Stability of phosphinidenes--are they synthetically accessible?

The relative stability of different singlet phosphinidenes (R-P) has been investigated by using isodesmic reactions. The energies of these reactions with several R groups were calculated with DFT and ab initio methods at different levels of theory. The best stabilising effect on the phosphinidene centre is exhibited by the R'2C=N-group, resulting in a singlet ground state. The analysis of the electron density in the parent H2C=N-P, indicates a considerable double bond character of the PN bond. Further tuning of the C=N pi-bond polarity is possible by variation of the R' substituents. Using trimethylsilyl substituents or incorporating the carbon atom in a pi-withdrawing pentafulvene ring the stabilization and the computed singlet triplet separation increases. The thermodynamics and the kinetics of dimerisation reactions of the most stabilised R'2C=N-P indicates that these compounds are likely synthetic targets.     

Surface smoothening mechanism of amorphous silicon thin films

An important concern in the deposition of thin hydrogenated amorphous silicon () films is to obtain smooth surfaces. Herein, we combine molecular-dynamics simulations with first-principles density functional theory calculations to elucidate the smoothening mechanism of plasma deposited thin films. We show that the deposition precursor may diffuse rapidly on the film surface via overcoordinated surface Si atoms and incorporate into the film preferentially in surface valleys, with activation barriers for incorporation dependent on the local surface morphology. Experimental data on smoothening and precursor diffusion are accounted for.     

Simple Current Actions of Cyclic Groups

Permutation actions of simple currents on the primaries of a Rational Conformal Field Theory are considered in the framework of admissible weighted permutation actions. The solution of admissibility conditions is presented for cyclic quadratic groups: an irreducible WPA corresponds to each subgroup of the quadratic group. As a consequence, the primaries of a RCFT with an order n integral or half-integral spin simple current may be arranged into multiplets of length k² (where k is a divisor of n) or 3k² if the spin of the simple current is half-integral and k is odd.Mathematical Subject Classifications (2000). 81T40.Work supported by grant OTKA TS044839.     

Markov inequality for polynomials of degree n with m distinct zeros

Let be the collection of all polynomials of degree at most n with real coefficients that have at most m distinct complex zeros. We prove thatfor every . This is far away from what we expect. We conjecture that the Markov factor 32·8^mn above may be replaced by cmn with an absolute constant c>0. We are not able to prove this conjecture at the moment. However, we think that our result above gives the best-known Markov-type inequality for on a finite interval when mc log n.     

Redox reactions of cobalt(III) complexes in aqueous organic mixtures effects: of single ion assumptions on initial state-transition state solvation analysis

Summary Solvent effects on the kinetics of redox reactions of cobalt(III) complexes were assessed in aqueous mixtures containing methanol,t-butanol, and acetone according to three different extra-thermodynamic assumptions —Wells, TATB, and TPTB^** — at 298.2 K. The calculated values of transfer functions of individual ions and initial and transition states were often markedly different. In some cases these differences led to different conclusions in the evaluation of the role of solvation in the reactions investigated.     

Improved mapping of protein binding sites

Computational mapping methods place molecular probes – small molecules or functional groups – on a protein surface in order to identify the most favorable binding positions by calculating an interaction potential. Mapping is an important step in a number of flexible docking and drug design algorithms. We have developed improved algorithms for mapping protein surfaces using small organic molecules as molecular probes. The calculations reproduce the binding of eight organic solvents to lysozyme as observed by NMR, as well as the binding of four solvents to thermolysin, in good agreement with x-ray data. Application to protein tyrosine phosphatase 1B shows that the information provided by the mapping can be very useful for drug design. We also studied why the organic solvents bind in the active site of proteins, in spite of the availability of alternative pockets that can very tightly accommodate some of the probes. A possible explanation is that the binding in the relatively large active site retains a number of rotational states, and hence leads to smaller entropy loss than the binding elsewhere else. Indeed, the mapping reveals that the clusters of the ligand molecules in the protein's active site contain different rotational-translational conformers, which represent different local minima of the free energy surface. In order to study the transitions between different conformers, reaction path and molecular dynamics calculations were performed. Results show that most of the rotational states are separated by low free energy barriers at the experimental temperature, and hence the entropy of binding in the active site is expected to be high.     

Theoretical study of low-lying triplet states of aniline

Multireference complete active space self-consistent-field CASSCF(10,12)/ANO and second-order perturbation theory MS-CASPT2 calculations were performed to determine the vertical low-lying singlet and triplet states of aniline. The sequence of the seven lower lying triplet states is T1(1(3)A'), T2(1(3)A' '), T3(2(3)A'), T4(3(3)A'), T5(2(3)A' '), T6(4(3)A'), and T7(3(3)A' '). The 3(3)A', 4(3)A', and 3(3)A' ' states are assigned as 3s, 3py, and 3pz Rydberg states, respectively, while other states correspond to pi <-- pi excitations. Both the T1 and T2 states are found to be below at the lowest-lying singlet S1 (1(1)A' ') state. Geometry, vibrational modes, and electron distribution of the lowest lying T1 state were determined using UB3LYP calculations. The vertical and adiabatic singlet-triplet energy gaps DeltaE(S0-T1) amount to 3.7 and 3.5 +/- 0.2 eV, respectively. In clear contrast with the S0 state, the triplet aniline is no longer aromatic, and its protonation occurs preferentially at the ring meta-carbon site, with a proton affinity PA = 243 +/- 3 kcal/mol.     

Stability of cyclic beta-hairpins: asymmetric contributions from side chains of a hydrogen-bonded cross-strand residue pair

Amino acid structural propensities measured in "host-guest" model studies are often used in protein structure prediction or to choose appropriate residues in de novo protein design. While this concept has proven useful for helical structures, it is more difficult to apply successfully to beta-sheets. We have developed a cyclic beta-hairpin scaffold as a host for measurement of individual residue contributions to hairpin structural stability. Previously, we have characterized substitutions in non-backbone-hydrogen-bonded strand sites; relative stability differences measured in the cyclic host are highly predictive of changes in folding free energy for linear beta-hairpin peptides. Here, we examine the hydrogen-bonded strand positions of our host. Surprisingly, we find a large favorable contribution to stability from a valine (or isoleucine) substitution immediately preceding the C-terminal cysteine of the host peptide, but not at the cross-strand position of the host or in either strand of a folded linear beta-hairpin (trpzip peptide). Further substitutions in the peptides and NMR structural analysis indicate that the stabilizing effect of valine is general for CX(8)C cyclic hairpins and cannot be explained by particular side-chain-side-chain interactions. Instead, a localized decrease in twist of the peptide backbone on the N-terminal side of the cysteine allows the valine side chain to adopt a unique conformation that decreases the solvent accessibility of the peptide backbone. The conformation differs from the highly twisted (coiled) conformation of the trpzip hairpins and is more typical of conformations present in multistranded beta-sheets. This unexpected structural fine-tuning may explain why cyclic hairpins selected from phage-displayed libraries often have valine in the same position, preceding the C-terminal cysteine. It also emphasizes the diversity of structures accessible to beta-strands and the importance of considering not only "beta-propensity", but also hydrogen-bonding pattern and strand twist, when designing beta structures. Finally, we observe correlated, cooperative stabilization from side-chain substitutions on opposite faces of the hairpin. This suggests that cooperative folding in beta-hairpins and other small beta-structures is driven by cooperative strand-strand association.