Clustering files of chemical structures using the fuzzy k-means clustering method

This paper evaluates the use of the fuzzy k-means clustering method for the clustering of files of 2D chemical structures. Simulated property prediction experiments with the Starlist file of logP values demonstrate that use of the fuzzy k-means method can, in some cases, yield results that are superior to those obtained with the conventional k-means method and with Ward's clustering method. Clustering of several small sets of agrochemical compounds demonstrate the ability of the fuzzy k-means method to highlight multicluster membership and to identify outlier compounds, although the former can be difficult to interpret in some cases.     

Intramolekulare Cyclisierung von Aminofluorsilanen

Aminofluorosilanes react with lithiated amines undergoing LiF-elimination and substitution (1). The acyclic silicon-nitrogen-compound2 is isolated in the reaction with a difluorosilane after renewed lithiation.2 is cyclisated in the reaction with butyllithium by butane- and LiF-elimination (3). Aminofluorosilanes with bulky (4) or mesomeric stabilized (5) ligands form stable lithioaminofluorosilanes, which react with fluorosilanes giving substitution products (6, 7).6 and7 react with the lithium salt oftert-butylamin in a molar ratio of 12 to give8 and9 by intramolecular cyclisation.—The mass,¹H and¹⁹F nmr spectra of the compounds are reported.     

Kristallstruktur und Phasenumwandlung von Betain-Borat, (CH3)3NCH2COO·B(OH)3

Summary Betaine borate undergoes a phase transition of strongly second order at 142.5 K. Crystals below this temperature belong to the ferroelastic Aizu species mmmF2/m. The crystal structures of both phases have been determined. Paraelastic phase: Pmcn,a=7.769(1),b=9.873(2),c=11.974(2)Å,Z=4,T=293K,R=0.041 for 519 unique observed reflections. Ferroelastic phase: P2₁/c,a=7.615(5),b=9.872(3),c=11.947(5)Å, =92.98(8)°,Z=4,T=130K,R=0.083 for 507 unique observed reflections. In both structures the betaine molecules are connected to B(OH)₃-groups via hydrogen bonds to form chains running parallel[001]. These chains are associated to each other by van der Waals forces.

     

Singular Sturm—Liouville problems with nonnegative and indefinite weights

This article is concerned with the oscillatory properties of the eigenfunctions of a class of singular Sturm—Liouville problems—(p y)+q y=w y on (a, b), where the weight functionw vanishes on a subinterval of positive measure, or where the weight functionw changes sign on (a, b).This work was supported by the Applied Mathematical Sciences Research Program (KC-04-02) of the Office of Energy Research of the U.S. Department of Energy under Contract W-31-109-Eng-38.     

Photochemical Preparation of Highly Water-Soluble Pendant [60]Fullerene-Aminopolymers

Abstract— In order to introduce fullerene cages into an aqueous environment, pendant [60]fullerene-poly(propionylethyle-neimine-co-ethyleneimine) was prepared photochemical-ly. The pendant polymer is highly water soluble, with equivalent aqueous solubilities of the polymer-bound [60]fullerene much higher than the solubility of [60]ful-lerene in toluene. The photochemical reaction between [60]fullerene and secondary amine moieties in the ami-nopolymers likely follows a photoinduced electron transfer-proton transfer mechanism. The pendant polymer structures, which are represented by dehydrogenated di-and tetra-aminofullerene linkages, were characterized by use of proton and 13C NMR, Fourier transform-infrared spectroscopy, gel-permeation chromatography and optical spectroscopic methods.     

Basis set convergence studies of Hartree-Fock calculations of molecular properties within the resolution of the identity approximation

Within the resolution of the identity (RI) method, the convergence of the Hartree-Fock (HF) total molecular energy and the multipole moments in the course of the combined regular expansion of the molecular and auxiliary (RI) basis sets is studied. Dunning's cc-pVXZ series is used for both the molecular and the RI basis sets. The results show the calculated quantities converge to the HF limit when both the molecular and the RI basis sets are expanded from correlation-consistent polarized valence double zeta to correlation-consistent polarized valence sextuple zeta. Combinations of molecular/RI basis sets sufficient for convergence of the total energy and of the multipole moments at various accuracy levels have been determined. A measure of the RI basis set incompleteness is suggested and discussed. As it is significantly faster than the standard HF algorithm for small and midsize molecules, the RI-HF method, together with appropriate expanding series of both molecular and RI basis sets, provide an efficient tool to estimate and control the error of the Hartree-Fock calculations due to the finite basis set.     

Excited-state characters and dynamics of [W(CO)(5)(4-cyanopyridine)] and [W(CO)(5)(piperidine)] studied by picosecond time-resolved IR and resonance Raman spectroscopy and DFT calculations: roles of W --> L and W --> CO MLCT and LF excited states revised

The characters, dynamics, and relaxation pathways of low-lying excited states of the complexes [W(CO)(5)L] [L = 4-cyanopyridine (pyCN) and piperidine (pip)] were investigated using theoretical and spectroscopic methods. DFT calculations revealed the delocalized character of chemically and spectroscopicaly relevant molecular orbitals and the presence of a low-lying manifold of CO pi-based unoccupied molecular orbitals. Traditional ligand-field arguments are not applicable. The lowest excited states of [W(CO)(5)(pyCN)] are W --> pyCN MLCT in character. They are closely followed in energy by W --> CO MLCT states. Excitation at 400 or 500 nm populates the (3)MLCT(pyCN) excited state, which was characterized by picosecond time-resolved IR and resonance Raman spectroscopy. Excited-state vibrations were assigned using DFT calculations. The (3)MLCT(pyCN) excited state is initially formed highly excited in low-frequency vibrations which cool with time constants between 1 and 20 ps, depending on the excitation wavelength, solvent, and particular high-frequency nu(CO) or nu(CN) mode. The lowest excited states of [W(CO)(5)(pip)] are W --> CO MLCT, as revealed by TD-DFT interpretation of a nanosecond time-resolved IR spectrum that was measured earlier in a low-temperature glass (Johnson, F. P. A.; George, M. W.; Morrison, S. L.; Turner, J. J. J. Chem. Soc., Chem. Commun. 1995, 391-393). MLCT(CO) excitation involves transfer of electron density from the W atom and, to a lesser extent, the trans CO to the pi orbitals of the four cis CO ligands. Optical excitation into MLCT(CO) transition of either complex in fluid solution triggers femtosecond dissociation of a W-N bond, producing [W(CO)(5)(solvent)]. It is initially vibrationally excited both in nu(CO) and anharmonicaly coupled low-frequency modes. Vibrational cooling occurs with time constants of 16-22 ps while the intramolecular vibrational energy redistribution from the v = 1 nu(CO) modes is much slower, 160-220 ps. No LF excited states have been found for the complexes studied in a spectroscopically relevant range up to 6-7 eV. It follows that spectroscopy, photophysics, and photochemistry of [W(CO)(5)L] and related complexes are well described by an interplay of close-lying MLCT(L) and MLCT(CO) excited states. The high-lying LF states play only an indirect photochemical role by modifying potential energy curves of MLCT(CO) states, making them dissociative.     

Reaktion von Alkyl- und Arylchlorsilanen mit Phosph(III) en-imidamiden

The reaction of RSiCl₃ (R=CH₃, C₂H₅, C₆H₅) and R₂SiCl₂ (R=CH₃) with one mole of the phosphenimidous amides R₂N–P=NR [R=R=Si(CH₃)₃; R=Si(CH₃)₃, R=C(CH₃)₃] yieds a four membered PN₂Si-ring system under elimination of (CH₃)₃SiCl.     

Substrate affinities for membrane transport proteins determined by 13C cross-polarization magic-angle spinning nuclear magnetic resonance spectroscopy

We have devised methods in which cross-polarization magic-angle spinning (CP-MAS) solid-state NMR is exploited to measure rigorous parameters for binding of (13)C-labeled substrates to membrane transport proteins. The methods were applied to two proteins from Escherichia coli: a nucleoside transporter, NupC, and a glucuronide transporter, GusB. A substantial signal for the binding of methyl [1-(13)C]-beta-d-glucuronide to GusB overexpressed in native membranes was achieved with a sample that contained as little as 20 nmol of GusB protein. The data were fitted to yield a K(D) value of 4.17 mM for the labeled ligand and 0.42 mM for an unlabeled ligand, p-nitrophenyl beta-d-glucuronide, which displaced the labeled compound. CP-MAS was also used to measure binding of [1'-(13)C]uridine to overexpressed NupC. The spectrum of NupC-enriched membranes containing [1'-(13)C]uridine exhibited a large peak from substrate bound to undefined sites other than the transport site, which obscured the signal from substrate bound to NupC. In a novel application of a cross-polarization/polarization-inversion (CPPI) NMR experiment, the signal from undefined binding was eliminated by use of appropriate inversion pulse lengths. By use of CPPI in a titration experiment, a K(D) value of 2.6 mM was determined for uridine bound to NupC. These approaches are broadly applicable to quantifying binding of substrates, inhibitors, drugs, and antibiotics to numerous membrane proteins.     

Design of a calcium-binding protein with desired structure in a cell adhesion molecule

Ca2+, "a signal of life and death", controls numerous cellular processes through interactions with proteins. An effective approach to understanding the role of Ca2+ is the design of a Ca2+-binding protein with predicted structural and functional properties. To design de novo Ca2+-binding sites in proteins is challenging due to the high coordination numbers and the incorporation of charged ligand residues, in addition to Ca2+-induced conformational change. Here, we demonstrate the successful design of a Ca2+-binding site in the non-Ca2+-binding cell adhesion protein CD2. This designed protein, Ca.CD2, exhibits selectivity for Ca2+ versus other di- and monovalent cations. In addition, La3+ (Kd 5.0 microM) and Tb3+ (Kd 6.6 microM) bind to the designed protein somewhat more tightly than does Ca2+ (Kd 1.4 mM). More interestingly, Ca.CD2 retains the native ability to associate with the natural target molecule. The solution structure reveals that Ca.CD2 binds Ca2+ at the intended site with the designed arrangement, which validates our general strategy for designing de novo Ca2+-binding proteins. The structural information also provides a close view of structural determinants that are necessary for a functional protein to accommodate the metal-binding site. This first success in designing Ca2+-binding proteins with desired structural and functional properties opens a new avenue in unveiling key determinants to Ca2+ binding, the mechanism of Ca2+ signaling, and Ca2+-dependent cell adhesion, while avoiding the complexities of the global conformational changes and cooperativity in natural Ca2+-binding proteins. It also represents a major achievement toward designing functional proteins controlled by Ca2+ binding.