The development of a knowledge base for basic active structures: an example case of dopamine agonists

<p>Abstract</p> <p>Background</p> <p>Chemical compounds affecting a bioactivity can usually be classified into several groups, each of which shares a characteristic substructure. We call these substructures "basic active structures" or BASs. The extraction of BASs is challenging when the database of compounds contains a variety of skeletons. Data mining technology, associated with the work of chemists, has enabled the systematic elaboration of BASs.</p> <p>Results</p> <p>This paper presents a BAS knowledge base, BASiC, which currently covers 46 activities and is available on the Internet. We use the dopamine agonists D1, D2, and Dauto as examples and illustrate the process of BAS extraction. The resulting BASs were reasonably interpreted after proposing a few template structures.</p> <p>Conclusions</p> <p>The knowledge base is useful for drug design. Proposed BASs and their supporting structures in the knowledge base will facilitate the development of new template structures for other activities, and will be useful in the design of new lead compounds via reasonable interpretations of active structures.</p

Exchange Interaction in Binuclear Complexes with Rare Earth and Copper Ions: A Many-Body Model Study

We have used a many-body model Hamiltonian to study the nature of the magnetic ground state of hetero-binuclear complexes involving rare-earth and copper ions. We have taken into account all diagonal repulsions involving the rare-earth 4f and 5d orbitals and the copper 3d orbital. Besides, we have included direct exchange interaction, crystal field splitting of the rare-earth atomic levels and spin-orbit interaction in the 4f orbitals. We have identified the inter-orbital $4f$ repulsion, U$_{ff}$ and crystal field parameter, $\Delta_f$ as the key parameters involved in controlling the type of exchange interaction between the rare earth $4f$ and copper 3d spins. We have explored the nature of the ground state in the parameter space of U$_{ff}$, $\Delta_f$, spin-orbit interaction strength $\lambda$ and the $4f$ filling n$_f$. We find that these systems show low-spin or high-spin ground state depending on the filling of the $4f$ levels of the rare-earth ion and ground state spin is critically dependent on U$_{ff}$ and $\Delta_f$. In case of half-filling (Gd(III)) we find a reentrant low-spin state as U$_{ff}$ is increased, for small values of $\Delta_f$, which explains the recently reported apparent anomalous anti-ferromagnetic behaviour of Gd(III)-radical complexes. By varying U$_{ff}$ we also observe a switch over in the ground state spin for other fillings . We have introduced a spin-orbit coupling scheme which goes beyond L-S or j-j coupling scheme and we find that spin-orbit coupling does not significantly alter the basic picture.Comment: 22 pages, 11 ps figure

Structural and Electronic Instabilities in Polyacenes: Density Matrix Renormalization Group Study of a Long--Range Interacting Model

We have carried out Density Matrix Renormalization Group (DMRG) calculations on the ground state of long polyacene oligomers within a Pariser-Parr-Pople (PPP) Hamiltonian. The PPP model includes long-range electron correlations which are required for physically realistic modeling of conjugated polymers. We have obtained the ground state energy as a function of the dimerization $\delta$ and various correlation functions and structure factors for $\delta=0$. From energetics, we find that while the nature of the Peierls' instabilityin polyacene is conditional and strong electron correlations enhance the dimerization. The {\it cis} form of the distortion is favoured over the {\it trans} form. However, from the analysis of correlation functions and associated structure factors, we find that polyacene is not susceptible to the formation of a bond order wave (BOW), spin density wave (SDW) or a charge density wave (CDW) in the ground state.Comment: 31 pages, latex, 13 figure

Application of the PM6 method to modeling the solid state

The applicability of the recently developed PM6 method for modeling various properties of a wide range of organic and inorganic crystalline solids has been investigated. Although the geometries of most systems examined were reproduced with good accuracy, severe errors were found in the predicted structures of a small number of solids. The origin of these errors was investigated, and a strategy for improving the method proposed

Functional Group and Substructure Searching as a Tool in Metabolomics

BACKGROUND: A direct link between the names and structures of compounds and the functional groups contained within them is important, not only because biochemists frequently rely on literature that uses a free-text format to describe functional groups, but also because metabolic models depend upon the connections between enzymes and substrates being known and appropriately stored in databases. METHODOLOGY: We have developed a database named "Biochemical Substructure Search Catalogue" (BiSSCat), which contains 489 functional groups, >200,000 compounds and >1,000,000 different computationally constructed substructures, to allow identification of chemical compounds of biological interest. CONCLUSIONS: This database and its associated web-based search program (http://bisscat.org/) can be used to find compounds containing selected combinations of substructures and functional groups. It can be used to determine possible additional substrates for known enzymes and for putative enzymes found in genome projects. Its applications to enzyme inhibitor design are also discussed

The correspondence between the molecular orbital and differential ionization energies methods

The correspondence between Self-Consistent Hückel MO methods and Differential Ionization Energies methods is discussed in terms of the approximations used for the diagonal matrix elements. The two methods are shown to be equivalent if electronic correlation is neglected. Ground-state properties of the hydrogen halides are calculated by these simple methods and shown to be in good overall agreement with experimental data. Die Übereinstimmung zwischen selbstkonsistenten Hückel MO-Methoden und Methoden der Differentiellen Ionisierungsenergien wird in Termen solcher Näherungen diskutiert, die für die diagonalen Matrixelemente benutzt werden. Es wird gezeigt, daß die beiden Methoden äquivalent sind, wenn die Elektronenkorrelation vernachlässigt wird. Grundzustandseigenschaften der “hydrogen halides” werden mit diesen einfachen Methoden ausgerechnet und zeigen sich in überall guter Übereinstimmung mit experimentellen Daten. La correspondance entre les méthodes SCF Hückel et d'énergie d'ionisation différentielle est discutée en fonction des approximations utilisées pour les éléments de matrice diagonaux. Les deux méthodes sont équivalentes si la corrélation électronique est négligée. Les propriétés de l'état fondamental des acides halogènés sont calculées par ces méthodes simples et l'on constate un accord raisonnable avec les données expérimentales.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/46451/1/214_2004_Article_BF00572780.pd