ACS Publications. Most Trusted. Most Cited. Most Read
DICE: A Monte Carlo Code for Molecular Simulation Including the Configurational Bias Monte Carlo Method

OR SEARCH CITATIONS

My Activity
Publications

Figure 1Loading Img
Download Hi-Res ImageDownload to MS-PowerPointCite This:J. Chem. Inf. Model. 2020, 60, 7, 3472-3488
    Computational Chemistry

    DICE: A Monte Carlo Code for Molecular Simulation Including the Configurational Bias Monte Carlo Method
    Click to copy article linkArticle link copied!

    Other Access OptionsSupporting Information (1)

    Journal of Chemical Information and Modeling

    Cite this: J. Chem. Inf. Model. 2020, 60, 7, 3472–3488
    Click to copy citationCitation copied!
    https://doi.org/10.1021/acs.jcim.0c00077
    Published May 29, 2020
    Copyright © 2020 American Chemical Society
    Request reuse permissions

    Abstract

    Click to copy section linkSection link copied!
    Abstract Image

    Solute–solvent systems are an important topic of study, as the effects of the solvent on the solute can drastically change its properties. Theoretical studies of these systems are done with ab initio methods, molecular simulations, or a combination of both. The simulations of molecular systems are usually performed with either molecular dynamics (MD) or Monte Carlo (MC) methods. Classical MD has evolved much in the last decades, both in algorithms and implementations, having several stable and efficient codes developed and available. Similarly, MC methods have also evolved, focusing mainly in creating and improving methods and implementations in available codes. In this paper, we provide some enhancements to a configurational bias Monte Carlo (CBMC) methodology to simulate flexible molecules using the molecular fragments concept. In our implementation the acceptance criterion of the CBMC method was simplified and a generalization was proposed to allow the simulation of molecules with any kind of fragments. We also introduce the new version of DICE, an MC code for molecular simulation (available at https://portal.if.usp.br/dice). This code was mainly developed to simulate solute–solvent systems in liquid and gas phases and in interfaces (gas–liquid and solid–liquid) that has been mostly used to generate configurations for a sequential quantum mechanics/molecular mechanics method (S-QM/MM). This new version introduces several improvements over the previous ones, with the ability of simulating flexible molecules with CBMC as one of them. Simulations of well-known molecules, such as n-octane and 1,2-dichloroethane in vacuum and in solution, are presented to validate the new implementations compared with MD simulations, experimental data, and other theoretical results. The efficiency of the conformational sampling was analyzed using the acceptance rates of different alkanes: n-octane, neopentane, and 4-ethylheptane. Furthermore, a very complex molecule, boron subphtalocyanine, was simulated in vacuum and in aqueous solution showing the versatility of the new implementation. We show that the CBMC is a very good method to perform conformation sampling of complex moderately sized molecules (up to 150 atoms) in solution following the Boltzmann thermodynamic equilibrium distribution.

    Copyright © 2020 American Chemical Society

    Subjects

    what are subjects

    Read this article

    To access this article, please review the available access options below.

    Get instant access

    Purchase Access

    Read this article for 48 hours. Check out below using your ACS ID or as a guest.

    Recommended

    Access through Your Institution

    You may have access to this article through your institution.

    Your institution does not have access to this content. Add or change your institution or let them know you’d like them to include access.

    Supporting Information

    Click to copy section linkSection link copied!

    The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.jcim.0c00077.

    • More information concerning the details about the DICE options, algorithms, parallelization efficiency, and input files and additional simulation data (PDF)

    Terms & Conditions

    Most electronic Supporting Information files are available without a subscription to ACS Web Editions. Such files may be downloaded by article for research use (if there is a public use license linked to the relevant article, that license may permit other uses). Permission may be obtained from ACS for other uses through requests via the RightsLink permission system: http://pubs.acs.org/page/copyright/permissions.html.

    Cited By

    Click to copy section linkSection link copied!

    This article is cited by 47 publications.

    1. Shehan M. Parmar, William Dean, Changwoo Do, James F. Browning, Jeffrey M. Klein, Burcu E. Gurkan, Jesse G. McDaniel. Structural Properties of [N1888][TFSI] Ionic Liquid: A Small Angle Neutron Scattering and Polarizable Molecular Dynamics Study. The Journal of Physical Chemistry B 2024, 128 (45) , 11313-11327. https://doi.org/10.1021/acs.jpcb.4c06255
    2. Mateus Bergami, Jorge Charry, Andres Reyes, Kaline Coutinho, Márcio T. do N. Varella. Does Positron Attachment Take Place in Water Solution?. The Journal of Physical Chemistry B 2024, 128 (41) , 10178-10188. https://doi.org/10.1021/acs.jpcb.4c03627
    3. Leandro Rezende Franco, Marcelo Hidalgo Cardenuto. Unraveling the Impact of Flexibility and Solvent Effects on the UV–Vis Absorption Spectrum of Subphthalocyanine in Liquid Chloroform within the Born–Oppenheimer Molecular Dynamics Approach. The Journal of Physical Chemistry A 2023, 127 (38) , 7937-7942. https://doi.org/10.1021/acs.jpca.3c04711
    4. Danillo Valverde, Lucas Modesto-Costa, Valdemir Ludwig, Zélia M. da Costa Ludwig. Chirality of Alanine Molecules in Water Solvent: A Theoretical Perspective. The Journal of Physical Chemistry A 2023, 127 (14) , 3096-3103. https://doi.org/10.1021/acs.jpca.3c00090
    5. Paulo M. C. de Oliveira, Jéssica I. R. de Souza, Juliana A. B. da Silva, Ricardo L. Longo. Temperature Dependence of Hydrogen Bond Networks of Liquid Water: Thermodynamic Properties and Structural Heterogeneity from Topological Descriptors. The Journal of Physical Chemistry B 2023, 127 (10) , 2250-2257. https://doi.org/10.1021/acs.jpcb.2c08873
    6. Patricio F. Provasi, Lucas Modesto-Costa, Felipe Sampaio, Tércio Silva, Antônio R. da Cunha, Tarciso Andrade-Filho, Rodrigo Gester. The Importance of the Density Functional Theory Exchange–Correlation Hartree–Fock Term in Magnetic Resonance: Application to an Aqueous Environment. The Journal of Physical Chemistry A 2023, 127 (3) , 619-626. https://doi.org/10.1021/acs.jpca.2c05623
    7. Alexsander C. Vendite, Thereza A. Soares, Kaline Coutinho. The Effect of Surface Composition on the Selective Capture of Atmospheric CO2 by ZIF Nanoparticles: The Case of ZIF-8. Journal of Chemical Information and Modeling 2022, 62 (24) , 6530-6543. https://doi.org/10.1021/acs.jcim.2c00579
    8. Danillo Valverde, Herbert C. Georg, Sylvio Canuto. Free-Energy Landscape of the SN2 Reaction CH3Br + Cl– → CH3Cl + Br– in Different Liquid Environments. The Journal of Physical Chemistry B 2022, 126 (20) , 3685-3692. https://doi.org/10.1021/acs.jpcb.1c10282
    9. Mateus Bergami, Andre L. D. Santana, Jorge Charry Martinez, Andres Reyes, Kaline Coutinho, Márcio T. do N. Varella. Multicomponent Quantum Mechanics/Molecular Mechanics Study of Hydrated Positronium. The Journal of Physical Chemistry B 2022, 126 (14) , 2699-2714. https://doi.org/10.1021/acs.jpcb.1c10124
    10. Dmitrii M. Nikolaev, Madushanka Manathunga, Yoelvis Orozco-Gonzalez, Andrey A. Shtyrov, Yansel Omar Guerrero Martínez, Samer Gozem, Mikhail N. Ryazantsev, Kaline Coutinho, Sylvio Canuto, Massimo Olivucci. Free Energy Computation for an Isomerizing Chromophore in a Molecular Cavity via the Average Solvent Electrostatic Configuration Model: Applications in Rhodopsin and Rhodopsin-Mimicking Systems. Journal of Chemical Theory and Computation 2021, 17 (9) , 5885-5895. https://doi.org/10.1021/acs.jctc.1c00221
    11. Adalberto Vasconcelos Sanches de Araújo, Danillo Valverde, Sylvio Canuto, Antonio Carlos Borin. Solvation Structures and Deactivation Pathways of Luminescent Isothiazole-Derived Nucleobases: tzA, tzG, and tzI. The Journal of Physical Chemistry A 2020, 124 (34) , 6834-6844. https://doi.org/10.1021/acs.jpca.0c03398
    12. Ignacio Aburto, Matías Vidal, Sebastián Yáñez, Carolina Aliaga, Moisés Domínguez. Orientation-dependent solvatochromism in ferrocenyl pyrimidinium conjugates: Comparative analysis and theoretical insights. Dyes and Pigments 2025, 233 , 112489. https://doi.org/10.1016/j.dyepig.2024.112489
    13. Gustavo Gomes de Sousa, João B. L. Martins, José Roberto dos Santos Politi. Exploring Mechanism and Kinetics of 1,4‐Dioxane Oxidative Degradation by OH Radical: A Computational Quantum Chemistry Investigation. Journal of Computational Chemistry 2025, 46 (2) https://doi.org/10.1002/jcc.70018
    14. Matheus Máximo‐Canadas, Lucas Modesto‐Costa, Itamar Borges. Ab initio electronic absorption spectra of para ‐nitroaniline in different solvents: Intramolecular charge transfer effects. Journal of Computational Chemistry 2024, 45 (32) , 2899-2911. https://doi.org/10.1002/jcc.27493
    15. Idney Brandão, Herbert C. Georg, Marcos A. Castro, Tertius L. Fonseca. Calculation of the geometry, absorption spectrum, and first hyperpolarizability of 4,5-dicyanoimidazole derivatives in solution. A multiscale ASEC–FEG study. The Journal of Chemical Physics 2024, 161 (3) https://doi.org/10.1063/5.0215931
    16. Jonas Capelasso Lucas Pinheiro, Marcello Ferreira Costa. Solvent effects on the Raman absorption spectrum of epinephrine and norepinephrine by Monte Carlo and QM computational methods. Journal of Molecular Structure 2024, 1302 , 137514. https://doi.org/10.1016/j.molstruc.2024.137514
    17. Karine Nascimento de Andrade, Bárbara Pereira Peixoto, José Walkimar de Mesquita Carneiro, Rodolfo Goetze Fiorot. Exploring borderline S N 1–S N 2 mechanisms: the role of explicit solvation protocols in the DFT investigation of isopropyl chloride. RSC Advances 2024, 14 (7) , 4692-4701. https://doi.org/10.1039/D4RA00066H
    18. Richard J. Sadus. Monte Carlo simulation. 2024, 215-241. https://doi.org/10.1016/B978-0-323-85398-9.00004-6
    19. Marcus V.A. Damasceno, Antônio R. Cunha, Patricio F. Provasi, Gabriel I. Pagola, Marcelo Siqueira, Vinícius Manzoni, Rodrigo Gester, Sylvio Canuto. Modulation of the NLO properties of p-coumaric acid by the solvent effects and proton dissociation. Journal of Molecular Liquids 2024, 394 , 123587. https://doi.org/10.1016/j.molliq.2023.123587
    20. Yu-Xin Lin, Chenghao Jiang, Yu-Bo Wang, Jia-Xin Wang, Bin Li, Guodong Qian. A fluorescent hydrogen-bonded organic framework for highly selective sensing of mono-nitrophenol isomers in water. Journal of Materials Chemistry A 2023, 12 (1) , 153-161. https://doi.org/10.1039/D3TA05309A
    21. Vinícius Manzoni, Yoelvis Orozco-Gonzalez, Jorge Peon, Sylvio Canuto. Theoretical study of the absorption and emission spectra of 1,2-Bis(9-anthryl)acetylene in cyclohexane and acetonitrile. Chemical Physics Letters 2023, 830 , 140775. https://doi.org/10.1016/j.cplett.2023.140775
    22. Neidy S.S. dos Santos, Sávio Fonseca, André Moura, Antonio R. da Cunha, Patricio F. Provasi, Tarciso Andrade-Filho, Rodrigo Gester. Nonlinear optical response of α -terpinolene and β -phellandrene chromophores: An octupolar gas-to-solvent enhancement able to retain light conduction. Optik 2023, 291 , 171199. https://doi.org/10.1016/j.ijleo.2023.171199
    23. Leandro Rezende Franco, Kalil Cristhian Figueiredo Toledo, Tiago Araujo Matias, C. Moyses Araujo, Koiti Araki, Kaline Coutinho. Theoretical investigation of solvent and oxidation/deprotonation effects on the electronic structure of a mononuclear Ru-aqua-polypyridine complex in aqueous solution. Physical Chemistry Chemical Physics 2023, 25 (36) , 24475-24494. https://doi.org/10.1039/D3CP02154H
    24. Leandro R. Franco, Tertius L. Fonseca, Kaline Coutinho, Herbert C. Georg. Elucidating the conformational change and electronic absorption spectrum of p -dimethylamino-cinnamaldehyde merocyanine across different solvent polarities. The Journal of Chemical Physics 2023, 159 (7) https://doi.org/10.1063/5.0158994
    25. Neidy S. S. dos Santos, Sávio Fonseca, Franco F. Almeida, Ezequiel Belo, Marcelo Siqueira, Edenilson dos Santos Niculau, Sebastião Silva, Darlisson A. Santos, Patricio F. Provasi, Tarciso Andrade-Filho, Rodrigo Gester, Antonio R. Cunha. Biotransformation of 1-nitro-2-phenylethane $$\longrightarrow $$ 2-phenylethanol from fungi species of the Amazon biome: an experimental and theoretical analysis. Journal of Molecular Modeling 2023, 29 (8) https://doi.org/10.1007/s00894-023-05595-4
    26. Sávio Fonseca, Neidy S. S. dos Santos, Antonio R. da Cunha, Sylvio Canuto, Patricio F. Provasi, Tarciso Andrade‐Filho, Rodrigo Gester. The Solute Polarization and Structural Effects on the Nonlinear Optical Response of Based Chromone Molecules. ChemPhysChem 2023, 24 (12) https://doi.org/10.1002/cphc.202300060
    27. Idney Brandão, Tertius L. Fonseca, Herbert C. Georg, Marcos A. Castro, Renato B. Pontes. Conformational Dependence of the First Hyperpolarizability of the Li@B10H14 in Solution. Liquids 2023, 3 (1) , 159-167. https://doi.org/10.3390/liquids3010012
    28. Guilherme Obeid, Gustavo O. Moraes, Tatiana C. Penna, Leonardo A. Schenberg, Lucas C. Ducati, Thiago C. Correra. Solvation effects on glyphosate protonation and deprotonation states evaluated by mass spectrometry and explicit solvation simulations. The Journal of Chemical Physics 2023, 158 (5) https://doi.org/10.1063/5.0134003
    29. Franco F. Almeida, Lucas Modesto-Costa, Antonio R. da Cunha, Darlisson A. Santos, Tarciso Andrade-Filho, Rodrigo Gester. Understanding the Stokes shift and nonlinear optical behavior of 1-nitro-2-phenylethane: A sequential Monte Carlo/Quantum Mechanics discussion. Chemical Physics Letters 2022, 804 , 139867. https://doi.org/10.1016/j.cplett.2022.139867
    30. Caio M. Porto, Lucas C. Santana, Nelson H. Morgon. Theoretical investigation of the cooperative effect of solvent: a case study. Physical Chemistry Chemical Physics 2022, 24 (23) , 14603-14615. https://doi.org/10.1039/D1CP05388D
    31. Idney Brandão, Tertius L. Fonseca, Leandro R. Franco, Herbert C. Georg, Marcos A. Castro. Density functional theory investigation of the second hyperpolarizability of the phenol blue in solution. Chemical Physics Letters 2022, 796 , 139549. https://doi.org/10.1016/j.cplett.2022.139549
    32. Leandro Rezende Franco, Kalil Cristhian Figueiredo Toledo, Tiago Araujo Matias, Paola Andrea Benavides, Henrique Musseli Cezar, C. Moyses Araujo, Kaline Coutinho, Koiti Araki. Unraveling the acid–base characterization and solvent effects on the structural and electronic properties of a bis-bidentate bridging ligand. Physical Chemistry Chemical Physics 2022, 24 (17) , 10222-10240. https://doi.org/10.1039/D1CP03912A
    33. Leonardo Bruno Assis Oliveira, Tertius L. Fonseca, Benedito J. C. Cabral, Kaline Coutinho, Sylvio Canuto. Preferential solvation and optical properties of eumelanin building blocks in binary mixture of methanol and water. The Journal of Chemical Physics 2021, 155 (17) https://doi.org/10.1063/5.0065723
    34. Miguel Herranz, Daniel Martínez-Fernández, Pablo Miguel Ramos, Katerina Foteinopoulou, Nikos Ch. Karayiannis, Manuel Laso. Simu-D: A Simulator-Descriptor Suite for Polymer-Based Systems under Extreme Conditions. International Journal of Molecular Sciences 2021, 22 (22) , 12464. https://doi.org/10.3390/ijms222212464
    35. Antonio Raiol, Antonio R. da Cunha, Vinícius Manzoni, Tarciso Andrade-Filho, Rodrigo Gester. Solvent enhancement and isomeric effects on the NLO properties of a photoinduced cis-trans azomethine chromophore: A sequential MC/QM study. Journal of Molecular Liquids 2021, 340 , 116887. https://doi.org/10.1016/j.molliq.2021.116887
    36. Vinícius Manzoni, Rogerio Gester, Antonio R. da Cunha, Tarciso Andrade-Filho, Rodrigo Gester. Solvent effects on Stokes shifts, and NLO response of thieno[3,4-b]pyrazine: A comprehensive QM/MM investigation. Journal of Molecular Liquids 2021, 335 , 115996. https://doi.org/10.1016/j.molliq.2021.115996
    37. Vlasis G. Mavrantzas. Using Monte Carlo to Simulate Complex Polymer Systems: Recent Progress and Outlook. Frontiers in Physics 2021, 9 https://doi.org/10.3389/fphy.2021.661367
    38. Guilherme Colherinhas. Updating atomic charge parameters of aliphatic amino acids: a quest to improve the performance of molecular modeling via sequential molecular dynamics and DFT-GIAO-NMR calculations. Physical Chemistry Chemical Physics 2021, 23 (14) , 8413-8425. https://doi.org/10.1039/D1CP00183C
    39. Alexandre Gonçalves, Antonio Raiol, Antonio R. da Cunha, Vinícius Manzoni, Tarciso Andrade-Filho, Rodrigo Gester. Insights on the crossing of the two lowest n - π ∗ and π - π ∗ absorption lines of thieno[3,4-b]pyrazine in an aqueous environment. Chemical Physics Letters 2021, 768 , 138366. https://doi.org/10.1016/j.cplett.2021.138366
    40. Marcelo Hidalgo Cardenuto, Henrique M. Cezar, Kurt V. Mikkelsen, Stephan P.A. Sauer, Kaline Coutinho, Sylvio Canuto. A QM/MM study of the conformation stability and electronic structure of the photochromic switches derivatives of DHA/VHF in acetonitrile solution. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 2021, 251 , 119434. https://doi.org/10.1016/j.saa.2021.119434
    41. Renata A. Grothe, Alnilan Lobato, Bassim Mounssef, Nikola Tasić, Ataualpa A. C. Braga, Adriano O. Maldaner, Leigh Aldous, Thiago R. L. C. Paixão, Luís Moreira Gonçalves. Electroanalytical profiling of cocaine samples by means of an electropolymerized molecularly imprinted polymer using benzocaine as the template molecule. The Analyst 2021, 146 (5) , 1747-1759. https://doi.org/10.1039/D0AN02274H
    42. Rosa A. S. Couto, Constantino Coelho, Bassim Mounssef, Sara F. de A. Morais, Camila D. Lima, Wallans T. P. dos Santos, Félix Carvalho, Cecília M. P. Rodrigues, Ataualpa A. C. Braga, Luís Moreira Gonçalves, M. Beatriz Quinaz. 3,4-Methylenedioxypyrovalerone (MDPV) Sensing Based on Electropolymerized Molecularly Imprinted Polymers on Silver Nanoparticles and Carboxylated Multi-Walled Carbon Nanotubes. Nanomaterials 2021, 11 (2) , 353. https://doi.org/10.3390/nano11020353
    43. Cíntia C. Vequi-Suplicy, Yoelvis Orozco-Gonzalez, M. Teresa Lamy, Sylvio Canuto, Kaline Coutinho. A new interpretation of the absorption and the dual fluorescence of Prodan in solution. The Journal of Chemical Physics 2020, 153 (24) https://doi.org/10.1063/5.0025013
    44. Valdemir Ludwig, Zélia M. da Costa Ludwig, Danillo Valverde, Herbert C. Georg, Sylvio Canuto. Free energy gradient for understanding the stability and properties of neutral and charged L-alanine molecule in water. Journal of Molecular Liquids 2020, 319 , 114109. https://doi.org/10.1016/j.molliq.2020.114109
    45. Rodrigo Gester, Marcus V.A. Damasceno, Sylvio Canuto, Vinícius Manzoni. A theoretical study of the magnetic shielding of 15N of formamide in liquid water. Journal of Molecular Liquids 2020, 320 , 114415. https://doi.org/10.1016/j.molliq.2020.114415
    46. Alina V. Kireeva, Tatiana A. Tarasova, Yaroslav V. Kalinin, Alexey P. Fedin, Evgeniy A. Marchuk, Mikhail S. Kochetov. On including the CA in polyimides polymerization modeling. 2020, 129-132. https://doi.org/10.1109/DCNAIR50402.2020.9216821
    47. Leonardo Bruno Assis Oliveira, Tertius L. Fonseca, Benedito J. C. Cabral. 15N NMR Shifts of Eumelanin Building Blocks in Water: A Combined Quantum Mechanics/Statistical Mechanics Approach. Molecules 2020, 25 (16) , 3616. https://doi.org/10.3390/molecules25163616
    Download PDF
    Go to Journal of Chemical Information and Modeling
    Get e-Alerts
    Get e-Alerts

    Journal of Chemical Information and Modeling

    Cite this: J. Chem. Inf. Model. 2020, 60, 7, 3472–3488
    Click to copy citationCitation copied!
    https://doi.org/10.1021/acs.jcim.0c00077
    Published May 29, 2020
    Copyright © 2020 American Chemical Society
    Request reuse permissions

    Article Views

    1915

    Altmetric

    -

    Citations

    47
    Learn about these metrics

    Article Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.

    Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.

    The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated.