On the molecular mechanism of drug intercalation into DNA: a simulation study of the intercalation pathway, free energy, and DNA structural changes

Intercalation into DNA (insertion between a pair of base pairs) is a critical step in the function of many anticancer drugs. Despite its importance, a detailed mechanistic understanding of this process at the molecular level is lacking. We have constructed, using extensive atomistic computer simulations and umbrella sampling techniques, a free energy landscape for the intercalation of the anticancer drug daunomycin into a twelve base pair B-DNA. A similar free energy landscape has been constructed for a probable intermediate DNA minor groove-bound state. These allow a molecular level understanding of aspects of the thermodynamics, DNA structural changes, and kinetic pathways of the intercalation process. Key DNA structural changes involve opening the future intercalation site base pairs toward the minor groove (positive roll), followed by an increase in the rise, accompanied by hydrogen bonding changes of the minor groove waters. The calculated intercalation free energy change is -12.3 kcal/mol, in reasonable agreement with the experimental estimate -9.4 kcal/mol. The results point to a mechanism in which the drug first binds to the minor groove and then intercalates into the DNA in an activated process, which is found to be in general agreement with experimental kinetic results.     

Infrared signatures of HNO3 and NO3(-) at a model aqueous surface. A theoretical study

The infrared signatures of nitric acid HNO3 and its conjugate anion NO3(-) at the surface of an aqueous layer are derived from electronic structure calculations at the HF/SBK+* level of theory on the HNO3 x (H2O)3 --> NO3(-) x H3O(+) x (H2O)2 model reaction system embedded in clusters comprising 33, 40, 45, and 50 classical, polarizable waters, mimicking various degrees of solvation [Bianco, R.; Wang, S.; Hynes, J. T. J. Phys. Chem. A 2007, 111, 11033]. The molecular level character of the various bands is discussed, and the solvation patterns are described in terms of hydrogen bonding and resulting polarization of the species' intramolecular bonds. Connection is made with assorted experimental results, including surface-sensitive Sum Frequency Generation spectroscopy of aqueous nitric acid solutions, infrared spectroscopy of amorphous thin films of nitric acid monohydrate (NAM) and dihydrate (NAD), and infrared and Raman spectroscopic results for bulk aqueous solutions of nitric acid and nitrate salts.     

Experimental and theoretical studies of the reaction of the OH radical with alkyl sulfides: 1. Direct observations of the formation of the OH-DMS adduct-pressure dependence of the forward rate of addition and development of a predictive expression at low temperature

A pulsed laser photolysis-pulsed laser-induced fluorescence (PLP-PLIF) system was employed to study the kinetics and mechanisms of reactions (1) OH + h6-DMS --> products and (2) OH + d6-DMS --> products. We report direct observations of the rate coefficients for the formation and dissociation of the h6-OHDMS and d6-OHDMS adducts over the pressure range 50-650 Torr and between 240 and 245 K, together with measurements of the oxygen dependence of the effective rate coefficients for reactions 1 and 2 under similar conditions. The effective rate coefficients increased as a function of O2 concentration reaching their limiting values in each case. The values of the adduct formation rate, obtained from the O2 dependencies, were in excellent agreement with values determined from direct observation of adduct equilibration in N2. OH regeneration is insignificant. The rate coefficients for the formation of the adduct isotopomers showed slight differences in their falloff behavior and do not approach the high-pressure limit in either case. The equilibrium constants obtained show no dependence on isotopomer and are in good agreement with previous work. A "second-law" analysis of the temperature dependence of the equilibrium constant gives an adduct bond strength (DeltaH degrees =-10.9 +/- 1.0 kcal mol(-1)), also in good agreement with previously reported values. Using the entropy calculated from the ab initio vibrational frequencies, we obtain a "third-law" value for the reaction enthalpy at 240 K, DeltaH(240K) degrees = -10.5 kcal mol(-1) in good agreement with the other approach. The rate coefficient for the reactions of the adducts with O2 was obtained from an analysis of the O2 dependence and was determined to be 6.3 +/- 1.2 x 10(-13) cm3 molecule(-1) s(-1), with no dependence on pressure or isotopomer. The pressure and temperature dependence for all of the elementary processes in the initial steps of the dimethylsulfide (DMS) oxidation mechanism have been characterized in the range 238-245 K, allowing the formulation of an expression which can be used to calculate the effective rate coefficient for reaction 1 at any pressure and oxygen concentration. The expression can calculate the effective rate coefficient for reaction 1 to +/- 40% over the range 220-260 K, with the largest errors at the extremes of this range. Gaussian 03 has been used to calculate the structure of the OH-DMS adduct and its deuterated isotopomer. We find similar bound structures for both isotopomers. The calculated enthalpies of formation of the adducts are lower than the experimentally determined values.     

Experimental and theoretical studies of the reaction of the OH radical with alkyl sulfides: 2. Kinetics and mechanism of the OH initiated oxidation of methylethyl and diethyl sulfides; observations of a two channel oxidation mechanism

A pulsed laser photolysis-pulsed laser induced fluorescence technique has been employed to measure rate coefficients for the OH initiated oxidation of methylethyl sulfide (MES) and diethylsulfide (DES). In the absence of oxygen and at low sulfide concentrations we measure rate coefficients that are independent of pressure and temperature. At high sulfide concentrations and a temperature of 245 K, we observed the equilibration of MESOH and DESOH adducts over the pressure range 100-600 Torr. In the presence of O(2) the observed rate coefficients show a dependence on the O(2) partial pressure. We measured the dependence of the overall rates of oxidation on the partial pressure of O(2) over the temperature range 240-295 K and at 200 and 600 Torr total pressures. All observations are consistent with oxidation proceeding via a two channel oxidation mechanism involving abstraction and addition channels, analogous to that observed in the OH initiated oxidation of dimethylsulfide (DMS). Structures and thermochemistry of the MESOH and DESOH adducts were calculated and all results compared to those for DMS. Calculated bond strengths of adducts increase with alkyl substitution but are comparable to that of the DMSOH adduct and are consistent with experimental observations.     

Synthesis of 2-aminoquinazolines from ortho-fluorobenzaldehydes

The reaction of guanidine carbonate with various ortho-fluorobenzaldehydes in N,N-diinethylacetamide was investigated as a potential route for preparing 2-aminoquinazolines. Eleven new 2-aminoquinazolines were elaborated in this manner in low to moderate yields. In general the best results were obtained with ortho-fluorobenzaldehydes possessing an electron withdrawing substituent at the other ortho position. Complex mixtures were obtained using 2-fluorobenzaldehyde, 2,5-difluorobenzaldehyde and 2-fluoro-5-methoxybenzaldehyde which were not resolved.     

Kinetics and mechanism of ligand substitution in binuclear nickel(II) and cobalt(II) complexes

The kinetics and mechanism of the removal of M²⁺ from bis-(heptane-2,4,6-trionato)M(II) [M = Ni, Co] by ethylenediminetetraacetic acid (EDTA), nitrilotriacetic acid (NAT), 1,2-cyclohexanediamine-N, N, N′, N′-tetraacetic acid (C_yDTA), and ethylenebis(oxyethylenenitrilo)tetraacetic acid (EGTA) have been investigated using stopped-flow spectrophotometry in methanol-water at 25°C and ionic strength 0.1 mol dm^?3 KNO₃. The reactions were investigated at a number of different pHs. An associative mechanism is proposed to account for the kinetic data. Although all the ligands have similar functional groups, their reactivity towards the parent complex is quite different. The pH dependence of the rate constants has been used to determine the relative reactivities of the various ligand species present. In the case of nitrilotriacetic acid, a nonlinear dependence on ligand concentration is observed, thus confirming the mechanism proposed. © 1995 John Wiley & Sons, Inc.     

Synthesis of 2-aminoquinazolines from ortho-fluoroketones

The reactions of ten ortho-fluoroketones with guanidine carbonate in N,N-dimethylacetamide were investigated as a new synthetic approach to 2-amino-4-alkyl- and 2-amino-4-arylquinazolines. The yields obtained ranged from low to moderate and were highly dependent upon the nature of the substituents on the reactant. Eight new quinazolines were elaborated in this study.