Complexes of graphene nanoribbons with porphyrins and metal-encapsulated C28 as molecular rectifiers: a theoretical study

The rectification properties of porphyrin–graphene nanoflake complexes and endohedral complexes of C28 fullerene with metal atoms have been studied using the fully ab initio method. D3 dispersion-corrected PBE/-def2-SVP model was used for the optimisations and the electronic energy evaluation. In porphyrin–graphene nanoflake complexes dispersion dominates, while in the endohedral complexes of C28 dispersion does not play an important role. All studied systems do rectify. In the case of fullerenes, the rectification is possible due to the reduction in the molecular symmetry of the fullerene caused by the interaction with electrodes and the endohedral complex formation. The origin of the rectification is the asymmetrical deformation of the electron density under direct and inverse voltages which creates different currents in opposite directions. It seems that peculiar geometry of Au-TPP-Cd/NF diode is responsible for its high rectification ratio. The Cd ion is notably out of the porphyrin plane making close contact with the neighbouring electrode, increasing the asymmetry of the diode compared to other TPP/NF complexes.     

Carbon nanotube functionalization with carboxylic derivatives: a DFT study

Chemical functionalization of a single-walled carbon nanotube (CNT) with different carboxylic derivatives including –COOX (X?=?H, CH₃, CH₂NH₂, CH₃Ph, CH₂NO₂, and CH₂CN) has been theoretically investigated in terms of geometric, energetic, and electronic properties. Reaction energies have been calculated to be in the range of ?0.23 to ?7.07 eV. The results reveal that the reaction energy is increased by increasing the electron withdrawing character of the functional groups so that the relative magnitude order is ?CH₂NO₂?>?CH₂CN?>?H?>?CH₂Ph?>?CH₃?>?CH₂NH₂. The chemical functionalization leads to an increase in HOMO/LUMO energy gap of CNT by about 0.32 to 0.35 eV (except for ?H). LUMO, HOMO, and Fermi level of the CNT are shifted to lower energies especially in the case of ?CH₂NO₂ and _?CH₂CN functional groups. Therefore, it leads to an increment in work function of the tube, impeding the field electron emission.     

Spermine-nucleic acid interactions: a theoretical study

The interaction of spermine with nucleic acids is simulated theoretically using refined semi-empirical energy formulae and an advanced minimization procedure. Various nucleic acids are considered: model homopolymeric DNA's, a dodecamer (CGCGAATTCGCG) of type B-DNA, as well as a transfer RNA, tRNA^Phe. The dominant role of electrostatic potential in determining the preferential binding sites of spermine is demonstrated in each of these cases and the role of counterions, nucleic acid structure, and base-pair sequence is analyzed.     

Conformational transitions of the quercetin molecule via the rotations of its rings: a comprehensive theoretical study

Abstract

Quercetin is an important flavonoid compound, usually extracted from plants, vegetables and fruits such as blueberries, apples, green tea, wine, onions and possessing broad range of pharmacological properties, in particular, powerful antioxidant, antitoxic, antiinflammation and antimicrobial effects due to its various reactive sites. The structure of this phenolic compound consists of three (A?+?C) and B rings, bearing five hydroxyl groups. Primarily, the chemical structure of quercetin determines its physico-chemical properties. Earlier, it was established that isolated quercetin molecule can acquire 48 stable conformations (24 planar and 24 non-planar) due to the mobility of its hydroxyl groups and (A?+?C) and B rings with relative Gibbs free energies in the range of 0.0–25.3?kcal·mol^?1 under normal conditions (Brovarets’ et al., 2019c Brovarets’, O. O., & Hovorun, D. M. (2019c). Conformational diversity of the quercetin molecule: A quantum-chemical view. Journal of Biomolecular Structure and Dynamics. doi: 10.1080/07391102.2019.1645734[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]). In this work by quantum-mechanical calculations at the MP2/6-311++G(2df,pd)//B3LYP/6-311++G(d,p) level of theory and Bader’s ‘Quantum Theory of Atoms in Molecules’, we have theoretically modeled the interconversions in the 24 pairs of the conformers of the quercetin molecule, occuring via the rotation of its non-deformable (A+С) and B rings around the С2-С1' bond through the quasi-orthogonal transition state with low values of the imaginary frequencies (28–33/29–36?cm^?1) and Gibbs free energies of activation in the range of 2.17–5.68/1.86–4.90?kcal·mol^?1 in the continuum with dielectric permittivity ε?=?1/ε?=?4 under normal conditions. Also, we studied the changes of the number of physico-chemical characteristics of all intramolecular-specific contacts – hydrogen bonds and attractive van der Waals contacts during these conformational rearrangements.

Communicated by Ramaswamy H. Sarma     

Mode of action of intercalators: a theoretical study

Mode of action of some intercalators has been theoretically investigated on the basis of quantum mechanical perturbation method. Energies of H-bond interaction between drug chromophore and base pairs have been calculated in all possible orientations. The stacking energy has also been calculated with the base pairs. The effect of these interactions on specific recognition has also been discussed. On the basis of these studies, a model for the interaction of these drugs has been proposed. This explains the relative activities of acridine intercalators and satisfies the experimental observations.     

Antibacterial functionalization of wool fabric via immobilizing lysozymes

Greater attention has been given to enzymatic processes of textiles as effective alternatives to conventional chemical treatments because of the non-toxic and eco-friendly characteristics of enzymes as well as the increasingly important requirement for reducing pollution in textile production. A new functionalization method for wool fabrics based on immobilization of lysozymes was investigated in this paper. Wool fabric was first activated with glutaraldehyde, and then employed to covalently immobilize lysozymes. Main immobilization parameters were optimized in terms of the activity of immobilized enzyme. A high activity of the immobilized enzyme was obtained when the fabric was activated at 25 °C for 6 h in a bath containing with 0.2% of glutaraldehyde followed by the immobilization at 4 °C and pH 7.0 for 6 h with 5 g l⁻¹ lysozyme. The scanning electron microscopy and staining tests based on modified Coomassie protein assay (Bradford method) revealed that the lysozyme was fixed covalently on the wool fabric. Wool fabrics immobilizing lysozymes presented a higher ratio of bacteriostasis to Staphylococcus aureus. The durability of antibacterial wool was assessed and the lysozyme immobilized on wool fabric retained ca. 43% of its activity after five cycles of use when taking the activity of the immobilized lysozyme before using as reference.     

Nonlinear buckling of blood vessels: a theoretical study

Tortuosity and kinking often occur in arteries and veins but the underlying mechanisms are poorly understood. It has been suggested recently that long arteries may buckle and become tortuosity due to reduced axial tension or hypertensive pressure, but very few studies have been done to establish the biomechanical basis for artery buckling. Here we developed the arterial buckling equation using a nonlinear elastic thick-walled cylindrical model with residual stress. Our results demonstrated that arteries may buckle due to high blood pressure or low axial tension and that residual stress in the arteries increases the buckling pressure. These results are in general agreement with the previous linear elastic model. The buckling equation provides a useful tool for studying artery tortuosity and kinking.     

A concise route to triazolobenzodiazepine derivatives via a one-pot alkyne-azide cycloaddition reaction

A new and efficient one-pot synthesis of [1,2,3]triazolo[1,5-a][1,4] benzodiazepin-6(4H)-ones is described starting from readily available anthranilic acids. A small array of the title compounds were assembled via a four-step sequence involving diazotisation, azide addition followed by amide bond formation employing polymer supported carbodiimide and subsequent 1,3-dipolar cycloaddition reaction.     

Duality between decomposition and gluing: a theoretical biology via adjoint functors

Two ideas in theoretical biology, ‘decomposition into functions’ and ‘gluing functions’, are formalized as endofunctors on the category of directed graphs. We prove that they constitute an adjunction. The invariant structures of the adjunction are obtained. They imply two biologically significant conditions: the existence of cycles in finite graphs and anticipatory diagrams.     

Sleep-induced periodic breathing and apnea: a theoretical study

To elucidate the mechanisms that lead to sleep-disordered breathing, we have developed a mathematical model that allows for dynamic interactions among the chemical control of respiration, changes in sleep-waking state, and changes in upper airway patency. The increase in steady-state arterial PCO2 accompanying sleep is shown to be inversely related to the ventilatory response to CO2. Chemical control of respiration becomes less stable during the light stage of sleep, despite a reduction in chemoresponsiveness, due to a concomitant increase in "plant gain" (i.e., responsiveness of blood gases to ventilatory changes). The withdrawal of the "wakefulness drive" during sleep onset represents a strong perturbation to respiratory control: higher magnitudes and rates of withdrawal of this drive favor instability. These results may account for the higher incidence of periodic breathing observed during light sleep and sleep onset. Periodic ventilation can also result from repetitive alternations between sleep onset and arousal. The potential for instability is further compounded if the possibility of upper airway occlusion is also included. In systems with high controller gains, instability is mediated primarily through chemoreflex overcompensation. However, in systems with depressed chemoresponsiveness, rapid sleep onset and large blood gas fluctuations trigger repetitive episodes of arousal and hyperpnea alternating with apneas that may or may not be obstructive. Between these extremes, more complex patterns can arise from the interaction between chemoreflex-mediated oscillations of shorter-cycle-duration (approximately 36 s) and longer-wavelength (approximately 60-80 s) state-driven oscillations.     

Potential infection of grazing cattle via contaminated water: a theoretical modelling approach

Wastewater discharge and agricultural activities may pose microbial risks to natural water sources. The impact of different sources can be assessed by water quality modelling. The aim of this study was to use hydrological and hydrodynamic models to illustrate the risk of exposing grazing animals to faecal pollutants in natural water sources, using three zoonotic faecal pathogens as model microbes and fictitious pastures in Sweden as examples. Microbial contamination by manure from fertilisation and grazing was modelled by use of a hydrological model (HYPE) and a hydrodynamic model (MIKE 3 FM), and microbial contamination from human wastewater was modelled by application of both models in a backwards process. The faecal pathogens Salmonella spp., verotoxin-producing Escherichia coli O157:H7 (VTEC) and Cryptosporidium parvum were chosen as model organisms. The pathogen loads on arable land and pastures were estimated based on pathogen concentration in cattle faeces, herd prevalence and within-herd prevalence. Contamination from human wastewater discharge was simulated by estimating the number of pathogens required from a fictitious wastewater discharge to reach a concentration high enough to cause infection in cattle using the points on the fictitious pastures as their primary source of drinking water. In the scenarios for pathogens from animal sources, none of the simulated concentrations of salmonella exceeded the concentrations needed to infect adult cattle. For VTEC, most of the simulated concentrations exceeded the concentration needed to infect calves. For C. parvum, all the simulated concentrations exceeded the concentration needed to infect calves. The pathogen loads needed at the release points for human wastewater to achieve infectious doses for cattle were mostly above the potential loads of salmonella and VTEC estimated to be present in a 24-h overflow from a medium-size Swedish wastewater treatment plant, while the required pathogen loads of C. parvum at the release points were below the potential loads of C. parvum in a 24-h wastewater overflow. Most estimates in this study assume a worst-case scenario. Controlling zoonotic infections at herd level prevents environmental contamination and subsequent human exposure. The potential for infection of grazing animals with faecal pathogens has implications for keeping animals on pastures with access to natural water sources. As the infectious dose for most pathogens is more easily reached for calves than for adult animals, and young calves are also the main shedders of C. parvum, keeping young calves on pastures adjacent to natural water sources is best avoided.     

Mechanism of osmoprotection by archaeal S-layers: a theoretical study

Many Archaea possess protein surface layers (S-layers) as the sole cell wall component. S-layers must therefore integrate the basic functions of mechanical and osmotic cell stabilisation. While the necessity is intuitively clear, the mechanism of structural osmoprotection by S-layers has not been elucidated yet. The theoretical analysis of a model S-layer-membrane assembly, derived from the typical cell envelope of Crenarchaeota, explains how S-layers impart lipid membranes with increased resistance to internal osmotic pressure and offers a quantitative assessment of S-layer stability. These considerations reveal the functional significance of S-layer symmetry and unit cell size and shed light on the rationale of S-layer architectures.     

Mechanism of mycolic acid cyclopropane synthase: a theoretical study

The reaction mechanism of mycolic acid cyclopropane synthase is investigated using hybrid density functional theory. The direct methylation mechanism is examined with a large model of the active site constructed on the basis of the crystal structure of the native enzyme. The important active site residue Glu140 is modeled in both ionized and neutral forms. We demonstrate that the reaction starts via the transfer of a methyl to the substrate double bond, followed by the transfer of a proton from the methyl cation to the bicarbonate present in the active site. The first step is calculated to be rate-limiting, in agreement with experimental kinetic results. The protonation state of Glu140 has a rather weak influence on the reaction energetics. In addition to the natural reaction, a possible side reaction, namely a carbocation rearrangement, is also considered and is shown to have a low barrier. Finally, the energetics for the sulfur ylide proposal, which has already been ruled out, is also estimated, showing a large energetic penalty for ylide formation.     

Salicylic acid is not a bacterial siderophore: a theoretical study

Using a newly available program for calculating the concentrations and speciation of various ions (Pettit, LD & Powell KJ, `SolEq' Academic Software, 1999), we have calculated that at pH 7 the amount of free Fe(III) present in an aqueous solution is 1.4×10^–9 M and not 10^–18 M as is usually quoted. In the presence of salicylic acid, included in the calculations at 10^–4 M, the solubility of Fe(III) is increased to only 9.8×10^–9 M suggesting that salicylate is unable to act as a siderophore although it is produced as an extracellular product by several bacterial genera when grown iron deficiently. In the presence of 40 mM phosphate, the soluble Fe(III) concentration is decreased by 10⁴ at pH 7 and again this is hardly affected by the presence of salicylate. Thus, for microorganisms grown either in vitro or in vivo, salicylate is unlikely to function as a iron solubilizing agent. The same conclusions may also apply to 2,3-dihydroxybenzoic acid.     

Vinyl sulfone functionalization: a feasible approach for the study of the lectin-carbohydrate interactions

Carbohydrate-mediated molecular recognition is involved in many biological aspects such as cellular adhesion, immune response, blood coagulation, inflammation, and infection. Considering the crucial importance of such biological events in which proteins are normally involved, synthetic saccharide-based systems have emerged as powerful tools for the understanding of protein-carbohydrate interactions. As a new approach to create saccharide-based systems, a set of representative monosaccharides (D-mannose, D-glucose, N-acetyl-D-glucosamine, and L-fucose) and disaccharides (lactose, maltose, and melibiose) were derivatized at their anomeric carbon with a vinyl sulfone group spanned by an ethylthio linker. This vinyl sulfone functionalization is demonstrated to be a general strategy for the covalent linkage of a saccharide in mild conditions via Michael-type additions with the amine and thiol groups from functionalized supports and those naturally present in biomolecules. The introduction of the ethylthio linker between the biorecognizable element (i.e., saccharide) and the reactive group (i.e., vinyl sulfone) was found to preserve the functionality of the former. The capability of the vinyl sulfone saccharides for the study of lectin-carbohydrate interactions was demonstrated by (i) immobilizing them on both amine-functionalized supports (glass slides and microwell plates) and polylysine-coated glass slides to create sugar arrays that selectively bind lectins (ii) coupling to model proteins to yield neoglycoproteins that are recognized by lectins and (iii) using vinyl sulfone saccharides as tags to allow the detection of the labeled biomolecule by HRP-lectins. The above results were further put tothe test with a real case: detection of carbohydrate binding proteins present in rice ( Oryza sativa ).     

The stereochemistry of a four-way DNA junction: a theoretical study.

The stereochemical conformation of the four-way helical junction in DNA (the Holliday junction; the postulated central intermediate of genetic recombination) has been analysed, using molecular mechanical computer modelling. A version of the AMBER program package was employed, that had been modified to include the influence of counterions and a global optimisation procedure. Starting from an extended planar structure, the conformation was varied in order to minimise the energy, and we discuss three structures obtained by this procedure. One structure is closely related to a square-planar cross, in which there is no stacking interaction between the four double helical stems. This structure is probably closely similar to that observed experimentally in the absence of cations. The remaining two structures are based on related, yet distinct, conformations, in which there is pairwise coaxial stacking of neighbouring stems. In these structures, the four DNA stems adopt the form of two quasi-continuous helices, in which base stacking is very similar to that found in standard B-DNA geometry. The two stacked helices so formed are not aligned parallel to each other, but subtend an angle of approximately 60 degrees. The strands that exchange between one stacked helix and the other are disposed about the smaller angle of the cross (i.e. 60 degrees rather than 120 degrees), generating an approximately antiparallel alignment of DNA sequences. This structure is precisely the stacked X-structure proposed on the basis of experimental data. The calculations indicate distortions from standard B-DNA conformation that are required to adopt the stacked X-structure; a widening of the minor groove at the junction, and reorientation of the central phosphate groups of the exchanging strands. An important feature of the stacked X-structure is that it presents two structurally distinct sides. These may be recognised differently by enzymes, providing a rationalisation for the points of cleavage by Holliday resolvases.