Book Chapters

• Modeling Microsolvation Features Involving Clusters, J.M.C. Marques, in Comprehensive Computational Chemistry, M. Yáñez and R. J. Boyd (eds.), Elsevier, Oxford, vol. 2, pp 509-522 (2024); doi: 10.1016/B978-0-12-821978-2.00143-4
• Revealing Energy Landscapes of Atomic Clusters by Applying Adaptive Bio-Inspired Algorithms, J.M.C. Marques, W.S. Jesus, F.V. Prudente, F.B. Pereira, and N. Lourenço, in Physical Chemistry for Chemists and Chemical Engineers Multidisciplinary Research Perspectives, A. V. Vakhrushev, R. Haghi, and J. V. de Julián-Ortiz (eds.), Innovations in Physical Chemistry: Monograph Series, Apple Academic Press, New York, chapter 3, pp 47-74 (2018); doi: 10.1201/b22413
• Aggregation of Cyclodextrins: Fundamental Issues and Applications, T.F.G.G. Cova, S.M.A. Cruz, A.J.M. Valente, P.E. Abreu, J.M.C. Marques and A.A.C.C. Pais, in Cyclodextrin: A Versatile Ingredient, Poonam Arora and Neelima Dhingra (eds.), IntechOpen, pp 45-66 (2018); doi: 10.5772/intechopen.69187
• Designing Efficient Evolutionary Algorithms for Cluster Optimization: A Study on Locality, F.B. Pereira, J.M.C. Marques, T. Leitão and J. Tavares, in Advances in Metaheuristics for Hard Optimization, P. Siarry and Z. Michalewicz (eds.), Springer, Berlin, pp 223-250 (2008); doi: 10.1007/978-3-540-72960-0_11

Papers

2024

• Magnetic Ionic Liquids: Current Achievements and Future Perspectives with a Focus on Computational Approaches, N.M. Figueiredo, I.V. Voroshylova, E.S.C. Ferreira, J.M.C. Marques and M.N.D.S. Cordeiro, Chem. Rev. 124 (2024) 3392-3415; doi: 10.1021/acs.chemrev.3c00678
   
• Structure and thermodynamics of Li⁺Ar_n clusters beyond the second solvation shell, J.M.C. Marques and F.V. Prudente, Symmetry 16 (2024) 229; doi: 10.3390/sym16020229

2023

• Aggregation paterns of curcumin and piperine mixtures in different polar media, J.R.C. Santos, P.E. Abreu and J.M.C. Marques, Phys. Chem. Chem. Phys. 25 (2023) 19899–19910; doi: 10.1039/d3cp00096f
• Reduced Chitosan as a Strategy for Removing Copper Ions from Water, P.M.C. Matias, J.F.M. Sousa, E.F. Bernardino, J.P. Vareda, L. Durães, P.E. Abreu, J.M.C. Marques, D. Murtinho and A.J.M. Valente, Molecules 28 (2023) 4110; doi: 10.3390/molecules28104110

2022

• Intermolecular forces: from atoms and molecules to nanostructures (editorial), J.M.C. Marques, F.V. Prudente and F. Pirani, Molecules 27 (2022) 3072; doi: 10.3390/molecules27103072
• The behaviour of aluminium ions in artificial saliva and the impact of the chlorhexidine digluconate on its removal - A diffusion model, S.I.G. Fangaia, P.M.G. Nicolau, F.A.D.R.A. Guerra, M. M. Rodrigo, A.C.F. Ribeiro, A.J.M. Valente, J.R.C. Santos, J.M.C. Marques and M.A. Esteso, J. Mol. Liq. 353 (2022) 118749; doi: 10.1016/j.molliq.2022.118749
• Thermodynamic signatures of structural transitions and dissociation of charged colloidal clusters: a parallel tempering Monte Carlo study, F.V. Prudente and J.M.C. Marques, Molecules 27 (2022) 2581; doi: 10.3390/molecules27082581
• On the transport and dynamics of disaccharides: H-bonding effect in sucrose and sucralose, C.V.M. Silva, J.R.C. Santos, M.M. Rodrigo, A.C.F. Ribeiro, A.J.M. Valente, P.E. Abreu, J.M.C. Marques and M.A. Esteso, J. Mol. Liq. 345 (2022) 117855; doi: 10.1016/j.molliq.2021.117855

2021

• Calculation of diffusion coefficients of pesticides by employing molecular dynamics simulations, J.R.C. Santos, P.E. Abreu and J.M.C. Marques, J. Mol. Liq. 340, 117106 (2021); doi: 10.1016/j.molliq.2021.117106
• On the stabilization of the Li⁺-Li⁺ interaction by microsolvation with rare-gas atoms, M.D. Andrade, W.S. Jesus, F.V. Prudente and J.M.C. Marques,Theor. Chem. Acc. 140, 65 (2021); Article's copy to download here; doi: 10.1007/s00214-021-02763-8
• Modeling microsolvation clusters with electronic-structure calculations guided by analytical potentials and predictive machine learning techniques, W.S. Jesus, F.V. Prudente, J.M.C. Marques and F.B. Pereira, Phys. Chem. Chem. Phys. 23, 1738-1749 (2021); Article's copy to download here; doi: 10.1039/D0CP05200K
• Aggregation of coronene: the effect of carboxyl and amine functional groups, C.F.O. Correia, J.M.C. Marques, M. Bartolomei, F. Pirani, E. Maçôas and J.M.G. Martinho, Phys. Chem. Chem. Phys. 23, 1500-1509 (2021); doi: 10.1039/D0CP05447J
• Effect of sodium chloride on the behavior of the lactose in aqueous solution studied from diffusion experiments and molecular dynamics simulations, M. Melia Rodrigo, A.C.F. Ribeiro, G. Moço, A.M.T.D.P.V. Cabral, A.J.M. Valente, M.A. Esteso, P.E. Abreu, J.R.C. Santos and J.M.C. Marques, J. Chem. Thermodyn. 155, 106370 (2021); doi: 10.1016/j.jct.2020.106370

2020

• A thermodynamic view on the microsolvation of ions by rare gas: application to Li⁺ with argon, M.N. Guimarães, M.M. de Almeida, J.M.C. Marques and F.V. Prudente, Phys. Chem. Chem. Phys. 22, 10882-10892 (2020); selected by Editors as a 2020 HOT PCCP article; doi: 10.1039/D0CP01283A
• Editorial: Application of Optimization Algorithms in Chemistry, J.M.C. Marques, E. Martínez-Núñez and W.L. Hase, Front. Chem. 8, 198 (2020); doi: 10.3389/fchem.2020.00198

2019

• Aggregation enhancement of coronene molecules by seeding with alkali-metal ions, M. Bartolomei, F. Pirani and J.M.C. Marques, Phys. Chem. Chem. Phys. 21, 16005-16016 (2019); selected by Editors as a 2019 HOT PCCP article; doi: 10.1039/C9CP02658D
• Microsolvation of Li⁺ in a Mixture of Argon and Krypton: Unveiling the Most Stable Structures of the Clusters, W.S. Jesus, F.V. Prudente and J.M.C. Marques, J. Phys. Chem. A 123, 2867-2873 (2019); Article's copy on request here; doi:  10.1021/acs.jpca.9b00960
• Exploring the first-shell and second-shell structures arising in the microsolvation of Li⁺ by rare gases, W.S. Jesus, J.M.C. Marques, F.V. Prudente and F.B. Pereira, Int. J. Quantum Chem. 119, e25860 (2019); doi: 10.1002/qua.25860
• Molecular dynamics insights for screening the ability of polymers to remove pesticides from water, F.G.A. Estrada, J.M.C. Marques and A.J.M. Valente, ChemistryOpen 8, 438-446 (2019); doi: 10.1002/open.201800293

2018

• Two-dimensional clusters from self-assembly of oppositely charged particles, S.G. Rodrigues, A.A.C.C. Pais and J.M.C. Marques, Chem. Phys. Lett. 706, 586-593 (2018); doi: 10.1016/j.cplett.2018.07.003
• Toward the Understanding of Micro-TLC Behavior of Various Dyes on Silica and Cellulose Stationary Phases Using A Data Mining Approach, J.C. Pereira, J.M.C. Marques, E. Włodarczyk, B. Fenert and P.K. Zarzycki, J. AOAC Int. 101, 1437-1447 (2018); doi: 10.5740/jaoacint.18-0061
• Correction: Solvation of Li⁺ by argon: how important are three-body forces?, F.V. Prudente, J.M.C. Marques and F.B. Pereira, Phys. Chem. Chem. Phys. 20, 16877-16882 (2018); doi:10.1039/C8CP91778G

2017

• Solvation of Li⁺ by argon: How important are three-body forces?, F.V. Prudente, J.M.C. Marques and F.B. Pereira, Phys. Chem. Chem. Phys. 19, 25707-25716 (2017); doi: 10.1039/C7CP04549B
• Modeling coronene nanostructures: analytical potential, stable configurations and ab initio energies, M. Bartolomei, F. Pirani and J.M.C. Marques, J. Phys. Chem. C 121, 14330-14338 (2017); doi: 10.1021/acs.jpcc.7b03691
• GAFit: a general-purpose, user-friendly program for fitting potential energy surfaces, R. Rodríguez-Fernández, F.B. Pereira, J.M.C. Marques, E. Martínez-Núñez and S.A. Vázquez,Comput. Phys. Commun. 217, 89-98 (2017); doi:10.1016/j.cpc.2017.02.008
• Low-energy structures of clusters modeled with competing repulsive and either long- or moderate short-range attractive interactions, S.M.A. Cruz and J.M.C. Marques, Comput. Theor. Chem. 1107, 82-93 (2017); doi: 10.1016/j.comptc.2017.01.035
• A global optimization perspective on molecular clusters, J.M.C. Marques, F.B. Pereira, J.L. Llanio-Trujillo, P.E. Abreu, M. Albertí, A. Aguilar, F. Pirani and M. Bartolomei, Phil. Trans. R. Soc. A 375, issue: 2092, 20160198 (2017); doi: 10.1098/rsta.2016.0198

2016

• Improved evolutionary algorithm for the global optimization of clusters with competing attractive and repulsive interactions, S.M.A. Cruz, J.M.C. Marques and F.B. Pereira, J. Chem. Phys. 145, 154109 (2016); doi: 10.1063/1.4964780
• A Detailed Study on the Low-Energy Structures of Charged Colloidal-Clusters, S.M.A. Cruz and J.M.C. Marques, J. Phys. Chem. B 120, 3455-3466 (2016); doi: 10.1021/acs.jpcb.6b01233

2015

• Low-energy structures of benzene clusters with a novel accurate potential surface, M. Bartolomei, F. Pirani and J.M.C. Marques, J. Comput. Chem. 36, 2291-2301 (2015); doi:10.1002/jcc.24201
• Colloidal clusters from a global optimization perspective, J.M.C. Marques and F.B. Pereira, J. Mol. Liq. 210, 51-63 (2015); doi: 10.1016/j.molliq.2015.03.009

2014

• On the lowest-energy structure of binary Zn-Cd nanoparticles: size and composition, C.M.A. Zanvettor and J.M.C. Marques, Chem. Phys. Lett. 608, 373-379 (2014); doi: 10.1016/j.cplett.2014.06.022
• Potassium Ion Surrounded by Aromatic Rings: Molecular Dynamics of the First Solvation Shell, M. Albertí, A. Aguilar and J.M.C. Marques, Eur. Phys. J. D 68, 364 (2014); doi: 10.1140/epjd/e2014-50579-2

2013

• Microsolvation of the potassium-ion with aromatic rings: comparison between hexafluorobenzene and benzene, J.M.C. Marques, J.L. Llanio-Trujillo, M. Albertí, A. Aguilar and F. Pirani, J. Phys. Chem. A 117, 8043-8053 (2013); doi: 10.1021/jp405295b
• New insights on lithium-cation microsolvation by solvents forming hydrogen-bonds: water versus methanol, J.L. Llanio-Trujillo, J.M.C. Marques and F.B. Pereira, Comput. Theoret. Chem. 1021, 124-134 (2013); doi: 10.1016/j.comptc.2013.06.043
• A detailed investigation on the global minimum structures of mixed rare-gas clusters: geometry, energetics and site occupancy, J.M.C. Marques and F.B. Pereira, J. Comput. Chem. 34, 505-517 (2013); doi: 10.1002/jcc.23161

2012

• Alkali-ion Microsolvation with Benzene Molecules, J.M.C. Marques, J.L. Llanio-Trujillo, M. Albertí, A. Aguilar and F. Pirani, J. Phys. Chem. A 116, 4947-4956 (2012); doi: 10.1021/jp302136u
• Intermolecular potentials for simulations of collisions of SiNCS⁺ and (CH₃)₂SiNCS⁺ ions with fluorinated self-assembled monolayers, J.J. Nogueira, A. Sanchez-Caronilla, J.M.C. Marques, W.L. Hase, E. Martínez-Núñez and S.A. Vázquez, Chem. Phys. 399, 193-204 (2012); doi: 10.1016/j.chemphys.2011.02.014
• On the use of big-bang method to generate low-energy structures of atomic
 clusters modeled with pair potentials of different ranges, J.M.C. Marques, A.A.C.C. Pais and P.E. Abreu, J. Comput. Chem. 33, 442-452 (2012); doi: 10.1002/jcc.21987

2011

• An evolutionary algorithm for the global optimization of molecular clusters: application to water, benzene, and benzene cation, J.L. Llanio-Trujillo, J.M.C. Marques and F.B. Pereira, J. Phys. Chem. A 115, 2130-2138 (2011); doi: 10.1021/jp1117695
• Electronic structure calculations on the Ar-C₆H₁₂ interaction: application to the microsolvation of the chair conformer, P.E. Abreu, J.M.C. Marques and F.B. Pereira, Comput. Theoret. Chem. 975, 83-91 (2011); doi: 10.1016/j.comptc.2011.02.014
• Direct fit of spectroscopic data of diatomic molecules by using genetic algorithms: II. the ground state of RbCs, M.M. Almeida, F.V.Prudente, C.E. Fellows, J.M.C. Marques and F.B. Pereira, J. Phys. B: At. Mol. Opt. Phys. 44, 225102 (2011); doi: 10.1088/0953-4075/44/22/225102

2010

• An evolutionary algorithm for global minimum search of binary atomic clusters, J.M.C. Marques and F.B. Pereira, Chem. Phys. Lett. 485, 211-216 (2010); doi: 10.1016/j.cplett.2009.11.059
• Transport properties of aqueous solutions of (1R,2S)-(-)- and (1S,2R)-(+)-ephedrine hydrochloride at different temperatures, A.J.M. Valente, A.C.F. Ribeiro, J.M.C. Marques, P.E. Abreu, V.M.M. Lobo and R. Kataky, J. Chem. Eng. Data 55, 1145-1152 (2010); doi: 10.1021/je9005757
• Generation and characterization of low-energy structures in atomic clusters, J.M.C. Marques, A.A.C.C. Pais and P.E. Abreu, J. Comput. Chem. 31, 1495-1503 (2010); doi: 10.1002/jcc.21436
• How Different Are Two Chemical Structures?, J.M.C. Marques, J.L. Llanio-Trujillo, P.E. Abreu and F.B. Pereira, J. Chem. Inf. Model. 50, 2129-2140 (2010); doi: 10.1021/ci100219f

2009

• Time-dependent wave packet calculation of the LiH+H reactive scattering on a new potential energy surface, F.V. Prudente, J.M.C. Marques and A.M. Maniero, Chem. Phys. Lett. 474, 18-22 (2009); doi: 10.1016/j.cplett.2009.04.016
• A study on diversity for cluster geometry optimization, F.B. Pereira and J.M.C. Marques, Evol. Intel. 2, 121-140 (2009); doi: 10.1007/s12065-009-0020-5

2008

• On the use of different potential energy functions in rare-gas cluster optimization by genetic algorithms: Application to argon clusters, J.M.C. Marques, F.B. Pereira and T. Leitão, J. Phys. Chem. A 112, 6079-6089 (2008); doi: 10.1021/jp711918t
• A new genetic algorithm to be used in the direct fit of potential energy curves to ab initio and spectroscopic data, J.M.C. Marques, F.V. Prudente, F.B. Pereira, M.M. Almeida, A.M. Maniero and C.E. Fellows, J. Phys. B: At. Mol. Opt. Phys. 41, 085103 (2008); doi: 10.1088/0953-4075/41/8/085103
• A quantum mechanics toolkit, J.P.M. Poiares, S.P.J. Rodrigues and J.M.C. Marques, J. Chem. Educ. 85, 591 (2008); doi: 10.1021/ed085p591

2007

• Symmetry numbers and chemical reaction rates, A. Fernández-Ramos, B.A. Ellingson, R. Meana-Pañeda, J.M. C. Marques and D.G. Truhlar, Theor. Chem. Acc. 118, 813-826 (2007); doi: 10.1007/s00214-007-0328-0
• Kinetics and dynamics of O+OClO reaction in a modified many-body expansion potential energy surface for ClO₃, O.B.M. Teixeira, J.M.C. Marques and A.J.C. Varandas, Int. J. Chem. Kinet. 39, 422-430 (2007); doi: 10.1002/kin.20257

2006

• Trajectory dynamics study of collision-induced dissociation of the Ar+CH4 reaction at hyperthermal conditions: vibrational excitation and isotope substitution, J.M.C. Marques, E. Martínez-Núñez and S.A. Vázquez, J. Phys. Chem. A 110, 7113-7121 (2006); doi: 10.1021/jp0611929

2005

• Trajectory dynamics study of the Ar+CH4 dissociation reaction at high temperatures: the importance of zero-point-energy effects, J.M.C. Marques, E. Martínez-Núñez, A. Fernández-Ramos and S.A. Vázquez, J. Phys. Chem. A 109, 5415-5423 (2005); doi: 10.1021/jp044707+
• Quasiclassical dynamics simulation of the collision-induced dissociation of Cr(CO)6+ with Xe, E. Martínez-Núñez, A. Fernández-Ramos, S.A. Vázquez, J.M.C. Marques, M. Xue and W.L. Hase, J. Chem. Phys. 123, 154311 (2005); doi: 10.1063/1.2044687

2004

• Quasiclassical trajectory study of the collision-induced dissociation of CH3SH⁺ + Ar, E. Martínez-Núñez, S.A. Vázquez and J.M.C. Marques, J. Chem. Phys. 121, 2571-2577 (2004); doi: 10.1063/1.1769364
• Dynamics study of ClO+O2 collisions and their role in the chemistry of stratospheric ozone, O.B.M. Teixeira, J.M.C. Marques and A.J.C. Varandas, Phys. Chem. Chem. Phys. 6, 2179-2184 (2004); doi: 10.1039/b316403a

2003

• Classical trajectory method: A+BC coplanar collisions., J.M.C. Marques, A. Riganelli and A.J.C. Varandas, Quim. Nova 26, 769-778 (2003); doi: 10.1590/S0100-40422003000500024
• Time dependent wave packet study of the electronically non-adiabatic Cl+H-2 reaction using a one-dimensional model, F.V. Prudente, A. Riganelli and J.M.C. Marques, Phys. Chem. Chem. Phys. 5, 2354-2359 (2003); doi: 10.1039/b301010d
• Dynamics calculations for the Cl+C2H6 abstraction reaction: Thermal rate constants and kinetic isotope effects, A. Fernández-Ramos, E. Martínez-Núñez, J.M.C. Marques and S.A. Vázquez, J. Chem. Phys. 118, 6280-6288 (2003); doi: 10.1063/1.1557453

2002

• Li+Li₂ dissociation reaction using the self-consistent potential and trajectory surface hopping methods, J.M.C. Marques, A.I. Voronin and A.J.C. Varandas, J. Phys. Chem. A 106, 3673-3680 (2002); doi: 10.1021/jp0144395

2001

• A direct dynamics study of the H2 elimination from 2,5-dihydrofuran, E. Martínez-Núñez, J.M.C. Marques and S.A. Vázquez, J. Chem. Phys. 115, 7872-7880 (2001); doi: 10.1063/1.1409359
• Reply to the 'Comment on "On the high pressure rate constants for the H/Mu+O2 addition reactions'' by L. B. Harding, J. Troe and V. G. Ushakov, Phys. Chem. Chem. Phys., 2001, 3, 2630', J.M.C. Marques and A.J.C. Varandas, Phys. Chem. Chem. Phys. 3, 2632-2633 (2001); doi: 10.1039/B102984N
• On the high pressure rate constants for the H/Mu+O-2 addition reactions, J.M.C. Marques and A.J.C. Varandas, Phys. Chem. Chem. Phys. 3, 505-507 (2001); doi: 10.1039/B010024M

2000

• Isotope effect on unimolecular dissociation of MuO2: a classical trajectory study, J.M.C. Marques, J.L. Llanio-Trujillo and A.J.C. Varandas, Phys. Chem. Chem. Phys. 2, 3583-3589 (2000); doi: 10.1039/B000469N

1999

• Comparative trajectory surface hopping study for the Li+Li2(X (1)Sigma(g) (+)), Na+Li2(X (1)Sigma(g) (+)) and Li+Na2(X (1)Sigma(g) (+)) dissociation reactions, J.M.C. Marques, A.I. Voronin and A.J.C. Varandas, Phys. Chem. Chem. Phys. 1, 2657-2665 (1999); doi: 10.1039/A901669D
• Mode specificity study in unimolecular dissociation of nonrotating H2O, DHO, and MuHO molecules, J.L. Llanio-Trujillo, J.M.C. Marques and A.J.C. Varandas, J. Phys. Chem. A 103, 10907-10914 (1999); doi: 10.1021/jp992461g

1998

• Trajectory surface hopping study of the Li+Li2(X-1 Sigma(+)(g)) dissociation reaction, A.I. Voronin, J.M.C. Marques and A.J.C. Varandas, J. Phys. Chem. A 102, 6057-6062 (1998): doi:10.1021/jp9805860

1997

• Classical trajectory study of mode specificity and rotational effects in unimolecular dissociation of HO2, J.M.C. Marques and A.J.C. Varandas, J. Phys. Chem. A 101, 5168-5173 (1997); doi: 10.1021/jp970960g

1996

• Dynamics study of the H+ArO2 multichannel reaction, J.M.C. Marques, W. Wang, A.A.C.C. Pais and A.J.C. Varandas, J. Phys. Chem. 100, 17513-17522 (1996); doi: 10.1021/jp961863a
• On the chaperon mechanism for association rate constants: The formation of HO2 and O3, A.J.C. Varandas, A.A.C.C. Pais, J.M.C. Marques and W. Wang, Chem. Phys. Lett. 249, 264-271 (1996); doi: 10.1016/0009-2614(95)01384-9

1992-1995 (PhD)

• Colisões moleculares em sistemas reactivos e o problema da energia de ponto-zero em dinâmica clássica, J.M.C. Marques, PhD thesis, Universidade de Coimbra (1995); link
• Caos determinístico em sistemas Hamiltonianos, J.M.C. Marques, Supplementary didactic work for the PhD qualifying examination, Universidade de Coimbra (1995); link
• Dynamics calculations and isotopic effect in O+OH(D) --> O2+H(D) at low temperatures, J.M.C. Marques, W. Wang and A.J.C. Varandas, J. Chem. Soc., Faraday Trans. 90, 2189-2200 (1994); doi: 10.1039/FT9949002189
• Method for quasiclassical trajectory calculations on potential energy surfaces defined from gradients and Hessians, and model to constrain the energy in vibrational modes, A.J.C. Varandas and J.M.C. Marques, J. Chem. Phys. 100, 1908-1920 (1994); doi: 10.1063/1.466544
• QCT-IEQMT calculations of thr O(3P)+OD(2Pi) reaction at low energies, J.M.C. Marques and A.J.C. Varandas, Anales de Fisica 90, 284-292 (1994); ISSN: 11330376
• A detailed state-to-state low-energy dynamics study of the reaction O(3P) + OH(2Pi) --> O2(X3Sigma(-)) + H2(2S) using a quasiclassical trajectory-internal-energy quantum-mechanical-threshold method, A.J.C. Varandas and J.M.C. Marques, J. Chem. Phys. 97, 4050-4065 (1992); doi: 10.1063/1.463934