Jose Lluch | Universitat Autònoma de Barcelona (original) (raw)
Papers by Jose Lluch
Physical Chemistry Chemical Physics, 2011
Angewandte Chemie (International ed. in English), 2015
Glycosyltransferases (GTs) comprise a prominent family of enzymes that play critical roles in a v... more Glycosyltransferases (GTs) comprise a prominent family of enzymes that play critical roles in a variety of cellular processes, including cell signaling, cell development, and host-pathogen interactions. Glycosyl transfer can proceed with either inversion or retention of the anomeric configuration with respect to the reaction substrates and products. The elucidation of the catalytic mechanism of retaining GTs remains a major challenge. A native ternary complex of a GT in a productive mode for catalysis is reported, that of the retaining glucosyl-3-phosphoglycerate synthase GpgS from M. tuberculosis in the presence of the sugar donor UDP-Glc, the acceptor substrate phosphoglycerate, and the divalent cation cofactor. Through a combination of structural, chemical, enzymatic, molecular dynamics, and quantum-mechanics/molecular-mechanics (QM/MM) calculations, the catalytic mechanism was unraveled, thereby providing a strong experimental support for a front-side substrate-assisted SN i-typ...
Journal of Physical Chemistry A, 2009
A dynamical study has been performed to determine from first principles the molecular volume of C... more A dynamical study has been performed to determine from first principles the molecular volume of C6H6 and C6D6 in the gas phase, starting from a normal-mode analysis and using anharmonic potential energy profiles at DFT level to determine vibrational eigenfunctions for all 30 degrees of freedom and using a Monte Carlo procedure to determine the appreciable ranges of variation of
Journal of The American Chemical Society, 1998
... Mireia Garcia-Viloca, Ricard Gelabert, Àngels González-Lafont, Miquel Moreno, and José M. Llu... more ... Mireia Garcia-Viloca, Ricard Gelabert, Àngels González-Lafont, Miquel Moreno, and José M. Lluch*. Contribution from the Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain. J. Am. Chem. Soc. ...
Organometallics, 1997
ABSTRACT
![Research paper thumbnail of Effect of the Spinning Motion of the Dihydrogen Ligand on the Properties of an Elongated Dihydrogen Complex. A Theoretical Study of the trans -[Os(H···H)Cl(H 2 PCH 2 CH 2 PH 2 ) 2 ] + Complex](https://attachments.academia-assets.com/44837730/thumbnails/1.jpg)
](Journal of The American Chemical Society, 1998
We present in this paper an electronic structure and quantum nuclear dynamics study of a modeled ... more We present in this paper an electronic structure and quantum nuclear dynamics study of a modeled version of trans-[Os(H‚‚‚H)Cl(dppe) 2 ] + , an elongated dihydrogen complex classified as being between the fast and slow H 2 spinning limits and whose J(H,D) coupling constant increases on increasing temperature. We have found that the librational potential energy barrier for the motion of the H 2 unit is quite low, in agreement with the spinning regime of the H 2 unit reported from experiment. Additionally, while the electronic structure study does not manage to describe the experimentally reported geometry obtained through neutron diffraction experiments, the quantum nuclear motion study reproduces the experimental findings very satisfactorily. Finally it is seen that only when the librational motion of the H 2 unit is taken into account in an explicit way in the quantum nuclear motion calculations the temperature dependence of the J(H,D) 1 H NMR coupling constant is also correctly accounted for. S0002-7863(98)00009-2 CCC: $15.00 Ĥ nuc Ψ nuc ) [T nuc + U(R)]Ψ nuc ) EΨ nuc (1) Study of the trans-[Os(H‚‚‚H)Cl(H 2 PCH 2 CH 2 PH 2 ) 2 ] +
Journal of The American Chemical Society, 2005
Complex [CpIr(dmpm)H(2)](2+) (dmpm = bis(dimethylphosphino)methane) has been reported to display ... more Complex [CpIr(dmpm)H(2)](2+) (dmpm = bis(dimethylphosphino)methane) has been reported to display temperature-dependent spin-spin coupling constant ((1)J(HD)) and isotope effect on the (1)H NMR chemical shift (Deltadelta). A combined electronic structure density functional theory + quantum nuclear dynamics study is used to determine from first-principles the unusual temperature dependence of the spin-spin coupling constant. It is found that the potential energy surface describing the motion of the Ir-H(2) unit has a deeper minimum in the dihydride region and is characterized by important anharmonicities. These anomalies affect the nature of the vibrational states of the unit and are the main reason for the unusual temperature dependence of (1)J(HD) and Deltadelta. These results suggest experimental tests to identify compressed dihydride transition metal complexes.
Journal of Molecular Structure: THEOCHEM, 2003
In this paper the need to use a second derivatives direct algorithm to refine the location of tra... more In this paper the need to use a second derivatives direct algorithm to refine the location of transition state structures obtained in enzymatic systems has been analyzed. The 25 approximate QM/MM transition state structures previously found by means of a reaction coordinate approach for the three mechanisms of racemization of mandelate and propargylglycolate by mandelate racemase enzyme have been refined using a modified micro-iterative optimization method developed in this work. The refinement of transition state structures is especially useful to assure that a structure, found as the highest potential energy point on a profile depicted by a particular reaction coordinate, lies in the correct quadratic region. This is more important in those steps of the enzymatic process where the selected reaction coordinate may not reflect quite accurately the geometrical changes taking place in the active site. q
The Journal of Physical Chemistry, 1996
structure structure (organic substances) K 9000 16 -034 H-Atom Transfer and Rotational Processes ... more structure structure (organic substances) K 9000 16 -034 H-Atom Transfer and Rotational Processes in the Ground and First Singlet Excited Electronic States of 2-(2'-Hydroxyphenyl)oxazole Derivatives: Experimental and Theoretical Studies. --(GUAL-LAR, V.; MORENO, M.; LLUCH, J. M.; AMAT-GUERRI, F.; DOUHAL, A.; J.
The objective of this paper is to compare the influence of two electron-withdrawing groups in the... more The objective of this paper is to compare the influence of two electron-withdrawing groups in the fragmentation of 2-methoxy-4-nitrophenyl benzyl ether and 4-cyanophenyl benzyl ether once these species are reduced. The stability of the corresponding radical anions depends essentially on those substituents. In our design we have chosen two species that are able to attach the electron but which have each a different capacity to retain it. An experimental study is carried out by EPR spectroscopy to analyze the different electronic nature of the generated radical anions. In addition, electronic structure calculations at the DFT level of theory have been performed to study those radical anions and their fragmentation pathways. The thermodynamics and kinetics of the two fragmentations are discussed and compared in detail.
Chemical Physics Letters, 2004
The photo-oxidation reactions between lipid model nona-3,6(c,c)-diene and singlet molecular oxyge... more The photo-oxidation reactions between lipid model nona-3,6(c,c)-diene and singlet molecular oxygen are investigated using density functional theory and polarized continuum models. Additions to both the 3- and 4-position of the lipid model (corresponding to the 9(13)- and 10(12)-positions of 9,12 lipid dienes such as linoleic acid) are explored. It is concluded that the modes of attack will lead to adduct
Journal of Physical Chemistry a, 2000
Equilibrium isotope effects (EIE) on the binding of H 2 and D 2 to transition metal complexes are... more Equilibrium isotope effects (EIE) on the binding of H 2 and D 2 to transition metal complexes are calculated for a modeled version of W(CO) 3 (PCy 3 ) 2 (η 2 -H 2 ), [Ru(H‚‚‚H)(C 5 Me 5 )(dppm)] + and trans-[Os(H‚‚‚H)Cl-(dppe) 2 ] + . Being probably unsatisfactorily described by the harmonic approach (specially in the elongated dihydrogen complexes), the thermodynamic contribution of the H-H stretching related modes is evaluated by means of nuclear motion quantum calculations. The Discrete Variable Representation (DVR) methodology is applied to obtain the anharmonic vibrational spectrum on the bidimensional B3LYP potential surface. From these results, the associated partition function is calculated and used to correct the harmonic EIE and other thermodynamic magnitudes. In agreement with experimental results, the anharmonically corrected EIE for the W complex turns out to be inverse (0.534 at 300 K). On the contrary, the corrected EIE for the Ru and Os complexes is clearly normal (1.217 and 1.685 at 300 K, respectively), predicting an unusual behavior for ML n H 2 compounds. Comparison with the pure harmonic EIE's leads to the conclusion that the harmonic approach is inadequate to describe the properties of the elongated dihydrogen complexes.
Journal of Physical Chemistry a, 2006
The proton-transfer dynamics in the aromatic Schiff base salicylidene methylamine has been theore... more The proton-transfer dynamics in the aromatic Schiff base salicylidene methylamine has been theoretically analyzed in the ground and first singlet (π,π*) excited electronic states by density functional theory calculations and quantum wave-packet dynamics. The potential energies obtained through electronic calculations that use the time-dependent density functional theory formalism, which predict a barrierless excited-state intramolecular proton transfer, are fitted to a reduced three-dimensional potential energy surface. The time evolution in this surface is solved by means of the multiconfiguration time-dependent Hartree algorithm applied to solve the time-dependent Schrödinger equation. It is shown that the excited-state proton transfer occurs within 11 fs for hydrogen and 25 fs for deuterium, so that a large kinetic isotope effect is predicted. These results are compared to those of the only previous theoretical work published on this system Grabowska, A. J. Chem. Phys. 2000, 113, 7845], reporting a configuration interaction singles barrier of 1.6 kcal mol -1 and time reactions of 30 and 115 fs for the hydrogen and deuterium transfers, respectively, evaluated with the semiclassical instanton approach.
Journal of Chemical Theory and Computation, 2013
The absorption spectrum of a fluorescent protein is determined by its chromophore, but the residu... more The absorption spectrum of a fluorescent protein is determined by its chromophore, but the residues that surround it also have a remarkable role, leading to noticeable spectral shifts. We have theoretically analyzed the monomeric protein Keima (mKeima), a red fluorescent protein most remarkable for an outstanding difference between the absorption and emission frequencies, and potentially suited for multicolor imaging applications. In the present work, we have performed excited state electronic calculations on the chromophore with an increasing number of atoms surrounding it, and we have compared these results with the excited states calculations on an ensemble of structures obtained from a molecular dynamics simulation of the complete protein. The importance of the inclusion of the effects of the whole protein in the electronic calculations has been proved, and it is concluded that only with the consideration of the thermal effects can the absorption spectra of the protein be properly characterized.
Journal of The American Chemical Society, 2007
The catechol functionality present in the catechins is responsible for the protective effects exe... more The catechol functionality present in the catechins is responsible for the protective effects exerted by green tea against a wide range of human diseases. High-level electronic structure calculations and canonical variational transition-state theory including multidimensional tunneling corrections have allowed us to understand the key factors of the antioxidant effectiveness of the catechol group. This catechol group forms two hydrogen bonds with the two oxygen atoms of the lipid peroxyl radical, leading to a very compact reactant complex. This fact produces an extremely narrow adiabatic potential-energy profile corresponding to the hydrogen abstraction by the peroxyl radical, which makes it possible for a huge tunneling contribution to take place. So, quantum-mechanical tunneling highly increases the corresponding rate constant value, in such a way that catechins become able to trap the lipid peroxyl radicals in a dominant competition with the very damaging free-radical chain-lipid peroxidation reaction.
Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta), 2002
We propose a methodology to locate stationary points on a quantum mechanical/molecular mechanical... more We propose a methodology to locate stationary points on a quantum mechanical/molecular mechanical potential-energy surface. This algorithm is based on a suitable approximation of an initial full Hessian matrix, either a modi®ed Broyden±Fletcher±Goldfarg± Shanno or a Powell update formula for the location of, respectively, a minimum or a transition state, and the socalled rational function optimization. The latter avoids the Hessian matrix inversion required by a quasi-Newton±Raphson method. Some examples are presented and analyzed.
Theoretical Chemistry Accounts, 2011
The reaction of cycloaddition of ketene and cyclopentadiene presents experimentally a competing m... more The reaction of cycloaddition of ketene and cyclopentadiene presents experimentally a competing mechanism where the branching ratio between the Woodward-Hoffmann allowed [4?2] and forbidden [2?2] cycloaddition product is 4.56 at -20°C, but because the minimum energy path misses the [2?2] product altogether, it has been claimed to lie beyond the scope of transition state theory. In this paper, a variational transition state theory study on this reaction is presented. It is found that the minimum energy path affording the [4?2] product travels through a potential energy plateau very close to the minimum energy path that describes the interconversion between both cycloaddition products, allowing the transfer between both and the direct formation of the forbidden [2?2] product, in this way acting as a means to circumvent the Woodward-Hooffmann rules. Within the domain of the competitive canonical unified statistical theory, a value for the branching ratio in very good agreement with experiment is computed.
The Journal of Physical Chemistry B, 2008
A nuclear quantum dynamical simulation of the proton shuttle operating in the green fluorescent p... more 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 ππ* 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 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 chromophore's phenolic O-H bond.
The Journal of Physical Chemistry B, 2005
The present work studies the reaction mechanism of the racemization of mandelate substrate by man... more The present work studies the reaction mechanism of the racemization of mandelate substrate by mandelate racemase enzyme. The reaction has some intriguing aspects such as the deprotonation of a nonacid hydrogen and the achievement of the pseudosymmetry necessary to obtain the racemic mixture. We will make use of a QM/MM potential energy surface to compute the free energy profiles associated with the reaction. The most favorable reaction mechanism consists of two proton transfers and the configuration inversion of the stereogenic carbon taking place in a concerted manner. We have also designed a suitable reaction coordinate to compute the free energy profiles for this rather complicated reaction. In addition, analysis of the electrostatic effects and bond distances along the reaction will explain how the enzyme accomplishes the catalysis. Finally, the enzymatic reaction will be compared to a model of the uncatalyzed reaction and the catalytic effect of mandelate racemase will be evaluated.
The Journal of Physical Chemistry B, 2004
The ultrafast enol-keto photoisomerization in the lowest singlet excited state of 2-(2′-hydroxyph... more The ultrafast enol-keto photoisomerization in the lowest singlet excited state of 2-(2′-hydroxyphenyl)-4methyloxazole (HPMO) is investigated using classical molecular dynamics in conjunction with an empirical valence bond potential. This process is studied in four different environments: the gas phase, dimethyl sulfoxide, water, and human serum albumin protein. The effects of the environment on the proton transfer time and the promoting-mode motions are analyzed. The ring-ring in-plane bending of HPMO is identified as the dominant low-frequency vibrational mode that decreases the proton donor-acceptor distance to facilitate proton transfer. The mean proton transfer times are 100-200 fs in all of the environments. The population decay of the enol tautomer in the S 1 state is significantly slower for the reaction in water than in DMSO and protein. The slower population decay in water is found to arise from configurations with intermolecular hydrogen bonds between HPMO and water molecules, leading to a disruption of the intramolecular hydrogen bond in HPMO. All of the condensed-phase environments are found to dampen the donor-acceptor vibrational mode after the proton transfer process, thereby stabilizing the keto tautomer. In the gas phase, the donor-acceptor mode oscillations continue to facilitate the forward and reverse isomerization processes. † Part of the special issue "Hans C. Andersen Festschrift".
Physical Chemistry Chemical Physics, 2011
Angewandte Chemie (International ed. in English), 2015
Glycosyltransferases (GTs) comprise a prominent family of enzymes that play critical roles in a v... more Glycosyltransferases (GTs) comprise a prominent family of enzymes that play critical roles in a variety of cellular processes, including cell signaling, cell development, and host-pathogen interactions. Glycosyl transfer can proceed with either inversion or retention of the anomeric configuration with respect to the reaction substrates and products. The elucidation of the catalytic mechanism of retaining GTs remains a major challenge. A native ternary complex of a GT in a productive mode for catalysis is reported, that of the retaining glucosyl-3-phosphoglycerate synthase GpgS from M. tuberculosis in the presence of the sugar donor UDP-Glc, the acceptor substrate phosphoglycerate, and the divalent cation cofactor. Through a combination of structural, chemical, enzymatic, molecular dynamics, and quantum-mechanics/molecular-mechanics (QM/MM) calculations, the catalytic mechanism was unraveled, thereby providing a strong experimental support for a front-side substrate-assisted SN i-typ...
Journal of Physical Chemistry A, 2009
A dynamical study has been performed to determine from first principles the molecular volume of C... more A dynamical study has been performed to determine from first principles the molecular volume of C6H6 and C6D6 in the gas phase, starting from a normal-mode analysis and using anharmonic potential energy profiles at DFT level to determine vibrational eigenfunctions for all 30 degrees of freedom and using a Monte Carlo procedure to determine the appreciable ranges of variation of
Journal of The American Chemical Society, 1998
... Mireia Garcia-Viloca, Ricard Gelabert, Àngels González-Lafont, Miquel Moreno, and José M. Llu... more ... Mireia Garcia-Viloca, Ricard Gelabert, Àngels González-Lafont, Miquel Moreno, and José M. Lluch*. Contribution from the Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain. J. Am. Chem. Soc. ...
Organometallics, 1997
ABSTRACT
Journal of The American Chemical Society, 1998
We present in this paper an electronic structure and quantum nuclear dynamics study of a modeled ... more We present in this paper an electronic structure and quantum nuclear dynamics study of a modeled version of trans-[Os(H‚‚‚H)Cl(dppe) 2 ] + , an elongated dihydrogen complex classified as being between the fast and slow H 2 spinning limits and whose J(H,D) coupling constant increases on increasing temperature. We have found that the librational potential energy barrier for the motion of the H 2 unit is quite low, in agreement with the spinning regime of the H 2 unit reported from experiment. Additionally, while the electronic structure study does not manage to describe the experimentally reported geometry obtained through neutron diffraction experiments, the quantum nuclear motion study reproduces the experimental findings very satisfactorily. Finally it is seen that only when the librational motion of the H 2 unit is taken into account in an explicit way in the quantum nuclear motion calculations the temperature dependence of the J(H,D) 1 H NMR coupling constant is also correctly accounted for. S0002-7863(98)00009-2 CCC: $15.00 Ĥ nuc Ψ nuc ) [T nuc + U(R)]Ψ nuc ) EΨ nuc (1) Study of the trans-[Os(H‚‚‚H)Cl(H 2 PCH 2 CH 2 PH 2 ) 2 ] +
Journal of The American Chemical Society, 2005
Complex [CpIr(dmpm)H(2)](2+) (dmpm = bis(dimethylphosphino)methane) has been reported to display ... more Complex [CpIr(dmpm)H(2)](2+) (dmpm = bis(dimethylphosphino)methane) has been reported to display temperature-dependent spin-spin coupling constant ((1)J(HD)) and isotope effect on the (1)H NMR chemical shift (Deltadelta). A combined electronic structure density functional theory + quantum nuclear dynamics study is used to determine from first-principles the unusual temperature dependence of the spin-spin coupling constant. It is found that the potential energy surface describing the motion of the Ir-H(2) unit has a deeper minimum in the dihydride region and is characterized by important anharmonicities. These anomalies affect the nature of the vibrational states of the unit and are the main reason for the unusual temperature dependence of (1)J(HD) and Deltadelta. These results suggest experimental tests to identify compressed dihydride transition metal complexes.
Journal of Molecular Structure: THEOCHEM, 2003
In this paper the need to use a second derivatives direct algorithm to refine the location of tra... more In this paper the need to use a second derivatives direct algorithm to refine the location of transition state structures obtained in enzymatic systems has been analyzed. The 25 approximate QM/MM transition state structures previously found by means of a reaction coordinate approach for the three mechanisms of racemization of mandelate and propargylglycolate by mandelate racemase enzyme have been refined using a modified micro-iterative optimization method developed in this work. The refinement of transition state structures is especially useful to assure that a structure, found as the highest potential energy point on a profile depicted by a particular reaction coordinate, lies in the correct quadratic region. This is more important in those steps of the enzymatic process where the selected reaction coordinate may not reflect quite accurately the geometrical changes taking place in the active site. q
The Journal of Physical Chemistry, 1996
structure structure (organic substances) K 9000 16 -034 H-Atom Transfer and Rotational Processes ... more structure structure (organic substances) K 9000 16 -034 H-Atom Transfer and Rotational Processes in the Ground and First Singlet Excited Electronic States of 2-(2'-Hydroxyphenyl)oxazole Derivatives: Experimental and Theoretical Studies. --(GUAL-LAR, V.; MORENO, M.; LLUCH, J. M.; AMAT-GUERRI, F.; DOUHAL, A.; J.
The objective of this paper is to compare the influence of two electron-withdrawing groups in the... more The objective of this paper is to compare the influence of two electron-withdrawing groups in the fragmentation of 2-methoxy-4-nitrophenyl benzyl ether and 4-cyanophenyl benzyl ether once these species are reduced. The stability of the corresponding radical anions depends essentially on those substituents. In our design we have chosen two species that are able to attach the electron but which have each a different capacity to retain it. An experimental study is carried out by EPR spectroscopy to analyze the different electronic nature of the generated radical anions. In addition, electronic structure calculations at the DFT level of theory have been performed to study those radical anions and their fragmentation pathways. The thermodynamics and kinetics of the two fragmentations are discussed and compared in detail.
Chemical Physics Letters, 2004
The photo-oxidation reactions between lipid model nona-3,6(c,c)-diene and singlet molecular oxyge... more The photo-oxidation reactions between lipid model nona-3,6(c,c)-diene and singlet molecular oxygen are investigated using density functional theory and polarized continuum models. Additions to both the 3- and 4-position of the lipid model (corresponding to the 9(13)- and 10(12)-positions of 9,12 lipid dienes such as linoleic acid) are explored. It is concluded that the modes of attack will lead to adduct
Journal of Physical Chemistry a, 2000
Equilibrium isotope effects (EIE) on the binding of H 2 and D 2 to transition metal complexes are... more Equilibrium isotope effects (EIE) on the binding of H 2 and D 2 to transition metal complexes are calculated for a modeled version of W(CO) 3 (PCy 3 ) 2 (η 2 -H 2 ), [Ru(H‚‚‚H)(C 5 Me 5 )(dppm)] + and trans-[Os(H‚‚‚H)Cl-(dppe) 2 ] + . Being probably unsatisfactorily described by the harmonic approach (specially in the elongated dihydrogen complexes), the thermodynamic contribution of the H-H stretching related modes is evaluated by means of nuclear motion quantum calculations. The Discrete Variable Representation (DVR) methodology is applied to obtain the anharmonic vibrational spectrum on the bidimensional B3LYP potential surface. From these results, the associated partition function is calculated and used to correct the harmonic EIE and other thermodynamic magnitudes. In agreement with experimental results, the anharmonically corrected EIE for the W complex turns out to be inverse (0.534 at 300 K). On the contrary, the corrected EIE for the Ru and Os complexes is clearly normal (1.217 and 1.685 at 300 K, respectively), predicting an unusual behavior for ML n H 2 compounds. Comparison with the pure harmonic EIE's leads to the conclusion that the harmonic approach is inadequate to describe the properties of the elongated dihydrogen complexes.
Journal of Physical Chemistry a, 2006
The proton-transfer dynamics in the aromatic Schiff base salicylidene methylamine has been theore... more The proton-transfer dynamics in the aromatic Schiff base salicylidene methylamine has been theoretically analyzed in the ground and first singlet (π,π*) excited electronic states by density functional theory calculations and quantum wave-packet dynamics. The potential energies obtained through electronic calculations that use the time-dependent density functional theory formalism, which predict a barrierless excited-state intramolecular proton transfer, are fitted to a reduced three-dimensional potential energy surface. The time evolution in this surface is solved by means of the multiconfiguration time-dependent Hartree algorithm applied to solve the time-dependent Schrödinger equation. It is shown that the excited-state proton transfer occurs within 11 fs for hydrogen and 25 fs for deuterium, so that a large kinetic isotope effect is predicted. These results are compared to those of the only previous theoretical work published on this system Grabowska, A. J. Chem. Phys. 2000, 113, 7845], reporting a configuration interaction singles barrier of 1.6 kcal mol -1 and time reactions of 30 and 115 fs for the hydrogen and deuterium transfers, respectively, evaluated with the semiclassical instanton approach.
Journal of Chemical Theory and Computation, 2013
The absorption spectrum of a fluorescent protein is determined by its chromophore, but the residu... more The absorption spectrum of a fluorescent protein is determined by its chromophore, but the residues that surround it also have a remarkable role, leading to noticeable spectral shifts. We have theoretically analyzed the monomeric protein Keima (mKeima), a red fluorescent protein most remarkable for an outstanding difference between the absorption and emission frequencies, and potentially suited for multicolor imaging applications. In the present work, we have performed excited state electronic calculations on the chromophore with an increasing number of atoms surrounding it, and we have compared these results with the excited states calculations on an ensemble of structures obtained from a molecular dynamics simulation of the complete protein. The importance of the inclusion of the effects of the whole protein in the electronic calculations has been proved, and it is concluded that only with the consideration of the thermal effects can the absorption spectra of the protein be properly characterized.
Journal of The American Chemical Society, 2007
The catechol functionality present in the catechins is responsible for the protective effects exe... more The catechol functionality present in the catechins is responsible for the protective effects exerted by green tea against a wide range of human diseases. High-level electronic structure calculations and canonical variational transition-state theory including multidimensional tunneling corrections have allowed us to understand the key factors of the antioxidant effectiveness of the catechol group. This catechol group forms two hydrogen bonds with the two oxygen atoms of the lipid peroxyl radical, leading to a very compact reactant complex. This fact produces an extremely narrow adiabatic potential-energy profile corresponding to the hydrogen abstraction by the peroxyl radical, which makes it possible for a huge tunneling contribution to take place. So, quantum-mechanical tunneling highly increases the corresponding rate constant value, in such a way that catechins become able to trap the lipid peroxyl radicals in a dominant competition with the very damaging free-radical chain-lipid peroxidation reaction.
Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta), 2002
We propose a methodology to locate stationary points on a quantum mechanical/molecular mechanical... more We propose a methodology to locate stationary points on a quantum mechanical/molecular mechanical potential-energy surface. This algorithm is based on a suitable approximation of an initial full Hessian matrix, either a modi®ed Broyden±Fletcher±Goldfarg± Shanno or a Powell update formula for the location of, respectively, a minimum or a transition state, and the socalled rational function optimization. The latter avoids the Hessian matrix inversion required by a quasi-Newton±Raphson method. Some examples are presented and analyzed.
Theoretical Chemistry Accounts, 2011
The reaction of cycloaddition of ketene and cyclopentadiene presents experimentally a competing m... more The reaction of cycloaddition of ketene and cyclopentadiene presents experimentally a competing mechanism where the branching ratio between the Woodward-Hoffmann allowed [4?2] and forbidden [2?2] cycloaddition product is 4.56 at -20°C, but because the minimum energy path misses the [2?2] product altogether, it has been claimed to lie beyond the scope of transition state theory. In this paper, a variational transition state theory study on this reaction is presented. It is found that the minimum energy path affording the [4?2] product travels through a potential energy plateau very close to the minimum energy path that describes the interconversion between both cycloaddition products, allowing the transfer between both and the direct formation of the forbidden [2?2] product, in this way acting as a means to circumvent the Woodward-Hooffmann rules. Within the domain of the competitive canonical unified statistical theory, a value for the branching ratio in very good agreement with experiment is computed.
The Journal of Physical Chemistry B, 2008
A nuclear quantum dynamical simulation of the proton shuttle operating in the green fluorescent p... more 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 ππ* 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 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 chromophore's phenolic O-H bond.
The Journal of Physical Chemistry B, 2005
The present work studies the reaction mechanism of the racemization of mandelate substrate by man... more The present work studies the reaction mechanism of the racemization of mandelate substrate by mandelate racemase enzyme. The reaction has some intriguing aspects such as the deprotonation of a nonacid hydrogen and the achievement of the pseudosymmetry necessary to obtain the racemic mixture. We will make use of a QM/MM potential energy surface to compute the free energy profiles associated with the reaction. The most favorable reaction mechanism consists of two proton transfers and the configuration inversion of the stereogenic carbon taking place in a concerted manner. We have also designed a suitable reaction coordinate to compute the free energy profiles for this rather complicated reaction. In addition, analysis of the electrostatic effects and bond distances along the reaction will explain how the enzyme accomplishes the catalysis. Finally, the enzymatic reaction will be compared to a model of the uncatalyzed reaction and the catalytic effect of mandelate racemase will be evaluated.
The Journal of Physical Chemistry B, 2004
The ultrafast enol-keto photoisomerization in the lowest singlet excited state of 2-(2′-hydroxyph... more The ultrafast enol-keto photoisomerization in the lowest singlet excited state of 2-(2′-hydroxyphenyl)-4methyloxazole (HPMO) is investigated using classical molecular dynamics in conjunction with an empirical valence bond potential. This process is studied in four different environments: the gas phase, dimethyl sulfoxide, water, and human serum albumin protein. The effects of the environment on the proton transfer time and the promoting-mode motions are analyzed. The ring-ring in-plane bending of HPMO is identified as the dominant low-frequency vibrational mode that decreases the proton donor-acceptor distance to facilitate proton transfer. The mean proton transfer times are 100-200 fs in all of the environments. The population decay of the enol tautomer in the S 1 state is significantly slower for the reaction in water than in DMSO and protein. The slower population decay in water is found to arise from configurations with intermolecular hydrogen bonds between HPMO and water molecules, leading to a disruption of the intramolecular hydrogen bond in HPMO. All of the condensed-phase environments are found to dampen the donor-acceptor vibrational mode after the proton transfer process, thereby stabilizing the keto tautomer. In the gas phase, the donor-acceptor mode oscillations continue to facilitate the forward and reverse isomerization processes. † Part of the special issue "Hans C. Andersen Festschrift".