-2020-

S. Martí "QMCube (QM3): An all‐purpose suite for multiscale QM/MM calculations" J. Comput. Chem. 42, 447-457 (2020) doi:10.1002/jcc.26465
Available as GitHub repository 

S. Velasco-Lozano, M. Roca, A. Leal-Duaso, J. A. Mayoral, E. Pires,  V. Moliner,  F. López-Gallego  "Selective oxidation of alkyl and aryl glyceryl monoethers catalysed by an engineered and immobilised glycerol dehydrogenase" Chem. Sci. 11, 12009-12020 (2020) doi:10.1039/D0SC04471G

W. Ren, M. Farren-Dai, N. Sannikova, K. Świderek, Y. Wang, O. Akintola, R. Britton, V. Moliner, A. J Bennet  "Glycoside Hydrolase Stabilization of Transition State Charge: New Directions for Inhibitor Design" Chem.Sci. 11, 10488-10495 (2020) doi:10.1039/D0SC04401F

S. Martí, I. Tuñón, V. Moliner, J. Bertran "Are heme dependent enzymes always using a redox mechanism? A Theoretical Study of the Kemp Elimination Catalysed by a promiscuous aldoxime dehydratase." ACS Catal. 10,  11110–11119 (2020) doi: 10.1021/acscatal.0c02215

M. Roca, I. H. Williams "Transition-State Vibrational Analysis and Isotope Effects for COMT-Catalyzed Methyl Transfer" 
J. Am. Chem. Soc. 142, 15548–15559 (2020) doi:10.1021/jacs.0c07344

M. Gabr, K. Świderek "Discovery of a histidine‐based scaffold as an inhibitor of gut microbial choline trimethylamine‐lyase."
ChemMedChem 15, 2273-2279 (2020) doi:10.1002/cmdc.202000571

K. Świderek, V. Moliner "Revealing the Molecular Mechanisms of Proteolysis of SARS-CoV-2 Mpro from QM/MM Computational Methods."
Chem. Sci. 11, 10626-10630 (2020) doi:10.1039/D0SC02823A ChemRxiv Preprint Doi: 10.26434/Chemrxiv.12283967.V1 featured on the front cover Issue 39, 2020.
This Article Is Part Of The Themed Collection: 2020 Chemical Science HOT Article Collection And Celebrating 10 Years Of Chemical Science


A.S. Adesina, K. Świderek, L.Y.P. Luk, V. Moliner, R.K. Allemann "Electric Field Measurements Reveal the Pivotal Role of Cofactor-Substrate Interaction in Dihydrofolate Reductase Catalysis"  ACS Catal. 10, 7907-7914 (2020) doi:10.1021/acscatal.0c01856

D. De Raffele, S. Martí, V. Moliner "Understanding the Directed Evolution of de novo Retro-Aldolases from QM/MM Studies."
ACS Catal. 10, 7871–7883 (2020) doi: 10.1021/acscatal.0c01165  Cover of Volume 10, Issue 14

V. Moliner "Bioquimica computational: una potente herramienta para desvalar el origen de la reactividad enzimatica" An. Quim. 116, 16-24 (2020)

M. Roca, S. Navas-Yuste, K. Zinovjev, M. López-Estepa, S. Gómez, F.J. Fernandez, M.C. Vega, I. Tuñón "Elucidating the Catalytic Reaction Mechanism of Orotate Phosphoribosyltransferase by means of X-ray Crystallography and Computational Simulations." ACS Catal. 10, 1871-1885 (2020) doi:10.1021/acscatal.9b05294

K. Świderek, A. Porter, C. M. Upfold, I. H. Williams "Influence of dielectric environment upon isotope effects on glycoside heterolysis: computational evaluation and atomic hessian analysis." J. Am. Chem. Soc. 142, 1556-1563 (2020) doi:10.1021/jacs.9b11988

K. Arafet, F.V. González, V. Moliner "Quantum mechanics/molecular mechanics studies of the mechanism of cysteine proteases inhibition by dipeptidyl nitroalkenes." Chem. Eur. J. 26, 2002-2012 (2020) doi:10.1002/chem.201904513

M.A. Galmés, E. García-Junceda, K. Świderek, V. Moliner "Exploring the Origin of Amidase Substrate Promiscuity in CALB by a Computational Approach." 
ACS Catal. 10, 1938-1946 (2020), ACS Editors' Choice doi:10.1021/acscatal.9b04002

-2019-

S. Martí, V. Moliner, K. Świderek "Examination of the performance of semiempirical methods in QM/MM studies of the SN2-like reaction of an adenylyl group transfer catalysed by ANT4′" Theor Chem Acc 138:120 (2019) doi:10.1007/s00214-019-2507-1

J.J. Ruiz-Pernía, I. Tuñón, V. Moliner, L. Y. P. Luk, R.K. Allemann "Loss of Hyperconjugative Effects Drives Hydride Transfer during Dihydrofolate Reductase Catalysis." 
ACS Catal. 9, 10343-10349 (2019) doi:10.1021/acscatal.9b02839

A. Krzeminska, K. Świderek "Molecular Insights into the Substrate-Assisted Mechanism of Viral DNA 3’-End Processing in Intasome of Prototype Foamy Virus Integrase from Molecular Dynamic and QM/MM Studies." J. Chem. Inf. Model. 59, 2995-3005 (2019) doi:10.1021/acs.jcim.9b00276

J.J. Ruiz-Pernía, I. Tuñón, V. Moliner, and R. K. Allemann "Why are some Enzymes Dimers? Flexibility and Catalysis in Thermotoga Maritima Dihydrofolate Reductase" ACS Catal. 9, 5902-5911 (2019) doi:10.1021/acscatal.9b01250

A.F. Scott, L.Y.P. Luk, I. Tuñón, V. Moliner, and R. K. Allemann "Heavy enzymes and the rational redesign of protein catalysts" Chem. Bio. Chem. 20, 1-7 (2019) 
doi:10.1002/cbic.201900134

S. G. Zárate, P. Morales, K. Świderek, V. M. Bolanos-Garcia, A. Bastida "A Molecular Modeling Approach to Identify Novel Inhibitors of the Major Facilitator Superfamily of Efflux Pump Transporters" Antibiotics  8, 25 (2019) doi:10.3390/antibiotics8010025

D. De Raffele, S. Martí, V. Moliner "QM/MM Theoretical Studies of a De Novo Retro-Aldolase Design" 
ACS Catal. 9, 2482-2492 (2019) DOI: 10.1021/acscatal.8b0445

N. Serrano-Aparicio, K. Świderek, V. Moliner "Theoretical study of the inhibition mechanism of human 20S proteasome by dihydroeponemycin."  
Eur. J. Med. Chem. 164, 399-407 (2019) DOI: 10.1016/j.ejmech.2018.12.062

S. Marti, A. Bastida, K. Świderek "Theoretical Studies on Mechanism of Inactivation of Kanamycin A by 4’-O-Nucleotidyltransferase."  
Front. Chem. 6, 660 (2019)  DOI: 10.3389/fchem.2018.00660

-2018-

K. Arafet, K. Świderek, V. Moliner "Computational Study of the Michaelis Complex Formation and the Effect on the Reaction Mechanism of Cruzain Cysteine Protease."  
ACS Omega 3, 18613-18622 (2018)  DOI: 10.1021/acsomega.8b03010

S.A. Kholodar, A. K. Ghosh, K. Świderek, V. Moliner, A. Kohen "Parallel reaction pathways and noncovalent intermediates in thymidylate synthase revealed by experimental and computational tools."  Proc. Nat. Acad. Sci. USA. 115, 10311-10314 (2018) DOI: 10.1073/pnas.1811059115

I. Gurevic, Z. Islam, K. Świderek, K. Trepka, A. K Ghosh, V. Moliner, A. Kohen "Experimental and computational studies delineate the role for asparagine 177 in hydride transfer for E. coli thymidylate synthase."  ACS Catal. 8, 10241-10253 (2018) DOI: 10.1021/acscatal.8b02554

M. Roca, J.J. Ruiz-Pernia, R. Castillo, M. Oliva, V. Moliner "Temperature dependence of dynamic, tunnelling and kinetic isotope effects in Formate Dehydrogenase"  
Phys. Chem. Chem. Phys. 20, 25722-25737 (2018)  DOI: 10.1039/C8CP04244F

W. Ren, R. Pengelly, M. Farren-Dai, S. Shamsi Kazem Abadi, V. Oehler, O. Akintola, J. Draper, M. Meanwell, S. Chakladar, K. Świderek, V. Moliner, R. Britton, T. M. Gloster, A. J. Bennet "Revealing the mechanism for covalent inhibition ofglycoside hydrolases by carbasugars at an atomiclevel"  Nat. Commun. 9: 3243 (2018) DOI: 10.1038/s41467-018-05702-7

A.R. Nödling, K. Świderek, R. Castillo, J.W.Hall, A. Angelastro, L.C. Morrill, Y. Jin, Y. Tsai, V. Moliner, L.Y.P. Luk  "Reactivity and Selectivity of Iminium Organocatalysis Improved by a Protein Host"  Angew. Chem. Int. Ed. 57, 12478-12482  (2018) F1000Prime Highlights DOI: 10.1002/anie.201806850

K. Świderek, I. Tuñón, I. H. Williams,V. Moliner "Insights on the origin of catalysis on glycine N-methyltransferase from computational modelling"  J. Am. Chem. Soc. 140, 4327–4334, (2018)  JACS Highlights, Biofisica Highlights, F1000Prime Highlights DOI: 10.1021/jacs.7b13655

E. M. Behiry, J.J. Ruiz-Pernia, L. Luk, I. Tuñón, V. Moliner, R.K. Allemann "Isotope substitution of promiscuous alcohol dehydrogenase reveals origin of substrate preference in transition state" Angew. Chem. Int. Ed. 57, 3128-3131, (2018)  Biofisica Highlights  DOI: 10.1002/anie.201712826

K. Świderek, A. R. Nödling, Y. Tsai, L. Y. P. Luk, V. Moliner "The Reaction Mechanism of Organocatalytic Michael Addition of Nitromethane to Cinnamaldehyde: A Case Study on Catalyst Regeneration and Solvent Effect" J. Phys. Chem. A, 122, 451–459, (2018) DOI: 10.1021/acs.jpca.7b11803

M.Roca, V. Moliner, I.Tuñón "On the origin of Enzymatic Kinetic Isotope Effects in Human Purine Nucleoside Phosphorylase" ACS Catal. 8, 815–827 (2018) DOI: 10.1021/acscatal.7b04199

-2017-

I. Bordes, R. Castillo, V. Moliner "A Theoretical Study of the Phosphoryl Transfer Reaction From ATP to Dha Catalyzed by DhaK From Escherichia Coli" 
J. Phys. Chem. B 121, 8878–8892, (2017)  DOI: 10.1021/acs.jpcb.7b04862

I. Bordes, E. García-Junceda, I. Sánchez-Moreno, R. Castillo, V. Moliner "Computational Study of the Phosphoryl Donor Activity of Dihydroxyacetone Kinase from ATP to Inorganic Polyphosphate." Int. J. Quantum Chem. (2017) DOI: 10.1021/acs.jpcb.7b04862

N. Gillet, B. Lévy, V. Moliner, I. Demachy, A. de la Lande "Theoretical estimation of redox potential of biological quinone cofactors" J. Comput. Chem.  38, 1612–1621, (2017)  
DOI: 10.1002/jcc.24802

K. Arafet, S. Ferrer, F. V. González, V. Moliner "Quantum Mechanics/Molecular Mechanics Studies of the Mechanism of Cysteine Protease Inhibition by Peptidyl-2,3-epoxyketones."  Phys. Chem. Chem. Phys. 19, 12740-12748, (2017) DOI: 10.1039/C7CP01726J

M. Delgado, S. Görlich, J.E. Longbotham, N.S. Scrutton, S. Hay, V. Moliner, I.Tuñón "Convergence of theory and experiment on the role of preorganization, quantum tunneling and enzyme motions into flavoenzyme-catalyzed hydride transfer" ACS Catal. 7, 3190–3198, (2017) DOI: 10.1021/acscatal.7b00201

K. Świderek, I. Tuñón, V. Moliner, J. Bertran "Revealing the origin of the efficiency of the de novo designed Kemp eliminase HG-3.17 by comparison with the former developed HG-3"  Chem. Eur. J. 23, 7582–7589, (2017) DOI: 10.1002/chem.201700807

K. Świderek, S. Marti, I. Tuñón, V. Moliner, J. Bertran "Molecular mechanism of the site-specific self-cleavage of the RNA phosphodiester backbone by a twister ribozyme" Theor Chem Acc 136:31, (2017) DOI: 10.1007/s00214-017-2060-8

K. Świderek, K. Arafet, A. Kohen, V. Moliner "Benchmarking QM/MM Methods on the Thymidylate Synthase Catalyzed Hydride Transfer."  
J. Chem. Theory Comput. 13, 1375–1388, (2017) DOI: 10.1021/acs.jctc.6b01032

K. Arafet, S. Ferrer, V. Moliner "A Computational Study of the Catalytic Mechanism of the Cruzain Cysteine Protease." ACS Catal. 7, 1207–1215, (2017) DOI: 10.1021/acscatal.6b03096

-2016-

Vicent Moliner, Iñaki Tuñón “Simulating Enzyme Catalysis” Biofísica Magazine 6, 1 (2016)

A. Krzemińska, V. Moliner, K. Świderek  "Dynamic and Electrostatic Effects on the Reaction Catalyzed by HIV-1 Protease." J. Am. Chem. Soc. 138, 16283–16298 (2016) DOI: 10.1021/jacs.6b06856

A. Vidal-Albalat, K. Świderek, J. Izquierdo,  S. Rodriguez, V. Moliner and F. V. Gonzalez  "Catalytic Enantioselective Epoxidation of Nitroalkenes" Chem Commun. 52, 10060-10063 (2016) DOI: 10.1039/C6CC03539F

N. Gillet, Jose J. Ruiz-Pernia, A. de la Lande, B. Lévy, F. Lederer, I. Demachy, V. Moliner  "QM/MM Study of L-Lactate Oxidation by Flavocytochrome b2"  Phys. Chem. Chem. Phys. 18, 15609-15618 (2016) DOI: 10.1039/C6CP00395H

I. Viciano, S. Marti "Theoretical Study of the Mechanism of Exemestane Hydroxylation Catalyzed by Human Aromatase Enzyme" J. Phys. Chem. B  120, 3331–3343 (2016) DOI: 10.1021/acs.jpcb.6b01014

J.J.Ruiz Pernía, E.M. Behiry, L.Y.P. Luk, E.J. Loveridge, I. Tuñon, V. Moliner, R.K. Allemann "Minimization of Dynamic Effects in the Evolution of Dihydrofolate Reductase" Chemical Science 7, 3248-3255 (2016) DOI: 10.1039/C5SC04209G

K. Świderek and V. Moliner "Computational Studies of Candida Antarctica Lipase B to Test Its Capability as a Starting Point to Redesign New Diels-Alderases" J. Phys. Chem. B  120, 2053-2070 (2016) DOI: 10.1021/acs.jpcb.5b10527