Subporphyrinoid systems: a theoretical study of the effects of the diheteroatom substitution in pyrrole subunits and of the nature of the bridging meso linkages.

A theoretical study of the geometry, the electronic structure, the electronic absorption spectra, and (1)H and (13)C NMR spectra of the [14]subporphine(1.1.1)-hydroxyboron(III) complex, free-base subporphyrin, and its dioxygen and dithio pyrrole substituted derivatives using CH, N, and P as bridging meso linkages was performed at the B3LYP/6-311+G(2d,p)//B3LYP/6-31G(d) theory level.

On the mechanism of cyclization of 5-hexenylchromate intermediates in the reactions of Fischer carbene complexes with a lithium enolate and allylmagnesium bromide.

The mechanisms for the evolution of pentacarbonyl-5-hexenylchromate complexes, unsubstituted and methyl substituted at C2, formed from a pentacarbonyl(alkoxy)carbene complex of chromium, the corresponding ketone lithium enolate, and allylmagnesium bromide, were theoretically investigated by using DFT (Density Functional Theory) at the B3PW91/6-31G* level (LANL2DZ for Cr and Br) taking into account the effect of THF solvent through the PCM model (Polarizable Continuum Model). Methyl substitution at C2 provokes a shortening of about 5 degrees in the C1-C2-C3 angle that favors the formation of the pentacyclic product. Also, the presence of this methyl substituent at C2 sterically disfavors the formation of the hexacyclic product.

Molecular magnetic properties of heteroporphyrins: a theoretical analysis.

B3LYP/6-31G(d) optimization of porphyrin, tetraphenylporphyrin and their 21,23-diheteroatom substituted derivatives with O, S, and Se heteroatoms was performed. A planar macrocycle was found in all cases except 21,23-dioxatetraphenylporphyrin which presents only slight deviations from planarity. A Bader analysis uncovers the presence of S-S and Se-Se interactions in the four corresponding heteroporphyrins, which appreciably distort the original unsubstituted macrocycles.

Quantum chemical study on the coordination environment of the catalytic zinc ion in matrix metalloproteinases.

X-ray analyses of matrix metalloproteinases (MMPs) have shown that the catalytic zinc ion (Zn1) can bind to one to three water molecules in addition to three conserved histidine residues. To estimate the relative stability of the possible Zn1 coordination structures in the active site of the MMPs, we carry out computational analyses on the coordination environment of the Zn1 ion in the gelatinase A enzyme (or matrix metalloproteinase 2; MMP-2). Four-, five-, and six-coordinated complexes representative of the Zn1 site are fully characterized by means of quantum mechanical (QM) methodologies.

Formation of trichlorinated dibenzo-p-dioxins from 2,4-dichlorophenol and 2,4,5-trichlorophenolate: a theoretical study.

The reaction of the 2,4,5-trichlorophenolate anion with 2,4-dichlorophenol to afford trichlorinated dibenzo-p-dioxins (T3CDDs) is investigated at the B3LYP/6-31+G(d) and B3LYP/6-311+G(3df,2p)//B3LYP/6-31+G(d)+ZPVE(B3LYP/6-31+G(d)) levels of theory. The first stage of the process corresponds to the formation of a predioxin, which can evolve through four different routes. Two of them lead directly to the products 2,3,7-T3CDD and 1,3,8-T3CDD, and the other two afford different predioxin-type intermediates, which in turn can evolve through all or some of the four routes to give new predioxins or T3CDD.

A theoretical study of rhodium(I) catalyzed carbonylative ring expansion of aziridines to beta-lactams: crucial activation of the breaking C-N bond by hyperconjugation.

The regioselectivity and enantiospecificity of the [Rh(CO)2Cl]2-catalyzed carbonylative ring expansions of N-tert-butyl-2-phenylaziridine to yield 2-azetidinone and the lack of reactivity of N-tert-butyl-2-methylaziridine along this process were investigated at the B3LYP/6-31G(d) (LANL2DZ for Rh) theory level taking into account solvent effects. According to our results, the regioselectivity in the ring expansion of N-tert-butyl-2-phenylaziridine and the unreactivity of N-tert-butyl-2-methylaziridine experimentally observed are determined by the different degree of activation of the breaking C-N bond in the initial aziridine-Rh(CO)2Cl complex due to its hyperconjugation interaction with the substituent on the carbon atom. When a phenyl substituent is present its hyperconjugation interaction with the C(alpha)-N bond facilitates the insertion of the metal atom into this bond.

A theoretical proposal for the synthesis of carbapenems from 4-(2-propynyl)azetidinones promoted by [W(CO)5] as an alternative to the Ag+-assisted process.

The synthesis of carbapenems from 4-(2-propynyl)azetidinones assisted by both Ag+ and [W(CO)5] was theoretically investigated by using the B3LYP/6-31+G(d)-LANL2DZ level, taking into account the effect of solvent by the PB-SCRF model implemented in Jaguar. According to our results, the silver-assisted cyclization is a concerted process for which the low yield experimentally observed could mainly stem from the alkaline hydrolysis of the beta-lactam ring. This process is very efficiently catalyzed by Ag+, making it competitive with the formation of the carbapenem.

Synthesis of beta-lactams by Ag+-induced ring expansion of 1-hydroxycyclopropylamines: a theoretical analysis.

A theoretical analysis of the silver-induced ring expansion of N-chloro-N-methyl-1-hydroxycyclopropylamine to form N-methyl-2-azetidinone, and of the Cl(-) elimination from this substrate without Ag(+) assistance, was performed using the B3LYP method and the 6-31+G(d) basis set for C, N, O, H, and Cl atoms and the relativistic effective core pseudopotential LANL2DZ complemented with one set of f polarization functions (zeta(f) = 0.473) for the Ag atom. The partial Ag(+)-assisted extrusion of Cl(-) at the rate-determining transition state provokes an important change in the nodal properties of the frontier molecular orbitals of the H(3)CClNCOHAg(+) fragment, thus making very stabilizing HOMO-LUMO interactions between this fragment and the C(2)H(4) moiety possible.

Radical ring expansion reactions of methylenecyclopropane derivatives: a theoretical study.

The evolution of the primary radicals from 1-(3-bromopropyl)-2-ethyl-3-methylenecyclopropane, 1-(3-bromopropyl)-1-trimethylsilyl-2-methylenecyclopropane, 1-(3-bromobutyl)-2-ethyl-3-methylenecyclopropane, and 1-(3-bromobutyl)-1-trimethylsilyl-2-methylenecyclopropane was theoretically studied at the ROMP2/6-311++G(d,p)//UB3LYP/6-31G(d,p) theory level taking into account the effect of solvent through a PCM-UAHF model. For the propyl-substituted radicals, the attack of the radical center on the double bond takes place most favorably in an exo fashion. The subsequent ring expansions yield the product corresponding to the rupture of the endo C-C bond as the most favorable one in accordance with the experimental results.

Assessing the protonation state of drug molecules: the case of aztreonam.

Herein we examine the viability of physicochemical approaches based on standard computational chemistry tools to characterize the structure and energetics of flexible drug molecules with various titratable sites. We focus on the case of the monobactam antibiotic aztreonam, whose structure and physicochemical properties have been ascribed to several tautomeric forms, although it is still unclear which protonation states are responsible for its biological activity. First, we experimentally determined the pKa values for aztreonam over the pH range 0.

Molecular dynamics simulations of class C beta-lactamase from Citrobacter freundii: insights into the base catalyst for acylation.

Herein, we present results from molecular dynamics (MD) simulations of the class C beta-lactamase from Citrobacter freundii and its Michaelis complex with aztreonam. Four different configurations of the active site were modeled in aqueous solution, and their relative stability was estimated by means of quantum mechanical energy calculations. For the free enzyme, the energetically most stable configurations present a neutral Lys67 residue or an anionic Tyr150 side chain.

Relative Gibbs energies in solution through continuum models: effect of the loss of translational degrees of freedom in bimolecular reactions on Gibbs energy barriers.

We present here a cell model for evaluating Gibbs energy barriers corresponding to bimolecular reactions (or processes of larger molecularity) in which a loss of translational degrees of freedom takes place along the reaction coordinate. With this model, we have studied the Walden inversion processes: Xa- + H3CXb --> XaCH3 + Xb- (X = F, Cl, Br, and I). In these processes, our model yields an increase of about 2.

Mechanism of cycloaddition reactions between ketene and N-silyl-, N-germyl-, and N-stannylimines: a theoretical investigation.

A theoretical study of the cycloaddition reactions of ketene and N-silyl-, N-germyl-, and N-stannylimines were performed at the B3LYP/6-311+G(d,p) theory level using the LANL2DZ effective core potential for Ge and Sn and taking into account the effect of diethyl ether solvent by means of the polarizable continuum model method. According to the obtained results the reaction between ketene and N-germylimine is a two-step process due to the effect of solvent, whereas the cycloaddition of ketene and N-silylimine follows a three-step mechanism because in this case the evolution of the electronic energy along the reaction coordinate predominates over the effect of solvent. For N-stannylimine the two- and three-step mechanisms are competitive.

Three-carbon Dowd-Beckwith ring expansion reaction versus intramolecular 1,5-hydrogen transfer reaction: a theoretical study.

[Reaction: see text]. The evolution of the primary radicals formed by addition of AIBN/HSnBu3 to methyl 1-(3-iodopropyl)-5-oxocyclopentanecarboxylate, methyl (1R,2R)-1-(3-iodopropyl)-2-methyl-5-oxocyclopentanecarboxylate, and methyl (1R,2S)-1-(3-iodopropyl)-2-methyl-5-oxocyclopentanecarboxylate in benzene has been theoretically investigated by ROMP2/6-311++G(2d,2p)//UB3LYP/6-31G(d,p) calculations taking into account the effect of solvent through a PCM-UAHF model. According to the theoretical results, for methyl 1-(3-iodopropyl)-5-oxocyclopentanecarboxylate and methyl (1R,2S)-1-(3-iodopropyl)-2-methyl-5-oxocyclopentanecarboxylate the major product is the cyclooctane derivative from the three-carbon ring expansion, whereas for methyl (1R,2R)-1-(3-iodopropyl)-2-methyl-5-oxocyclopentanecarboxylate the major product is that corresponding to the 1,5-H transposition in agreement with the experimental findings.

A theoretical analysis of the coordination modes of CuII with penicillins: activation of the beta-lactam C-N bond.

The interaction of CuII with 6-formylamino-3alpha-carboxypenam and 6-acetylamino-3alpha-carboxypenam was investigated by means of DFT calculations with the UB3LYP functional. Nine different modes of complexation between CuII and 6-formylamino-3alpha-carboxypenam were located. When two water molecules directly bonded to CuII are included in the calculations on 6-acetylamino-3alpha-carboxypenam as penicillin model, only six CuII(H2O)2-6-acetylamino-3alpha-carboxypenam complexes (1S-6S) are found.

Insights into the base catalysis exerted by the DD-transpeptidase from Streptomyces K15: a molecular dynamics study.

Herein, we present results from molecular dynamics simulations of the DD-transpeptidase/penicillin-binding protein from Streptomyces K15 and its Michaelis complex with benzylpenicillin. For the apo-enzyme, six different configurations of the active site were modeled in aqueous solution and their relative stabilities were estimated by means of quantum mechanical energy calculations. The energetically most stable configuration has a neutral Lys(213) residue.

Molecular dynamics simulations of the TEM-1 beta-lactamase complexed with cephalothin.

Herein, we present theoretical results aimed at elucidating the origin of the kinetic preference for penicillins over cephalosporins characteristic of the TEM/SHV subgroup of class A beta-lactamases. First, we study the conformational properties of cephalothin showing that the C2-down conformer of the dihydrothiazine ring is preferred over the C2-up one by approximately 2 kcal/mol in solution (0.4-1.

Stereodynamics of bond rotation in tertiary 1-naphthoic acid amides: a computational study.

Computations sho that independent N-CO rotation is not possible in N,N-diethyl-1-naphthamide, and that the coalescence signal corresponding to methyl equivalence observed in the VT NMR spectrum of this system is caused by a complex process whose rate-determining step implies concerted N-CO, Ar-CO, and ethyl rotations. The calculated Gibbs energy barriers for these processes in solution are in good agreement with the experimental values.

Conformational properties of penicillins: quantum chemical calculations and molecular dynamics simulations of benzylpenicillin.

Herein, we present theoretical results on the conformational properties of benzylpenicillin, which are characterized by means of quantum chemical calculations (MP2/6-31G* and B3LYP/6-31G*) and classical molecular dynamics simulations (5 ns) both in the gas phase and in aqueous solution. In the gas phase, the benzylpenicillin conformer in which the thiazolidine ring has the carboxylate group oriented axially is the most favored one. Both intramolecular CH.

Theoretical study of the mechanism of the formation of 3-unsubstituted 4,4-disubstituted beta-lactams by silver-induced ring expansion of alkoxycyclopropylamines: a new synthetic route to 4-alkoxycarbonyl-4-alkyl-2-azetidinones.

The mechanisms of formation of 4,4-dialkyl- and 4-alkoxycarbonyl-4-alkyl-2-azetidinones by silver-induced ring expansion of the corresponding 2,2-disubstituted N-chloro-1-hydroxycyclopropylamines were theoretically investigated by means of the B3LYP method and the PCM solvation model. The obtained results indicate that these reactions are facile two-step regioselective processes proceeding through a short-life nitrenium intermediate. The theoretical results thus predict that this synthetic strategy, which has already been used to obtain 4,4-dialkyl-2-azetidinones, could also be a new route to efficiently obtain in a regio- and stereoselective way 4-alkoxycarbonyl-4-alkyl-2-azetidinones, which are precursors of conformationally constrained amino acids.

Intramolecular aromatic 1,5-hydrogen transfer in free radical reactions III. Reactivity of diaryl ketones, ethers, thioethers, sulfoxydes, and sulfones. An experimental and theoretical study.

[reaction: see text] Experiments show that free radical hydrogen shift is significant in the Pschorr cyclization of diphenyl ethers (X = O) and thioethers (X = S) and does not take place with sufoxides (X = SO) and sulfones (X = SO(2)). DFT calculations of the product ratios, activation energies, rate constants for H-transfers, and ring-closings at the UB3PW91/6-31G(d,p) level are in excellent agreement with the experimental results reported here and elsewhere in the literature.

Synthesis of beta-lactams from a N-rhenaimine: effect of the transition metal on the energetic profile of the Staudinger reaction.

As depicted in the scheme, the alkylidenamido complex 1, a N-rhenaimine, reacts with ketenes to afford the beta-lactams 2-4, which possess a {Re(CO)3(bpy)} fragment as substituent at nitrogen. Clean demetalations using HOTf or MeOTf yield the free beta-lactams or N-methyl-beta-lactams along with [Re(OTf)(CO)3(bpy)]. DFT calculations help to rationalize why the reaction is faster than those of non transition metal N-substituted imines.

Insights into the acylation mechanism of class A beta-lactamases from molecular dynamics simulations of the TEM-1 enzyme complexed with benzylpenicillin.

Herein, we present results from molecular dynamics MD simulations ( approximately 1 ns) of the TEM-1 beta-lactamase in aqueous solution. Both the free form of the enzyme and its complex with benzylpenicillin were studied. During the simulation of the free enzyme, the conformation of the Omega loop and the interresidue contacts defining the complex H-bond network in the active site were quite stable.

Water-assisted alkaline hydrolysis of monobactams: a theoretical study.

A theoretical study of the water-assisted alkaline hydrolysis of 2-azetidinone, 3-formylamino-2-azetidinone and 3-formylamino-2-azetidine-1-sulfonate ion is carried out at the B3LYP/6-31+G* level. The effect of bulk solvent is taken into account using the PCM solvation model while specific solvent effects are represented by the inclusion of an ancillary water molecule along the reaction profile. The calculated free energy barriers in solution are in reasonable agreement with experimental values.