Octachloronaphthalene (OCN), a serious environmental pollutant, has been investigated by charge density analysis to unravel several unexplored factors responsible for steric overcrowding. The topological features of the enigmatic peri interactions contributing to steric overcrowding are qualified and quantified from experimental and theoretical charge-density studies. A new facet in the fundame...

Optimization algorithms are iterative procedures that evolve from guessed starting points (SP) to the desired global minimum. Their performance can be greatly improved [1], if a neural network (NN) is created to select suitable SP. Here, we have trained NN’s to select possible groundstate geometries for silicon clusters. A genetic algorithm uses these candidates as initial population and perfor...

We present a model to describe electrical transport in dense films of conjugated polymers. The essential physical features of the model are as follows: (i) thermal fluctuations in the molecular geometry of the polymer modify the energy levels of localized electronic states in the material, and (ii) the primary restoring force for these fluctuations is steric, which leads to spatial correlation ...

The advantages and disadvantages of the use of direct geometry spectrometers for molecular spectroscopy and catalysis studies are described. We show that both direct and indirect geometry INS spectrometers are important tools for the study of industrially relevant areas such as catalysis, proton conductors and gas separation. We propose a novel hybrid instrument, Cerberus, that would offer high...

Grover’s algorithm is a quantum algorithm for searching in unstructured databases. Due to the properties of quantum mechanics, it provides a quadratic speedup over its classical counterparts. We present a new application of the algorithm to the Molecular Distance Geometry Problem. This problem is related to the determination of the tridimensional structure of a molecule based on the knowledge o...

The existence of an embedding in R satisfying a set of exact distances can be verified by the Cayley-Menger conditions [2]. In the MDGP, a set of distances is embeddable if and only if all Cayley-Menger determinants of 3 and 4 points have the correct sign(corresponding to the triangular and tetrangular inequalities) and the ones of 5 and 6 points vanish. Another way to verify the embeddability ...

In this paper we consider global optimization algorithms based on multiple local searches for the Molecular Distance Geometry Problem (MDGP). Three distinct approaches (Multistart, Monotonic Bain Hopping, Population Basin Hopping) are presented and for each of them a computational analysis is performed. The results are also compared with those of two other approaches in the literature, the DGSO...

From ligand-receptor binding to DNA hybridization, molecular recognition plays a central role in biology. Over the past several decades, chemists have successfully reproduced the exquisite specificity of biomolecular interactions. However, engineering multiple specific interactions in synthetic systems remains difficult. DNA retains its position as the best medium with which to create orthogona...

We examine how the shape of cells and the geometry of experiment affect the reaction-diffusion kinetics at the binding between target and probe molecules on molecular biochips. In particular, we compare the binding kinetics for the probes immobilized on surface of the semispherical and flat circular cells, the limit of thin slab of analyte solution over probe cell as well as hemispherical gel p...