Geometry optimization of molecular structures in solution by the polarizable continuum model

A new implementation of analytical gradients for the polarizable continuum model is presented, which allows Hartree-Fock and density functional calculations taking into account both electrostatic and nonelectrostatic contributions to energies and gradients for closed and open shell systems. Simplified procedures neglecting the derivatives of the cavity surface and/or using single spheres for XH_n groups have also been implemented and tested. The solvent-induced geometry relaxation has been studied for a number of representative systems in order to test the efficiency of the procedure and to investigate the role of different contributions. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 404–417, 1998     

Embeddings of Spherical Homogeneous Spaces

We review in these notes the theory of equivariant embeddings of spherical homogeneous spaces. Given a spherical homogeneous space G/H, the normal equivariant embeddings of G/H are classified by combinatorial objects called colored fans, which generalize the fans appearing in the classification of toric varieties and which encode several geometric properties of the corresponding variety.     

Mechanics of tubular helical assemblies: ensemble response to axial compression and extension

Acta Mechanica Sinica - Nature and technology often adopt structures that can be described as tubular helical assemblies. However, the role and mechanisms of these structures remain elusive. In...     

An improved iterative solution to solve the electrostatic problem in the polarizable continuum model

 We present a discrete iterative interpolation scheme (DIIS) to improve the convergence rate of electrostatic calculations in the polarizable continuum model (PCM) to describe solvent effects on molecular solutes. The electrostatic calculations may easily become the bottleneck of the calculation when the solute size is large. For large molecules iterative procedures turn out to be computationally more convenient than matrix inversion or closure methods. The DIIS scheme is compared here to another iterative procedure (DAMP) and to the biconjugate gradient (BCG) method. The comparisons show that DIIS leads to a sizeable saving of computational time for the C-PCM and IEF-PCM methods (average 40%) compared to DAMP, and more than 50% with respect to the BCG method. Received: 5 October 2000 / Accepted: 13 November 2000 / Published online: 19 January 2001     

Counterpoise corrections to the components of bimolecular energy interactions: An examination of three methods of decomposition

Counterpoise corrections for the basis set superposition error to the components of the bimolecular interaction energy are defined for three methods of decomposition. The results for the case of the NH₃ + BH₃ interaction are presented and discussed.     

Optical necklace states in Anderson localized 1D systems

We report on the observation of nonlocalized modes or necklace states of light waves in disordered systems in the Anderson localized regime. The samples consist of positional-disordered binary multilayer systems. Anderson localized modes manifest themselves as narrow high-transmission peaks in the transmission spectrum, whereas the average of the logarithm of the transmission coefficient decreases linearly with thickness. Optical necklace states are observed as modes with a characteristic multiresonance time response and relatively fast decay time.     

Covalent docking of selected boron-based serine beta-lactamase inhibitors

Journal of Computer-Aided Molecular Design - AmpC β-lactamase is a hydrolytic enzyme conferring resistance to β-lactam antibiotics in multiple Gram-negative bacteria. Therefore,...