DFT and metal-metal bonding: a dys-functional treatment for multiply charged complexes?

Density functional theory (DFT) calculations are reported for 16 binuclear transition-metal complexes. Structural motifs studied include face-shared and edge-shared bioctahedra, carboxylate-bridged "paddlewheel" complexes, and nonbridged dimers possessing direct metal-metal bonds. Most of these structure types are represented both by multiply charged (tri- and tetra-anionic, and tetracationic) and by neutral or singly charged examples. Geometry optimizations for these species, in the vacuum phase, use the "broken-symmetry" approach coupled with nine different DFT methods. We find a clear dichotomy in the performance of different DFT approaches. For the eight neutral or singly charged complexes, orthodox gradient-corrected DFT methods such as BP and PBE perform generally very well in reproducing in vacuo the complex geometries obtained from X-ray crystallographic studies. In contrast, these orthodox approaches fail to reliably mimic the crystalline geometries for more highly charged complexes such as Mo(2)Cl(9)(3-), Cr(2)(CH(3))(8)(4-), and Rh(2)(NCCH(3))(10)(4+). Much closer agreement with experimental condensed-phase structures for the multiply charged dinuclear complexes is seen for two "local-density-approximation" approaches, X alpha and VWN, and for VWN+B-LYP, an unorthodox combination of the VWN local and B-LYP nonlocal density functionals. The very good performance of the latter approaches arises from an essentially fortuitous cancellation of errors: while the generally overbinding nature of these approaches suggests that they will not reliably describe true gas-phase structures, this overbinding compensates very well for the coulombic distortion expected when complexes are removed from the charge-stabilizing environment of the crystalline or solvated state. We recommend that, as an alternative to the (computationally expensive) incorporation of solvent-field corrections, VWN+B-LYP is the preferred method for structural characterization of triply or more highly charged dinuclear complexes, while orthodox approaches such as PBE perform best for neutral or mildly charged complexes.     

How to obtain accurate results with molecular iodine and density functional theory?

Molecular iodine is found in many organic synthetic methodologies, both as reagent and as catalyst. Naturally, many groups have carried out computational studies involving this element. However, the choice of computational method proves to be more challenging than for other non-metals. We quantify herein the errors that some common theory levels can introduce in terms of both structural and energetic deviations. We also evaluate multiple post hoc corrections, namely, vibrational entropy, dispersion, and counter-poise corrections. Our results indicate the triple- $$ basis sets are essential to obtain quality results and that post hoc corrections are overall detrimental.     

NMR and molecular modelling studies on the interaction of fluconazole with β-cyclodextrin

Background  

Fluconazole (FLZ) is a synthetic, bistriazole antifungal agent, effective in treating superficial and systemic infections caused by Candida species. Major challenges in formulating this drug for clinical applications include solubility enhancement and improving stability in biological systems. Cyclodextrins (CDs) are chiral, truncated cone shaped macrocyles, and can easily encapsulate fluconazole inside their hydrophobic cavity. NMR spectroscopy has been recognized as an important tool for the interaction study of cyclodextrin and pharmaceutical compounds in solution state.     

Polypeptoids: A perfect match for molecular definition and macromolecular engineering?

Precision synthesis of polymers has been a hot topic in recent years. While this is notoriously difficult to address for polymers with a C? C backbone, Merrifield has discovered a way many decades ago for polypeptides. Using a similar approach, N‐substituted polypeptides, so‐called polypeptoids have been synthesized and studied for about 20 years. In contrast, the living ring‐opening polymerization (ROP) of N‐substituted N‐carboxyanhydrides was among the first living polymerizations to be discovered. More recently, a surge in new synthetic approaches led to the efficient synthesis of cyclic or linear multiblock copolypeptoids. Thus, polypeptoids can be synthesized either by solid phase synthesis to yield complex and exactly defined oligo‐ and small polymers or by ROP of appropriately N‐substituted N‐carboxyanhydrides (NNCA) to give linear, cyclic, or star‐like polymers. Together with an excellent biocompatibility, this polymer family may have a bright future ahead as biomaterials. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2013, 51, 2731–2752     

Blends of some non-flexible and flexible polymers: Routes to molecular composites?

The definition of a molecular composite is a blend of a rigid rod polymer and a flexible coil polymer that is miscible at the molecular level. This concept has been tested using systems in which the chain flexibilities differ as widely as possible as judged by the difference in glass transition temperatures (δTg). The biggest variation (δT ∼360°C) was obtained by mixing poly benzimidazole with copolymers of poly(vinyl acetate-ran-vinyl alcohol). It was observed that the blends were distinctly two phase when the hydroxyl content was less than 50 mol %. Above this value clear blends were obtained with finely dispersed phases although it is doubtful if mixing at the molecular level takes place. Miscible blends could be obtained from combinations of the sodium salt of poly(phenylene terephthalamide) with poly(4-vinylpyridine) and mixtures of poly(phenyl imino-1,4-phenyleneoxyterephthalate) with poly(styrene-stat-hydroxylstyrene) where coulombic interactions and hydrogen bonding respectively promoted the miscibility.     

Synthesis, molecular structure and intramolecular aromatic-ring stacking interaction of a novel binuclear Cu(Ⅱ) complex with 1, 10-phenanthroline and phenylacetate

The complex [Cu(phen)2(POAc)3]ClO·4H2O has been synthesized and investigated by elemental analysis, IR spec-troscopy and X-ray diffraction methods, where phen = 1,10-phenanthroline, POAc = phenylacetate group). The complex crystallizes in the triclinic space group PI with two molecules in a unit cell of dimensions a = 1.0579(2) nm, b = 1.2423(3) nm, c = 1.9190(4) nm, α = 71.84(1)°, β = 80.50(2)°, γ = 88.60(1)°, V = 2.3625(9) nm3, R = 0.0407 and Rw = 0.0656. The complex results from bridging of two Cu(phen)2 units by three carboxylate groups, and each Cu2 ion is in a distorted square pyramidal geometry with two nitrogen atoms of phen and three carboxylate oxygen atoms of POAc. It has been showed that intramolecular stacking interactions occur between the phenyl moieties of POAc and aromatic rings of phen, leading to a novel molecule structure with two coordinating modes of carboxylate ligands, of which two phenylacetates are μ2-carboxylate-O-bridging ligands, and the other is a μ2-carboxylate-     

Synthesis of conjugates of β-cyclodextrin with polyamidoamine dendrimers and their molecular inclusion interaction with levofloxacin lactate

Polyamidoamine (PAMAM) dendrimers of different generations (G2 and G4) conjugated with β-cyclodextrin (β-CD), PAMAM (G2, G4)-CD, were synthesized using substitution reaction from mono-6-iodine-β-cyclodextrin and PAMAM dendrimers. The resulting molecular structures were characterized by NMR, IR. The molecular interaction between various dendrimers and levofloxacin lactate (LFL) were investigated by monitoring the fluorescence of LFL in the presence of dendrimers in buffer solution (pH 7.4) at 25?°C. It was found that the PAMAM (G2, G4)-CD possesses higher sensitizing ability than that of the corresponding parent dendrimers and natural β-CD, and increases concomitantly with the increases of generation and content of β-CD, suggesting that the PAMAM (G2, G4)-CD possesses stronger inclusion ability with LFL. The possible interaction mechanism between PAMAM-CD and LFL was proposed by ¹H NMR analysis and theoretical calculation. The results show that the LFL molecule is located at the amine end of dendrimer molecule and along the side of cyclodextrin cavities to form supramolecular complexes. Furthermore, results indicate that the main driving force of the complex could be attributed to the electrostatic interactions and hydrogen bonding between LFL and PAMAM-CD, as well as the synergistic effect of intermolecular forces.     

In vitro antitumor activity of titanocene alanine complex and its interaction with nucleic acids

Titanocene alanine complex, Cp2Ti(O2CCH(CH3)NH3+Cl-)2, has been found to have in vitro antitumor activity against Ehrlich ascites tumor cells. Study of the interaction between Cp2Ti(O2CCH(CH3)NH+Cl-)2 and DNA by UV-VIS spectra, fluorescence spectra, agarose gel elec-trophoresis reveals that Cp2Ti(O2CCH(CH3)NH3 Cl-)2 forms a stable compound with DNA in molar ratio 1:1 and reduces the migration rate of ccc-DNA band and oc-DNA band. However, unlike cis-platin, the complex does not induce nicking of DNA even after a long incubation at a high ratio of the complex to DNA. The results suggest that titanocene-based antitumor agents have different mechanism of action from cisplatin-like antitumor agents.     

Why does electron sharing lead to covalent bonding? A variational analysis

Ground state energy differences between related systems can be elucidated by a comparative variational analysis of the energy functional, in which the concepts of variational kinetic pressure and variational electrostatic potential pull are found useful. This approach is applied to the formation of the bond in the hydrogen molecule ion. A highly accurate wavefunction is shown to be the superposition of two quasiatomic orbitals, each of which consists to 94% of the respective atomic 1s orbital, the remaining 6% deformation being 73% spherical and 27% nonspherical in character. The spherical deformation can be recovered to 99.9% by scaling the 1s orbital. These results quantify the conceptual metamorphosis of the free-atom wavefunction into the molecular wavefunction by orbital sharing, orbital contraction, and orbital polarization. Starting with the 1s orbital on one atom as the initial trial function, the value of the energy functional of the molecule at the equilibrium distance is stepwise lowered along several sequences of wavefunction modifications, whose energies monotonically decrease to the ground state energy of H2+. The contributions of sharing, contraction and polarization to the overall lowering of the energy functional and their kinetic and potential components exhibit a consistent pattern that can be related to the wavefunction changes on the basis of physical reasoning, including the virial theorem. It is found that orbital sharing lowers the variational kinetic energy pressure and that this is the essential cause of covalent bonding in this molecule.     

Interaction and reaction of the hydroxyl ion with β-d-galactose and its hydrated complex: an ab initio molecular dynamics study

The interaction of OH(-) with the sugar β-d-galactose is studied computationally, with Ab Initio Molecular Dynamics (AIMD) as the prime tool. The main findings are: (1) the OH(-) abstracts a proton from the sugar in a barrier-less process, yielding H(2)O and a Deprotonated beta-d-Galactose anion, (Dep-beta-d-G)(-). (2) This reaction can be reversed when two additional H(2)O molecules are present in the sugar. (3) At 500 K, a ring-opening reaction occurs in (Dep-beta-d-G)(-) within a timescale of 10 ps. The (neutral) sugar itself is stable over this timescale, and well beyond. This indicates that OH(-) can catalyze the degradation of β-d-galactose. Implications of this process are briefly discussed.     

Encapsulation of dicinnamalacetone in β-cyclodextrin: A physicochemical evaluation and molecular modeling approach on 1:2 inclusion complex

The aim of this research is to prepare and characterize the inclusion complex between Dicinnamalacetone (DCA) and β-CD. The inclusion complex of Dicinnamalacetone [DCA] and Beta-cyclodextrin [β-CD] was characterized both in solution and solid state by UV-visible spectroscopy, Fluorescence spectroscopy, Nano second time resolved fluorescence study, Fourier Transform Infra-red spectroscopy (FT-IR), Differential Scanning Calorimetry (DSC), Scanning Electron Microscopy (SEM), Powder X-ray diffractometry (XRD), Atomic Force Microscopy (AFM) and molecular modeling test. The 1:2 soichiometry of inclusion complex and binding constant values were determined by Benesi-Hildebrand plot and confirmed by Job's continuous variation method. FT-IR study indicated that the aromatic rings of the Dicinnamalacetone molecule were included in the β-CD cavities. The nano second time resolved fluorescence study revealed that DCA exhibits single exponential decay in aqueous medium and bi-exponential decay in β-CD medium indicating the formation of inclusion complex. From the DSC study it is observed that the thermal stability of the inclusion complex was significantly enhanced when compared with the pure compound due to strong interaction between DCA and β-CD. Furthermore, implementation of molecular modeling test confirmed that the complexation could reduce the energy of the system. The experimental studies revealed that the most predominant structure of 1:2 inclusion complex is the one in which the two aromatic ends of DCA were inserted into the cavities of two β-CD molecules.     

Intramolecular nonbonded S?O interaction in acetazolamide and thiadiazolinethione molecules in their dimeric crystalline structures and complex crystalline structures with enzymes

The dimeric crystalline structure of acetazolamide 1 and thiadiazolinethione 2 bearing intramolecular nonbonded S?O interactions, in each different hydrogen-bonding manner was clarified by their X-ray crystallographic analysis. Existence of the dimeric structure of 1 and 2 in a MeOH solution could be suggested on the basis of their cold-spray ionization mass spectrometry. The intramolecular nonbonded S?O interaction was precisely recognized in the complex crystalline structures of carbonic anhydrase I inhibitor 1 and stromelysin inhibitors 2-4 with each specific enzyme. The computational evaluation of the possible monomeric seven conformers of 1 and two model compounds 5 and 6 of 2-4 based on DFT calculations defined that the conformer bearing the intramolecular nonbonded S?O interaction is most stable.     

Syntheses of molecular wires containing redox center： Reversible redox property and good energy level matching with Au electrode

Molecular wires with tetrathiafulvalene （TTF） as redox center were synthesized and characterized. UV-vis spectra and cyclic voltammetry showed these wires had good reversible redox behavior under ambient conditions and their HOMO energy levels （--5.0 eV） matched well with the Fermi level of Au （--5.1 eV）.     

A molecular Debye-Hückel theory and its applications to electrolyte solutions

In this report, a molecular Debye-Hu?ckel theory for ionic fluids is developed. Starting from the macroscopic Maxwell equations for bulk systems, the dispersion relation leads to a generalized Debye-Hu?ckel theory which is related to the dressed ion theory in the static case. Due to the multi-pole structure of dielectric function of ionic fluids, the electric potential around a single ion has a multi-Yukawa form. Given the dielectric function, the multi-Yukawa potential can be determined from our molecular Debye-Hu?ckel theory, hence, the electrostatic contributions to thermodynamic properties of ionic fluids can be obtained. Applications to binary as well as multi-component primitive models of electrolyte solutions demonstrated the accuracy of our approach. More importantly, for electrolyte solution models with soft short-ranged interactions, it is shown that the traditional perturbation theory can be extended to ionic fluids successfully just as the perturbation theory has been successfully used for short-ranged systems.     

Aromaticity and π-bond covalency: prominent intermolecular covalent bonding interaction of a Kekulé hydrocarbon with very significant singlet biradical character

An anthracene-linked bisphenalenyl Kekulé molecule with very significant singlet biradical character has shown a prominent covalent bonding interaction between molecules in a molecular aggregate. High aromatic stabilization energy in the anthracene linker is responsible for the significant singlet biradical character.     

A copper(II) complex with 2-(2′-pyridyl)benzimidazole and l-arginine: synthesis,structure, antibacterial activities,and DNA interaction

A Cu(II) complex with 2-(2′-pyridyl)benzimidazole and l-arginine has been synthesized and investigated by elemental analysis, molar conductivity, IR, UV/vis, and X-ray diffraction. The complex crystallizes in the triclinic space group P1 with six molecules in a unit cell of dimensions a?=?10.6397(5)?Å, b?=?19.2178(8)?Å, c?=?20.0387(9)?Å, α?=?75.3670(10)°, β?=?79.4670(10)°, γ?=?87.4470(10)°, V?=?3897.6(3)?ų, R ₁?=?0.0408, and wR ₂?=?0.0502. The complex contains six crystallographically independent complexes, Cu1, Cu2, Cu3, Cu4, Cu5, and Cu6, which have a distorted square-pyramidal geometry. The complex was screened for its in vitro antibacterial activities against two Gram-positive (Bacillus subtilis and Staphylococcus aureus) and two Gram-negative (Escherichia coli and Salmonella) micro-organisms. The complex exhibited good antibacterial activities against the micro-organisms compared with HPB and Cu(ClO₄)₂. Interaction of the complex with DNA was studied by electronic absorption spectroscopy, fluorescence spectroscopy, circular dichroic spectroscopy, viscosity measurements, and agarose gel electrophoresis. Results suggest that the complex could bind to CT-DNA via partial intercalation, and cleave the plasmid DNA with involvement of hydroxyl radicals, and probably singlet oxygen-like copper-oxo species in the presence of ascorbate.     

A molecular modeling study of complex formation and self-aggregation behavior of a porphyrin–β-cyclodextrin conjugate

This paper reports a molecular modeling study of complex formation and aggregation behavior of a supramolecular system comprising three different moieties forming two distinct molecules. One molecule is a phenol derivative of porphyrin conjugated to a macrocyclic oligosaccharide, β-cyclodextrin (β-CD), and the other is 1-adamantanol (ADM). The inclusion complex of the latter molecule with the porphyrin–β-cyclodextrin (β-CD) conjugate, and the dimeric aggregates of the conjugate both in the presence and in the absence of the guest are investigated through molecular mechanics and molecular dynamics methods in vacuo, since the systems are scarcely soluble in polar solvents. In this way, we can find the most likely geometry of the complexes or aggregates and characterize the competitive inclusion behavior of ADM and of a porphyrin phenol within the β-CD cavity in terms of the various energy contributions stabilizing the resulting aggregates and/or inclusion complexes.     

A radiation-chemical and quantum-chemical study of ascorbic acid interaction with α-hydroxyethyl radicals

The effect of ascorbic acid and its analogue 5,6-O-isopropylidenyl-2,3-O-dimethylascorbic acid (I), which has been synthesized for the purpose and does not contain mobile hydrogen atoms, on the formation of the products of continuous radiolysis of deaerated ethanol and its aqueous solutions has been studied. The ionization potentials, the molecular orbital energies, the enthalpies of homolytic dissociation of C-H and O-H bonds, and the enthalpies of H atom addition to the C=O group of the test compounds have been calculated by ab initio methods. The array of the experimental and calculated theoretical data suggests that both ascorbic acid in the undissociated form and compound I can oxidize α-hydroxyethyl radicals, whereas the monoanion of ascorbic acid acts as a reducing agent in the reactions with these transient radicals. The reduction of α-hydroxyethyl radicals in aqueous solutions by the ascorbic acid monoanion can follow both the hydrogen transfer and electron transfer mechanisms.     

A prelude of the 2004 Antwerp Quality Conference: Targets and target values—integrating quality management and costing

Questions about the value of services in the health care sector and the quality of them have been addressed frequently during the last decade, but as separate issues. In this article a method is proposed to combine these two issues. The starting point is the observation that competition will become fiercer among providers in the health care sector . Moreover, the patients opinion about quality in terms of convenience, emotional attention, etc., will be important in a competitive environment and will determine which health care service providers will be successful. These developments will have an impact on the engineering of the health care chain. Methods are discussed to integrate the determination of the value of innovations and new products, and the design of quality systems. The system of target costing is focused upon. It takes the outcome of care processes as desired by customers or the users as the starting point both for pricing the services as well as for designing the delivery system. This will not only improve cost control, but also quality improvements in two ways. First, the delivery system will be better adapted (and integrated if more health care providers are involved) to the needs of the patients, and second quality will improve as health care providers analyze, redesign, and monitor their processes more extensively.Presented at the 9th Conference on Quality in the Spotlight, 18–19 March 2004, Antwerp, Belgium