On the coherent description of diffusion-influenced fluorescence quenching experiments

The fluorescence quenching by electron transfer of a fluorophore, 2,5-bis(dimethylamino)-1,3-benzenedicarbonitrile, to 1,3-dimethyl-2-nitrobenzene, has been studied by means of time-resolved and steady-state experiments at different viscosities and up to large quencher concentrations. Differential Encounter Theory (DET) has been used to rationalize the results, in combination with electron transfer modelled by the Marcus theory. Additionally, the solvent structure and the hydrodynamic effect on the diffusion coefficient have been taken into account. Any simpler model failed to simultaneously fit all the results. The large number of quencher concentrations used is crucial to unambiguously extract the electron transfer parameters.     

A unified view of the theoretical description of magnetic coupling in molecular chemistry and solid state physics

The magnetic interactions in organic diradicals, dinuclear inorganic complexes and ionic solids are presented from a unified point of view. Effective Hamiltonian theory is revised to show that, for a given system, it permits the definition of a general, unbiased, spin model Hamiltonian. Mapping procedures are described which in most cases permit one to extract the relevant magnetic coupling constants from ab initio calculations of the energies of the pertinent electronic states. Density functional theory calculations within the broken symmetry approach are critically revised showing the contradictions of this procedure when applied to molecules and solids without the guidelines of the appropriate mapping. These concepts are illustrated by describing the application of state-of-the-art methods of electronic structure calculations to a series of representative molecular and solid state systems.     

The Berry phase in molecular physics

The geometric phase of quantum mechanics is introduced, and its physical effects are then studied in the context of molecular physics. By performing the most general Born–Oppenheimer procedure, we show how gauge groups appear in the study of molecules. This method is then applied to the doubly degenerate Λ-levels of a diatomic molecule. The resulting dynamics for the slow angular motion of the dumbbell is equivalent to that of a Dirac monopole.     

Detectors for high energy nuclear physics experiments

High energy nuclear physics experiments started about a decade ago with the aim of studying quark gluon plasmas (QGP) in the laboratory. Statistical QCD predicts that in nuclear collisions at ultra-relativistic energies the quarks and gluons in hadrons will be momentarily deconfined into a phase of matter containing free quarks and gluons in the form of a plasma. This quark gluon plasma is also thought to have existed in the very early history of the evolution of the Universe, some 10 microseconds after the Big Bang when the extremely hot blob of energy started to cool and be converted into matter. Thus the study of ultra-relativistic nuclear collisions is important from the point of view of nuclear and high energy physics, astrophysics and cosmology. In these studies new detectors are required.     

A molecular description of the evolution of resistance

BACKGROUND: In vitro evolution has been used to obtain nucleic acid molecules with interesting functional properties. The evolution process usually is carried out in a stepwise manner, involving successive rounds of selection, amplification and mutation. Recently, a continuous in vitro evolution system was devised for RNAs that catalyze the ligation of oligonucleotide substrates, allowing the evolution of catalytic function to be studied in real time. RESULTS: Continuous in vitro evolution of an RNA ligase ribozyme was carried out in the presence of a DNA enzyme that was capable of cleaving, and thereby inactivating, the ribozyme. The DNA concentration was increased steadily over 33.5 hours of evolution, reaching a final concentration that would have been sufficient to inactivate the starting population in one second. The evolved population of ribozymes developed resistance to the DNA enzyme, reducing their vulnerability to cleavage by 2000-fold but retaining their own catalytic function. Based on sequencing and kinetic analysis of the ribozymes, two mechanisms are proposed for this resistance. One involves three nucleotide substitutions, together with two compensatory mutations, that alter the site at which the DNA enzyme binds the ribozyme. The other involves enhancement of the ribozyme's ability to bind its own substrate in a way that protects it from cleavage by the DNA enzyme. CONCLUSIONS: The ability to direct the evolution of an enzyme's biochemical properties in response to the behavior of another macromolecule provides insight into the evolution of resistance and may be useful in developing enzymes with novel or enhanced function.     

Localized orbitals for the description of molecular interaction

The intermolecular interaction between the molecules CH₂O and NH₃ was investigated by the supermolecule method. The interaction energies were first calculated at the ab initio SCF level, and the electron correlation was included via second-order Møller-Plesset perturbation theory (MP 2). The basis set superposition error (BSSE ) was taken into account by the counter-poise (CP ) method. The occupied and the virtual canonical molecular orbitals (CMOS ) of the supermolecule were separately localized by the Boys' procedure. The correlation correction was calculated by the many-body perturbation theory (MBPT ) in the localized representation. Contributions of the third- and fourth-order localized diagrams were added to those of the second-order canonical diagram. This procedure gives a correction nearly equivalent to that of MP 2. The possibility to separate LMO contributions responsible for the dispersion interaction was investigated.     

The chemistry and physics of molecular surfaces

Configuration interaction calculations are carried out to study the potential energy surface for the system Ar-Ar ₂ ⁺ . An all-electron as well as a pseudopotential treatment is employed. It is found that in the perpendicular Ar approach the Ar ₂ ⁺ partner remains essentially unchanged and the potential can be characterized by an electrostatic ion-induced dipole interaction. In the collinear mode of Ar approach the Ar ₂ ⁺ bond separation increases considerably, the charge is redistributed and the interaction can be characterized as chemical bonding. The minimum on the surface is found to be the linear symmetric molecule with bond lengths of 2.62 Å. The optimum structure in the perpendicular approach lies 0.13 eV above the minimum and is the T-shaped molecule in which the Ar is 3.65 Å away from the midpoint of the Ar ₂ ⁺ (r=2.46 Å) system; the best equilateral triangle structure has a bond length of 2.99 Å but is found to lie 0.64 eV above the Ar ₃ ⁺ minimum. The dissociation energy into Ar ₂ ⁺ + Ar is calculated to be 0.16 eV in reasonable agreement with experimental values of 0.21 eV. The potential curves for the four lowest states of Ar ₂ ⁺ are also treated.     

On the description of reactions in solution

A formulation for diffusion-influenced reactions in solution is given in which reactive and translational contributions are separated, steady state rate-limiting step formulations are generalized to the dynamical case and the influence of different experimental initial conditions is isolated.     

On the determination of molecular weight distributions of asphaltenes and their aggregates in laser desorption ionization experiments

Molecular weight distributions (MWD) of asphaltenes and their aggregates have been investigated in laser desorption ionization (LDI) mass spectrometric experiments. A systematic investigation of the dependence of the measured MWD on the asphaltene sample density and on the laser pulse energy allows the assignment of most probable molecular weights within 300-500 amu and average molecular weights of 800-1000 amu for the monomeric asphaltenes, as well as for the estimation of the contribution from asphaltene clusters in typical LDI measurements. The results serve to reconcile the existing controversy between earlier mass spectrometric characterizations of asphaltenes based on laser desorption techniques by different groups. Furthermore, the MWD measurements performed on particularly dense samples yield an additional differentiated broad band peaking around 9000-10,000 amu and extending over 20,000 amu, not observed previously in LDI experiments, thereby revealing a strong propensity of the asphaltenes to form clusters with specific aggregation numbers, which is in qualitative agreement with previous theoretical predictions and with the interpretation of measurements performed with other techniques.     

A theoretical description of elastic pillar substrates in biophysical experiments.

Arrays of elastic pillars are used in biophysical experiments as sensors for traction forces. The evaluation of the forces can be complicated if they are coupled to the pillar displacements over large distances. This is the case if many of the pillars are interconnected by elastic linkages as, for example, in fiber networks that are grown on top of pillars. To calculate the traction forces in such a network, we developed a set of nonlinear inhomogeneous equations relating the forces in the linking elements to the resulting pillar deflections. We chose a homogeneous, activated two-dimensional network of cytoskeletal actin filaments to illustrate that a pillar substrate is generally not a force sensor but a force-gradient sensor. In homogeneous networks the forces acting along the filaments can be approximated by analyzing only pillar deflections in the edge zones of the substrate and by integration over the corresponding force gradients.     

Relaxation rates in molecular beam maser experiments

A theoretical explanation is given of recent measurements by Kukolich, Wang and Oates on the relaxation of pure inversion states and superposition states in a molecular-beam ammonia maser spectrometer. The Feynman-Vernon-Hellwarth representation is used, combined with an impact theory of collision damping, to derive the rate equations. It is shown, in agreement with experiment, that the longitudinal-component decay rate (analogous to a T₁ process in the Bloch equiations in magnetic resonance) is larger than the transverse-component decay rate (the analog of a T₂ process), in contrast to the usual magnetic-resonance case. The difference between the two rates depends on the efficiency of inelastic collisions in mixing the two maser levels, and is therefore more likely to occur with polar scattering gases having appropriate energy level spacings and populations.     

Multiple collisions in molecular beam scattering experiments

Due to the forward peaked differential cross section for elastic atom—atom scattering the effect of multiple collisions has to be considered in the analysis of crossed beam measurements of the total cross section and especially of the small angle differential cross section at large values of the beam attenuation. At angles θ ≈ θ₀, with θ₀ the quantum mechanical scaling angle of the elastic differential cross section, the correction for the latter case amounts to 20% at beam attenuations I/I₀ = exp(?1). Firstly, a careful analysis of the probabilities for single and multiple scattering is given, resulting in an expression for the measured beam signals which is correct for all values of the beam attenuation. The probability for multiple scattering is then calculated for an inverse power potential V(r) = ?C_sr^?s, with s = 4 through s = 7, which include both the case of ion—atom scattering (s = 4) and atom—atom scattering (s = 6). The results are given as effective differential cross sections σ_n(θ) for n-fold scattering. They are described by a single, simple analytical function with four free parameters that have been determined for n = 2, 3 and 4 by a least squares method. The σ_n(θ) are normalised to the total cross section Q.     

Another scientific practice separating chemistry from physics: thought experiments

Thought experiments in the history of science display a striking asymmetry between chemistry and physics, namely that chemistry seems to lack well-known examples, whereas physics presents many famous examples. This asymmetry, I argue, is not independent data concerning the chemistry/physics distinction. The laws of chemistry such as the periodic table are incurably special, in that they make testable predictions only for a very restricted range of physical conditions in the universe which are necessarily conditioned by the contingences of chemical investigation. The argument depends on how ‚thought experiment’ is construed. Here, several recent accounts of thought experiments are surveyed to help formulate what I call ‚crucial’ thought experiments. These have a historical role in helping to judge between hypotheses in physics, but are not helpful in chemistry past or present.     

Determination of the molecular structure of diacetylene from high-resolution FTIR spectroscopy

The high-resolution infrared absorption spectra of eight²H or¹³C substituted isotopomers of diacetylene have been recorded, and the bands corresponding to thev ₄ fundamental andv ₆ combination of the major isotopomer have been analyzed using a Loomis-Wood-type program. Effective ground-state rotational constants have been obtained from ground-state combination differences. A number ofr ₀,r _s,r _m , and (r _m )_corr structures have been calculated from the available data and are compared to those obtained by ab initio methods. The (r _m )_corr structure, which is a reliable near-equilibrium structure of diacetylene, isr _C–H=106.131(13) pm;r _C–C=137.081(16) pm;r _C-C=120.964(14). (r _m )_corr structures of the related molecules cyanogen, cyanoacetylene, and cyanodiacetylene have been calculated, and near-equilibrium structures of triacetylene and dicyanoacetylene have been predicted.