Supramolecular recognition: association of palladium molecular clefts with planar platinum complexes

The crystal structures of two new molecular recognition adducts formed between a dicationic, di-terpyridyl-Pd-Cl molecular cleft and two square planar platinum complexes are reported. In both structures, the planar platinum-containing guests are located within the molecular cleft formed by the two parallel disposed terpyridyl-Pd-Cl⁺ units of the receptor. The crystal structure of the adduct formed between the molecular cleft and a neutral platinum complex has interplanar distances between the host and guest of 3.24 Å, a distance shorter than that usually ascribed to π-stacking interaction (∼3.45 Å). The short distance is likely the result of metal-metal interaction between the host and guest. The second adduct, that between the dicationic molecular receptor and an anionic platinum complex, also bears the guest within the molecular cleft. The interplanar distances between the cationic terpyridyl-Pd-Cl units of the host and the anionic guest (3.21 and 3.29 Å) are also shorter than typical π-stacking distances but no metal-metal interaction is present. Coulombic attraction between the host and guest is believed to be responsible for the short interplanar separation. These data are discussed in relation to analogous systems that associate through π-π and metal-metal interaction.     

Computer Simulation by Molecular Dynamics as a Tool for Modelling of Molecular Systems

Abstract

A survey is given of methods for simulation of molecular systems on a computer. The various assumptions, approximations and limitations are discussed and the possibility of making comparisons with experimental quantities is assessed. Finally, a number of practical applications of molecular dynamics simulation techniques in chemistry are reviewed.     

蓖麻毒素A链突变体(MRTA)的分子设计

利用同源模建的方法,借助分子力学优化,分子力学模拟退火设计构建了删除部分氨基酸序列的蓖麻毒素Ａ链突变体。采用泊松－玻尔兹曼方程对比分析了蓖麻毒素Ａ链与ＭＲＴＡ表现静电势分布,研究了ＲＴＡ与ＭＲＴＡ蛋白表面静电性质;     

蓖麻毒素A链突变体(MRTA)的分子设计

利用同源模建的方法,借助分子力学优化、分子动力学模拟退火设计构建了删除部分氨基酸序列的蓖麻毒素Ａ链突变体（ＭＲＴＡ）。采用泊松—玻尔兹曼方程对比分析了蓖麻毒素Ａ链（ＲＴＡ）与ＭＲＴＡ表观静电势分布,研究ＲＴＡ与ＭＲＴＡ蛋白表面静电性质;通过半经验量子化学ＡＭ１与分子力学结合方法探讨ＲＴＡ与ＭＲＴＡ功能域氨基酸前线分子轨道性质、能级分布,从理论上预测ＭＲＴＡ功能活性     

Spatial Separation of Molecular Conformers and Clusters

Gas-phase molecular physics and physical chemistry experiments commonly use supersonic expansions through pulsed valves for the production of cold molecular beams. However, these beams often contain multiple conformers and clusters, even at low rotational temperatures. We present an experimental methodology that allows the spatial separation of these constituent parts of a molecular beam expansion. Using an electric deflector the beam is separated by its mass-to-dipole moment ratio, analogous to a bender or an electric sector mass spectrometer spatially dispersing charged molecules on the basis of their mass-to-charge ratio. This deflector exploits the Stark effect in an inhomogeneous electric field and allows the separation of individual species of polar neutral molecules and clusters. It furthermore allows the selection of the coldest part of a molecular beam, as low-energy rotational quantum states generally experience the largest deflection. Different structural isomers (conformers) of a species can be separated due to the different arrangement of functional groups, which leads to distinct dipole moments. These are exploited by the electrostatic deflector for the production of a conformationally pure sample from a molecular beam. Similarly, specific cluster stoichiometries can be selected, as the mass and dipole moment of a given cluster depends on the degree of solvation around the parent molecule. This allows experiments on specific cluster sizes and structures, enabling the systematic study of solvation of neutral molecules.     

An approach to peptide-based ATP receptors by a combination of random selection, rational design, and molecular imprinting

Random selection, rational design and molecular imprinting were cooperatively utilized to develop peptide-based ATP synthetic receptors. In this fusion strategy, combinatorial chemistry was utilized for screening a precursor peptide useful for construction of ATP receptors, and rational design was employed in modification of the selected precursor peptide for higher affinity and selectivity. Finally, molecular imprinting was used for pre-organizing the conformation of the precursor peptide as complementary to a target molecule ATP. The fusion strategy appeared to have advantage to sole use of the individual strategy: (1) a low hit-rate of combinatorial chemistry will be improved by customizing a higher order structure of a selected peptide by molecular imprinting, (2) combinatorial chemistry allows us to semi-automatically select components of water-compatible synthetic receptors, (3) rational design improves the selected peptide sequence for better molecularly imprinted receptors.A peptide consisting of a randomly selected sequence and a rationally designed sequence (Resin-Lys-Gly-Arg-Gly-Lys-Gly-Gly-Gly-Glu-Lys-Tyr-Leu-Lys-NHAc) was designed and synthesized as a precursor peptide. The rational design was made according to the sequence of the adenine binding site of biotin carboxylase. The on-beads peptide was cross-linked with dimethyl adipimidate in the presence of ATP. In the saturation binding tests, the cross-linked on-beads peptide showed 5.3 times higher affinity compared to the non-cross-linked peptide with the same sequence. Furthermore, the cross-linked peptide showed improved selectivity; the ratios of binding constants, K_(ATP)/K_(ADP) and K_(ATP)/K_(GTP), were increased from 2.4 to 19, and from 0.8 to 10, respectively. It would be notable that the peptide without the rationally designed sequence showed no discrimination between ATP and GTP (K_(ATP)/K_(GTP) as 0.9), suggesting that the rationally designed site was successfully engaged for recognition of the adenine base.     

鳞翅目昆虫病原微孢子虫研究进展

微孢子虫广泛存在于鳞翅目昆虫中,是一类重要的病原微生物。微孢子虫病一方面影响野外昆虫种群的自然平衡,另一方面对家蚕、柞蚕等经济和资源昆虫造成了严重的危害。微孢子虫分子生物学研究基础相对薄弱,再加上微孢子虫表面坚厚的孢壁,无疑增加了研究难度。随着核酸、蛋白质等生物大分子分离制备方法和高通量测序技术的不断更新发展,基于各种组学(Omics)研究微孢子虫的工作方兴未艾,并且有了一些重要的发现。本文综述了微孢子虫与鳞翅目昆虫寄主的相互作用及寄生于鳞翅目昆虫的病原微孢子虫基因组、转录组和蛋白质组进展情况,以期为微孢子虫的深入研究提供参考。这些昆虫微生物研究将为鳞翅目害虫生物防治提供新的思路,并对家蚕等经济昆虫微粒子病的诊断、防控及治疗产生积极影响。     

Synthesis,antibacterial studies,and molecular modeling studies of 3,4-dihydropyrimidinone compounds

The syntheses of dihydropyrimidinones (DHPMs) using solvent-free grindstone chemistry method. All the synthesized compounds exhibited significant activity against pathogenic bacteria. The current effort has been developed to obtain new DHPM derivatives that focus on the bacterial ribosomal A site RNA as a drug target. Molecular docking simulation analysis was applied to confirm the target specificity of DHPMs. The crystal structure of bacterial 16S rRNA and human 40S rRNA was taken as receptors for docking. Finally, the docking score, binding site interaction analysis revealed that DHPMs exhibit more specificity towards 16S rRNA than known antibiotic amikacin. Accordingly, targeting the bacterial ribosomal A site RNA with potential drug leads promises to overcome the bacterial drug resistance. Even though, anti-neoplastic activities of DHPMs were also predicted through prediction of activity spectra for substances (PASS) tool. Further, the results establish that the DHPMs can serve as perfect leads against bacterial drug resistance.     

Electronic structure and surface properties of the mixed-valence doughnut shaped polyoxomolybdate nanocapsule Mo57V6

We report a detailed analysis of the electronic structure and results of molecular dynamics simulations for the large polyoxomolybdate [H₃Mo₅₇V₆(NO)₆O₁₈₃(H₂O)₁₈]²¹⁻ (Mo₅₇V₆) which is a highly symmetric anion with a complex electronic structure and exhibiting a unique variety of multifunctionality. The six vanadium centres are reduced with one electron each, the six Mo centres are bonded to non-innocent NO ligands and the additional six 4d electrons are mostly delocalised over the rest of molybdenum atoms. DFT calculations carried out with the solvent - modelled by a continuum approach - suggest that despite the large charge of the anion, the Mo₅₇V₆ framework can be easily reduced in polar solvents. Furthermore, the Mo₅₇V₆ cluster has 18 water molecules trapped in its internal cavity. Molecular dynamics simulations carried out with different solvent conditions suggest that the water molecules inside the cavity have a high ordered structure over a wide range of temperatures and give important information about the cluster anion interactions with the cations present in solution. The obtained results allow a better understanding of related properties of the giant ball-shaped polyoxometalates/Keplerates as the present cluster contains similar building blocks - like the (metal)₆O₆ type pores with crown ether-like structure.     

Computational study on the difference between the Co–C bond dissociation energy in methylcobalamin and adenosylcobalamin

The bond dissociation energies of the Co–C bonds in the cobalamin cofactors methylcobalamin and adenosylcobalamin were calculated using the hybrid quantum mechanics/molecular mechanics method IMOMM (integrated molecular orbital and molecular mechanics). Calculations were performed on models of differing complexities as well as on the full systems. We investigated the origin of the different experimental values for the Co–C bond dissociation energies in methylcobalamin and adenosylcobalamin, and have provided an explanation for the difficulties encountered when we attempt to reproduce this difference in quantum chemistry. Additional calculations have been performed using the Miertus–Scrocco–Tomasi method in order to estimate the influence of solvent effects on the homolytic Co–C bond cleavage. Introduction of these solvation effects is shown to be necessary for the correct reproduction of experimental trends in bond dissociation energies in solution, which consequently have no direct correlation with dissociation processes in the enzyme.     

Recent developments of the quantum chemical cluster approach for modeling enzyme reactions

The quantum chemical cluster approach for modeling enzyme reactions is reviewed. Recent applications have used cluster models much larger than before which have given new modeling insights. One important and rather surprising feature is the fast convergence with cluster size of the energetics of the reactions. Even for reactions with significant charge separation it has in some cases been possible to obtain full convergence in the sense that dielectric cavity effects from outside the cluster do not contribute to any significant extent. Direct comparisons between quantum mechanics (QM)-only and QM/molecular mechanics (MM) calculations for quite large clusters in a case where the results differ significantly have shown that care has to be taken when using the QM/MM approach where there is strong charge polarization. Insights from the methods used, generally hybrid density functional methods, have also led to possibilities to give reasonable error limits for the results. Examples are finally given from the most extensive study using the cluster model, the one of oxygen formation at the oxygen-evolving complex in photosystem II.

The BRAIN Initiative: developing technology to catalyse neuroscience discovery

The evolution of the field of neuroscience has been propelled by the advent of novel technological capabilities, and the pace at which these capabilities are being developed has accelerated dramatically in the past decade. Capitalizing on this momentum, the United States launched the Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative to develop and apply new tools and technologies for revolutionizing our understanding of the brain. In this article, we review the scientific vision for this initiative set forth by the National Institutes of Health and discuss its implications for the future of neuroscience research. Particular emphasis is given to its potential impact on the mapping and study of neural circuits, and how this knowledge will transform our understanding of the complexity of the human brain and its diverse array of behaviours, perceptions, thoughts and emotions.     

Preparation of Silica Nanoparticles Through Microwave-assisted Acid-catalysis

Microwave-assisted synthetic techniques were used to quickly and reproducibly produce silica nanoparticle sols using an acid catalyst with nanoparticle diameters ranging from 30-250 nm by varying the reaction conditions. Through the selection of a microwave compatible solvent, silicic acid precursor, catalyst, and microwave irradiation time, these microwave-assisted methods were capable of overcoming the previously reported shortcomings associated with synthesis of silica nanoparticles using microwave reactors. The siloxane precursor was hydrolyzed using the acid catalyst, HCl. Acetone, a low-tan δ solvent, mediates the condensation reactions and has minimal interaction with the electromagnetic field. Condensation reactions begin when the silicic acid precursor couples with the microwave radiation, leading to silica nanoparticle sol formation. The silica nanoparticles were characterized by dynamic light scattering data and scanning electron microscopy, which show the materials'' morphology and size to be dependent on the reaction conditions. Microwave-assisted reactions produce silica nanoparticles with roughened textured surfaces that are atypical for silica sols produced by Stöber''s methods, which have smooth surfaces.     

金纳米微粒辅助细胞激光热作用疗法研究

金纳米微粒对可见光的强吸收特性使得光能可以高效地转换为热能.由于金纳米微粒的尺度在几十纳米范围,并且很容易与其他生物体结合,因此可以在局部范围进行激光选择性加热,这非常适合作为分子或细胞的靶向.采用这种金纳米微粒辅助激光热作用方法,对牛肠碱性磷酸酯酶(alkaline phosphatase aP)的选择性破坏,细胞膜的通透性提高以及对细胞的选择性灭活进行了试验并得到了很好的结果.此外,还讨论了用这种方法进行基因转染以及选择性光热治疗一些疾病的可能性.