On assignment of fundamental vibrational modes of hypophosphite anion and its deuterated analogue

Results of ab initio and density functional theory calculations on the structure and vibrational frequencies of hypophosphite anion indicate earlier experimental assignments of the fundamental vibrational modes are correct while the recent reassignments of several modes proposed by Bickley et al. are inconsistent with the calculated results.     

A simple sum rule for total radiative decay rates in diatomics

The quantity (ν³μ_e²), which occurs in expressions for the total radiative decay rate for an excited vibronic state of a diatomic, is evaluated as a simple expectation value for the initial state. In test calculations this expectation value agrees with the exact sum over states within ≈0.2%.     

A convergent approach to huperzine A and analogues

We describe a concise and convergent synthesis of (rac)-5-methoxy-6-azatricyclco[7.3.1.0(2,7)]trideca-2(7),3,5,11-tetraen-13-ol, which has the basic ring system of huperzine A, a potent inhibitor of acetylcholinesterase. We also describe the synthesis of the novel system 5-methoxy-6-azatricyclo[7.2.2.0(2,7)]trideca-2(7),3,5-trien-10-one and a series of related systems.     

Particle circulation and oxygen mass transfer in an immobilized cell bioreactor

Two important considerations in the design of an aerobic particulate immobilized cell bioreactor are the provision of sufficient oxygen to maintain the desired metabolism of the immobilized organism, and the biomass holdup (which is proportional to the number of immobilized cell particles in the reactor). The Circulating Bed Reactor, a reactor developed for use with those forms of immobilization that result in particles of essentially neutral buoyancy, operates with an expanded bed of circulating particles. The particle number density attainable in such a reactor has been found to be dependent upon the circulation cell aspect ratio, the individual particle properties, the static bed voidage of the particles, and the superficial gas velocity. The oxygen mass transfer characteristics have been found to be dependent upon the circulatory nature of the system, the particle (solids) holdup, the particle porosity, and the superficial gas velocity.     

A cell model of a liquid droplet

An expression for the free energy of a droplet composed of attracting hard spheres is found using a simple cell model. The hard-sphere repulsion is assumed to act only between molecules in the same cell, whereas attraction extends over many cells. A maximum term analysis gives rise to a mean-field free energy which includes terms proportional to the first and second power of the droplet radius R with coefficients which can be related to the planar surface tension and Tolman length. Certain Gaussian fluctuations about the maximum term are also considered, corresponding to droplet translation and capillary wave fluctuations. Inclusion of these fluctuations is necessary to ensure that the nucleation rate is proportional to the system volume. They also reduce the planar surface tension and introduce a logarithmic term, -4/3 ln R, into the free energy. The inclusion of other fluctuations and the relationship between these equations and those arising in density-functional theories of nucleation is discussed.     

Metallaborane reaction chemistry. A facile and reversible dioxygen capture by a B-frame-supported bimetallic: structure of [(PMe2Ph)4(O2)Pt2B10H10

[(PMe2Ph)4Pt2B10H10] reversibly takes up atmospheric dioxygen to give the fluxional dioxygen-dimetallaborane complex [(PMe2Ph)4(O2)Pt2B10H10], which has Pt-Pt 2.7143(3), Pt-O 2.141(4) and 2.151(4) and O-O 1.434(6)A.     

How does huperzine A enter and leave the binding gorge of acetylcholinesterase? Steered molecular dynamics simulations

The entering and leaving processes of Huperzine A (HupA) binding with the long active-site gorge of Torpedo californica acetylcholinesterase (TcAChE) have been investigated by using steered molecular dynamics simulations. The analysis of the force required along the pathway shows that it is easier for HupA to bind to the active site of AChE than to disassociate from it, which for the first time interprets at the atomic level the previous experimental result that unbinding process of HupA is much slower than its binding process to AChE. The direct hydrogen bonds, water bridges, and hydrophobic interactions were analyzed during two steered molecular dynamics (SMD) simulations. Break of the direct hydrogen bond needs a great pulling force. The steric hindrance of bottleneck might be the most important factor to produce the maximal rupture force for HupA to leave the binding site but it has a little effect on the binding process of HupA with AChE. Residue Asp72 forms a lot of water bridges with HupA leaving and entering the AChE binding gorge, acting as a clamp to take out HupA from or put HupA into the active site. The flip of the peptide bond between Gly117 and Gly118 has been detected during both the conventional MD and SMD simulations. The simulation results indicate that this flip phenomenon could be an intrinsic property of AChE and the Gly117-Gly118 peptide bond in both HupA bound and unbound AChE structures tends to adopt the native enzyme structure. At last, in a vacuum the rupture force is increased up to 1500 pN while in water solution the greatest rupture force is about 800 pN, which means water molecules in the binding gorge act as lubricant to facilitate HupA entering or leaving the binding gorge.     

Stereocontrol in Organic Synthesis Using the Diphenylphosphoryl Group

In 1959, Horner showed that metalated alkyldiphenylphosphane oxides react with aldehydes or ketones to give alkenes. With this reaction, the diphenylphosphoryl (Ph₂PO) group made its entrance into synthetic organic chemistry. In the thirty-six years since that date, extensive research has shown that this olefination, the Horner–Wittig reaction, has unique properties that make it much more than simply the phosphane oxide cousin of the more famous phosphorus-based olefinations—the Wittig reaction (based on phosphonium salts) and the Wadsworth–Emmons reaction (based on phosphonate esters). Early work on the Horner–Wittig reaction concentrated on the reactivity of phosphane oxides and the regioselectivity of their reactions, but more recently the power of the Ph₂PO group to control the stereochemistry of alkenes, and to produce “on demand” either stereoisomer in high stereochemical purity, has emerged. From the study of these stereocontrolled Horner–Wittig reactions arose the realization that the Ph₂PO group is useful not only for the control of the two-dimensional stereochemistry of alkenes, but also of three-dimensional stereochemistry in general. After a brief introduction to phosphane oxide chemistry, this review will examine the Horner–Wittig reaction, in both its original and “stereocontrolled” varieties. From there, we will move on to an account of the stereoselective construction of molecules containing the Ph₂PO group, concentrating on the stereochemical directing effects of the Ph₂PO group and on the role of its unique combination of attributes—steric bulk, electronegativity, and Lewis basicity—in controlling these reactions. Finally, we will present what is intended as a practical guide to this chemistry, covering the type of functionalized alkenes that have been made with the help of the Ph₂PO group and giving guidelines that we hope will help the organic chemist to make the most of the chemistry the Ph₂PO group has to offer.     

Paradigms and paradoxes: patterns and estimation of the entropy of formation of aqueous hydrogen containing mono and polynuclear oxyanions

“Simple” energetic patterns, where simple means the use of parameters derived only from the stoichiometry of these species, are relatively rarely discussed in the literature. In addition, entropy studies have been dominated by derivation of the absolute quantity S° rather than the entropy of formation (TΔ_f S ^o). Relationships between the entropy of formation and different parameters such as negative value of the charge of the species, the number of oxygen atoms, the natural logarithm of the molecular weight, the total number of atoms and the number of central atoms that are gases were recently discussed by us for aqueous polynuclear oxyanions. As shown here hydrogen containing anions do not follow this pattern. In this study, new approaches for the estimation of the entropy of formation of aqueous hydrogen containing mono and polynuclear oxyanions are suggested, evaluated and recommended.     

A sequential molecular mechanics/quantum mechanics study of the electronic spectra of amides

We report gas-phase electronic spectra of formamide, N-methyformamide, acetamide, and N-methylacetamide at 300 K calculated using a combination of classical molecular dynamics and time-dependent density functional theory (TDDFT). In comparison to excitation energies computed using the global minima structures, the valence npi* and pi(nb)pi* states show a significant red-shift of 0.1-0.35 eV, while smaller shifts are found for the n3s and pi(nb)3s Rydberg states. In this work, we have identified the physical origin of these shifts arising from variations of the molecular structure. We present simple relationships between key geometrical parameters and spectral shifts. Consequently, electronic spectra can be generated directly from ground-state structures, without additional quantum chemical calculations. The electronic spectrum of formamide in aqueous solution is computed using TDDFT using an explicit solvent model. This provides a quantitative determination of the condensed-phase spectrum. In general, this study shows that temperature effects can change the predicted excitation energies significantly and demonstrates how electronic spectra at elevated temperatures can be computed in a computationally efficient way.