We compare the strategy found by the optimal control theory in a complex molecular system according to the active subspace coupled to the field. The model is the isomerization during a Cope rearrangement of Thiele's ester that is the most stable dimer obtained by the dimerization of methyl-cyclopentadienenylcarboxylate. The crudest partitioning consists in retaining in the active space only the reaction coordinate, coupled to a dissipative bath of harmonic oscillators which are not coupled to the field. The control then fights against dissipation by accelerating the passage across the transition region which is very wide and flat in a Cope reaction. This mechanism has been observed in our previous simulations [Chenel et al., J. Phys. Chem. A 116, 11273 (2012)]. We compare here, the response of the control field when the reaction path is coupled to a second active mode. Constraints on the integrated intensity and on the maximum amplitude of the fields are imposed limiting the control landscape. Then, optimum field from one-dimensional simulation cannot provide a very high yield. Better guess fields based on the two-dimensional model allow the control to exploit different mechanisms providing a high control yield. By coupling the reaction surface to a bath, we confirm the link between the robustness of the field against dissipation and the time spent in the delocalized states above the transition barrier.

We present a preliminary simulation toward the control of the Cope rearrangement of the most stable isomer of methyl-cyclopentadienylcarboxylate dimer. An experimental investigation of the dimerization of methyl-cyclopentadienylcarboxylate has been carried out. It shows that the most stable isomer of the dimer, the Thiele's ester, is the major product of the dimerization. The simulation takes it as the initial state for the further control of the Cope reaction. The aim of the simulation is to examine the possibility of laser control to form the target product, not detected during the dimerization. The relevant stationary states have been characterized at the DFT B3LYP level, particularly the Cope transition state in which the dimer is connected only by a single bond r(1). A minimum energy potential surface has been computed in a two-dimensional subspace of two bounds r(2) and r(3) which achieve the dimerization and have a very high weight in the reaction path from the Cope TS to the two adducts. Quantum wave packet optimal control simulation has been studied in a one-dimensional model using an active coordinate r(-) - r(3) - r(2) which nearly corresponds to the reaction path. The stability of the optimal field against dissipation is examined by a non-Markovian master equation approach, which is perturbative in the system-bath coupling but without limitation on the strength of the field.

In this work, we present optimal control calculations in a dissipative environment.To this end, the auxiliary density matrix method describing the dissipative quantum dynamics is combined with optimal control theory.The resulting approach, which is nonperturbative in the lasersystem interaction, is applied to model the control of Cope's isomerization of the methyl-cyclopentadienylcarboxylate dimer, described as the motion along a one-dimensional reaction path.The construction of the reaction path model as well as the dipole moments required for the laser interaction are obtained from DFT quantum chemistry calculations.As a main result, we show that the proposed methodology, which includes the environment at the design stage of the control, leads to control fields which can react on dissipative effects during the dynamics and lead to an increased control objective, as compared to control fields obtained without dissipation.The chosen example is analyzed in detail, and the physical mechanisms of the control under dissipation are elucidated.

The triplet Hartree–Fock (HF) instability is investigated through the examples of substituted ethylenes and the small linear conjugated systems butadiene, hexatriene, octatetraene. A statistical analysis is performed for several conformations of the latters. The second eigenvalue of the instability matrix appears to be able to discriminate the groups of unsaturated compounds. The HF instability is largely influenced by conjugation and mesomeric effects and thus by the geometry. The number of π electrons is also an important factor. The electronic correlation related to the HF instability is not quantified by the energy difference between the post-HF and HF levels.

We present a complete analysis of the laser control of a model molecular system using both optimal control theory and adiabatic techniques. This molecule has a particular potential energy surface with a bifurcating region connecting three potential wells which allows a variety of processes such as isomerization, tunneling, or implementation of quantum gates on one or two qubits. The parameters of the model have been chosen so as to reproduce the main features of H3CO which is a molecule benchmark for such dynamics. We show the feasibility of different processes and we investigate their robustness against variations of laser field. We discuss the conditions under which each method of control gives the best results. We also point out the relation between optimal control theory and local control.

The inclusion complexes of tagitinin C with beta-, 2,6-di-O-methyl-beta- and gamma-cyclodextrin (CyD) was investigated in aqueous medium. The stoichiometric ratios and stability constants (K(f)) which describe the extent of formation of the complexes have been determined by UV spectroscopy and direct current tast polarography (DC(tast)), respectively. For each complex, a 1:1 molar ratio was formed in solution and the trend of stability constants was K(f) (2,6-di-O-methyl-beta-CyD)>K(f) (gamma-CyD)>K(f) (beta-CyD). The effect of molecular encapsulation on the photochemical conversion of tagitinin C was evaluated. No significant protection efficacy was noticed with beta- and gamma-CyD for the complexed drug with the respect to the free one. On the other hand, the photochemical conversion rate was slowed in presence of 2,6-di-O-methyl-beta-CyD. Data from (1)H NMR and ROESY experiments provided a clear evidence of formation of inclusion complexes. The lactone, the ester and the unsaturated ketone parts of tagitinin C inserted into the wide rim of the CyDs torus. These experimental results were confirmed by the molecular modeling using semiempirical Austin Model 1 (AM1) method.

Quantum dynamics in a valley ridge inflection (VRI) point region is analyzed in the case of the Diels-Alder endo-dimerization of cyclopentadiene pointed out recently by [Caramella et al., J. Am. Chem. Soc. 124, 1130 (2002)]. The VRI point is located along the reaction path connecting the bispericyclic symmetrical transition structure put in evidence by Caramella et al. and the transition state of the Cope rearrangement. Dynamics is carried out by using constrained Hamiltonian methodology. The active coordinates are the first formed C-C bond length and the difference between the two other C-C bond lengths which achieve the dimerization as 4+2 or 2+4 adducts. A two-dimensional (2D) minimum-energy surface have been computed at the Becke 3 Lee-Yong-Parr6-31G* level. The energy landscape can be classified as an uphill ridge-pitchfork VRI bifurcation according to a recent classification of bifurcation events [W. Quapp, J. Mol. Struct. 695-696, 95 (2004)]. Dynamics does not describe the thermal reaction but concerns wave packets which could be prepared by pulse reagents, i.e., by coherent control. We analyze how the shape and initial location on the ground potential-energy surface are linked to the synchronous or asynchronous mechanism of the final step after the first transition state. We use a one-dimensional model of optimum control theory to check the feasibility of such a coherent preparation. The wave-packet evolution in the VRI domain is well explained by semiclassical predictions even with the negative curvature of the unstable ridge. Finally, a crude model of dissipation has been introduced to test the stability of the 2D predictions.

RGD (Arg-Gly-Asp) peptidomimetics have been designed for covalent anchorage on biomaterials. The tyrosine template was thus equipped with (i) a basic side chain of various flexibility, (ii) an acidic side chain, which incorporated the XPS fluorine tag, and (iii) a spacer-arm terminated by a primary amine for surface grafting. The most active compounds showed IC50 values in the nanomolar range versus isolated human integrins αVβ3 and αIIbβ3. Preincubation of CaCo2 cells with soluble peptidomimetics (2 and 19a) prevented cellular adhesion on culture plates coated with vitronectin. On the other hand, peptidomimetics (19a and 19b) immobilized on a poly(ethylene)terephthalate membrane (PET) promoted CaCo2 cells adhesion. A modeling study at the ab initio level in MINI-1′ basis allowed to compare the various synthetic ligands of integrins and to propose novel pharmacophore structures.

Vertical ionization energies (IE) as a function of the conformation are determined at the quantum chemistry level for eighteen α-L-amino acids. Geometry optimization of the neutrals are performed within the Density Functional Theory (DFT) framework using the hybrid method B3LYP and the 6-31G**(5d) basis set. Few comparisons are made with wave-function-based ab initio correlated methods like MP2, QCISD or CCSD. For each amino acid, several conformations are considered that lie in the range 10-15 kJ/mol by reference to the more stable one. Their IE are calculated using the Outer-Valence-Green's-Functions (OVGF) method at the neutrals' geometry. Few comparisons are made with MP2 and QCISD IE. It turns out that the OVGF results are satisfactory but an uncertainty relative to the most stable conformer at the B3LYP level persists. Moreover, the value of the IE can largely depend on the conformation due to the fact that the ionized molecular orbitals (MO) can change a lot as a function of the nuclear structure.

4-(Alkylamino)carbonyl-1-(alkoxy)carbonyl-2-azetidinones (9–11) have been prepared in five steps from 4-(benzyloxy)carbonyl-1-(t-butyldimethyl)silyl-2-azetidinone (1). The β-lactam reactivity of 9 has been established by 1H NMR experiment. Compound 11 was a good reversible inhibitor of PPE and HLE. Based on theoretical design, series of 2-azetidinones (12–17) and 4-(alkoxy)carbonyl-2-azetidinones (18–21) bearing various carbonyl (ester, thiolester, amide) and thiocarbonyl (thioamide) functionalities at position N1 were similarly prepared. In the absence of C4-substituent, the compounds were inactive against elastases. On the other hand, 4-(benzyloxy)carbonyl-1-(ethylthioxy)carbonyl-2-azetidinone (19) and 4-(benzyloxy)carbonyl-1-(benzylamino)thiocarbonyl-2-azetidinone (21) were both good reversible inhibitors, but acting most probably via different mechanisms (enzymic processing of the exocyclic ester function or β-lactam ring opening).

The ability of cyclodextrins (CDs) to increase the solubility of cyproterone acetate (CPA) was previously shown by phase-solubility and NMR studies [1]. In the present work, the influence of various CDs on the stability of CPA was studied in pH 6 and pH 8 aqueous solutions at 25 °C. Different CDs were tested: hydroxypropyl-β-cyclodextrin (HPβCD), randomly methylated β-cyclodextrin (RAMEB), hydroxypropyl-γ-cyclodextrin (HPγCD) and γ-cyclodextrin (γCD). At pH 6, the presence of these CDs reduces the degradation of CPA. Nevertheless, at pH 8, the γ-CD derivatives are ineffective against the degradation of CPA, whereas the β-CD derivatives (HPβCD and RAMEB) allow decreasing CPA hydrolysis. Molecular modeling was performed to theoretically calculate some of the most energetically favorable conformations for γ-CD and RAMEB complexes with CPA. The position of the ester group in the CD cavity seems to be the most important factor influencing the hydrolysis of CPA. Other factors, such as the size of the cavity, the substitution of the CD hydroxyls and the stability constant also have a strong incidence on CPA stability.

A new asymmetric synthesis of 2-substituted chiral chromanes has been achieved. The key step is the intramolecular conjugate addition of a phenolic nucleophile on a α,β-unsaturated ester catalyzed by Cinchona alkaloids. The high ee’s obtained with cinchonine and its derivatives have been rationalized by ab initio quantum chemistry calculations of transition state structures.

The problem of bifurcating reaction paths is revisited by wave packet (WP) dynamics. The pitchfork model connecting five stationary points—a reactive, two transition structures and two enantiomeric products—is characterized by a Valley Ridge inflection point (VRI) where WP could leave the standard intrinsic reaction path. We question the role of such a VRI point to determine whether the mechanism is sequential or concerted. WP simulations on two-dimensional minimum energy surfaces are carried out in the benchmark case of the methoxy radical isomerization H3CO→H2COH. The ab initio potential energy surface (PES) is fitted to an analytical model which is bent to analyze the incidence of geometrical parameters on the WP behavior. For each of these generated PES, the WP width in the entrance valley is the main factor which conditions the behavior on the unstable ridge. The WP evolution is also analyzed in terms of nonadiabatic transitions among adiabatic channels along the reaction coordinate. Finally, the location of VRI points according to an invariant definition is discussed.

A strategy to obtain quantum corrections to the cumulative reaction probability from a subspace of active coordinates is analyzed. The kinetic energy operator exactly takes into account the constraints due to inactive coordinates. The geometry of the inactive skeleton is adiabatically adjusted to the dynamical variables or simply frozen according to the coupling to the active space. Dynamics is carried out using the curvilinear coordinates of the Z-matrix so that computation of the potential energy surface and dynamics are coupled. The cumulative reaction probability N(E) is obtained directly in a large range of energy by a time independent formulation of the Zhang and Light transition state wave packet method. NnD(E) is first computed in the active n-dimensional space and then convoluted with a bath. The efficiency of the Chebyshev expansion of the microcanonical projection operator δ(E−ĤnD) appearing in the quantum expression of NnD(E) is checked. The method is implemented for the study of tunneling effect in H transfer. The coordinates are three spherical coordinates referred to the frozen or adiabatic skeleton. We compare the quantum corrections brought about by different 2D groups of internal coordinates.

The total number of possible retrosynthetic bisections Of C-60 leads to nine different isometric C-30 fragments. These molecules include five chiral units, four of which derive from partitions corresponding to four distinct "Coupes du Roi". The energies, curvatures, and homodesmotic stabilization energies of the C-30 fragments are evaluated at the ab initio 6-31G level.

A series of 1,4-bis(alkoxycarbonyl)azetidin-2-ones, designed as potential suicide-inhibitors of serine proteases, has been synthesized and evaluated against porcine pancreatic elastase (PPE). The most active compound (Ki∼10μM; reversible inhibitor) was equipped with phenethyloxycarbonyl and benzyloxycarbonyl side-chains at positions N1 and C4, respectively, with the (S)-configuration. 1H NMR spectroscopic analysis of the reaction mixtures showed that the ester function is preferentially hydrolyzed, in both chemical and enzyme-catalyzed reactions, with regard to the azetidinone and urethane functions. Considering the three potentially sensitive carbonyl functions and the two stereoisomers, ab initio calculations were performed to determine the energetic barriers required to reach the transition state structures of hydrolysis in a model of the enzyme pocket.

The Bacillus licheniformis BS3 beta-lactamase catalyzes the hydrolysis of the beta-lactam ring of penicillins, cephalosporins, and related compounds. The production of beta-lactamases is the most common and thoroughly studied cause of antibiotic resistance. Although they escape the hydrolytic activity of the prototypical Staphylococcus aureus beta-lactamase, many cephems are good substrates for a large number of beta-lactamases. However, the introduction of a 7alpha-methoxy substituent, as in cefoxitin, extends their antibacterial spectrum to many cephalosporin-resistant Gram-negative bacteria. The 7alpha-methoxy group selectively reduces the hydrolytic action of many beta-lactamases without having a significant effect on the affinity for the target enzymes, the membrane penicillin-binding proteins. We report here the crystallographic structures of the BS3 enzyme and its acyl-enzyme adduct with cefoxitin at 1.7 A resolution. The comparison of the two structures reveals a covalent acyl-enzyme adduct with perturbed active site geometry, involving a different conformation of the omega-loop that bears the essential catalytic Glu166 residue. This deformation is induced by the cefoxitin side chain whose position is constrained by the presence of the alpha-methoxy group. The hydrolytic water molecule is also removed from the active site by the 7beta-carbonyl of the acyl intermediate. In light of the interactions and steric hindrances in the active site of the structure of the BS3-cefoxitin acyl-enzyme adduct, the crucial role of the conserved Asn132 residue is confirmed and a better understanding of the kinetic results emerges.