Nucleophilic properties of purine bases : inherent reactivity versus reaction conditions

In the present study, nucleophilic properties of adenine and guanine are examined by means of density functional theory. H+ is used as a model electrophile. Two modes of H+ attack on the bases are considered: on the neutral molecule and on the anion. Solvent effects are modeled by means of polarizable continuum model. Regioselectivity of attack is studied by analyzing two contributions. The first one is the energetic ordering of the tautomers. The second is the relative inherent reactivity of nucleophilic sites in the bases. Atomic softnesses calculated by means of charge sensitivity analysis are employed for this purpose. The most reactive sites in various tautomers are identified on the ground of Li–Evans model. For adenine, it is demonstrated that both in basic and in neutral pH N7 atom possesses the most nucleophilic character. In polar solvents, N7 substitution is also most favored energetically. In basic pH and nonpolar solvents as well as in the gas phase, N9 substitution is slightly more probable. For guanine, a mixture of N7- and N9-substituted products can be expected in basic pH. In neutral pH, inherent reactivity and energy trends are opposite to each other; therefore, the substitution does not occur. Experimentally observed products of reactions with various electrophiles and in various conditions confirm the results obtained in this study

Formation of β-cyclodextrin complexes in an anhydrous environment

The formation of inclusion complexes of β-cyclodextrin was studied at the melting temperature of guest compounds by differential scanning calorimetry. The complexes of long-chain n-alkanes, polyaromatics, and organic acids were investigated by calorimetry and IR spectroscopy. The complexation ratio of β-cyclodextrin was compared with results obtained in an aqueous environment. The stability and structure of inclusion complexes with various stoichiometries were estimated by quantum chemistry and molecular dynamics calculations. Comparison of experimental and theoretical results confirmed the possible formation of multiple inclusion complexes with guest molecules capable of forming hydrogen bonds. This finding gives new insight into the mechanism of formation of host–guest complexes and shows that hydrophobic interactions play a secondary role in this case. [Figure: see text] ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00894-016-3061-6) contains supplementary material, which is available to authorized users

Nucleoside analog reverse-transcriptase inhibitors in membrane environment : molecular dynamics simulations

The behavior of four drugs from the family of nucleoside analog reverse-transcriptase inhibitors (zalcitabine, stavudine, didanosine, and apricitabine) in a membrane environment was traced using molecular dynamics simulations. The simulation models included bilayers and monolayers composed of POPC and POPG phospholipids. It was demonstrated that the drugs have a higher affinity towards POPG membranes than POPC membranes due to attractive long-range electrostatic interactions. The results obtained for monolayers were consistent with those obtained for bilayers. The drugs accumulated in the phospholipid polar headgroup region. Two adsorption modes were distinguished. They differed in the degree of penetration of the hydrophilic headgroup region. Hydrogen bonds between drug molecules and phospholipid heads were responsible for adsorption. It was shown that apricitabine penetrated the hydrophilic part of the POPC and POPG membranes more effectively than the other drugs. Van der Waals interactions between S atoms and lipids were responsible for this

A way to introducing a hydrophilic bioactive agent into model lipid membranes : the role of cetyl palmitate in the interaction of curcumin with 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine monolayers

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Metoda wydłużania w wariancie zrównoleglonym

Pokazano, że technika obcięcia zastosowana w metodzie wydłużania istotnie przyspiesza obliczenia kwantowo-chemiczne w formaliźmie Hartreego-Focka (HF). Metoda ta sprawdza się wyjątkowo dobrze w obliczeniach przeprowadzanych na wielu procesorach. W pracy porównano zarówno całkowity czas obliczeń, jak i jego najbardziej czasochłonnych części, z tradycyjnym schematem obliczeniowym metody HF.It is demonstrated that the elongation cutoff technique (ECT) substantially speeds up the quantum-chemical calculation at Hartree-Fock (HF) level of theory and is especially well suited for parallel performance. A comparison of ECT timings for water chains with the reference HF calculations is given. The analysis includes the overall CPU (central processing unit) time and its most time consuming steps

Electrophilic Benzylation of the Pyridine Ring; a Charge Sensitivity and MNDO Study

The sensitivity of carbon and nitrogen atoms in two structures of 2- benzylaminopyridine (I,II) and its cations (III,IV) to an electrophilic agent attack were investigated in order to determine which are responsible for its 5-benzyl and AT-benzyl derivative formation in the reaction with benzyl cation. For predicting the most sensitive centres, net atomic charges and HOMO electron density plots were calculated by the MNDO-method, as well as the Fukui function (FF) indices and relaxed chemical potentials of atoms-in- molecules (AIM) within a charge sensitivity (CS) scheme. The analysis indicates that only in structures I and II the sensitivity of the carbon and nitrogen atoms explains the experimental facts. The analysis also shows that 2-benzylaminopyridine cations (m and IV) did not participate in the 5-benzyl and IV-benzyl derivatives of 2-benzylaminopyridine formation. Their presence in the reaction mixture influenced the formation and stabilization of the benzyl cation

Protonation of Pyrrole: A Model Hardness (Softness) Sensitivity Study

The protonation mechanism of pyrrole is investigated in terms of various global and regional (fragment) hardness (softness) parameters and related quantities in order to identify the most sensitive criteria indicating the known a-preference for electrophilic substitution in this molecule. Both rigid and relaxed hardness data are discussed. Numerical results for the H+... pyrrole system, obtained from a realistic semiempirical Atoms-in-a- Molecule (AIM) hardness matrix, clearly show that the resultant AIM hardness (the inverse of the AIM softness) provides the most sensitive reactivity index. It measures the effective AIM hardness in a given molecular environment and predicts the a-carbons to be effectively much harder than b-carbons, for all alternative approaches of proton. Relaxational contributions to the relevant hardnesses, representing the effect of moderating electron redistributions outside the response and displacement molecular fragments, are shown to be very small and to have practically no effect on the selectivity of protonation

Generalized charge sensitivity analysis

Charge sensitivity analysis was originally introduced in the trivial-atom resolution. Here, we extend this resolution into force-field atoms. The AMBERff99 force-field resolution was employed. The effective elec- tronegativities and hardnesses were derived for five dif- ferent population analyses (Mulliken, Hirschfeld, AIM, NPA and Voronoi charges) by applying evolutionary algorithms

Protonation of Pyrrole: A Model Hardness (Softness) Sensitivity Study

The protonation mechanism of pyrrole is investigated in terms of various global and regional (fragment) hardness (softness) parameters and related quantities in order to identify the most sensitive criteria indicating the known a-preference for electrophilic substitution in this molecule. Both rigid and relaxed hardness data are discussed. Numerical results for the H+... pyrrole system, obtained from a realistic semiempirical Atoms-in-a- Molecule (AIM) hardness matrix, clearly show that the resultant AIM hardness (the inverse of the AIM softness) provides the most sensitive reactivity index. It measures the effective AIM hardness in a given molecular environment and predicts the a-carbons to be effectively much harder than b-carbons, for all alternative approaches of proton. Relaxational contributions to the relevant hardnesses, representing the effect of moderating electron redistributions outside the response and displacement molecular fragments, are shown to be very small and to have practically no effect on the selectivity of protonation