A finite temperature linear tetrahedron method for electronic structure calculations of periodic systems

A finite-temperature linear tetrahedron method for electronic structure calculations of periodic systems is developed. When compared to widely used simple temperature broadening, the number of k points necessary for accurate integration at finite temperatures is reduced. The utility of the method is demonstrated with benchmark calculations on 1D, 2D, and 3D systems.     

Frequency stabilization and transverse mode discrimination in injection-seeded unstable resonator TEA CO2 lasers

Longitudinal mode selection by injection has been demonstrated as a viable technique for TEA-CO₂ lasers with pulse energies of a Joule or greater. Once reliable generation of single-longitudinal-mode (SLM) pulses is obtained, one can study the characteristics and the causes of intrapulse frequency variation. These include the effect of the decaying plasma, the thermal gradient due to the energy dissipation associated with the laser mechanism itself, and the pressure shift of the center frequency of the laser transition. The use of the positive-branch unstable resonator as an efficient means of coupling a discharge with large spatial dimensions to an optical cavity mode introduces another concern: namely, what can be done to emphasize transverse mode discrimination in an unstable resonator cavity while maintaining high coupling efficiency. These issues are discussed in this paper, and relevant experimental results are included.     

Simulating periodic trends in the structure and catalytic activity of coinage metal nanoribbons

We present a systematic density functional theory (DFT) study of the structure and catalytic activity of group 10 (Ni, Pd, Pt) and group 11 (Cu, Ag, Au) coinage metal nanoribbons. These infinite, periodic, quasi‐one‐dimensional structures are conceptually important as intermediates between small metal clusters and close‐packed metal surfaces, and have been shown experimentally to be practical catalysts. We find that nanoribbons have significantly higher predicted H₂ dissociation activity than close‐packed metal surfaces consistent with their lower coordination numbers. Computed periodic trends are reasonable, with late transition states and low barriers for H₂ dissociation over late group 10 nanoribbons, suggesting their promise as practical catalysts. These trends are consistent with the isolated nanoribbons' computed molecular electrostatic potentials. Calculations also predict nearly linear Brønsted–Evans–Polanyi relationships between the nanoribbons' H₂ dissociation energies and dissociation barriers. We also test new meta‐generalized gradient approximation (GGA) and hybrid DFT approximations for H₂ dissociation over these nanoribbons. These new functionals increase the (generally underestimated) dissociation barriers predicted by standard GGAs, motivating their continued application in surface chemistry. © 2015 Wiley Periodicals, Inc.     

Structure control within poly(amidoamine) dendrimers: size, shape and regio-chemical mimicry of globular proteins

This work describes the syntheses of a new poly(amidoamine) (PAMAM) dendrimer family possessing a disulfide function (cystamine) in its core. Traditional redox-chemistry associated with the disulfide core in these dendrimer structures, provides a versatile strategy for designing unique sizes, shapes and controlling the regio-disposition of chemical groups on the surface of these dendrimers. Various single site, sulfhydryl functionalized dendron reactants may be generated in situ, under standard reducing conditions (i.e. dithiothreitol (DTT)). Facile control of size, shape and chemical functionality placement involves covalent hybridization of these single point, sulfhydryl reactive dendron components. This is accomplished by re-oxidation in the presence of air, to yield generation/surface chemistry differentiated cross-over products which may be isolated by preparative thin layer or column chromatography. Differentiated cystamine core dendrimers derived from combination and permutation of lower generation (i.e. Gen.=0-3) sulfhydryl functionalized dendrons possessing amino, hydroxyl, acetamido or dansyl surface groups, were synthesized and isolated. They were characterized by a variety of methods including; ¹³C NMR, capillary electrophoresis (CE), gel electrophoresis (PAGE), thin layer chromatography (TLC) and electrospray (ES) or matrix assisted laser desorption ionization (MALDI-TOF) mass spectrometry. This general strategy has broad implications for the systematic size, shape and regio-chemical control of a wide range of dendritic nanostructures, many of which may be designed to mimic the sizes, shapes and regio specific chemo-domains observed for globular proteins.     

Ligand Displacement Reaction Paths in a Diiron Hydrogenase Active Site Model Complex

The mechanism and energetics of CO, 1‐hexene, and 1‐hexyne substitution from the complexes (SBenz)₂[Fe₂(CO)₆] (SBenz=SCH₂Ph) ( 1 ‐CO), (SBenz)₂[Fe₂(CO)₅(η²‐1‐hexene)] ( 1 ‐(η²‐1‐hexene)), and (SBenz)₂[Fe₂(CO)₅(η²‐1‐hexyne)] ( 1 ‐(η²‐1‐hexyne)) were studied by using time‐resolved infrared spectroscopy. Exchange of both CO and 1‐hexyne by P(OEt)₃ and pyridine, respectively, proceeds by a bimolecular mechanism. As similar activation enthalpies are obtained for both reactions, the rate‐determining step in both cases is assumed to be the rotation of the Fe(CO)₂L (L=CO or 1‐hexyne) unit to accommodate the incoming ligand. The kinetic profile for the displacement of 1‐hexene is quite different than that for the alkyne and, in this case, both reaction channels, that is, dissociative (S_N1) and associative (S_N2), were found to be competitive. Because DFT calculations predict similar binding enthalpies of alkene and alkyne to the iron center, the results indicate that the bimolecular pathway in the case of the alkyne is lower in free energy than that of the alkene. In complexes of this type, subtle changes in the departing ligand characteristics and the nature of the mercapto bridge can influence the exchange mechanism, such that more than one reaction pathway is available for ligand substitution. The difference between this and the analogous study of (μ‐pdt)[Fe(CO)₃]₂ (pdt=S(CH₂)₃S) underscores the unique characteristics of a three‐atom S?S linker in the active site of diiron hydrogenases.     

Porphyrin complexes containing coordinated BOB groups: synthesis, chemical reactivity and the structure of [BOB(tpClpp)]2+

The reactions of boron halides with free base porphyrins under conditions where partial hydrolysis of the boron halides can occur give diboron porphyrin complexes containing BOB moieties in which each boron is bonded to two porphyrin nitrogen atoms. BF(3).OEt(2) with H(2)(por) gives B(2)OF(2)(por) (por = tpp, ttp, tpClpp, oep) which has an asymmetric structure in which one boron lies in the porphyrin plane (B(ip)) while the other lies above it (B(oop)). BCl(3).MeCN with H(2)(por) gives B(2)O(2)(BCl(3))(2)(por) which contains a four-membered B(2)O(2) ring and is stable only in the presence of excess BCl(3). BBr(3) with Li(2)(tpClpp) gives the dicationic complex [B(2)O(tpClpp)](2+) as its [BBr(4)](-) salt, and is the first example of a boron porphyrin containing three-coordinate boron to be structurally characterised. B(2)O(2)(BCl(3))(2)(por) can be chromatographed on basic alumina to give the hydroxyboron complex B(2)O(OH)(2)(por), which is deduced from its NMR spectra and DFT calculations to have a structure analogous to B(2)OF(2)(por). The OH protons are shifted upfield to near delta -4 (B(oop)-OH) and -10 (B(ip)-OH) by the diamagnetic porphyrin ring current. The reaction of either B(2)O(2)(BCl(3))(2)(por) or B(2)O(OH)(2)(por) (por = ttp, tpClpp) with alcohols (ROH, R = Et, 4-C(6)H(4)CH(3)) gives B(2)O(OR)(2)(por), which can in turn be converted to B(2)O(OR)(OH)(por) by repeated chromatography. The reaction of PhBCl(2) with H(2)(por) (por = ttp, tpClpp) gives B(2)O(Ph)(OH)(por) which has been characterised by spectroscopy in concert with DFT calculations. It is a further example of the B(2)OF(2)(por) structural type, in which the phenyl group is coordinated to the out-of-plane boron and the OH group to the in-plane boron, as are its derivatives B(2)O(Ph)(X)(tpClpp) (X = F, OEt). Steric drivers for the facile hydrolysis of haloboron porphyrins relative to their dipyrromethene and expanded porphyrin counterparts are discussed.     

A toxicity evaluation and predictive system based on neural networks and wavelets

A computational approach has been developed for performing efficient and reasonably accurate toxicity evaluation and prediction. The approach is based on computational neural networks linked to modern computational chemistry and wavelet methods. In this paper, we present details of this approach and results demonstrating its accuracy and flexibility for predicting diverse biological endpoints including metabolic processes, mode of action, and hepato- and neurotoxicity. The approach also can be used for automatic processing of microarray data to predict modes of action.