Data Analysis WorkbeNch (DAWN) Basham, Mark; Filik, Jacob; Wharmby, Michael T. ...
Journal of synchrotron radiation,
20/May , Volume:
22, Issue:
3
Journal Article
Peer reviewed
Open access
Synchrotron light source facilities worldwide generate terabytes of data in numerous incompatible data formats from a wide range of experiment types. The Data Analysis WorkbeNch (DAWN) was developed ...to address the challenge of providing a single visualization and analysis platform for data from any synchrotron experiment (including single‐crystal and powder diffraction, tomography and spectroscopy), whilst also being sufficiently extensible for new specific use case analysis environments to be incorporated (e.g. ARPES, PEEM). In this work, the history and current state of DAWN are presented, with two case studies to demonstrate specific functionality. The first is an example of a data processing and reduction problem using the generic tools, whilst the second shows how these tools can be targeted to a specific scientific area.
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FZAB, GIS, IJS, IZUM, KILJ, NLZOH, NUK, OILJ, PILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK
A wavefunction model to chemical bonding Náray‐Szabó, Gábor; Mezey, Paul G.
International journal of quantum chemistry,
April 15, 2022, Volume:
122, Issue:
8
Journal Article
Peer reviewed
Open access
In this paper we give a brief survey on some specific aspects of a wavefunction model for chemical bonding which are connected to or have been motivated in part by the work of the late István Mayer ...and colleagues. After a brief description of the early wavefunction models as reflected in Mayer's works, naturally leading to electron densities, we discuss localized molecular orbitals, and summarize some of the early initiatives and applications. The concept of the Chemical Hamiltonian, as introduced by Mayer, its extensions and some classical and some more advanced connections will be discussed. The twofold motivating role of Mayer in the development of the earliest, ab initio level macromolecular linear scaling methods, giving proven “ab initio quality” protein energy results by the adjustable density matrix assembler method, and in some other molecular fragment advances will be also pointed out.
Specific aspects of the wavefunction model for chemical bonding and its quantum mechanical interpretation are discussed. We treat localized molecular orbitals, limits to their transferability and the Chemical Hamiltonian concept. Linear scaling computation of electron correlation as well as macromolecular methods for the calculation of ab initio quality protein energy results are also discussed shortly.
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BFBNIB, FZAB, GIS, IJS, IZUM, KILJ, NLZOH, NUK, OILJ, PILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK
To date, chemistry has provided more than a hundred million new compounds, most of which are non-natural species that have never existed before and are a source of an enormous amount of pollution. ...With the increased amount of these "man-made" chemicals being synthesised and environmental concerns of chemical processes, chemists have become very aware of these potential risks and dangers. As an answer to this challenge, Green Chemistry emerged and brought with it a list of necessary measures to be followed in the laboratory that has been gradually completed. Herein, we present evidence for the manifestation of two related principles within Green Chemistry: (i)
conservative evolution
, which refers to the observation that throughout the history of the universe, old construction blocks, such as elementary particles, amino acids, or living cells remained conserved while the world evolved in its complexity, and (ii) the practice of
industrial metabolism
that is a manifestation of conservative evolution in human activity referring to the application of biological metabolism in the production of goods for our civilization. Related concepts of Green Chemistry, such as the atom economy, as a metric of green chemistry, the application of safer chemicals and solvents, the utilization of catalysis, the utilization of renewable resources, and
in situ
spectroscopy, are discussed, providing examples to students and researchers from academy to industry involving the work of Professor István T. Horváth.
Chemical substances and processes that play a fundamental role in the 12 principles of Green Chemistry representing conservative evolution and/or industrial metabolism were reviewed.
Most enzyme reactions involve formation and cleavage of covalent bonds, while electrostatic effects, as well as dynamics of the active site and surrounding protein regions, may also be crucial. ...Accordingly, special computational methods are needed to provide an adequate description, which combine quantum mechanics for the reactive region with molecular mechanics and molecular dynamics describing the environment and dynamic effects, respectively. In this review we intend to give an overview to non-specialists on various enzyme models as well as established computational methods and describe applications to some specific cases. For the treatment of various enzyme mechanisms, special approaches are often needed to obtain results, which adequately refer to experimental data. As a result of the spectacular progress in the last two decades, most enzyme reactions can be quite precisely treated by various computational methods.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
Three novel, N-acyl-pro-pyrrolidine-type, inhibitors of prolyl oligopeptidase (POP) with nanomolar activities were synthesized and their binding analyzed to the host enzyme in the light of X-ray ...diffraction and molecular modeling studies. We were interested in the alteration in the binding affinity at the S3 site as a function of the properties of the N-terminal group of the inhibitors. Our studies revealed that, for inhibitors with flat aromatic terminal groups, the optimal length of the linker chain is three C−C bonds, but this increases to four C−C bonds if there is a bulky group in the terminal position. Molecular dynamics calculations indicate that this is due to the better fit into the binding pocket. A 4-fold enhancement of the inhibitor activity upon replacement of the 4-CH2 group of the proline ring by CF2 is a consequence of a weak hydrogen bond formed between the fluorine atom and the hydroxy group of Tyr473 of the host enzyme. There is notably good agreement between the calculated and experimental free energies of binding; the average error in the IC50 values is around 1 order of magnitude.
C1r is a modular serine protease which is the autoactivating component of the C1 complex of the classical pathway of the complement system. We have determined the first crystal structure of the ...entire active catalytic region of human C1r. This fragment contains the C-terminal serine protease (SP) domain and the preceding two complement control protein (CCP) modules. The activated CCP1–CCP2–SP fragment makes up a dimer in a head-to-tail fashion similarly to the previously characterized zymogen. The present structure shows an increased number of stabilizing interactions. Moreover, in the crystal lattice there is an enzyme–product relationship between the C1r molecules of neighboring dimers. This enzyme–product complex exhibits the crucial S1–P1 salt bridge between Asp631 and Arg446 residues, and intermolecular interaction between the CCP2 module and the SP domain. Based on these novel structural information we propose a new split-and-reassembly model for the autoactivation of the C1r. This model is consistent with experimental results that have not been explained adequately by previous models. It allows autoactivation of C1r without large-scale, directed movement of C1q arms. The model is concordant with the stability of the C1 complex during activation of the next complement components.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
Phosphate ester hydrolysis is a key step in several enzymatic processes, which follow either a dissociative or an associative mechanism. While in the aqueous phase both pathways are favoured to about ...the same extent, the associative mechanism is relatively rarely observed. In this paper we report on quantum mechanical calculations for three enzymes HIV integrase, β-phosphoglucomutase and dUTPase, and try to find an explanation for the preference of the associative mechanism in a given enzyme. It is reasonable to suppose that the stabilisation of the pentacovalent, trigonal bipyramidal phosphorane moiety by formation of a covalent bond, one or more hydrogen bonds, or by co-ordination of a divalent metal cation with the equatorial oxygen atoms is the key factor. In all three enzymes studied one of the equatorial oxygen atoms is co-ordinated to a magnesium dication, while a second one is involved in a covalent bond. While in HIV integrase the third oxygen atom may only form a weak hydrogen bond with a solvent water molecule, in β-phosphoglucomutase this atom is stabilised by two strong hydrogen bonds with adjacent protein side chains and in dUTPase it is involved in a covalent bond.
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DOBA, EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, IZUM, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UILJ, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
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