Silambarasan, D., Iyakutti, K. & Vasu, V. Functionalization of single-walled carbon nanotubes with uracil, guanine, thymine and l-alanine. Chem. Phys. Lett. 604, 83–88 (2014).
Google Scholar
Liu, X. et al. Understanding the interaction of single-walled carbon nanotube (SWCNT) on estrogen receptor: A combined molecular dynamics and experimental study. Ecotoxicol. Environ. Saf. 172, 373–379 (2019).
Google Scholar
Zamani, F. et al. Nanostructures for Drug Delivery 239–270 (Elsevier, 2017).
Sheikhi, M. et al. Adsorption properties of the molecule resveratrol on CNT (8, 0–10) nanotube: geometry optimization, molecular structure, spectroscopic (NMR, UV/Vis, excited state), FMO, MEP and HOMO-LUMO investigations. J. Mol. Struct. 1160, 479–487 (2018).
Google Scholar
Lotfi, M., Morsali, A. & Bozorgmehr, M. R. Comprehensive quantum chemical insight into the mechanistic understanding of the surface functionalization of carbon nanotube as a nanocarrier with cladribine anticancer drug. Appl. Surf. Sci. 462, 720–729 (2018).
Google Scholar
Khorram, R., Raissi, H. & Morsali, A. Assessment of solvent effects on the interaction of Carmustine drug with the pristine and COOH-functionalized single-walled carbon nanotubes: A DFT perspective. J. Mol. Liq. 240, 87–97 (2017).
Google Scholar
Mousavi, S. Z., Amjad-Iranagh, S., Nademi, Y. & Modarress, H. Carbon nanotube-encapsulated drug penetration through the cell membrane: An investigation based on steered molecular dynamics simulation. J. Membr. Biol. 246, 697–704 (2013).
Google Scholar
Barzegar, A., Mansouri, A. & Azamat, J. Molecular dynamics simulation of non-covalent single-walled carbon nanotube functionalization with surfactant peptides. J. Mol. Graph. Model. 64, 75–84 (2016).
Google Scholar
Amjad-Iranagh, S., Yousefpour, A., Haghighi, P. & Modarress, H. Effects of protein binding on a lipid bilayer containing local anesthetic articaine, and the potential of mean force calculation: A molecular dynamics simulation approach. J. Mol. Model. 19, 3831–3842 (2013).
Google Scholar
Kavyani, S., Dadvar, M., Modarress, H. & Amjad-Iranagh, S. Molecular perspective mechanism for drug loading on carbon nanotube–dendrimer: A coarse-grained molecular dynamics study. J. Phys. Chem. B 122, 7956–7969 (2018).
Google Scholar
Kavyani, S., Dadvar, M., Modarress, H. & Amjad-Iranagh, S. A coarse grained molecular dynamics simulation study on the structural properties of carbon nanotube–dendrimer composites. Soft Matter 14, 3151–3163 (2018).
Google Scholar
Kordzadeh, A., Amjad-Iranagh, S., Zarif, M. & Modarress, H. Adsorption and encapsulation of the drug doxorubicin on covalent functionalized carbon nanotubes: A scrutinized study by using molecular dynamics simulation and quantum mechanics calculation. J. Mol. Graph. Model. 88, 11–22 (2019).
Google Scholar
Kamel, M., Raissi, H., Morsali, A. & Shahabi, M. Assessment of the adsorption mechanism of Flutamide anticancer drug on the functionalized single-walled carbon nanotube surface as a drug delivery vehicle: An alternative theoretical approach based on DFT and MD. Appl. Surf. Sci. 434, 492–503 (2018).
Google Scholar
Li, Z., Tozer, T. & Alisaraie, L. Molecular dynamics studies for optimization of noncovalent loading of vinblastine on single-walled carbon nanotube. J. Phys. Chem. C 120, 4061–4070 (2016).
Google Scholar
Dehneshin, N., Raissi, H., Hasanzade, Z. & Farzad, F. Using molecular dynamics simulation to explore the binding of the three potent anticancer drugs sorafenib, streptozotocin, and sunitinib to functionalized carbon nanotubes. J. Mol. Model. 25, 1–15 (2019).
Google Scholar
Wang, C., Li, S., Zhang, R. & Lin, Z. Adsorption and properties of aromatic amino acids on single-walled carbon nanotubes. Nanoscale 4, 1146–1153 (2012).
Google Scholar
Wang, C., Yang, G. & Jiang, Y. Structure and property of multiple amino acids assembled on the surface of a CNT. Phys. E 85, 7–12 (2017).
Google Scholar
Deborah, M., Jawahar, A., Mathavan, T., Dhas, M. K. & Franklin Benial, A. M. Spectroscopic studies on valine-functionalized single-walled carbon nanotubes. Fullerenes Nanotubes Carbon Nanostruct. 23, 649–657 (2015).
Google Scholar
Mallakpour, S. & Zadehnazari, A. A facile, efficient, and rapid covalent functionalization of multi-walled carbon nanotubes with natural amino acids under microwave irradiation. Prog. Org. Coat. 77, 679–684 (2014).
Google Scholar
Rahmani, L. & Ketabi, S. Solvation of alanine and histidine functionalized carbon nanotubes in aqueous media: A Monte Carlo simulation study. J. Mol. Liq. 208, 191–195 (2015).
Google Scholar
Liu, X. et al. Biocompatible multi-walled carbon nanotube–chitosan–folic acid nanoparticle hybrids as GFP gene delivery materials. Colloids Surf. B 111, 224–231 (2013).
Google Scholar
Modupe, O., Siddiqui, J., Jonnalagadda, A. & Diosady, L. L. Folic acid fortification of double fortified salt. Sci. Rep. 11, 1–10 (2021).
Castillo, J. J. et al. Computational and experimental studies of the interaction between single-walled carbon nanotubes and folic acid. Chem. Phys. Lett. 564, 60–64 (2013).
Google Scholar
Depan, D., Shah, J. & Misra, R. Controlled release of drug from folate-decorated and graphene mediated drug delivery system: Synthesis, loading efficiency, and drug release response. Mater. Sci. Eng. C 31, 1305–1312 (2011).
Google Scholar
Wolski, P., Narkiewicz-Michalek, J., Panczyk, M., Pastorin, G. & Panczyk, T. Molecular dynamics modeling of the encapsulation and de-encapsulation of the carmustine anticancer drug in the inner volume of a carbon nanotube. J. Phys. Chem. C 121, 18922–18934 (2017).
Google Scholar
Merzel, R. L. et al. Folate binding protein: Therapeutic natural nanotechnology for folic acid, methotrexate, and leucovorin. Nanoscale 9, 2603–2615 (2017).
Google Scholar
Gupta, R., Kalita, P., Patil, O. & Mohanty, S. An investigation of folic acid–protein association sites and the effect of this association on folic acid self-assembly. J. Mol. Model. 21, 1–8 (2015).
Google Scholar
Talaulikar, V. & Arulkumaran, S. Folic acid in pregnancy. Obstet. Gynaecol. Reprod. Med. 23, 286–288 (2013).
Tavakolifard, S., Biazar, E., Pourshamsian, K. & Moslemin, M. H. Synthesis and evaluation of single-wall carbon nanotube–paclitaxel–folic acid conjugate as an anti-cancer targeting agent. Artif. Cells Nanomed. Biotechnol. 44, 1247–1253 (2016).
Google Scholar
Mehra, N. K. & Jain, N. K. One platform comparison of estrone and folic acid anchored surface engineered MWCNTs for doxorubicin delivery. Mol. Pharm. 12, 630–643 (2015).
Google Scholar
Ellison, M. D. & Chorney, M. Reaction of folic acid with single-walled carbon nanotubes. Surf. Sci. 652, 300–303 (2016).
Google Scholar
Karnati, K. R. & Wang, Y. Understanding the co-loading and releasing of doxorubicin and paclitaxel using chitosan functionalized single-walled carbon nanotubes by molecular dynamics simulations. Phys. Chem. Chem. Phys. 20, 9389–9400 (2018).
Google Scholar
Wu, H. et al. Prostate stem cell antigen antibody-conjugated multiwalled carbon nanotubes for targeted ultrasound imaging and drug delivery. Biomaterials 35, 5369–5380 (2014).
Google Scholar
Ganji, M. D., Mirzaei, S. & Dalirandeh, Z. Molecular origin of drug release by water boiling inside carbon nanotubes from reactive molecular dynamics simulation and DFT perspectives. Sci. Rep. 7, 1–13 (2017).
Google Scholar
Izadyar, A., Farhadian, N. & Chenarani, N. Molecular dynamics simulation of doxorubicin adsorption on a bundle of functionalized CNT. J. Biomol. Struct. Dyn. 34, 1797–1805 (2016).
Google Scholar
Wolski, P., Nieszporek, K. & Panczyk, T. Pegylated and folic acid functionalized carbon nanotubes as pH controlled carriers of doxorubicin. Molecular dynamics analysis of the stability and drug release mechanism. Phys. Chem. Chem. Phys. 19, 9300–9312 (2017).
Google Scholar
Kavyani, S., Amjad-Iranagh, S. & Modarress, H. Aqueous poly (amidoamine) dendrimer G3 and G4 generations with several interior cores at pHs 5 and 7: A molecular dynamics simulation study. J. Phys. Chem. B 118, 3257–3266 (2014).
Google Scholar
Panczyk, T., Wolski, P. & Lajtar, L. Coadsorption of doxorubicin and selected dyes on carbon nanotubes. Theoretical investigation of potential application as a pH-controlled drug delivery system. Langmuir 32, 4719–4728 (2016).
Google Scholar
Yousefpour, A., Amjad-Iranagh, S., Goharpey, F. & Modarress, H. Effect of drug amlodipine on the charged lipid bilayer cell membranes DMPS and DMPS+ DMPC: A molecular dynamics simulation study. Eur. Biophys. J. 47, 939–950 (2018).
Google Scholar
Yousefpour, A., Amjad Iranagh, S., Nademi, Y. & Modarress, H. Molecular dynamics simulation of nonsteroidal antiinflammatory drugs, naproxen and relafen, in a lipid bilayer membrane. Int. J. Quantum Chem. 113, 1919–1930 (2013).
Google Scholar
Nademi, Y., Iranagh, S. A., Yousefpour, A., Mousavi, S. Z. & Modarress, H. Molecular dynamics simulations and free energy profile of Paracetamol in DPPC and DMPC lipid bilayers. J. Chem. Sci. 126, 637–647 (2014).
Google Scholar
Yousefpour, A., Modarress, H., Goharpey, F. & Amjad-Iranagh, S. Combination of anti-hypertensive drugs: A molecular dynamics simulation study. J. Mol. Model. 23, 1–18 (2017).
Google Scholar
Wenninger, J. et al. Associations between tryptophan and iron metabolism observed in individuals with and without iron deficiency. Sci. Rep. 9, 1–9 (2019).
Google Scholar
Nanotube modeler, http://www.jcrystal.com/products/wincnt/ (2019).
Drugbank, http://www.drugbank.ca (2019).
Yousefpour, A., Modarress, H., Goharpey, F. & Amjad-Iranagh, S. Interaction of PEGylated anti-hypertensive drugs, amlodipine, atenolol and lisinopril with lipid bilayer membrane: A molecular dynamics simulation study. Biochim. Biophys. Acta BBA Biomembr. 1848, 1687–1698 (2015).
Google Scholar
Schmidt, M. W. et al. General atomic and molecular electronic structure system. J. Comput. Chem. 14, 1347–1363 (1993).
Google Scholar
pubchem, http://pubchem.ncbi.nlm.nih.gov (2019).
Hess, B., Kutzner, C., Van Der Spoel, D. & Lindahl, E. GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. J. Chem. Theory Comput. 4, 435–447 (2008).
Google Scholar
Yousefpour, A., Modarress, H., Goharpey, F. & Amjad-Iranagh, S. Interaction of drugs amlodipine and paroxetine with the metabolizing enzyme CYP2B4: A molecular dynamics simulation study. J. Mol. Model. 24, 1–11 (2018).
Google Scholar
Kavyani, S., Amjad-Iranagh, S., Dadvar, M. & Modarress, H. Hybrid dendrimers of PPI (core)–PAMAM (shell): A molecular dynamics simulation study. J. Phys. Chem. B 120, 9564–9575 (2016).
Google Scholar
Az’hari, S. & Ghayeb, Y. Effect of chirality, length and diameter of carbon nanotubes on the adsorption of 20 amino acids: A molecular dynamics simulation study. Mol. Simul. 40, 392–398 (2014).
Google Scholar
He, Z. & Zhou, J. Probing carbon nanotube–amino acid interactions in aqueous solution with molecular dynamics simulations. Carbon 78, 500–509 (2014).
Google Scholar
Swissparam, http://www.swissparam.ch/ (2019).
Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W. & Klein, M. L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926–935 (1983).
Google Scholar
Berendsen, H. J., Postma, J. V., van Gunsteren, W. F., DiNola, A. & Haak, J. R. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81, 3684–3690 (1984).
Google Scholar
Parrinello, M. & Rahman, A. Polymorphic transitions in single crystals: A new molecular dynamics method. J. Appl. Phys. 52, 7182–7190 (1981).
Google Scholar
Rahimi, A., Amjad-Iranagh, S. & Modarress, H. Molecular dynamics simulation of coarse-grained poly (l-lysine) dendrimers. J. Mol. Model. 22, 59 (2016).
Google Scholar
Darden, T., York, D. & Pedersen, L. Particle mesh Ewald: An N⋅ log (N) method for Ewald sums in large systems. J. Chem. Phys. 98, 10089–10092 (1993).
Google Scholar
Amjad-Iranagh, S., Golzar, K. & Modarress, H. Molecular simulation study of PAMAM dendrimer composite membranes. J. Mol. Model. 20, 1–20 (2014).
Google Scholar
Humphrey, W., Dalke, A. & Schulten, K. VMD: Visual molecular dynamics. J. Mol. Graph. 14, 33–38 (1996).
Google Scholar
Anzar, N., Hasan, R., Tyagi, M., Yadav, N. & Narang, J. Carbon nanotube-A review on synthesis, properties and plethora of applications in the field of biomedical science. Sens. Int. 1, 100003 (2020).
Eisenberg, D. & McLachlan, A. D. Solvation energy in protein folding and binding. Nature 319, 199–203 (1986).
Google Scholar
Hasanzade, Z. & Raissi, H. Molecular mechanism for the encapsulation of the Doxorubicin in the cucurbit [n] urils cavity and the effects of diameter, protonation on loading and releasing of the anticancer drug: Mixed quantum mechanical/molecular dynamics simulations. Comput. Methods Prog. Biomed. 196, 105563 (2020).
Razmimanesh, F., Amjad-Iranagh, S. & Modarress, H. Molecular dynamics simulation study of chitosan and gemcitabine as a drug delivery system. J. Mol. Model. 21, 1–14 (2015).
Google Scholar
Qiu, L. Y. & Yan, M. Q. Constructing doxorubicin-loaded polymeric micelles through amphiphilic graft polyphosphazenes containing ethyl tryptophan and PEG segments. Acta Biomater. 5, 2132–2141 (2009).
Google Scholar
Chen, T., Li, M. & Liu, J. π–π stacking interaction: A nondestructive and facile means in material engineering for bioapplications. Cryst. Growth Des. 18, 2765–2783. https://doi.org/10.1021/acs.cgd.7b01503 (2018).
Google Scholar

