Metals in biology: Electronic structure,properties and charge transfer for copper complexes of glyoxal and dithiene

Summary In an attempt to study the role of metals in biologyab initio SCF calculations have been performed on a model complex simulating the binding between metals and biological materials. There is a certain distinction between the copper complexes compared to the other transition metals and in many cases the copper complexes are more similar to the Li and Be complexes than to other transition metal complexes. One special feature of the copper complexes is their strong ability for an easy transfer between the Cu(I) and Cu(II) states, allowing for a very flexible charge transfer with small energies required for the redox processes. These processes have been described in terms of orbital energies and Mulliken populations.Dedicated to Professor Inga Fischer-Hjalmars on the occasion of her 75th birthday     

Theoretical studies on the electronic structures and absorption spectra of substituted benzenes with one- and two-dimensional charge transfer character

The electronic structures and absorption spectra of one- and two-dimensional charge transfer (CT) molecules based on para-nitroaniline (pNA) and 1,3-diamino-4,6-dinitro- benzene (DADB) have been studied theoretically via semi-empirical and ab initio methods. It is found that the behaviors of optical absorption are strongly influenced by the dimension of CT. Different from the well-known one-dimensional CT molecule of pNA, which shows one intense absorption related to the π → π^* CT transition, two-dimensional CT molecule of DADB exhibits more absorption peaks associated with various low-lying CT transitions in near ultraviolet range. In addition, the relative orientations of transition dipole moment and ground state dipole moment in one- and two-dimensional charge transfer molecules were also discussed.     

Atomic decomposition of identity: General formalism for population analysis and energy decomposition

The concept of “atomic resolution of identity” has been introduced, leading to a very simple general formalism for generating different decomposition schemes of molecular quantities. Thus, different population analysis and energy partitioning schemes can be treated as special cases of a common framework. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

A simple and convenient method for the preparation of diborane from tetrabutylammonium borohydride and benzyl chloride for application in organic synthesis

Diborane is readily generated in situ at 25 °C in toluene using the Bu₄NBH₄/PhCH₂Cl and Bu₄NBH₄/I₂ reagent systems. The reagent prepared in this way is used for the reduction of carbonyl compounds and hydroboration-oxidation of olefins to obtain the corresponding alcohols in good yields.     

Orbital correlation effects: The independent pair-potential approximation with application to the ground state and first ionized state of boron hydride

A new method is proposed for calculating correlation effects in atomic and molecular systems. The basis of the method is the formulation of a set of partial configuration expansions which yield directly variational orbital correlation corrections which are appropriately summed in order to obtain an estimate of the total correlation energy. This method is applied to the ground state of boron hydride and its cation at the equilibrium distance of BH. The results of the method are compared in detail with independent electron pair results and second order CI results. It is further shown that multiple substitutions are approximately accounted for in this method and the extent to which they are included is compared with other approximations. Finally, three methods of increasing accuracy, aimed at reducing the necessary computational effort, are given for determining the vertical ionization potential. The most economical method yields an IP of 9.70 eV or 0.03 eV less than the experimental IP. Completion of the basis is estimated to improve this value to 9.77 eV.     

Effect of charge state and stoichiometry on the structure and reactivity of nickel oxide clusters with CO

The collision induced fragmentation and reactivity of cationic and anionic nickel oxide clusters with carbon monoxide were studied experimentally using guided-ion-beam mass spectrometry. Anionic clusters with a stoichiometry containing one more oxygen atom than nickel atom (NiO₂⁻, Ni₂O₃⁻, Ni₃O₄⁻ and Ni₄O₅⁻) were found to exhibit dominant products resulting from the transfer of a single oxygen atom to CO, suggesting the formation of CO₂. Of these four species, Ni₂O₃⁻ and Ni₄O₅⁻ were observed to be the most reactive having oxygen transfer products accounting for approximately 5% and 10% of the total ion intensity at a maximum pressure of 15 mTorr of CO. Our findings, therefore, indicate that anionic nickel oxide clusters containing an even number of nickel atoms and an odd number of oxygen atoms are more reactive than those with an odd number of nickel atoms and an even number of oxygen atoms. The majority of cationic nickel oxides, in contrast to anionic species, reacted preferentially through the adsorption of CO onto the cluster accompanied by the loss of either molecular O₂ or nickel oxide units. The adsorption of CO onto positively charged nickel oxides, therefore, is exothermic enough to break apart the gas-phase clusters. Collision induced dissociation experiments, employing inert xenon gas, were also conducted to gain insight into the structural properties of nickel oxide clusters. The fragmentation products were found to vary considerably with size and stoichiometry as well as ionic charge state. In general, cationic clusters favored the collisional loss of molecular O₂ while anionic clusters fragmented through the loss of both atomic oxygen and nickel oxide units. Our results provide insight into the effect of ionic charge state on the structure of nickel oxide clusters. Furthermore, we establish how the size and stoichiometry of nickel oxide clusters influences their ability to oxidize CO, an important reaction for environmental pollution abatement.     

All-solid-state electronic tongue and its application for beverage analysis

Disposable all-solid-state planar-type potentiometric electronic tongue has been developed with the carbon paste electrode array screen-printed on a polymeric substrate. Highly cross-sensitive solvent polymeric membranes based on different matrices [e.g. poly(vinyl chloride) (PVC), aromatic polyurethane, and polypyrrole (Ppy)] and doped with common electroactive components for potentiometric measurements (e.g. various plasticizers, and cation- and anion-selective ionophores) were deposited on the screen-printed carbon paste electrodes (SCPEs). It was observed that an incorporation of 10 wt.% of Prussian Blue (PB; Fe₄(III)[Fe(II)(CN)₆]₃) into a commercially available carbon paste and electrochemical preanodization of SCPEs in KCl solution at 1.6 V provide the all-solid-state planar-type electrodes with significantly improved potentiometric stability. The proposed fabrication method gives possibility for simple and reproducible mass-production of low-cost disposable electronic tongue microsystems. The practical utility of all-solid-state disposable electronic tongue chips has been demonstrated with a flow injection cell for the analysis of potable waters, soft drinks, and beers. It is shown that the potentiometric measurements with the SCPE-based all-solid-state chips and the combined use of chemometric methods (e.g. principal components analysis, partial least regression (PLS), and principal component regression (PCR)) for the analysis of obtained data sets successfully discriminate various types of samples according to their tastes.     

Applications of the virtual charge model to the electronic structures and spectra of benzaldehyde and acetophenone

Summary The virtual charge model (Tapia model) in conjunction with the CNDO/S-CI approximation in the frame of SCF-MO theory was employed to study the effects of solvent on the electronic structures and spectra of benzaldehyde and acetophenone molecules. The CNDO/S calculations in presence of solvation indicate a satisfactory interpretation of the medium effects on the electronic structures and spectra of the molecules investigated. The prediction of our MO calculations by means of the Tapia model concerning the solvochromic shifts of n * and * transitions are in accord with the observed trends which indicate a blue shift for the n * band and a red shift for the * band upon a change of solvent from non-polar to polar solvents.

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Anwendung des Virtual Charge-Modells auf die Elektronenstrukturen und Spektren von Benzaldehyd und Acetophenon

Zusammenfassung Das Virtual-Charge-Modell (Tapia-Modell) im Zusammenhang mit der CNDO/S-CI-Näherung im Rahmen der SCF-MO-Theorie wurde zum Studium der Lösungsmitteleffekte auf die Elektronenstrukturen und Spektren von Benzaldehyd und Acetophenon herangezogen. Die CNDO/S-Rechnungen bei Anwesenheit von Solvens erlauben eine befriedigende Interpretation der Mediumeffekte auf Elektronenstrukturen und Spektren der untersuchten Verbindungen. Die aus MO-Rechnungen folgenden Voraussagen ergeben auf Basis des Tapia-Modells solvatochrome Verschiebungen für die n *- und *-Übergänge. Die vorausgesagten Effekte stehen im Einklang mit den experimentell beobachteten Trends: Blauverschiebung für die n *-Bande und Rotverschiebung für die *-Bande beim Wechsel von nichtpolarem zu polarem Lösungsmittel.

     

Using electronic pressure programming to reduce the decomposition of labile compounds during splitless injection

A split/splitless capillary injection port has been developed for electronic pressure programming (EPP) in gas chromatography. The inlet may be operated in several modes: constant pressure, constant flow, vacuum compensation (for gas chromatography–mass spectrometry (GC-MS)), pressure-programmed, or a combination mode enabling a pressure program to be followed by constant flow. A pressure-programming technique has been tried which uses high pressure (high column flow rate) at the time of injection followed by reduction in inlet pressure to a value required for normal chromatography. Sample is swept rapidly from the inlet and into the column, reducing contact with the hot, active inlet surfaces which cause sample decomposition. The decomposition of endrin and 4,4′-DDT, two labile pesticides, can be substantially reduced using this technique and modest improvements were also observed with the carbamate pesticide carbaryl.     

Symmetry analysis of the potential energy surfaces for the photochemical decomposition of formaldehyde

Orbital Correspondence Analysis in Maximum Symmetry (OCAMS) is applied to the decomposition pathways of formaldehyde to H₂ + CO and to H + HCO. The symmetry adapted nuclear motions, which are preferentially incorporated in the energetically favoured fragmentation pathways on both the ground and excited state surfaces are singled out. The results of this analysis are in full agreement with those of published potential energy surfaces and consistent with the results of experimental investigations reported in the literature. The nuclear motions favouring the various processes thus appear to be deducible from considerations of orbital symmetry.This work was carried out during tenure of a Minerva Foundation grant to one of us. (E.A.H.)     

Energy decomposition in molecular complexes: implications for the treatment of polarization in molecular simulations

This study examines the contribution of electrostatic and polarization to the interaction energy in a variety of molecular complexes. The results obtained from the Kitaura-Morokuma (KM) energy decomposition analysis at the HF/6-31G(d) level indicate that, for intermolecular distances around the equilibrium geometries, the polarization energy can be determined as the addition of the polarization energies of interacting blocks, as the mixed polarization term is typically negligible. Comparison of KM and QM/MM results shows that the electrostatic energy determined in the KM method is underestimated (in absolute value) by QM/MM methods. The reason of such underestimation can be attributed to the simplified representation of treating the interaction between overlapping charge distribution by the interaction of a QM molecule with a set of point charges. Nevertheless, the polarization energies calculated by KM and QM/MM methods are in close agreement. Finally, a consistent, automated strategy to derive charge distributions that include implicitly polarization effects in pairwise, additive force fields is presented. The strategy relies in the simultaneous fitting of electrostatic and polarization energies computed by placing a suitable perturbing particle at selected points around the molecule. The suitability of these charges to describe molecular interactions is discussed.     

Theoretical investigation of electronic structures and excitation energies of hexaphyrin and its group 11 transition metal (III) complexes

Density functional theory is carried out to study hexaphyrin and its bis-metal and mixed bis-metal (M = Cu³⁺, Ag³⁺, and Au³⁺) complexes. The electronic structures and bonding situations of them are studied by using natural bond orbital approach and the topological analysis of the electron localization function. Electronic spectra are investigated by using time-dependent density functional theory. The introduction of group 11 transition metals leads to red shifts in the spectra of these metal complexes with respect to that of hexaphyrin. Moreover, it is noteworthy that the spectra of copper contained complexes are mainly derived from combination of ligand-to-metal charge transfer and ligand-to-ligand charge transfer transitions. In addition, the relativistic time-dependent density functional theory with spin-orbit coupling calculations indicate that the effects of spin-orbit coupling on the excitation energies are so small that it is safe enough to neglect spin-orbit coupling for these systems.     

Pressure relaxation of polystyrene and its comparison to the shear response

Isothermal pressure relaxation as a function of temperature in two pressure ranges has been measured for polystyrene using a self-built pressurizable dilatometer. A master curve for pressure relaxation in each pressure regime is obtained based on the time–temperature superposition principle, and time–pressure superposition of the two master curves is found to be applicable when the master curves are referenced to their pressure-dependent T_g. The pressure relaxation master curves, the shift factors, and retardation spectra obtained from these curves are compared with those obtained from shear creep compliance measurements for the same material. The shift factors for the bulk and shear responses have the same temperature dependence, and the retardation spectra overlap at short times. Our results suggest that the bulk and shear response have similar molecular origin, but that long-time chain mechanisms available to shear are lost in the bulk response. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 3375–3385, 2007     

Computational investigation of tuning the electronic ability and featured for heterofullerene based dye sensitized solar cells

The structural characteristics of the heteroatom substituted fullerene to improve its physical and chemical properties are discussed in this work, highlighting possible applications in aromaticity, photocatalysis, solar cells, and superconducting materials. The energy gap of doped fullerene lowers significantly, making C₃₁Nb a more reactive material and transforming it into an efficient superconductor. The molecular structure, energy and relative stabilities of the heterofullerene were examined and evaluated to determine the material's identification. According to the results analysis, the extra niobium atom and substituted carbon atom improve the electronic stability of heterofullerene. Using ¹³C NMR nuclear independent chemical shift, the stability of each fullerene and aromatic found in nature is discovered. Furthermore, the simulated infrared spectra of fullerene are reviewed, and the major distinctive peaks are given to different functional groups. NBO study which shows the intermolecular charge transfer from the donor to the acceptor in doped fullerene, demonstrates that the strong intermolecular contact between carbon and niobium atoms makes this material a notable material for NLO property.     

Characterization and kinetics analysis of the thermal decomposition of the humic substance from hazelnut husk

A humic substance was obtained from hazelnut husk using an alkali extraction. The chemical and morphological structure of the humic matter was characterized via elemental analysis, Fourier transform infrared spectrometry (FTIR), nuclear magnetic resonance, Brunauer-Emmet-Teller (BET) analysis, scanning electron microscopy (SEM), and thermogravimetric-FTIR (TG-FTIR). In addition, thermal analysis measurements TG analysis-differential thermogravimetry/differential scanning calorimetry (TGA-DTG/DSC) were performed under dynamic air conditions to better determine the origin, physical and chemical structure, and decomposition process of the humic matter. The Kissinger-Akahira-Sunose (KAS) and Flynn-Wall-Ozawa (FWO) methods were used to calculate the kinetic parameters of the high-temperature decomposition process. It was observed that the activation energy values were almost constant at certain conversion and temperature intervals. In addition, the structure of the humic substance at different temperatures was also investigated via FTIR analysis. It was found that the obtained humic substance had a very stable structure and decomposed at a high temperature. The stability of the humic matter can be a useful tool in the environmental quality research of soil.     

Theoretical investigation of the GaF molecule and its positive ion

Coupled pair approximation and configuration interaction calculations were carried out on the gallium fluoride molecule and its positive ion with flexible basis sets. Spectroscopic constants of these species were examined in detail through step-wise extensions of correlating space. The contribution from correlations of the semi-core 3d electrons in Ga was found to be sizable. The bonding character was revealed to be highly ionic even for the positive ion. Received: 13 June 1998/Accepted: 28 August 1998 / Published online: 7 December 1998     

SurfinPES: Performing automated analysis of activation strain,energy decomposition,and reaction force

Analyzing activation strain, energy decomposition, and reaction force models is crucial for studying chemical reactivity and gaining quantitative insights into the factors that control energy barriers. However, manually preparing and processing the necessary data can be challenging and prone to errors. To address this issue, we introduce SurfinPES, a Python-based module in Eyringpy that automates data extraction and processing for these analyses. SurfinPES also allows monitoring of the evolution of primitive properties (geometrical and electronic) along the reaction coordinate. The module is user-friendly with a simple input format, making it accessible to any user in the field of computational chemistry.     

Outer product analysis of electronic nose and visible spectra: application to the measurement of peach fruit characteristics

Visual aspect and aroma are among the most important features of fruit that determine consumer preferences. Electronic nose and spectroscopic techniques have shown positive results in evaluating some basic analytical parameters of fruit and global features such as the cultivar.In this paper, we illustrate and discuss a study aimed at evaluating the improvement derived by the fusion of visible spectra and electronic nose data. These experiments were performed on a population of yellow peaches belonging to two cultivars. Each sample was measured by visible optical spectroscopy and by electronic nose. In addition, a number of reference parameters were also measured by conventional destructive methodologies.Collected data were analysed individually and then fused together in order to classify the two cultivars and to estimate the reference parameters. Data fusion was performed building the outer product matrix for each measurement. The set of matrices was then successively unfolded and analysed by conventional chemometrics tools.Results were improved using outer products, for instance in classification average percentage errors of 25, 10, and 7 for electronic nose, spectra, and outer product, respectively was achieved. Regression analysis provides the evidence of a substantial orthogonal appearance of the datasets, which offer former hidden information on fruit classification.     

Direct estimate of the strength of conjugation and hyperconjugation by the energy decomposition analysis method

The intrinsic strength of pi interactions in conjugated and hyperconjugated molecules has been calculated using density functional theory by energy decomposition analysis (EDA) of the interaction energy between the conjugating fragments. The results of the EDA of the trans-polyenes H2C=CH-(HC=CH)n-CH=CH2 (n = 1-3) show that the strength of pi conjugation for each C=C moiety is higher than in trans-1,3-butadiene. The absolute values for the conjugation between Si=Si pi bonds are around two-thirds of the conjugation between C=C bonds but the relative contributions of DeltaE pi to DeltaE orb in the all-silicon systems are higher than in the carbon compounds. The pi conjugation between C=C and C=O or C=NH bonds in H2C=CH--C(H)=O and H2C=CH-C(H)=NH is comparable to the strength of the conjugation between C=C bonds. The pi conjugation in H2C=CH-C(R)=O decreases when R = Me, OH, and NH2 while it increases when R = halogen. The hyperconjugation in ethane is around a quarter as strong as the pi conjugation in ethyne. Very strong hyperconjugation is found in the central C-C bonds in cubylcubane and tetrahedranyltetrahedrane. The hyperconjugation in substituted ethanes X3C-CY3 (X,Y = Me, SiH3, F, Cl) is stronger than in the parent compound particularly when X,Y = SiH3 and Cl. The hyperconjugation in donor-acceptor-substituted ethanes may be very strong; the largest DeltaE pi value was calculated for (SiH3)3C-CCl3 in which the hyperconjugation is stronger than the conjugation in ethene. The breakdown of the hyperconjugation in X3C-CY3 shows that donation of the donor-substituted moiety to the acceptor group is as expected the most important contribution but the reverse interaction is not negligible. The relative strengths of the pi interactions between two C=C double bonds, one C=C double bond and CH3 or CMe3 substituents, and between two CH3 or CMe3 groups, which are separated by one C-C single bond, are in a ratio of 4:2:1. Very strong hyperconjugation is found in HC[triple bond]C-C(SiH3)3 and HC[triple bond]C-CCl3. The extra stabilization of alkenes and alkynes with central multiple bonds over their terminal isomers coming from hyperconjugation is bigger than the total energy difference between the isomeric species. The hyperconjugation in Me-C(R)=O is half as strong as the conjugation in H2C=CH-C(R)=O and shows the same trend for different substituents R. Bond energies and lengths should not be used as indicators of the strength of hyperconjugation because the effect of sigma interactions and electrostatic forces may compensate for the hyperconjugative effect.     

Energy and capacity time correlation functions for investigation of vibrational energy relaxation

Vibrational energy relaxation of a diatomic solute in a liquid solvent is investigated by means of the generalized Langevin equation. The vibrational energy, velocity and capacity time correlation functions (TCFs) are considered. It is shown that the detailed structure of the energy TCF contains an initial fast (subpicosecond) decay segment that is followed by weak oscillations on the background of an exponential relaxation curve. The direct method for evaluating the relaxation rate constant from equilibrium molecular dynamics simulations of a flexible solute is proposed and implemented. The closed form expressions for the memory function and for the relaxation rate constant in terms of quantities accessible from the simulations are derived. The simulation results for rigid and flexible solutes are compared and analyzed.