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.     

Tetrameric Cubic Structures of Two Solvated Lithium Enolates

The structures of the crystalline lithium enolates derived from 3, 3-dimethyl-2-butanone and from cyclopentanone have been determined by X-ray analysis. Both structures are tetrameric aggregates based on a Li₄O₄-cube, each Li⁺-ion being additionally bonded to the O-atom of a tetrahydrofuran solvent molecule.     

Influence of Process Parameters on the Reaction Kinetics of the Chromium‐Catalyzed Trimerization of Ethylene

In this paper we report the results of an extensive experimental kinetic study carried out on the novel ethylene trimerization catalyst system, comprising the chromium source [CrCl₃(thf)₃] (thf=tetrahydrofuran), a Ph₂P‐N(iPr)‐P(Ph)‐N(iPr)H (PNPNH) ligand (Ph=phenyl, iPr=isopropyl), and triethylaluminum (AlEt₃) as activator. It could be shown that the initial activity shows a first‐order dependency on the ethylene concentration. Also, a first‐order dependency was found for the catalyst concentration. The initial activity follows a typical Arrhenius behavior with an experimentally determined activation energy of 52.6 kJ mol^?1. At elevated temperatures (ca. 80 °C), a significant deactivation was observed, which can be tentatively traced back to a ligand rearrangement in the presence of AlEt₃. After a fast initial phase, a pronounced ‘kink’ in the ethylene‐uptake curve is observed, followed by a slow, almost linear, further increase of the total ethylene consumption. The catalyst composition, in particular the ligand/chromium and the cocatalyst/chromium molar ratio, has a strong impact on the catalytic performance of the trimerization of ethylene.     

Structural and redox properties of VOx and Pd/VOx thin film model catalysts studied by TEM and SAED

The oxidation of pure V(2)O(3) and Pd/V(2)O(3) films was studied by Transmission Electron Microscopy (TEM) and Selected Area Electron Diffraction (SAED) in the temperature range 673-773 K. Thin films of V(2)O(3) were prepared by reactive deposition of V metal in 10(-2) Pa O(2) on NaCl(001) cleavage faces. Pd particles were epitaxially grown on NaCl(001) and subsequently embedded in V(2)O(3). Oxidation of both pure V(2)O(3) and Pd/V(2)O(3) at 673 K transforms V(2)O(3) into a platelet-like V(2)O(5) structure. At temperatures T>or= 773 K, a reconstruction of the platelet-like V(2)O(5) structure into an array of oblong and needle-type V(2)O(5) nanocrystals of different size occurs. Subsequent reduction of the so-prepared structures in 1 bar H(2) at 573-673 K results in the formation of the cubic VO phase, whereby the external shape of the original crystals is partially maintained. Upon oxidation at 723 K, Pd is transformed into PdO, but its formation is suppressed in comparison with Pd supported on Al(2)O(3) and occurs only at an about 100 K higher temperature than on Pd/Al(2)O(3). The Pd particles are stabilized against oxidation up to 673 K, PdO decomposes upon reduction in hydrogen between 573 and 673 K.