Counterexamples to Cyvin's conjecture

A conjuctured bound for the number of internal vertices in a simply connected mono-q-polyhex is disproved     

Optical ring resonators for biochemical and chemical sensing

In the past few years optical ring resonators have emerged as a new sensing technology for highly sensitive detection of analytes in liquid or gas. This article introduces the ring resonator sensing principle, describes various ring resonator sensor designs, reviews the current state of the field, and presents an outlook of possible applications and related research and development directions.     

The primary events in chemical sensory perception: Olfaction as a model for selective chemical sensing

Early theories of olfaction are summarized after brief introductions to the anatomy of the human olfactory system and direct electrical measurements on receptor cells (electro-olfactography). The problems of odourant convection-diffusion, and transduction are discussed in terms of the physical chemistry of interfacial partitioning and membrane-receptor behaviour, respectively. Speculation is presented regarding the significant features of receptor structure required for analytical selectivity. Stimulant—receptor interaction at the membrane surface can lead to changes in membrane permeability to ions in a number of distinct ways. Current knowledge regarding the structure and membrane electrochemistry of the important neurotransmitter receptor for acetylcholine, is examined as a role model for the biological activity of olfactory receptors. Finally the olfactory system is compared concisely to existing chemical sensor technology. Although parallels exist, significant differences are obvious; an example is the particular chemistry exhibited by molecular receptors and the hybrid of digital and analogue coding for transduction.     

15N NMR chemical shifts of ring substituted benzonitriles

15N chemical shifts in an extensive series of para (15) and meta (15) as well as ortho (8) substituted benzonitriles, X-C6H4-CN, were measured in deuteriochloroform solutions, using three different methods of referencing. The standard error of the average chemical shift was less than 0.03 ppm in most cases. The results are discussed for both empirical correlations with substituent parameters and quantum chemical calculations. The 15N chemical shifts calculated at the GIAO/B3LYP/6-31 + G*//B3LYP/6-31 + G* level reproduce the experimental values well, and include nitrogen atoms in the substituent groups (range of 300 ppm with slope 0.98 and R = 0.998, n = 43). The 15N shifts in hydroxybenzonitriles are affected by interaction with the OH group. Therefore, these derivatives are excluded from the correlation analysis. The resultant 15N chemical shift correlates well with substituent constants, both in the simple Hammett or DSP relationships and the 13C substituent-induced chemical shifts of the CN carbon.     

Substituent effect on ring proton chemical shifts in PMR spectra of monosubstituted pyridines

The relative chemical shifts of ring protons in PMR spectra of 2-, 3-, and 4-monosubstituted pyridines (in DMSO-D₆) are correlated with the F- and R-constants of the substitutents by using a two-parameter approach. Transmission factors characterizing the transfer of inductive and resonance effects in pyridine, pyrimidine, and s-triazine rings are analyzed.Deceased.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 11, pp. 1520–1523, November, 1989.     

A refined ring polymer molecular dynamics theory of chemical reaction rates

We further develop the ring polymer molecular dynamics (RPMD) method for calculating chemical reaction rates [I. R. Craig and D. E. Manolopoulos, J. Chem. Phys. 122, 084106 (2005)]. We begin by showing how the rate coefficient we obtained before can be calculated in a more efficient way by considering the side functions of the ring-polymer centroids, rather than averaging over the side functions of the individual ring-polymer beads. This has two distinct advantages. First, the statistics of the phase-space average over the ring-polymer coordinates and momenta are greatly improved. Second, the resulting flux-side correlation function converges to its long-time limit much more rapidly. Indeed the short-time limit of this flux-side correlation function already provides a "quantum transition state theory" approximation to the final rate coefficient. In cases where transition state recrossing effects are negligible, and the transition state dividing surface is put in the right place, the RPMD rate is therefore obtained almost instantly. We then go on to show that the long-time limit of the new flux-side correlation function, and hence the fully converged RPMD reaction rate, is rigorously independent of the choice of the transition state dividing surface. This is especially significant because the optimum dividing surface can often be very difficult to determine for reactions in complex chemical systems.     

Calculations of the contribution of ring currents to the chemical shielding anisotropy

Ring currents can exert a large effect upon the chemical shielding of NMR resonances. The analytical expression developed by Waugh and Fessenden (Waugh, J. S.; Fessenden, R. W. J. Am. Chem. Soc. 1957, 79, 846) and Johnson and Bovey (Johnson, C. E.; Bovey, F. A. J. Chem. Phys. 1957, 29, 1012) only quantifies the contribution of ring currents to the isotropic component of the shielding tensor. In the work described here an additional analytical expression is developed so that the contribution of ring currents to the full shielding tensor can be calculated, allowing an estimate of the influence of ring currents upon the chemical shielding anisotropy (CSA, Deltasigma). To test that this pair of analytical expressions can provide a reasonable estimate of the contribution of ring currents to the full shielding tensor a series of density functional calculations (DFT) were carried out. A shielding tensor in a model compound was calculated in two distinct ways. For the first series, DFT shielding calculations of the model compound were carried out in the presence of a benzene ring. For the second series a ring current contribution to the shielding tensor was calculated via the new expressions, and this was added to the result of a DFT shielding calculation which used in place of benzene the nonaromatic analogue 1,3 cyclohexadiene. The two series of results proved to be in excellent agreement. The pair of analytical expressions are used to calculate ring current contributions to the CSA (Deltasigma) of 1H(N) backbone amide resonances in a structure of the second type 2 module from the protein fibronectin. Significant CSA variations are predicted in particular for the 1H(N) of G42 which is most likely involved in a N-H...tpi aromatic hydrogen bond.     

Uncoupled Hartree-Fock calculations of the ring current contribution to the chemical shifts in conjugated hydrocarbons

Uncoupled Hartree-Fock perturbation theory is adapted for the calculation of the ring current contribution to the chemical shifts in a number of conjugated hydrocarbons. The results compare favourably with those of the coupled form of the theory. It is also shown that the Hückel approach may be modified so as to give values close to those of the SCF theory.

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Zusammenfassung Für einige konjugierte Kohlenwasserstoffe wird zur Berechnung des Anteils des Ringstroms an der chemischen Verschiebung die ungekoppelte Hartree-Fock-Störungstheorie verwandt. Die Ergebnisse stimmen gut mit denen überein, die man mit der gekoppelten Form der Theorie erhält. Ferner wird gezeigt, daß der Ansatz nach Hückel derart modifiziert werden kann, daß die Ergebnisse den aus der SCF-Theorie erhaltenen nahekommen.

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Résumé La théorie de perturbation Hartree-Fock non couplé est adaptée pour le calcul de la contribution du «courant cyclique» aux déplacements chimiques dans un certain nombre d'hydrocarbures conjugués. Les résultats se comparent favorablement à ceux de la théorie de Hartree-Fock couplé. On montre que par ailleurs l'approximation de type Hückel peut être modifiée de manière à donner des valeurs proches de celles de la théorie SCF.

     

Counterexamples to a proposed algorithm for Fries structures of benzenoids

The Fries number of a benzenoid is the maximum number of benzenoid hexagons over all of its Kekulé structures (perfect matchings), and a Fries canonical structure is a perfect matching that realises this maximum. A recently published algorithm claims to determine Fries canonical structures of benzenoids via iterated Hadamard products based on the adjacency matrix (Ciesielski et?al. in Symmetry 2:1390–1400, 2010). This algorithm is re-examined here. Convergence is typically rapid and often yields a single candidate perfect matching, but the algorithm can give an exponential number of choices, of which only a small number are canonical. More worryingly, the algorithm is found to give incorrect results for the Fries number for some benzenoids with as few as seven hexagonal faces. We give a combinatorial reformulation of the algorithm in terms of linear combinations of perfect matchings (with weights at each stage proportional to the products of weights of the edges included in a matching). In all the cases we have examined, the algorithm converges to a maximum-weight matching (or combination of maximum-weight matchings), and where the algorithm fails, either no best Fries matching is of maximum weight, or a best Fries matching is of maximum weight but a sub-optimal matching of the same weight is chosen.     

Model of peptide bond-aromatic ring interaction: correlated ab initio quantum chemical study

Aromatic ring-peptide bond interactions (modeled as benzene and formamide, N-methylformamide and N-methylacetamide) are studied by means of advanced computational chemistry methods: second-order M?ller-Plesset (MP2), coupled-cluster single and double excitation model [CCSD(T)], and density functional theory with dispersion (DFT-D). The geometrical preferences of these interactions as well as their interaction energy content, in both parallel and T-shaped arrangements, are investigated. The stabilization energy reaches a value of over 5 kcal/mol for the N-methylformamide-benzene complex at the CCSD(T)/complete basis set (CBS) level. Decomposition of interaction energy by the DFT-symmetry-adapted perturbation treatment (SAPT) technique shows that the parallel and T-shaped arrangements, although similar in their total interaction energies, differ significantly in the proportion of electrostatic and dispersion terms.     

二环丁烷[1.1.0]开环反应的量子化学研究

本文用MNDO方法研究了二环丁烷[1.1.0]开环反应的反应途径, 并优化了该反应的反应物、产物和过渡态的结构, 在理论上证明了此开环反应的反应机理。     

Cyclic tetrapeptides via the ring contraction strategy: chemical techniques useful for their identification

Cyclic tetrapeptides are a class of natural products that have been shown to have broad ranging biological activities and good pharmacokinetic properties. In order to synthesise these highly strained compounds a ring contraction strategy had previously been reported. This strategy was further optimised and a suite of techniques, including the Edman degradation and mass spectrometry/mass spectrometry, were developed to enable characterisation of cyclic tetrapeptide isomers. An NMR solution structure of a cyclic tetrapeptide was also generated. To illustrate the success of this strategy a library of cyclic tetrapeptides was synthesised.     

Contributions of quantum chemistry to the development of ring opening polymerizations and chemical recycling

Quantum chemistry has increasingly become an integral component for the development of homogeneous catalytic processes to form polymers and to break them down. This review examines how quantum chemistry has been utilized to gain insights on mechanisms and selectivities in polymerization and depolymerization reactions by homogeneous catalysts, from some of the earliest uses of theory to the most recent efforts. Key aspects of catalysis by transition-metal catalysts, organocatalytic bases and organic acids will be highlighted.     

Theoretical characterization of the chemical bonds of some three-membered ring compounds through QTAIM theory

Structural Chemistry - In this paper, we investigate the nature of the carbonyl and the intraring C–C, C–N, C–O, N–N, O–O and N–O bonds of cyclopropanone and the...