Pseudo-point groups and chronality in enumeration of reaction pairs

Summary The pseudo-point group is constructed to characterize the symmetry of a basic pair of hexagonal reaction graphs having no par-bonds on its edges. Any pairs of reaction graphs (reaction pairs) are considered to be obtained by adding par-bonds to the edges of the basic pair; they are counted by the USCI (unit-subduced-cycle-index) approach. Thus, the six edges of the basic pair are assigned to the coset representation (/C _2v ). After the subduction of the is calculated, the partial-cycle-index method of the USCI approach is applied to the combinatorial enumeration of reactions pairs.Reaction pairs are classified to two categories, i.e. isoenergetic and anisoenergetic. An isoenergetic pair is concluded to be a self-reaction pair, while an anisoenergetic pair corresponds to a non-self-reaction pair. The concept of chronality is also discussed to clarify the symmetrical nature of the resulting orbits.     

Reaction pathways of the Simmons-Smith reaction

The cyclopropanation reaction of an alkene with a metal carbenoid has been studied by means of the B3LYP hybrid density functional method. The cyclopropanation of ethylene with a lithium carbenoid or a zinc carbenoid [Simmons-Smith (SS) reagent] goes through two competing pathways, methylene transfer and carbometalation. Both processes are fast for the lithium carbenoid, while, for the zinc carbenoid, only the former is fast enough to be experimentally feasible. The reaction of an SS reagent (ClZnCH(2)Cl) with ethylene and an allyl alcohol in the presence of ZnCl(2) was also studied. The allyl alcohol reaction was modeled with an SS reagent/alkoxide complex (ClCH(2)ZnOCH(2)CH=CH(2)) formed from the SS reagent and allyl alcohol. Two modes of acceleration were found. The first involves the well-accepted mechanism of 1,2-chlorine migration, and the second involves a five-centered bond alternation. The latter was found to be more facile than the former and to operate equally well both with ethylene and with aggregates of SS reagent/alkoxide complexes. Calculations on the SS reaction with 2-cyclohexen-1-ol offer a reasonable model for the hydroxy-directed diastereoselective SS reaction, which has been used for a long time in organic synthesis.     

Iterated reaction graphs: simulating complex Maillard reaction pathways

This study investigates a new method of simulating a complex chemical system including feedback loops and parallel reactions. The practical purpose of this approach is to model the actual reactions that take place in the Maillard process, a set of food browning reactions, in sufficient detail to be able to predict the volatile composition of the Maillard products. The developed framework, called iterated reaction graphs, consists of two main elements: a soup of molecules and a reaction base of Maillard reactions. An iterative process loops through the reaction base, taking reactants from and feeding products back to the soup. This produces a reaction graph, with molecules as nodes and reactions as arcs. The iterated reaction graph is updated and validated by comparing output with the main products found by classical gas-chromatographic/mass spectrometric analysis. To ensure a realistic output and convergence to desired volatiles only, the approach contains a number of novel elements: rate kinetics are treated as reaction probabilities; only a subset of the true chemistry is modeled; and the reactions are blocked into groups.     

Computer enumeration of polyhexes using the compact naming approach

The enumeration of polyhexes can be easily carried out by utilizing a compact name (CN) approach to code chemical structures. The Fortran program performing generation of benzenoid hydrocarbons with 1–10 rings is presented. The computed structures are divided into various classes according to their cata- or peri- as well and non- or radicaloid character. Use of the additive nodal increments (ANI) approach leads to algorithm producing representative samples of the polyhexes' sets which can be applicable in testing of various topological formulae.     

Fluctuations in the ensemble of reaction pathways

The dominant reaction pathway is a rigorous framework to microscopically compute the most probable trajectories, in nonequilibrium transitions. In the low-temperature regime, such dominant pathways encode the information about the reaction mechanism and can be used to estimate nonequilibrium averages of arbitrary observables. On the other hand, at sufficiently high temperatures, the stochastic fluctuations around the dominant paths become important and have to be taken into account. In this work, we develop a technique to systematically include the effects of such stochastic fluctuations, to order k(B)T. This method is used to compute the probability for a transition to take place through a specific reaction channel and to evaluate the reaction rate.     

Theoretical study of reaction pathways to borazine

Four reaction pathways from diborane and ammonia to borazine, (HBNH)3, have been studied computationally at the density functional level (B3LYP/6-311+G(2d,p)//B3LYP/6-31G(d)). The cycloaddition of H2BNH2 to 1,3-diaza-2,4-diborabuta-1,3-diene and subsequent elimination of two molecules of H2 was found to be the lowest-energy pathway to (HBNH)3. In the other pathways, the formation and conversion of the intermediates 1,3,5-triaza-2,4,6-triborahexatriene, cyclotriborazane, and 1,3,5-triaza-2,4,6-triborahexa-1,5-diene into (HBNH)3 were investigated. The formation of 1,3-diaza-2,4-diborabuta-1,3-diene and, subsequently, the formation and electrocyclization of 1,3,5-triaza-2,4,6-triborahexatriene and the cycloaddition of H2BNH2 to 1,3-diaza-2,4-diborabuta-1,3-diene are predicted to be the kinetically favored pathways to (HBNH)3 in the gas phase. At low concentrations of 1,3-diaza-2,4-diborabutene, high concentrations of H2BNH2, and a temperature of 298.15 K, the formation of the polyolefins H3BNH2(H2BNH2)nNHBH2 (n=1,2) is predicted to be competitive with the formation of 1,3-diaza-2,4-diborabuta-1,3-diene.     

De novo peptide sequencing using exhaustive enumeration of peptide composition

We introduce the use of a peptide composition lookup table indexed by residual mass and number of amino acids for de novo sequencing of polypeptides. Polypeptides of 1600 Daltons (Da) or more can be sequenced effectively through exhaustive compositional analysis of MS/MS spectra obtained by unimolecular decomposition (without CID) in a MALDI TOF/TOF despite a fragment mass accuracy of 50 mDa. Peaks are referenced against the lookup table to obtain a complete profile of amino acid combinations, and combinations are assembled into series of increasing length. Concatenating the differences between successive entries in compositional series yields peptide sequences that can be scored and ranked according to signal intensity. While the current work involves measurements acquired on MALDI TOF-TOF, such general treatment of the data anticipates extension to other types of mass analyzers.     

Normal,abnormal and pseudo-abnormal reaction pathways for the imine-peroxyacid reaction

Steric and mesomeric effects have a marked influence upon the formation of oxaziridine (normal pathway) or nitrone (abnormal pathway) products from the imine-peroxyacid reaction; n.m.r. studies of the thermal isomerization of oxaziridines to nitrones provide evidence of a pseudo-abnormal oxidation pathway.     

Integrating steepest-descent reaction pathways for large molecules

Exploring potential energy surfaces of large molecular systems can be quite challenging due to the increased number of nuclear degrees of freedom. Many techniques that are well-suited for small and moderate size systems require diagonalization of the energy second-derivative matrix. Since the cost of this step scales as O(N(atoms)(3)) (where N(atoms) is the number of atomic centers), such methods quickly become infeasible and are eventually rendered cost prohibitive. In this work, the recently developed Euler-based predictor-corrector reaction path integration method [H. P. Hratchian, M. J. Frisch, and H. B. Schlegel, J. Chem. Phys. 133, 224101 (2010)] is enhanced and proposed as a useful alternative to conventional reaction path following schemes in studies on very large systems. Because this integrator does not require Hessian diagonalization, the O(N(atoms)(3)) bottleneck afflicting other approaches is completely avoided. The effectiveness of the integrator in large system studies is demonstrated with an enzyme-catalyzed reaction employing an ONIOM (QM:MM) model chemistry and involving 5368 atomic centers.     

Characterization of protein folding by dominant reaction pathways

We assess the reliability of the recently developed approach denominated dominant reaction pathways (DRP) by studying the folding of a 16 residue beta-hairpin, within a coarse-grained Go-type model. We show that the DRP predictions are in quantitative agreement with the results of molecular dynamics simulations performed in the same model. On the other hand, in the DRP approach, the computational difficulties associated with the decoupling of time scales are rigorously bypassed. The analysis of the important transition pathways supports a picture of the beta-hairpin folding, in which the reaction is initiated by the collapse of the hydrophobic cluster.     

Efficient enumeration of stereoisomers of tree structured molecules using dynamic programming

Nonredundant and exhaustive generation of stereoisomers of a chemical compound with a specified constitution is one of the important tools for molecular structure elucidation and molecular design. In this paper, we deal with chemical compounds composed of carbon, hydrogen, oxygen and nitrogen atoms whose graphical structures are tree-like graphs because these compounds are most fundamental, and consider stereoisomers that can be generated by asymmetric carbon atoms and double bonds between two adjacent carbon atoms. Based on dynamic programming, we propose an algorithm of generating all stereoisomers without duplication. We treat a given tree-like graph as a tree rooted at its structural center. Our algorithm first computes recursively the numbers of stereoisomers of the subgraphs induced by the descendants of each vertex, and then constructs each stereoisomer by backtracking the process of computing the numbers of stereoisomers. Our algorithm correctly counts the number of stereoisomers in O(n) time and space, and correctly enumerates all the stereoisomers in O(n) space and in O(n) time per stereoisomer, where n is the number of atoms in a given structure. The source code of the program implementing the proposed algorithm is freely available for academic use upon request.     

Efficient enumeration of stereoisomers of outerplanar chemical graphs using dynamic programming

Exhaustive and nonredundant generation of stereoisomers of a chemical compound with a specified constitution is an important tool for molecular structure elucidation and molecular design. It is known that many chemical compounds have outerplanar graph structures. In this paper we deal with chemical compounds composed of carbon, hydrogen, oxygen, and nitrogen atoms whose graphical structures are outerplanar and consider stereoisomers caused only by asymmetry around carbon atoms. Based on dynamic programming, we propose an algorithm of generating all stereoisomers without duplication. We treat a given outerplanar graph as a graph rooted at its structural center. Our algorithm first recursively computes the number of stereoisomers of the subgraph induced by the descendants of each vertex and then constructs each stereoisomer by backtracking the process of computing the numbers of stereoisomers. Our algorithm correctly counts the number of stereoisomers in O(n) time and space and correctly enumerates all of the stereoisomers in O(n3) time per stereoisomer on average and in O(n) space, where n is the number of atoms in a given structure.     

The direct aldol reaction using bifunctional catalysts

In this paper, we describe an approach to the direct aldol reaction using a bifunctional catalyst containing Lewis acidic and basic functional groups. To achieve this novel means of catalysis we have developed new tertiary amine-zinc catalysts, which perform the aldol reaction between acetone and p-nitrobenzaldehyde.     

Gold-catalyzed cyanosilylation reaction: homogeneous and heterogeneous pathways

Gold had been considered to be an extremely inert metal, but recently it was found that nanometer-sized gold particles on metal-oxide supports acted as catalysts for simple organic reactions, such as oxidation and hydrogenation, even at or below room temperature. Herein, we report that gold nanoparticles (AuNPs) of zero oxidation state (Au0) are catalytically active for a C--C bond-forming reaction, the cyanosilylation of aldehydes. The AuNP-catalyzed cyanosilylation proceeded smoothly at room temperature with 0.2 wt % loading of AuNPs. The reactions of aromatic aldehydes were almost quantitative, except for benzaldehyde derivatives containing the electron-withdrawing NO2 group, and alpha,beta-unsaturated aromatic aldehydes were the most reactive substrates. The reactions also went smoothly for aliphatic aldehydes. Mechanistic studies indicated that the reactions proceeded both homogeneously and heterogeneously: homogeneous catalysis by leached gold species and heterogeneous catalysis by the adsorption of the reactants (aldehydes and trimethylsilyl cyanide) onto AuNPs. The ratio of homogeneous and heterogeneous catalysis was estimated to be approximately 4:1.