Ab initio study on the photoisomers of a nitro-substituted spiropyran

Structural and spectroscopic properties of the photoisomers of a nitro-substituted spiropyran have been investigated by performing ab initio molecular orbital (MO) calculations both in vacuo and in hexafluoro-2-propanol solution. Full geometry optimisation of the closed form and of the transoid conformations of the open form has been carried out. Dipole moments of both photoisomers have been determined, the ratio of which agrees with recent experimental results. Net atomic charges have also been determined according to three different approaches.

A Molecular Dynamics Study of the Structure of an Aqueous KC1 Solution

A molecular dynamics simulation of a 2.2 molal aqueous KCl solution has been performed using the ST2 water model. The simulation extended over 5ps at an average temperature of 288 K. The basic box has a side length of 18.74 A and contained 200 water molecules, 8 cations and 8 anions. The structure of the solution is discussed by radial distribution functions, the orientation of the water molecules, and their geometrical arrangement in the first hydration shells. The first shells of K+ and Cl- extend up to 3.52 and 3.84 A, respectively, with the corresponding hydration numbers 7.8 and 7.6. The results are compared with recent neutron and X-ray diffraction data and with findings of previous M…

Concurrent Molecular Dynamics Simulation of ST2 Water on a Transputer Array

Abstract A concurrent implementation of a Molecular Dynamics program for ST2 water molecules is presented, which exploits the great potentialities of the Transputer arrays for statistical mechanical calculations. High load-balance efficiency is obtained using a new task decomposition algorithm which evenly distributes particles and interaction calculations among the processors. This approach can also help to solve efficiently the more general problem of task distribution in parallel computing of symmetric pairwise system properties.

Demixing and polymerization in systems of anisotropic globular particles: A molecular dynamics simulation study

We report a first set of results of Molecular Dynamics simulations of phase separation in a two-dimensional system of identical particles bearing attachment sites at their surface. Morphology of regions of aggregation so obtained appear similar to images of biologically self-assembled structures. Also, they evidence the relevance of the region of thermodynamic instability and of the presence and range of interaction of specific attachment sites. Particles of our system are apt to represent indifferently, though grossly, globular proteins or rigid cells, bearing specific and fixed adhesion sites at their surface. Results illustrate some basic aspects of the origin of the morphology of extend…

Hydrophobic interactions and stacking forces: A convenient model system

Abstract We consider solvent–biomolecule interactions and the role of solvent structural and isotopic alterations on the thermodynamic stability of biomolecular structures. Approaches to this problem range from the study of biomolecular functional stability, to that of the stability of small structural entities suitable of being taken as model systems for (parts of) larger molecules. We shall focus on this latter case and shall consider the dimerization process of small planar molecules (Methylene Blue). These are a convenient model system for the study of interactions responsible e.g. for base stacking in DNA. As an additional advantage, they do not form hydrogen bonds. The experimental st…

Transputer-based parallel system for acquisition and on-line analysis of single-fiber electromyographic signals.

Abstract We describe a transputer-based system suitable for accurate measurements of single-fiber electromyographic jitter. It consists of a conventional electromyograph, a home-made interface and a commercially available transputer-based board installed within a PC/AT compatible. Taking advantage of the concurrent operation of two transputer modules, the system features simultaneous data acquisition and statistical signal processing: while data are acquired and analyzed, a real-time visualization of the signal latency and its variability is provided. In the present configuration, the system can acquire and analyze up to 40,000 consecutive action potentials, which can be grouped into up to …

A molecular dynamics study of large-scale reversible aggregation of anisotropic particles

We report findings of 1000 ps molecular dynamics simulations of a bidimensional system of 4050 Lennard–Jones particles with electric dipoles, undergoing spinodal separation. This simple system is used to model the reversible aggregation of building blocks bearing specific and fixed adhesion sites at their surface. Aggregation regions so obtained resemble images of self-assembled biological structures. Statistical analyses of these regions evidence the interplay of thermodynamic instability and of interaction range between the attachment sites. They also illustrate some basic aspects of the morphogenesis of extended biomolecular/cellular structures, self-organized from initially homogeneous …

On the systolic calculation of all-pairs interactions using transputer arrays

Solute-induced Water Structure: Computer Simulation on a Model System

Abstract Two series of Monte Carlo simulations have been carried out on a system consisting of 125 water molecules, one of which is kept fixed to simulate a water molecule whose mobility is restricted by a solute. The results are checked against similar simulations without restrictions, used as a control, and they show how the blocked molecule helps increase both the structural order and the connectivity of the hydrogen bond network. Cooperativity originating from proton polarizability of H-bonds and/or from many-body terms of interaction potentials cannot be involved since we use a rigid water model and ab initio pair potentials. The present findings are interpreted as indicative of a moti…

Ab initio calculations and vibrational spectroscopy on the phenylenediamine isomers

Molecular orbital calculations at HF and MP2 levels have been performed using the 6-3IG** basis set for full geometry optimization of the phenylenediamine isomers. Our results show that only a transoid conformer is found for o-phenylenediamine, whereas cis and trans conformers exist for m- and p-phenylenediamine. Vibrational normal modes have been also analyzed for the gas phase and in chloroform solution, and compared with experimental data we have obtained using FTIR spectroscopy. © 1998 Elsevier Science B.V.

Biomolecular-solvent stereodynamic coupling probed by deuteration.

Thermodynamic interpretation of experiments with isotopically perturbed solvent supports the view that solvent stereodynamics is directly relevant to thermodynamic stability of biomolecules. According with the current understanding of the structure of the aqueous solvent, in any stereodynamic configuration of the latter, connectivity pathways are identifiable for their topologic and order properties. Perturbing the solvent by isotopic substitution or, e.g., by addition of co-solvents, can therefore be viewed as reinforcing or otherwise perturbing these topologic structures. This microscopic model readily visualizes thermodynamic interpretation. In conclusion, the topologic stereodynamic str…

Ion transport through membranes: A computer experiment

Abstract Gramicidin-A is a linear pentadecapeptide antibiotic, which forms transmembrane channels; these have a number of interesting conductance characteristics [1, 2 and Refs. therein], as for example high specific ion fluxes (a single channel carries about 10 7 sodium ions/sec at 25 °C, 1 M NaCl and 100 mV transmembrane d.d.p.) have a remarkable ion selectivity among the monovalent cations. The permeability ratios with respect to sodium were found to be in following order H + (150) > NH 4 + (8.9) > Cs + (5.8) > Rb + (5.5) > K + (3.9) > Na + (1.0) > Li + (0.33). The channel is impermeable to anions and to divalent cations and it exhibits saturation and maxima in conductance as a function …