Fully atomistic molecular dynamics simulations are employed to study impregnation of the poly(methyl methacrylate) (PMMA) matrix with carbamazepine (CBZ) in supercritical carbon dioxide. The simulation box consists of 108 macromolecules of the polymer sample with the polymerization degree of 100, 57 molecules of CBZ, and 242,522 CO2 molecules. The simulation is performed at 333 K and 20 MPa. It is found that by the end of the simulation, the CBZ uptake reaches 1.09 wt % and 50 molecules are sorbed by PMMA. The main type of interaction between PMMA and CBZ is hydrogen bonding between the carbonyl oxygen of PMMA and the hydrogen atoms of the CBZ NH2-group. At the polymer surface, CBZ exists not only in the molecular form, as inside the polymer and in the bulk solution, but also in the form of dimers and trimers. The energy of formation of the hydrogen-bonded complexes is estimated within ab initio calculations.
The development of advanced electrochemical devices for energy conversion and storage requires fine tuning of electrode reactions, which can be accomplished by altering the electrode/solution interface structure. Particularly, in case of an alkali-salt electrolyte the electric double layer (EDL) composition can be managed by introducing organic cations (e.g. room temperature ionic liquid cations) that may possess polar fragments. To explore this approach, we develop a theoretical model predicting the efficient replacement of simple (alkali) cations with dipolar (organic) ones within the EDL. For the typical values of the molecular dipole moment ($2-4~D$) the effect manifests itself at the surface charge densities higher than 30 $\mu C/cm^2$. We show that the predicted behavior of the system is in qualitative agreement with the molecular dynamics simulation results.
Due to their high durability and immobilization properties, cementitious materials have found a considerable application in the design and construction of radioactive waste repositories in the last decades. During cement paste production, organic additives are introduced to modify various properties of cement. The presence of such organic complexants may negatively affect the immobilizing properties of cement with respect to radionuclides. For better understanding and prediction of the effects of interactions between organic molecules and cementitious materials with radionuclides, we have developed several representative models consisting of three principal components: (i) calcium silicate hydrate (C-S-H) phase - the main binding phase of cement; (ii) gluconate, a simple well-described molecule, as a representative of organic additives; (iii) U(VI), as one of the most studied radionuclides of the actinide series. The C-S-H phase with low Ca/Si ratio (~0.83) typical for â€œlow-pHâ€ and degraded cement pastes has been selected for this modelling study. Structural, and energetic aspects of the sorption processes of uranyl, gluconate, and their mutual correlations on the surface of cement were quantitatively modeled by classical molecular dynamics (MD) and potential of mean force (PMF) calculations. The ternary surface complex formation between uranyl hydroxides and Ca2+ cations at the C-S-H aqueous interfaces is shown to have an important role in the overall sorption process. In the presence of gluconate, U(VI) sorption on C-S-H is facilitated by weakening the Ca2+ binding with the surface. Additionally, Na+ is proven to be an important competitor for certain surface sorption sites and can potentially affect the equilibrium properties of the interface.
We performed constant reservoir composition molecular dynamics (CRC-MD) simulations at 323 K and 124 bar to quantitatively study the partitioning of fluid species between the nano- and mesopores of clay and a bulk reservoir containing an equimolar mixture of CO2 and CH4. The results show that the basal (001) and protonated edge (010) surfaces of illite both demonstrate a strong preference for CO2 over CH4 adsorption; that the (001) surfaces show a stronger preference for CO2 than the (010) surfaces, especially with K+ as the exchangeable cation; and that the structuring of the near-surface CO2 by K+ is stronger than that by Na+. The protonated (010) surfaces have a somewhat greater preference for CH4, with the concentration near them close to that in the bulk fluid. The effects of the surfaces on the fluid composition extend to approximately 2.0 nm from them, with the fluid composition at the center of the pore becoming essentially the same as the bulk composition at a pore thickness of ~5.7 nm. The preference of nano- and mesopores bounded by clay minerals for CO2 over CH4 suggests that injection of CO2 into tight reservoirs is likely to displace CH4 into larger pores, thus enhancing its production.
Statistical information on the edge surface area and edge crystallographic orientation of clay nanoparticle surfaces is essential for proper accounting of the protonation-deprotonation reactions as a part of mechanistic surface complexation models. A combination of atomic-force microscopy (AFM) measurements and molecular dynamics computer simulations made it possible to quantify the relative contributions of the most frequently occurring montmorillonite edge surfaces to the total edge surface area. Edge surfaces normal to the  and  crystallographic directions are found to be the most abundant (~60% and ~20%, respectively), in agreement with previous estimations.
First representatives of a novel class of compounds containing an electron-accepting hydrazonocyclopentadiene moiety, π-conjugated phenylene spacer, and electron-donating triphenylamine moiety have been synthesized. Investigation of their optical, electrochemical and photovoltaic properties revealed a high potential of the hydrazonocyclopentadiene acceptor moiety in the design of donor-acceptor compounds for organic photovoltaics.
Reductive amination plays a paramount role in pharmaceutical and medicinal chemistry owing to its synthetic merits and the ubiquitous presence of amines among biologically active compounds. It is one of the key approaches to C–N bond construction due to its operational easiness and a wide toolbox of protocols. Recent studies show that at least a quarter of C–N bond-forming reactions in the pharmaceutical industry are performed via reductive amination. This Review concisely compiles information on 71 medical substances that are synthesized by reductive amination. Compounds are grouped according to the principle of action, which includes drugs affecting the central nervous system, drugs affecting the cardiovascular system, anticancer drugs, antibiotics, antiviral and antifungal medicines, drugs affecting the urinary system, drugs affecting the respiratory system, antidiabetic medications, drugs affecting the gastrointestinal tract, and drugs regulating metabolic processes. A general synthetic scheme is provided for each compound, and the description is focused on reductive amination steps. The green chemistry metric of reaction mass efficiency was calculated for all reactions.
Non-turnover voltammetry is a sensitive tool to characterize the electrochemical properties of redox proteins. However, the catalytically competent oxidation states of most peroxidases do not display the required electrochemical reversibility. In this report, we circumvent this limitation and exploit the voltammetric response associated with the Fe(III)/Fe(II) redox couple of tobacco peroxidase to probe the energetics and electronic connectivity of the heme pocket. We have applied this approach to rationalize the previously reported influence of the immobilization protocol on the electrocatalytic activity of tobacco peroxidase. To decouple proton and electron transfer steps, measurements have been carried out over the 3 ≤ pH ≤ 9 range and a 1e − /2H + ladder scheme has been adopted for their analysis. At each pH, thermodynamic and kinetic parameters associated with the Fe(III)/Fe(II) redox conversion were determined as a function of temperature in the 0-30 °C range. Reduction entropies and reorganization energies displayed different values for covalently immobilized and physisorbed enzymes, pointing to a larger involvement of the solvent in the last case. These findings, together with a larger electronic coupling between the prosthetic group and the electrode, are indicative of a partial denaturation of the physisorbed enzymes as the origin of their lower electrocatalytic activity.
The carboxypeptidase T (CPT) from Thermoactinomyces vulgaris has an active site structure and 3D organization similar to pancreatic carboxypeptidases A and B (CPA and CPB), but differs in broader substrate specificity. The crystal structures of CPT complexes with the transition state analogs N-sulfamoyl-L-leucine and N-sulfamoyl-L-glutamate (SLeu and SGlu) were determined and compared with previously determined structures of CPT complexes with N-sulfamoyl-L-arginine and N-sulfamoyl-L-phenylalanine (SArg and SPhe). The conformations of residues Tyr255 and Glu270, the distances between these residues and the corresponding ligand groups, and the Zn-S gap between the zinc ion and the sulfur atom in the ligand's sulfamoyl group that simulates a distance between the zinc ion and the tetrahedral sp3-hybridized carbon atom of the converted peptide bond, vary depending on the nature of the side chain in the substrate's C-terminus. The increasing affinity of CPT with the transition state analogs in the order SGlu, SArg, SPhe, SLeu correlates well with a decreasing Zn-S gap in these complexes and the increasing efficiency of CPT-catalyzed hydrolysis of the corresponding tripeptide substrates (ZAAL > ZAAF > ZAAR > ZAAE). Thus, the side chain of the ligand that interacts with the primary specificity pocket of CPT, determines the geometry of the transition complex, the relative orientation of the bond to be cleaved by the catalytic groups of the active site and the catalytic properties of the enzyme. In the case of CPB, the relative orientation of the catalytic amino acid residues, as well as the distance between Glu270 and SArg/SPhe, is much less dependent on the nature of the corresponding side chain of the substrate. The influence of the nature of the substrate side chain on the structural organization of the transition state determines catalytic activity and broad substrate specificity of the carboxypeptidase T.