Theoretical study of geometrical and nonlinear optical properties of pyridinum N-phenolate betaine dyes

This paper presents an ab initio quantum chemical investigation of the geometrical structures and the non-linear optical properties (NLO) of three structural isomers of pyridinium N-phenolate betaine dye. The ground state geometrical parameters and the first-order hyperpolarizabilities were calculated using the Hartree-Fock (HF) as well as the second-order perturbation Møller-Pleset (MP2) method with the 6–31G, 6–31G(d), 6–31G(d,p), 6–31+G(d), 6–31++G(d,p), 6–311+G(d), aug-cc-PVDZ and the recently developed Z3PolX basis sets. Moreover, the first-order hyperpolarizability was calculated at the coupled cluster singles and doubles (CCSD/6–31+G(d)) level of theory. The analysis of the results of calculations for the investigated isomers indicates that there are important differences in their NLO activities. Additionally, it was shown that Z3PolX basis set works reasonable well for betaine dyes.

Linear and nonlinear optical responses in bacteriochlorophyll a

Nonlinear optical responses of bacteriochlorophyll a (BChl a) were investigated by means of the three-pulse four-wave mixing (FWM) technique under the resonant excitation into the Q _y band. The experimental results are explained by a theoretical model calculation including the Brownian oscillation mode of the solvent. We have determined the spectral density, which is the most important function with which to calculate optical signals. The linear absorption spectrum can be reproduced fairly well when the vibronic oscillation modes of the solvent together with those of BChl a are properly taken into consideration. The FWM signal was also calculated using the spectral density. It was found that a simple two-level model could not explain the experimental result. The effect of the higher-order interactions is discussed.     

The effects of geometrical parameters on synaptic transmission: a Monte Carlo simulation study

Monte Carlo simulations of transmitter diffusion and its interactions with postsynaptic receptors have been used to study properties of quantal responses at central synapses. Fast synaptic responses characteristic of those recorded at glycinergic junctions on the teleost Mauthner cell (time to peak approximately 0.3-0.4 ms and decay time constant approximately 3-6 ms) served as the initial reference, and smaller contacts with fewer postsynaptic receptors were also modeled. Consistent with experimental findings, diffusion, simulated using a random walk algorithm and assuming a diffusion coefficient of 0.5-1.0 x 10(-5) cm2 s(-1), was sufficiently fast to account for transmitter removal from the synaptic cleft. Transmitter-receptor interactions were modeled as a two-step binding process, with the double-bound state having opened and closed conformations. Addition of a third binding step only slightly decreased response amplitude but significantly slowed both its rising and decay phases. The model allowed us to assess the sources of response variability and the likelihood of postsynaptic saturation as functions of multiple kinetic and spatial parameters. The method of nonstationary fluctuation analysis, typically used to estimate the number of functional channels at a synapse and single channel current, proved unreliable, presumably because the receptors in the postsynaptic matrix are not uniformly exposed to the same profile of transmitter concentration. Thus, the time course of the probability of channel opening most likely varies among receptors. Finally, possible substrates for phenomena of synaptic plasticity, such as long-term potentiation, were explored, including the diameter of the contact zone, defined by the region of pre- and postsynaptic apposition, the number and distribution of the receptors, and the degree of vesicle filling. Surprisingly, response amplitude is quite sensitive to the size of the receptor-free annulus surrounding the receptor cluster, such that expansion of the contact zone could produce an appreciable increase in quantal size, normally attributed to either the presence of more receptors or the release of more transmitter molecules.     

Design and studies of novel polyoxysterol-based porphyrin conjugates

New types of steroid-porphyrin conjugates derived from 20-hydroxyecdysone (20E) and 24-epibrassinolide (EBl) were synthesized. An exceptional regioselectivity in the reaction of both steroids with porphyrin boronic acids was found to give side-chain-conjugated boronic esters as sole products. UV-Vis-, fluorescence and NMR spectroscopy yielded similar data for all the studied compounds confirming the solvent driven supramolecular assembly with formation of J-aggregates. CD measurements of water diluted solutions showed a clear difference between 20E and EBl conjugates. The latter showed a strong supramolecular chirality, whereas 20E J-aggregates did not.     

Theoretical studies on alpha-helix--DNA interactions

The interaction energies between (Ala)10 and alpha-helix fragment and different nucleotide sequences in right-handed B-form have been optimized using semi-empirical potential energy functions. The energies are calculated for two different orientations of the alpha-helix, viz., when the alpha-helix axis taken in the N----C direction is (i) parallel and (ii) antiparallel to the 5'-3' ascending strand of DNA, proximal to it. When both the DNA molecule as well as the alpha-helix are treated as rigid molecules it is found that a polyalanine alpha-helix has slightly more favourable contacts when it is in the proximity of a four nucleotide sequence of 5'-(N-A-T-N)-3' type, where N is either a purine or a pyrimidine. However, when the two interacting molecules are allowed to undergo local structural variations then the interaction energy appears to be independent of the base sequence confirming the non-specific nature of these interactions.     

Stress responses and specific metal exclusion on mine soils based on germination and growth studies by Australian golden wattle

We reported the Australian golden wattle as a copper stabilizer in abandoned copper mine soils earlier. Here we investigate to confirm this plant’s suitability to grow on metal contaminated mine soils based on stress indication. The seeds of Acacia pycnantha collected from mining area were germinated after heat and no heat treatment on two types of irrigation. The daily irrigated and heat treated seeds gave up to 85% germination on sandy soil. The A. pycnantha was grown under greenhouse condition in six different soils collected from abandoned copper mine at Kapunda in South Australia. Among the six soil samples, soil-1 with the highest copper concentration produced 2.05 mmol g⁻¹ tissue of proline. Proline expression was prominent in more saline soils (1, 5 and 6) having electrical conductivity (EC) 1184, 1364 and 1256 μS, respectively. Chlorophyll a, b and carotenoid levels in plants showed a gradually decreasing trend in all the soils as experiment progressed. The plants grown on soil sample-1, containing 4083 ± 103 mg kg⁻¹ of copper resulted in 18 ± 2 mg kg⁻¹ accumulation in its leaf. The calcium accumulation was significant up to 11648 ± 1209 mg kg⁻¹ in leaf. Although pore water samples showed higher Cu concentration in soils, an increased mobility of arsenic and lead was observed in all the soil samples. Our experiment points out the need for proper monitoring of revegetation processes to avoid revegetation and reclamation failure.     

Theoretical study of the geometrical and electronic structures and thermochemistry of spherophanes

A set of supramolecular cage-structures—spherophanes—was studied at the density functional B3LYP level. Full geometrical structure optimisations were made with 6–31G and 6–31G(d) basis sets followed by frequency calculations, and electronic energies were evaluated at B3LYP/6–31++G(d,p). Three different symmetries were considered: C1, Ci, and Oh. It was found that the bonds between the benzene rings are very long to allow π-electron delocalisation between them. These spherophanes show portal openings of 2.596 Å in Spher1, 4.000 Å in Meth2, 3.659 Å in Oxa3, and 4.412 Å in Thia4. From the point of view of potential host–guest interaction studies, it should also be noted that the atoms nearest to the centre of the cavities are carbons bonded to X groups. These supramolecules seem to exhibit relatively large gap HOMO?LUMO: 2.89 eV(Spher1), 5.26 eV(Meth2), 5.73 eV(Oxa3), and 4.82 eV(Thia4). The calculated ΔH°_f (298.15 K) values at B3LYP/6–31G(d) are (in kcal mol^?1) 750.98, 229.78, ?10.97, and 482.49 for Spher1, Meth2, Oxa3, and Thia4, respectively. Using homodesmotic reactions, relative to Spher1, the spherophanes Meth2, Oxa3, and Thia4 are less strained by ?399.13 kcal mol^?1, ?390.40 kcal mol^?1, and ?411.38 kcal mol^?1, respectively. Their infrared and ¹³C NMR calculated spectra are reported.     

Theoretical studies on farnesyltransferase: the distances paradox explained

In spite of the enormous interest that has been devoted to its study, the mechanism of the enzyme farnesyltransferase (FTase) remains the subject of several crucial doubts. In this article, we shed a new light in one of the most fundamental dilemmas that characterize the mechanism of this puzzling enzyme commonly referred to as the "distances paradox", which arises from the existence of a large 8-A distance between the two reactive atoms in the reaction catalyzed by this enzyme: a Zn-bound cysteine sulphur atom from a peptidic substrate and the farnesyldiphosphate (FPP) carbon 1. This distance must be overcome for the reaction to occur. In this study, the two possible alternatives were evaluated by combining molecular mechanics (AMBER) and quantum chemical calculations (B3LYP). Basically, our results have shown that an activation of the Zn-bound cysteine thiolate with subsequent displacement from the zinc coordination sphere towards the FPP carbon 1 is not a realistic hypothesis of overcoming the large distance reported in the crystallographic structures of the ternary complexes between the two reactive atoms, but that a rotation involving the FPP molecule can bring the two atoms closer with moderate energetic cost, coherent with previous experimental data. This conclusion opens the door to an understanding of the chemical step in the farnesylation reaction.     

Multiscale simulation studies of geometrical effects on solution transport through nanopores

Due to intrinsic properties, solid-state nanopores are widely used in nanopore technology. Different geometries (cylindrical (CY), hourglass (HG) and conical (CO)) of artificial nanopores have been fabricated and studied. Each was found to promote different transport abilities experimentally. To explore such pore effects, the combination of finite element (FE) and molecular dynamics (MD) simulations with applied electric filed (150 mV) were performed. The dimension of anion-selective protein pore was used as a nanopore template. Different pore geometries with a narrowest diameter ranging from 1.8 to 1.8 μm were studied here. Firstly, we found that the narrowest regions at a pore orifice in CO and constriction site in HG maximise water velocity and consequently control a water flow rate. Secondly, CY triggers the highest water flux, but low ion selectivity, whilst the funnel-like geometries (HG and CO) enhance the ion selectivity significantly. Both HG and CO show similar degrees of permeant flux and selectivity. The orifice and constriction site in CO and HG are the main player for selectivity and permeation control. Thirdly, the transport properties are tuneable by changing the flow direction in asymmetric CO pore. The tip-to-base flow in CO obviously promotes stronger anion selectivity than the base-to-tip one.     

Insight into the nature of the interactions of furan and thiophene with hydrogen halides and lithium halides: ab initio and QTAIM studies

The nature of the interactions of furan and thiophene with hydrogen halides and lithium halides has been investigated using ab initio calculations and QTAIM analysis. The concept of molecule formation density difference (MFDD) is introduced to study weak hydrogen bond (HB) and lithium bond (LB) interactions. The results have shown the molecular electrostatic potentials of furan and thiophene, as well as of the hydrogen halides and lithium halides, determine the geometries of the complexes. Both the studied HB and LB interactions can be classified as “closed-shell” weak interactions. The topological properties and energy properties at the bond critical points of HB and LB have been shown to be exponentially dependent on intermolecular distances d(H-bond) and d(Li-bond), which enables interpretation of the strength of the HB and LB interactions in terms of these ρ(r) properties. Electron transfer plays a more important role in the formation of HB than in that of LB, while electrostatic interaction in LB is more dominant than that in HB.     

Third-order nonlinear optical materials: practical issues and theoretical challenges

The renewed interest in all-optical switching has led to more detailed experimental investigations of nonlinear optical properties of materials within wide wavelength ranges. The objectives of these studies are discussed here in the context of the availability of suitable computational data that might be compared with the results of the experimental research. It is concluded that the currently available data are insufficient and should be augmented to provide better guidance for experimental work.     

Theoretical and simulation studies on voltage-gated sodium channels

Voltage-gated sodium (Na_v) channels are indispensable membrane elements for the generation and propagation of electric signals in excitable cells. The successes in the crystallographic studies on prokaryotic Na_v channels in recent years greatly promote the mechanistic investigation of these proteins and their eukaryotic counterparts. In this paper, we mainly review the progress in computational studies, especially the simulation studies, on these proteins in the past years.     

捕食者-猎物关系的理论和应用研究

捕食者和猎物相互关系的研究,长期以来一直是动物生态学研究的中心课题之一。这种研究可区分为3种类型:第一是理论研究,即组建各种数学模型以便模拟捕食者和猎物间的相互关系;第二是实验种群研究,通常是在实验室内选用原生动物和节肢动物实验种群对捕食一猎物间的动态关系进行观察,并将观察结果与理论模型进行比较;第三是在田间对自然种群中的捕食者-猎物关系进行研究,并利用从理论研究和实验种群研究中所总结出来的各种基本原理对观察资料进行分析。在应用生态学领域中,常常靠引进新的更加有效的天敌来控制各种害虫。这些实际工作有些已获得成功,也有不少未取得预期效果,不管成功与否,它们都可被看作是对捕食者-猎物关系所进行的田间实验.     

Induction and memory of chirality in porphyrin hetero-aggregates: the role of the central metal ion

The anionic H2TPPS porphyrin and its copper derivative, CuTPPS, form in aqueous solution hetero-aggregates with the cationic H2T4 porphyrin and its copper derivative, CuT4. In the presence of poly-L-glutamate, at pH 4.0, a CD signal appears in the Soret region of the spectrum, indicating that the polypeptide has induced chirality into the structure of the aggregates. These species exhibit remarkable inertness due to the strength and number of the coulombic interactions between the anionic and the cationic porphyrins. This property allows them to preserve the chiral structure, even when the matrix changes or loses its chiral conformation, demonstrating that these aggregates are capable of memorizing the chiral information. The remarkable properties of the title systems may find various applications (chiral amplification, discrimination, and separation) that, on the other hand, require a more strict control of the aggregate dimension. Here, we show that the central copper of these macrocycles is crucial for determining the aggregate dimension.