Chemistry

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We report a study on the feasibility of using an intramolecular dipole to enhance charge separation for organic photovoltaic applications. We have developed a poly(1,4-phenylenevinylene) derivative, poly{2-[(9,9-di-n-propyl-9H-7-nitrofluoren-2-yl)]-5-(2-ethylhexyloxy)-1,4-phenylenevinylene} 12, which has electronically asymmetric chromophores as a result of the para attachment of alkoxy and nitrofluorenyl groups on the phenyl units of the polymer backbone. The luminescence of the polymer with the electronically asymmetric chromophores was found to be smaller by a factor of eight when compared to the equivalent polymer but without the nitro group attached to the fluorenyl unit. Light-induced electron spin resonance experiments showed that the polymer with the electronically asymmetric chromophores had more photo-induced spins, showing that the quenching of the luminescence was due to intramolecular charge separation. Single layer photovoltaic devices containing neat films of 12 showed efficiencies similar to other single layer devices and this was ascribed to poor transport of the separated charges. This was confirmed by a strong improvement in device power efficiency to 0.52% at AM1.5 by blending the polymer with an electron transporting material. © 2007 Elsevier B.V. All rights reserved.

(SoNS) School of Natural Sciences

World University root node

Organic Electronics

Electronically asymmetric poly(1,4-phenylenevinylene)s for photovoltaic cells

The structure of L-valinol [(S)-(+)-2-amino-3-methylbutan-1-ol or hydroxylated L-valine], C5H13NO, has been determined at 100 K by single-crystal X-ray diffraction. The independent atom model geometry, Flack parameter and figures of merit are compared with results from an invariom structure refinement. The latter provides H-atom positions free of independent atom model bias and therefore yields a more accurate hydrogen-bond pattern, and the geometry from invariom refinement shows an improved agreement with results from a quantum chemical geometry optimization. © 2006 International Union of Crystallography.

Acta Crystallographica Section C: Crystal Structure Communications

Invariom-model refinement of L-valinol

Detailed investigation of the charge density distribution in concomitant polymorphs of 3-acetylcoumarin in terms of experimental and theoretical densities shows significant differences in the intermolecular features when analyzed based on the topological properties via the quantum theory of atoms in molecules. The two forms, triclinic and monoclinic (Form A and Form B), pack in the crystal lattice via weak C-H⋯O and C-H⋯π interactions. Form A results in a head-to-head molecular stack, while Form B generates a head-to-tail stack. Form A crystallizes in P1̄ (Z′ = 2) and Form B crystallizes in P21/n (Z′ = 1). The electron density maps of the polymorphs demonstrate the differences in the nature of the charge density distribution in general. The charges derived from experimental and theoretical analysis show significant differences with respect to the polymorphic forms. The molecular dipole moments differ significantly for the two forms. The lattice energies evaluated at the HF and DFT (B3LYP) methods with 6-31G** basis set for the two forms clearly suggest that Form A is the thermodynamically stable form as compared to Form B. Mapping of electrostatic potential over the molecular surface shows dominant variations in the electronegative region, which bring out the differences between the two forms. © 2006 American Chemical Society.

Crystal Growth and Design

Topological analysis of charge density distribution in concomitant polymorphs of 3-acetylcoumarin, a case of packing polymorphism

We have illustrated the utility of WTs throughout this chapter, for cleaning, smoothing, and denoising data, as well as the benefits of their direct use as molecular property descriptors. It is clear from the examples cited that this versatile technology can identify and quantify important features within spectra or property distributions of chemical interest for use in both classification and regression models, to achieve near-linear scaling in electronic structure calculations and serve to control the quality of a basis set in ab initio molecular dynamics simulations. The evolution of wavelets in chemistry parallels the development of ever more sophisticated computational methods and hardware performance. In a relatively short period of time, wavelet methods have grown in importance from a noise filter and baseline correction tool to a fundamental component of modern data analysis, computational chemistry, and knowledge discovery. Copyright © 2006 Wiley-VCH, John Wiley & Sons, Inc.

Reviews in Computational Chemistry

Wavelets in chemistry and cheminformatics

The reaction of poly(allyl azide) (PAA; number-average molecular weight = 1800 g/mol) with N-phenyl maleimide, 4,4′-bis(maleimidodiphenyl) ether, 4,4′-(bismaleimidodiphenyl) sulfone, and 1,6-bismaleimido hexane is described in this article. As indicated by Fourier transform infrared studies, the azido group reacted with the highly electron-deficient olefinic bond of N-phenyl maleimide or bismaleimides in a 3 + 2 cycloaddition reaction under mild reaction conditions. The curing of PAA with bismaleimides (10-30 phr) was monitored with differential scanning calorimetry. In freshly prepared samples of PAA and bismaleimides, a broad exothermic transition was observed in the temperature range of 150-280°C and could be attributed to the loss of N 2 from PAA and the curing of bismaleimides. The heat of the exothermic reaction (ΔH) depended on the structure and composition and was in the range of 800-1413 J/g. Isothermal heating in an air oven at 40°C (2 days) followed by 60°C (5-6 days) resulted in the conversion of a sticky, viscous liquid into an elastic, nonsticky material. No significant difference in the ΔH values of uncured and cured samples was observed, and this indicated the reaction of fewer azido groups with the bismaleimides (dipolarophiles). In the thermogravimetry traces, a mass loss was indicated in the temperature range of 130-280°C due to the loss of nitrogen from the azido group. © 2006 Wiley Periodicals, Inc.

Journal of Applied Polymer Science

Curing and thermal behavior of poly(allyl azide) and bismaleimides

The electron transfer reactions involving ascorbic acid as electron donor are in general very fast. The present work is an example of electron transfer between ascorbic acid and a (μ-oxo) diiron(III,III) complex, where the otherwise very fast process has been slowed down by the presence of large excess of chloride ion. The complex ion [Fe2III(μ-O)(phen)4(H2O)2]4+(1) (phen = 1,10-phenanthroline) and its H2O acid dissociated derivatives [Fe2III(μ-O)(phen)4(H2O)(OH)]3+(1a)and[Fe2III(μ-O)(phen)4(OH)2]2+(2a) coexist in rapid equilibria in the range pH 3.95-5.09 in presence of excess phen (pKa1 = 3.71 ± 0.11, pKa2 = 5.28 ± 0.10). The complex solution reacts with ascorbic acid in presence of excess phenanthroline to produce tris(phenanthroline)iron(II) and dehydroascorbic acid. All the three forms of the complex ion are kinetically active, whereas the ascorbate ion and not the free ascorbic acid has been found to be the reactive species. The observed rate constants exhibit a first-order dependence on the total concentration of ascorbic acid and an inverse square dependence on chloride ion concentration, while the dependence on [H+] is complex in nature. Kinetic and stoichiometric results indicate that one ascorbate ion reacts with one complex molecule in an inner sphere pathway. The kinetic experiments were carried out at 25°C in aqueous media. The ionic strengths of the reaction media were kept 1.0 M using NaNO3. © 2005 Elsevier Ltd. All rights reserved.

Polyhedron

Electron transfer between ascorbic acid and a (μ-oxo) diiron(III,III) complex: An example of chloride inhibition

In an attempt to investigate the putative S-H⋯N hydrogen bond, we have studied the title compound, 1-formyl-3-thiosemicarbazide, which was revealed in a CSD search as a crystal structure which might show such an interaction. However, a redetermination of the structure at room temperature and careful analysis showed that the earlier study [Saxena et al (1991). Acta Cryst. C47, 2374-2376] on which the CSD search was based was in error and that the possibility of an S-H⋯N hydrogen bond is negated. The presence of five other varieties of hydrogen bond (N-H⋯O, N-H⋯S, N-H⋯N, C-H⋯O, C-H⋯S) in the crystal packing prompted us to redirect our efforts and to undertake a study of the charge-density distribution at 90 K. The topological analysis of these five varieties of hydrogen bond was carried out with Bader's quantum theory of 'atoms in molecules' and by applying Koch-Popelier's criteria. The analysis reveals that the hydrogen-bond strength is highest for N-H⋯O and lowest for C-H⋯S with N-H⋯S, N-H⋯N and C-H⋯O forming the middle order. © 2006 International Union of Crystallography Printed in Great Britain - all rights reserved.

Acta Crystallographica Section B: Structural Science

Five varieties of hydrogen bond in 1-formyl-3-thiosemicarbazide: An electron density study

The topological features of the charge densities, ρ(r), of three bioactive molecules, 2-thiouracil [2,3-dihydro-2-thioxopyrimidin-4(1H)-one], cytosine [4-aminopyrimidin-2(1H)-one] monohydrate and salicylic acid (2-hydroxybenzoic acid), have been determined from high-resolution X-ray diffraction data at 90 K. The corresponding results are compared with the periodic theoretical calculations, based on theoretical structure factors, performed using DFT (density-functional theory) at the B3LYP/6-31G** level. The molecules pack in the crystal lattices via weak intermolecular interactions as well as strong hydrogen bonds. All the chemical bonds, including the intra- and intermolecular interactions in all three compounds, have been quantitatively described by topological analysis based on Bader's quantum theory of 'Atoms In Molecules'. The roles of interactions such as C-H⋯O, C-H⋯S, C-H⋯π and π⋯π have been investigated quantitatively in the presence of strong hydrogen bonds such as O-H⋯O, N-H⋯O and N-H⋯S, based on the criteria proposed by Koch and Popelier to characterize hydrogen bonds and van der Waals interactions. The features of weak intermolecular interactions, such as S⋯S in 2-thiouracil, the hydrogen bonds generated from the water molecule in cytosine monohydrate and the formation of the dimer via strong hydrogen bonds in salicylic acid, are highlighted on a quantum basis. Three-dimensional electrostatic potentials over the molecular surfaces emphasize the preferable binding sites in the structure and the interaction features of the atoms in the molecules, which are crucial for drug-receptor recognition. © 2006 International Union of Crystallography Printed in Great Britain - all rights reserved.

Intra- and intermolecular interactions in small bioactive molecules: Cooperative features from experimental and theoretical charge-density analysis

We have developed a novel structure-based chemoinformatics approach to search for Complimentary Ligands Based on Receptor Information (CoLiBRI). CoLiBRI is based on the representation of both receptor binding sites and their respective ligands in a space of universal chemical descriptors. The binding site atoms involved in the interaction with ligands are identified by the means of a computational geometry technique known as Delaunay tessellation as applied to X-ray characterized ligand-receptor complexes. TAE/RECON multiple chemical descriptors are calculated independently for each ligand as well as for its active site atoms. The representation of both ligands and active sites using chemical descriptors allows the application of well-known chemometric techniques in order to correlate chemical similarities between active sites and their respective ligands. We have established a protocol to map patterns of nearest neighbor active site vectors in a multidimensional TAE/RECON space onto those of their complementary ligands and vice versa. This protocol affords the prediction of a virtual complementary ligand vector in the ligand chemical space from the position of a known active site vector. This prediction is followed by chemical similarity calculations between this virtual ligand vector and those calculated for molecules in a chemical database to identify real compounds most similar to the virtual ligand. Consequently, the knowledge of the receptor active site structure affords straightforward and efficient identification of its complementary ligands in large databases of chemical compounds using rapid chemical similarity searches. Conversely, starting from the ligand chemical structure, one may identify possible complementary receptor cavities as well. We have applied the CoLiBRI approach to a data set of 800 X-ray characterized ligand-receptor complexes in the PDBbind database. Using a k nearest neighbor (kNN) pattern recognition approach and variable selection, we have shown that knowledge of the active site structure affords identification of its complimentary ligand among the top 1% of a large chemical database in over 90% of all test active sites when a binding site of the same protein family was present in the training set. In the case where test receptors are highly dissimilar and not present among the receptor families in the training set, the prediction accuracy is decreased; however, CoLiBRI was still able to quickly eliminate 75% of the chemical database as improbable ligands. CoLiBRI affords rapid prefiltering of a large chemical database to eliminate compounds that have little chance of binding to a receptor active site. © 2006 American Chemical Society.

Fulltext

Journal of Chemical Information and Modeling

Chemometric analysis of ligand receptor Complementarity: Identifying Complementary Ligands Based on Receptor Information (CoLiBRI)

The laterally nonsymmetric aza cryptand Lo readily forms mononuclear inclusion complexes with metal ions like CuII, Ni II, AgI, TlI, and so forth. However, when the secondary amines present in the three bridges are substituted by a cyanomethyl group to yield a new cryptand L, its metal-binding properties are drastically altered. Thus, while Lo binds AgI at the tren end, showing AgN4 coordination, in L, the bridgehead nitrogen atoms are pulled inside to form a two-coordinate complex of AgI and none of the O or N atoms present in the three bridges are involved in coordination. This is probably the first example where the two bridgehead atoms are pulled inside to the maximum to bind the metal ion. Likewise, the TlI ion shows TlN4 coordination with Lo, while in L it is loosely bound at the tren end, showing TlN3 coordination. Upon treatment with a AgI salt, the TlI can be replaced almost instantaneously. On the other hand, with copper(II) tetrafluoroborate salt in moist DMF, two of the cyanide groups in L are converted to carboxylic acid groups and bind the metal ion from outside. The CuII ion in this complex shows distorted octahedral coordination where the two O atoms from the two carboxylic acid groups and the two corresponding N atoms in the two bridges are bound equatorially. The two axial sites are occupied by the nearby bridgehead N atom and the O atom of a DMF molecule. All five complexes and the free ligands are characterized by spectroscopic and X-ray crystallographic studies. © Wiley-VCH Verlag GmbH &amp; Co. KGaA, 2006.

European Journal of Inorganic Chemistry

Alteration in the binding property of a laterally nonsymmetric aza cryptand toward CuII, AgI, and TlI ions upon derivatization with a cyanomethyl group