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Representation of molecular structures of organoelement compounds as hypergraphs with different degrees of detailing and different types of labels is considered. As opposed to the graph model, the hypergraph model contains not only ordinary edges connecting pairs of vertices and corresponding to ordinary covalent bonds but also hyperedges, each connecting more than two vertices and corresponding to delocalized multicenter bonds. Symbolic, numerical, and structural labels are proposed as labels of hypergraph vertices and edges. Structural labels involve substitutions and transformations on the sets of vertices and edges of a hypergraph. Choosing a method of representation is determined by conditions of a particular problem. Institute of Mathematics, Siberian Branch, Russian Academy of Sciences (Novosibirsk). Translated fromZhurnal Strukturnoi Khimii, Vol. 39, No. 2, pp. 328–337, March–April, 1998.  相似文献   

3.
An algorithm, based on "vertex priority values" has been proposed to uniquely sequence and represent connectivity matrices of chemical structures of cyclic/acyclic functionalized achiral hydrocarbons and their derivatives. In this method, "vertex priority values" have been assigned in terms of atomic weights, subgraph lengths, loops, and heteroatom contents. Subsequently, the terminal vertices have been considered upon completing the sequencing of the core vertices. This approach provides a multilayered connectivity graph, which can be put to use in comparing two or more structures or parts thereof for any given purpose. Furthermore, the basic vertex connection tables generated here are useful in the computation of characteristic matrices/topological indices and automorphism groups and in storing, sorting, and retrieving chemical structures from databases.  相似文献   

4.
A new algorithm is proposed for approximation to the molecular surface. It starts with a triangular mesh built on an ellipsoid embracing the whole molecular surface. The triangular mesh is obtained from an icosahedron subdivision sphere with highly uniform vertex distribution, and the embracing surface is deflated stepwise to the best adherence of its triangles onto the surface of the molecule. The deflating direction of each vertex of a triangle is defined by the vector normal at this point to the previous deflated embracing surface. Our results show that the speed of the triangulation embracing ellipsoid method and the quality of the surface obtained by the method are faster and better than the method that starts with a quadrilateral mesh built from meridian and parallel representations on an embracing sphere to get the molecular surface. Furthermore, the surface obtained by the method can be used directly to approximate the molecular surface by spherical harmonic expansions. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1805–1815, 1998  相似文献   

5.
A new canonical coding method for representation of three-dimensional structures, CAST (CAnonical representation of STereochemistry), is described. CAST canonically codes stereochemistry around an atom in a molecule. The same CAST notations are given for atoms of molecules in the same conformation. The CAST code is based on the dihedral angles of four atoms that are uniquely defined by a molecular tree structure. CAST has successfully represented similarities and differences between several conformers.  相似文献   

6.
Summary A triangulation algorithm for a dotted surface (i.e. a surface defined by point coordinates in three dimensions) is given. The individual triangles are generated on the basis of a hierarchy of strategies according to increasing surface complexity. While for small molecules an elementary algorithm is sufficient to triangulate the surface, large molecules-like proteins-generally need all steps of the hierarchy. Although this program has been developed with the aim of triangulating molecular surfaces, it can in principle be applied to any surface defined by 3D point coordinates.  相似文献   

7.
The combinatorial-topological modeling of 3D periodic packings of layers composed of T12 polyhedral clusters (t-hpr tiles in the form of hexagonal prisms) was carried out. The T12 clusters are among the most abundant units in the crystal structures of zeolites. The layers were produced by decoration of the vertices of the square and hexagonal (graphite-like) nets with T12 clusters. All combinatorially possible patterns of 3D frameworks, which were constructed based on packings of decorated square nets, correspond to known zeolite structures: CHA (mineral chabazite, Ca6(H2O)40Al12Si24O72), AEI (AlPO-18, Al24P24O96), SAV ((C18H42N6)2(H2O)7Mg5Al19P24O96), and KFI (Na30(H2O)98Al30Si66O192). The modeling using the same scheme and a decorated hexagonal net gave rise to the frameworks of three known zeolites, GME (gmelinite, (Ca,Na)4(H2O)24Al8Si16O48), AFX (SAPO-56, H3Al23Si5P20O96), and AFT (AlPO-52, Al36P36O144), as well as of one previously unknown hypothetical zeolite ISC-2 with the unit cell parameters a = 13.90 Å, c = 30.00 Å, V = 5019.7 Å3, sp. gr. \(P\bar 6m2\). Zeolite ISC-2 contains a cavity with a new t-isc-2 topology [421.62.815], which is responsible for its unique framework. An analysis of the specially created database of topological types of molecules (TTM collection) containing geometric and topological characteristics of more than 300000 different molecules suggested an organic structure-directing agent, which stabilizes the t-isc-2 cavity and which can be used for the synthesis of ISC-2.  相似文献   

8.
A “frozen-orbital” diabatic basis has been constructed for an impact parameter treatment of collisions of He+ with metastable He(23S) at 1000 eV laboratory ion energy. Except for the two highest states used, the diabatic states correlate very well with the separated-atom energies, and the Σ-Π rotational couplings deviate little from the proper asymptotic behaviour (≈R?2). Cross sections and transition probabilities are presented for some elastic and inelastic channels.  相似文献   

9.
We here report a unique cyclic peptide structure, "helix triangle", as a unique example of peptide-based molecular architecture. The cyclic peptide is designed to have a triangular shape in which three 9mer helical peptide units make the sides and three pyrene derivatives make the apexes. The helical peptide units are ideally linear, and the pyrene units are ideal 60 degrees angular components. The yield of the cyclic peptide was relatively high despite its large cycle size. Absorption and fluorescence spectroscopy revealed that the three pyrene units do not interact with each other electronically, and circular dichroism spectroscopy indicated that the helical peptide units take 3(10)-helical conformation. Geometry optimization by the semi-empirical molecular orbital method gave a triangular structure with 3(10)-helices as the plausible molecular structure. To gain more information on the geometry and demonstrate one example of its self-assemblies, the monolayer of the cyclic peptide was prepared at the air/water interface, and its surface pressure-molecular area isotherm was studied. The isotherm indicated formation of a stable monolayer and suggested that the cyclic peptide actually takes the triangular structure predicted by the geometry optimization. The monolayer was then transferred onto a substrate and characterized by various methods. Ellipsometry and infrared reflection-absorption spectroscopy confirmed that the cyclic peptide has horizontal orientation to the surface in the monolayer. Furthermore, absorption and fluorescence spectroscopy showed that the isolated electronic properties of the pyrene units are intact even in a condensed state in the monolayer.  相似文献   

10.
We propose a 4-D representation of RNA secondary structures. The four-dimensional representation resolves structures’ degeneracy and avoids loss of information and the limitation that different structures correspond the same plot set (or presentation). The RNA pseudoknpts also can be represented as four-dimensional representations. Based on this representation, we outline an approach to compute the similarities between six RNA secondary structures for illustrating the utility of our approach.  相似文献   

11.
Summary A non-local representation of the effective potential due to a molecular fragment is proposed here. Using this technique one can reproduce both Coulomb and exchange operators with kernels made up by molecular orbitals localized on a given molecular fragment. Such an approach seems particularly effective for large molecules with well-defined chemical fragments since in this case the kernel orbitals can be prepared through separate calculations on each fragment. The performance of the method is illustrated through calculations on specific molecular examples.  相似文献   

12.
A new Tamm–Dancoff method for the ground and excited states of molecular electronic systems is developed. The method begins with a number-projected BCS (PBCS ) wave function and is generated by excitations of particle pairs from the degenerate geminals in the PBCS wave function. A direct optimization of the PBCS wave function is accomplished with successive Bogoliubov transformations so that one-pair excitation terms in the Tamm-Dancoff expansion of the ground state vanish (the generalized Brillouin theorem). The spin-symmetry adapted first- and second-order Tamm–Dancoff bases and matrix elements are calculated by means of the CI expansion of the PBCS wave function with natural orbitals that diagonalize the BCS geminal matrix. Numerical calculations are presented for the H4 system with D2h and D4h conformations and for methylene. The PBCS wave function is not a very good approximation for the ground state, accounting for only about half of the correlation energy. The second-order Tamm–Dancoff correction improves the result as much as the double excitation CI . The Tamm–Dancoff terms consisting of two triplet pairs coupled to a singlet, and those relaxing the constraint imposed on the pairwise excitations in the PBCS wave function are important.  相似文献   

13.
Within the last decade, the advance of miniaturization has opened the window to new systems that permit digital and molecular science to intersect, suggesting a new role for organic chemistry. Currently, fusion of molecules and electronic digits, as well as molecular-based digital structures, have expanded the conventional interpretation of the digit. This emergence has already generated new technological platforms with unique applications for molecular analysis and computation. We provide a brief overview of the conventional understanding of digital devices, examine the concept of molecular-based digits, and suggest new architectures by examining studies conducted on the compact discs. This analysis presents a perspective for the unique interaction of molecules and digits and the development of digital-based platforms for molecular analysis.  相似文献   

14.
A number of force fields of the molecular mechanics type have been tested for their ability to represent as an energy minimum, the observed crystal structure for three cyclic hexapeptides, cyclo-(-Ala-Ala-Gly-Gly-Ala-Gly-), cyclo-(-Ala-Ala-Gly-Gly-Ala-Gly-), and cyclo-(-D-Ala-D-Ala-Gly-Gly-Gly-Gly-). The most effective force field tested was that recently proposed by Kollman and co-workers, notwithstanding its use of “united” atoms for CH, CH2, and CH3 groups. Fields proposed by Levitt, and adaptations of that of Scheraga and co-workers, were also effective. Force fields in which hydrogens bonded to electronegative atoms were not specified explicitly were less accurate in representation.  相似文献   

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The photodissociation and low-energy collision-induced dissociation of p-nitrotoluene and p-ethylnitrobenzene molecular ions were studied using Fourier transform ion cyclotron resonance mass spectrometry. The dissociation of these ions is highly dependent on the time-scale of the experiment and the pressure of the nitroaromatic compound. Collisions of the ions with nitroaromatic neutral species increase the abundance of fragment ions due to NO elimination, while collisions with inert gases such as sulfur hexafluoride and argon have no effect. Evidence is presented for the occurrence of an ion–molecule reaction between p-alkylnitrobenzene ions and nitroaromatic neutral species that induces isomerization of the ion. This isomerization is proposed to involve a nitro-to-nitrite rearrangement. Although the mechanism of this process is unknown, isotopic labeling experiments have shown that it does not involve nitrogen atom transfer between the two reactants. The dissociations of o-nitrotoluene, m-nitrotoluene and nitrobenzene ions are also discussed. For these ions, no pressure- or time-scale-dependent behavior was observed, indicating that an isomerization did not occur.  相似文献   

17.
A. N. Nesmeyanov Institute of Organometallic Chemistry. Translated from Zhurnal Strukturnoi Khimii, Vol. 29, No. 1, pp. 26–31, January–February, 1988.  相似文献   

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19.
In calixarene chemistry there is a continuous search for new shaping units or substructures useful for molecular recognition or for the binding of ions. The problem of assigning their molecular conformations cannot be dealt with by the use of the dihedral angles as done until now, because this method contains intrinsic ambiguities. The new approach, proposed here, is based on the use of the set ofn pairs of torsion angles (conformational parameters) which involve the flexible part of the calixarene and it is free of ambiguities. Moreover, knowledge of the set of conformational parameters allows one to build straightforwardly three-dimensional molecular models. A symbolic representation of the molecular conformation of any calix[n]arene may be obtained by combining the Schöenflies symbol of the molecular symmetry together with the signs of the conformational parameters.  相似文献   

20.
Additivity models have been widely employed to approximate unknown molecular properties based on previously measured or calculated data for similar molecules. This paper proposes an improved formulation of additivity, which is based on high-dimensional model representation (HDMR). HDMR is a general function-mapping technique that expresses the output of a multivariate system in terms of a hierarchy of cooperative effects among its input variables. HDMR rests on the general observation that, for many physical systems, only relatively low-order input variable cooperativity is significant. A molecule is expressed as a multivariate system by defining binary-valued input variables corresponding to the presence or absence of a chemical bond, with the molecular property as the output. Conventional additivity decomposes a molecular property into contributions from nonoverlapping subcomponents of fixed size. On the other hand, HDMR decomposes a molecular property into the exact contributions from the full hierarchy of its variable-sized subcomponents and contains additivity as a special case. The complete hierarchical structure of HDMR can in many cases lead to a much more accurate estimate than conventional additivity. Also, when full group additivity is not possible, HDMR gives an expression for a lower-order approximation for the missing group additivity value, greatly expanding the scope of HDMR compared to additivity. The component terms in an HDMR approximation have well-defined physical significance. Moreover, HDMR gives an exact expression for the truncation error in any given HDMR approximation, also with a well-defined physical significance. The HDMR model is tested for the enthalpy of formation of a broad range of organic molecules, and its advantages over additivity are illustrated.  相似文献   

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