{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,12]],"date-time":"2025-10-12T01:23:34Z","timestamp":1760232214807,"version":"build-2065373602"},"reference-count":72,"publisher":"MDPI AG","issue":"21","license":[{"start":{"date-parts":[[2022,10,26]],"date-time":"2022-10-26T00:00:00Z","timestamp":1666742400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001871","name":"Portuguese Foundation for Science and Technology (FCT) in the framework of the Strategic Funding","doi-asserted-by":"publisher","award":["UIDB\/04650\/2020","POCI-01-442 0145-FEDER-028108","EXPL\/FIS-MAC\/0947\/2021"],"award-info":[{"award-number":["UIDB\/04650\/2020","POCI-01-442 0145-FEDER-028108","EXPL\/FIS-MAC\/0947\/2021"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"SATRAP","doi-asserted-by":"publisher","award":["UIDB\/04650\/2020","POCI-01-442 0145-FEDER-028108","EXPL\/FIS-MAC\/0947\/2021"],"award-info":[{"award-number":["UIDB\/04650\/2020","POCI-01-442 0145-FEDER-028108","EXPL\/FIS-MAC\/0947\/2021"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"SATRAP-PLUS","doi-asserted-by":"publisher","award":["UIDB\/04650\/2020","POCI-01-442 0145-FEDER-028108","EXPL\/FIS-MAC\/0947\/2021"],"award-info":[{"award-number":["UIDB\/04650\/2020","POCI-01-442 0145-FEDER-028108","EXPL\/FIS-MAC\/0947\/2021"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Polymers"],"abstract":"<jats:p>Manipulation of nanoscale objects using molecular self-assembly is a potent tool to achieve large scale nanopatterning with small effort. Coordination polymers of bis-salphen compounds based on zinc have demonstrated their ability to align carbon nanotubes into micro-scale networks with an unusual \u201crings-and-rods\u201d pattern. This paper investigates how the compounds interact with pristine and functionalized graphene using density functional theory calculations and molecular dynamic simulations. Using the free energy perturbation method we will show how the addition of phenyl side groups to the core compound and functionalization of graphene affect the stability, mobility and conformation adopted by a dimer of bis-(Zn)salphen compound adsorbed on graphene surface and what it can reveal about the arrangement of chains of bis-(Zn)salphen polymer around carbon nanotubes during the self-assembly of microscale networks.<\/jats:p>","DOI":"10.3390\/polym14214525","type":"journal-article","created":{"date-parts":[[2022,10,26]],"date-time":"2022-10-26T05:11:33Z","timestamp":1666761093000},"page":"4525","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Adhesion of Bis-Salphen-Based Coordination Polymers to Graphene: Insights from Free Energy Perturbation Study"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5180-2175","authenticated-orcid":false,"given":"Sergey","family":"Pyrlin","sequence":"first","affiliation":[{"name":"Physics Center of Minho and Porto Universities (CF-UM-UP), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3633-1966","authenticated-orcid":false,"given":"Veniero","family":"Lenzi","sequence":"additional","affiliation":[{"name":"Physics Center of Minho and Porto Universities (CF-UM-UP), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexandre","family":"Silva","sequence":"additional","affiliation":[{"name":"Physics Center of Minho and Porto Universities (CF-UM-UP), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marta","family":"Ramos","sequence":"additional","affiliation":[{"name":"Physics Center of Minho and Porto Universities (CF-UM-UP), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7477-6934","authenticated-orcid":false,"given":"Lu\u00eds","family":"Marques","sequence":"additional","affiliation":[{"name":"Physics Center of Minho and Porto Universities (CF-UM-UP), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2022,10,26]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"2458","DOI":"10.1016\/j.joule.2020.09.001","article-title":"Liquid Thermo-Responsive Smart Window Derived from Hydrogel","volume":"4","author":"Zhou","year":"2020","journal-title":"Joule"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1146\/annurev-matsci-070214-020901","article-title":"Materials for Flexible, Stretchable Electronics: Graphene and 2D Materials","volume":"45","author":"Kim","year":"2015","journal-title":"Annu. Rev. Mater. Res."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"2767","DOI":"10.1021\/nn9006237","article-title":"Nanoengineering Heat Transfer Performance at Carbon Nanotube Interfaces","volume":"3","author":"Xu","year":"2009","journal-title":"ACS Nano"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1016\/j.commatsci.2018.05.044","article-title":"Thermoelectric Effect in Superlattices; Applicability of Coherent and Incoherent Transport Models","volume":"153","author":"Musland","year":"2018","journal-title":"Comput. Mater. Sci."},{"doi-asserted-by":"crossref","unstructured":"Coropceanu, I., Boles, M.A., and Talapin, D.V. (J. Am. Chem. Soc., 2019). Systematic Mapping of Binary Nanocrystal Superlattices: The Role of Topology in Phase Selection, J. Am. Chem. Soc., Just Accepted Manuscript.","key":"ref_5","DOI":"10.1021\/jacs.8b12539"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1705704","DOI":"10.1002\/adma.201705704","article-title":"Graphene and Carbon-Nanotube Nanohybrids Covalently Functionalized by Porphyrins and Phthalocyanines for Optoelectronic Properties","volume":"30","author":"Wang","year":"2018","journal-title":"Adv. Mater."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"692","DOI":"10.3762\/bjnano.3.79","article-title":"Influence of the Diameter of Single-Walled Carbon Nanotube Bundles on the Optoelectronic Performance of Dry-Deposited Thin Films","volume":"3","author":"Mustonen","year":"2012","journal-title":"Beilstein J. Nanotechnol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"2648","DOI":"10.1038\/ncomms3648","article-title":"Nanorings and Rods Interconnected by Self-Assembly Mimicking an Artificial Network of Neurons","volume":"4","author":"Pyrlin","year":"2013","journal-title":"Nat Commun"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1002\/adfm.200800135","article-title":"Directed Self-Assembly of Gradient Concentric Carbon Nanotube Rings","volume":"18","author":"Hong","year":"2008","journal-title":"Adv. Funct. Mater."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"117961","DOI":"10.1016\/j.ces.2022.117961","article-title":"Dewetting Assisted Self-Assembly of Carbon Nanotube into Circular Nanorings","volume":"261","author":"Basu","year":"2022","journal-title":"Chem Eng Sci"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1038\/s41557-022-00908-1","article-title":"Porous Covalent Organic Nanotubes and Their Assembly in Loops and Toroids","volume":"14","author":"Koner","year":"2022","journal-title":"Nat. Chem."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"400","DOI":"10.1038\/s41586-020-2445-z","article-title":"Self-Assembled Poly-Catenanes from Supramolecular Toroidal Building Blocks","volume":"583","author":"Datta","year":"2020","journal-title":"400 Nat."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"1181","DOI":"10.1039\/C7SM02371E","article-title":"Self-Assembly of Bis-Salphen Compounds: From Semiflexible Chains to Webs of Nanorings","volume":"14","author":"Pyrlin","year":"2018","journal-title":"Soft Matter"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"3890","DOI":"10.1021\/nl9020914","article-title":"Electrical Connectivity in Single-Walled Carbon Nanotube Networks","volume":"9","author":"Nirmalraj","year":"2009","journal-title":"Nano. Lett."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"161403","DOI":"10.1103\/PhysRevB.63.161403","article-title":"Contact Resistance between Carbon Nanotubes","volume":"63","author":"Buldum","year":"2001","journal-title":"Phys. Rev. B"},{"key":"ref_16","first-page":"3295","article-title":"Mobility of Polymer Melts in a Regular Array of Carbon Nanotubes","volume":"18","author":"Alberti","year":"2021","journal-title":"J. Chem. Theory Comput."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"6174","DOI":"10.1039\/C5CP00288E","article-title":"A Review of Methods for the Calculation of Solution Free Energies and the Modelling of Systems in Solution","volume":"17","author":"Skyner","year":"2015","journal-title":"Phys. Chem. Chem. Phys."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1420","DOI":"10.1063\/1.1740409","article-title":"High-Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases","volume":"22","author":"Zwanzig","year":"1954","journal-title":"J. Chem. Phys."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"932","DOI":"10.1002\/wcms.66","article-title":"Umbrella Sampling","volume":"1","year":"2011","journal-title":"Wiley Interdiscip. Rev. Comput. Mol. Sci."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"10925","DOI":"10.1063\/1.1739216","article-title":"Calculation of Free Energy through Successive Umbrella Sampling","volume":"120","author":"Virnau","year":"2004","journal-title":"J. Chem. Phys."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1011","DOI":"10.1002\/jcc.540130812","article-title":"THE Weighted Histogram Analysis Method for Free-Energy Calculations on Biomolecules. I. The Method","volume":"13","author":"Kumar","year":"1992","journal-title":"J. Comput. Chem."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"2690","DOI":"10.1103\/PhysRevLett.78.2690","article-title":"Nonequilibrium Equality for Free Energy Differences","volume":"78","author":"Jarzynski","year":"1997","journal-title":"Phys. Rev. Lett."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"5946","DOI":"10.1063\/1.1651473","article-title":"Calculating Potentials of Mean Force from Steered Molecular Dynamics Simulations","volume":"120","author":"Park","year":"2004","journal-title":"J. Chem. Phys."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"3559","DOI":"10.1063\/1.1590311","article-title":"Free Energy Calculation from Steered Molecular Dynamics Simulations Using Jarzynski\u2019s Equality","volume":"119","author":"Park","year":"2003","journal-title":"J. Chem. Phys."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1129","DOI":"10.1021\/jp506633n","article-title":"The Adaptive Biasing Force Method: Everything You Always Wanted to Know but Were Afraid to Ask","volume":"119","author":"Comer","year":"2015","journal-title":"J. Phys. Chem. B"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1509","DOI":"10.1021\/ct900587b","article-title":"Prediction of Absolute Solvation Free Energies Using Molecular Dynamics Free Energy Perturbation and the Opls Force Field","volume":"6","author":"Shivakumar","year":"2010","journal-title":"J. Chem. Theory Comput."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"10235","DOI":"10.1021\/jp102971x","article-title":"Good Practices in Free-Energy Calculations","volume":"114","author":"Pohorille","year":"2010","journal-title":"J. Phys. Chem. B"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"794","DOI":"10.1021\/ct3008099","article-title":"Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy?","volume":"9","author":"Gumbart","year":"2013","journal-title":"J. Chem. Theory Comput."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1016\/0021-9991(76)90078-4","article-title":"Efficient Estimation of Free Energy Differences from Monte Carlo Data","volume":"22","author":"Bennett","year":"1976","journal-title":"J. Comput. Phys."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"164103","DOI":"10.1063\/1.3701766","article-title":"Bennett\u2019s Acceptance Ratio and Histogram Analysis Methods Enhanced by Umbrella Sampling along a Reaction Coordinate in Configurational Space","volume":"136","author":"Kim","year":"2012","journal-title":"J. Chem. Phys."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"074115","DOI":"10.1063\/1.2232082","article-title":"Efficient and Precise Solvation Free Energies via Alchemical Adiabatic Molecular Dynamics","volume":"125","author":"Abrams","year":"2006","journal-title":"J. Chem. Phys."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"2911","DOI":"10.1021\/acs.jcim.7b00564","article-title":"Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations","volume":"57","author":"Cournia","year":"2017","journal-title":"J. Chem. Inf. Model"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"638","DOI":"10.1021\/acs.jmedchem.7b00681","article-title":"Free Energy Methods in Drug Design: Prospects of \u201cAlchemical Perturbation\u201d in Medicinal Chemistry","volume":"61","author":"Yuriev","year":"2018","journal-title":"J. Med. Chem."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"22157","DOI":"10.1039\/D0CP03128C","article-title":"Disentangling the Liquid Phase Exfoliation of Two-Dimensional Materials: An \u201cin Silico\u201d Perspective","volume":"22","author":"Mukhopadhyay","year":"2020","journal-title":"Phys. Chem. Chem. Phys."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1016\/j.cocis.2016.09.001","article-title":"DNA Adsorbed on Graphene and Graphene Oxide: Fundamental Interactions, Desorption and Applications","volume":"26","author":"Liu","year":"2016","journal-title":"Curr. Opin. Colloid Interface Sci."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"21625","DOI":"10.1021\/jp108688m","article-title":"First-Principle Study of Hydroxyl Functional Groups on Pristine, Defected Graphene, and Graphene Epoxide","volume":"114","author":"Ghaderi","year":"2010","journal-title":"J. Phys. Chem. C"},{"doi-asserted-by":"crossref","unstructured":"Mehandzhiyski, A.Y., Morita, M., Oya, Y., Kato, N., Mori, K., and Koyanagi, J. (2022). Effect of Electrostatic Interactions on the Interfacial Energy between Thermoplastic Polymers and Graphene Oxide: A Molecular Dynamics Study. Polymers, 14.","key":"ref_37","DOI":"10.3390\/polym14132579"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"2745","DOI":"10.1088\/0953-8984\/14\/11\/302","article-title":"The SIESTA Method for Ab Initio Order- N Materials Simulation","volume":"14","author":"Soler","year":"2002","journal-title":"J. Phys. Condens. Matter"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"3865","DOI":"10.1103\/PhysRevLett.77.3865","article-title":"Generalized Gradient Approximation Made Simple","volume":"77","author":"Perdew","year":"1996","journal-title":"Phys. Rev. Lett."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"235111","DOI":"10.1103\/PhysRevB.64.235111","article-title":"Numerical Atomic Orbitals for Linear-Scaling Calculations","volume":"64","author":"Junquera","year":"2001","journal-title":"Phys. Rev. B"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1993","DOI":"10.1103\/PhysRevB.43.1993","article-title":"Efficient Pseudopotentials for Plane-Wave Calculations","volume":"43","author":"Troullier","year":"1991","journal-title":"Phys. Rev. B"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"1787","DOI":"10.1002\/jcc.20495","article-title":"Semiempirical GGA-Type Density Functional Constructed with a Long-Range Dispersion Correction","volume":"27","author":"Grimme","year":"2006","journal-title":"J. Comput. Chem."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1007\/BF00528320","article-title":"On the Counterpoise Correction for the Basis Set Superposition Error in Large Systems","volume":"74","author":"Sordo","year":"1988","journal-title":"Theor. Chim. Acta"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"108171","DOI":"10.1016\/j.cpc.2021.108171","article-title":"LAMMPS\u2014A Flexible Simulation Tool for Particle-Based Materials Modeling at the Atomic, Meso, and Continuum Scales","volume":"271","author":"Thompson","year":"2022","journal-title":"Comput. Phys. Commun."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1080\/08927029408022004","article-title":"A Comparison of Particle-Particle, Particle-Mesh and Ewald Methods for Calculating Electrostatic Interactions in Periodic Molecular Systems","volume":"14","author":"Luty","year":"1994","journal-title":"Mol. Simul."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"7821","DOI":"10.1039\/c0cp00111b","article-title":"The R.E.D. Tools: Advances in RESP and ESP Charge Derivation and Force Field Library Building","volume":"12","author":"Dupradeau","year":"2010","journal-title":"Phys. Chem. Chem. Phys."},{"key":"ref_47","first-page":"1748","article-title":"Gaussian 03, Revision C.02","volume":"24","author":"Frisch","year":"2004","journal-title":"J. Comput. Chem."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1002\/prot.340230104","article-title":"Zinc Binding in Proteins and Solution: A Simple but Accurate Nonbonded Representation","volume":"23","author":"Stote","year":"1995","journal-title":"Proteins Struct. Funct. Genet."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1016\/0009-2614(94)00397-1","article-title":"Avoiding Singularities and Numerical Instabilities in Free Energy Calculations Based on Molecular Simulations","volume":"222","author":"Beutler","year":"1994","journal-title":"Chem. Phys. Lett."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"11225","DOI":"10.1021\/ja9621760","article-title":"Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids","volume":"118","author":"Jorgensen","year":"1996","journal-title":"J. Am. Chem. Soc."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"6474","DOI":"10.1021\/jp003919d","article-title":"Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides","volume":"105","author":"Kaminski","year":"2001","journal-title":"J. Phys. Chem. B"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"1752","DOI":"10.1002\/jcc.20292","article-title":"Integrated Modeling Program, Applied Chemical Theory (IMPACT)","volume":"26","author":"Banks","year":"2005","journal-title":"J. Comput. Chem."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"4482","DOI":"10.1021\/acs.jctc.2c00015","article-title":"Development of OPLS-AA\/M Parameters for Simulations of G Protein-Coupled Receptors and Other Membrane Proteins","volume":"18","author":"Robertson","year":"2022","journal-title":"J. Chem. Theory Comput."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"6131","DOI":"10.1021\/acs.jctc.7b00520","article-title":"Revisiting OPLS Force Field Parameters for Ionic Liquid Simulations","volume":"13","author":"Doherty","year":"2017","journal-title":"J. Chem. Theory Comput."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1021\/acs.jctc.5b00864","article-title":"OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins","volume":"12","author":"Harder","year":"2016","journal-title":"J. Chem. Theory Comput."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"4291","DOI":"10.1021\/acs.jctc.1c00302","article-title":"OPLS4: Improving Force Field Accuracy on Challenging Regimes of Chemical Space","volume":"17","author":"Lu","year":"2021","journal-title":"J. Chem. Theory Comput."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"26895","DOI":"10.1039\/D2RA04015H","article-title":"In Vitro and Computational Investigations of Novel Synthetic Carboxamide-Linked Pyridopyrrolopyrimidines with Potent Activity as SARS-CoV-2-M Pro Inhibitors","volume":"12","author":"Aljuhani","year":"2022","journal-title":"RSC Adv."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"2023","DOI":"10.1002\/jcc.27001","article-title":"A Computational Approach for Modeling Electronic Circular Dichroism of Solvated Chromophores","volume":"15","author":"Monti","year":"2022","journal-title":"J. Comput. Chem."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"44470","DOI":"10.1021\/acsami.2c13517","article-title":"Tuning the Solvent Alkyl Chain to Tailor Electrolyte Solvation for Stable Li-Metal Batteries","volume":"14","author":"Ding","year":"2022","journal-title":"ACS Appl. Mater. Interfaces"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"166841","DOI":"10.1016\/j.jmb.2021.166841","article-title":"Moltemplate: A Tool for Coarse-Grained Modeling of Complex Biological Matter and Soft Condensed Matter Physics","volume":"433","author":"Jewett","year":"2021","journal-title":"J. Mol. Biol."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"2338","DOI":"10.1103\/PhysRevE.52.2338","article-title":"Thermostatted Molecular Dynamics: How to Avoid the Toda Demon Hidden in Nose-Hoover Dynamics","volume":"52","author":"Holian","year":"1995","journal-title":"Phys. Rev. E"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"1302","DOI":"10.1103\/PhysRevB.17.1302","article-title":"Molecular-Dynamics Study of a Three-Dimensional One-Component Model for Distortive Phase Transitions","volume":"17","author":"Schneider","year":"1978","journal-title":"Phys. Rev. B"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","article-title":"VMD: Visual Molecular Dynamics","volume":"14","author":"Humphrey","year":"1996","journal-title":"J. Mol. Graph."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"214108","DOI":"10.1063\/1.2799191","article-title":"Nonlinear Scaling Schemes for Lennard-Jones Interactions in Free Energy Calculations","volume":"127","author":"Steinbrecher","year":"2007","journal-title":"J. Chem. Phys."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"144107","DOI":"10.1063\/1.1873592","article-title":"Comparison of Efficiency and Bias of Free Energies Computed by Exponential Averaging, the Bennett Acceptance Ratio, and Thermodynamic Integration","volume":"122","author":"Shirts","year":"2005","journal-title":"J. Chem. Phys."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"397","DOI":"10.1007\/s10822-015-9840-9","article-title":"Guidelines for the Analysis of Free Energy Calculations","volume":"29","author":"Klimovich","year":"2015","journal-title":"J. Comput. Aided Mol. Des."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"1961","DOI":"10.1016\/j.cpc.2009.05.011","article-title":"PLUMED: A Portable Plugin for Free-Energy Calculations with Molecular Dynamics","volume":"180","author":"Bonomi","year":"2009","journal-title":"Comput. Phys. Commun."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"68760","DOI":"10.1039\/C6RA13187E","article-title":"The Dispersion, Solubilization and Stabilization in \u201cSolution\u201d of Single-Walled Carbon Nanotubes","volume":"6","author":"Kharisov","year":"2016","journal-title":"RSC Adv."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"6964","DOI":"10.1039\/C5NR08576D","article-title":"A Theoretical Study of Dispersion-to-Aggregation of Nanoparticles in Adsorbing Polymers Using Molecular Dynamics Simulations","volume":"8","author":"Cao","year":"2016","journal-title":"Nanoscale"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1007\/s11709-015-0325-7","article-title":"Acid-Treated Carbon Nanotubes and Their Effects on Mortar Strength","volume":"10","author":"Elkashef","year":"2015","journal-title":"Front. Struct. Civ. Eng."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"3513","DOI":"10.1007\/s10853-015-9671-z","article-title":"Multi-Walled Carbon Nanotubes Functionalized with a Ultrahigh Fraction of Carboxyl and Hydroxyl Groups by Ultrasound-Assisted Oxidation","volume":"51","author":"Liang","year":"2016","journal-title":"J. Mater. Sci."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"833","DOI":"10.1016\/j.carbon.2008.02.012","article-title":"Chemical Oxidation of Multiwalled Carbon Nanotubes","volume":"46","author":"Datsyuk","year":"2008","journal-title":"Carbon N. 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