Ab initio correlation corrections to the Hartree-Fock quasi band-structure of periodic systems employing Wannier-type orbitals

A size-consistent ab initio formalism to calculate correlation corrections to ionization potentials as well as electron affinities of periodic systems is presented. Our approach is based on a Hartree-Fock scheme which directly yields local orbitals without any a posteriori localization step. The use of local orbitals implies non-zero off-diagonal matrix elements of the Fock operator, which are treated as an additional perturbation and give rise to localization diagrams. Based on the obtained local orbitals, an effective Bloch Hamiltonian is constructed to second order of perturbation theory with all third-order localization diagrams included. In addition, the summation of certain classes of diagrams up to infinite order in the off-diagonal Fock elements as well as the Epstein-Nesbet partitioning of the full Hamiltonian are discussed. The problem of intruder states, frequently encountered in many-body perturbation theory, is dealt with by employing the theory of intermediate Hamiltonians. As model systems we have chosen cyclic periodic structures up to an oligoethylene ring in double-zeta basis; however, the theory presented here straightforwardly carries over to infinite periodic systems. Received: 30 April 1998 / Accepted: 27 July 1998 /  Published online: 7 October 1998     

The unrestricted natural orbital-restricted active space method: methodology and implementation

The full configuration interaction method in the space of fractionally occupied unrestricted natural orbitals (UNO-CAS method) is extended to excited states as well as to strongly correlated and reactive systems with large active spaces. This is accomplished by␣using restricted active space (RAS) wave functions introduced by Olsen et al. [(1988) J Chem Phys 89: 2185] and using the UNOs without the expensive orbital optimization step. In RAS, the space of active orbitals is subdivided into three groups: a group with essentially doubly occupied orbitals (RAS1), the usual CAS space (RAS2), and a space with weakly occupied active orbitals (RAS3). We select these spaces on the basis of the occupation numbers of the UNOs. All possible electron distributions are allowed in the usual CAS space, but the number of vacancies is limited in RAS1 and the number of electrons is limited in RAS3. We discuss an efficient algorithm for generating a RAS wave function. This is based on the Handy-Knowles determinantal expansion with an addressing scheme adopted for the restricted expansion. Results for both ground and excited states of azulene and free base porphyrin are presented. Received: 16 July 1998 / Accepted: 7 August 1998 / Published online: 19 October 1998     

Electrochemical redox reactions studied in frozen tetrabutylammonium halide hydrates

The electrochemical redox reactions: Fe(CN)₆ ⁴⁻−e⁻↔ Fe(CN)₆ ³⁻, Ru(NH₃)₆ ³⁺+e⁻↔ Ru (NH₃)₆ ²⁺ and Fc(CH₂OH)₂−e⁻↔ Fc(CH₂OH)₂ ⁺ (Fc–ferrocene) were investigated in tetrabutylammonium halide hydrates at temperatures below and above the electrolyte melting point. They were studied by cyclic voltammetry, potential step chronoamperometry and impedance spectroscopy. Freezing of the electrolyte affects both the shape and position of the cyclic voltammogram on the potential scale. Also the shapes of the current-time relationship and the impedance spectra change at temperatures below the melting point. It has been proposed that this behaviour is caused by slow transport of the reactant and the heterogeneous nature of the electrolyte. The activation energies of reactant transport are about four times larger in frozen electrolytes than those in liquid. It has been concluded that reactant transport is restricted to the intergrain space of the electrolyte. Received: 16 December 1997 / Accepted: 10 February 1998     

Molecular meccano for light-sensitive and light-emitting nanosized systems based on unsaturated and macrocyclic compounds

The review presents the results of the development of an universal approach to the molecular design of light-sensitive and light-emitting nanosized systems with desired properties based on unsaturated and macrocyclic compounds. Within the same class of compounds, various nanosized systems were constructed using a limited number of structural fragments. These nanosized systems are susceptible to all main types of photoprocesses, such as fluorescence, photodissociation, photoisomerization, photocycloaddition, photoelectrocyclization, excimer formation, charge-transfer complex formation, the formation of the twisted intramolecular charge-transfer state (TICT state), and the electron transfer. The use of photostructural transformations for controlling the complexation and mechanical movements in molecular devices and machines is discussed. The prospects of application of the new strategy are exemplified by the design of the previously unknown types of molecular switches, materials for optical chemosensors, optical data recording and storage media, photoswitchable molecular devices, and photocontrolled molecular machines. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 7, pp. 1299–1323, July, 2008.     

The role of initiation in the synthesis of silica/poly(methyl methacrylate) nanocomposite latex particles through emulsion polymerization

Silica/poly(methyl methacrylate) nanocomposite latex particles have been synthesized by emulsion polymerization of methyl methacrylate using a nonionic surfactant: nonylphenol poly(oxyethylene) and three different initiators, namely: 2,2′-azobis(2-amidinopropane) dihydrochloride (AIBA), potassium persulfate (KPS) and azobis(isobutyronitrile) (AIBN), being cationic, anionic and nonionic, respectively. A silica sol with an average diameter of 68 nm was used as the seed. The polymerization reaction was conducted under alkaline conditions in order to evaluate the role of the surface charge of the hydrophilic silica on the coating reaction. AIBA was found to be adsorbed on the silica surface owing to electrostatic interactions of the amidine function of the cationic initiator with the silanolate groups of the oxide surface, while the anionic and the nonionic initiators did not adsorb on silica under the same conditions. Nonetheless, whatever the nature of the initiator, polymerization took place on the silica particles as evidenced by transmission electron microscopy. The extent of interaction between the inorganic surface and the polymer particles was quantified by means of ultracentrifugation and a material balance. As much as 65% by weight of the total polymer formed was found to be present at the silica surface using AIBA, while only 40% for KPS and 25% for AIBN was found to cover the silica particles under alkaline conditions. We demonstrate that by using a cationic initiator and by controlling the pH of the suspension it is possible to significantly decrease the amount of free polymer. Coating of the silica particles took place through a kind of in situ heterocoagulation mechanism. Received: 8 December 2000 Accepted: 22 February 2001     

Adsorption of neutral polymers on negatively charged liposomes. A novel quantitative method to measure the rate of polymer adsorption on the liposomal surface

We studied the adsorption of two neutral polymers [poly(vinyl pyrrolidone) and poly(vinyl alcohol) (PVA)] on negatively charged liposomes composed of 25:2:3 (molar ratio) soy lecithin/dicetyl phosphate/cholesterol.The liposomes were prepared in buffered solution at pH 7.4 and were mixed with the solution of the polymers in the desired polymer/lipid ratios. Adsorption was measured by determination of the equilibrium bulk concentration of the polymer. Protamine hydrochloride was used to aggregate the liposomes with polymers adsorbed on their surface and to facilitate their separation from the equilibrium bulk solution. In the case of PVA, quantitative adsorption measurements with a specific reagent were possible. Adsorption isotherms were recorded at 25 ± 0.2 °C. It was concluded that adsorbed and nonadsorbed PVA molecules are in equilibrium even at low polymer/lipide ratios. The results were confirmed by dynamic laser light scattering, X-ray diffraction and thermal activity monitoring experiments. Received: 13 October 2000 Accepted: 8 March 2001     

Adsorption of styrene on micron-sized, monodisperse, cross-linked polymer particles in a snowman-shaped state by utilizing the dynamic swelling method

Polystyrene/styrene–divinylbenzene copolymer composite particles with different cross-linking densities were produced by seeded copolymerization for (styrene/divinylbenzene)-swollen polystyrene particles prepared by utilizing the dynamic swelling method (DSM) which was proposed by the authors in 1991. Using the cross-linked, composite particles as seeds, styrene-adsorbed (swollen) composite particles having snowman shapes were prepared by the DSM. With a decrease in the cross-linking density in the composite particles, the volume of the composite particle which was embedded in a spherical styrene phase in the snowman-shaped, styrene-adsorbed particle increased and the contact angle of the styrene phase on the composite particle decreased. In the DSM process, the absorption stage of styrene in the composite particles and the adsorption stage thereon were clearly observed. This suggests that the cross-linking density of the composite particles greatly affects the morphology of the snowman-shaped particles. Received: 13 December 2000 Accepted: 14 March 2001     

Structure and stabilities of (HA1NH)n (n = 2–4)

Ab initio molecular electronic structure methods have been used to study the relative stability of the planar inorganic ring (HAlNH)_n (n = 2–4) during homodesmotic and monomer polymerization reactions. Optimized geometries, frequencies and energies through restricted Hartree-Fock/6-31G* are reported, and energies at the self-consistent field optimized geometries including M?ller-Plesset fourth perturbation theory with single, double and quadruple excitation (MP4SDQ) corrections are also reported for both reactions. Homodesmotic reactions with MP4SDQ −28.5 kcal/mol for (AlN)₂, 1.9 kcal/mol for (AlN)₃ and −0.97 kcal/mol for (AlN)₄. On analysing a π-molecular orbitals diagram, only one, three and three strongly bonding π-molecular orbitals exist for the planar four-, six- and eight-membered AlN rings, respectively. Received: 9 March 1998 / Accepted: 19 March 1998 / Published online: 23 June 1998     

Gaussian-3 and related methods for accurate thermochemistry

In this paper, we present an overview of Gaussian-3 (G3) theory, a composite technique that employs a sequence of ab initio molecular orbital calculations to derive a total energy of a given molecular species. This method provides accurate energies of molecular systems for the calculation of enthalpies of formation, ionization potentials, electron affinities, proton affinities, etc. Also covered in this review are several variants of G3 theory including one based on scale factors (G3S) and an extended version (G3X) that uses improved geometries and larger Hartree-Fock basis sets. Finally, the G3/99 test set of accurate experimental data that is used for critical assessment is described. Overall, G3 theory has a mean absolute deviation from experiment of 1.07 kcal mol⁻¹ for the G3/99 test set and G3S theory has a similar accuracy of 1.08 kcal mol⁻¹. G3X theory is significantly more accurate with the mean absolute deviation from experiment decreasing from 1.07 kcal mol⁻¹ (G3) to 0.95 kcal mol⁻¹ (G3X). The scaled version of G3X theory shows a similar improvement. Received: 23 January 2002 / Accepted: 7 April 2002 / Published online: 4 July 2002     

Effect of amorphous precipitated silica on the properties and structure of poly(p-phenylene sulfide)

Using a precipitation technique, silicas were obtained from sodium metasilicate solution employing an acidic agent. Alcohol solutions were used in the process of production of highly dispersed silicas, which resulted in partial blocking of the silica surface silanol groups. Moreover, studies on morphology and microstructure using transmission electron microscopy and scanning electron microscopy were performed. The size distributions of primary particles and aggregate and agglomerate structures were determined using a ZetaPlus instrument using the dynamic light scattering method. The structure and molecular dynamics of the nanocomposite, consisting of poly (p-phenylene sulfide) (PPS) and of the precipitated silica, were studied using atomic force microscopy and nuclear magnetic resonance. It was proved that during annealing the fragmentation of PPS agglomerates takes place. This phenomena probably resulted from repulsion forces existing between agglomerates and aggregates. Fragmentation in the polymer network probably resulted from repulsion forces between agglomerates and smaller aggregates. Received: 7 November 2000 Accepted: 5 April 2001     

A density functional theory study of bridging and terminal oxotitanium(IV) oligomeric and polymeric linear titanoxanes

 This work deals with theoretical investigations on the oxygen–transition metal bond in systems containing linear chains of Ti–O units. From an experimental point of view, in the recent past a number of systems containing linearly arranged Ti–O units were synthesized, in which the Ti atom is complexed with Schiff bases such as acacen and salen. The theoretical study presented here has been carried out applying the density functional theory to model compounds of these systems, in order to shed light on the interactions between the transition metal and oxygen. Calculations have been performed on Ti–O oligomers (dimers, trimers and tetramers) by means of density functional theory at the gradient-corrected level of theory, optimizing the molecular geometries. Calculations have also been performed on linear polymers of the same systems, applying periodic boundary conditions, in order to compare the results with those of oligomeric analogues. Received: 12 January 2002 / Accepted: 16 April 2002 / Published online: 5 July 2002     

Determination of DNA by Use of the Molecular “Light Switch” Complex of Ru(bipy)2(dppz)2+

 A novel fluorimetric method has been developed for selective determination of DNA with the molecular “Light Switch” complex of Ru(bipy)₂(dppz)²⁺. The maximum fluorescence intensity was produced in the pH range of 9.3–11.5, with the maximum excitation and emission wavelength of 471.8 nm and 599.8 nm, respectively. Under the optimum conditions, the fluorescence intensity was in proportion to the concentration of DNA. The linear range for calf thymus DNA salmon sperm DNA and herring sperm DNA reaches from the limit of determination to 1.5 μg/mL. The limits of determination for calf thymus DNA salmon sperm DNA and herring sperm DNA are 3.3 ng/mL, 2.8 ng/mL and 4.4 ng/mL, respectively. When the proposed method was used to determine DNA in the presence of some coexisting substances, a satisfactory result was obtained. Received December 29, 1998. Revision June 28, 1999.     

An overlap criterion for selection of core orbitals

 An overlap criterion is defined that connects the identification of core orbitals in a molecular system, which can be problematic, to that in isolated atoms, which is well defined. This approach has been tested on a variety of troublesome systems that have been identified in the literature, including molecules containing third-row main-group elements, and is shown to remove errors of up to 100 kcal/mol arising from an inconsistent treatment of core orbitals at different locations on a potential-energy surface. For some systems and choices of core orbitals, errors as large as 19 kcal/mol can be introduced even when consistent sets of orbitals are frozen, and the new method is shown to identify these cases of substantial core–valence mixing. Finally, even when there is limited core–valence mixing, the frozen-core approximation can introduce errors of more than 5 kcal/mol, which is much larger than the presumed accuracy of models such as G2 and CBS-QB3. The source of these errors includes interatomic core–core and core–valence dispersion forces. Received: 31 August 2001 / Accepted: 11 October 2001 / Published online: 9 January 2002     

Exploring the quantum mechanical/molecular mechanical replica path method: a pathway optimization of the chorismate to prephenate Claisen rearrangement catalyzed by chorismate mutase

 A replica path method has been developed and extended for use in complex systems involving hybrid quantum/classical (quantum mechanical/molecular mechanical) coupled potentials. This method involves the definition of a reaction path via replication of a set of macromolecular atoms. An “important” subset of these replicated atoms is restrained with a penalty function based on weighted root-mean-square rotation/translation best-fit distances between adjacent (i±1) and next adjacent (i±2) pathway steps. An independent subset of the replicated atoms may be treated quantum mechanically using the computational engine Gamess-UK. This treatment can be performed in a highly parallel manner in which many dozens of processors can be efficiently employed. Computed forces may be projected onto a reference pathway and integrated to yield a potential of mean force (PMF). This PMF, which does not suffer from large errors associated with calculated potential-energy differences, is extremely advantageous. As an example, the QM/MM replica path method is applied to the study of the Claisen rearrangement of chorismate to prephenate which is catalyzed by the Bacillus subtilis isolated, chorismate mutase. Results of the QM/MM pathway minimizations yielded an activation enthalpy ΔH ^†† of 14.9 kcal/mol and a reaction enthalpy of −19.5 kcal/mol at the B3LYP/6-31G(d) level of theory. The resultant pathway was compared and contrasted with one obtained using a forced transition approach based on a reaction coordinate constrained repeated walk procedure (ΔH ^†† =20.1 kcal/mol, ΔH _rxn = −20.1 kcal/mol, RHF/4-31G). The optimized replica path results compare favorably to the experimental activation enthalpy of 12.7±0.4 kcal/mol. Received: 16 December 2001 / Accepted: 6 September 2002 / Published online: 8 April 2003 Contribution to the Proceedings of the Symposium on Combined QM/MM Methods at the 22nd National Meeting of the American Chemical Society, 2001. Correspondence to: H.L. Woodcock e-mail: hlwood@ccqc.uga.edu Acknowledgements. The authors thank Eric Billings, Xiongwu Wu, and Stephen Bogusz for helpful discussions and related work. The authors also show grateful appreciation to The National Institutes of Health and The National Science Foundation for support of the current research.     

Reparameterization of hybrid functionals based on energy differences of states of different multiplicity

 Low-spin/high-spin energy splittings for Fe(II) transition-metal complexes – particularly in weak ligand fields – cannot be well described by density functional methods. Different density functionals yield results which differ by up to 1 eV in transition-metal complexes with sulfur-rich first coordination spheres. We attribute this failure to the fact that the high-spin state is systematically favoured in Hartree–Fock-type theories, because Fermi correlation is included in the exact exchange, while Coulomb correlation is not. We thus expect that the admixture of exact exchange to a given density functional will heavily influence the energy splitting between states of different multiplicity. We demonstrate that the energy splitting depends linearly on the coefficient of exact exchange admixture. This remarkable result is found for all the Fe(II)–S complexes studied. From this observation we conclude in connection with experimental results that Becke's 20% admixture should be reduced to about 15% if meaningful energetics are sought for transition-metal compounds. We rationalize that this reduction by 5% will not affect the quality of the hybrid functional since we arrive at a slightly modified functional, which lies between the pure density functional and the hybrid density functional, which both give good results for “standard” systems. Received: 13 July 2001 / Accepted: 31 August 2001 /  Published online: 16 November 2001     

Accuracy assessment of semiempirical molecular electrostatic potential of proteins

 Accurate electrostatic maps of proteins are of great importance in research of protein interaction with ligands, solvent media, drugs, and other biomolecules. The large size of real-life proteins imposes severe limitations on computational methods one can use for obtaining the electrostatic map. Well-known accurate second-order M?ller–Plesset and density functional theory methods are not routinely applicable to systems larger than several hundred atoms. Conventional semiempirical tools, as less resource demanding ones, could be an attractive solution but they do not yield sufficiently accurate calculation results with reference to protein systems, as our analysis demonstrates. The present work performs a thorough analysis of the accuracy issues of the modified neglect of differential overlap type semiempirical Hamiltonians AM1 and PM3 on example of the calculation of the molecular electrostatic potential and the dipole moment of natural amino acids. Real capabilities and limitations of these methods with application to protein modeling are discussed. Received: 26 April 2002 / Accepted: 19 September 2002 / Published online: 14 February 2003     

Comparison of a homology model and the crystallographic structure of human 11β-hydroxysteroid dehydrogenase type 1 (11βHSD1) in a structure-based identification of inhibitors

Summary Human 11β-hydroxysteroid dehydrogenase type 1 (11βHSD1) catalyzes the interconversion of cortisone into active cortisol. 11βHSD1 inhibition is a tempting target for the treatment of a host of human disorders that might benefit from blockade of glucocorticoid action, such as obesity, metabolic syndrome, and diabetes type 2. Here, we report an in silico screening study aimed at identifying new selective inhibitors of human 11βHSD1 enzyme. In the first step, homology modeling was employed to build the 3D structure of 11βHSD1. Further, molecular docking was used to validate the predicted model by showing that it was able to discriminate between known 11βHSD1 inhibitors or substrates and non-inhibitors. The homology model was found to reproduce closely the crystal structure that became publicly available in the final stages of this work. Finally, we carried out structure-based virtual screening experiments on both the homology model and the crystallographic structure with a database of 114’000 natural molecules. Among these, 15 molecules were consistently selected as inhibitors based on both the model and crystal structures of the enzyme, implying a good quality for the homology model. Among these putative 11βHSD1 inhibitors, two were flavonone derivatives that have already been shown to be potent inhibitors of the enzyme.     

Π delocalisation in 1,3-butadiene: a nonempirical molecular orbital study

A value of −0.33 eV or −7.6 kcal mol⁻¹ has been obtained for the vertical delocalisation energy of trans-1,3-butadiene from a nonempirical molecular orbital calculation on the π system. The result agrees well enough with ab initio calculations to suggest that a simplified approach need not be semiempirical. In a basis of orthogonalised atomic orbitals the central bond order is found to be 0.295 (Hückel value 0.447) for the delocalised structure and 0.125 for the localised (Hückel value zero). Core resonance integrals between neighbouring atoms, the analogues of Hückel's β, have theoretical values of −3.9 and −3.2 eV compared with −3.6 eV in benzene. Received: 11 May 1999 / Accepted: 22 July 1999 / Published online: 2 November 1999     

Self-consistent reaction field calculation of solvent reorganization energy in electron transfer: a dipole-reaction field interaction model

Based on the continuum dielectric model, this work has established the relationship between the solvent reorganization energy of electron transfer (ET) and the equilibrium solvation free energy. The dipole-reaction field interaction model has been proposed to describe the electrostatic solute-solvent interaction. The self-consistent reaction field (SCRF) approach has been applied to the calculation of the solvent reorganization energy in self-exchange reactions. A series of redox couples, O₂/O⁻ ₂, NO/NO⁺, O₃/O⁻ ₃, N₃/N⁻ ₃, NO₂/NO⁺ ₂, CO₂/CO⁻ ₂, SO₂/SO⁻ ₂, and ClO₂/ClO⁻ ₂, as well as (CH₂)₂C-(-CH₂-) _n -C(CH₂)₂ (n=1 ∼ 3) model systems have been investigated using ab initio calculation. For these ET systems, solvent reorganization energies have been estimated. Comparisons between our single-sphere approximation and the Marcus two-sphere model have also been made. For the inner reorganization energies of inorganic redox couples, errors are found not larger than 15% when comparing our SCRF results with those obtained from the experimental estimation. While for the (CH₂)₂C–(–CH₂–) _n –C(CH₂)₂ (n=1 ∼ 3) systems, the results reveal that the solvent reorganization energy strongly depends on the bridge length due to the variation of the dipole moment of the ionic solute, and that solvent reorganization energies for different systems lead to slightly different two-sphere radii. Received: 19 April 2000 / Accepted: 6 July 2000 / Published online: 27 September 2000