Research applications of the Cambridge Structural Database (CSD)

Crystal structure data are of fundamental importance in a wide spectrum of scientific activities. This tutorial review summarises the principal application areas, so far, for the data from more than 300,000 crystal structures of small organic and metal-organic compounds that are stored in the Cambridge Structural Database (CSD). Direct use of the accumulated data is valuable in establishing standard molecular dimensions, determining conformational preferences and in the study of intermolecular interactions, all of which are crucial in structural chemistry and rational drug design. More recently, information derived from the CSD has been used to construct two dynamic libraries of structural knowledge: Mogul, which stores intramolecular information, and IsoStar, which stores information about intermolecular interactions. These electronic libraries provide information "at the touch of a button". In their turn, the libraries also serve as sources of structural knowledge for applications software that address specific problems in small-molecule and biological chemistry.     

Proteomic analysis of the endoplasmic reticulum from developing and germinating seed of castor (Ricinus communis)

Endoplasmic reticulum (ER) has been prepared and analysed from germinating and developing castor bean endosperm. A combination of one- and two-dimensional (1-D and 2-D) gel electrophoresis was used to study the complexity of sample and protein differences between the two stages. The ER of the developing oilseed is central to the synthesis, sorting and storage of protein and lipid reserves while the germinating seed is concerned with their degradation. Sample complexity has been reduced by separation of ER proteins into lumenal, peripheral membrane and integral membrane subfractions. Membrane proteins pose specific problems in aggregation and binding to passive surfaces. We have overcome this by collection of membranes at density gradient interfaces and by silanization of plastic ware. Several major components have been identified from 1-D gels by N-terminal sequencing and matrix-assisted laser desorption/ionization (MALDI) peptide mass fingerprints. These include protein disulphide isomerase (PDI), calreticulin and developing-ER-specific oleate-12-hydroxylase involved in the biosynthesis of ricinoleic acid. In excess of 300 spots are detectable in each developmental fraction by high sensitivity 2-D gels. This is the first 2-D electrophoretic analysis of plant ER. These gels reveal significant differences between germinating and developing ER. Preparative loading 2-D gels of germinating ER have been run and 14 selected spots characterized by quadrupole time of flight tandem mass spectrometry (Q-TOF MS/MS). Ten of these proteins were assigned function on the basis of identity with existing castor database entries, or by homology with other species. Two proteins, aspartate proteinase precursor and N-carbamyl-L-aminohydrolase-like protein, appear to be absent from developing profiles. Most of the proteins identified are concerned with roles in protein processing and storage, and lipid metabolism which occur in the ER. Data from three of the assigned spots included unidentified peptides indicating the presence of more than one protein in these spots following 2-D electrophoresis. More extensive analysis will have to await developments in genomics but the basic separation technologies to simplify sample identity for a plant ER preparation have been established.     

Organometallic reagents in organic synthesis—V: An organocuprate conjugate addition—Aldol condensation synthetic procedure for sequential formation of two carbon-carbon bonds

The enolates produced from the conjugate addition reaction of lithium dialkylcuprates with α,β- unsaturated ketones react with aldehydes in the presence of zinc chloride to give overall β-alkyl α-hydroxyalkyl addition to the original alkene. Reaction of these enolates with carbon dioxide and ethyl formate is also reported.     

DEPENDENCE OF THE TRIPLET YIELD ON EXCITATION ENERGY IN ALL-TRANS AND 11-CIS RETINAL*

Abstract. The triplet-triplet absorption of all-trans and 11- cis retinal was measured as a function of the exciting radiation from 423 nm to 365 nm in a glass of 3-methylpentane at 77 K. This experiment was also accomplished with all-trans retinal in hexane at ambient temperature. The relative triplet formation quantum yields of all-trans and 11-cis retinal at 77 K were found to be independent (±10%) of the frequency of the exciting radiation. At room temperature we measured an increase in this relative quantum yield for all- trans retinal from 1.0 at 365 nm to 1.82 at 423 nm [Bensasson et al. (1975) measured an absolute quantum yield of 0.45 at 353 nm]. These results are used to evaluate previous interpretations for photophysical decay processes in all-trans retinal, and previous suggestions for wavelength dependent radiationless transitions are shown to be unacceptable. High energy excitation of 300 K solutions of all- trans retinal produce excited states that result in less efficient intersystem crossing. These states appear to be inaccessible in the 77 K matrices. We suggest that steric restrictions introduced by the retinal matrix interaction at 77 K are able to block this new internal conversion pathway back to the ground state.     

A nonequilibrium entropy for dynamical systems

It is proposed to define entropy for nonequilibrium ensembles using a method of coarse graining which partitions phase space into sets which typically have zero measure. These are chosen by considering the totality of future possibilities for observation on the system. It is shown that this entropy is necessarily a nondecreasing function of the timet. There is no contradiction with the reversibility of the laws of motion because this method of coarse graining is asymmetric under time reversal. Under suitable conditions (which are stated explicitly) this entropy approaches the equilibrium entropy ast+ and the fine-grained entropy ast–. In particular, the conditions can always be satisfied if the system is aK-system, as in the Sinai billiard models. Some theorems are given which give information about whether it is possible to generate the partition used here for coarse graining from time translates of a finite partition, and at the same time elucidate the connection between our concept of entropy and the entropy invariant of Kolmogorov and Sinai.Research supported in part by NSF grants PHY78-03816 and PHY78-15920.     

Di- and tri-alkylphosphine adducts of S-donor palladacycles as catalysts in the Suzuki coupling of aryl chlorides

The reaction of tricyclohexylphosphine with the S-based palladacycle [(Pd(mu-OAc)(kappa2-S,C-C(6)H(4)CH(2)SMe))(2)] gives several products, regardless of stoichiometry, one of which, [Pd(kappa1-OAc)(eta1-C(6)H(4)CH(2)SMe)(PCy3)2], has been characterised crystallographically. Despite this, catalysts formed in situ from di- and tri-alkylphosphines and [(Pd(mu-OAc)(kappa2-S,C-C(6)H(4)CH(2)SMe))2] show excellent activity in the Suzuki coupling of a range of deactivated, non-activated and activated aryl chloride substrates.     

Carbene-catalyzed activation of cyclopropylcarbaldehydes for mannich reaction and δ-lactam formation: remote enantioselecitvity control and dynamic kinetic asymmetric transformation

An N-heterocyclic carbene(NHC)-catalyzed enantioselective Mannich reaction of the remote γ-carbon of cyclopropylcarbaldehydes is disclosed for the first time. Diastereo-and enantiomerically enriched multicyclic δ-lactam compound is afforded as the main product from 8 possible stereo-specific isomers through dynamic kinetic asymmetric transformation(DYKAT) processes. Multiple chiral functional molecules can be afforded from the lactam products through simple protocols with retentions of the optical purities.     

Fracture initiation in the contact region under shear

In the contact region between sliding elastic bodies, there are subregions where the interacting shores are bonded and subregions where they can slide along each other. It is convenient to interpret the latter as transverse shear cracks with slip resistance forces acting on their closed shores. In the end regions of such a crack, stress concentration may lead to fracture initiation in the contacting bodies. Experimental results and an analytic model of the phenomenon are given for a situation where the fracture intersects the contact plane tilted with respect to the direction of the loads.     

Simulation of variations in mechanical properties of polyurethane elastomers modified with carbon nanotubes

The addition of extremely small portions of single-wall carbon nanotubes causes an anomalous change in mechanical properties of a cross-linked polyurethane-amide-urea elastomer containing 10% of polyamide-6; namely, with a nanofiller content of hundredths and thousandths of a percent, local maxima of elastic modulus and ultimate stress are observed. In the work, the anomalous variation in the elastic modulus is simulated relying on the concept of intermediate phase layer formation at the boundary of contacting particles of the initial material.