing purine 3′:5′‐cyclic nucleotides have been obtained and structurally characterized, namely adenosine 3′:5′‐cyclic phosphate dihydrate, C₁₀H₁₂N₅O₆P·2H₂O or cAMP·2H₂O, (I), adenosine 3′:5′‐cyclic phosphate 0.3‐hydrate, C₁₀H₁₂N₅O₆P·0.3H₂O or cAMP·0.3H₂O, (II), guanosine 3′:5′‐cyclic phosphate pentahydrate, C₁₀H₁₂N₅O₇P·5H₂O or cGMP·5H₂O, (III), sodium guanosine 3′:5′‐cyclic phosphate tetrahydrate, Na⁺·C₁₀H₁₁N₅O₇P⁻·4H₂O or Na(cGMP)·4H₂O, (IV), and sodium inosine 3′:5′‐cyclic phosphate tetrahydrate, Na⁺·C₁₀H₁₀N₄O₇P⁻·4H₂O or Na(cIMP)·4H₂O, (V). Most of the cyclic nucleotide zwitterions/anions [two from four cAMP present in total in (I) and (II), cGMP in (III), cGMP⁻ in (IV) and cIMP⁻ in (V)] are syn conformers about the N‐glycosidic bond, and this nucleobase arrangement is accompanied by C_rib—H…N_pur hydrogen bonds (rib = ribose and pur = purine). The base orientation is tuned by the ribose pucker. An analysis of data obtained from the Cambridge Structural Database made in the context of syn–anti conformational preferences has revealed that among the syn conformers of various purine nucleotides, cyclic nucleotides and dinucleotides predominate significantly. The interactions stabilizing the syn conformation have been indicated. The inter‐nucleotide contacts in (I)–(V) have been systematized in terms of the chemical groups involved. All five structures display three‐dimensional hydrogen‐bonded networks.     

Simplified Box Orbitals (SBO) for H To Ar atoms: Exact expressions,SBO‐3G approximations,and relations with the ZDO approximation

Simplified Box Orbitals (SBO) are a kind of spatially restricted basis functions. SBOs have a similar use and value to Slater functions but, because they fulfill a version of the zero‐differential overlap approximation, they allow for a drastic reduction in the number of two‐electron integrals to be calculated when dealing with huge systems, and they seem to be specially adapted to study confined systems such as molecules in solution. In a previous study, the mathematical shape of SBOs was discussed and the necessary parameters were obtained by means of the variational method. In the present study, the parameters of each SBO were obtained by applying the condition that it is as similar as possible to the STO that would be used in a basis set without spatial restrictions. We have developed a method to achieve this likeness and deduced simple formulas to describe all the SBOs of any atom. We also present the SBO‐3G expansions of the SBOs obtained, making it possible to use these SBOs with standard quantum chemistry calculation software. Simple formulas were also deduced to directly write the SBOs and SBO‐3G corresponding to the atoms with a Z value of between 1 and 18. Finally, as a first example of the usefulness of this kind of functions, an optimized SBO‐3G basis set is proposed for atoms from H to Cl in molecules. © 2016 Wiley Periodicals, Inc.     

Density functional theory calculation of cyclic carboxylic phosphorus mixed anhydrides as possible intermediates in biochemical reactions: Implications for the Pro‐Tide approach

Cyclic acyl phosphoramidates (CAPAs) are important components in several fundamental biological reactions such as protein synthesis and phosphorylation. These structures are particularly interesting in the nucleotide pro‐drug approach, Pro‐Tide, since they are putative intermediates in one of the hydrolysis steps required for activation. The central role played by the amino acid carboxylate function suggests first the formation of a cyclic mixed phosphorus anhydride, rapidly followed by water attack. To investigate such speculations, we performed quantum mechanical calculations using the B3LYP/6‐311+G** level of theory for the plausible mechanisms of action considered. In the five‐membered ring case, transition state theory demonstrated how the overall, gas‐phase, mechanism of action could be split into two in‐line addition–elimination (A–E) steps separated by a penta‐coordinate phosphorane intermediate. The difference between five‐membered and six‐membered ring first A–E was also explored, revealing a single step, unimolecular reaction for the six‐membered ring A–E profile. Implicit solvent contribution further confirmed the importance of CAPAs as reactive intermediates in such kind of reactions. Lastly, the second A–E pathway was analyzed to understand the complete pathway of the reaction. This analysis is the first attempt to clarify the putative mechanism of action involved in the activation of Pro‐Tides and casts light also on the possible mechanism of action involved in primordial protein syntheses, strengthening the hypothesis of a common cyclic mixed phosphorus anhydride species as a common intermediate. © 2012 Wiley Periodicals, Inc.     

Solution of periodic Poisson's equation and the Hartree–Fock approach for solids with extended electron states: Application to linear augmented plane wave method

We formulate a Hartree–Fock‐LAPW method for electronic band structure calculations. The method is based on the Hartree–Fock–Roothaan approach for solids with extended electron states and closed core shells where the basis functions of itinerant electrons are linear augmented plane waves. All interactions within the restricted Hartree–Fock approach are analyzed and in principle can be taken into account. In particular, we obtained the matrix elements for the exchange interactions of extended states and the crystal electric field effects. To calculate the matrix elements of exchange for extended states, we first introduce an auxiliary potential and then integrate it with an effective charge density corresponding to the electron exchange transition under consideration. The problem of finding the auxiliary potential is solved by using the strategy of the full potential LAPW approach, which is based on the general solution of periodic Poisson's equation. Here, we use an original technique for the general solution of periodic Poisson's equation and multipole expansions of electron densities. We apply the technique to obtain periodic potentials of the face‐centered cubic lattice and discuss its accuracy and convergence in comparison with other methods. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

A three‐dimensional coordination polymer based on the Zn4(μ3‐OH)2 unit: poly[[(μ4‐benzene‐1,4‐dicarboxylato)bis(μ3‐benzene‐1,4‐dicarboxylato)bis(μ3‐hydroxido)bis(1,10‐phenanthroline‐5,6‐dione)tetrazinc] dihydrate]

The title compound, {[Zn₄(C₈H₄O₄)₃(OH)₂(C₁₂H₆N₂O₂)₂]·2H₂O}_n, has been prepared hydrothermally by the reaction of Zn(NO₃)₂·6H₂O with benzene‐1,4‐dicarboxylic acid (H₂bdc) and 1,10‐phenanthroline‐5,6‐dione (pdon) in H₂O. In the crystal structure, a tetranuclear Zn₄(OH)₂ fragment is located on a crystallographic inversion centre which relates two subunits, each containing a [ZnN₂O₄] octahedron and a [ZnO₄] tetrahedron bridged by a μ₃‐OH group. The pdon ligand chelates to zinc through its two N atoms to form part of the [ZnN₂O₄] octahedron. The two crystallographically independent bdc²⁻ ligands are fully deprotonated and adopt μ₃‐κO:κO′:κO′′ and μ₄‐κO:κO′:κO′′:κO′′′ coordination modes, bridging three or four Zn^II cations, respectively, from two Zn₄(OH)₂ units. The Zn₄(OH)₂ fragment connects six neighbouring tetranuclear units through four μ₃‐bdc²⁻ and two μ₄‐bdc²⁻ ligands, forming a three‐dimensional framework with uninodal 6‐connected α‐Po topology, in which the tetranuclear Zn₄(OH)₂ units are considered as 6‐connected nodes and the bdc²⁻ ligands act as linkers. The uncoordinated water molecules are located on opposite sides of the Zn₄(OH)₂ unit and are connected to it through hydrogen‐bonding interactions involving hydroxide and carboxylate groups. The structure is further stabilized by extensive π–π interactions between the pdon and μ₄‐bdc²⁻ ligands.     

Structural and Spectral Studies on the Ni(II) Complexes of 1,5‐Diazacyclooctane (DACO) Bearing Heterocyclic Pendants: Formation of a Two‐dimensional Network via Hydrogen Bonds and π‐π Stacking Interactions

A penta‐coordinated Ni(II) complex with a 1,5‐diazacyclooctane (DACO) ligand functionalized by two imidazole donor pendants, [NiL¹Cl] (ClO₄) H₂O (1) (where L¹ = 1,5‐bis (imidazol‐4‐ylmethyl)‐l,5‐diazacyclooctane) has been synthesized and characterized by X‐ray diffraction, infrared spectra, elemental analyses, conductance, thermal analyses and UV‐Vis techniques. Complex 1 crystallizes in triclinic crystal system, P‐l space group with a = 0.74782(7), b = 1.15082 (10), c = 1.23781(11) nm, α = 82.090(2), β = 73.011(2), γ = 83.462(2)°, V = 1.00603(16) nm³, M, = 486.00, Z = 2, D_c = 1.604 g/cm³, final R = 0.0435, and wR = 0.1244. The structures of 1 and its related complexes show that in all the three mononuclear complexes, each Ni(II) center is penta‐coordinated with a near regular square pyramid (RSP) to distorted square‐pyramidal (DSP) coordination environment due to the boat/chair configuration of DACO ring in these complexes, and the degree of distortion increases with the augment of the size of the heterocyclic pendants. In addition, the most striking feature of complex 1 resides in the formation of a two‐dimensional network structure through hydrogen bonds and stabilized by π‐π stacking. The solution behaviors of the Ni(II) complexes are also discussed in detail.     

BaxC60 fullerides: π Electronic peculiarities of the C60 molecule and their consequences for the solid state

The electronic structure of Ba_xC₆₀ fullerides was studied theoretically under special consideration of π electronic effects in the C₆₀ molecule. Band structure data were derived by an intermediate neglect of differential overlap (INDO) crystal orbital (CO) approach. Different electronic configuration were evaluated in the Ba-doped C₆₀ fullerides. Ba_xC₆₀ solids with x=0, 3, 4, 6 are insulators. For a Ba₅C₆₀ model extrapolated from the crystal structure of Ba₆C₆₀, a finite band gap is also predicted. For a Ca₅C₆₀-like structure of Ba₅C₆₀, a quasi-degeneracy between a metallic configuration and an insulating Mott-like state was found. With an increasing Ba-to-C₆₀ charge transfer (CT), sizable changes in the π system of C₆₀ occur. In the neural molecule and for not too high an electron count, the π electrons form more or less electronically isolated hexagon–hexagon (6–6) “double” bonds with only minor hexagon–pentagon (6–5) “double-bond” admixtures. In the vicinity of C₆₀¹²⁻, the 6–6 bonds have lost most of their double-bond character while it is enhanced for the 6–5 bonds. In highly charged anions, the π electron system of the soccer ball approaches a configuration with 12 decoupled 6π electron pentagons. For electron numbers between C₆₀ and C₆₀¹²⁻, the net π bonding is not weakened. The INDO CO results of the Ba_xC₆₀ solids are supplemented by INDO MO and ab initio (3-21 G* split-valence basis) calculations of molecular C₆₀ and some highly charged anions. Ab initio geometry optimizations show that the bond alternation of C₆₀ with short 6–6 and long 6–5 bonds is inverted in C¹²⁻₆₀. The high acceptor capability of C₆₀ is explained microscopically on the basis of quantum statistical arguments. In the π electron configurations of C₆₀ and C₆₀¹²⁻, the influence of the Pauli antisymmetry principle (PAP) is minimized. The quantum statistics of (π) electron ensembles with a deactivated PAP is of the so-called hard-core bosonic (hcb) type. In these ensembles, the on-site interaction is fermionic while the intersite interaction is bosonic. Energetic consequences of the quantum statistical peculiarities of π systems are explained with the aid of simple model systems; we selected annulenes and polyenes. Computational tools in this step are Green's function quantum Monte Carlo (GF QMC) and full configuration interaction (CI) calculations for the π electrons of the model systems. These many-body techniques were combined with a Pariser–Parr–Pople (PPP) Hamiltonian. © 1997 John Wiley & Sons, Inc. Int J Quant Chem 65 : 333–373, 1997