About MSSM
(Modelagem e Simulação de Sistemas Moleculares)

Our research at MSSM (Modeling and Simulation of Molecular Systems) focuses on the development and application of molecular models and computational methods. We pay special attention to molecular dynamics (MD) simulation and force field development. MD simulation consists in numerically solving Newton’s equation of motion. In classical MD, an empirical potential energy function, namely a force field, is employed to describe the interactions between a system of particles. The quality of which basically determines the accuracy of such simulations provided that an adequate sampling is achieved. More specifically, our group currently aims at four research lines: (i) the development of force fields for simulating biological and nanotechnological systems; (ii) the development of novel nature-inspired optimization techniques based on evolutionary approaches; (iii) the applications towards biological systems such as virus proteins and chemokines; and (iv) the simulation of nanosystems for drug delivery applications.

Research Topics

Development of force fields for simulating biological and nanotechnological systems

Development of novel nature-inspired optimization techniques based on evolutionary approaches

Applications towards biological systems such as Zika virus proteins and chemokines

Simulation of nanosystems for drug delivery applications



de Sousa Rodrigues, FA; Gonçalves, YMH; Horta, BAC; da Silva Santos, I; Silva, BV; D’Elia, E. Experimental and theoretical studies of isonitrosoacetanilides derivatives as corrosion inhibitors for mild steel in 1 mol L−1 HCl. J. Mol. Struct. (In Press).

Hoelscher, F; Cardoso, PB; Candiotto, G; Guindani, C; Feuser, P; Araújo, PHH; Sayer, C
In Vitro Degradation and Cytotoxicity Response of Biobased Nanoparticles Prepared by Thiol-ene Polymerization in Miniemulsion. J. Polym. Environ. v. 1, 1-11, 2021.

Benassi, JC; Barbosa, FAR; Candiotto, G; Grinevicius, VMAS; Filho, DW; Braga, AL; Pedrosa, RC
Docking and molecular dynamics predicted B-DNA and dihydropyrimidinone selenoesters interactions elucidating antiproliferative effects on breast adenocarcinoma cells. J. Biomol. Struct. Dyn. v. 1, 1-14, 2021.

da Silva, GCQ; Oliveira, FG; de Souza, WF; de Oliveira, MCK; Esteves, PM; Horta, BAC
Effects of paraffin, fatty acid and long alkyl chain phenol on the solidification of n-hexadecane under harsh subcooling condition: A molecular dynamics simulation study. FUEL, 285, 119029, 2021.

Farias, AB; Candiotto, G; Siragusa, L; Goracci, L; Cruciani, G; Oliveira, ERA; Horta, BAC
Targeting Nsp9 as an anti-SARS-CoV-2 strategy. New J. Chem. v. 45, 522-525, 2021.

Ramos, MC; Quoika, PK; Horta, VAC; Dias, DM; Costa, EG; do Amaral, JLM; Ribeiro, LM; Liedl, KR; Horta; BAC
pyPolyBuilder: Automated Preparation of Molecular Topologies and Initial Configurations for Molecular Dynamics Simulations of Arbitrary Supramolecules. J. Chem. Inf. Model. 61, 4, 1539–1544, 2021.

Ramos, MC; Horta, BAC
Drug-Loading Capacity of PAMAM Dendrimers Encapsulating Quercetin Molecules: A Molecular Dynamics Study with the 2016H66 Force Field. J. Chem. Inf. Model. 61, 987, 2021.

van Gunsteren, WF; Daura, X; Fuchs, PFJ; Hansen, N; Horta, BAC; Hünenberger, PH; Mark, AE; Pechlaner, M; Riniker, S; Oostenbrink, C
On the Effect of the Various Assumptions and Approximations used in Molecular Simulations on the Properties of Bio-Molecular Systems: Overview and Perspective on Issues. ChemPhysChem 22, 264, 2021.


Candiotto, G; Giro, R; Horta, BAC; Rosselli, FP; de Cicco, M; Achete, CA; Cremona, M; Capaz, RB
Emission redshift in DCM2-doped Alq 3 caused by nonlinear Stark shifts and Förster-mediated exciton diffusion. Phys. Rev. B, v. 102, 235401-1-235401-7, 2020.

Guindani, C; Candiotto, G; Araújo, PHH; Ferreira, SRS; de Oliveira, D; Wurm, FR; Landfester, K
Controlling the biodegradation rates of poly(globalide-co-ε-caprolactone) copolymers by post polymerization modification. Polym. Degrad. Stab. v. 179, 109287, 2020.

Kashefolgheta, S; Oliveira, MP; Rieder, SR; Horta, BAC; Acree Jr, WE; Hünenberger, PH
Evaluating Classical Force Fields against Experimental Cross-Solvation Free Energies. J. Chem. Theory Comput. 16, 7556, 2020.

Oliveira, MP; Andrey, M; Rieder, SR; Kern, L; Hahn, DF; Riniker, S; Horta, BAC; Hünenberger, PH
Systematic Optimization of a Fragment-Based Force Field against Experimental Pure-Liquid Properties Considering Large Compound Families: Application to Saturated Haloalkanes. J. Chem. Theory Comput.  16, 7525, 2020.

da Silva, GCQ; Silva, GM; Tavares, FW; Fleming, FP; Horta, BAC
Are all-atom any better than united-atom force fields for the description of liquid properties of alkanes? J. Mol. Model. 26, 296, 2020.

Candiotto, C; Giro, R; Horta, BAC; Rosselli, FP; de Cicco, M; Achete, CA; Cremona, M; Capaz, RB
Emission redshift in DCM2-doped Alq 3 caused by nonlinear Stark shifts and Förster-mediated exciton diffusion. Phys. Rev. B 102, 235401, 2020.

dos Santos, TJP; Abreu, CRA; Horta, BAC; Tavares, FW
Self-diffusion coefficients of methane/n-hexane mixtures at high pressures: an evaluation of the finite-size effect and a comparison of force fields. J. Supercrit. Fluids 155, 104639/1-104639/9, 2020.

Simões, TRG; do Pim, WD; Metz, KC; Ribeiro, MA; Valente, DCA; Cardozo, TM; Pinheiro, CB; Pedroso, EF; Horta, BAC; Pereira, CLM; de Souza, GP; Stumpf, HO
Dinuclear copper(II) complexes containing oxamate and blocking ligands: Crystal structure, magnetic properties and DFT calculations. New. J. Chem. 44, 2597-2608, 2020.

Pannuzzo, M; Horta, BAC; La Rosa, C; Decuzzi, P
Predicting the miscibility and rigidity of PLGA/PEG blends via molecular dynamics simulations. Macromolecules, 53, 3643-3654, 2020.

da Silva, GCQ; Giro, R; Neumann, RF; Horta, BAC; Engel, M; Steiner, M
Effects of additives on oil displacement in nanocapillaries: a mesoscale simulation study. J. Mol. Liq. 312, 112953, 2020.

Carvalho, BBPP; Amaral, AAP; de Castro, PP; Ferreira, FCM; Horta, BAC; Amarante, GW.
On the Development of a Nucleophilic Methylthiolation Methodology. Org. Biomol. Chem. 2020 (in press)


Póvoa, RCBL; Koshiyama, AS; Dias, DM; Souza, PL; Horta, BAC
Unimodal optimization using a genetic-programming-based method with periodic boundary conditions. Genet. Program Evol. M. (online), 2019.

Batista, GMF; De Castro, PP; Carpanez, AG; Horta, BAC; Amarante, GW
gem-Dichlorocyclopropanation of dicarbonyl derivatives. Chem. Eur. J. 25, 16555-16563, 2019.

Gonçalves, YMH; Senac, C; Fuchs, PFJ; Hünenberger, PH; Horta, BAC
Influence of the treatment of non-bonded interactions on thermodynamic and transport properties of pure liquids calculated using the 2016H66 force field. J. Chem. Theory Comput. 15, 1806–1826, 2019.

Ramos, MC; Horta, VAC; Horta, BAC
Molecular dynamics simulations of PAMAM and PPI dendrimers using the GROMOS-compatible 2016H66 forcefield. J. Chem. Inf. Model. 59, 1444-1457, 2019.


da Silva, GC; Cardozo, TM; Amarante, GW; Abreu, CRA; Horta, BAC
Solvent effects on the decarboxylation of trichloroacetic acid: insights from ab initio molecular dynamics simulations. Phys. Chem. Chem. Phys. 20, 21988-21998, 2018.

Melo, IL; Lube, LM; Terra, WS; Fernandes, C; Matos, CRR; Franco, RWA; Resende, JALC; Valente, DCA; Horta, BAC; Cardozo, TM; Horn Jr., A
Experimental and theoretical studies of a greener catalytic system for cyclohexane chlorination promoted by trichloroisocyanuric acid and a copper(II) compound. Appl. Catal. A 562, 150-158, 2018.

Póvoa, RCBL; Koshiyama, AS; Dias, DM; Souza, PL; Horta, BAC
Multi-modal optimization by multi-gene genetic programming. IEEE Congress on Evolutionary Computation, 2172-2179, 2018. [conference paper]

Sueges, NS; Rodriguez, AA; Diederichs, CC; de Souza, SP; Leão, RAC; Miranda, LSM; Horta, BAC; Pedraza, SF; de Carvalho, OV; Pais, KC; Terra, JHC; de Souza, ROMA
Continuous-flow synthesis of (R)-propylene carbonate: an important intermediate in the synthesis of tenofovir. Eur. J. Org. Chem. 2018, 2931-2938, 2018.

da Silva, RP; Ambrósio, MFS; Piovesan, LA; Freitas, MCR; de Aguiar, DLM; Horta, BAC; Epprecht, E; San Gil, RAS; Visentin, LC
New solvatomorphic form of dexamethasone acetate monohydrate (DEX-II). J. Pharm. Sci. 107, 672-681, 2018.


Senac, C; Urbach, W; Kurtisovski, E; Hünenberger, PH; Horta, BAC; Taulier, N; Fuchs, PFJ
Simulating bilayers of nonionic CiEj surfactants with the GROMOS-compatible 2016H66 force field. Langmuir 33, 10225-10238, 2017.

Oliveira, ERA; de Alencastro, RB; Horta, BAC
New insights into flavivirus biology: the influence of pH over interactions between prM and E proteins. J. Comput. Aided Mol. Des. 31, 1009-1019, 2017.

Tavara, EGM; Vellasco, MMBR; Horta, BAC; Custodio, FL
Feature importance calculation and protein quality assessment on the decoy discrimination problem. 2017 International Joint Conference on Neural Networks (IJCNN) [conference paper]

David, KS; Oliveira, ERA; Horta, BAC; Valente, AP; de Paula, VS
Insights into chemokine ligand 2 – chemokine receptor 2 molecular recognition: a step forward towards anti-chemotactic agents. Biochemistry 56, 3197-3210, 2017 .

Oliveira, ER; Mohana-Borges, R; de Alencastro, RB; Horta, BAC
The flavivirus capsid protein: Structure, function and perspectives towards drug design. Virus Res. 227, 115-123, 2017.

Pereira, AA; Pereira, AS; de Mello, AC; Carpanez, AG; Horta, BAC; Amarante, GW
Methylsulfenylation of electrophilic carbons: Reaction development, scope, and mechanism. Eur. J. Org. Chem. 2017, 1578-1582, 2017.


Oliveira, ERA; de Alencastro, RB; Horta, BAC
The mechanism by which P250L mutation impairs flavivirus-NS1 dimerization: an investigation based on molecular dynamics simulations. Eur. Biophys. J. 45, 573-580, 2016.

Horta, BAC; Merz, PT; Fuchs, PFJ; Dolenc, J; Riniker, S; Hünenberger, PH
A GROMOS-compatible force field for small organic molecules in the condensed phase: The 2016H66 parameter set. J. Chem. Theory Comput. 12, 3825-3850, 2016.

Collazos, SO; Gonçalves, YMH; Horta, BAC; Picciani, PHS; Louro, SRW; Oliveira Jr, ON; Pimentel, AS
Langmuir films and Mechanical Properties of Polyethyleneglycol Fatty Acid Esters at the Air-Water Interface. Coll. Surf. A 498, 50-57, 2016.


Bellini, RG; Guimarães, AP; Pacheco, MAC; Dias, DM; Furtado, VR; de Alencastro, RB; Horta, BAC
Association of the anti-tuberculosis drug rifampicin with a PAMAM dendrimer. J. Mol. Graph. Model. 60, 34-42, 2015.

de Miranda, AS; Simon, RC; Grischek, B; de Paula, GC; Horta, BAC; de Miranda, LSM; Kroutil, W; Kappe, CO; de Souza, ROMA
Chiral chlorohydrins from the biocatalyzed reduction of chloroketones: chiral building blocks for antiretroviral drugs. ChemCatChem 7, 984-992, 2015.

Laner, M; Horta, BAC; Hünenberger, PH
Long-timescale motions in glycerol-monopalmitate lipid bilayers investigated using molecular dynamics simulation. J. Mol. Graph. Model. 55, 48-64, 2015.


Laner, M; Horta, BAC; Hünenberger, PH
Effect of the cosolutes trehalose and methanol on the equilibrium and phase-transition properties of glycerol-monopalmitate lipid bilayers investigated using molecular dynamics simulations. Eur. Biophys. J. Biophys. Lett. 43, 517-544, 2014.

Campomanes, P; Neri, M; Horta, BAC; Roehrig, UF; Vanni, S; Tavernelli, I; Röthlisberger, U
Origin of the Spectral Shifts among the Early Intermediates of the Rhodopsin Photocycle. J. Am. Chem. Soc. 136, 3842-3851, 2014.

Rusu, VH; Horta, VAH; Horta, BAC; Lins, RD; Baron R
MDWiZ: A platform for the automated translation of molecular dynamics simulations. J. Mol. Graph. Model. 48, 80, 2014.


Fuchs, PFJ; Hansen, HS; Hünenberger, PH; Horta, BAC
A GROMOS parameter set for vicinal diether functions: properties of polyethyleneoxide and polyethyleneglycol. J. Chem. Theory Comput. 8, 3943, 2012.

Horta, BAC; Lin, Z; Huang, W; Riniker, S; van Gunsteren, WF; Hünenberger, PH
Reoptimized interaction parameters for the peptide-backbone model compound N-methylacetamide in the GROMOS force field: Influence on the folding properties of two β-peptides in methanol. J. Comput. Chem. 33, 1907, 2012.

Riniker, S; Horta, BAC; Thijssen, B; Gupta, S; van Gunsteren, WF; Hünenberger, PH
Temperature dependence of the dielectric permittivity of acetic acid, propionic acid and their methyl esters: A molecular dynamics simulation study. ChemPhysChem 13, 1182-1190, 2012.

Kunz, APE; Allison, J.; Geerke, DP; Horta, BAC; Hünenberger, PH; Riniker, S; Schmid, N; van Gunsteren, WF
New functionalities in the GROMOS biomolecular simulation software. J. Comput. Chem. 33, 340, 2012.


Eichenberger, AP; Allison, J.; Dolenc, J; Geerke, DP; Horta, BAC; Meier, K; Oostenbrink, C; Schmid, N; Steiner, D; Wang, D; van Gunsteren, WF
The GROMOS++ software for the analysis of biomolecular simulation trajectories. J. Chem. Theory Comput. 7, 3379, 2011.

Hoelz, LVB; Ribeiro, AAST; Bernardi, R; Horta, BAC; Araújo, JQ; Albuquerque, MG; Silva, JFM; Pascutti, P; Alencastro, RB
The role of helices 5 and 6 on the human β1-adrenoceptor activation mechanism. Mol. Sim. 38, 236, 2011.

Hoelz, LVB; Bernardi, R; Horta, BAC; Araújo, JQ; Albuquerque, MG; Silva, JFM; Pascutti, P; Alencastro, RB
Dynamical behaviour of the human β1-adrenoceptor under agonist binding. Mol. Sim. 37, 907, 2011.

Horta, BAC; Hünenberger, PH
Enantiomeric segregation in the gel phase of lipid bilayers. J. Am. Chem. Soc. 133, 8464, 2011.

Horta, BAC; Alencastro, RB
Structural and dynamic effects of changing the pattern of disulfide bonds in the vascular endothelial growth factor. Rev. Virtual Quim. 3, 37, 2011.

Horta, BAC; Fuchs, PFJ; van Gunsteren, WF; Hünenberger, PH
New interaction parameters for oxygen compounds in the GROMOS force field: improved pure-liquid and solvation properties for alcohols, ethers, aldehydes, ketones, carboxylic acids and esters. J. Chem. Theory Comput. 7, 1016, 2011.


Horta, BAC; Perić-Hassler, L; Hünenberger, PH
Interaction of the disaccharides trehalose and gentiobiose with lipid bilayers: A comparative molecular dynamics study. J. Mol. Graph. Model. 29, 331, 2010.

Horta, BAC; De Vries, AH; Hünenberger, PH
Simulating the transition between gel and liquid-crystal phases of lipid bilayers: dependence of the transition temperature on the hydration level. J. Chem. Theory. Comput. 6, 2488, 2010.

Hoelz, LVB; Horta, BAC; Araújo, JQ; Albuquerque, MG, Alencastro, RB; Silva, JFM
Quantitative structure-activity relationship of antioxidant phenolic compounds. J. Chem. Pharm. Res. 2, 291, 2010.


Horta, BAC; Sodero, ACR; Alencastro, RB
Investigating the differential activation of vascular endothelial growth factor (VEGF) receptors. J. Mol. Graph. Model. 28, 287, 2009.

Silva, BV; Horta, BAC; Alencastro, RB; Pinto, AC
Kinase protein: structural features and chemical inhibitors. Química Nova, 32, 453, 2009.


Horta, BAC; Cirino, JJV; Alencastro, R B
On the Structure, interactions, and dynamics of bound vascular endothelial growth factor. J. Mol. Graph. Model. 26, 1091, 2008.

Ribeiro, AAST; Horta, BAC; Alencastro, RB
MKTOP: A program for automatic construction of molecular topologies. J. Braz. Chem. Soc. 19, 1433, 2008.

Miranda, J; Silva, CJ; Moura, L.; Herbst, M; Horta, BAC; Alencastro, RB; Albuquerque, M
Deamination process in the formation of a copper(II) complex with glutamic acid and a new ligand derived from guanidinoacetic acid: Synthesis, characterization, and molecular modeling studies. Polyhedron, 27, 2386, 2008.

Horta, BAC; Cirino, JJV; Alencastro, RB
Dynamical behavior of the vascular endothelial growth factor: Biological implications. Proteins, 67, 517, 2007. With erratum: Proteins, 70, 307, 2008.


Chou, TF; Tikh, IB; Horta, BAC; Gosh, B; Alencastro, RB; Wagner, CR
Engineered monomeric human histidine triad nucleotide binding protein 1 (hHint1) hydrolyzes fluorogenic acyl adenylate and LysRS generated lysyl-adenylate. J. Biol. Chem. 282, 15137, 2007.


Esteves, PM; Araujo, CL; Horta, BAC; Alvarez, LJ; Zicovich-Wilson, CM; Ramirez-Solis, A
The isobutylene-isobutane alkylation process in liquid HF revisited. J. Phys. Chem. B, 109, 12946, 2005.

Development and Application of Molecular
Models and Computational Methods 


Prof. Bruno A. C. Horta
MSSM - Group Leader

Graziâni Candiotto
MSSM - Postdoctoral Researcher

Mayk C. Ramos
MSSM - PhD Student
André B. Farias
MSSM - PhD Student

Yan M. H. Gonçalves
MSSM - PhD Student

Ricardo M. A. Silva
MSSM - Master Student

Marcel C. V. Milani
MSSM - Undergraduate Student

Former Group Members

Guilherme C. Q. da Silva
MSSM - Former PhD Student

Dr. Rogério C. B. L. Póvoa
MSSM - Former PhD Student

Dr. Edson R. A. Oliveira
MSSM - Former Postdoc

Luciano M. da Silva Junior
MSSM - Undergraduate Student

Contact Us

Instituto de Química UFRJ
Av. Athos da Silveira Ramos, 149
Centro de Tecnologia, Bloco A, Sala 609
21941-909, Cidade Universitária
Rio de Janeiro – RJ, Brazil