{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,1]],"date-time":"2026-07-01T20:12:04Z","timestamp":1782936724982,"version":"3.54.5"},"reference-count":95,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2026,2,10]],"date-time":"2026-02-10T00:00:00Z","timestamp":1770681600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Directorate of Research and Community Service, Ministry of Higher Education, Science, and Technology","award":["124\/C3\/DT.05.00\/PL\/2025"],"award-info":[{"award-number":["124\/C3\/DT.05.00\/PL\/2025"]}]},{"name":"Directorate of Research and Community Service, Ministry of Higher Education, Science, and Technology","award":["0982\/LL3\/AL.04\/2025"],"award-info":[{"award-number":["0982\/LL3\/AL.04\/2025"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Molecules"],"abstract":"<jats:p>Mitragyna speciosa, commonly referred to as kratom, is known for its active compound, mitragynine, which is classified as a new psychoactive substance. The availability of mitragynine standards remains a challenge, highlighting the need for effective and efficient methods for isolating this compound from kratom. This study aimed to computationally design a molecularly imprinted polymer (MIP) for the selective isolation of mitragynine. Computational studies were conducted using the B3LYP def2TZVP method with DFT-D4 dispersion, and the results were verified by a laboratory experiment and a molecular dynamics study. The study revealed that methacrylic acid was the optimal monomer for MIP interactions in methanol. Laboratory experiments, employing the association constant and Job plot methods, confirmed that methanol was the ideal solvent for the pre-polymerization complex, with an equilibrium template-to-monomer ratio of 1:3. Radial distribution function analysis from molecular dynamics simulations further supported that the 1:3 template-to-monomer ratio was optimal, aligning with experimental findings. This study\u2019s findings suggest that computational analysis may be employed for the rational design of improved MIPs and for further laboratory investigation into the selective isolation of mitragynine from plants.<\/jats:p>","DOI":"10.3390\/molecules31040610","type":"journal-article","created":{"date-parts":[[2026,2,11]],"date-time":"2026-02-11T09:16:08Z","timestamp":1770801368000},"page":"610","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Unravelling Rational Design of Molecularly Imprinted Polymer for Selective Mitragynine Isolation from Kratom: Quantum Mechanical, Molecular Dynamics, and Experimental Insights"],"prefix":"10.3390","volume":"31","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6931-0910","authenticated-orcid":false,"given":"Untung","family":"Gunawan","sequence":"first","affiliation":[{"name":"Department of Pharmacy, School of Medicine and Health Sciences, Atma Jaya Catholic University of Indonesia, Jakarta 14440, Indonesia"},{"name":"Research Center for Cheminformatics and Molecular Modeling, Atma Jaya Catholic University of Indonesia, Jakarta 14440, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7641-861X","authenticated-orcid":false,"given":"Eko Adi","family":"Prasetyanto","sequence":"additional","affiliation":[{"name":"Department of Pharmacy, School of Medicine and Health Sciences, Atma Jaya Catholic University of Indonesia, Jakarta 14440, Indonesia"},{"name":"The Indonesian Center for Drugs Research (ICDR), Atma Jaya Catholic University of Indonesia, Jakarta 14440, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pretty Falena Atmanda","family":"Kambira","sequence":"additional","affiliation":[{"name":"Department of Pharmacy, School of Medicine and Health Sciences, Atma Jaya Catholic University of Indonesia, Jakarta 14440, Indonesia"},{"name":"Research Center for Cheminformatics and Molecular Modeling, Atma Jaya Catholic University of Indonesia, Jakarta 14440, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7376-3517","authenticated-orcid":false,"given":"Dion","family":"Notario","sequence":"additional","affiliation":[{"name":"Department of Pharmacy, School of Medicine and Health Sciences, Atma Jaya Catholic University of Indonesia, Jakarta 14440, Indonesia"},{"name":"The Indonesian Center for Drugs Research (ICDR), Atma Jaya Catholic University of Indonesia, Jakarta 14440, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erna","family":"Wulandari","sequence":"additional","affiliation":[{"name":"Department of Pharmacy, School of Medicine and Health Sciences, Atma Jaya Catholic University of Indonesia, Jakarta 14440, Indonesia"},{"name":"The Indonesian Center for Drugs Research (ICDR), Atma Jaya Catholic University of Indonesia, Jakarta 14440, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8344-5587","authenticated-orcid":false,"given":"Enade Perdana","family":"Istyastono","sequence":"additional","affiliation":[{"name":"Department of Pharmacy, School of Medicine and Health Sciences, Atma Jaya Catholic University of Indonesia, Jakarta 14440, Indonesia"},{"name":"The Indonesian Center for Drugs Research (ICDR), Atma Jaya Catholic University of Indonesia, Jakarta 14440, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrea Tirta","family":"Wening","sequence":"additional","affiliation":[{"name":"Department of Pharmacy, School of Medicine and Health Sciences, Atma Jaya Catholic University of Indonesia, Jakarta 14440, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kellie","family":"Irlianto","sequence":"additional","affiliation":[{"name":"Department of Pharmacy, School of Medicine and Health Sciences, Atma Jaya Catholic University of Indonesia, Jakarta 14440, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Atthar Luqman","family":"Ivansyah","sequence":"additional","affiliation":[{"name":"Inorganic and Physical Chemistry Division, Department of Chemistry, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Bandung 40132, Indonesia"},{"name":"Master Program in Computational Science, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Bandung 40132, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,2,10]]},"reference":[{"key":"ref_1","first-page":"29","article-title":"Extraction Methods, Qualitative and Quantitative Techniques for Screening of Phytochemicals from Plants","volume":"5","author":"Oshadie","year":"2017","journal-title":"Am. J. Essent. Oils Nat. Prod."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Swamy, M.K., and Akhtar, M.S. (2019). Techniques for Extraction, Isolation, and Standardization of Bio-Active Compounds from Medicinal Plants. Natural Bio-Active Compounds: Volume 2: Chemistry, Pharmacology and Health Care Practices, Springer.","DOI":"10.1007\/978-981-13-7205-6"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"31","DOI":"10.9734\/ajrimps\/2020\/v9i230152","article-title":"An Overview of Methods of Extraction, Isolation and Characterization of Natural Medicinal Plant Products in Improved Traditional Medicine Research","volume":"9","author":"Fonmboh","year":"2020","journal-title":"Asian J. Res. Med. Pharm. Sci."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1186\/s13020-018-0177-x","article-title":"Techniques for Extraction and Isolation of Natural Products: A Comprehensive Review","volume":"13","author":"Zhang","year":"2018","journal-title":"Chin. Med."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"400","DOI":"10.1080\/19476337.2017.1411978","article-title":"Green Technologies for the Extraction of Bioactive Compounds in Fruits and Vegetables","volume":"16","author":"Soquetta","year":"2018","journal-title":"CYTA\u2013J. Food"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"426","DOI":"10.1016\/j.jfoodeng.2013.01.014","article-title":"Techniques for Extraction of Bioactive Compounds from Plant Materials: A Review","volume":"117","author":"Azmir","year":"2013","journal-title":"J. Food Eng."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1","DOI":"10.4103\/jpbs.JPBS_175_19","article-title":"Preparation of Medicinal Plants: Basic Extraction and Fractionation Procedures for Experimental Purposes","volume":"12","author":"Abubakar","year":"2020","journal-title":"J. Pharm. Bioallied Sci."},{"key":"ref_8","first-page":"1","article-title":"Extraction, Isolation and Characterization of Natural Products from Medicinal Plants","volume":"2","author":"Rasul","year":"2018","journal-title":"Int. J. Basic Sci. Appl. Comput."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"100157","DOI":"10.1016\/j.scenv.2024.100157","article-title":"Green Extraction of Secondary Metabolites from Plants: Obstacles, Current Status, and Trends","volume":"8","year":"2024","journal-title":"Sustain. Chem. Environ."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"2200499","DOI":"10.1002\/mame.202200499","article-title":"Application of Molecularly Imprinted Polymers in Plant Natural Products: Current Progress and Future Perspectives","volume":"308","author":"Zuo","year":"2023","journal-title":"Macromol. Mater. Eng."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1007\/s40122-020-00151-x","article-title":"Kratom\u2014Pharmacology, Clinical Implications, and Outlook: A Comprehensive Review","volume":"9","author":"Eastlack","year":"2020","journal-title":"Pain Ther."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"126367","DOI":"10.1016\/j.jnc.2023.126367","article-title":"Survey for Threatened Plants in Riparian Fragmented Forests: A Case Study on Three Vatica (Dipterocarpaceae) Species in Kapuas Hulu, West Kalimantan","volume":"72","author":"Primananda","year":"2023","journal-title":"J. Nat. Conserv."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"190","DOI":"10.25026\/mpc.v14i1.555","article-title":"Uji Toksisitas Ekstrak Berbasis Nades Dari Daun Kadamba (Mitragyna speciosa Korth) Terhadap Mencit (Mus musculus)","volume":"14","author":"Afandi","year":"2021","journal-title":"Proceeding Mulawarman Pharm. Conf."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Zhang, M., Sharma, A., Le\u00f3n, F., Avery, B., Kjelgren, R., McCurdy, C.R., and Pearson, B.J. (2022). Plant Growth and Phytoactive Alkaloid Synthesis in Kratom [Mitragyna speciosa (Korth.)] in Response to Varying Radiance. PLoS ONE, 17.","DOI":"10.1371\/journal.pone.0259326"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1016\/j.neubiorev.2012.11.012","article-title":"From Kratom to Mitragynine and Its Derivatives: Physiological and Behavioural Effects Related to Use, Abuse, and Addiction","volume":"37","author":"Hassan","year":"2013","journal-title":"Neurosci. Biobehav. Rev."},{"key":"ref_16","first-page":"165","article-title":"Mitragynine: A Review of Its Extraction, Identification, and Purification Methods","volume":"3","author":"Amrianto","year":"2021","journal-title":"Curr. Res. Biosci. Biotechnol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"o1441","DOI":"10.1107\/S1600536809017309","article-title":"(E)-Methyl 2-[(2S,3S,12bR)-3-Ethyl-8-Meth-Oxy-1,2,3,4,6,7,12,12b-Octa- Hydro-Indolo[2,3-a]Quinolizin-2-Yl]-3-Methoxy-Acrylate Ethanol Solvate","volume":"65","author":"Carvalho","year":"2009","journal-title":"Acta Crystallogr. Sect. E Struct. Rep. Online"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"120195","DOI":"10.1016\/j.molliq.2022.120195","article-title":"Theoretical Insight and Molecular Recognition of Oxatub[4]Arene-Based Organic Macrocycle as a Supramolecular Host for Antipsychotic Drug Risperidone","volume":"366","author":"Akmal","year":"2022","journal-title":"J. Mol. Liq."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1383","DOI":"10.1021\/jacsau.2c00085","article-title":"Describing Chemical Reactivity with Frontier Molecular Orbitalets","volume":"2","author":"Yu","year":"2022","journal-title":"JACS Au"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"19158","DOI":"10.1039\/D5RA03211C","article-title":"Theoretical Insight and Molecular Recognition of Fluconazole Molecularly Imprinted Polymers: A Combined Computational and Experimental Analysis","volume":"15","author":"Gunawan","year":"2025","journal-title":"RSC Adv."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1321","DOI":"10.1002\/slct.201702541","article-title":"Computational Unravelling of the Role of Alkyl Groups on the Host-Guest Complexation of Pillar[5]Arenes with Neutral Dihalobutanes","volume":"3","author":"Panneerselvam","year":"2018","journal-title":"ChemistrySelect"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1305","DOI":"10.1039\/C0CS00062K","article-title":"Determining Association Constants from Titration Experiments in Supramolecular Chemistry","volume":"40","author":"Thordarson","year":"2011","journal-title":"Chem. Soc. Rev."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"11998","DOI":"10.1002\/anie.201304157","article-title":"Method of Continuous Variations: Applications of Job Plots to the Study of Molecular Associations in Organometallic Chemistry","volume":"52","author":"Renny","year":"2013","journal-title":"Angew. Chem. Int. Ed."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"107267","DOI":"10.1016\/j.jobe.2023.107267","article-title":"Molecular Dynamics Simulation in Concrete Research: A Systematic Review of Techniques, Models and Future Directions","volume":"76","author":"Barbhuiya","year":"2023","journal-title":"J. Build. Eng."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"785","DOI":"10.1103\/PhysRevB.37.785","article-title":"Development of the Colle-Salvetti Correlation-Energy Formula into a Functional of the Electron Density","volume":"37","author":"Lee","year":"1988","journal-title":"Phys. Rev. B"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"2315","DOI":"10.1080\/00268976.2017.1333644","article-title":"Thirty Years of Density Functional Theory in Computational Chemistry: An Overview and Extensive Assessment of 200 Density Functionals","volume":"115","author":"Mardirossian","year":"2017","journal-title":"Mol. Phys."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"e202205735","DOI":"10.1002\/anie.202205735","article-title":"Best-Practice DFT Protocols for Basic Molecular Computational Chemistry","volume":"61","author":"Bursch","year":"2022","journal-title":"Angew. Chem. Int. Ed."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"154122","DOI":"10.1063\/1.5090222","article-title":"A Generally Applicable Atomic-Charge Dependent London Dispersion Correction","volume":"150","author":"Caldeweyher","year":"2019","journal-title":"J. Chem. Phys."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"8499","DOI":"10.1039\/D0CP00502A","article-title":"Extension and Evaluation of the D4 London-Dispersion Model for Periodic Systems","volume":"22","author":"Caldeweyher","year":"2020","journal-title":"Phys. Chem. Chem. Phys."},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Pantsar, T., and Poso, A. (2018). Binding Affinity via Docking: Fact and Fiction. Molecules, 23.","DOI":"10.3390\/molecules23081899"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"100072","DOI":"10.1016\/j.talo.2021.100072","article-title":"A Brief Overview of Molecularly Imprinted Polymers: Highlighting Computational Design, Nano and Photo-Responsive Imprinting","volume":"4","author":"Sajini","year":"2021","journal-title":"Talanta Open"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1007\/s10822-020-00357-3","article-title":"SAMPL7: Host\u2013Guest Binding Prediction by Molecular Dynamics and Quantum Mechanics","volume":"35","author":"Eken","year":"2021","journal-title":"J. Comput. Aided. Mol. Des."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"24673","DOI":"10.1039\/D1RA04614D","article-title":"Betaine Host\u2013Guest Complexation with a Calixarene Receptor: Enhanced in Vitro Anticancer Effect","volume":"11","author":"Fahmy","year":"2021","journal-title":"RSC Adv."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"9498","DOI":"10.1021\/acs.jpca.9b02340","article-title":"Improving Performance of the SMD Solvation Model: Bondi Radii Improve Predicted Aqueous Solvation Free Energies of Ions and PKa Values of Thiols","volume":"123","author":"Mirzaei","year":"2019","journal-title":"J. Phys. Chem. A"},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"V\u00e1radi, M., Keszei, S.J., G\u00f6m\u00f6ry, \u00c1., Kov\u00e1cs, M., K\u00e9gl, T., Fodor, L., and Skoda-F\u00f6ldes, R. (2024). Investigation of Host\u2013Guest Interactions in 2-Ureido-4-Ferrocenylpyrimidine Derivatives. Int. J. Mol. Sci., 25.","DOI":"10.3390\/ijms252413552"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"726","DOI":"10.1016\/j.snb.2015.10.075","article-title":"Computationally Modelled Receptors for Drug Monitoring Using an Optical Based Biomimetic SPR Sensor","volume":"224","author":"Altintas","year":"2016","journal-title":"Sens. Actuators B Chem."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"020083","DOI":"10.1063\/1.5005416","article-title":"Rational Computational Design for the Development of Andrographolide Molecularly Imprinted Polymer","volume":"1891","author":"Krishnan","year":"2017","journal-title":"AIP Conf. Proc."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"122130","DOI":"10.1016\/j.molliq.2023.122130","article-title":"Insights into the Selective Imprinted Polymer of Voriconazole from Host-Guest Interaction Perspective","volume":"383","author":"Gunawan","year":"2023","journal-title":"J. Mol. Liq."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1007\/s00214-019-2502-6","article-title":"A Density Functional Theory Study on Complexation Processes and Intermolecular Interactions of Triptycene-Derived Oxacalixarenes","volume":"138","author":"Jia","year":"2019","journal-title":"Theor. Chem. Acc."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1007\/s10847-017-0759-8","article-title":"Solvent Effect on Complexation Reactions","volume":"89","author":"Payehghadr","year":"2017","journal-title":"J. Incl. Phenom. Macrocycl. Chem."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1922","DOI":"10.1021\/ja983494x","article-title":"Electrophilicity Index","volume":"121","author":"Parr","year":"1999","journal-title":"J. Am. Chem. Soc."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"1854","DOI":"10.1021\/ja00005a072","article-title":"Principle of Maximum Hardness","volume":"113","author":"Parr","year":"1991","journal-title":"J. Am. Chem. Soc."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"7512","DOI":"10.1021\/ja00364a005","article-title":"Absolute Hardness: Companion Parameter to Absolute Electronegativity","volume":"105","author":"Parr","year":"1983","journal-title":"J. Am. Chem. Soc."},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Fukui, K., and Pullman, B. (1980). Density Functional Theory of Atoms and Molecules. Horizons of Quantum Chemistry, Springer.","DOI":"10.1007\/978-94-009-9027-2"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"9357","DOI":"10.1021\/acs.jpca.3c04847","article-title":"Site-Specific Ionization Potentials and Electron Affinities in Large Molecular Systems at Coupled Cluster Level","volume":"127","author":"Fedorov","year":"2023","journal-title":"J. Phys. Chem. A"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"474","DOI":"10.1016\/j.molstruc.2018.12.086","article-title":"Spectroscopic Behavior, FMO, NLO and NBO Analysis of Two Novel Aryl Boronic Acid Derivatives: Experimental and Theoretical Insights","volume":"1181","author":"Sharma","year":"2019","journal-title":"J. Mol. Struct."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1002\/qua.560340840","article-title":"Molecular Hardness and Softness Parameters and Their Use in Chemistry","volume":"34","author":"Nalewajski","year":"1988","journal-title":"Int. J. Quantum Chem."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1016\/j.molstruc.2016.01.068","article-title":"Molecular Structure, Vibrational Spectral Assignments (FT-IR and FT-RAMAN), NMR, NBO, HOMO-LUMO and NLO Properties of O-Methoxybenzaldehyde Based on DFT Calculations","volume":"1111","author":"Vennila","year":"2016","journal-title":"J. Mol. Struct."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1007\/s10847-016-0690-4","article-title":"Host-Guest Complex of Nabumetone: \u03b2-Cyclodextrin: Quantum Chemical Study and QTAIM Analysis","volume":"87","author":"Bensouilah","year":"2017","journal-title":"J. Incl. Phenom. Macrocycl. Chem."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.chemphys.2019.05.003","article-title":"A DFT Approach for Theoretical and Experimental Study of Structure, Electronic, Hirshfeld Surface and Spectroscopic Properties of 12-(4-Bromophenyl)-2-(Prop-2-Ynyloxy)-9,10-Dihydro-8H-Benzo[a]Xanthen-11(12H)-on Single Crystal","volume":"524","author":"Singh","year":"2019","journal-title":"Chem. Phys."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"2065","DOI":"10.1021\/cr040109f","article-title":"Electrophilicity Index","volume":"106","author":"Chattaraj","year":"2006","journal-title":"Chem. Rev."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"111426","DOI":"10.1016\/j.chemphys.2021.111426","article-title":"Calix[4]Pyrrole Based Scrupulous Probe for Track on of Tryptophan: Host-Guest Interaction, in Silico Modeling and Molecular Docking Insights","volume":"554","author":"Desai","year":"2022","journal-title":"Chem. Phys."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"4924","DOI":"10.1039\/D3RA00259D","article-title":"Unraveling the Effect of Solvents on the Excited State Dynamics of C540A by Experimental and Theoretical Study","volume":"13","author":"Ge","year":"2023","journal-title":"RSC Adv."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"2958","DOI":"10.1039\/D0AY00533A","article-title":"Sample Treatment Based on Molecularly Imprinted Polymers for the Analysis of Veterinary Drugs in Food Samples: A Review","volume":"12","author":"Ibarra","year":"2020","journal-title":"Anal. Methods"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"2400353","DOI":"10.1002\/jssc.202400353","article-title":"Advances in the Selection of Functional Monomers for Molecularly Imprinted Polymers: A Review","volume":"47","author":"Niu","year":"2024","journal-title":"J. Sep. Sci."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"7756","DOI":"10.1021\/ja00134a021","article-title":"The Fukui Function: A Key Concept Linking Frontier Molecular Orbital Theory and the Hard-Soft-Acid-Base Principle","volume":"117","author":"Li","year":"1995","journal-title":"J. Am. Chem. Soc."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1016\/S0009-2614(98)00036-0","article-title":"Hydrogen Bond Strengths Revealed by Topological Analyses of Experimentally Observed Electron Densities","volume":"285","author":"Espinosa","year":"1998","journal-title":"Chem. Phys. Lett."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"11154","DOI":"10.1021\/ja0017864","article-title":"Behavior of Ylides Containing N, O, and C Atoms as Hydrogen Bond Acceptors","volume":"122","author":"Rozas","year":"2000","journal-title":"J. Am. Chem. Soc."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1002\/qua.1613","article-title":"Theoretical Study of the Si-H Group as Potential Hydrogen Bond Donor","volume":"86","author":"Alkorta","year":"2001","journal-title":"Int. J. Quantum Chem."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"9747","DOI":"10.1021\/j100024a016","article-title":"Characterization of C-H-O Hydrogen Bonds on the Basis of the Charge Density","volume":"99","author":"Koch","year":"1995","journal-title":"J. Phys. Chem."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"22603","DOI":"10.1021\/acsomega.1c02570","article-title":"Sulfation of Diethylaminoethyl-Cellulose: QTAIM Topological Analysis and Experimental and DFT Studies of the Properties","volume":"6","author":"Kazachenko","year":"2021","journal-title":"ACS Omega"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"6498","DOI":"10.1021\/ja100936w","article-title":"Revealing Noncovalent Interactions","volume":"132","author":"Johnson","year":"2010","journal-title":"J. Am. Chem. Soc."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1002\/cmtd.202100007","article-title":"Interaction Region Indicator: A Simple Real Space Function Clearly Revealing Both Chemical Bonds and Weak Interactions","volume":"1","author":"Lu","year":"2021","journal-title":"Chem. Methods"},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"724","DOI":"10.1002\/cphc.201701325","article-title":"The Independent Gradient Model: A New Approach for Probing Strong and Weak Interactions in Molecules from Wave Function Calculations","volume":"19","author":"Lefebvre","year":"2018","journal-title":"ChemPhysChem"},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1002\/jcc.26812","article-title":"Independent Gradient Model Based on Hirshfeld Partition: A New Method for Visual Study of Interactions in Chemical Systems","volume":"43","author":"Lu","year":"2022","journal-title":"J. Comput. Chem."},{"key":"ref_66","doi-asserted-by":"crossref","unstructured":"Kou, X., Jin, J., Wang, Y., Li, Y., and Hou, F. (2021). The Catalysis Effect of Na and Point Defect on No Heterogeneous Adsorption on Carbon during High-Sodium Zhundong Coal Reburning: Structures, Interactions and Thermodynamic Characteristics. Catalysts, 11.","DOI":"10.3390\/catal11091046"},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"4448","DOI":"10.1093\/bioinformatics\/btz278","article-title":"ORCA: A Comprehensive Bioinformatics Container Environment for Education and Research","volume":"35","author":"Jackman","year":"2019","journal-title":"Bioinformatics"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"1652","DOI":"10.1021\/acs.jctc.8b01176","article-title":"GFN2-XTB\u2014An Accurate and Broadly Parametrized Self-Consistent Tight-Binding Quantum Chemical Method with Multipole Electrostatics and Density-Dependent Dispersion Contributions","volume":"15","author":"Bannwarth","year":"2019","journal-title":"J. Chem. Theory Comput."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"22149","DOI":"10.1038\/s41598-020-79153-w","article-title":"Comparison of Computational Chemistry Methods for the Discovery of Quinone-Based Electroactive Compounds for Energy Storage","volume":"10","author":"Zhang","year":"2020","journal-title":"Sci. Rep."},{"key":"ref_70","first-page":"339","article-title":"Unraveling the Molecular Recognition Mechanism of Voriconazole and Functional Monomers in Molecularly Imprinted Polymer Design","volume":"55","author":"Prasetyanto","year":"2026","journal-title":"S. Afr. J. Chem. Eng."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"1353","DOI":"10.1016\/S1872-1508(07)60071-0","article-title":"Validity and Reliability of Benesi-Hildebrand Method","volume":"23","author":"Wang","year":"2007","journal-title":"Acta Phys. Chim. Sin."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"336","DOI":"10.1016\/j.saa.2009.06.009","article-title":"Molecular Interactions of Monosulfonate Tetraphenylporphyrin (TPPS1) and Meso-Tetra(4-Sulfonatophenyl)Porphyrin (TPPS) with Dimethyl Methylphosphonate (DMMP)","volume":"74","author":"Huo","year":"2009","journal-title":"Spectrochim. Acta A Mol. Biomol. Spectrosc."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"2623","DOI":"10.1039\/c2an35228a","article-title":"Rational Design of Molecularly Imprinted Polymer: The Choice of Cross-Linker","volume":"137","author":"Muhammad","year":"2012","journal-title":"Analyst"},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1016\/j.eurpolymj.2016.01.008","article-title":"The Effect of Crosslinking Density on Molecularly Imprinted Polymer Morphology and Recognition","volume":"75","author":"Golker","year":"2016","journal-title":"Eur. Polym. J."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"105915","DOI":"10.1016\/j.reactfunctpolym.2024.105915","article-title":"Unraveling Multi-Template Molecularly Imprinted Polymer for Selective Extraction of Triazole Antifungals: Theoretical and Experimental Investigation","volume":"200","author":"Gunawan","year":"2024","journal-title":"React. Funct. Polym."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1002\/(SICI)1096-987X(20000130)21:2<132::AID-JCC5>3.0.CO;2-P","article-title":"Fast, Efficient Generation of High-Quality Atomic Charges. AM1-BCC Model: I. Method","volume":"21","author":"Jakalian","year":"2000","journal-title":"J. Comput. Chem."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"1623","DOI":"10.1002\/jcc.10128","article-title":"Fast, Efficient Generation of High-Quality Atomic Charges. AM1-BCC Model: II. Parameterization and Validation","volume":"23","author":"Jakalian","year":"2002","journal-title":"J. Comput. Chem."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1016\/j.sbi.2021.11.011","article-title":"Recent Progress in General Force Fields of Small Molecules","volume":"72","author":"He","year":"2022","journal-title":"Curr. Opin. Struct. Biol."},{"key":"ref_79","doi-asserted-by":"crossref","unstructured":"Fasman, G.D. (1989). The Role of Energy Minimization in Simulation Strategies of Biomolecular Systems. Prediction of Protein Structure and the Principles of Protein Conformation, Springer.","DOI":"10.1007\/978-1-4613-1571-1"},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"747","DOI":"10.1039\/b102799a","article-title":"Molecularly Imprinted Polymers in Analytical Chemistry","volume":"126","author":"Haupt","year":"2001","journal-title":"Analyst"},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"120116","DOI":"10.1016\/j.molliq.2022.120116","article-title":"Effects of Thermostats\/Barostats on Physical Properties of Liquids by Molecular Dynamics Simulations","volume":"365","author":"Ke","year":"2022","journal-title":"J. Mol. Liq."},{"key":"ref_82","doi-asserted-by":"crossref","unstructured":"Filipe, H.A.L., and Loura, L.M.S. (2022). Molecular Dynamics Simulations: Advances and Applications. Molecules, 27.","DOI":"10.3390\/molecules27072105"},{"key":"ref_83","doi-asserted-by":"crossref","unstructured":"Suryana, S., Mutakin, M., Rosandi, Y., and Hasanah, A.N. (2022). Molecular Dynamic Study of Mechanism Underlying Nature of Molecular Recognition and the Role of Crosslinker in the Synthesis of Salmeterol-Targeting Molecularly Imprinted Polymer for Analysis of Salmeterol Xinafoate in Biological Fluid. Molecules, 27.","DOI":"10.3390\/molecules27113619"},{"key":"ref_84","doi-asserted-by":"crossref","unstructured":"Hasanah, A.N., Safitri, N., Zulfa, A., Neli, N., and Rahayu, D. (2021). Factors Affecting Preparation of Molecularly Imprinted Polymer and Methods on Finding Template-Monomer Interaction as the Key of Selective Properties of the Materials. Molecules, 26.","DOI":"10.3390\/molecules26185612"},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1186\/1758-2946-4-17","article-title":"Avogadro: An Advanced Semantic Chemical Editor, Visualization, and Analysis Platform","volume":"4","author":"Hanwell","year":"2012","journal-title":"J. Cheminform."},{"key":"ref_86","unstructured":"Frisch, M.J., Trucks, G.W., Schlegel, H.B., Scuseria, G.E., Robb, M.A., Cheeseman, J.R., Scalmani, G., Barone, V., Mennucci, B., and Petersson, G.A. (2009). Gaussian 09 Revision A.2 2009, Gaussian, Inc."},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"2981","DOI":"10.1093\/bioinformatics\/btu426","article-title":"YASARA View\u2014Molecular Graphics for All Devices\u2014From Smartphones to Workstations","volume":"30","author":"Krieger","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_88","unstructured":"Dassault Syst\u00e8mes (2016). BIOVIA Discovery Studio 2016, Dassault Syst\u00e8mes."},{"key":"ref_89","unstructured":"(2025, February 01). Chemcraft\u2014Graphical Software for Visualization of Quantum Chemistry Computations. Version 1.8, Build 682. Available online: https:\/\/www.chemcraftprog.com."},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"580","DOI":"10.1002\/jcc.22885","article-title":"Multiwfn: A Multifunctional Wavefunction Analyzer","volume":"33","author":"Lu","year":"2012","journal-title":"J. Comput. Chem."},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"27\u201328,33-38","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_92","unstructured":"Janert, P.K. (2016). Gnuplot in Action, Second Edition: Understanding Data with Graphs, Manning."},{"key":"ref_93","unstructured":"GIMP Development Team (2025). GIMP 3.0.2, GIMP Development Team."},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1016\/0010-4655(95)00042-E","article-title":"GROMACS: A Message-Passing Parallel Molecular Dynamics Implementation","volume":"91","author":"Berendsen","year":"1995","journal-title":"Comput. Phys. Commun."},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/j.softx.2015.06.001","article-title":"GROMACS: High Performance Molecular Simulations through Multi-Level Parallelism from Laptops to Supercomputers","volume":"1","author":"Abraham","year":"2015","journal-title":"SoftwareX"}],"container-title":["Molecules"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1420-3049\/31\/4\/610\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,2,11]],"date-time":"2026-02-11T09:16:59Z","timestamp":1770801419000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1420-3049\/31\/4\/610"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,2,10]]},"references-count":95,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2026,2]]}},"alternative-id":["molecules31040610"],"URL":"https:\/\/doi.org\/10.3390\/molecules31040610","relation":{},"ISSN":["1420-3049"],"issn-type":[{"value":"1420-3049","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,2,10]]}}}