Direct experimental evaluation of charge scheme performance by a molecular charge-meter

The remarkable advances accomplished in the past two decades in theoretical and computational capabilities have made the in silico study of complex chemical systems feasible. However, this progress is in strong contrast to the lag in experimental capabilities relating to the measurement of fundamental chemical quantities within convoluted environments such as solvents or protein milieu. As a result, many works rely extensively on predictions provided by ab initio methodologies without having independent experimental support. Such a proliferation of theory and computational approaches without being substantiated by appropriate experimental data is undesirable. The feasibility of using nickel-bacteriochlorophyll as a molecular potentiometer was recently demonstrated for the systematic evaluation of fragmental charge density transfer for metal complexes in solution, thus providing an experimental assay with high accuracy and sensitivity (better than +/-0.005 e(-); Yerushalmi, R.; Baldridge, K. K.; Scherz, A. J. Am. Chem. Soc. 2003, 125, 12706-12707). Here the experimentally determined fragmental charge density transfer values measured by the molecular potentiometer for metal complexes in solvent are used to provide, for the first time, an independent and critical experimental evaluation of theoretical approaches commonly used in determining atomic charges and fragmental charge density transfer among interacting molecular systems. Importantly, these findings indicate that the natural population analysis (NPA) charge analysis is highly robust and well-suited for determining charge transfer processes involving donor-acceptor coordination interactions. The majority of computational charge schemes fail to provide an accurate chemical picture for the whole range of systems considered here. In cases where the role of electronic correlation varies significantly among chemically related structures, as with mono- and biligated complexes, the widely used electrostatic potential fit-based methods for evaluating atomic charges may prove to be problematic for predictive studies. In such cases, alternative methods that do not rely on the net dipole moment or other higher multipoles of the system for determining charges should be employed.     

PowerMV: a software environment for molecular viewing, descriptor generation, data analysis and hit evaluation

Ideally, a team of biologists, medicinal chemists and information specialists will evaluate the hits from high throughput screening. In practice, it often falls to nonmedicinal chemists to make the initial evaluation of HTS hits. Chemical genetics and high content screening both rely on screening in cells or animals where the biological target may not be known. There is a need to place active compounds into a context to suggest potential biological mechanisms. Our idea is to build an operating environment to help the biologist make the initial evaluation of HTS data. To this end the operating environment provides viewing of compound structure files, computation of basic biologically relevant chemical properties and searching against biologically annotated chemical structure databases. The benefit is to help the nonmedicinal chemist, biologist and statistician put compounds into a potentially informative biological context. Although there are several similar public and private programs used in the pharmaceutical industry to help evaluate hits, these programs are often built for computational chemists. Our program is designed for use by biologists and statisticians.     

Design and evaluation of a crystalline hybrid of molecular conductors and molecular rotors

Combining recent concepts from the fields of molecular conductivity and molecular machinery we set out to design a crystalline molecular conductor that also possesses a molecular rotor. We report on the structures, electronic and physical properties, and dynamics of two solids with a common 1,4-bis(carboxyethynyl)bicyclo[2.2.2]octane (BABCO) functional rotor. One, [nBu(4)N(+)](2)[BABCO][BABCO(-)](2), is a colorless insulator where the dicarboxylic acid cocrystallizes with two of its monoanionic conjugated bases. The other is self-assembled by electrocrystallization in the form of black, shiny needles, with highly conducting molecular slabs of (EDT-TTF-CONH(2))(2)(+) (EDT-TTF = ethylenedithiotetrathiafulvalene) and anionic [BABCO(-)] rotors. Using variable-temperature (5-300 K) proton spin-lattice relaxation, (1)H T(1)(-1), we were able to assign two types of Brownian rotators in [nBu(4)N(+)](2)[BABCO][BABCO(-)](2). We showed that neutral BABCO groups have a rotational frequency of 120 GHz at 300 K with a rotational barrier of 2.03 kcal mol(-1). Rotors on the BABCO(-) sites experience stochastic 32 GHz jumps at the same temperature over a rotational barrier of 2.72 kcal mol(-1). In contrast, the BABCO(-) rotors within the highly conducting crystals of (EDT-TTF-CONH(2))(2)(+)[BABCO(-)] are essentially "braked" at room temperature. Notably, these crystals possess a conductivity of 5 S cm(-1) at 1 bar, which increases rapidly with pressure up to 50 S cm(-1) at 11.5 kbar. Two regimes with different activation energies E(a) for the resistivity (180 K above 50 and 400 K below) are observed at ambient pressure; a metallic state is stabilized at ca. 8 kbar, and an insulating ground state remains below 50 K at all pressures. We discuss two likely channels by which the motion of the rotors might become slowed down in the highly conducting solid. One is defined as a low-velocity viscous regime inherent to a noncovalent, physical coupling induced by the cooperativity between five C(sp3)-H···O hydrogen bonds engaging any rotor and five BABCO units in its environment. The rotational barrier calculated with the effect of this set of hydrogen bonds amounts to 7.3 kcal mol(-1). Another is quantum dissipation, a phenomenon addressing the difference of dynamics of the rotors in the two solids with different electrical properties, by which the large number of degrees of freedom of the low dimensional electron gas may serve as a bath for the dissipation of the energy of the rotor motion, the two systems being coupled by the Coulomb interaction between the charges of the rotors (local moments and induced dipoles) and the charges of the carriers.     

An evaluation of the implementation of the Cramer classification scheme in the Toxtree software

Risk assessment for most human health effects is based on the threshold of a toxicological effect, usually derived from animal experiments. The Threshold of Toxicological Concern (TTC) is a concept that refers to the establishment of a level of exposure for all chemicals below which there would be no appreciable risk to human health. When carefully applied, the TTC concept can provide a means of waiving testing based on knowledge of exposure limits. Two main approaches exist; the first of these is a General Threshold of Toxicological Concern; the second approach is a TTC in relation to structural information and/or toxicological data of chemicals. The structural scheme most routinely used is that of Cramer and co-workers from 1978. Recently this scheme was encoded into a software program called Toxtree, specifically commissioned by the European Chemicals Bureau (ECB). Here we evaluate two published datasets using Toxtree to demonstrate its concordance and highlight potential software modifications. The results were promising with an overall good concordance between the reported classifications and those generated by Toxtree. Further evaluation of these results highlighted a number of inconsistencies which were examined in turn and rationalised as far as possible. Improvements for Toxtree were proposed where appropriate. Notable of these is a necessity to update the lists of common food components and normal body constituents as these accounted for the majority of false classifications observed. Overall Toxtree was found to be a useful tool in facilitating the systematic evaluation of compounds through the Cramer scheme.     

Theoretical studies on the adsorption from non-ideal binary liquid mixtures on heterogeneous surfaces involving difference in molecular sizes of components

An equation for the phenomenon of competetive adsorption from binary liquid mixtures onto solids has been derived using the kinetic approach. In this equation the difference of the molecular sizes, the non-ideality of both bulk surface phases, and the energetic heterogeneity of the solid surface have been taken into account.

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Theoretische Untersuchungen zur Adsorption aus nichtidealen binären Lösungsmittelgemischen an heterogene Oberflächen fester Körper unter Berücksichtigung der Unterschiede in den molekularen Größen der Komponenten

Zusammenfassung Auf Grund kinetischer Erwägungen wurde eine Gleichung, die die Konkurrenzadsorption aus binären Lösungsmittelgemischen an den Oberflächen fester Körper beschreibt, aufgestellt. In der Gleichung wurde der Größenunterschied der Teilchen, die Nichtidealität der Lösung in der Volumen- und Oberflächenphase, sowie die energetische Heterogenität der Oberfläche des festen Körpers berücksichtigt.

     

Photochemical transformation of a dithioacetal S-oxide into the corresponding aldehyde

Irradiation of an aldehyde dithioacetal S-oxide gives the corresponding aldehyde. The mechanism of this photochemical transformation is discussed and its application to organic synthesis is also described.     

Optimal descriptor as a translator of eclectic information into the prediction of thermal conductivity of micro-electro-mechanical systems

Micro-electro-mechanical systems (MEMS) are involved in various fields of nanotechnology. MEMS are characterized by complex and unclear molecular architecture. However, in most cases information about chemical composition and conditions of synthesis is available. One-variable models for thermal conductivity of MEMS are suggested. These models are based on the representation of MEMS by their chemical composition and technological attributes. We have examined three random splits of available data into the training set and validation set. The average statistical characteristics of these models are quite good. Development of suggested here models is carried out without information on molecular architecture of MEMS.     

Molybdenum-catalyzed transformation of molecular dinitrogen into silylamine: experimental and DFT study on the remarkable role of ferrocenyldiphosphine ligands

A molybdenum-dinitrogen complex bearing two ancillary ferrocenyldiphosphine ligands, trans-[Mo(N(2))(2)(depf)(2)] (depf = 1,1'-bis(diethylphosphino)ferrocene), catalyzes the conversion of molecular dinitrogen (N(2)) into silylamine (N(SiMe(3))(3)), which can be readily converted into NH(3) by acid treatment. The conversion has been achieved in the presence of Me(3)SiCl and Na at room temperature with a turnover number (TON) of 226 for the N(SiMe(3))(3) generation for 200 h. This TON is significantly improved relative to those ever reported by Hidai's group for mononuclear molybdenum complexes having monophosphine coligands [J. Am. Chem. Soc.1989, 111, 1939]. Density functional theory (DFT) calculations have been performed to figure out the mechanism of the catalytic N(2) conversion. On the basis of some pieces of experimental information, SiMe(3) radical is assumed to serve as an active species in the catalytic cycle. Calculated results also support that SiMe(3) radical is capable of working as an active species. The formation of five-coordinate intermediates, in which one of the N(2) ligands or one of the Mo-P bonds is dissociated, is essential in an early stage of the N(2) conversion. The SiMe(3) addition to a "hydrazido(2-)" intermediate having the NN(SiMe(3))(2) group will give a "hydrazido(1-)" intermediate having the (Me(3)Si)NN(SiMe(3))(2) group rather than a pair of a nitrido (≡N) intermediate and N(SiMe(3))(3). The N(SiMe(3))(3) generation would not occur at the Mo center but proceed after the (Me(3)Si)NN(SiMe(3))(2) group is released from the Mo center. The flexibility of the Mo-P bond between Mo and depf would play a vital role in the high catalysis of the Mo-Fe complex.     

Design,synthesis, biological evaluation and molecular dynamics of LAR inhibitors

In this study, firstly, the pharmacophore model was established based on LAR inhibitors. ZINC database and drug-like database were screened by Hypo-1-LAR model, and the embryonic compound ZINC71414996 was obtained. Based on this compound, we designed 9 compounds. Secondly, the synthetic route of the compound was determined by consulting Reaxys and Scifinder databases, and 9 compounds (1a-1i) were synthesized by nucleophilic substitution, Suzuki reaction and so on. Meanwhile, their structures were confirmed by ¹H NMR and ¹³C NMR. Thirdly, the Enzymatic assays was carried out, the biological evaluation of compounds 1a-1i led to the identification of a novel PTP-LAR inhibitor 1c, which displayed an IC₅₀ value of 4.8 μM. At last, molecular dynamics simulation showed that compounds could interact strongly with the key amino acids LYS1350, LYS1352, ARG1354, TYR1355, LYS1433, ASP1435, TRP1488, ASP1490, VAL1493, SER1523, ARG1528, ARG1561, GLN1570, LYS1681, thereby inhibiting the protein activity. This study constructed the pharmacophore model of LAR protein, designed small-molecule inhibitors, conducted compound synthesis and enzyme activity screening, so as to provide a basis for searching for drug-capable lead compounds.