Role of the tautomerism of 2-azaadenine and 2-azahypoxanthine in substrate recognition by xanthine oxidase

The tautomerism of 2-azaadenine and 2-hypoxanthine has been examined in the gas phase and in aqueous solution. The tautomerism in the gas phase has been studied by means of semiempirical and ab initio quantum-mechanical computations, as well as density-functional calculations. The influence of the aqueous solvent on the relative stability between tautomers has been estimated from self-consistent reaction field calculations performed with different high-level continuum models. The results provide a detailed picture of the tautomeric preference for these purine bases. The importance of tautomerism in the substrate recognition by xanthine oxidase is discussed. Finally, the rate of oxidation of 2-azaadenine and 2- hypoxanthine by xanthine oxidase is discussed in terms of the recognition model at the enzyme active site.     

PRIRODA-04: a quantum-chemical program suite. New possibilities in the study of molecular systems with the application of parallel computing

Main characteristics are described of the PRIRODA quantum-chemical program suite designed for the study of complex molecular systems by the density functional theory, at the MP2, MP3, and MP4 levels of multiparticle perturbation theory, and by the coupled-cluster single and double excitations method (CCSD) with the application of parallel computing. A number of examples of calculations are presented.__________Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 804–810, March, 2005.     

Patterning porous matrices and planar substrates with quantum dots

Silica hydrogels and planar substrates were patterned with CdS nanoparticles using a photolithographic method based on the photo dissociation of thiols and cadmium-thiolate complexes. Silica hydrogels were prepared via a standard base-catalyzed route. The solvent was exchanged with an aqueous solution of CdSO₄ and 2-mercaptoethanol, and the samples were then exposed to a focused ultraviolet beam. Planar substrates were patterned by illuminating a precursor solution spin coated on the substrates. CdS nanoparticles formed in the illuminated spots, and had a diameter below about 2 nm. The diameter of the spots illuminated by the UV beam could be varied from a few hundred to a few μm, on both hydrogels and planar substrates. Samples were characterized with transmission electron microscopy, X-ray photoelectron spectroscopy, X-ray diffraction, and optical absorption, photoluminescence and Raman spectroscopies. All these techniques confirmed the chemical identity of the CdS nanoparticles. To investigate the mechanism of nanoparticle formation, we took absorption spectra of the precursor solution as a function of irradiation time. In unirradiated solutions, we noticed a maximum at 250 nm, characteristic of Cd-thiolate complexes. The absorption at 250 nm decreased with increasing irradiation time. A new band appeared at 265 nm for exposures around 5 min, and that band shifted to 290 nm in samples exposed for 10 min. A yellow precipitate formed after about 30 min. XRD showed that the precipitate was cubic CdS, with a mean particle size of 1.4 nm. We attribute formation of CdS to the photodissociation of the thiols and of the Cd-thiolates. UV irradiation of these precursors yields a series of species that can react with Cd²⁺, such as RS^·, S²⁻ and H₂S. Small CdS nanoparticles form in the initial stages of illumination, and present absorption bands in the 265–290 nm region. These CdS aggregates grow, coalesce and precipitate for longer irradiation times.     

Surface-modified CdSe quantum dots as luminescent probes for cyanide determination

Luminescent surface-modified CdSe semiconductor quantum dots (QDs), with nanoparticle (NP) size distribution in the order of 2-7 nm, have been synthesized for optical determination of cyanide ions. The nanoparticles have been functionalised with tert-butyl-N-(2-mercaptoethyl)-carbamate (BMC) groups and exhibit a strong fluorescent emission at about 580 nm with rather long fluorescence lifetimes (several hundred nanoseconds) in aerated methanolic solution. The observed luminescence emitted by the synthesized nanocrystals was tremendously increased by photo-activation under sunlight exposure. The functionalised QDs turned out to exhibit excellent long-term stability when stored in the dark (no significant changes in QDs luminescence emission intensity was observed even after two months from synthesis). The functionalisation of the NPs with carbamate ligand allowed a highly sensitive determination of free cyanide via analyte-induced changes in the photoluminescence (fluorescence quenching of intensity at 580 nm and lifetime changes) of the modified quantum dots (excited at 400 nm). A detection limit of 1.1 × 10⁻⁷ M (2.9 μg l⁻¹) of cyanide ions was obtained, while the interfering effect of other inorganic anions (including NO₃⁻, Cl⁻ or SCN⁻) was negligible even at 200-fold level concentrations in excess of cyanide.     

The complete symmetrization of quantum operators: new thoughts on an old problem

The complete symmetrization with respect to x, p _x,... of the operators associated with dynamical properties can sometimes lead to results different from those obtained by the conventional quantum formalism based on the rule op (A ²)=(op A)². For example, angular momentum operators M _z ² and M ² are modified by the additive constants ²/2 and 3 ²/2 respectively (M ²0 for electron in the ground state of H atom, rotator never at rest, but spectra unchanged); the average quadratic dispersion of energy is different from zero. These results can be interpreted by assuming that the system is never strictly isolated but communicates with the other systems of the universe by means of electromagnetic interactions. Quantum mechanics would give only average values over a sufficiently long time and would exhibit a quasi-ergodic character. Examples supporting this possibility are given, in particular that of arsines for which quantum forecasts correspond to average values over one year.Dedicated to Professor J. Koutecký on the occasion of his 65th birthday     

Variational reactive scattering calculations: computational optimization strategies

Summary We have developed efficient and accurate techniques for the calculation of quantum mechanical reaction probabilities of atom-diatom exchange reactions in the gas phase, and we have optimized a computer code employing these techniques and applied it sucessfully to several systems. In this paper we consider further strategies for improving the algorithm to allow even more demanding applications. In this context, improvement means that equivalent results can be obtained using fewer computational resources (computer time or storage) or that an equivalent expenditure of resources can yield higher accuracy. The new strategies discussed here lead to improvement in both of these areas. Two areas of special focus in the present paper are (i) the finite difference boundary value method used for calculating distorted wave Green's functions and regular solutions for scattering by the distortion potential and (ii) the choice of the distortion potential itself. Among other results included here is the first application of the outgoing wave or scattered wave variational principle to reactive scattering.     

NMR chemical shifts in the low–pH form of a-chymotrypsin. A QM/MM and ONIOM–NMR study

 The relationship between hydrogen bonding and NMR chemical shifts in the catalytic triad of low-pH α-chymotrypsin is investigated by combined use of the effective fragment potential [(2001) J Phys Chem A 105:293] and ONIOM–NMR [(2000) Chem Phys Lett 317:589] methods. Our study shows that while the His57 N^δ1−H bond is stretched by a relatively modest amount (to about 1.060 ?) this lengthening, combined with the polarization due to the molecular environment, is sufficient to explain the experimentally observed chemical shifts of 18.2 ppm. Furthermore, the unusual down-field shift of H^ɛ1 (9.2 ppm) observed experimentally is reproduced and shown to be induced by interactions with the C=O group of Ser214 as previously postulated. The free-energy cost of moving H^δ1 from His57 to Asp102 is predicted to be 5.5 kcal/mol. Received: 26 September 2001 / Accepted: 6 September 2002 / Published online: 21 January 2003 Contribution to the Proceedings of the Symposium on Combined QM/MM Methods at the 222nd National Meeting of the American Chemical Society, 2001 Correspondence to: J. H. Jensen e-mail: jan-jensen@uiowa.edu Acknowledgements. This work was supported by a Research Innovation Award from the Research Corporation and a type G starter grant from the Petroleum Research Fund. The calculations were performed on IBM RS/6000 workstations obtained through a CRIF grant from the NSF (CHE-9974502) and on supercomputers at the National Center for Supercomputer Applications at Urbana-Champaign. The authors are indebted to Visvaldas Kairys for help with the CHARMM program, and to Daniel Quinn for many helpful discussions.     

A parallel implementation of the COLUMBUS multireference configuration interaction program

Summary In this work a parallel implementation of the COLUMBUS MRSDCI program system is presented. A coarse grain parallelization approach using message passing via the portable toolkit TCGMSG is used. The program is very well portable and runs on shared memory machines like the Cray Y-MP, Alliant FX/2800 or Convex C2 and on distributed memory machines like the iPSC/860. Further implementations on a network of workstations and on the Intel Touchstone Delta are in progress. Overall, results are quite satisfactory considering the complexity and the prodigious requirements, especially the I/O bandwidth, of MRCI programs in general. For our largest test case we obtain a speedup of a factor of 7.2 on an eight processor Cray Y-MP for that section of the program (hamiltonian matrix times trial vector product) which has been parallelized. The speedup for one complete diagonalization iteration amounts to 5.9. An absolute speed close to 1 GFLOPS is found. Results for the iPSC/860 show that ordinary disk I/O is certainly not sufficient in order to guarantee a satisfactory performance. As a solution for that problem, the implementation of a fully asynchronous distributed-memory model for certain data files is in preparation. On leave from: Bereich Informatik, Universität Leipzig, Augustusplatz 10/11, O-7010 Leipzig, Germany     

Benchmark studies of the BCRLM reactive scattering code: Implications for accurate quantum calculations

Summary The Bending Corrected Rotating Linear Model (BCRLM), developed by Hayes and Walker, is a simple approximation to the true multidimensional scattering problem for reactions of the type: A + BC AB + C. While the BCRLM method is simpler than methods designed to obtain accurate three-dimensional quantum scattering results, this turns out to be a major advantage in terms of our benchmarking studies. The computer code used to obtain BCRLM scattering results is written for the most part in standard FORTRAN and has been ported to several scalar, vector, and parallel architecture computers including the IBM 3090-600J, the Cray XMP and YMP, the Ardent Titan, IBM RISC System/6000, Convex C-1 and the MIPS 2000. Benchmark results will be reported for each of these machines with an emphasis on comparing the scalar, vector, and parallel performance for the standard code with minimum modifications. Detailed analysis of the mapping of the BCRLM approach onto both shared and distributed memory parallel architecture machines indicates the importance of introducing several key changes in the basic strategy and algorithms used to calculate scattering results. This analysis of the BCRLM approach provides some insights into optimal strategies for mapping three-dimensional quantum scattering methods, such as the Parker-Pack method, onto shared or distributed memory parallel computers.     

Homologies cyclique et de Hochschild de certains espaces homogènes quantiques

Nous quantifions certaines inclusions d'algèbres de Lie semi-simpleshg. Nous calculons les homologies associées aux quantifications, surC((h)), d'une part des algèbres de fonctions formelles surG/H, pourHG une inclusion de groupes de Lie semi-simples associée, et d'autre part des fonctions algébriques sur SL(2,C)/T.We quantize certain inclusions of semisimple Lie algebrashg. We compute the cyclic and Hochschild homologies for theC((h))-quantizations of