Shellability and homology of q-complexes and q-matroids

Journal of Algebraic Combinatorics - We consider a q-analogue of abstract simplicial complexes, called q-complexes, and discuss the notion of shellability for such complexes. It is shown that...     

Kinetics of the Antibody Recognition Site in the Third IgG‐Binding Domain of Protein G

Protein dynamics occurring on a wide range of timescales play a crucial role in governing protein function. Particularly, motions between the globular rotational correlation time ( ) and 40 μs (supra‐ window), strongly influence molecular recognition. This supra‐ window was previously hidden, owing to a lack of experimental methods. Recently, we have developed a high‐power relaxation dispersion (RD) experiment for measuring kinetics as fast as 4 μs. For the first time, this method, performed under super‐cooled conditions, enabled us to detect a global motion in the first β‐turn of the third IgG‐binding domain of protein G (GB3), which was extrapolated to 371±115 ns at 310 K. Furthermore, the same residues show the plasticity in the model‐free residual dipolar coupling (RDC) order parameters and in an ensemble encoding the supra‐ dynamics. This β‐turn is involved in antibody binding, exhibiting the potential link of the observed supra‐ motion with molecular recognition.     

Studies towards the synthesis of epothilone A via organoboranes

Studies towards the synthesis of epothilone A via organoboranes have been described. A modified procedure for the large-scale preparation of B-gamma,gamma-dimethylallyldiisopinocampheylborane from prenyl alcohol has been developed. This reagent, upon reaction with various aldehydes, provides the corresponding alpha,alpha-dimethylhomoallylic alcohols in high enantioselectivities. The application of this reagent for the synthesis of the C1-C6 subunit of epothilone has been demonstrated. Alternatively, inter- and intramolecular asymmetric reduction protocols have also been utilized for the synthesis of the C1-C6 subunit of epothilone A. The synthesis of the C7-C21 fragment of epothilone A involving asymmetric alkoxyallyl- and crotylboration using alpha-pinene-derived reagents has also been described.     

Electron solvation in water-ammonia mixed clusters: Structure, energetics, and the nature of localization states of the excess electron

The structure and energetics of water-ammonia mixed clusters with an excess electron, [(H2O)n(NH3)m]- with m=1, n=2-6 and m=2, n=2, and also the corresponding neutral clusters are investigated in detail by means of ab initio quantum chemical calculations. The authors focus on the localization structure of the excess electron with respect to its surface versus interiorlike states, its binding to ammonia versus water molecules, the spatial and orientational arrangement of solvent molecules around the excess electron, the changes of the overall hydrogen-bonded structure of the clusters as compared to those of the neutral ones and associated dipole moment changes, vertical detachment energies of the anionic clusters, and also the vertical attachment energies of the neutral clusters. It is found that the hydrogen-bonded structure of the anionic clusters are very different from those of the neutral clusters unlike the case of water-ammonia dimer anion, and these changes in structural arrangements lead to drastically different dipole moments of the anionic and the neutral clusters. The spatial distribution of the singly occupied molecular orbital holding the excess electron shows only surface states for the smaller clusters. However, for n=5 and 6, both surface and interiorlike binding states are found to exist for the excess electron. For the surface states, the excess electron can be bound to the dangling hydrogens of either an ammonia or a water molecule with different degrees of stability and vertical detachment energies. The interiorlike states, wherever they exist, are found to have a higher vertical detachment energy than any of the surface states of the same cluster. Also, for interiorlike states, the ammonia molecule with its dangling hydrogens is always found to stay on top or on a far side of the charge density of the excess electron without participating in the hydrogen bond network of the cluster; the intermolecular hydrogen bonds are formed by the water molecules only which add to the overall stability of these anionic clusters.     

Microscopic solvation of a lithium atom in water-ammonia mixed clusters: solvent coordination and electron localization in presence of a counterion

The microsolvation structures and energetics of water-ammonia mixed clusters containing a lithium atom, i.e., Li(H(2)O)(n)(NH(3)), n = 1-5, are investigated by means of ab initio theoretical calculations. Several structural aspects such as the solvent coordination to the metal ion and binding motifs of the free valence electron of the metal are investigated. We also study the energetics aspects such as the dependence of vertical ionization energies on the cluster size, and all these structural and energetics aspects are compared to the corresponding results of previously studied anionic water-ammonia clusters without a metal ion. It is found that the Li-O and Li-N interactions play a very important role in stabilizing the lithium-water-ammonia clusters, and the presence of these metal ion-solvent interactions also affect the characteristics of electron solvation in these clusters. This is seen from the spatial distribution of the singly occupied molecular orbital (SOMO) which holds the ejected valence electron of the Li atom. For very small clusters, SOMO electron density is found to exist mainly at the vicinity of the Li atom, whereas for larger clusters, it is distributed outside the first solvation shell. The free dangling hydrogens of water and ammonia molecules are involved in capturing the SOMO electron density. In some of the conformers, OH{e}HO and OH{e}HN types of interactions are found to be present. The presence of the metal ion at the center of the cluster ensures that the ejected electron is solvated at a surface state only, whereas both surface and interiorlike states were found for the free electron in the corresponding anionic clusters without a metal ion. The vertical ionization energies of the present clusters are found to be higher than the vertical detachment energies of the corresponding anionic clusters which signify a relatively stronger binding of the free electron in the presence of the positive metal counterion. The shifts in different vibrational frequencies are also calculated for the larger clusters, and the results are discussed for some of the selective modes of water and ammonia molecules that are directly influenced by the location and hydrogen bonding state of these molecules in the clusters.     

Population Shuffling of Protein Conformations

Motions play a vital role in the functions of many proteins. Discrete conformational transitions to excited states, happening on timescales of hundreds of microseconds, have been extensively characterized. On the other hand, the dynamics of the ground state are widely unexplored. Newly developed high‐power relaxation dispersion experiments allow the detection of motions up to a one‐digit microsecond timescale. These experiments showed that side chains in the hydrophobic core as well as at protein–protein interaction surfaces of both ubiquitin and the third immunoglobulin binding domain of protein G move on the microsecond timescale. Both proteins exhibit plasticity to this microsecond motion through redistribution of the populations of their side‐chain rotamers, which interconvert on the picosecond to nanosecond timescale, making it likely that this “population shuffling” process is a general mechanism.     

Synthesis,characterization, crystal structure and catalytic activity of amido azo palladium(II) complex

Transition Metal Chemistry - The newly designed tridentate ligand, 2-((2-aminophenyl)diazenyl)-N-benzylaniline, 1 has been synthesized by the reaction between 2,2′-diaminoazobenzene and...     

A Designed Conformational Shift To Control Protein Binding Specificity

In a conformational selection scenario, manipulating the populations of binding‐competent states should be expected to affect protein binding. We demonstrate how in silico designed point mutations within the core of ubiquitin, remote from the binding interface, change the binding specificity by shifting the conformational equilibrium of the ground‐state ensemble between open and closed substates that have a similar population in the wild‐type protein. Binding affinities determined by NMR titration experiments agree with the predictions, thereby showing that, indeed, a shift in the conformational equilibrium enables us to alter ubiquitin’s binding specificity and hence its function. Thus, we present a novel route towards designing specific binding by a conformational shift through exploiting the fact that conformational selection depends on the concentration of binding‐competent substates.     

Stereoselective synthesis of the C7C21 segment of epothilone A via asymmetric alkoxyallyl- and crotylboration

The synthesis of the C₇C₂₁ fragment of epothilone A involving asymmetric alkoxyallyl- and crotylboration using α-pinene-derived reagents is described.     

A Remote ‘Imidazole’‐Based Ruthenium(II) Para‐Cymene Pre‐catalyst for the Selective Oxidation Reaction of Alkyl Arenes and Alcohols

Herein we disclosed the use of a remote ‘imidazole’‐based precatalyst [(para‐cymene)Ru^II(L)Cl]⁺, C‐1 where L=2‐(4‐substituted‐phenyl)‐1H‐imidazo[4,5‐f]^[1,10] phenanthroline) for the selective oxidation of a variety of alkyl arenes/heteroarenes and alcohols to their corresponding aldehydes or ketones in presence of tert‐butyl hydroperoxide (TBHP). The remote ‘imidazole’ moiety present in the complex facilitates the activation of oxidant and subsequent generation of active species via the release of para‐cymene from C‐1 , which in‐turn was less effective without the ‘imidazole’ moiety. The mechanistic features of C‐1 promoted oxidation of alkyl arenes were also assessed from spectroscopic, kinetic, and few control experiments. The substrate scope for C‐1 promoted oxidation reaction was assessed based on the selective oxidation of 27‐different alkyl arenes/heteroarenes and 25 different alcohols to their corresponding aldehydes/ketones in moderate to good yields.