Black and white local invariants of mappings from surfaces into three-space

Goryunov proved that the space of local invariants of Vassiliev type for generic maps from surfaces to three-space is three-dimensional. The basic invariants were the number of pinch points, the number of triple points and one linked to a Rokhlin type invariant. In this paper we show that, by colouring the complement of the image of the map with a chess board pattern, we can produce a six-dimensional space of local invariants. These are essentially black and white versions of the above. Simple examples show how these are more effective. This revised version was published online in August 2006 with corrections to the Cover Date.     

BonDNet: a graph neural network for the prediction of bond dissociation energies for charged molecules

A broad collection of technologies, including e.g. drug metabolism, biofuel combustion, photochemical decontamination of water, and interfacial passivation in energy production/storage systems rely on chemical processes that involve bond-breaking molecular reactions. In this context, a fundamental thermodynamic property of interest is the bond dissociation energy (BDE) which measures the strength of a chemical bond. Fast and accurate prediction of BDEs for arbitrary molecules would lay the groundwork for data-driven projections of complex reaction cascades and hence a deeper understanding of these critical chemical processes and, ultimately, how to reverse design them. In this paper, we propose a chemically inspired graph neural network machine learning model, BonDNet, for the rapid and accurate prediction of BDEs. BonDNet maps the difference between the molecular representations of the reactants and products to the reaction BDE. Because of the use of this difference representation and the introduction of global features, including molecular charge, it is the first machine learning model capable of predicting both homolytic and heterolytic BDEs for molecules of any charge. To test the model, we have constructed a dataset of both homolytic and heterolytic BDEs for neutral and charged (−1 and +1) molecules. BonDNet achieves a mean absolute error (MAE) of 0.022 eV for unseen test data, significantly below chemical accuracy (0.043 eV). Besides the ability to handle complex bond dissociation reactions that no previous model could consider, BonDNet distinguishes itself even in only predicting homolytic BDEs for neutral molecules; it achieves an MAE of 0.020 eV on the PubChem BDE dataset, a 20% improvement over the previous best performing model. We gain additional insight into the model''s predictions by analyzing the patterns in the features representing the molecules and the bond dissociation reactions, which are qualitatively consistent with chemical rules and intuition. BonDNet is just one application of our general approach to representing and learning chemical reactivity, and it could be easily extended to the prediction of other reaction properties in the future.

Prediction of bond dissociation energies for charged molecules with a graph neural network enabled by global molecular features and reaction difference features between products and reactants.     

General approach for the synthesis of chiral perylenequinones via catalytic enantioselective oxidative biaryl coupling

By using oxygen as the terminal oxidant, copper complexes derived from chiral 1,5-diaza-cis-decalin catalyze the enantioselective oxidative biaryl coupling of highly functionalized naphthols to provide octa- and decasubstituted binaphthalenes with high selectivity (86-90% ee). Products containing very electron-rich naphthalenes were prone to epimerization under the reaction conditions. This epimerization could be suppressed by employing naphthol starting materials with phenol protecting groups that attenuated the electron-rich nature of the naphthalenes. Direct oxidation of the resultant chiral 1,1'-binaphthol framework completed the first asymmetric synthesis of a perylenequinone containing only an axial chirality element.     

Photochemical and Acid-Catalyzed Rearrangements of 4-Carbomethoxy-4-methyl-3-(trimethylsilyl)-2,5-cyclohexadien-1-one

The synthesis of 4-carbomethoxy-4-methyl-3-(trimethylsilyl)-2,5-cyclohexadien-1-one (1) in 60% overall yield from benzaldehyde is described. Irradiation (366 nm) of 1 in benzene solution gave products of type A photorearrangement; e.g., diastereomers of the 4-(trimethylsilyl)- and 5-(trimethylsilyl)bicyclo[3.1.0]hex-3-en-2-ones 8 and 9. Bicyclohexenones 9a and 9b could not be isolated, but underwent acid-catalyzed protiodesilylative rearrangements on attempted chromatography (silica gel) to give a 1:1 mixture of (E)- and (Z)-4-(carbomethoxymethylmethylene)cyclopent-2-en-1-ones 12 and 13. Irradiation (366 nm) of either 12 or 13 resulted in photoisomerization to a photostationary state that was also a 1:1 mixture. Irradiation of 8a or 8b gave equivalent mixtures of phenols 14 and 15 by way of the type B oxyallyl zwitterion 17. The available experimental evidence suggests that both 9a and 9b undergo regiospecific photorearrangement to phenol 16 with no trace of 3-methyl-4-carbomethoxyphenol (19), the product of ipso substitution of the Me(3)Si group at C(4). Phenol 15 was isolated in 65% yield from the photoreaction of 1 in benzene with 20 equiv of CF(3)CO(2)H. The acid-catalyzed rearrangement of 1 to 3-carbomethoxy-4-methylphenol (21) occurs in 91% yield by way of CO(2)Me group rearrangement to C(3) to give the Me(3)Si-stabilized carbocation 23.     

Interplanar torsion in the S1<--S0 electronic spectrum of jet cooled 1-phenylimidazole

The S(1)<--S(0) transition of 1-phenylimidazole (1PI) has been studied in a supersonic jet expansion by resonant two-photon ionization. The origin band at 36 075 cm(-1) is accompanied by a low frequency progression associated with torsion about the bond connecting phenyl and imidazole groups. Torsional potentials have been determined for both states. In S(0), phi(min)=37.2+/-0.5 degrees and the planar barrier is 339+/-20 cm(-1), while in S(1), phi(min)=17.6+/-0.5 degrees and the planar barrier is 57+/-2 cm(-1). The transition moment alignment is observed to be consistent with an excited state of L(b) character, in spite of the "off-axis" conjugation provided by the imidazole ring. These results are compared with ab initio calculations on both states, performed using Hartree-Fock, M?ller-Plesset second-order perturbation, density functional theory with the Becke3-Lee-Yang-Parr functional, time-dependent density functional theory, configuration interaction singles, and complete active space self-consistent field methods. Solution-phase UV spectra of neutral and protonated 1PI are also reported.     

Molecular models of lipopeptide detergents: large coiled-coils with hydrocarbon interiors

We have constructed molecular models of octameric micelles formed by a recently developed lipopeptide detergent consisting of a single amphipathic alpha-helix coupled to two acyl chains at either end of the helix. The models explain the experimentally observed aggregation behavior of peptides with different acyl chain lengths. The octameric micelles form a unique coiled-coil structure, with the acyl chains in a nearly frozen conformation inside the cylindrical assemblies. Two extreme models with helices either all parallel or in an alternating orientation suggest that the alternating orientation is energetically more favorable. The models suggest several new directions for further diversifying this new class of detergents for the structural studies of membrane proteins.     

Copper(II) coordination to ligands immobilized on photoluminescent porous silicon

Increased preorganization can be achieved by immobilizing ligands on solid supports. Photoluminescent porous silicon, which can undergo facile hydrosilylation, was used as a support for open chain neutral N- and O-donor ligands. The abilities of these ligands to bind the divalent metal ions Ni(2+), Cu(2+), Zn(2+), and Pb(2+) are examined. Immobilized ligands selectively complexed Cu(II) over the other metal ions studied. Ligands immobilized on photoluminescent porous silicon also removed a significant amount, up to 98%, of Cu(II) from copper(II)-spiked, organic-rich, seawater samples.     

The role of acidic residues and of sodium ion adduction on the gas-phase H/D exchange of peptides and peptide dimers

Gas-phase H/D exchange is widely used for characterizing the structure of ions. However, many structural parameters that affect the rate of H/D exchange are poorly understood, which complicates the interpretation of experimental data. Here, the effects of sodium ion adduction on the rate of H/D exchange with D₂O for a series of peptides and peptide dimers with varying numbers of acidic residues are described. The maximum number of sodium ion adducts that can be accommodated by the peptides and peptide dimers in this study is N + 1, where N is the number of free carboxylic acid groups. The formation of methyl-esters at all carboxylic acid groups, or the replacement of all the acidic hydrogens with sodium ions, effectively shuts down H/D exchange with D₂O. In contrast, both the rate and the extent of H/D exchange with D₂O are increased for most of the peptides and peptide dimers by the adduction of an intermediate number of sodium ions. These results are consistent with the H/D exchange occurring via a salt-bridge mechanism and show that the presence of two carboxylic acid groups is much better than one. The results with peptide dimers also indicate that surface accessibility may not be a dominant factor in the extent of H/D exchange for these ions.     

Quantum yields for product formation in the 120-133 nm photodissociation of O2

The photodissociation of O(2) in the region from 120-133 nm has been investigated using product imaging. The spectrum in this region is dominated by transitions from the ground state to the first three vibrational levels of the E (3)Sigma(u) (-) state. The O((1)D)+O((3)P) channel is the only product channel observed by product imaging for dissociation at either 124.4 nm or 120.4 nm. The O((1)D(2)) product is aligned in the molecular frame in such a way that its J vector is perpendicular to the relative velocity vector between the O((1)D) and the O((3)P). The variation in the anisotropy of dissociation is approximately predicted by considering transitions on individual lines and then taking into account the coherent excitation of overlapping resonances. At 132.7 nm, both the O((1)D)+O((3)P) and the O((3)P)+O((3)P) channels are observed with branching ratios of 0.40+/-0.08 and 0.60+/-0.09, respectively. At 130.2 nm, the quantum yield for production of O((1)D) is 0.76+/-0.28.     

Controlling the morphology of cross beta-sheet assemblies by rational design

Low molecular weight peptidomimetics with simple amphiphilic sequences can help to elucidate the structures of cross beta-sheet assemblies, such as amyloid fibrils. The peptidomimetics described herein comprise a dibenzofuran template, two peptide strands made up of alternating hydrophilic and hydrophobic residues, and carboxyl termini, each of which can be varied to probe the structural requirements for beta-sheet self-assembly processes. The dibenzofuran template positions the strands approximately 10 A apart, allowing corresponding hydrophobic side chains in the strands to pack into a collapsed U-shaped structure. This conformation is stabilized by hydrophobic interactions, not intramolecular hydrogen bonds. Intermolecular stacking of the collapsed peptidomimetics, enabled by intermolecular hydrogen bonding and hydrophobic interactions, affords 25-27 A wide protofilaments having a cross beta-sheet structure. Association of protofilaments, mediated by the dibenzofuran substructures and driven by the hydrophobic effect, affords 50-60 A wide filaments. These widths can be controlled by changing the length of the peptide strands. Further assembly of the filaments into fibrils or ribbons can be controlled by modification of the template, C-terminus, and buffer ion composition.