List of works - Vicent Moliner

A Novel Strategy to Study Electrostatic Effects in Chemical Reactions: Differences between the Role of Solvent and the Active Site of Chalcone Isomerase in a Michael Addition

scientific article published on 10 April 2012

A QM/MM Exploration of the Potential Energy Surface of Pyruvate to Lactate Transformation Catalyzed by LDH. Improving the Accuracy of Semiempirical Descriptions

scientific article published on 01 July 2005

A QM/MM study of the complexes formed by aluminum and iron with serum transferrin at neutral and acidic pH

scientific article published on 02 August 2011

A Theoretical Study of the Favorskii Rearrangement. Calculation of Gas-Phase Reaction Paths and Solvation Effects on the Molecular Mechanism for the Transposition of the α-Chlorocyclobutanone

scientific article published in 1997

A density functional study of flavonoid compounds with anti-HIV activity

scientific article published on 13 March 2006

A hybrid potential reaction path and free energy study of the chorismate mutase reaction

scientific article published in February 2001

A quantum mechanic/molecular mechanic study of the wild-type and N155S mutant HIV-1 integrase complexed with diketo acid.

scientific article published on 2 November 2007

A quantum mechanics/molecular mechanics study of the catalytic mechanism of the thymidylate synthase.

scientific article published in March 2007

A quantum mechanics/molecular mechanics study of the protein-ligand interaction for inhibitors of HIV-1 integrase

scientific article published on 01 January 2007

A quantum mechanics/molecular mechanics study of the protein-ligand interaction of two potent inhibitors of human O-GlcNAcase: PUGNAc and NAG-thiazoline

scientific article

A theoretical analysis of rate constants and kinetic isotope effects corresponding to different reactant valleys in lactate dehydrogenase

scientific article published on 01 December 2006

A theoretical study of carbon–carbon bond formation by a Michael-type addition

scientific article published on 21 June 2012

A theoretical study of the catalytic mechanism of formate dehydrogenase.

scientific article

Ab initio perturbed ion calculations on Ni2+·KZnF3 and Ni2+ ·KMgF3. A structural study

Activation Free Energy of CatecholO-Methyltransferase. Corrections to the Potential of Mean Force†

scientific article published in January 2006

An AM1 theoretical study on the effect of Zn2+ Lewis acid catalysis on the mechanism of the cycloaddition between 3-phenyl-1-(2-pyridyl)-2-propen-1-one and cyclopentadiene

Application of Grote−Hynes Theory to the Reaction Catalyzed by Thymidylate Synthase

scientific article published on 28 October 2010

Author Correction: Revealing the mechanism for covalent inhibition of glycoside hydrolases by carbasugars at an atomic level

scientific article published in Nature Communications

Benchmarking Quantum Mechanics/Molecular Mechanics (QM/MM) Methods on the Thymidylate Synthase-Catalyzed Hydride Transfer.

scientific article published on 13 February 2017

Binding isotope effects as a tool for distinguishing hydrophobic and hydrophilic binding sites of HIV-1 RT.

scientific article published on 25 August 2014

Calculation of binding energy using BLYP/MM for the HIV-1 integrase complexed with the S-1360 and two analogues

scientific article published on 13 March 2007

Catalysis in glycine N-methyltransferase: testing the electrostatic stabilization and compression hypothesis

scientific article published on 01 December 2006

Catalytic enantioselective epoxidation of nitroalkenes.

scientific article published on 25 July 2016

Chemical Ligation and Isotope Labeling to Locate Dynamic Effects during Catalysis by Dihydrofolate Reductase

scientific article

Computational Studies of Candida Antarctica Lipase B to Test Its Capability as a Starting Point To Redesign New Diels-Alderases

scientific article published on December 2015

Computational analysis of human OGA structure in complex with PUGNAc and NAG-thiazoline derivatives

scientific article published on 18 September 2012

Computational design of biological catalysts.

scientific article published on 06 October 2008

Computational strategies for the design of new enzymatic functions

scientific article

Computational study on hydrolysis of cefotaxime in gas phase and in aqueous solution

scientific article published on 07 June 2012

Computer-aided rational design of catalytic antibodies: The 1F7 case

scientific article published on 01 January 2007

Computing kinetic isotope effects for chorismate mutase with high accuracy. A new DFT/MM strategy.

scientific article published in March 2005

Convergence of theory and experiment on the role of preorganization, quantum tunneling and enzyme motions into flavoenzyme-catalyzed hydride transfer.

scientific article

Coupling between protein and reaction dynamics in enzymatic processes: application of Grote-Hynes Theory to catechol O-methyltransferase.

scientific article published in May 2006

Coupling of the guanosine glycosidic bond conformation and the ribonucleotide cleavage reaction: implications for barnase catalysis

scientific article published in February 2008

Dependence of enzyme reaction mechanism on protonation state of titratable residues and QM level description: lactate dehydrogenase

scientific article published on 14 October 2005

Dioxygen activation by mononuclear copper enzymes: insights from a tripodal ligand mimicking their Cu(M) coordination sphere

scientific article published on 01 August 2009

Do zwitterionic species exist in the non-enzymatic peptide bond formation?

scientific article published on 01 November 2012

Dynamic and Electrostatic Effects on the Reaction Catalyzed by HIV-1 Protease

scientific article published on 09 December 2016

Dynamic effects on reaction rates in a Michael addition catalyzed by chalcone isomerase. Beyond the frozen environment approach.

scientific article published on 14 May 2008

Electron and Hydrogen Atom Transfers in the Hydride Carrier Protein EmoB.

scientific article published in November 2014

Enzymatic Δ 1 -Dehydrogenation of 3-Ketosteroids—Reconciliation of Kinetic Isotope Effects with the Reaction Mechanism

scientific article published on 20 June 2021

Enzyme molecular mechanism as a starting point to design new inhibitors: a theoretical study of O-GlcNAcase

scientific article published on 04 May 2011

Experimental and Computational Studies Delineate the Role of Asparagine 177 in Hydride Transfer for E. coli Thymidylate Synthase

scientific article published on 20 September 2018

First quantum mechanics/molecular mechanics studies of the inhibition mechanism of cruzain by peptidyl halomethyl ketones

scientific article published on 20 May 2015

Heavy enzymes--experimental and computational insights in enzyme dynamics

scientific article published on 05 April 2014

Hybrid schemes based on quantum mechanics/molecular mechanics simulations goals to success, problems, and perspectives.

scientific article published on January 2011

Hydrolysis of phosphotriesters: a theoretical analysis of the enzymatic and solution mechanisms.

scientific article published on 28 June 2012

Improving the QM/MM Description of Chemical Processes: A Dual Level Strategy To Explore the Potential Energy Surface in Very Large Systems

scientific article

Increased dynamic effects in a catalytically compromised variant of Escherichia coli dihydrofolate reductase.

scientific article published on 26 November 2013

Insights on the origin of catalysis on glycine N-methyltransferase from computational modelling.

scientific article published on 20 February 2018

Intrinsically Competitive Photoinduced Polycyclization and Double-Bond Shift through a Boatlike Conical Intersection This work was supported by the Università di Siena (P.A.R. 99/00), the Università di Bologna (MURST ex-60 %), NATO (CRG 950748), an

scientific article published on 01 April 2001

Investigation of the hydroxylation mechanism of noncoupled copper oxygenases by ab initio molecular dynamics simulations.

scientific article published on 20 November 2013

Ionic structures as intercalation compound host lattices. An ab initio perturbed ion study on lattice stretching

Is Promiscuous CALB a Good Scaffold for Designing New Epoxidases?

article

Long distance electron-transfer mechanism in peptidylglycine alpha-hydroxylating monooxygenase: a perfect fitting for a water bridge

scientific article published on 01 September 2007

Mechanism and plasticity of isochorismate pyruvate lyase: a computational study

scientific article published in November 2009

Minimization of dynamic effects in the evolution of dihydrofolate reductase† †Electronic supplementary information (ESI) available: Full experimental procedures; mass spectra of purified proteins; circular dichroism spectra, tabulated experimental d

scientific article published on 3 February 2016

Modeling methods for studying post-translational and transcriptional modifying enzymes.

scientific article

On the nature of the transition state in catechol O-methyltransferase. A complementary study based on molecular dynamics and potential energy surface explorations

scientific article published in August 2005

Parallel reaction pathways and noncovalent intermediates in thymidylate synthase revealed by experimental and computational tools

article published in the Proceedings of the National Academy of Sciences of the United States of America

Peptide Bond Formation Mechanism Catalyzed by Ribosome

scientific article

Predicting an improvement of secondary catalytic activity of promiscuous isochorismate pyruvate lyase by computational design.

scientific article

Preorganization and reorganization as related factors in enzyme catalysis: the chorismate mutase case

scientific article published in February 2003

Promiscuity in alkaline phosphatase superfamily. Unraveling evolution through molecular simulations.

scientific article

Protein Conformational Landscapes and Catalysis. Influence of Active Site Conformations in the Reaction Catalyzed by L-Lactate Dehydrogenase

scientific article

Protein isotope effects in dihydrofolate reductase from Geobacillus stearothermophilus show entropic-enthalpic compensatory effects on the rate constant

scientific article published on 26 November 2014

QM/MM calculations of kinetic isotope effects in the chorismate mutase active site

scientific article published in February 2003

QM/MM determination of kinetic isotope effects for COMT-catalyzed methyl transfer does not support compression hypothesis

scientific article published in July 2004

QM/MM study of l-lactate oxidation by flavocytochrome b2.

scientific article published on 25 May 2016

QM/MM study of thymidylate synthase: enzymatic motions and the temperature dependence of the rate limiting step.

scientific article

Quantum Mechanics/Molecular Mechanics Studies of the Mechanism of Cysteine Proteases Inhibition by Dipeptidyl Nitroalkenes

scientific article published on 20 January 2020

Quantum mechanical/molecular mechanical molecular dynamics simulation of wild-type and seven mutants of CpNagJ in complex with PUGNAc.

scientific article published in May 2010

Quantum mechanics/molecular mechanics studies of the mechanism of cysteine protease inhibition by peptidyl-2,3-epoxyketones.

scientific article

Quantum mechanics/molecular mechanics studies of the mechanism of falcipain-2 inhibition by the epoxysuccinate E64.

scientific article published on 15 May 2014

Reaction Mechanism of Organocatalytic Michael Addition of Nitromethane to Cinnamaldehyde: A Case Study on Catalyst Regeneration and Solvent Effects.

scientific article

Reactivity and Selectivity of Iminium Organocatalysis Improved by a Protein Host.

scientific article published on 23 August 2018

Revealing the Origin of the Efficiency of the De Novo Designed Kemp Eliminase HG-3.17 by Comparison with the Former Developed HG-3.

scientific article published on 23 March 2017

Revealing the mechanism for covalent inhibition of glycoside hydrolases by carbasugars at an atomic level

scientific article published in Nature Communications

Role of solvent on nonenzymatic peptide bond formation mechanisms and kinetic isotope effects.

scientific article published on 29 May 2013

Secondary Amine Catalysis in Enzyme Design: Broadening Protein Template Diversity through Genetic Code Expansion

scientific article published in 2024

Singlet-triplet gaps in large multireference systems: spin-flip-driven alternatives for bioinorganic modeling

scientific article published on January 2007

Special issue in computational modeling on biological systems

scientific article published on 26 July 2015

Stereoselectivity behavior of the AZ28 antibody catalyzed oxy-Cope rearrangement

scientific article published on 01 January 2006

Studying the role of protein dynamics in an SN2 enzyme reaction using free-energy surfaces and solvent coordinates

scientific article

Temperature dependence of dynamic, tunnelling and kinetic isotope effects in formate dehydrogenase

article published in 2018

The catalytic mechanism of glyceraldehyde 3-phosphate dehydrogenase from Trypanosoma cruzi elucidated via the QM/MM approach

scientific article published on 01 March 2013

The influence of active site conformations on the hydride transfer step of the thymidylate synthase reaction mechanism

scientific article

Theoretical Modeling on the Reaction Mechanism of p-Nitrophenylmethylphosphate Alkaline Hydrolysis and its Kinetic Isotope Effects

scientific article published on March 2009

Theoretical QM/MM studies of enzymatic pericyclic reactions.

scientific article published on 28 January 2010

Theoretical Study of the Phosphoryl Transfer Reaction from ATP to Dha Catalyzed by DhaK from Escherichia coli

scientific article published on 29 August 2017

Theoretical estimation of redox potential of biological quinone cofactors

scientific article published on 3 May 2017

Theoretical exploration of the oxidative properties of a [(tren Me1)CuO2]+ adduct relevant to copper monooxygenase enzymes: insights into competitive dehydrogenation versus hydroxylation reaction pathways.

scientific article published in January 2008

Theoretical modeling of enzyme catalytic power: analysis of "cratic" and electrostatic factors in catechol O-methyltransferase

scientific article

Theoretical modeling of the reaction mechanism of phosphate monoester hydrolysis in alkaline phosphatase

scientific article published on 01 June 2009

Theoretical modelling of tripodal CuN3 and CuN4 cuprous complexes interacting with O2, CO or CH3CN

scientific article published on 17 May 2006

Theoretical site-directed mutagenesis: Asp168Ala mutant of lactate dehydrogenase.

scientific article published in December 2008

Theoretical studies of HIV-1 reverse transcriptase inhibition.

scientific article

Theoretical studies of the hydrolysis of antibiotics catalyzed by a metallo-β-lactamase.

scientific article published on 23 January 2015

Theoretical study of catalytic efficiency of a Diels-Alderase catalytic antibody: an indirect effect produced during the maturation process

scientific article published on 01 January 2008

Theoretical study of phosphodiester hydrolysis in nucleotide pyrophosphatase/phosphodiesterase. Environmental effects on the reaction mechanism.

scientific article

Theoretical study of the inhibition mechanism of human 20S proteasome by dihydroeponemycin.

scientific article published on 25 December 2018

Theoretical study of the temperature dependence of dynamic effects in thymidylate synthase

scientific article published on 16 August 2010

Towards a rational design of antibody catalysts through computational chemistry

scientific article published on 01 January 2005

Transfer hydrogenations catalyzed by streptavidin-hosted secondary amine organocatalysts

scientific article

Understanding the different activities of highly promiscuous MbtI by computational methods

scientific article published on 03 February 2012

Unraveling the role of protein dynamics in dihydrofolate reductase catalysis

scientific article published on 24 September 2013

Using Grote−Hynes Theory To Quantify Dynamical Effects on the Reaction Rate of Enzymatic Processes. The Case of Methyltransferases†

scientific article published in January 2008

Why are some Enzymes Dimers? Flexibility and Catalysis in Thermotoga Maritima Dihydrofolate Reductase

scientific article published on 13 May 2019

List of works by Vicent Moliner

A Novel Strategy to Study Electrostatic Effects in Chemical Reactions: Differences between the Role of Solvent and the Active Site of Chalcone Isomerase in a Michael Addition

A QM/MM Exploration of the Potential Energy Surface of Pyruvate to Lactate Transformation Catalyzed by LDH. Improving the Accuracy of Semiempirical Descriptions

A QM/MM study of the complexes formed by aluminum and iron with serum transferrin at neutral and acidic pH

A Theoretical Study of the Favorskii Rearrangement. Calculation of Gas-Phase Reaction Paths and Solvation Effects on the Molecular Mechanism for the Transposition of the α-Chlorocyclobutanone

A density functional study of flavonoid compounds with anti-HIV activity

A hybrid potential reaction path and free energy study of the chorismate mutase reaction

A quantum mechanic/molecular mechanic study of the wild-type and N155S mutant HIV-1 integrase complexed with diketo acid.

A quantum mechanics/molecular mechanics study of the catalytic mechanism of the thymidylate synthase.

A quantum mechanics/molecular mechanics study of the protein-ligand interaction for inhibitors of HIV-1 integrase

A quantum mechanics/molecular mechanics study of the protein-ligand interaction of two potent inhibitors of human O-GlcNAcase: PUGNAc and NAG-thiazoline

A theoretical analysis of rate constants and kinetic isotope effects corresponding to different reactant valleys in lactate dehydrogenase

A theoretical study of carbon–carbon bond formation by a Michael-type addition

A theoretical study of the catalytic mechanism of formate dehydrogenase.

Ab initio perturbed ion calculations on Ni2+·KZnF3 and Ni2+ ·KMgF3. A structural study

Activation Free Energy of CatecholO-Methyltransferase. Corrections to the Potential of Mean Force†

An AM1 theoretical study on the effect of Zn2+ Lewis acid catalysis on the mechanism of the cycloaddition between 3-phenyl-1-(2-pyridyl)-2-propen-1-one and cyclopentadiene

Application of Grote−Hynes Theory to the Reaction Catalyzed by Thymidylate Synthase

Author Correction: Revealing the mechanism for covalent inhibition of glycoside hydrolases by carbasugars at an atomic level

Benchmarking Quantum Mechanics/Molecular Mechanics (QM/MM) Methods on the Thymidylate Synthase-Catalyzed Hydride Transfer.

Binding isotope effects as a tool for distinguishing hydrophobic and hydrophilic binding sites of HIV-1 RT.

Calculation of binding energy using BLYP/MM for the HIV-1 integrase complexed with the S-1360 and two analogues

Catalysis in glycine N-methyltransferase: testing the electrostatic stabilization and compression hypothesis

Catalytic enantioselective epoxidation of nitroalkenes.

Chemical Ligation and Isotope Labeling to Locate Dynamic Effects during Catalysis by Dihydrofolate Reductase

Computational Studies of Candida Antarctica Lipase B to Test Its Capability as a Starting Point To Redesign New Diels-Alderases

Computational analysis of human OGA structure in complex with PUGNAc and NAG-thiazoline derivatives

Computational design of biological catalysts.

Computational strategies for the design of new enzymatic functions

Computational study on hydrolysis of cefotaxime in gas phase and in aqueous solution

Computer-aided rational design of catalytic antibodies: The 1F7 case

Computing kinetic isotope effects for chorismate mutase with high accuracy. A new DFT/MM strategy.

Convergence of theory and experiment on the role of preorganization, quantum tunneling and enzyme motions into flavoenzyme-catalyzed hydride transfer.

Coupling between protein and reaction dynamics in enzymatic processes: application of Grote-Hynes Theory to catechol O-methyltransferase.

Coupling of the guanosine glycosidic bond conformation and the ribonucleotide cleavage reaction: implications for barnase catalysis

Dependence of enzyme reaction mechanism on protonation state of titratable residues and QM level description: lactate dehydrogenase

Dioxygen activation by mononuclear copper enzymes: insights from a tripodal ligand mimicking their Cu(M) coordination sphere

Do zwitterionic species exist in the non-enzymatic peptide bond formation?

Dynamic and Electrostatic Effects on the Reaction Catalyzed by HIV-1 Protease

Dynamic effects on reaction rates in a Michael addition catalyzed by chalcone isomerase. Beyond the frozen environment approach.

Electron and Hydrogen Atom Transfers in the Hydride Carrier Protein EmoB.

Enzymatic Δ 1 -Dehydrogenation of 3-Ketosteroids—Reconciliation of Kinetic Isotope Effects with the Reaction Mechanism

Enzyme molecular mechanism as a starting point to design new inhibitors: a theoretical study of O-GlcNAcase

Experimental and Computational Studies Delineate the Role of Asparagine 177 in Hydride Transfer for E. coli Thymidylate Synthase

First quantum mechanics/molecular mechanics studies of the inhibition mechanism of cruzain by peptidyl halomethyl ketones

Heavy enzymes--experimental and computational insights in enzyme dynamics

Hybrid schemes based on quantum mechanics/molecular mechanics simulations goals to success, problems, and perspectives.

Hydrolysis of phosphotriesters: a theoretical analysis of the enzymatic and solution mechanisms.

Improving the QM/MM Description of Chemical Processes: A Dual Level Strategy To Explore the Potential Energy Surface in Very Large Systems

Increased dynamic effects in a catalytically compromised variant of Escherichia coli dihydrofolate reductase.

Insights on the origin of catalysis on glycine N-methyltransferase from computational modelling.

Intrinsically Competitive Photoinduced Polycyclization and Double-Bond Shift through a Boatlike Conical Intersection This work was supported by the Università di Siena (P.A.R. 99/00), the Università di Bologna (MURST ex-60 %), NATO (CRG 950748), an

Investigation of the hydroxylation mechanism of noncoupled copper oxygenases by ab initio molecular dynamics simulations.

Ionic structures as intercalation compound host lattices. An ab initio perturbed ion study on lattice stretching

Is Promiscuous CALB a Good Scaffold for Designing New Epoxidases?

Long distance electron-transfer mechanism in peptidylglycine alpha-hydroxylating monooxygenase: a perfect fitting for a water bridge

Mechanism and plasticity of isochorismate pyruvate lyase: a computational study

Minimization of dynamic effects in the evolution of dihydrofolate reductase† †Electronic supplementary information (ESI) available: Full experimental procedures; mass spectra of purified proteins; circular dichroism spectra, tabulated experimental d

Modeling methods for studying post-translational and transcriptional modifying enzymes.

On the nature of the transition state in catechol O-methyltransferase. A complementary study based on molecular dynamics and potential energy surface explorations

Parallel reaction pathways and noncovalent intermediates in thymidylate synthase revealed by experimental and computational tools

Peptide Bond Formation Mechanism Catalyzed by Ribosome

Predicting an improvement of secondary catalytic activity of promiscuous isochorismate pyruvate lyase by computational design.

Preorganization and reorganization as related factors in enzyme catalysis: the chorismate mutase case

Promiscuity in alkaline phosphatase superfamily. Unraveling evolution through molecular simulations.

Protein Conformational Landscapes and Catalysis. Influence of Active Site Conformations in the Reaction Catalyzed by L-Lactate Dehydrogenase

Protein isotope effects in dihydrofolate reductase from Geobacillus stearothermophilus show entropic-enthalpic compensatory effects on the rate constant

QM/MM calculations of kinetic isotope effects in the chorismate mutase active site

QM/MM determination of kinetic isotope effects for COMT-catalyzed methyl transfer does not support compression hypothesis

QM/MM study of l-lactate oxidation by flavocytochrome b2.

QM/MM study of thymidylate synthase: enzymatic motions and the temperature dependence of the rate limiting step.

Quantum Mechanics/Molecular Mechanics Studies of the Mechanism of Cysteine Proteases Inhibition by Dipeptidyl Nitroalkenes

Quantum mechanical/molecular mechanical molecular dynamics simulation of wild-type and seven mutants of CpNagJ in complex with PUGNAc.

Quantum mechanics/molecular mechanics studies of the mechanism of cysteine protease inhibition by peptidyl-2,3-epoxyketones.

Quantum mechanics/molecular mechanics studies of the mechanism of falcipain-2 inhibition by the epoxysuccinate E64.

Reaction Mechanism of Organocatalytic Michael Addition of Nitromethane to Cinnamaldehyde: A Case Study on Catalyst Regeneration and Solvent Effects.

Reactivity and Selectivity of Iminium Organocatalysis Improved by a Protein Host.

Revealing the Origin of the Efficiency of the De Novo Designed Kemp Eliminase HG-3.17 by Comparison with the Former Developed HG-3.

Revealing the mechanism for covalent inhibition of glycoside hydrolases by carbasugars at an atomic level

Role of solvent on nonenzymatic peptide bond formation mechanisms and kinetic isotope effects.