In silico engineering of tailored ink-binding ability at molecular printboards.

Molecular recognition between guest ink molecules and beta-cyclodextrin (beta-CD) cavities at self-assembled monolayers provides a molecular printboard for nanopatterning applications. We recently used molecular dynamics (MD) simulations to describe the specificity of ink-printboard binding and here extend the simulations to include charged cyclodextrin hosts, necessary to broaden the chemistry of molecular printboards and bind charged inks such as the ferrocenium cation. Shifting to high pH, or alternatively grafting a charged sidearm onto beta-CD, created three distinct types of anionic beta-CD cavity and we used electronic structure calculations and MD simulations to measure host-guest charge transfer and binding strengths. We find that steric recognition of uncharged organic molecules is retained at the charged printboards, and that improved guest-host electrostatic contacts can strengthen binding of larger inks while penalising small inks, enhancing the level of discrimination. A prudent choice of complementary host-guest shape and charge states thus provides a means of tuning both ink binding strength and specificity at molecular printboards.     

Computation of cross sections for the F+H2(v=0,j=0) → FH(v′j)+H reaction by the hyperspherical method

Summary A quantum mechanical calculation of cross sections for the reaction F+H₂(v=0,j=0) FH(vj)+H has been performed on the T5A semiempirical potential surface using hyperspherical coordinates. State-to-state integral and differential cross sections converge rapidly with the number of components of the total angular momentum projection onto the axis of least inertia. Thev=3 differential cross section has a forward peak whose magnitude increases with energy whereas thev=2 differential cross section has a backward maximum, in qualitative agreement with cross-beam experiments. Thev=2 andv=3 rotational distributions are in rather good agreement with experiment, but not the vibrational branching ratios.     

Determining molecular structures and conformations directly from electron diffraction using a genetic algorithm.

A global optimization strategy, based upon application of a genetic algorithm (GA), is demonstrated as an approach for determining the structures of molecules possessing significant conformational flexibility directly from gas-phase electron diffraction data. In contrast to the common approach to molecular structure determination, based on trial-and-error assessment of structures available from quantum chemical calculations, the GA approach described here does not require expensive quantum mechanical calculations or manual searching of the potential energy surface of the sample molecule, relying instead upon simple comparison between the experimental and calculated diffraction pattern derived from a proposed trial molecular structure. Structures as complex as all-trans retinal and p-coumaric acid, both important chromophores in photosensing processes, may be determined by this approach. In the examples presented here, we find that the GA approach can determine the correct conformation of a flexible molecule described by 11 independent torsion angles. We also demonstrate applications to samples comprising a mixture of two distinct molecular conformations. With these results we conclude that applications of this approach are very promising in elucidating the structures of large molecules directly from electron diffraction data.     

I NQR and spectroscopic investigation of impurity-doped and mixed lithium iodate Li1−xHxIO3 crystals

The ¹²⁷I NQR, IR absorption and Raman spectra of impurity-doped and mixed lithium iodate Li_1−xH_xIO₃ crystals grown from water solutions with different LiIO₃/HIO₃ ratios were investigated depending on the content of the impurity hydrogen x. The NQR results suggested that, at small concentration of doping iodic acid x<0.22, the lattice dynamics of the crystal grown from water solution changes significantly though the crystal retains hexagonal symmetry. Spectroscopic studies are compatible with average hexagonal symmetry of the grown doped crystals. From the results of Raman studies at room temperature and 100 K, the concentration range of hydrogen dopant 0.22<x<0.36 was found where disordered solid solution crystals Li_1−xH_xIO₃ are formed.     

The photoisomerization mechanism of azobenzene: a semiclassical simulation of nonadiabatic dynamics

We have simulated the photoisomerization dynamics of azobenzene, taking into account internal conversion and geometrical relaxation processes, by means of a semiclassical surface hopping approach. Both n-->pi* and pi-->pi* excitations and both cis-->trans and trans-->cis conversions have been considered. We show that in all cases the torsion around the N==N double bond is the preferred mechanism. The quantum yields measured are correctly reproduced and the observed differences are explained as a result of the competition between the inertia of the torsional motion and the premature deactivation of the excited state. Recent time-resolved spectroscopic experiments are interpreted in the light of the simulated dynamics.     

Watching photoinduced chemistry and molecular energy flow in solution in real time

Energized molecules are the essential actors in chemical transformations in solution. As the rearrangement of bonds requires a movement of nuclei, vibrational energy is often the driving force for a reaction. Vibrational energy can be redistributed within the "hot" molecule, or relaxation can occur when molecules interact. Both processes govern the rates, pathways, and quantum yields of chemical transformations in solution. Unfortunately, energy transfer and the breaking, formation, and rearrangement of bonds take place on ultrafast timescales. This Review highlights experimental approaches for the direct, ultrafast measurement of photoinduced femtochemistry and energy flow in solution. In the first part of this Review, we summarize recent experiments on intra- and intermolecular energy transfer. The second part discusses photoinduced decomposition of large organic peroxides, which are used as initiators in free radical polymerization. The mechanisms and timescales of their decarboxylation determine the initial steps of polymerization and the microstructure of the polymer product.     

Structure formation and dynamics of water in strong external electric fields

We have performed molecular dynamics computer simulations of water in homogeneous external electric fields which were varied in a wide range of field strengths. The dielectric response is found to be linear up to fields E₀≈0.01 V/Å from where dielectric saturation effects become important. At fields of E₀≈3 V/Å a phase transition into an ordered, ice-like structure is observed, which is stabilized through hydrogen-bonds. With an increasing external electric field, the frequency spectrum of the water dynamics shows a remarkable red shift of the intramolecular modes and a blue shift of the librational motions, where the frequency varies quadratically with the field strength. A simple analytical model is discussed which reproduces the observed behavior.     

Molecular potential-energy surfaces for chemical reaction dynamics

This paper reviews the construction of molecular potential-energy surfaces by an interpolation method which has been developed over the last several years. The method uses ab initio quantum chemistry calculations of the molecular electronic energy in an automated procedure to construct global potential- energy surfaces which can be used to simulate chemical reactions with either classical or quantum dynamics. The methodology is explained and several applications are presented to illustrate the approach. Received: 22 February 2002 / Accepted: 2 May 2002 / Published online: 6 November 2002 Correspondence to: M. A. Collins e-mail: collins@rsc.anu.edu.au Acknowledgements. The methods described in this overview are the result of collaborations with former members of my group, in particular with Josef Ischtwan, Meredith Jordon, Keiran Thompson and Ryan Bettens. I am also indebted for inspiration gained from many discussions with my colleagues Leo Radom and Donghui Zhang (National University of Singapore). This work has been supported by the Supercomputer Facility of the Australian National University and the Australian Partnership for Advanced Computing.