Electronic and vibrational contributions to first hyperpolarizability of donor-acceptor-substituted azobenzene

In this study we report on the electronic and vibrational (hyper)polarizabilities of donor–acceptorsubstituted azobenzene. It is observed that both electronic and vibrational contributions to the electric dipole first hyperpolarizability of investigated photoactive molecule substantially depend on the conformation. The contributions to the nuclear relaxation first hyperpolarizability are found to be quite important in the case of two considered isomers (cis and trans). Although the double-harmonic term is found to be the largest in terms of magnitude, it is shown that the total value of the nuclear relaxation contribution to vibrational first hyperpolarizability is a result of subtle interplay of higher-order contributions. As a part of the study, we also assess the performance of long-range-corrected density functional theory in determining vibrational contributions to electric dipole (hyper)polarizabilities. In most cases, the applied long-range-corrected exchange correlation potentials amend the drawbacks of their conventional counterparts

Mechanism of action of cyclic antimicrobial peptides

This PhD thesis is the result of the combination of experimental and computational techniques with the aim of understanding the mechanism of action of de novo cyclic decapeptides with high antimicrobial activity. By experimental techniques the influence of the replacement of the phenylalanine for tryptophan residue in their antimicrobial activity was tested and the stability in human serum was also analyzed, in order to evaluate their potential therapeutic application as antitumor agents. On the other hand, the interaction amongst the peptide BPC194 c(KKLKKFKKLQ), the best candidate from the whole library of cyclic peptides, and a model anionic membrane was simulated. The results showed a structure-function relationship derived from the stable conformation of the peptides involved in the membrane permeabilization. As a result, a rational design was performed being BPC490 the peptide with best antimicrobial activity compared with the best active peptide from the original library.

Developments in near infrared spectroscopy

Vibrational spectroscopy at high excitation is an important research frontier for two reasons. Firstly, the near infrared is proving to be an important area for the analytical applications of spectroscopy, and we would therefore like to understand how the spectra we observe relate to the molecular structure of the absorbing species. Secondly, there is a fundamental interest in understanding molecular dynamics and energy flow within a polyatomic molecule at high excitation, because this is the boundary between spectroscopy and chemistry through which we try to understand the details of a chemical reaction. In this presentation I shall survey recent progress in this field.

Dinuclear copper and zinc complexes of a hexaazamacrocycle containing p-xylyl spacers and bridging anions: theoretical and spectroscopic studies

The hexaazamacrocycle 7,22-dimethyl-3,7,11,18,22,26-hexaazatricyclo[26.2.2.2(13,16)] tetratriaconta-1(30), 13,15,28,31,33- hexaene (Me-2[30] pbz(2)N(6)) was synthesized and characterised by single crystal X-ray diffraction. The macrocycle adopts a conformation with the two aromatic rings almost parallel at a distance of ca. 4.24 Angstrom, but displaced relative to each other by ca. 1.51 Angstrom. The protonation constants of this compound and the stability constants of its complexes with Cu2+ and Zn2+, were determined in water - methanol (9 : 1 v/v) at 25 degreesC with ionic strength 0.10 mol dm(-3) in KCl. The potentiometric and spectroscopic studies (NMR of zinc, cadmium and lead complexes, and EPR of the copper complexes) indicate the formation of only dinuclear complexes. The association constants of the dinuclear copper complex with anions ( thiocyanate, terephthalate and glyphosate) and neutral molecules (1,4-benzenedimethanol, p-xylylenediamine and terephthalic acid) were determined at 20 degreesC in methanol. The structural preferences of this ligand and of its dinuclear copper(II) complex with a variety of bridging ligands were evaluated theoretically by molecular mechanics calculations (MM) and molecular dynamics (MD) using quenching techniques.

Metal complexes of a dipyridine octaazamacrocycle: stability constants, structural and modelling studies

Two 28-membered octaazamacrocycles, [28]py(2)N(6) and Me-2[28]py(2)N(6), have been synthesized. The protonation constants of the N-methyl. derivative and the stability constants of its complexes with Ni2+, Cu2+, Zn2+, Cd2+, and Pb2+ were determined at 25degreesC in 0.10 mol dm(-3) KNO3. The high overall basicity of Me-2[28]py(2)N(6) is ascribed to the weaker repulsion between protonated contiguous charged ammonium sites separated by propyl chains. These studies together with NMR, UV-vis and EPR spectroscopies indicated the presence of mono- and di-nuclear species, The single crystal structure of the complex [Ni-2([28]py(2)N(6))(H2O)(4)]Cl-4.3H(2)O was determined, and showed each nickel centre in a distorted octahedral co-ordination environment. The nickel centres are held within the macrocycle at a large distance of 6.991(g) Angstrom from each other. The formation of mononuclear complexes was evaluated theoretically via molecular mechanics (MM) and molecular dynamics (MD) calculations and showed that these large macrocycles have sufficient flexibility to encapsulate metal ions with different stereo-electronic sizes. Structures for small and large metal ions are proposed.

Synthesis and properties of polyaromatic dendrimers possessing a repetitive amide-ester coupling sequence

A series of novel polyaromatic dendrimers that feature tris-(2-ethylamino)amine as the central core unit has been synthesized up to the third generation by employing a convergent growth strategy. The building blocks 1,3-diamino-2-hydroxypropane and 4-carboxybenzaldehyde were used for dendron construction, a process that involved the cyclic repetition of esterification, oxidation and selective amidation steps. Molecular modelling of this class of dendrimers has been used to predict potential solution state conformations employing molecular mechanics and molecular dynamic simulations. In addition, the results of preliminary metal binding studies using the first generation dendritic system are also outlined. (C) 2003 Elsevier Science Ltd. All rights reserved.

Kinetic multi-layer model of gas-particle interactions in aerosols and clouds (KM-GAP): linking condensation, evaporation and chemical reactions of organics, oxidants and water

We present a novel kinetic multi-layer model for gas-particle interactions in aerosols and clouds (KM-GAP) that treats explicitly all steps of mass transport and chemical reaction of semi-volatile species partitioning between gas phase, particle surface and particle bulk. KM-GAP is based on the PRA model framework (Pöschl-Rudich-Ammann, 2007), and it includes gas phase diffusion, reversible adsorption, surface reactions, bulk diffusion and reaction, as well as condensation, evaporation and heat transfer. The size change of atmospheric particles and the temporal evolution and spatial profile of the concentration of individual chemical species can be modelled along with gas uptake and accommodation coefficients. Depending on the complexity of the investigated system, unlimited numbers of semi-volatile species, chemical reactions, and physical processes can be treated, and the model shall help to bridge gaps in the understanding and quantification of multiphase chemistry and microphysics in atmo- spheric aerosols and clouds. In this study we demonstrate how KM-GAP can be used to analyze, interpret and design experimental investigations of changes in particle size and chemical composition in response to condensation, evaporation, and chemical reaction. For the condensational growth of water droplets, our kinetic model results provide a direct link between laboratory observations and molecular dynamic simulations, confirming that the accommodation coefficient of water at 270 K is close to unity. Literature data on the evaporation of dioctyl phthalate as a function of particle size and time can be reproduced, and the model results suggest that changes in the experimental conditions like aerosol particle concentration and chamber geometry may influence the evaporation kinetics and can be optimized for eðcient probing of specific physical effects and parameters. With regard to oxidative aging of organic aerosol particles, we illustrate how the formation and evaporation of volatile reaction products like nonanal can cause a decrease in the size of oleic acid particles exposed to ozone.

Kinetic multi-layer model of gas-particle interactions in aerosols and clouds (KM-GAP): linking condensation, evaporation and chemical reactions of organics, oxidants and water

We present a novel kinetic multi-layer model for gas-particle interactions in aerosols and clouds (KMGAP) that treats explicitly all steps of mass transport and chemical reaction of semi-volatile species partitioning between gas phase, particle surface and particle bulk. KMGAP is based on the PRA model framework (P¨oschl-Rudich- Ammann, 2007), and it includes gas phase diffusion, reversible adsorption, surface reactions, bulk diffusion and reaction, as well as condensation, evaporation and heat transfer. The size change of atmospheric particles and the temporal evolution and spatial profile of the concentration of individual chemical species can be modeled along with gas uptake and accommodation coefficients. Depending on the complexity of the investigated system and the computational constraints, unlimited numbers of semi-volatile species, chemical reactions, and physical processes can be treated, and the model shall help to bridge gaps in the understanding and quantification of multiphase chemistry and microphysics in atmospheric aerosols and clouds. In this study we demonstrate how KM-GAP can be used to analyze, interpret and design experimental investigations of changes in particle size and chemical composition in response to condensation, evaporation, and chemical reaction. For the condensational growth of water droplets, our kinetic model results provide a direct link between laboratory observations and molecular dynamic simulations, confirming that the accommodation coefficient of water at 270K is close to unity (Winkler et al., 2006). Literature data on the evaporation of dioctyl phthalate as a function of particle size and time can be reproduced, and the model results suggest that changes in the experimental conditions like aerosol particle concentration and chamber geometry may influence the evaporation kinetics and can be optimized for efficient probing of specific physical effects and parameters. With regard to oxidative aging of organic aerosol particles, we illustrate how the formation and evaporation of volatile reaction products like nonanal can cause a decrease in the size of oleic acid particles exposed to ozone.

Relaxation of surface tension in the free-surface boundary layers of simple Lennard-Jones liquids

In this paper we use molecular dynamics to answer a classical question: how does the surface tension on a liquid/gas interface appear? After defining surface tension from the first principles and performing several consistency checks, we perform a dynamic experiment with a single simple liquid nanodroplet. At time zero, we remove all molecules of the interfacial layer of molecules, creating a fresh bare interface with the bulk arrangement of molecules. After that the system evolves towards equilibrium, and the expected surface tension is re-established. We found that the system relaxation consists of three distinct stages. First, the mechanical balance is quickly re-established. During this process the notion of surface tension is meaningless. In the second stage, the surface tension equilibrates, and the density profile broadens to a value which we call “intrinsic” interfacial width. During the third stage, the density profile continues to broaden due to capillary wave excitations, which does not however affect the surface tension.We have observed this scenario for monatomic Lennard-Jones (LJ) liquid as well as for binary LJ mixtures at different temperatures, monitoring a wide range of physical observables.

Temperature-dependent orientational ordering on a spherical surface modeled with a lattice spin model

We study the orientational ordering on the surface of a sphere using Monte Carlo and Brownian dynamics simulations of rods interacting with an anisotropic potential. We restrict the orientations to the local tangent plane of the spherical surface and fix the position of each rod to be at a discrete point on the spherical surface. On the surface of a sphere, orientational ordering cannot be perfectly nematic due to the inevitable presence of defects. We find that the ground state of four +1/2 point defects is stable across a broad range of temperatures. We investigate the transition from disordered to ordered phase by decreasing the temperature and find a very smooth transition. We use fluctuations of the local directors to estimate the Frank elastic constant on the surface of a sphere and compare it to the planar case. We observe subdiffusive behavior in the mean square displacement of the defect cores and estimate their diffusion constants.

Structure and viscoelasticity of an electrorheological fluid in oscillatory shear: computer simulation investigation

The three-dimensional molecular dynamics simulation method has been used to study the dynamic responses of an electrorheological (ER) fluid in oscillatory shear. The structure and related viscoelastic behaviour of the fluid are found to be sensitive to the amplitude of the strain. With the increase of the strain amplitude, the structure formed by the particles changes from isolated columns to sheet-like structures which may be perpendicular or parallel to the oscillating direction. Along with the structure evolution, the field-induced moduli decrease significantly with an increase in strain amplitude. The viscoelastic behaviour of the structures obtained in the cases of different strain amplitudes was examined in the linear response regime and an evident structure dependence of the moduli was found. The reason for this lies in the anisotropy of the arrangement of the particles in these structures. Short-range interactions between the particles cannot be neglected in determining the viscoelastic behaviour of ER fluids at small strain amplitude, especially for parallel sheets. The simulation results were compared with available experimental data and good agreement was reached for most of them.

Computer simulation study of equilibrium properties of magnetic dipolar fluids

Langevin dynamics simulations are used to investigate the equilibrium magnetization properties and structure of magnetic dipolar fluids. The influence of using different boundary conditions are systematically studied. Simulation results on the initial susceptibility and magnetization curves are compared with theoretical predictions. The effect of particle aggregation is discussed in detail by performing a cluster analysis of the microstructure.

The effect of electric field direction on the-shear stress of ER fluids

The effect of the direction of external electric field on the shear stress of an ER fluid has been studied by molecular-dynamics simulation. Due to the formation of inclined chains, the shear stress strongly depends on the direction of the field, and it may be very large under some special field direction. And theoretical model of ideal microstructure of ER fluids has proved this result. Thus the ER effect may be greatly enhanced just by choosing an optimum direction for the field without any additional requirement, suggesting a promising way to the practical application of ER fluids.

Structure-based energetics of protein interfaces guides foot-and-mouth disease virus vaccine design

Virus capsids are primed for disassembly, yet capsid integrity is key to generating a protective immune response. Foot-and-mouth disease virus (FMDV) capsids comprise identical pentameric protein subunits held together by tenuous noncovalent interactions and are often unstable. Chemically inactivated or recombinant empty capsids, which could form the basis of future vaccines, are even less stable than live virus. Here we devised a computational method to assess the relative stability of protein-protein interfaces and used it to design improved candidate vaccines for two poorly stable, but globally important, serotypes of FMDV: O and SAT2. We used a restrained molecular dynamics strategy to rank mutations predicted to strengthen the pentamer interfaces and applied the results to produce stabilized capsids. Structural analyses and stability assays confirmed the predictions, and vaccinated animals generated improved neutralizing-antibody responses to stabilized particles compared to parental viruses and wild-type capsids.

Repulsion-induced surface-migration, by ballistics and bounce

The motion of adsorbate molecules across surfaces is fundamental to self-assembly, material growth, and heterogeneous catalysis. Recent Scanning Tunneling Microscopy studies have demonstrated the electron-induced long-range surface-migration of ethylene, benzene, and related molecules, moving tens of Angstroms across Si(100). We present a model of the previously unexplained long-range recoil of chemisorbed ethylene across the surface of silicon. The molecular dynamics reveal two key elements for directed long-range migration: first ‘ballistic’ motion that causes the molecule to leave the ab initio slab of the surface traveling 3–8 Å above it out of range of its roughness, and thereafter skipping-stone ‘bounces’ that transport it further to the observed long distances. Using a previously tested Impulsive Two-State model, we predict comparable long-range recoil of atomic chlorine following electron-induced dissociation of chlorophenyl chemisorbed at Cu(110)