Theoretical study of the 1,3-hydrogen shift of triazene in water

The 1,3-hydrogen shift of triazene in aqueous solution was studied with a combination of QM/MM methods. First, the different species involved were characterized and the activation free-energies calculated with ASEP/MD, a method that makes use of the mean field approximation. Then the reaction dynamics was simulated with a QM/MM/MD method. A very strong influence of the solvent was observed, both specific, with the participation of a water molecule, and from the rest of the solvent. The effect of solvation on the geometry and electron distribution of triazene is important: N-N bond lengths tend to be more similar and the molecule acquires a planar structure. For the transition state structure, a substantial degree of ionic nature was found. Dynamic solvent effects were also analyzed.     

The proton momentum distribution in strongly H-bonded phases of water: a critical test of electrostatic models

Water is often viewed as a collection of monomers interacting electrostatically with each other. We compare the water proton momentum distributions from recent neutron scattering data with those calculated from two electronic structure-based models. We find that below 500 K these electrostatic models, one based on a multipole expansion, which includes the polarizability of the monomers, are not able to even qualitatively account for the sizable vibrational zero-point contribution to the enthalpy of vaporization. This discrepancy is evidence that the change in the proton well upon solvation cannot be entirely explained by electrostatic effects alone, but requires correlations of the electronic states on the molecules involved in the hydrogen bonds to produce the observed softening of the well.     

Sol-gel derived ceramic-carbon enzyme electrodes: Glucose oxidase as a test case

Several types of amperometric biosensors comprised of immobilized glucose oxidase in chemically-modified ceramic-carbon matrices are compared. The electrodes are comprised of several building blocks each performing a specific function. Glucose oxidase is used to catalyze the bio-oxidation of glucose; carbon powder imparts conductivity and favorable electrochemical characteristics; the Ormosil network provides rigidity and porosity; and the organic modification of the Ormosil imparts controlled surface polarity. Additionally, hydrophilic chemical modifiers are incorporated in order to control the size of the wetted, electroactive layer; high dispersion of inert metal catalysts is used to enhance hydrogen peroxide oxidation and redox mediators may be co-immobilized when oxygen independent response is desirable. The electrodes can be prepared either in the form of thick supported film, useful for disposable electrodes or as bulk-modified, disk shape electrodes, which can be used as renewable surface electrodes.     

d-d Spectra of transition-metal carbodiimides and hydrocyanamides as derived from many-particle effective Hamiltonian calculations

We apply the local many-particle method of the Effective Hamiltonian of Crystal Field (EHCF) to analyze the magnetic ground state and the low-energy excitation spectra of the transition-metal carbodiimides MNCN with M = Fe-Ni. Experimentally, these materials represent a uniform group of (high-spin) antiferromagnetic, optically transparent, colored insulators with absorption lines in the visible spectrum. These findings are fully supported by the EHCF numerical modeling. In all three cases, we arrive at high-spin ground states in agreement with the results of previous magnetic measurements as well as the presence of the d-d intrashell transitions for the visible absorption spectra. Remarkably enough, the EHCF approach resolves the controversial case of FeNCN which was earlier predicted to be metallic by density-functional theory even when including explicit electronic correlation (GGA+U). We also address the ground state and the low-energy excitation spectra of the transition-metal hydrocyanamides of the general formula M(NCNH)(2) with M = Fe-Ni, another uniform group of optically transparent colored insulators. EHCF also arrives at high-spin ground states and visible d-d intrashell transitions.     

Improved consistency in 2D gel electrophoresis: Sheep plasma as a test case

Two‐dimensional (2D) gel electrophoresis is a well‐proven proteomic technique; however, sample‐specific optimisation can often be necessary in order to get consistent quantitation. In particular, plasma samples are often smeared on 2D gels making spot matching difficult. A variety of different sample preparation and 2D methods were tested by using sheep plasma, and it was found that lowering sample pH prior to precipitation, using a long voltage gradient for isoelectric focusing and the inclusion of carrier ampholytes in the electrode wicks, improved both the quality and consistency of spot resolution. Analysis of the internal standards from two different DIGE experiments, one with conventional methodology and one with the improved method, showed that along with substantially improving the number of spots resolved, the average CV (coefficient of variation) of matched standards was lower with the new method. 428 matched spots were found using the improved method compared to 208 matched spots using conventional methodology. For the 174 spots that were matched between the two DIGE experiments, the average CV's of spot volumes were also significantly lower, at 0.20 for the new method compared to 0.24 for the conventional method (p < 0.001).     

Normalized irreducible tensorial matrix expansions applied to an effective sp-type Hamiltonian for the PES of water

Any matrix can be expanded on a basis of SU(2) normalized irreducible tensorial matrices, NITM , defined in terms of 3-j symbols or coupling coefficients of SU (2). The NITM transform under rotations according to Wigner's matrices. If one dimension of an NITM is odd and the other even, the tensor has half-integer rank. A simple NITM basis consists of all NITM having the same numbers of rows and columns as the expanded matrix. A compound NITM basis consists of two or more simple bases, each spanning a corresponding block in the expanded matrix. The choice of NITM basis for expanding an effective Hamiltonian matrix is a crucial step in formulating a model. To illustrate the use of a compound NITM basis, including nonsquare NITM , an effective sp-type overlap-free superposition Hamiltonian is constructed and applied to the photoelectron ionization potential spectrum of water.     

Improving description of hydrogen bonds at the semiempirical level: water–water interactions as test case

Hydrogen bonding is not well described by available semiempirical theories. This is an important restriction because hydrogen bonds represent a key feature in many chemical and biochemical processes, besides being responsible for the singular properties of water. In this study, we describe a possible solution to this problem. The basic idea is to replace the nonphysical gaussian correction functions (GCF) appearing in the core–core repulsion terms of most MNDO‐based semiempirical methods by a simple function exhibiting the correct physical behavior in the whole range of intermolecular separation distances. The parameterized interaction function (PIF) is the sum of atom‐pair contributions, each one having five adjustable parameters. In this work, the approach is used to study water–water interactions. The parameters are optimized to reproduce a reference ab initio intermolecular energy surface for the water–water dimer obtained at the MP2/aug‐cc‐pVQZ level. OO, OH, and HH parameters are reported for the PM3 method. The results of PM3‐PIF calculations remarkably improve qualitatively and quantitatively those obtained at the standard PM3 level, both for water–dimer properties and for water clusters up to the hexamer. For example, the root‐mean‐square deviation of the PM3‐PIF interaction energies, with respect to ab initio values obtained using 700 points of the water dimer surface, is only 0.47 kcal/mol. This value is much smaller than that obtained using the standard PM3 method (4.2 kcal/mol). The PM3‐PIF water dimer energy minimum (−5.0 kcal/mol) is also much closer to ab initio data (−5.0±0.01 kcal/mol) than PM3 (−3.50 kcal/mol). The method is therefore promising for the development of new semiempirical approaches as well as for application of combined quantum mechanics and molecular mechanics techniques to investigate chemical processes in water. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 572–581, 2000     

Comparison of three methods for measuring 222Rn in drinking water

Three techniques were used to measure ²²²Rn in drinking water: the degassing method followed by counting in an ionisation chamber (IC); gamma spectrometry (GS); and liquid scintillation counting (LSC). Environmental samples were measured in the field using the IC, and the same samples were measured in the laboratory using GS and LSC. The results obtained using the three techniques are compared and discussed in the context of the new Euratom Drinking Water Directive (2013/51/Euratom), which sets out general principles for monitoring radioactive substances such as radon.

     

Predictive-property-ranked variable reduction in partial least squares modelling with final complexity adapted models: Comparison of properties for ranking

The calibration performance of partial least squares regression for one response (PLS1) can be improved by eliminating uninformative variables. Many variable-reduction methods are based on so-called predictor-variable properties or predictive properties, which are functions of various PLS-model parameters, and which may change during the steps of the variable-reduction process. Recently, a new predictive-property-ranked variable reduction method with final complexity adapted models, denoted as PPRVR-FCAM or simply FCAM, was introduced. It is a backward variable elimination method applied on the predictive-property-ranked variables. The variable number is first reduced, with constant PLS1 model complexity A, until A variables remain, followed by a further decrease in PLS complexity, allowing the final selection of small numbers of variables.     

Electronic states of the benzene dimer: a simple case of complexity

Electronic structure calculations of the excited states of the benzene dimer using equation-of-motion coupled-cluster method are reported. The calculations reveal large density of electronic states, including multiple valence, Rydberg, and mixed Rydberg-valence states. The calculations of the oscillator strengths for the transitions between the excimer state (i.e., the lowest excited state of the dimer, 1(1)B(1g)) and other excited states allowed us to identify the target state responsible for the excimer absorption as the E(1u) state of a mixed Rydberg-valence character at 3.04 eV above the excimer (1(1)B(1g)). Although at D(6h) the 1(1)B(1g) → E(1u) transition is symmetry-forbidden, small geometric displacements (to D(2h)) that have a negligible effect on the excitation energy split this degenerate state into the dark (4B(3u)) and bright (4B(2u)) components (oscillator strength of 0.3 au). The excitation energy for this transition depends strongly on the dimer structure, which explains the broad character of the experimentally observed excimer absorption spectrum.     

Integrated computational approach to vibrationally resolved electronic spectra: anisole as a test case

A new general and effective procedure to compute Franck-Condon spectra from first principles is exploited to elucidate the subtle features of the vibrationally resolved optical spectra of anisole. Methods based on the density functional theory and its time-dependent extension for electronic excited states [B3LYP6-311+G(d,p) and TD-B3LYP6-311+G(d,p)] have been applied to geometry optimizations and harmonic frequency calculations. Perturbative anharmonic frequencies [J. Chem. Phys. 122, 014108 (2005)] have been calculated for the ground state, and the Duschinsky matrix elements have been used to evaluate the corresponding anharmonic corrections for the first excited electronic state. The relative energetics of both electronic states has been refined by single point calculations at the coupled clusters (CC) level with the aug-cc-pVDZ basis set. Theoretical spectra have been evaluated using a new optimized implementation for the effective computation of Franck-Condon factors. The remarkable agreement between theoretical and experimental spectra allowed for revision of some assignments of fundamental vibrations in the S(1) state of anisole.     

Allene and pentatetraene cations as models for intramolecular charge transfer: vibronic coupling Hamiltonian and conical intersections

We consider the vibronic coupling effects involving cationic states with degenerate components that can be represented as charge localized at either end of the short cumulene molecules allene and pentatetraene. Our aim is to simulate dynamically the charge transfer process when one component is artificially depopulated. We model the Jahn-Teller vibronic interaction within these states as well as their pseudo-Jahn-Teller coupling with some neighboring states. For the manifold of these states, we have calculated cross sections of the ab initio adiabatic potential energy surfaces along all nuclear degrees of freedom, including points at large distances from the equilibrium to increase the physical significance of our model. Ab initio calculations for the cationic states of allene and pentatetraene were based on the fourth-order M?ller-Plesset method and the outer valence Green's function method. In some cases we had to go beyond this method and use the more involved third-order algebraic diagrammatic construction method to include intersections with satellite states. The parameters for a five-state, all-mode diabatic vibronic coupling model Hamiltonian were least-square fitted to these potentials. The coupling parameters for the diabatic model Hamiltonian are such that, in comparison to allene, an enhanced preference for indirect charge transfer is predicted for pentatetraene.     

Incorporating protein flexibility in structure-based drug discovery: using HIV-1 protease as a test case

We have developed a receptor-based pharmacophore method which utilizes a collection of protein structures to account for inherent protein flexibility in structure-based drug design. Several procedures were systematically evaluated to derive the most general protocol for using multiple protein structures. Most notably, incorporating more protein flexibility improved the performance of the method. The pharmacophore models successfully discriminate known inhibitors from drug-like non-inhibitors. Furthermore, the models correctly identify the bound conformations of some ligands. We used unliganded HIV-1 protease to develop and validate this method. Drug design is always initiated with a protein-ligand structure, and such success with unbound protein structures is remarkable - particularly in the case of HIV-1 protease, which has a large conformational change upon binding. This technique holds the promise of successful computer-based drug design before bound crystal structures are even discovered, which can mean a jump-start of 1-3 years in tackling some medically relevant systems with computational methods.     

Palladium-catalyzed ortho-olefination of 2-arylpyrrolidines: A tool for increasing structural complexity in nitrogen heterocycles

The dual role of the (2-pyridyl)sulfonyl unit as directing functionality and readily removable N-protecting group has enabled an efficient and practical transformation of 2-arylpyrrolidine derivatives into more complex tricyclic frameworks via palladium-catalyzed ortho-olefination with electron deficient alkenes and subsequent cyclization upon N-deprotection under mild conditions. The key cross coupling step in the presence of N-fluoro-2,4,6-trimethylpyridinium triflate ([F+]) as the terminal oxidant is both highly efficient and tolerant to a variety of steric and electronic changes at both coupling partners. By adequate choice of reductive conditions, the N-sulfonyl deprotection can be directed to the selective formation of benzo-fused pyrrolizidine or fused pyrrolidino-benzazapine frameworks.     

Role and effective treatment of dispersive forces in materials: Polyethylene and graphite crystals as test cases

A semiempirical addition of dispersive forces to conventional density functionals (DFT-D) has been implemented into a pseudopotential plane-wave code. Test calculations on the benzene dimer reproduced the results obtained by using localized basis set, provided that the latter are corrected for the basis set superposition error. By applying the DFT-D/plane-wave approach a substantial agreement with experiments is found for the structure and energetics of polyethylene and graphite, two typical solids that are badly described by standard local and semilocal density functionals.     

Photochemistry of the three carboxypyridines in water: a pH dependent reaction

The photochemistry of ortho, meta and para-carboxypyridines (pK(a)(1)= 1.0-2.1 and pK(a)(2)= 4.7-5.3) in aqueous medium was studied by laser-flash photolysis and product studies. At pH < pK(a)(1), hydroxylated compounds are produced with low quantum yields. Within the pH range 4-7, ortho and meta isomers undergo dimerization together with decarboxylation with a quantum yield showing a very sharp maximum around pK(a)(2)([small phi](max)= 0.09 and 0.01, respectively) while the para isomer is photostable. End-of-pulse transients assigned to triplet states were detected by laser-flash photolysis at pH < pK(a)(1) and pH > 4. Additionally, the carboxypyridinyl radicals were detected as secondary intermediates at pH < pK(a)(1) and 4 < pH < 7 and the OH-adduct radicals at pH < pK(a)(1). This is in favour of an electron transfer reaction between triplet and starting compound producing a charge transfer species. The radical anion would escape as carboxypyridinyl radical while the radical cation may add water at pH < pK(a)(1) yielding the OH-adduct radical or may undergo decarboxylation at pH > 4. The high quantum yield of phototransformation of the ortho isomer at pH > 4 is due to an easy decarboxylation process. A reaction scheme is proposed accounting for the dependences of [small phi] on both the pH and the carboxypyridines concentration. This study points out the distinct pattern of reactivity of carboxypyridines depending on the ionisation state of starting compounds and isomeric substitution.     

Arynic species II: Tosyl and triazene as leaving group in the generation of arynes from polymer-bound reagents

o-Benzyne and its 4-methyl, 4-chloro and 4-bromo-derivatives were generated in the thermal decomposition of two new kinds of polymer-bound precursors: 1(2-carboxyaryl)triazenes and 2-carboxyaryl-sulphonates. New kinds of trapping polymers for these elusive species are also presented.     

Conservation of ultrafast photoprotective mechanisms with increasing molecular complexity in sinapoyl malate derivatives

Sinapoyl malate is a natural plant sunscreen molecule which protects leaves from harmful ultraviolet radiation. Here, the ultrafast dynamics of three sinapoyl malate derivatives, sinapoyl L-dimethyl malate, sinapoyl L-diethyl malate and sinapoyl L-di-t-butyl malate, have been studied using transient electronic absorption spectroscopy, in a dioxane and methanol solvent environment to investigate how well preserved these dynamics remain with increasing molecular complexity. In all cases it was found that, upon photoexcitation, deactivation occurs via a trans-cis isomerisation pathway within ∼20–30 ps. This cis-photoproduct, formed during photodeactivation, is stable and longed-lived for all molecules in both solvents. The incredible levels of conservation of the isomerisation pathway with increased molecular complexity demonstrate the efficacy of these molecules as ultraviolet photoprotectors, even in strongly perturbing solvents. As such, we suggest these molecules might be well-suited for augmentations to further improve their photoprotective efficacy or chemical compatibility with other components of sunscreen mixtures, whilst conserving their underlying photodynamic properties.