Evolution of physics-based methodology for exploring the conformational energy landscape of proteins

The evolution of our physics-based computational methods for determining protein conformation without the introduction of secondary-structure predictions, homology modeling, threading, or fragment coupling is described. Initial use of a hard-sphere potential captured much of the structural properties of polypeptide chains, and subsequent more refined force fields, together with efficient methods of global optimization provide indications that progress is being made toward an understanding of the interresidue interactions that underlie protein folding.     

Role of surface crossings in the photochemistry of nitromethane

The photodissociation dynamics of nitromethane (CH(3)NO(2)) starting at the S(3) excited state has been studied at the complete active space self-consistent field level of theory in conjunction with atomic natural orbital type basis sets. In addition, the energies of all the critical points and the energy profiles connecting them have been recomputed with the multiconfigurational second-order perturbation method. It is found that the key step in the reaction mechanism is a radiationless decay through an S(3)S(2) conical intersection. The branching space spanned by the gradient difference and nonadiabatic coupling vectors of this crossing point comprises dissociation into excited nitromethane plus singlet atomic oxygen [CH(3)NO(1A")+O((1)D)] and S(3)-->S(2) deactivation, respectively. Furthermore, deactivated nitromethane S(n (n<3)) can decompose in subsequent steps into CH(3)+NO(2), where NO(2) is generated at least in two different electronic states (1 (2)B(2) and 1 (2)A(1)). It is shown that formation of excited nitric oxide NO(A (2)Sigma) arises from CH(3)NO(1A") generated in the previous step. In addition, four crossings between singlet and triplet states are localized; however, no evidence is found for a relevant role of such crossings in the photochemistry of CH(3)NO(2) initiated at S(3) state in the gas phase.     

Supramolecular H-bonded assemblies of redox-active metallodendrimers and positive and unusual dendritic effects on the recognition of H2PO4-

The DSM polyamine dendrimers dend-DAB-(NH2)x of generations 1 (x = 4) to 4 (x = 32) form H-bonded dendritic assemblies with the phenol AB3 units p-HOC6H4C(CH2CHCH2)3 and p-HOC6H4C{(CH2)3SiCH2NHCOFc}3 (Fc = ferrocenyl), as shown by the shifts of the NH2 and OH signals giving a concentration-dependent common signal between 2.4 and 4.1 ppm in CDCl3. The supramolecular dendrimers efficiently recognize H2PO4- anions with positive and unusual dendritic effects upon electrochemical titration involving half-stoichiometry for G1, a sudden cyclovoltammetry wave change at the equivalent point, and a dramatic intensity decrease of the new wave.     

A new approach to micropatterning: application of potential-assisted ion transfer at the liquid-liquid interface for the local metal deposition

A new approach to micropatterning is demonstrated. The approach is based on driving an electrochemical process at the solid-liquid interface through the formation of a flux of ions from a micropipet that is held in close proximity to the surface. The flux of ions is generated by the so-called potential assisted ion transfer at the interface between two immiscible electrolyte solutions (ITIES). As a model system, the local deposition of silver was examined. Specifically, a constant potential, which was applied to a micropipet filled with an aqueous solution of silver ions, caused the transfer of Ag(+) into the outer nitrobenzene (NB) solution that consisted of an electrolyte, tetrabutylammonium tetrakis[4-chlorophenyl]borate (TBATPBCl). To facilitate the transfer of silver ions a macrocyclic ligand, that is, dibenzo-24-crown-8 (DB24C8), was added to the organic phase. The Faradaic current of this micro-ITIES was used as a means of controlling the tip-surface distance in scanning electrochemical microscopy (SECM) and depositing silver microstructures on a gold substrate.     

Interfacial polymerisation of anilinium at Langmuir monolayers

Anilinium is strongly adsorbed at monolayers of the phospholipid L-alpha-dimyristoylphosphatidic acid (DMPA) and hexadecanesulfonic acid (HDSA) at the air-water interface, and undergoes chemical polymerisation under conditions where bulk polymerisation does not occur.     

Aza-Claisen Rearrangement: Synthesis of 5′-branched 5′-aminothymidines

The syntheses of both diastereoisomers of 5′-ethyl-substituted thymidine dimers, the (5′R)- and (5′S)-configurated 33a and 33b respectively, in which the natural phosphodiester linkage is replaced by an amide group (C(3′)-CH₂CONH-CH(5′)(Et)), arc described. Their fully protected derivatives 35a and 35b , respectively, are suitable for incorporation into antisense oligonucleotides. Unexpectedly, an attempted Pd^II-catalysed aza-Claisen rearrangement of trichloroacetimidate 7 provided the diastereoisomerically pure cyclopropane derivative 17 , whose structure was confirmed by X-ray analysis.     

Potential energy surface discontinuities in local correlation methods

We have examined the occurrence of discontinuities in bond-breaking potential energy surfaces given by local correlation methods based on the Pulay-Saeb? orbital domain approach. Our analysis focuses on three prototypical dissociating systems: the C-F bond in fluoromethane, the C-C bond in singlet, ketene, and the central C-C bond in propadienone. We find that such discontinuities do not occur in cases of homolytic bond cleavage due to the inability of the Pipek-Mezey orbital localization method to separate singlet-coupled charges on distant fragments. However, for heterolytic bond cleavage, such as that observed in singlet ketene and propadienone, discontinuities occur both at stretched geometries and near equilibrium. These discontinuities are usually small, but may be of the same order of magnitude as the localization error in some cases.     

Waiting Time Variability in some Single-Server Queueing Systems

This paper considers the range of values of the coefficient of variation of waiting time in some general single-server queueing systems. It is shown that in M/G/1 systems with given ρ, the square of this coefficient increases linearly with m₁m₃/m²₂, where m_i is the ith moment of the service distribution. This implies always a lower bound, and for some widely used distributions an upper bound as well. A few ranges are illustrated and compared to those implied in two GI/M/1 systems. The usefulness of knowing such ranges for modelling purposes is explained.     

On the singular graph and the Weyr characteristic of anM-matrix

LetA be anM-matrix in standard lower block triangular form, with diagonal blocksA _ii irreducible. LetS be the set of indices such that the diagonal blockA is singular. We define the singular graph ofA to be the setS with partial order defined by > if there exists a chain of non-zero blocksA _i, A_ij, , A_l.Let ₁ be the set of maximal elements ofS, and define thep-th level _p ,p = 2, 3, , inductively as the set of maximal elements ofS \( _{1 p-1}). Denote by _p the number of elements in _p . The Weyr characteristic (associated with 0) ofA is defined to be (A) = ( ₁, ₂,, _h ), where ₁ + + _p = dim KerA ^p ,p = 1, 2, , and _h > 0, _h+1 = 0.Using a special type of basis, called anS-basis, for the generalized eigenspaceE(A) of 0 ofA, we associate a matrixD withA. We show that(A) = ( ₁, , _h) if and only if certain submatricesD _p,p+1 ,p = 1, , h – 1, ofD have full column rank. This condition is also necessary and sufficient forE(A) to have a basis consisting of non-negative vectors, which is a Jordan basis for –A. We also consider a given finite partially ordered setS, and we find a necessary and sufficient condition that allM-matricesA with singular graphS have(A) = ( ₁, , _h). This condition is satisfied ifS is a rooted forest.The work of the second-named author was partly supported by the National Science Foundation, under grant MPS-08618 A02.     

Flow constant-current stripping analysis for antimony(III) and antimony(V) with gold fibre working electrodes : Application to Natural Waters

Antimony(III) is determined by means of electrolysis at ?0.40 V vs. Ag/AgCl on a gold-coated gold fibre electrode for 0.5–10 min in a redox buffer containing 0.01 M iron(II) in 0.10 M hydrochloric acid, and subsequent stripping with a constant current of 0.50μA either in 2 M hydrochloric acid or in 4 M hydrochloric acid/4 M calcium chloride. Antimony(V) is determined by the same procedure in 4 M hydrochloric acid medium. Bismuth(III) is masked by the addition of iodide to the sample prior to electrolysis. Antimony(III) and antimony(V) are determined by standard addition methods; the whole procedure including digital and graphical evaluation of the results is fully automated. The antimony(V) concentrations in the river water reference sample SLRS-1 and the seawater reference sample NASS-1 were found to be 0.63 and 0.31 μg l^?1 with standard deviations of 0.046 and 0.051 μg l^?1, respectively (n=15). The certified value for SLRS- 1 is 0.63±0.05 μg l^?1; no certified value is available for NASS-1.