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. The geometrical structure of these systems is mainly determined by the internal area delimited by the meso atoms and the alpha-carbon atoms of the pyrrolic rings, and by the number and nature of the atoms located on this area. All the hydroxyboron subporphyrins and dioxo and dithio subporphyrins with CH meso connectors display a conical shaped geometry. The presence of strong repulsions between the atoms on the central zone of the remaining systems provokes a correlative tilting of one of the three rings with loss of the conical shape with important consequences on spectroscopic properties. A particularly interesting case is the dioxosubporphyrin with P connectors in which the large area of the central zone determined by these connectors allows for an almost planar geometry that endows it with special features. The molecules presenting a tilted ring display weak absorption bands. Generally, the intensity of the bands moderately increases when the geometry is cone shaped. The dioxo heterosubporphyrins with CH (conical shape) and P (almost planar) connectors present strong absorption bands. (1)H and (13)C chemical shifts clearly reflect the effect of geometry distortion provoked by the repulsion among the atoms of the central area of the system indicating a deep perturbation of the pi system of the molecules.

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. Thus, our results yield the hexacyclic system as the most favored product for the evolution of the unsubstituted alkylpentacarbonylchromate complex, and the pentacyclic product in the case of the substituted system, in good agreement with the experimental findings. The stereochemistry of the products experimentally observed is determined at the transition state for the migration of the Cr(CO)(5) fragment from C1 to C6 and the conformational rearrangement of the C1-C6 skeleton. Amine molecules, present in the reaction medium, can play a catalytic role by assisting the 1,2-H migration in the last step for the formation of hexacyclic products.

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. On one hand, B3LYP/LACVP* minimizations of various cluster models of the MMP-2 active site show that the trigonal bipyramidal geometry is energetically favored in the gas phase and that continuum solvent effects stabilize preferentially the tetrahedral complexes. On the other hand, B3LYP/OPLS-AA hybrid QM/molecular mechanical calculations in the solvated catalytic domain of the MMP-2 enzyme complemented with electrostatic Poisson-Boltzmann calculations show that the mature enzyme presents most likely a Zn1 ion coordinated by three histidine residues and two water molecules, while the active site glutamic acid is negatively charged. In consonance with X-ray diffraction data, other possible Zn1 configurations, a six-coordinated structure with Zn1-water as well as four- and five-coordinated complexes with a Zn1-bound hydroxide, are predicted to be very close in energy.

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. On the other hand, when the substituent is a methyl group, a larger stability of the initial complex along with a lower stabilization through hyperconjugation of the TS for insertion of the Rh atom into the C(alpha)-N bond make the ring expansion of N-tert-butyl-2-methylaziridine unviable. The enantiospecificity experimentally observed is also reproduced by our calculations given that the stereogenic center is never perturbed to change its configuration.

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. The cycloisomerization of 4-(2-propynyl)azetidinone promoted by [W(CO)5] is proposed as an alternative synthetic strategy to obtain the carbapenem. The endo cycloisomerization is by far the most favorable one. When the process is assisted by [(thf)W(CO)5], although the main product is the carbapenem, the formation of a carbene complex represents a certain competition. The presence of a Me3N molecule from the very start of the reaction causes an important catalytic effect considerably reducing the energy barriers corresponding to the H atom transfers and rendering a very efficient process. Moreover, this catalytic action determines the evolution of the system through only one mechanistic route which produces the carbapenem, hindering the formation of the carbene. Therefore, the cycloisomerization of 4-(2-propynyl)azetidinone promoted by [(Me3N)W(CO)5] constitutes an interesting alternative to the silver-assisted cyclization.

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. In the case of 1-(3-bromobutyl)-2-ethyl-3-methylenecyclopropane, the Gibbs energy barriers for the endo and exo attacks are the same, and the subsequent reversible evolution yields the product corresponding to the rupture of the exo C-C bond as the most favorable one through thermodynamic control in agreement with experiment. Finally, for 1-(3-bromobutyl)-1-trimethylsilyl-2-methylenecyclopropane, our calculations predict that the endo attack is 0.8 kcal/mol more favorable than the exo one. In the subsequent reversible ring expansion, the product corresponding to the rupture of the endo C-C bond is kinetically the most favored one in reasonable agreement with the experimental observations.

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 0.8-7.0 using both 1H NMR and 13C NMR spectroscopy. Second, we carried out quantum chemical calculations on snapshots extracted from classical molecular dynamics simulations. Various levels of approximation were used in the energy calculations: ONIOM(HF/3-21G*:AMBER) for geometry relaxation, B3LYP/6-31+G** for electronic and electrostatic solvation energies, and molecular mechanics for attractive dispersion energy. The value of the free energy of solvation of a proton was treated as a parameter and chosen to give the best match between calculated and experimental pKa values for small molecules. Overall, this computational scheme can give satisfactory results in the pKa calculations for drug molecules.

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. Our calculations predict that these two configurations are quite close in terms of free energy, the anionic Tyr150 state being favored by approximately 1 kcal/mol. In contrast, for the noncovalent complex formed between the C. freundii enzyme and aztreonam, the energetic analyses predict that the configuration with the neutral Lys67 residue is much more stable than the anionic Tyr150 one (approximately 20 kcal/mol). Moreover, the MD simulations reveal that the neutral Lys67 state results in a proper enzyme-aztreonam orientation for nucleophilic attack and in a very stable contact between the nucleophilic hydroxyl group of Ser64 and the neutral amino side chain of Lys67. Thus, both the computed free energies and the structural analyses support the assignation of Lys67 as the base catalyst for the acylation step in the native form of the C. freundii enzyme.

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 2.3-3.4 kcal/mol in Gibbs energy in solution corresponding to the loss of the translational degrees of freedom when passing from separate reactants to the TS in good agreement with experimental data. The corresponding value in the gas phase is about 6.7-7.1 kcal/mol. When the difference between these two figures is used to correct the results obtained by the standard UAHF implementation of the continuum model, the theoretical results are brought significantly closer to the experimental ones. This seems to indicate that for these reactions the parametrization used does not adequately introduce the increase in Gibbs energy corresponding to the constriction of the translational motion of the species along the reaction coordinate when passing from the gas phase to solution. Therefore, we believe that continuum models could perform much better if we released the parametrization process from the task of taking into account the constriction in translation motion in solution, which could be more adequately evaluated using the cell model proposed here, thus allowing it to focus on better reproducing all the remaining solvation effects.

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. In all the cases the rate-determining barrier corresponds to the evolution of the azadiene intermediate. The cycloaddition of ketene and N-germylimine is kinetically the most favorable reaction of the three studied by us and can take place as a domino process. In the three cases the isomerization of the imine through the inversion at the nitrogen atom is easier than the formation of the azadiene intermediate so that the three processes would afford the trans-beta-lactam.

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. This different behavior is a consequence of several factors determining the relative energy barriers. The methyl substituent destabilizes the ring expansion process for methyl (1R,2R)-1-(3-iodopropyl)-2-methyl-5-oxocyclopentanecarboxylate because of steric repulsion but favors it in the case of the beta-trans-substituted substrate because it makes possible the evolution of the system along more favorable conformations. The methyl group also favors the 1,5-H transposition rendering the transposed product a tertiary radical. The second stage of the ring expansion process is stabilized by resonance.

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. In this configuration, the nucleophilic Ser(35) hydroxyl group interchanges with a water molecule in the "oxy-anion hole" and the Lys(38)/Lys(213) ammonium/amino groups are connected through the Ser(96) hydroxyl group. Subsequently, the enzyme-penicillin complexes corresponding to the four most stable configurations of the apo-enzyme were modeled. In the presence of the beta-lactam antibiotic, the configuration with a neutral Lys(38) residue is favored energetically and shows the best orientation for nucleophilic attack. In addition, a very stable contact between the Ser(35) hydroxyl group and the neutral amino group of Lys(38) supports the assignation of Lys(38) as the base catalyst for the acylation step. Finally, some mechanistic implications of enzyme-inhibitor contacts involving the benzylpenicillin carboxylate group are also discussed.

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. In solution the four most stable complexes obtained from our calculations, 6S, 1S, 2S, and 3S, exhibit CuII in square-planar coordination with at least one bond to the carboxylate group, in agreement with experimental evidence. Complexes 6S, 1S, and 3S were previously suggested by available experimental evidence. In three of the most stable complexes (6S, 2S, and 3S) the beta-lactam C-N bond is remarkably activated and displays C-N bond lengths similar to those found in some tetrahedral intermediates located for the hydrolysis of 2-azetidinones. This suggests that these kinds of complexes belong to the reaction coordinate for the degradation of beta-lactam antibiotics in the presence of CuII.

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 (0.4-1.4 kcal/mol in the gas phase). Second, the TEM-1 beta-lactamase complexed with cephalothin is investigated by carrying out a molecular dynamics simulation. The DeltaG(binding) energy is then estimated using molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) and quantum chemical PBSA (QM-PBSA) computational schemes. The preferential binding of benzylpenicillin over cephalothin is reproduced by the different energetic calculations, which predict relative DeltaDeltaG(binding) energies ranging from 1.8 to 5.7 kcal/mol. The benzylpenicillin/cephalothin DeltaDeltaG(binding) energy is most likely due to the lower efficacy of cephalosporins than that of penicillins in order to simultaneously bind the "carboxylate pocket" and the "oxyanion hole" in the TEM-1 active site.

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.

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. This interaction leads to the ring opening and release of most of the strain energy, giving rise to a low energy barrier for the process. Also, by assisting the Cl(-) extrusion, Ag(+) avoids the elimination of the hydroxyl hydrogen atom, which would provoke the fragmentation of the system instead of the formation of the beta-lactam.

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. O and dispersion interactions contribute to stabilize the axial conformer with respect to the equatorial one. In aqueous solution, a molecular dynamics simulation predicts a relative population of the axial:equatorial conformers of 0.70:0.30 in consonance with NMR experimental data. Overall, the quantum chemical calculations as well as the simulations give insight into substituent effects, the conformational dynamics of benzylpenicillin, the frequency of ring-puckering motions, and the correlation of side chain and ring-puckering motions.

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.