Statistical Theory of Unimolecular Reactions and Intramolecular Dynamics

In the present lecture we review experimental and theoretical developments in the field of intramolecular dynamics during the past sixty years. In a concluding section we consider possible implications for intramolecular laser selective chemistry

Dynamic Arrest in Polymer Melts: Competition between Packing and Intramolecular Barriers

We present molecular dynamics simulations of a simple model for polymer melts with intramolecular barriers. We investigate structural relaxation as a function of the barrier strength. Dynamic correlators can be consistently analyzed within the framework of the Mode Coupling Theory (MCT) of the glass transition. Control parameters are tuned in order to induce a competition between general packing effects and polymer-specific intramolecular barriers as mechanisms for dynamic arrest. This competition yields unusually large values of the so-called MCT exponent parameter and rationalize qualitatively different observations for simple bead-spring and realistic polymers. The systematic study of the effect of intramolecular barriers presented here also establishes a fundamental difference between the nature of the glass transition in polymers and in simple glass-formers.Comment: 4 pages, 3 figures, 2 table

Unusual structure-energy correlations in intramolecular Diels–Alder reaction transition states

Detailed analysis of calculated data from an experimental/computational study of intramolecular furan Diels–Alder reactions has led to the unusual discovery that the mean contraction of the newly forming C-C σ-bonds from the transition state to the product shows a linear correlation with both reaction Gibbs free energies and reverse energy barriers. There is evidence for a similar correlation in other intramolecular Diels–Alder reactions involving non-aromatic dienes. No such correlation is found for intermolecular Diels–Alder reactions

Thermal rectification in carbon nanotube intramolecular junctions: Molecular dynamics calculations

We study heat conduction in (n, 0)/(2n, 0) intramolecular junctions by using molecular dynamics method. It is found that the heat conduction is asymmetric, namely, heat transports preferably in one direction. This phenomenon is also called thermal rectification. The rectification is weakly dependent on the detailed structure of connection part, but is strongly dependent on the temperature gradient. We also study the effect of the tube radius and intramolecular junction length on the rectification. Our study shows that the tensile stress can increase rectification. The physical mechanism of the rectification is explained

Picosecond-jet spectroscopy and photochemistry. Energy redistribution and its impact on coherence, isomerization, dissociation and solvation

The development of the picosecond-jet technique is presented. The applications of the technique to the studies of coherence (quantum beats), photodissociation, isomerization and partial solvation of molecules in supersonic-jet beams are detailed with emphasis on the role of intramolecular energy redistribution. Experimental evidence for intramolecular threshold effect for rates as a function of excess molecular energy is given and explained using simple theory for the redistribution of energy among certain modes. Comparison with R.R.K.M. calculation is also made to assess the nature of the statistical behaviour of the energy redistribution

A perturbation density functional theory for the competition between inter and intramolecular association

Using the framework of Wertheim's thermodynamic perturbation theory we develop the first density functional theory which accounts for intramolecular association in chain molecules. To test the theory new Monte Carlo simulations are performed at a fluid solid interface for a 4 segment chain which can both intra and intermolecularly associate. The theory and simulation results are found to be in excellent agreement. It is shown that the inclusion of intramolecular association can have profound effects on interfacial properties such as interfacial tension and the partition coefficient

On the Theory of Intramolecular Energy Transfer

We consider the distinguishing features of two main types of classical anharmonic motion in molecules, their quantum parallels, and conditions that classical chaos also be sufficient for “quantum chaos”. Implications are considered for experimental reaction rates, R.R.K.M. theory, spectra and a possible type of system for intramolecular laser-selective chemistry. A theory of intramolecular energy transfer between two ligands of a heavy atom is described for a system which may contain many coordinates. It is partly statistical and, for the modes of each ligand which communicate through the heavy atom, dynamical

Analysis of the conformational profiles of fenamates shows route towards novel, higher accuracy, force-fields for pharmaceuticals

In traditional molecular mechanics force fields, intramolecular non-bonded interactions are modelled as intermolecular interactions, and the form of the torsion potential is based on the conformational profiles of small organic molecules. We investigate how a separate model for the intramolecular forces in pharmaceuticals could be more realistic by analysing the low barrier to rotation of the phenyl ring in the fenamates (substituted N-phenyl-aminobenzoic acids), that results in a wide range of observed angles in the numerous fenamate crystal structures. Although the conformational energy changes by significantly less than 10 kJmol-1 for a complete rotation of the phenyl ring for fenamic acid, the barrier is only small because of small correlated changes in the other bond and torsion angles. The maxima for conformations where the two aromatic rings approach coplanarity arise from steric repulsion, but the maxima when the two rings are approximately perpendicular arise from a combination of an electronic effect and intramolecular dispersion. Representing the ab initio conformational energy profiles as a cosine series alone is ineffective; however, combining a cos2ξ term to represent the electronic barrier with an intramolecular atom-atom exp-6 term for all atom pairs separated by three or more bonds (1-4 interactions) provides a very effective representation. Thus we propose a new, physically motivated, generic analytical model of conformational energy, which could be combined with an intermolecular model to form more accurate force-fields for modelling the condensed phases of pharmaceutical-like organic molecules

Intramolecular fluorescence correlation spectroscopy in a feedback tracking microscope

We derive the statistics of the signals generated by shape fluctuations of large molecules studied by feedback tracking microscopy. We account for the influence of intramolecular dynamics on the response of the tracking system, and derive a general expression for the fluorescence autocorrelation function that applies when those dynamics are linear. We show that tracking provides enhanced sensitivity to translational diffusion, molecular size, heterogeneity and long time-scale decays in comparison to traditional fluorescence correlation spectroscopy. We demonstrate our approach by using a three-dimensional tracking microscope to study genomic $\lambda$-phage DNA molecules with various fluorescence label configurations.Comment: 11 pages, 5 figures, supplemental info: http://minty.stanford.edu/papers/Publications/McHale10aSI.pd

Resonant hot charge-transfer excitations in fullerene-porphyrin complexes: a many-body Bethe-Salpeter study

We study within the many-body Green's function GW and Bethe-Salpeter approaches the neutral singlet excitations of the zinctetraphenylporphyrin and C70 fullerene donor-acceptor complex. The lowest transition is a charge-transfer excitation between the donor and the acceptor with an energy in excellent agreement with recent constrained density functional theory calculations. Beyond the lowest charge-transfer state, of which the energy can be determined with simple electrostatic models that we validate, the Bethe-Salpeter approach provides the full excitation spectrum. We evidence the existence of hot electron-hole states which are resonant in energy with the lowest donor intramolecular excitation and show an hybrid intramolecular and charge-transfer character, favouring the transition towards charge separation. These findings support the recently proposed scenario for charge separation at donor-acceptor interfaces through delocalized hot charge-transfer states.Comment: 9 pages, 4 figure