Molecular structure calculations without clamping the nuclei

A number of recent papers have considered ways in which molecular structure may be calculated when both the electrons and the nuclei are treated from the outset as quantum particles. This is in contrast to the conventional approach in which the nuclei initially have their positions fixed and so merely provide a potential for electronic motion. The usual approach is generally assumed to be justified by the 1927 work of Born and Oppenheimer. In this paper we discuss what precisely might be anticipated in the way of molecular structure from a mathematical consideration of the spectral properties of the full Coulomb Hamiltonian, to what extent the very idea of molecular structure might be dependent upon treating the nuclei simply as providing a potential and the extent to which the work of Born and Oppenheimer can be used to support this position.     

Photoionization dynamics of glycine adsorbed on a silicon cluster: "on-the-fly" simulations

Dynamics of glycine chemisorbed on the surface of a silicon cluster is studied for a process that involves single-photon ionization, followed by recombination with the electron after a selected time delay. The process is studied by "on-the-fly" molecular dynamics simulations, using the semiempirical parametric method number 3 (PM3) potential energy surface. The system is taken to be in the ground state prior to photoionization, and time delays from 5 to 50 fs before the recombination are considered. The time evolution is computed over 10 ps. The main findings are (1) the positive charge after ionization is initially mostly distributed on the silicon cluster. (2) After ionization the major structural changes are on the silicon cluster. These include Si-Si bond breaking and formation and hydrogen transfer between different silicon atoms. (3) The transient ionization event gives rise to dynamical behavior that depends sensitively on the ion state lifetime. Subsequent to 45 fs evolution in the charged state, the glycine molecule starts to rotate on the silicon cluster. Implications of the results to various processes that are induced by transient transition to a charged state are discussed. These include inelastic tunneling in molecular devices, photochemistry on conducting surfaces, and electron-molecule scattering.     

Cyclen based bis-macrocyclic ligands as phosphates receptors. A potentiometric and NMR study

The host-guest interaction between orthophosphate, pyrophosphate and triphosphate anions and four cyclen based bis-macrocycles ligands possessing ortho-(BOC), meta-(BMC), para-xylenyl (BPC) or 2,6-pyridinyl (BPyC) linker was investigated by potentiometric measurements and NMR spectroscopy. Each ligand gave protonated species in aqueous solution that further formed ternary complexes after binding with anions; these complexes were analyzed as a result of hydrogen bond formation and Coulombic attraction between the organic host and the inorganic guest. The equilibrium constants for all the detected species are reported and the selectivity, illustrated with species distribution diagrams, is discussed. The results unambiguously showed the importance of the distance between the two cyclen cores and underlined, especially for the triphosphate species, the contribution of the nitrogen atom of the pyridinyl spacer as a supplementary anchoring point in acidic medium.     

Charge calculations in molecular mechanics. IX. A general parameterisation of the scheme for saturated halogen,oxygen and nitrogen compounds

Summary The CHARGE2 program for the calculation of partial atomic charges has been amended to include bond parameters for a number of organic functional groups, including halogens, nitrogen and oxygen. These minor amendments to the original scheme produce dipole moments for the fluoro and chloro compounds which are in complete agreement with the observed values.The less complete data sets for the bromo and iodo compounds are also well reproduced, and the dipole moments of a variety of mixed halo compounds are now in better agreement with experiment than previously.The calculated dipole moments of the saturated nitrogen and oxygen compounds are now in much better agreement than in the original scheme, thus the revised parameterisation may be employed with confidence to predict the electrostatic energies of these compounds.Furthermore, the revised scheme now gives a precise proportionality between the charge on the proton in a CH group and the ¹H chemical shift of the corresponding proton, allowing the general prediction, in principle, of ¹H chemical shifts. In addition, attempts to include variable electronegativity in the effect are described for fluoro compounds.For part VIII see Ref. 1.     

Damaging Effects of Ultraviolet Radiation on the Cornea

The cornea sits at the anterior aspect of the eye and, like the skin, is highly exposed to ultraviolet radiation (UVR). The cornea blocks a significant proportion of UVB from reaching the posterior structures of the eye. However, UVA can penetrate the full thickness of the cornea, even reaching the anterior portion of the lens. Epidemiological data indicate that UVR is a contributing factor for a multitude of diseases of the cornea including pterygium, photokeratitis, climatic droplet keratopathy and ocular surface squamous neoplasia (OSSN), although the pathogenic mechanisms of each require further elucidation. UVR is a well‐known genotoxic agent, and its effects have been well characterized in organs such as the skin. However, we are only beginning to identify its effects on the cornea, such as the UVR signature C → T and CC → TT transversions identified by sequencing and increased proliferative and shedding rates in response to UVR exposure. Alarmingly, a single low‐dose exposure of UVR to the cornea is sufficient to elicit genetic, molecular and cellular changes, supporting the consideration of using protective measures, such as wearing sunglasses when outdoors. The aim of this review was to describe the adverse effects of UVR on the cornea.     

Computational Fluid Dynamic Design of Jet Stirred Reactors for Measuring Intrinsic Kinetics of Gas‐Phase and Gas‐Solid Reactions

Nonreactive and reactive computational fluid dynamic simulations were applied to optimize the design of a laboratory scale jet stirred reactor for measuring intrinsic kinetics of gas‐phase and gas‐solid reactions, i.e. kinetics determined by chemical steps only and not by heat or mass transfer. In the past these reactors were designed and tested based on empirical design criteria and residence time distribution experiments. This work shows that these do not always capture important local effects that are vital for kinetic studies. First the degree of macro–mixing was evaluated for three different geometries (down case, 45° case and 90° case) by performing in silico residence time distribution experiments at 900 K, showing that with these type of experiments only minor differences are observed. However, the ethane steam cracking simulations revealed major differences, with the 45° case being the most uniform in terms of temperature and the 90° case being by far the worst. The species nonuniformity in all geometries was acceptable and was in some cases even partly masked by important shortcut streams such as those observed in the 90° case. The existing gradients on the substrate surface are sufficiently small to be neglected in modeling efforts. As temperature is the major parameter determining the rate of the surface reactions, the 45° case is suggested as the best geometry for measuring intrinsic kinetics.     

Synthesis and Characterisation of a Thiocarbonyl containing Osmium Cluster

Reaction of CS₂ with H₂Os₃(CO)₈(MeCN)S in cyclohexane yields a product H₂Os₃(CO)₇(CS)S₂. this has been characterised by NMR and mass spectroscopy, and by X-ray analysis, and has been shown to contain a terminal thiocarbonyl ligand.     

Inorganic reactions of iodine(III) in acidic solutions and free energy of iodous acid formation

An analysis of the former works devoted to the reactions of I(III) in acidic nonbuffered solutions gives new thermodynamic and kinetic information. At low iodide concentrations, the rate law of the reaction IO + I^? + 2H⁺ ? IO₂H + IOH is k_+B [IO][I^?][H⁺]² – k_?B [IO₂H][IOH] with k_+B = 4.5 × 10³ M^?3s^?1 and k_?B = 240 M^?1s^?1 at 25°C and zero ionic strength. The rate law of the reaction IO₂H + I^? + H⁺ ? 2IOH is k_+C [IO₂H][I^?][H⁺] – k_?C [IOH]² with k_+C = 1.9 × 10¹⁰ M^?2s^?1 and k_?C = 25 M^?1s^?1. These values lead to a Gibbs free energy of IO₂H formation of ?95 kJ mol^?1. The pK_a of iodous acid should be about 6, leading to a Gibbs free energy of IO formation of about ?61 kJ mol^?1. Estimations of the four rate constants at 50°C give, respectively, 1.2 × 10⁴ M^?3s^?1, 590 M^?1s^?1, 2 × 10⁹ M^?2s^?1, and 20 M^?1 s^?1. Mechanisms of these reactions involving the protonation IO₂H + H⁺ ? IO₂H and an explanation of the decrease of the last two rate constants when the temperature increases, are proposed. © 2008 Wiley Periodicals, Inc. Int J Chem Kinet 40: 647–652, 2008     

Cyclic (alkyl)(amino)carbene gold(I) complexes: A synthetic and structural investigation

A series of mono- and dicarbene gold(I) complexes of types Au(CAAC)(Cl) [CAAC = cyclic (alkyl)(amino)carbene] (1) and [Au(CAAC)₂]⁺[X]^? (X = Cl, AuCl₂) (2) have been prepared through reaction of AuCl(SMe₂) with free carbenes a–e, and structurally characterized by single X-ray diffraction studies (1a, 1b, 2d, 2e). In addition two new free cyclic (alkyl)(amino)carbenes (c and e) have been synthesized.