Chemical applications of group theory and topology

The following procedure is described for investigating the qualitative dynamics of simple chemical systems: 1) A so-called influence diagram is generated representing the relationships between the reference reactants (phase-determining intermediates); 2) This influence diagram is used to generate a truth table indicating possible transitions between state vectors representing the signs of the time derivatives of of the reference reactant concentrations; 3) The truth table is used to determine a state transition diagram representing the flow topology around unstable equilibrium points; 4) The characteristic equation of the adjacency matrix of the influence diagram is solved in order to determine the presence of such unstable equilibrium points. The two types of qualitative dynamics possible for chemical systems containing two reference reactants and one feedback circuit are bifurcation between two attracting regions (bistability) and limit cycle oscillation. However, in two reference reactant systems oscillation requires an additional self-activating loop to generate the unstable equilibrium point required for its realization. Bistability and limit cycle oscillation are also two of the possible types of qualitative dynamics for chemical systems containing three reference reactants. However, chemical systems with three reference reactants and two or more feedback circuits can also contain interlocking limit cycles, which can lead to toroidal oscillations or chaos. The influence diagrams are given for the systems exhibiting these various types of dynamic behavior along with a summary of the important properties of all 729 possible influences for simple chemical systems containing three reference reactants.     

The importance of nonconventional structures in the binding of Ni<Superscript>+</Superscript> to ethynylsilanes and ethynylgermanes

The influence of the nature of the heteroatom on the Ni⁺ gas-phase binding energies of HCC–XH₃ (X is C, Si, or Ge) compounds has been investigated through the use of high-level density functional theory methods. The structures of the corresponding Ni⁺ complexes were optimized at the B3LYP/6-311G(d,p) level of theory. Final energies were obtained in single-point B3LYP/6-311+G(2df,2p) calculations. Nonconventional complexes, in which the metal cation interacts simultaneously with the CC system and with one of the X–H bonds of the substituent XH₃ group, play a significant role in the binding of Ni⁺ to HCC–XH₃ (X is Si or Ge) derivatives. Conversely, such nonconventional complexes are not local minima of the propyne–Ni⁺ potential-energy surface. This establishes a clear distinction between unsaturated carbon derivatives and the Si- and Ge-containing analogues as far as bonding to transition-metal monocations is concerned. Actually, the attachment of Ni⁺ to HCC–XH₃ (X is Si or Ge) compounds in the gas phase yields a mixture of conventional and nonconventional complexes. These agostic-type interactions can be viewed as a dative bond from the X–H bonding orbital toward the empty s orbital of the metal, and a back-donation from the valence electron pairs of the metal into the X–H antibonding orbital of the neutral species.Proceedings of the 11th International Congress of Quantum Chemistry satellite meeting in honor of Jean-Louis Rivail     

Highly conformationally constrained halogenated 6-spiroepoxypenicillins as probes for the bioactive side-chain conformation of benzylpenicillin

Summary The halogenated 6-spiroepoxypenicillins are a series of novel semisynthetic-lactam compounds with highly conformationally restricted side chains incorporating an epoxide. Their biological activity profiles depend crucially on the configuration at position C-3 of that epoxide. In derivatives with aromatic-containing side chains, e.g., anilide, the 3R-compounds possess notable Gram-positive antibacterial activity and potent-lactamase inhibitory properties. The comparable 3S-compounds are antibacterially inactive, but retain-lactamase inhibitory activity.Using the molecular simulation programs COSMIC and ASTRAL, we attempted to map a putative, lipophilic accessory binding site on the PBPs that must interact with the side-chain aromatic residue. Comparative computer-assisted modelling of the 3R, and 3S-anilides, along with benzylpenicillin, indicated that the available conformational space at room temperature for the side chains of the 3R and the 3S-anilides was mutually exclusive. The conformational space for the more flexible benzylpenicillin could accommodate the side chains ofboth the constrained penicillin derivatives. By a combination of van der Waals surface calculations and a pharmacophoric distance approach, closely coincident conformers of the 3R-anilide and benzylpenicillin were identified. These conformers must be related to the antibacterial, bioactive conformer for the classical-lactam antibiotics. From these proposed bioactive conformations, a model for the binding of benzylpenicillin to the PBPs relating the three-dimensional arrangement of a putative lipophilic S₂-subsite, specific for the side-chain aromatic moiety, and the 3-carboxylate functionality is presented.This work has been reported in preliminary form at the 4th Royal Society of Chemistry International Symposium on Recent Advances in the Chemistry of-lactam Antibiotics, Churchill College, Cambridge, U.K., 3–6 July 1988.     

RNA Methylation m6A: A New Code and Drug Target?

The m⁶A‐RNA modification is a dynamic and reversible process, which has emerged as a new RNA code for the regulation of gene expression. The functional network of methyltransferases (writers), demethylases (erasers), and binding proteins (readers) modulate the level of m⁶A modification. Dysfunction of RNA methylation has been associated with various fundamental biological processes and human diseases. Herein, we briefly introduce an understanding‐enabled manipulation on m⁶A‐RNA modification with an emphasis on the use of small‐molecule intervention.      

Reaction of 4,4′-dimethyldiphenyl ether with phosphorus trichloride in the presence of anhydrous aluminum chloride

The reaction of 4,4-dimethyldiphenyl ether with phosphorus trichloride in the presence of anhydrous aluminum chloride was studied. This reaction affords 2,8-dimethyl-10H-10⁵-phenoxaphosphine 10-oxide as virtually the only product. In air, the latter in an alkaline solution is quantitatively transformed into 10-hydroxy-2,8-dimethyl-10H-10⁵-phenoxaphosphine 10-oxide.__________Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 12, pp. 2762–2765, December, 2004.     

双峰倍增配平法用于同步、导数-同步荧光法同时测定邻羟基苯甲酸和间羟基苯甲酸

邻羟基苯甲酸（ｏＨＢＡ）和间羟基苯甲酸（ｍＨＢＡ）荧光光谱严重重叠，同步及导数技术虽使选择性有所改善，但仍不能完全分辨开重叠谱。用双峰倍增配平计算法结合同步、一阶导数－同步荧光法对双组分体系（邻羟基苯甲酸／间羟基苯甲酸，ｐＨ１２介质）同时测定。结合计算的两种测定方法精密度、回收率和不同组分间浓度比范围均优于一阶导数－同步荧光法。     

On the singular graph and the Weyr characteristic of anM-matrix

LetA be anM-matrix in standard lower block triangular form, with diagonal blocksA _ii irreducible. LetS be the set of indices such that the diagonal blockA is singular. We define the singular graph ofA to be the setS with partial order defined by > if there exists a chain of non-zero blocksA _i, A_ij, , A_l.Let ₁ be the set of maximal elements ofS, and define thep-th level _p ,p = 2, 3, , inductively as the set of maximal elements ofS \( _{1 p-1}). Denote by _p the number of elements in _p . The Weyr characteristic (associated with 0) ofA is defined to be (A) = ( ₁, ₂,, _h ), where ₁ + + _p = dim KerA ^p ,p = 1, 2, , and _h > 0, _h+1 = 0.Using a special type of basis, called anS-basis, for the generalized eigenspaceE(A) of 0 ofA, we associate a matrixD withA. We show that(A) = ( ₁, , _h) if and only if certain submatricesD _p,p+1 ,p = 1, , h – 1, ofD have full column rank. This condition is also necessary and sufficient forE(A) to have a basis consisting of non-negative vectors, which is a Jordan basis for –A. We also consider a given finite partially ordered setS, and we find a necessary and sufficient condition that allM-matricesA with singular graphS have(A) = ( ₁, , _h). This condition is satisfied ifS is a rooted forest.The work of the second-named author was partly supported by the National Science Foundation, under grant MPS-08618 A02.     

Organoruthenaborane Chemistry. X. The SM2-catalysed formation of [ l-(η6-C6Me6)-isocloso-RuB9H9], and some B-phenylamino derivatives. NMR and X-ray diffraction studies

The action of SMe₂ on the ten-vertex nido-ruthenaborane [6-(η⁶-C₆Me₆)RuB₉H_l3] ( 1 ) provides a high-yield route to the unsubstituted isocloso-ruthenaborane [1-(η⁶-C₆Me₆)RuB₉H₉] (2). The benzene analogue [1-(η⁶-C₆Me₆)RuB₉H₉] is prepared similarly. By contrast, reaction of (1) with PhNH₂ gives a variety of B-phenylamino isocloso derivatives, including orange crystals of [1-(η⁶-C₆Me₆)-2-(PhNH)-isocloso-1-RuB 9 H₈] ( 3 ), red-orange [1-(η⁶-C₆Me₆)-2,3-(PhNH)₂-isocloso-1-RuB₉H₇] ( 4 ) and dark-red [1-(η⁶-C₆Me₆)-5,6,7-(PhNH)₃-isocloso-1-RuB₉H₆] ( 5 ). Detailed ¹H and ¹¹B nmr properties of these various compounds are described. The structure of ( 3 ) has been established by a single-crystal X-ray diffraction study of the solvate [1-(η⁶-C₆Me₆)-2-(PhNH)-isocloso-1-RuB₉H₈] · 1/2 CH₂Cl₂; the crystals were monoclinic, space group C2/c, with a = 1895.1(3), b = 1556.6(3), c = 1716.4(3) pm, β = 104.37(1)° and z = 8.     

An investigation of microbore reverse-phase columns containing 3 μm packing materials

A procedure for packing 15 cm × 1 mm id reverse-phase microbore columns with 3 μm silicas obtained from different manufacturers is described. The speed of analysis and detection limits are compared to those obtained with a 50 cm × 1 mm id column packed with 10 μm ODS. The effect of detector time constant on the system, and flow rates on column efficiency are also examined.