Antihydrophobic solvent effects: an experimental probe for the hydrophobic contribution to enzyme-inhibitor binding

The hydrophobic component to the binding affinities of one acyclic phosphinate (4) and three macrocyclic phosphonamidate inhibitors (1-3) to the zinc peptidase thermolysin was probed by varying the solvent composition. Increasing the percentage of ethanol in the buffer solution over the range 0-9% increases the inhibition constants, K(i), by up to an order of magnitude. This approach represents an experimental method for distinguishing solvation from conformational or other effects on protein-ligand binding. The size of the "antihydrophobic effect" is correlated with the amount of hydrophobic surface area sequestered from solvent on association of the inhibitor and enzyme, although it is attenuated from that calculated from the surface tension of ethanol-water mixtures. The results are consistent with the Lum-Chandler-Weeks explanation for the size dependence of the hydrophobic effect.     

A crystallite packing model for pseudoboehmite formed during the hydrolysis of trisecbutoxyaluminium to explain the peptizability

A model for pseudoboehmite crystallite packing formed during the hydrolysis of trisecbutoxyaluminium is postulated. The model describes platelike crystallites of pseudoboehmite stacked in a sharing edges only configuration. With this type of stacking, the pore sizes detected are approximately equal to the crystallite sizes of the hydrolysates. The hydrolysates age via a dissolution re-precipitation reaction. This increases the size of the crystallite size of the pseudoboehmite formed, speeding peptization by allowing nitrate ions to enter pores and access the surfaces of the crystallites. This type of model also allows an explanation for the peptization kinetics of systems containing sec-butanol formed during the hydrolysis of trisecbutoxyaluminium.     

Singular value decomposition applied to the compression of T3 amplitude for the coupled cluster method

We apply the singular value decomposition to compress the degrees of freedom of T3 amplitude for the CCSDT-1 method (compressed CCSDT-1). This method enables us to make the number of the T3 amplitudes less than that of the T2 amplitudes, making CCSDT-1 calculations much less expensive without losing accuracy. We perform test calculations on some atoms and molecules to investigate the applicability of this method. Computational results for the electronic energies as well as timings of these calculations are presented.     

Identification of novel macrocyclic peptidase substrates via on-bead enzymatic cyclization

Peptidase-catalyzed formation of macrocyclic lactams on solid phase identifies ring systems that are favorably bound in the enzyme active site. We evaluated several cyclic peptide motifs linked by ester bonds between the P2 and P1' or the P1 and P2' side chains. The depsipeptide represented by structure 5 was readily generated by a variety of peptidases from precursor omega-amino acids or omega-amino esters. This strategy for identifying ring systems for potential macrocyclic transition state analogues was demonstrated with the serine peptidases trypsin and chymotrypsin, with the aspartic peptidase pepsin, and with the zinc peptidase thermolysin.     

Zeolites with Continuously Tuneable Porosity

Zeolites are important materials whose utility in industry depends on the nature of their porous structure. Control over microporosity is therefore a vitally important target. Unfortunately, traditional methods for controlling porosity, in particular the use of organic structure‐directing agents, are relatively coarse and provide almost no opportunity to tune the porosity as required. Here we show how zeolites with a continuously tuneable surface area and micropore volume over a wide range can be prepared. This means that a particular surface area or micropore volume can be precisely tuned. The range of porosity we can target covers the whole range of useful zeolite porosity: from small pores consisting of 8‐rings all the way to extra‐large pores consisting of 14‐rings.     

Determination of diisopropylfluorophosphate in rat plasma and brain tissue by headspace solid-phase microextraction gas chromatography/mass spectrometry

A simple, sensitive and rapid method for the determination of diisopropylfluorophosphate (DFP) in rat plasma and brain tissue using headspace solid-phase microextraction (HS-SPME) and gas chromatography/mass spectrometry (GC/MS) is presented. A 65 microm polydimethylsiloxane/divinylbenzene (PDMS/DVB) fiber was selected for sampling. The main parameters affecting the SPME process such as extraction and desorption temperature, extraction and desorption time, salt addition, and fiber preheating time were optimized in each matrix to enhance the extraction efficiency of the method. The lower limits of quantitation for DFP in plasma and brain tissue were 1 ng/mL and 3 ng/g, respectively. The method showed good linearity over the range from 1-100 ng/mL in plasma and 3-300 ng/g in brain tissue with correlation coefficient (R(2)) values higher than 0.995. The precision and accuracy for intra-day and inter-day were less than 10%. The relative recoveries in plasma and brain for DFP were greater than 50%. Stability tests including autosampler and freeze and thaw were also investigated. This validated method was successfully applied to study the neurobehavioral effects of low-level organophosphate exposures. Copyright (c) 2008 John Wiley & Sons, Ltd.     

Natural linear-scaled coupled-cluster theory with local transferable triple excitations: applications to peptides

The natural linear-scaled coupled-cluster (NLSCC) method ( Flocke, N.; Bartlett, R. J. J. Chem. Phys. 2004, 121, 10935 ) is extended to include approximate triple excitations via a coupled-cluster with single, double, and triple excitation method (CCSDT-3). The triples contribution can potentially be embedded in a larger singles and doubles region. NLSCC exploits the extensivity of the CC wave function to represent it in terms of transferable natural localized molecular orbitals (NLMOs) or functional groups thereof that are obtained from small quantum mechanical (QM) regions. Both occupied and virtual NLMOs are local because they derive from the single-particle density matrix. Noncanonical triples amplitudes are avoided by applying the unitary localization matrix to the canonical CC wave function for a QM region. A generalized NLMO code interfaced to the ACES II quantum chemistry software package provides NLMOs for the relevant number of atoms in a given functional group. Applications include linear polyglycine and the pentapeptide met-enkephalin, which was chosen as a more realistic three-dimensional system with nontrivial side chains. The results show that the triples contributions are quite large for aromatic bonds suggesting an interesting active space method for triples in which different bonds require different excitation levels. The NLSCC approach recovers a very large percentage (>99%) of the CCSD or CCSDT-3 correlation energy.     

Use of an on-line imprinted polymer pre-column, for the liquid chromatographic-UV absorbance determination of carbaryl and its metabolite in complex matrices

A carbaryl and 1-naphtol molecular imprinted polymers (MIP1 and MIP 2, respectively) were prepared using suspension polymerization and tested for selective and reversible binding to carbaryl and 1-naphtol, respectively. In the suspension polymerization technique used, polymers of methacrylic acid (MAA), highly cross-linked with ethylene dimethacrylate, provide a specific binding sites for the carbaryl molecule and its metabolite when using it as a template to be removed after polymerization. The molecular imprinted polymer with a particle size of approximately 5 microm were isolated and packed into a pre-column (50 mm x 4.6 mm id) that was used to isolate carbaryl and its metabolite from complex matrices injected on a high performance liquid chromatography system using ultra-violet detection without extensive sample preparation and clean up. The HPLC method had a detection limit of 1.00 ng/mL and a linear response (r2 > 0.98) over the concentration range of 1.00-10.0 ng/mL.     

Comparing ab initio density-functional and wave function theories: the impact of correlation on the electronic density and the role of the correlation potential

The framework of ab initio density-functional theory (DFT) has been introduced as a way to provide a seamless connection between the Kohn-Sham (KS) formulation of DFT and wave-function based ab initio approaches [R. J. Bartlett, I. Grabowski, S. Hirata, and S. Ivanov, J. Chem. Phys. 122, 034104 (2005)]. Recently, an analysis of the impact of dynamical correlation effects on the density of the neon atom was presented [K. Jankowski, K. Nowakowski, I. Grabowski, and J. Wasilewski, J. Chem. Phys. 130, 164102 (2009)], contrasting the behaviour for a variety of standard density functionals with that of ab initio approaches based on second-order M?ller-Plesset (MP2) and coupled cluster theories at the singles-doubles (CCSD) and singles-doubles perturbative triples [CCSD(T)] levels. In the present work, we consider ab initio density functionals based on second-order many-body perturbation theory and coupled cluster perturbation theory in a similar manner, for a range of small atomic and molecular systems. For comparison, we also consider results obtained from MP2, CCSD, and CCSD(T) calculations. In addition to this density based analysis, we determine the KS correlation potentials corresponding to these densities and compare them with those obtained for a range of ab initio density functionals via the optimized effective potential method. The correlation energies, densities, and potentials calculated using ab initio DFT display a similar systematic behaviour to those derived from electronic densities calculated using ab initio wave function theories. In contrast, typical explicit density functionals for the correlation energy, such as VWN5 and LYP, do not show behaviour consistent with this picture of dynamical correlation, although they may provide some degree of correction for already erroneous explicitly density-dependent exchange-only functionals. The results presented here using orbital dependent ab initio density functionals show that they provide a treatment of exchange and correlation contributions within the KS framework that is more consistent with traditional ab initio wave function based methods.