Co‐Conformational Distribution of Nanosized [2]Catenanes Determined by Pulse EPR Measurements

The co‐conformational ensembles of three differently sized [2]catenanes were studied by measuring pair correlation functions corresponding to the separation of nitroxide spin labels—one attached to each of the two macrocycles—with the double electron–electron resonance (DEER) experiment. A geometric model for the [2]catenanes was derived that approximates the macrocycles by circles and takes into account the topological constraint. Comparison of the experimental to the theoretically predicted pair correlation functions gives insight into the co‐conformational distribution and the size of the macrocycles. It was found that the macrocycles of the medium‐ and large‐sized catenanes in chloroform are close to fully expanded, while they are partially collapsed in glassy o‐terphenyl. For the small‐sized catenane, moderate interaction between the unsaturated sections of the macrocycles in chloroform is indicated by a slight overrepresentation of short label‐to‐label separations in the pair correlation function.     

Binding Ensembles of p53-MDM2 Peptide Inhibitors by Combining Bayesian Inference and Atomistic Simulations

Designing peptide inhibitors of the p53-MDM2 interaction against cancer is of wide interest. Computational modeling and virtual screening are a well established step in the rational design of small molecules. But they face challenges for binding flexible peptide molecules that fold upon binding. We look at the ability of five different peptides, three of which are intrinsically disordered, to bind to MDM2 with a new Bayesian inference approach (MELD × MD). The method is able to capture the folding upon binding mechanism and differentiate binding preferences between the five peptides. Processing the ensembles with statistical mechanics tools depicts the most likely bound conformations and hints at differences in the binding mechanism. Finally, the study shows the importance of capturing two driving forces to binding in this system: the ability of peptides to adopt bound conformations (ΔGconformation) and the interaction between interface residues (ΔGinteraction).     

Molecular caps for full quantum mechanical computation of peptide-water interaction energy

We present a systematic study of numerical accuracy of various forms of molecular caps that are employed in a recently developed molecular fractionation scheme for full quantum mechanical computation of protein-molecule interaction energy. A previously studied pentapeptide (Gly-Ser-Ala-Asp-Val) or P5 interacting with a water molecule is used as a benchmark system for numerical testing. One-dimensional potential energy curves are generated for a number of peptide-water interaction pathways. Our study shows that various forms of caps all give consistently accurate energies compared to the corresponding full system calculation with only small deviations. We also tested the accuracy of cutting peptide backbone at different positions and comparisons of results are presented.     

Electronically-coupled MM quadruply-bonded complexes of molybdenum and tungsten

The reaction of M2(O2CBu(t))4 (M = Mo, W) with a dicarboxylic acid in toluene yields compounds of general formula [M2]-O2C-X-CO2-[M2] ([M2] = M2(O2CBu(t))3; X = conjugated spacer). The M2 units are electronically coupled via interactions between the M2 delta and dicarboxylate pi* orbitals, and the magnitude of this coupling is revealed by electronic structure calculations and spectroscopic data. These compounds show intense metal to ligand charge transfer (MLCT) absorptions in the visible region of the electronic spectrum that are temperature and solvent dependent. Evidence of electronic coupling is seen in their cyclic voltammograms, which show two successive one-electron oxidations. The extent of electronic coupling in the mixed valence radical cations [M2]-O2C-X-CO2-[M2]+, generated by oxidation with one equivalent of AgPF6 or FeCp2PF6, is evaluated by EPR and UV-vis-NIR spectroscopic data, and delocalized behavior is observed in compounds with W2 units separated by up to 13.6 angstroms. The simplicity of the frontier M2 orbital interactions with the bridge pi orbitals provides a convenient system with which to study electron transfer in mixed valence systems, as compared to the extensively studied, but more complicated, dinuclear t(2g)6/t(2g)5 mixed valence compounds. Oligomeric and polymeric compounds incorporating M2 units have also been synthesized, having general formula [M2(O2CR)2(O2C-Thio-CO2)]n (Thio = n-hexyl substituted ter- and quinque-thiophenes). They can be deposited as thin films by spin coating, and show photoluminescence and electroluminescence. These metallo-polythiophenes show potential for application in electronic materials. (     

Own N-layered integrated molecular orbital and molecular mechanics study of the reaction of OH<Superscript>−</Superscript> with polychlorinated hydrocarbons CH<Subscript>(4−n)</Subscript>Cl<Subscript>n</Subscript> (n=2–4)

The reliability of the two-layer own N-layered integrated molecular orbital and molecular mechanics (ONIOM) method was examined for the S_N2 reaction CH_(4–n)Cl_n+OH^–. In the ONIOM calculation, only the methyl chloride and OH^–were treated at a high level and the effect of polychlorination was taken into account only at a low level. The ONIOM results were compared with the target CCSD(T)/aug-cc-pVDZ//MP2/aug-cc-pVDZ results obtained by Borisov etal. [(2001) J. Phys. Chem. A 105:7724]. The ONIOM[MP2/aug-cc-pVDZ:B3LYP/6-31+G(d)] was found to reproduce well the target geometry and energy at the MP2/aug-cc-pVDZ level. The single-point improved energetics at the ONIOM[CCSD(T)/aug-cc-pVDZ:MP2/6-31+G(d)] is found to give results nearly as accurate as the target CCSD(T)/aug-cc-pVDZ//MP2/aug-cc-pVDZ results. The substantially reduced cost, 20% for optimization and 5% for single-point improved energy of the target cost for n=4, as well as small errors suggest that ONIOM is a powerful tool for accurate potential-energy surfaces of the reaction of large polyhalohydrocarbons.     

A computational model of the nicotinic acetylcholine binding site

We have derived a model of the nicotinic acetylcholine binding site. This was accomplished by using three known agonists (acetylcholine, nicotine and epibatidine) as templates around which polypeptide side chains, found to be part of the receptor cavity from published molecular biology studies, are allowed to flow freely in molecular dynamics simulations and mold themselves around these templates. The resulting supramolecular complex should thus be a complement, both in terms of steric effects as well as electronic effects, to the agonists and it should be a good estimation of the true receptor cavity structure. The shapes of those minireceptor cavities equilibrated rapidly on the simulation time scale and their structural congruence is very high, implying that a satisfactory model of the nicotinic acetylcholine binding site has been achieved. The computational methodology was internally tested against two rigid and specific antagonists (dihydro--erytroidine and erysoidine), that are expected to give rise to a somewhat differently shaped binding site compared to that derived from the agonists. Using these antagonists as templates there were structural reorganizations of the initial receptor cavities leading to distinctly different cavities compared to agonists. This indicates that adequate times and temperatures were used in our computational protocols to achieve equilibrium structures for the agonists. Overall, both minireceptor geometries for agonists and antagonists are similar with the exception of one amino acid (ARG209).     

受限于纳米碳管中的乙醇分子的结构和扩散的分子模拟研究

利用分子模拟研究了常温常压下受限于(8,8) (管径1.081 nm)和(15,15) (管径 2.035 nm)单壁纳米碳管中的乙醇分子. 对受限分子的径向密度分布和氢键等静态性质以及扩散性质进行了分析. 结果显示在管内乙醇分子的平均氢键数目和主体相一致. 乙醇分子在(8,8)碳管内具有高度有序的结构, 而在(15,15)碳管内由于空间的增大导致结构有序度的降低, 其中分子取向已呈随机分布. 进一步对扩散系数的分析发现, 在管内乙醇分子的轴向扩散系数低于主体相, 特别在(8,8)碳管内乙醇分子几乎丧失了轴向扩散能力.     

Principal component analysis of the effects of wavefunction modification on the electrostatic potential of indole

The molecular electrostatic potential (MEP) of the indole molecule was calculated in a three‐dimensional grid in which the molecule was centered at the origin. To evaluate the dependence of MEP on the type of calculation, semiempirical, ab initio, and density functional theory methods with different basis sets were employed. The data matrix generated by these calculations was analyzed by principal component analysis (PCA). The appearance of outliers and the effect of wavefunction modifications such as the introduction of electron correlations and diffuse functions were highlighted by the use of PCA. The spatial localization of such effects around the molecule was possible from the loadings values associated with the graphical analysis of the grid points. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Solvation of uranyl(II), europium(III) and europium(II) cations in "basic" room-temperature ionic liquids: a theoretical study

We report a molecular dynamics study of the solvation of UO2(2+), Eu3+ and Eu2+ ions in two "basic" (Lewis acidity) room-temperature ionic liquids (IL) composed of the 1-ethyl-3-methylimidazolium cation (EMI+) and a mixture of AlCl4- and Cl- anions, in which the Cl-/AlCl4- ratio is about 1 and 3, respectively. The study reveals the importance of the [UO2Cl4]2- species, which spontaneously form during most simulations, and that the first solvation shell of europium is filled with Cl- and AlCl4- ions embedded in a cationic EMI+ shell. The stability of the [UO2Cl4]2- and [Eu(III)Cl6]3- complexes is supported by quantum mechanical calculations, according to which the uranyl and europium cations intrinsically prefer Cl- to the AlCl4- ion. In the gas phase, however, [Eu(III)Cl6]3- and [Eu(II)Cl6]4- complexes are predicted to be metastable and to lose two to three Cl- ions. This contrasts with the results of simulations of complexes in ILs, in which the "solvation" of the europium complexes increases with the number of coordinated chlorides, leading to an equilibrium between different chloro species. The behavior of the hydrated [Eu(OH2)8]3+ complex is considered in the basic liquids; the complex exchanges H2O molecules with Cl- ions to form mixed [EuCl3(OH2)4] and [EuCl4(OH2)3]- complexes. The results of the simulations allow us to better understand the microscopic nature and solvation of lanthanide and actinide complexes in "basic" ionic liquids.     

Shape-persistent cyclyne-type azamacrocycles: synthesis, unusual light-emitting characteristics, and specific recognition of the Sb(V) ion

Simple members of arene-azaarenecyclynes as a novel family of geometrically-controlled and shape-persistent azamacrocycles have been synthesized. Noteworthy is the specific recognition function for Sb(V). The synthesized azamacrocycles, in particular the Sb(V) complex, have unusually strong light-emitting property.