José M. Lluch

The use of quantum mechanics calculations for the study of corrosion inhibitors

Abstract In order to study the ability of quantum chemistry to select corrosion inhibitors, quantum mechanics calculations have been applied to different linear chain diols, diamines and aliphatic aminoalcohols. The corresponding structures have been optimized, and the energies and coefficients of their molecular orbitals have been calculated, using the semi-empirical method MINDO/3. Finally, the theoretical results obtained have been compared with the experimental data.

Elongated dihydrogen complexes: what remains of the H–H Bond?

Of the several hundred examples of transition metal dihydrogen complexes that have been reported to date, the vast majority have H-H distances of less than 1.0 Angstrom. A small number of complexes have been reported with distances in the range of 1.1 to 1.5 Angstrom. These complexes have been termed elongated dihydrogen complexes. In this review, experimental methods for structure determination of such complexes are summarized, along with computational approaches which have proven useful in understanding the structures of these molecules.

Electronic-structure and quantum dynamical study of the photochromism of the aromatic Schiff base salicylideneaniline

The ultrafast proton transfer dynamics of salicylideneaniline has been theoretically analyzed in the ground and first singlet excited electronic states using density functional theory (DFT) and time-dependent DFT calculations, which predict a (pi,pi( *)) barrierless excited state intramolecular proton transfer (ESIPT). In addition to this, the photochemistry of salicylideneaniline is experimentally known to present fast depopulation processes of the photoexcited species before and after the proton transfer reaction. Such processes are explained by means of conical intersections between the ground and first singlet (pi,pi( *)) excited electronic states. The electronic energies obtained by the time-dependent density functional theory formalism have been fitted to a monodimensional potential energy surface in order to perform quantum dynamics study of the processes. Our results show that the proton transfer and deactivation of the photoexcited species before the ESIPT processes are completed within 49.6 and 37.7 fs, respectively, which is in remarkable good agreement with experiments.

Bidimensional tunneling dynamics of malonaldehyde and hydrogenoxalate anion. A comparative study

One‐dimensional and bidimensional tunneling splittings have been calculated in malonaldehyde (MA) and hydrogenoxalate anion (HX) systems. Two different monodimensional paths have been considered: the intrinsic reaction path (IRP) and the linear reaction path (LRP). A bidimensional model that includes the coupling between the proton transfer motion and the vibration of the heavy atoms is then used. We find that with the bidimensional model the splittings are 2 orders of magnitude greater than the monodimensional ones, and close to the previous experimental and theoretical values for the MA when zero point energy is introduced. At all levels of calculation we obtain that the splitting is greater in the MA than in the HX. This fact is attributed to the different size of the rings through which the proton transfer occurs.

Retaining Glycosyltransferase Mechanism Studied by QM/MM Methods: Lipopolysaccharyl-α-1,4-galactosyltransferase C Transfers α-Galactose via an Oxocarbenium Ion-like Transition State

Glycosyltransferases (GTs) catalyze the highly specific biosynthesis of glycosidic bonds and, as such, are important both as drug targets and for biotechnological purposes. Despite their broad interest, fundamental questions about their reaction mechanism remain to be answered, especially for those GTs that transfer the sugar with net retention of the configuration at the anomeric carbon (retaining glycosyltransferases, ret-GTs). In the present work, we focus on the reaction catalyzed by lipopolysaccharyl-α-1,4-galactosyltransferase C (LgtC) from Neisseria meningitides. We study and compare the different proposed mechanisms (S(N)i, S(N)i-like, and double displacement mechanism via a covalent glycosyl-enzyme intermediate, CGE) by using density functional theory (DFT) and quantum mechanics/molecular mechanics (QM/MM) calculations on the full enzyme. We characterize a dissociative single-displacement (S(N)i) mechanism consistent with the experimental data, in which the acceptor substrate attacks on the side of the UDP leaving group that acts as a catalytic base. We identify several key interactions that help this front-side attack by stabilizing the transition state. Among them, Gln189, the putative nucleophile in a double displacement mechanism, is shown to favor the charge development at the anomeric center by about 2 kcal/mol, compatible with experimental mutagenesis data. We predict that using 3-deoxylactose as acceptor would result in a reduction of k(cat) to 0.6-3% of that for the unmodified substrates. The reactions of the Q189A and Q189E mutants have also been investigated. For Q189E, there is a change in mechanism since a CGE can be formed which, however, is not able to evolve to products. The current findings are discussed in the light of the available experimental data and compared with those for other ret-GTs.

Theoretical study of molecular dynamics in model base pairs

Abstract Ab initio calculations (4-31G basis set at CIS and CIS-MP2 levels) were carried out to investigate the nature of the double proton-transfer process of the 7-azaindole base-pair in both S 0 and S 1 states. The result is in agreement with the stepwise mechanism recently observed for S 1 , and reveals a diffuse transition state for the reaction in S 0 . The stepwise nature of the phototautomerization originates from a localized electronic excitation in one part of the pair. Compression of the internal hydrogen bonds is crucial for the occurrence of the reaction in both states.

Operation of the Proton Wire in Green Fluorescent Protein. A Quantum Dynamics Simulation

A nuclear quantum dynamical simulation of the proton shuttle operating in the green fluorescent protein has been carried out on a high-quality, high-dimensionality potential energy surface describing the photoactive pipi* excited state, and including motion of both the three protons and of the donor and acceptor atoms of the hydrogen bonds in a closed proton wire. The results of the simulations show that proton transfer along the wire is essentially concerted, synchronous, and very fast, with a substantial amount of the green fluorescent species forming within several tens of femtoseconds. In this regard, analysis of the population of the fluorescent species indicates that at least two dynamical regimes are present for its formation. Within the first hundreds of femtoseconds, dynamics is very fast and impulsive. Later on, a slower pace of formation appears. It is discussed that the two largest decay times for the protonated chromophore reported experimentally (Chattoraj, M.; King, B. A.; Bublitz, G. U.; Boxer, S. G. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 8362-8367) might correspond to some irreversible process occurring after formation of the fluorescent species, rather than to cleavage of the chromophores phenolic O-H bond.

A theoretical study of the ground and first excited singlet state proton transfer reaction in isolated 7-azaindole–water complexes

Abstract A systematic study of the proton transfer in the 7-azaindole–water clusters ( 7 -AI ( H 2 O ) n ; n=1–4 ) in both the ground and first excited singlet electronic states is undertaken. DFT(B3LYP) calculations for the ground electronic state shows that the more stable geometry of the initial normal tautomer presents a cyclic set of hydrogen bonds that links the two nitrogen atoms of the base across the waters. For the n=4 cluster the water molecules adopt a double ring structure so that two cycles of hydrogen bonds are found there. From this structure full tautomerization implies only one transition state so that a concerted but non-synchronous process is predicted by our theoretical calculations. This behavior is found both in the ground and the excited states where CIS geometry optimizations and TD(B3LYP) energy calculations are performed. The difference between both states is the height of the energy barrier that is much lower in the excited state. Another clear difference between both electronic states is that full tautomerization is an endergonic process in the ground state whereas it is clearly exergonic (then favorable) in the excited state. This is so because electronic excitation implies a charge transfer from the five-member cycle to the six-member one of 7-azaindole so that the proton transfer from the pyrrolic side to the pyridinic one is favored. These results clearly indicate that full tautomerization will not likely occur in the ground state but it will be quite easy (and fast) in the excited state. Reaction is already feasible in the S 1 1:1 complex but it is faster in the 1:2 complex. However the reaction slows again for the 1:3 complex and, finally, reaches a new maximum for the largest cluster studied here, the n=4 case. These results, which are in agreement with experimental data, are explained in terms of the number of hydrogen bonds that are involved in the transfer. The proton transfer through a ring formed by the substrate and two water molecules is found to be the more efficient one, at least in this system.

Bidimensional tunneling splitting in the à 1B2 and X̃ 1A1 states of tropolone

The intramolecular proton transfer in tropolone has been theoretically analyzed. Ab initio calculations using a variety of basis sets have been performed for both the singlet ground state (X 1A1) and the first excited singlet state (A 1B2). A configuration interaction all single excitation method (CIS) has been used to deal with the excited singlet state. Tunneling splittings in both electronic states have been obtained by fitting a bidimensional surface into the ab initio results. This way, a new strategy designed to avoid calculations of the intrinsic reaction coordinate (IRC), which require a very long computer time, is proposed and shown to give accurate results. Our calculations provide a theoretical interpretation of previous extensive spectroscopical data from which the tunneling splitting for the excited A 1B2 state was shown to be clearly higher than for the ground X 1A1 state. Finally, the experimentally observed diminution of the splitting upon deuteration of the transferring hydrogen is al...

Testing electronic structure methods for describing intermolecular H · · · H interactions in supramolecular chemistry

In this article a wide variety of computational approaches (molecular mechanics force fields, semiempirical formalisms, and hybrid methods, namely ONIOM calculations) have been used to calculate the energy and geometry of the supramolecular system 2‐(2′‐hydroxyphenyl)‐4‐methyloxazole (HPMO) encapsulated in β‐cyclodextrin (β‐CD). The main objective of the present study has been to examine the performance of these computational methods when describing the short range H · · · H intermolecular interactions between guest (HPMO) and host (β‐CD) molecules. The analyzed molecular mechanics methods do not provide unphysical short H · · · H contacts, but it is obvious that their applicability to the study of supramolecular systems is rather limited. For the semiempirical methods, MNDO is found to generate more reliable geometries than AM1, PM3 and the two recently developed schemes PDDG/MNDO and PDDG/PM3. MNDO results only give one slightly short H · · · H distance, whereas the NDDO formalisms with modifications of the Core Repulsion Function (CRF) via Gaussians exhibit a large number of short to very short and unphysical H · · · H intermolecular distances. In contrast, the PM5 method, which is the successor to PM3, gives very promising results. Our ONIOM calculations indicate that the unphysical optimized geometries from PM3 are retained when this semiempirical method is used as the low level layer in a QM:QM formulation. On the other hand, ab initio methods involving good enough basis sets, at least for the high level layer in a hybrid ONIOM calculation, behave well, but they may be too expensive in practice for most supramolecular chemistry applications. Finally, the performance of the evaluated computational methods has also been tested by evaluating the energetic difference between the two most stable conformations of the host(β‐CD)‐guest(HPMO) system.