Classification of polyhedral matroids

This paper establishes polyhedral properties of matroidal structures. Classical problems such as enumeration and classification of polyhedra matroids, the characterization of face complexes, the metric properties of graphs of polymatroids are considered. Supported by DAAD and Belarussian Fundamental Science Fund     

A unified model description of mobile and localized adsorption: I. MFA with nonadditive lateral interactions — an application to disordered adsorbed monolayer on a structureless substrate

A simple model is used to treat mobile adsorption on a structureless substrate. The influence of temperature on the state of motion of adsorbed particles is described by means of an interpolation formula used earlier in the theory of hindered rotation, whereas the influence of the nearest-neighbour potential with varying degree of coverage is accounted for in terms of a “free area”, available for individual particle motion, for which a simple analytical expression, based on an harmonic oscillator approximation, is obtained. An irregularity in the long range order of the adsorbed monolayer is introduced in terms of “varying distances”, resp. of varying energy bonds between the particles in dependence of the number of nearest neighbours actually present in the first coordination sphere of each particle (nonadditivity of the bonds).     

Stereoselective electrocatalytic transformation of malonate and alkylidenecyanoacetates into (E)-3-substituted 2-cyanocyclopropane-1,1,2-tricarboxylates

Electrolysis of malonate and alkylidenecyanoacetates in alcohols in an undivided cell in the presence of NaBr results in stereoselective formation of (E)-3-substituted 2-cyanocyclopropane-1,1,2-tricarboxylates in 75-90% yields.     

A unified model description of mobile and localized adsorption: II. Adsorption on crystalline surfaces — a gradual transition between mobile and localized adsorption

The model used in Part I is now extended to account for the periodic potential of the substrate. The influence of the energetical structure of the substrate on the state of motion of a single particle is allowed for at varying degree of coverage so that the gradual transition from localized to mobile adsorption with growing temperature may be described. The impact of the energetical characteristics of adsorbate and adsorbent on the critical parameters of the adsorption isotherms is investigated. These parameters are also considerably influenced when non-additivity of the lateral bonds is taken into account. On a perfectly smooth substrate, as well as in the case of potential wells of the substrate coinciding in size with the diameter of the adatoms, the model predicts the impossibility of a first order phase transition between “additive” and “nonadditive” phases. The last result could be related to the problem of 2D melting, provided the degree of disorder in both adsorbate phases is adequately expressed in terms of varying nonadditivity of the energy bonds.     

Selective and efficient electrocatalytic way to spirobarbituric dihydrofurans

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A graph-theoretical kinetic Monte Carlo framework for on-lattice chemical kinetics

Existing kinetic Monte Carlo (KMC) frameworks for the simulation of adsorption, desorption, diffusion, and reaction on a lattice often assume that each participating species occupies a single site and represent elementary events involving a maximum of two sites. However, these assumptions may be inadequate, especially in the case of complex chemistries, involving multidentate species or complex coverage and neighboring patterns between several lattice sites. We have developed a novel approach that employs graph-theoretical ideas to overcome these challenges and treat easily complex chemistries. As a benchmark, the Ziff-Gulari-Barshad system is simulated and comparisons of the computational times of the graph-theoretical KMC and a simpler KMC approach are made. Further, to demonstrate the capabilities of our framework, the water-gas shift chemistry on Pt(111) is simulated.     

Energetics of a protein disorder–order transition in small molecule recognition

Many proteins recognise other proteins via mechanisms that involve the folding of intrinsically disordered regions upon complex formation. Here we investigate how the selectivity of a drug-like small molecule arises from its modulation of a protein disorder-to-order transition. Binding of the compound AM-7209 has been reported to confer order upon an intrinsically disordered ‘lid’ region of the oncoprotein MDM2. Calorimetric measurements revealed that truncation of the lid region of MDM2 increases the apparent dissociation constant of AM-7209 250-fold. By contrast, lid truncation has little effect on the binding of the ligand Nutlin-3a. Insights into these differential binding energetics were obtained via a complete thermodynamic analysis that featured adaptive absolute alchemical free energy of binding calculations with enhanced-sampling molecular dynamics simulations. The simulations reveal that in apo MDM2 the ordered lid state is energetically disfavoured. AM-7209, but not Nutlin-3a, shows a significant energetic preference for ordered lid conformations, thus shifting the balance towards ordering of the lid in the AM-7209/MDM2 complex. The methodology reported herein should facilitate broader targeting of intrinsically disordered regions in medicinal chemistry.

Molecular simulations and biophysical measurements elucidate why the ligand AM-7209 orders a disordered region of the protein MDM2 on binding. This work expands strategies available to medicinal chemists for targeting disordered proteins.     

Electrochemically induced Henry reaction of nitromethane and carbonyl compounds

The electrolysis of carbonyl compounds and nitromethane in methanol or in the mixture of methanol and DMF in an undivided cell results in the formation of corresponding β-nitroalcohols in 60-75% yields. Thus, the simple electrocatalytic system can produce under mild conditions an electrochemically induced Henry reaction.