Insight into the activation mechanism of carbonic anhydrase(II) through 2-(2-aminoethyl)-pyridine: a promising pathway for enhanced enzymatic activity.

Activation of human carbonic anhydrase II (hCA II) holds great promise for treating memory loss symptoms associated with Alzheimer's disease. Despite its importance, the activation mechanism of hCA II has been largely overlooked in favor of the well-studied inhibition mechanism. To address this unexplored realm, we use first-principles calculations to tease out the activation mechanism of hCA II using 2-(2-aminoethyl)-pyridine (2-2AEPy), a promising in vitro activator. We explored both stepwise and concerted mechanisms via both available nitrogen sites of 2-2AEPy: (i) aminoethyl group (Nα) and (ii) pyridine ring (Nß). Our results show that a concerted mechanism via Nα holds the key to hCA II activation. The activation process of the concerted mechanism exhibits the characteristics of an exergonic reaction, wherein the transition state resembles the reactant with a notably low imaginary frequency of 452.4i cm-1 and barrier height of 5.2 kcal mol-1. Such meager transition barriers propel the activation of hCA II at in vivo temperatures. These findings initiate future research into hCA II activation mechanisms and the development of efficient activators, which may lead to promising therapeutic interventions for Alzheimer's disease.

Non-enzymatic electrochemical cholesterol sensor based on strong host-guest interactions with a polymer of intrinsic microporosity (PIM) with DFT study.

Advances in materials science have accelerated the development of diagnostic tools with the last decade witnessing the development of enzyme-free sensors, owing to the improved stability, low cost and simple fabrication of component materials. However, the specificity of non-enzymatic sensors for certain analytes still represents a challenging task, for example the determination of cholesterol level in blood is vital due to its medical relevance. In this work, a reagent displacement assay for cholesterol sensing in serum samples was developed. It is based on coating of a glassy carbon electrode with a polymer of intrinsic microporosity (PIM) that forms a host-guest complex with methylene blue (MB). In the presence of cholesterol, the MB electroactive probe was displaced due to the stronger association of cholesterol guest to the PIM host. The decrease in the oxidative current was proportional to the cholesterol concentration achieving a detection limit of approximately 0.1 nM. Moreover, to further assist the experimental studies, comprehensive theoretical calculations are also performed by using density functional theory (DFT) calculations.

Quantum mechanical study on the activation mechanism of human carbonic anhydrase VII cluster model with bis-histamine schiff bases and bis-spinaceamine derivatives.

The activation mechanism of human carbonic anhydrase (hCA) isoform VII, hCA VII, with histamine, histamine bis-Schiff bases and bis-spinaceamine derivatives has been investigated using quantum mechanical calculations. The DFT-D3 method has been employed to calculate in detail the electronic structure and electronic energy of different compounds and complexes throughout the reaction pathway. The model system of hCA VII included the core catalytic center, the Zn2+ ion, its three histidine ligands and a hydroxide ion or water molecule coordinated to it. Furthermore, Thr199, Glu106 and the deep water molecule were considered in the model. Five activators of this enzyme, including histamine as standard, in complex with the cluster model of hCA VII were investigated. Thermodynamic functions for the overall reaction and for the complexation between activators and hCA VII were evaluated. Our results demonstrate that the protonatable moiety of these activators participates in proton transfer reactions from the zinc-bound water molecule to the reaction medium, promoting the formation of the catalytically active zinc hydroxide species of the enzyme. The QM analysis revealed that the electrostatic interactions between activators and hCA VII are the driving force of the enzyme-activator complex formation.

Separation of CH4, H2S, N2 and CO2 gases using four types of nanoporous graphene cluster model: a quantum chemical investigation.

Nanoporous graphene is being regarded as a promising candidate for reliable gas separation and purification applications. In the present research, the permeation barrier, selectivity and all thermodynamic functions for passing of four different molecules including CH4, H2S, N2 and CO2 gases on four types of porous graphene which is doped by two, three and six nitrogen atoms using quantum mechanical modelling, based on the density functional theory, B97D, and cc-pVTZ basis set have been evaluated. We find that the permeation barrier of all studied gases especially carbon dioxide decreased by considering the functionalized porous graphene by two, three and six nitrogens-doped, respectively. The results of our study propose using a porous graphene sheet as highly efficient and highly selective membranes for gas separations.

Exploring the effect of phosphorus doping on the utility of g-C3N4 as an electrode material in Na-ion batteries using DFT method.

The suitability of P-doped g-C3N4 for sodium storage was assessed using density functional theory. The electronic structure of P-doped g-C3N4 was calculated and the results indicate that the presence of the P atom causes the band gap of g-C3N4 to narrow. Na adsorption on a P-g-C3N4 sheet was investigated. Projected density of states (PDOS) analysis revealed that pyridinic nitrogen atoms in g-C3N4 play the main role in Na adsorption. High binding energies were calculated for Na storage on g-C3N4, leading to a high voltage range (1-3 V) and a high Na diffusion barrier (2.3 eV). Doping the substrate with more P atoms resulted in lower voltages (below 2.2 V), easier Na diffusion (with a barrier of 1.2 eV), and therefore a material that was better suited than g-C3N4 for use in anodes.

Dynamic stereochemistry of Topiramate (anticonvulsant drug) in solution: theoretical approaches and experimental validation.

Topiramate, an antiepileptic drug, was synthesized with an improved protocol and identified by (1)H NMR, (13)C NMR, (1)H-(1)H COSY, HMQC and HMBC spectrum. In parallel, density functional theory (DFT) using B3LYP functional and split-valance 6-311++G** basis set has been used to optimize the structures and conformers of Topiramate. Also experimental and theoretical methods have been used to correlate the dependencies of (1)J and (2)J involving (1)H and (13)C on the C1-C2 (ω) and C1-O1 (θ) torsion angles in the glycosidic part of Topiramate. New Karplus equations are proposed to assist in the structural interpretation of these couplings. Importantly, due to the sensitivity of some couplings, most notably (2)J(H1R,H1S), (2)J(C2,H1R) and (2)J(C2,H1S) values depend on both C-C (ω) and C-O (θ) torsion angles. Analyses of experimental coupling constants for protons on the pyranose ring of Topiramate indicate a twist boat structure for Topiramate in solution. In all calculations solvent effects were considered using a polarized continuum model (PCM).

Quantum mechanical study of antioxidative ability and antioxidative mechanism of rutin (vitamin P) in solution.

A quantum mechanical approach has been used to shed light on the antioxidative mechanism for scavenging hydroxyl radicals (()OH) and superoxide radicals (O2-) by rutin in the solution phase. Density-functional theory (DFT) using B(3)LYP and UB(3)LYP functional and split-valance 6-311+G(∗∗) basis sets were used to optimize rutin and its different radical forms. Analysis of the theoretical bond dissociation enthalpy (BDE) values for all OH sites of rutin in solution clearly shows the importance of the B-ring and the 3'-OH and 4'-OH groups in the antioxidant activity. We have also investigated the spin density of the radicals to determine the delocalization possibilities. The results of the calculations showed that the oxidation of rutin by both the hydroxyl radical and superoxide radical is an exothermic reaction. In all calculations solvent effects were considered using a polarized continuum model (PCM).

Dynamic stereochemistry of rutin (vitamin P) in solution: theoretical approaches and experimental validation.

Rutin, vitamin P, was extracted from Salvia macrosiphon and identified by (1)H, (13)C, (1)H-(1)H COSY, HMQC, and HMBC spectroscopy. In parallel, density functional theory (DFT) using B(3)LYP functional and split-valance 6-311G * * basis set has been used to optimize the structures and conformers of rutin. Also experimental and theoretical methods have been used to correlate the dependencies of (1)J, (2)J, and (3)J involving (1)H and (13)C on the C5''-C6'' (omega), C6''-O6'' (theta), and C1'''-O6'' (phi) torsion angles in the glycosidic moiety. New Karplus equations are proposed to assist in the structural interpretation of these couplings. (3)J(HH) depends mainly on the C-C (omega) torsion angle, as expected, and (2)J(HH) values depend on both C-C (omega) and C-O (theta) torsions. (1)J(CH) values within hydroxymethyl fragments were also examined and found to depend on r(CH), which is modulated by specific bond orientation and stereoelectronic factors. In all calculations solvent effects were considered using a polarized continuum model (PCM).

Noninnocent effect of axial ligand on the heme degradation process: a theoretical approach to hydrolysis pathway of verdoheme to biliverdin.

Conversion of iron(II) verdoheme to iron(II) biliverdin in the presence of hydroxyl ion as a nucleophile and imidazole, pyridine, water, hydroxyl, cyanide, phenolate, chloride, thiolate and imidazolate as axial ligands was investigated using the B3LYP method and the 6-31G basis set. In the five-coordinated pathway the reactants and products are in the ground triplet state. In this path, hydroxyl ion directly attacks the macrocycle. The exothermic energy for addition of hydroxyl ion to iron(II) verdoheme with various ligands is 169.55, 166.34 and 164 kcal mol(-1) for water, pyridine and imidazole, energies which are around 30-60 kcal mol(-1) more exothermic than those for the other axial ligands used in this study. Therefore, imidazole, water and pyridine axial ligands can facilitate hydrolytic cleavage of iron(II) verdoheme to form open-chained helical iron(II) biliverdin complexes. The activation barrier for the conversion of iron(II) verdoheme hydroxyl species to the iron(II) biliverdin complex is estimated to be 5.2, 4.2, 4.35, 13.76 and 14.05 kcal mol(-1) for imidazole, water, cyanide, thiolate and imidazolate, respectively.

Dynamic stereochemistry of erigeroside by measurement of 1H-1H and 13C-1H coupling constants.

Erigeroside was extracted from Satureja khuzistanica Jamzad (Marzeh Khuzistani in Persian, family of lamiaceae), and (1)H, (13)C, (13)C{(1)H}, (1)H-(1)H COSY, HMQC and J-HMBC were obtained to identify this compound and determine a complete set of J-coupling constants ((1)J(C-H), (2)J(C-H), (3)J(C-H) and (3)J(H-H)) values within the exocyclic hydroxymethyl group (CH(2)OH) and anomeric center. In parallel, density functional theory (DFT) using B3LYP functional and split-valance 6-311++G** basis set has been used to optimized the structures and conformers of erigeroside. In all calculations solvent effects were considered using a polarized continuum (overlapping spheres) model (PCM). The dependencies of (1)J, (2)J and (3)J involving (1)H and (13)C on the C(5')-C(6') (omega), C(6')-O(6') (theta) and C(1')-O(1') (phi) torsion angles in erigeroside were computed using DFT method. Complete hyper surfaces for (1)J(C1',H1'), (2)J(C5',H6'R), (2)J(C5',H6'S), (2)J(C6',H5'), (3)J(C4',H6'R), (3)J(C4',H6'S) and (2)J(H6'R-H5'S) as well as (3)J(H5',H6'R) were obtained and used to derive Karplus equations to correlate these couplings to omega, theta and phi. These calculated J-couplings are in agreement with experimental values. These results confirm the reliability of DFT calculated coupling constants in aqueous solution.

New Karplus equations for 2JHH, 3JHH, 2JCH, 3JCH, 3JCOCH, 3JCSCH, and 3JCCCH in some aldohexopyranoside derivatives as determined using NMR spectroscopy and density functional theory calculations.

The (1)H-(13)C coupling constants of methyl alpha- and beta-pyranosides of D-glucose and D-galactose have been measured by one-dimensional and two-dimensional (1)H-(13)C heteronuclear zero and double quantum, phase sensitive J-HMBC spectra to determine a complete set of coupling constants ((1)J(CH), (2)J(CH), (3)J(CH), (2)J(HH), and (3)J(HH)) within the exocyclic hydroxymethyl group (CH(2)OH) for each compound. In parallel with these experimental studies, structure, energy, and potential energy surfaces of the hydroxymethyl group for these compounds were determined employing quantum mechanical calculations at the B3LYP level using the 6-311++G( * *) basis set. Values of the vicinal coupling constants involving (1)H and (13)C in the C5-C6 (omega) and C6-O6 (theta) torsion angles in the aldohexopyranoside model compounds were calculated with water as the solvent using the PCM method. To test the relationship between (3)J(CXCH) (X=C, O, S) and torsion angle C1-X (phi) around the anomeric center, the conformations of 24 derivatives of glucose and galactose, which represent sequences of atoms at the anomeric center of C-glycosides (C-C bond), O-glycosides (C-O bond), thioglycosides (C-S bond), glycosylamines (C-N bond), and glycosyl halides (C-halogen (F/Cl) bond) have been calculated. Nonlinear regression analysis of the coupling constants (1)J(C1,H1), (2)J(C5,H6R), (2)J(C5,H6S), (2)J(C6,H5), (3)J(C4,H6R), (3)J(C4,H6S), (2)J(H6R,H5), and (3)J(H5,H6R) as well as (3)J(CXCH) (X=C, O, S) on the dihedral angles omega, theta, and phi have yielded new Karplus equations. Good agreement between calculated and experimentally measured coupling constants revealed that the DFT method was able to accurately predict J-couplings in aqueous solutions.

QSARs and activity predicting models for competitive inhibitors of adenosine deaminase.

Combinations of multiple linear regressions, genetic algorithms and artificial neural networks were utilized to develop models for seeking quantitative structure-activity relationships that correlate structural descriptors and inhibition activity of adenosine deaminase competitive inhibitors. Many quantitative descriptors were generated to express the physicochemical properties of 70 compounds with optimized structures in aqueous solution. Multiple linear regressions were used to linearly select different subsets of descriptors and develop linear models for prediction of log(k(i)). The best subset then fed artificial neural networks to develop nonlinear predictors. A committee of six hybrid models - that included genetic algorithm routines together with neural networks - was also utilized to nonlinearly select most efficient subsets of descriptors in a cross-validation procedure for nonlinear log(k(i)) prediction. The best prediction model was found to be an 8-3-1 artificial neural network which was fed by the most frequently selected descriptors among these subsets. This prediction model resulted in train set root mean sum square error (RMSE) of 0.84 log(k(i)) and prediction set RMSE of 0.85 log(k(i)) (both equivalent of 0.10 in normal range of log(k(i))) and correlation coefficient (r(2)) of 0.91.