First principles and classical molecular dynamics simulations of solvated benzene

We have performed extensive ab initio and classical molecular dynamics (MD) simulations of benzene in water in order to examine the unique solvation structures that are formed. Qualitative differences between classical and ab initio MD simulations are found and the importance of various technical simulation parameters is examined. Our comparison indicates that nonpolarizable classical models are not capable of describing the solute-water interface correctly if local interactions become energetically comparable to water hydrogen bonds. In addition, a comparison is made between a rigid water model and fully flexible water within ab initio MD simulations which shows that both models agree qualitatively for this challenging system.     

Chemoenzymatic Synthesis of Enantiopure Amino Alcohols from Simple Methyl Ketones

This study highlights the straight-forward synthesis of substituted 1,2-amino alcohols from simple and readily available aromatic methyl ketones. Starting from acetophenone derivatives, the straight-forward synthesis strategy involved an initial bromination of the alpha-positioned methyl group in the first step, followed by a simple hydrolysis to the hydroxyketone (2-hydroxyacetophenone). The hydroxylated intermediate was subsequently converted from Silicibacter pomeroyi to the final 1,2-amino alcohol by using the transaminase. The transaminase-catalyzed reaction proceeded with yields up to 62 % and always excellent enantiomeric excess of >99 %. Interestingly, the keto-enol-tautomerism of the hydroxyl ketone yields an unexpected amino alcohol isomer.     

Lattice theory of ultrafast excitonic and charge-transfer dynamics in DNA

We propose a lattice fermion model suitable for studying the ultrafast photoexcitation dynamics of ordered chains of deoxyribonucleic acid (DNA) polymers. The model includes both parallel (intrachain) and perpendicular (cross-chain) terms as well as diagonal cross-chain terms coupling neighboring bases. The general form of our Hamiltonian is borrowed from lattice fermion models of quantum chromodynamics. The band structure for this model can be determined analytically, and we use this as a basis for computing the singly excited states of the poly(dA)poly(dT) DNA duplex using configuration interaction singles. Parameters for the model are taken from various literature sources and our own ab initio calculations. Results indicate that the excited states consist of a low energy band of dark charge-separated states followed by separate bands of delocalized excitonic states which have weak mixing between the thymidine and adenosine sides of the DNA chain. We then propose a lattice exciton model based upon the transition dipole-dipole couplings between bases and compare the analytical results for the survival probability of an initially localized exciton to exact numerical results. The results herein underscore the competing role of excitonic and charge-transfer dynamics in these systems.     

Stepwise hydration of protonated proline

Using an ab initio strategy accounting for the basis set superposition error and electron-correlation effects, we have investigated the stepwise hydration of the proline cation. Structures with 0-3 surrounding water molecules have been obtained, and major differences with respect to protonated glycine are highlighted. Several structures with similar energies actually coexist at each step, and we give indications that should help removing experimental doubts. The theoretical enthalpies and entropies meet the experimental observations, though the computed entropic changes when adding the third water molecule are overestimated.     

Square versus tetrahedral iron clusters with polyoxometalate ligands

Two new insoluble transition metal substituted phosphotungstates, (C2N2H10)11[{(B-alpha-PW9O34)Fe3(OH)3}4(PO4)4Fe].38H2O(1) and K4(C2N2H10)12[(alpha-PW10Fe2O39)4].30H2O(2), have been isolated by the hydrothermal reaction of [A-alpha-PW9O34]9-, Fe(III) ions and ethylenediamine. Compound 1 has a tetrahedral symmetry and contains a Fe13 core built from the assembly of four Fe(III) trisubstituted [B-alpha-PW9O34]9- anions around a central disordered iron ion via four phosphato ligands. The anion in 2 can be described as a square of disubstituted [PW10O37]9- anions linked by Fe(III)-O-Fe(III) bridges. Magnetic measurements performed on 1 and 2 have shown the occurrence of antiferromagnetic interactions between the iron ions and have allowed the coupling constants between the magnetic centers to be determined.     

Crystal structure, Raman spectroscopy, and ab initio calculations of a new bialkali alanate K2LiAlH6

A new bialkali alanate K2LiAlH6 was synthesized at 320-330 degrees C and 100-700 bar. It was structurally characterized by powder X-ray diffraction. It crystallizes in space group R3m (No. 166) with unit cell parameters a = 5.62068(8) and c = 27.3986(6) A. The Li and K cation sites are mutually exclusive, and Rietveld refinement finds no cation mixing. First-principles total energy calculations were performed for nine competing database structures of the stoichiometry A2BCX6, taken from fluoride and oxide compounds in the Inorganic Crystal Structure Database (ICSD). The relaxed structures were compared via their total energies and their agreement with experimental diffraction spectra. Two database structures K2LiAlF6 (R3m) and Cs2NaAlF6 (C2/m) were found to have the lowest total energies, but with the Rietveld method the K2LiAlF6 structure type was shown to be the most favorable. Ab initio total energy calculations support the validity of the structure determination. First-principles calculations also indicate that cation mixing is energetically unfavorable. Hydride properties such as plateau pressure are therefore more difficult to manipulate through alloying in this class of compounds.     

31P NMR chemical shifts in hypervalent oxyphosphoranes and polymeric orthophosphates

We report the first quantum chemical investigation of the solid- and solution-state 31P NMR chemical shifts in models for phosphoryl transfer enzyme reaction intermediates and in polymeric inorganic phosphates. The 31P NMR chemical shifts of five- and six-coordinate oxyphosphoranes containing a variety of substitutions at phosphorus, as well as four-coordinate polymeric orthophosphates and four-coordinate phosphonates, are predicted with a slope of 1.00 and an R2= 0.993 (N = 34), corresponding to a 3.8 ppm (or 2.1%) error over the entire 178.3 ppm experimental chemical shift range, using Hartree-Fock methods. For the oxyphosphoranes, we used either experimental crystallographic structures or, when these were not available, fully geometry optimized molecular structures. For the four-coordinate phosphonates we used X-ray structures together with charge field perturbation, to represent lattice interactions. For the three-dimensional orthophosphates (BPO4, AlPO4, GaPO4 we again used X-ray structures, but for these inorganic systems we employed a self-consistent charge field perturbation approach on large clusters, to deduce peripheral atom charges. For pentaoxyphosphoranes, the solvent effect on 31P NMR chemical shieldings was found to be very small (<0.5 ppm). The 31P NMR chemical shielding tensors in the pentaoxyphosphoranes were in most cases found to be close to axially symmetric and were dominated by changes in the shielding tensor components in the equatorial plane (sigma22 and sigma33). The isotropic shifts were highly correlated (R2= 0.923) with phosphorus natural bonding orbital charges, with the larger charges being associated with shorter axial P-O bond lengths and, hence, more shielding. Overall, these results should facilitate the use of 31P NMR techniques in investigating the structures of more complex systems, such as phosphoryl transfer enzymes, as well as in investigating other, complex oxide structures.     

Copper(I/II) complexes of a bis(tetrathiafulvalene)-2,2'-bipyridine: synthesis, characterization, magnetic and electrochemical properties

The coordination ability of the electroactive TTF-based chelating ligand 5,5'-bis(4,5-bis(thiomethyl)-4'-carbamoyltetrathiafulvalene)-2,2'-bipyridine (L) has been tested with Cu(I) and Cu(II) centres. [(L)2Cu(I)](PF6), [(L)2Cu(II)](OTf)2 and [(L)Cu(II)(DMF)3](OTf)2 have been synthesized. A single-crystal X-ray analysis was performed on [(L)Cu(II)(DMF)3](OTf)2, showing a distorted octahedral geometry around the Cu(II) centre, and the formation of dimeric units in the solid state through weak coordination in apical position of an amide oxygen atom from a neighbouring complex. Magnetic data show that the paramagnetic metallic centres are isolated, in agreement with the solid-state structure. Electrochemical measurements were performed on the three complexes and in all cases the Cu(I)/Cu(II) and TTF/TTF+*/TTF2+ redox processes were observed.     

Deposition of DNA-functionalized gold nanospheres into nanoporous surfaces

We report the deposition of DNA-conjugated gold nanospheres into arrays of surface nanopores obtained from hexagonally ordered thin polystyrene-b-poly(methyl methacrylate) (PS-b-PMMA) diblock copolymer films on silicon. The deposition occurs spontaneously from aqueous solution and is driven by either electrostatic interactions or specific DNA hybridization events between the DNA nanospheres and the surface nanopores. To mitigate this spontaneous deposition, we have chemically modified the nanopores with either positively charged aminosilanes or oligonucleotide probe sequences. The deposition of DNA nanospheres into the surface nanopores was characterized by atomic force microscopy (AFM) and X-ray photoelectron spectroscopy (XPS). We have observed preferential immobilization of individual DNA nanospheres within the nanopores, based on the size matching between the two entities. The inclusion density and selectivity of DNA nanosphere deposition into the surface nanopores was found to depend predominantly on the methods through which the nanoporous surfaces were prepared and chemically functionalized.