A. Oliva

Universitat Autònoma de Barcelona

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J. Bertrán

Universitat Autònoma de Barcelona

Vicenç Branchadell

Universitat Autònoma de Barcelona

José M. Lluch

Universitat Autònoma de Barcelona

Mariona Sodupe

Universitat Autònoma de Barcelona

Carles Acosta‐Silva

Institute for High Energy Physics

R. M. ORTUNO

Rede de Química e Tecnologia

Josep Font

Universitat Autònoma de Barcelona

Rosa M. Ortuño

Universitat Autònoma de Barcelona

ÀG

Àngels González‐Lafont

Universitat Autònoma de Barcelona

Javier Ibarzo

Universitat Autònoma de Barcelona

Cooperative Institutions

Universitat Autònoma de Barcelona

Centre National de la Recherche Scientifique

Universitat de Barcelona

Centre de Recerca Matemàtica

Rede de Química e Tecnologia

University of Girona

Institut de Ciència de Materials de Barcelona

Consejo Superior de Investigaciones Científicas

Centre for Research on Ecology and Forestry Applications

Université Toulouse III - Paul Sabatier

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ChemInform Abstract: 5‐Methylene‐2(5H)‐furanone in Diels‐Alder Reactions with Cyclic Dienes: endo/exo Selectivity.

ChemInform (1990)

Daniel F. Alonso Vicenç Branchadell Josep Font A. Oliva R. M. ORTUNO

Abstract The Diels‐Alder reactions between the title compound (I) and cyclopentadiene (IIa) or cyclohexadiene (IIb) occur exclusively at the exocyclic C=C bond of (I) to yield mixtures of the endo (III) and exo spiro adducts (IV).

Cyclopentadiene

Methylene

Diels–Alder reaction

Bridged compounds

10.1002/chin.199041069

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Citations (0)

Dynamic model to predict reactivity effects of core temperature biasing in Slowpoke-2

A. Oliva Cormier J. S. Hewitt

Source

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ChemInform Abstract: Ab initio Study of endo/exo and Diastereofacial Selectivities in Diels‐ Alder Reactions Between Chiral Butenolides and Cyclopentadiene.

ChemInform (1996)

Abdelouahid Sbai Vicenç Branchadell A. Oliva

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

Cyclopentadiene

Diels–Alder reaction

10.1002/chin.199623045

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Phosphoryl Transfer Reaction in RNA: Is the Substrate-Assisted Catalysis a Possible Mechanism in Certain Solvents?

The Journal of Physical Chemistry A (2017)

Carles Acosta‐Silva J. Bertrán Vicenç Branchadell A. Oliva

A proton shuttle mechanism for the phosphoryl transfer reaction in RNA, in which a proton is transferred from the nucleophile to the leaving group through a nonbridged oxygen atom of the phosphate, was explored using the MO6-2X density functional method and the solvent continuum model. This reaction is the initial step of the RNA hydrolysis. We used different solvents characterized by their dielectric constant, and, for each of them, we studied the nuclear and electronic relaxation, produced by the solvent reaction field, for the stationary points. Given that RNA has a poor leaving group, the bond breaking corresponds to the rate-determining step. If the O atom is substituted by a S atom, the leaving group is now good, and the rate-determining step is now the nucleophilic attack concerted with the proton transfer. The most relevant result we found is that none of the solvents we studied has a free energy of activation that is smaller than the one in water. This suggests that the enzyme catalysis following this mechanism must be due to the permanent electric field that is created by a preorganized charge distribution but not to the solvent reaction field.

Leaving group

Concerted reaction

10.1021/acs.jpca.7b09156

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Citations (4)

Quantum Mechanical Study on the Mechanism of Peptide Release in the Ribosome

The Journal of Physical Chemistry B (2013)

Carles Acosta‐Silva J. Bertrán Vicenç Branchadell A. Oliva

A quantum mechanical study of different concerted mechanisms of peptide release in the ribosome has been carried out using the M06-2X density functional. Reoptimization with MP2 has also been carried out for the stationary points of some selected mechanisms. The uncatalyzed processes in solution have been treated with the SMD solvation model. We conclude that the 2′-OH plays an important catalytic role and that it takes place via a zwitterionic transition state, this TS being stabilized by the presence of oxyanion holes or by the solvent. The comparison with our previous study on the peptide bond formation shows that both processes proceed via two different mechanisms, in such a way that the TS of the aminolysis has an ion-pair instead of a zwitterionic character. So, despite the limitations of the model we have used, we can conclude that there is catalytic promiscuity at the peptidyl transferase center (PTC) of the ribosome.

Peptidyl transferase

Aminolysis

Peptide bond

10.1021/jp3110248

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Citations (4)

Solvent effect in the Diels-Alder reaction

Journal of Molecular Structure THEOCHEM (1983)

Leonardo Pardo Vicenç Branchadell A. Oliva J. Bertrán

Diels–Alder reaction

10.1016/0166-1280(83)80109-2

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Citations (3)

Theoretical Study on Two-Step Mechanisms of Peptide Release in the Ribosome

The Journal of Physical Chemistry B (2014)

Carles Acosta‐Silva J. Bertrán Vicenç Branchadell A. Oliva

A quantum mechanical study of different two-step mechanisms of peptide release in the ribosome has been carried out using the M06-2X density functional. Reoptimization with MP2 has also been carried out for the stationary points of some selected mechanisms. The uncatalyzed processes in solution have been treated with the SMD solvation model. From the results obtained in this paper for the peptide release process we can conclude that the energy barriers for the two-step mechanisms are lower than the ones for the concerted process, that the 2'OH plays also an important role in the catalytic process and that the side chain does not only accommodate a nucleophilic water molecule in the PTC, but it also contributes to activate this molecule through electron transfer to the water oxygen. We have also found that the second step is the rate-determining one, and that the two most favorable mechanisms, in which a water or a formamide molecule is added, follow a quite different strategy to catalyze the reaction. The main conclusion of our work is that the two-step mechanisms cannot be disregarded, since they can contribute to clarify the complex and yet unsolved problem of the mechanism of the peptide release process.

10.1021/jp501246a

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Citations (2)

ChemInform Abstract: THE LOCATION OF TRANSITION STATES FOR THE ADDITION OF SINGLET METHYLENE TO SUBSTITUTED ETHYLENES

Chemischer Informationsdienst (1985)

M. MORENO J. M. LLUCH A. Oliva J. Bertrán

Methylene

Spillage

10.1002/chin.198517102

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Mutual Relationship between Stacking and Hydrogen Bonding in DNA. Theoretical Study of Guanine−Cytosine, Guanine−5-methylcytosine, and Their Dimers

The Journal of Physical Chemistry B (2010)

Carles Acosta‐Silva Vicenç Branchadell J. Bertrán A. Oliva

The mutual relationship between stacking and hydrogen-bonding and the possible influence of stacking in the different behavior of cytosine (C) and 5-methylcytosine (C′) in DNA have been studied through complete DFT optimization of different structures of G-C and G-C′ dimers (i.e., G-C/C-G and G-C′/C′-G), using four different functionals. Our results show that stacking leads to an increase of the O6···H−N4 hydrogen bond length and to a simultaneous decrease of the N2−H···O2 one, in such a way that both lengths approach each other and, in some cases, an inversion occurs. These results suggest that stacking can be a factor to explain the disparity between theory and experiment on the relative strength of the two lateral hydrogen bonds. Regarding the difference between cytosine and 5-methylcytosine, we have shown that methylation enhances the stacking interactions, mainly due to the increase of polarizability. Methylation also favors the existence of slid structures which can produce local distortions of DNA.

Cytosine

5-Methylcytosine

10.1021/jp103850h

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Citations (76)

The role of proton transfer in acid-catalyzed diels-alder reactions: A theoretical study

Journal of Molecular Catalysis (1986)

Vicenç Branchadell A. Oliva J. Bertrán

MINDO

Diels–Alder reaction

Acrolein

Acid catalysis

10.1016/0304-5102(86)85055-6

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