Does the topological approach characterize the hydrogen bond?

 The topological analysis of the electron localization function has been applied to complexes representative of the weak, medium and strong hydrogen bond. For both the weak and the medium hydrogen bonds, the number of basins in the complexes is the sum of those of the moieties. In this case, the formation of a weak or a medium hydrogen-bonded complex does not involve a chemical reaction. In the weak hydrogen bond case, the reduction of the localization domain yields two domains in the first step, which can be partitioned afterwards into valence and core domains. In contrast, for medium complexes the core–valence separation is the first event which occurs during the reduction process and therefore the complex should be considered as a single molecular species. Moreover, the analysis of the basin population variance indicates in this case a noticeable delocalization between the V(A, H) and V(B) basins. Finally, the symmetrical strong hydrogen bond has a protonated basin V(H) at the bond midpoint. Such a topology corresponds to an incomplete proton transfer and to a rather covalent bond. Received: 19 April 1999 / Accepted: 22 July 1999 / Published online: 17 January 2000     

Rearrangement of symmetrical dicubane clusters into topological analogues of the P cluster of nitrogenase: nature's choice?

Reaction schemes have been developed that lead to clusters having the topology of the PN cluster of nitrogenase. The single cubane clusters [(Tp)MFe3S4Cl3]z (M = Mo, z = 1-; M = V, z = 2-) react with PEt3 to give [(Tp)MFe3S4(PEt3)3]1+, which are reduced to the neutral edge-bridged double cubanes [(Tp)2M2Fe6S8(PEt3)4] with highly reduced (2[MFe3S4]1+) cores. Reaction of these clusters in acetonitrile with (Et4N)(HS) results in the formation of [(Tp)2Mo2Fe6S9(SH)2]3- and [(Tp)2V2Fe6S9(SH)2]4-. X-ray structures of the Et4N+ salts reveal the bridging pattern M2Fe6(mu2-S)2(mu3-S)6(mu6-S) in which two cuboidal MFe3(mu3-S)3 units share the common bridge atom mu6-S and are externally bridged by two mu2-S atoms. The M sites possess trigonal octahedral, and the Fe sites, distorted tetrahedral coordination. Hydrosulfide ligands and sulfide atoms simulate terminal cysteinate ligation and mu2 bridges, respectively, in the protein-bound cluster Fe8S7(mu2-SCys)2(SCys)4. The synthetic clusters have the same bridging pattern as the PN cluster and approach congruency with it. These clusters are the first molecular topological analogues of a PN cluster. Like the latter, they are substantially reduced (majority of Fe(II)).     

Phenomenology of polymorphism and topological pressure–temperature diagrams

Although polymorphism of drug molecules is often studied with extensive and excellent experimental data, pressure appears to be a forgotten variable. In this article, an analysis is provided of the phase behavior of Atovaquone using available literature data. A pressure–temperature diagram is constructed topologically by way of the Clapeyron equation. The method leads to the conclusion that Atovaquone phase I and III behave enantiotropically, like α- and β-sulfur do in their paradigmatic P–T diagram, and that phase I is stable at room temperature and under “ordinary” pressure.     

Effect of γ-irradiation on the molecular–topological structure of a copolymer of tetrafluoroethylene and perfluoro(propyl vinyl ether)

The molecular–topological structure of a copolymer of tetrafluoroethylene and perfluoro(propyl vinyl ether) before and after γ-irradiation has been studied for the first time. The pseudo-network structure of the copolymer contains an amorphous block and the crystalline segments of macromolecules serve as branching points. After γ-irradiation to a dose of 15 to 2380 kGy, polyassociative cluster-type entities have appeared in the initial copolymer in place of the crystalline branching points with simultaneous structure amorphization and a decrease in the onset temperature of molecular flow.     

Features of the molecular–topological structure of γ-irradiated powdered tetrafluoroethylene–perfluoro(propyl vinyl ether) copolymer

With the use of thermomechanical spectrometry in two modes, coaxial, when the load application vector is coplanar with the compacting pressure vector (semicrystalline copolymer) during the measurement of the deformation of a copolymer of tetrafluoroethylene with perfluoro(propyl vinyl ether), and mutually perpendicular (completely amorphous copolymer), it has been established that the axial compression of the copolymer brought its topological structure to an absolutely anisotropic state. After γ-irradiation, the semicrystalline structure of the copolymer was retained regardless of the radiation dose. The minimum values of the glass transition temperature of the amorphous block and the degree of crystallinity were observed in the copolymer irradiated to a dose of 150 kGy. The molecular weight distribution functions of interjunction chains in the networks of the amorphous blocks of the initial copolymer and its γ-irradiated analogs are bimodal.     

Effect of γ-irradiation and thermal annealing on the molecular–topological structure of a copolymer of tetrafluoroethylene and perfluoro(propyl vinyl ether)

The molecular–topological structure of a copolymer of tetrafluoroethylene and perfluoro(propyl vinyl ether) subjected to γ-irradiation and thermal annealing has been studied for the first time with the use of thermomechanical spectrometry. The pseudonetwork structure of the copolymer contains an amorphous block (interjunction chains) and crystalline segments (branching points). The diblock amorphous and crystalline structure with a crystal structure fraction of 0.21 transformed into an almost completely amorphous structure with a crystallite fraction of 0.06 after the irradiation of the copolymer at a dose of 600 kGy. Thermal annealing at 483 K formed a new structure: a high-temperature amorphous block.     

Fully analytical integration over the 3D volume bounded by the β sphere in topological atoms

Atomic properties of a topological atom are obtained by 3D integration over the volume of its atomic basin. Algorithms that compute atomic properties typically integrate over two subspaces: the volume bounded by the so-called β sphere, which is centered at the nucleus and completely contained within the atomic basin, and the volume of the remaining part of the basin. Here we show how the usual quadrature over the β sphere volume can be replaced by a fully analytical 3D integration leading to the atomic charge (monopole moment) for s, p, and d functions. Spherical tensor multipole moments have also been implemented and tested up to hexadecupole for s functions only, and up to quadrupole for s and p functions. The new algorithm is illustrated by operating on capped glycine (HF/6-31G, 35 molecular orbitals (MOs), 322 Gaussian primitives, 19 nuclei), the protein crambin (HF/3-21G, 1260 MOs, 5922 primitives and 642 nuclei), and tin (Z = 50) in Sn(2)(CH(3))(2) (B3LYP/cc-pVTZ and LANL2DZ, 59 MOs, 1352 primitives).     

Can QTAIM topological parameters be a measure of hydrogen bonding strength?

The block-localized wave function (BLW) method, which is the simplest variant of ab initio valence bond (VB) theory, together with the quantum theory of atoms in molecules (QTAIM) approach, have been used to probe the intramolecular hydrogen bonding interactions in a series of representative systems of resonance-assisted hydrogen bonds (RAHBs). RAHB is characteristic of the cooperativity between the π-electron delocalization and hydrogen bonding interactions and is identified in many biological systems. While the deactivation of the π resonance in these RAHB systems by the use of the BLW method is expected to considerably weaken the hydrogen bonding strength, little change on the topological properties of electron densities at hydrogen bond critical points (HBCPs) is observed. This raises a question of whether the QTAIM topological parameters can be an effective measure of hydrogen bond strength.     

SIMS accurate determination of matrix composition of topological crystalline insulator material Pb1 − xSnxSe

Substitutional alloy Pb_1 − xSn_xSe is a new class of electronic materials called topological crystalline insulators, which at the temperature range from 0 K to 300 K exhibit topological state at compositions in the range 0.18 < x < 0.40 (in the rock-salt structure). In this report, we present a secondary ion mass spectrometry (SIMS) analysis technique to provide accurate Pb and Sn composition based on the measurement of PbCs⁺ and SnCs⁺ cluster ions intensities. Studies of Pb_1 − xSn_xSe bulk samples with various values of x show that x/(1 − x) is linear in relation to the intensity ratio of PbCs⁺/SnCs⁺ over the range from x = 0.15 to x = 0.41. This technique allows us to obtain an accurate Sn content for multilayered heterostructures, quantum wells containing Pb_1 − xSn_xSe with different x values for each layer.     

The influence of protecting the hydroxyl group of β-oxy-α-diazo carbonyl compounds in the competition between Wolff rearrangement and [1,2]-hydrogen shift. Density functional theory study and topological analysis of the charge density

The influence of protecting the hydroxyl group of a β-oxy-α-diazo carbonyl compound on the competition between the Wolff rearrangement (WR) and the [1,2]-hydrogen shift (HS) was investigated theoretically. Stationary points on the potential-energy surface were located with the B3LYP density functional and the 6-31G** basis set. For the basic system geometry optimisations at B3LYP/6-311+G** were performed to validate the reliability of the B3LYP/6-31G** calculations. Single-point energy calculations were carried out at the B3LYP/6-311+G** level on the B3LYP/6-31G**-optimised geometries. Further insight into the processes was achieved with the aid of the theory of “atoms in molecules” of Bader. The calculated energy barriers qualitatively predicted the yields of HS and WR obtained experimentally. In order to rationalise the calculated energy barriers, it was necessary to take into account not only the electronegativity of the protective groups but also the alignment of the migrating groups with the depletion sites at the carbene centre. Further, when the hydroxyl group was not protected the existence of an intramolecular hydrogen bond played an important role in both HS and WR. Received: 30 December 1998 / Accepted: 7 May 1999 / Published online: 4 October 1999     

Single-step preparation of topological gels using vinyl-modified β-cyclodextrin as a figure-of-six cross-linker

Herein, we have proposed a single-step preparation of topological gels using vinyl-modified β-cyclodextrin (V-β-CyD) and isoprene. Copolymerization of V-β-CyD and isoprene in an aqueous solution resulted in gelation due to V-β-CyD acting as a novel type of copolymer chain cross-linker. The vinyl moiety of V-β-CyD becomes a part of the copolymer, while the β-CyD moiety of V-β-CyD simultaneously incorporates the isoprene component of the copolymer. V-β-CyD is capable of two different modes of cross-linking at each end, i.e., chemically bonding and mechanically interlocking. Due to the shape of the cross-linking point, we refer to it as figure-of-six cross-linking. Nuclear magnetic resonance analysis showed that the gel contained V-β-CyD and isoprene in an approximately 1:0.3 stoichiometry. The relatively high content of β-CyD was reflected in the character of the gel; the gel swelled in dimethylformamide which is a good solvent of β-CyD. A fluorometric analysis using 6-(p-toluidino)-2-naphthalenesulfonic acid showed that the appended β-CyD was able to accommodate guest molecules. Introduction of an additional vinyl monomer into the gel was also successful. Addition of 4-vinylphenylboronic acid to the preparation procedure yielded a sugar-responsive gel that swelled in the presence of d-fructose.     

Theory of cluster self-organization of crystal-forming systems: geometrical–topological modeling of nanocluster precursors with a hierarchical structure

The current state of the art related with the self-organization of crystal-forming systems, where long-range order spontaneously appears in the arrangement of structural units of any nature (micro- and macromolecules or atomic clusters), is considered. Three partially overlapping stages of self-organization of a system accepted in physical models of ??order?Cdisorder?? kinetic transitions are matched to those used in supramolecular chemistry. An algorithmically constructed model of transition from disordered to hierarchically ordered systems is considered. The geometrical and topological modeling of density fluctuations of n-atomic species (clusters) A_n in a crystal-forming medium is carried out. Clusters A_n of a higher level of the system self-organization (the time moment t_i) were determined as assemblies of specially selected clusters at the lower level (the time moment t_(i?1)). Such clusters are built of equivalent clusters and, therefore, have a hierarchical structure; i.e., the simplest clusters are integrated into the clusters of the next higher level. Also, the mechanism of self-assembly of symmetrically and topologically different chains and microlayers (in the form of planar nets) from cyclic clusters A_n is considered in the model system. The 45 obtained nets correspond to 11 uninodal Shubnikov nets and new binodal nets. Algorithms are presented for combinatorial and topological analysis to search for precursor clusters and restore a three-dimensional net of covalent and non-covalent bonds in a crystal structure by the matrix (cluster) self-assembly mechanism. The developed model is universal. The mechanism of self-assembly has been modeled for O₃ (ozone), C₆H₆ (benzene), C₂H₂ (acetylene), NaAlSi₃O₈ (albite), K_2.25Na_0.31Ca_2.25Ba_1.44 (Al_11.5Si_30.5O₈₄H_1.4) (H₂O)₂₅ (paulingite, PAU), B(OH)₃, H₃B₃O₆, H₂SeO₃, the Friauf?CLaves structure family(which counts in 1,400 of binary and ternary compounds): MgCu₂ (cF24), MgZn₂ (hP12), and MgNi₂ (hP24), the icosahedral structures: B₁₂, C₂₀H₂₀, C₆₀, ZrZn₂₂ (cF184), and NaCd₂ (cF1192) Samson Phase.     

Large-scale prediction of drug–target interactions using protein sequences and drug topological structures

The identification of interactions between drugs and target proteins plays a key role in the process of genomic drug discovery. It is both consuming and costly to determine drug–target interactions by experiments alone. Therefore, there is an urgent need to develop new in silico prediction approaches capable of identifying these potential drug–target interactions in a timely manner. In this article, we aim at extending current structure–activity relationship (SAR) methodology to fulfill such requirements. In some sense, a drug–target interaction can be regarded as an event or property triggered by many influence factors from drugs and target proteins. Thus, each interaction pair can be represented theoretically by using these factors which are based on the structural and physicochemical properties simultaneously from drugs and proteins. To realize this, drug molecules are encoded with MACCS substructure fingerings representing existence of certain functional groups or fragments; and proteins are encoded with some biochemical and physicochemical properties. Four classes of drug–target interaction networks in humans involving enzymes, ion channels, G-protein-coupled receptors (GPCRs) and nuclear receptors, are independently used for establishing predictive models with support vector machines (SVMs). The SVM models gave prediction accuracy of 90.31%, 88.91%, 84.68% and 83.74% for four datasets, respectively. In conclusion, the results demonstrate the ability of our proposed method to predict the drug–target interactions, and show a general compatibility between the new scheme and current SAR methodology. They open the way to a host of new investigations on the diversity analysis and prediction of drug–target interactions.     

Construction of the Skeleton of Phthalascidin, Mechanism of the Formation of the Key Tricyclic Lactam Intermediate

Phthalascidin is a structurally simplified version of Et-743, which is a potent anti-tumor marine natural product isolated from Ecteinascidia turbinata. Its antiproliferative activity is greater than that of the agents taxol, camptothecin, adriamycin, mitomycin C, cisplatin, bleomycin, and etoposide by 1-3 orders of magnitude. An elegant synthesis of Et-743 and phthalascidin has been reported by E. J. Corey and co-workers1,2. As part of our continuing program, we have also engaged in dev…     

Studies of the dissociation and the protonation of TB-chlorosulphophenol

The dissociation constant of each step for TB-chlorosulphophenol has been determined by potentiometric method, and the thermodynamic constants, △G°, △H° and △S°, of the dissociation process have been calculated. The protonation constants were measured by the spectrophotometric method. The pH values of various forms of anions of the chromogenic reagent at their concentrations were also calculated.