Unexpected dimerization of 1,3‐dimethyl‐5‐methylenebarbituric acid revealed by a combined experimental and computational study

A comparison of experimental and calculated ¹³C‐nuclear magnetic resonance chemical shifts reveals the molecular structure of a dimer that was obtained by an unexpected dimerization of 1,3‐dimethyl‐5‐methylenebarbituric acid. Furthermore, the puckering angle of the cyclobutane unit linking the six‐membered rings is discussed in detail. The influence of substituents on 1,3‐position of the cyclobutane ring on the puckering angle is demonstrated based on 1,1,3,3‐tetramethylcyclobutane. Copyright © 2015 John Wiley & Sons, Ltd.     

The Dirac Operator on Nilmanifolds and Collapsing Circle Bundles

We compute the spectrum of the Dirac operator on 3-dimensional Heisenberg manifolds. The behavior under collapse to the 2-torus is studied. Depending on the spin structure either all eigenvalues tend to ± or there are eigenvalues converging to those of the torus. This is shown to be true in general for collapsing circle bundles with totally geodesic fibers. Using the Hopf fibration we use this fact to compute the Dirac eigenvalues on complex projective space including the multiplicities.Finally, we show that there are 1-parameter families of Riemannian nilmanifolds such that the Laplacian on functions and the Dirac operator for certain spin structures have constant spectrum while the Laplacian on 1-forms and the Dirac operator for the other spin structures have nonconstant spectrum. The marked length spectrum is also constant for these families.     

Bidirectional molecular dynamics: Interpretation in terms of a modern formulation of classical mechanics

The validity and applicability of bidirectional molecular dynamics is shown in terms of modern classical mechanics. A simple interpretation of bidirectional molecular dynamics is given. This interpretation justifies an easy approach to start from an equilibrium configuration, to perform simulations in parallel in “forward” and “backward” time direction, and to combine the two obtained trajectories into a single one for proper evaluation of statistical quantities. Practical results, obtained for liquid ammonia, are presented. © 1996 by John Wiley & Sons, Inc.     

Nitrogen‐Doped Ordered Mesoporous Carbon Supported Bimetallic PtCo Nanoparticles for Upgrading of Biophenolics

Hydrodeoxygenation (HDO) is an attractive route for the upgrading of bio‐oils produced from lignocellulose. Current catalysts require harsh conditions to effect HDO, decreasing the process efficiency in terms of energy and carbon balance. Herein we report a novel and facile method for synthesizing bimetallic PtCo nanoparticle catalysts (ca. 1.5 nm) highly dispersed in the framework of nitrogen‐doped ordered mesoporous carbon (NOMC) for this reaction. We demonstrate that NOMC with either 2D hexagonal (p6m) or 3D cubic (Im m) structure can be easily synthesized by simply adjusting the polymerization temperature. We also demonstrate that PtCo/NOMC (metal loading: Pt 9.90 wt %; Co 3.31 wt %) is a highly effective catalyst for HDO of phenolic compounds and “real‐world” biomass‐derived phenolic streams. In the presence of PtCo/NOMC, full deoxygenation of phenolic compounds and a biomass‐derived phenolic stream is achieved under conditions of low severity.     

Self-assembling cyclic peptides: molecular dynamics studies of dimers in polar and nonpolar solvents

The self-assembly of cyclic D,L-alpha-peptides into hollow nanotubes is a crucial mechanistic step in their application as antibacterial and drug-delivery agents. To understand this process, molecular dynamics (MD) simulations were performed on dimers of cyclic peptides formed from cyclo [(-L-Trp-D-N-MeLeu-)4-]2 and cyclo [(-L-Trp-D-Leu-)4-]2 subunits in nonpolar (nonane) and polar (water) solvent. The dimers were observed to be stable only in nonpolar solvent over the full 10 ns length of the MD trajectory. The behavior of the dimers in different solvents is rationalized in terms of the intersubunit hydrogen bonding, hydrogen bonding with the solvent, and planarity of the rings. It is shown that the phi and psi dihedral angles of a single uncapped ring in nonane lie in the beta-sheet region of the Ramachandran plot, and the ring stays in a flat conformation. Steered MD (SMD) simulations based on Jarzynski's equality were performed to obtain the potential of mean force as a function of the distance between the two rings of the capped dimer in nonane. It is also shown that a single peptide subunit prefers to reside close to the nonane/water interface rather than in bulk solvent because of the amphiphilic character of the peptide ring. The present MD results build the foundation for using MD simulations to study the mechanism of the formation of cyclic peptide nanotubes in lipid bilayers.     

Propagation with distributed Gaussians as a sparse, adaptive basis for higher-dimensional quantum dynamics

A simple quantum wavepacket propagation algorithm is presented, designed to produce a very compact, non-direct product representation in higher-dimensional cases. Instead of moving basis functions around, localized basis functions at pre-defined centers are added to and deleted from the representation, generating an active basis function set strictly localized to the region where the moving wavepacket has significantly non-zero values. Simple one-dimensional examples prove this property, as well as the ability of the algorithm to accommodate splitting and rejoining of an arbitrary number of wavefunction pieces, and tunnelling through potential energy barriers. It is argued that future applications to higher-dimensional examples will be less expensive than with traditional direct-product bases, since making the basis adaptive has a lower scaling than the elementary steps necessary for any propagation algorithm itself.     

Small molecule conformational preferences derived from crystal structure data. A medicinal chemistry focused analysis

Based on torsion angle distributions of frequently occurring substructures, conformation preferences of druglike molecules are presented, accompanied by a review of the relevant literature. First, the relevance of the Cambridge Structural Database (CSD) for drug design is demonstrated by comparing substructures present in compounds entering clinical trials with those found in the CSD and protein-bound ligands in the Protein Data Bank (PDB). Next, we briefly highlight preferred conformations of elementary acyclic systems, followed by a discussion of sulfonamide conformations. Due to their central role in medicinal chemistry, we discuss properties of aryl ring substituents in depth, including biaryl systems and systems of two aryl rings connected by two acyclic bonds. For a subset of torsion motifs, we also compare torsion angle histograms derived from CSD structures with those derived from ligands in the PDB. Furthermore, selected properties of some six- and seven-membered ring systems are discussed. The article closes with a section on attractive sulfur-oxygen contacts.     

The tandem ring-closing metathesis-isomerization approach to 6-deoxyglycals

Protected 3,6-dideoxyglycals have been synthesized de novo as single isomers starting from ethyl lactate by using the tandem RCM-isomerization reaction as the key step. Different relative configurations become accessible by addition of vinyl- or allyl-metal compounds to protected lactaldehydes under Cram-chelate or Felkin-Anh control. The concept is exemplified for glycals of L-rhodinose and L-amicetose, as well as for ring-expanded non-natural analogues thereof. This novel approach to glycals is also applicable to the synthesis of disaccharide glycals via a reiterative strategy, as exemplified for the dimer of L-rhodinose and its non-natural ring expanded analogue.