{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,1]],"date-time":"2026-08-01T04:59:11Z","timestamp":1785560351152,"version":"3.56.0"},"reference-count":58,"publisher":"MDPI AG","issue":"15","license":[{"start":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T00:00:00Z","timestamp":1785369600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100006769","name":"Russian Science Foundation","doi-asserted-by":"crossref","award":["25-26-00488"],"award-info":[{"award-number":["25-26-00488"]}],"id":[{"id":"10.13039\/501100006769","id-type":"DOI","asserted-by":"crossref"}]},{"award":["25-26-00488"],"award-info":[{"award-number":["25-26-00488"]}],"id":[{"id":"https:\/\/ror.org\/03y2gwe85","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Molecules"],"abstract":"<jats:p>Natural plant extracts rich in polyphenols are increasingly being studied as multifunctional food ingredients with antioxidant and stabilizing properties. In this study, Ocimum basilicum L. extracts were evaluated as biological cryoprotective agents for Streptococcus thermophilus. The extracts contained high levels of phenolic compounds (~1350\u20132200 mg GAE equivalents\/L) and exhibited strong antioxidant activity (up to 5.6 mM Trolox equivalents). Density functional theory calculations showed low O\u2013H bond dissociation energies (~72\u201374 kcal\/mol in ethanol) for key components, including luteolin and rosmarinic acid. These calculations indicate a high hydrogen donation capacity comparable to or exceeding that of ascorbic acid. Molecular dynamics simulations demonstrated the preferential localization of major phenolic compounds at the membrane\u2013water interface in a POPC bilayer membrane. The interaction of molecules with POPC increased membrane thickness and formed stable hydrogen-bond networks with lipid head groups. Experiments showed that systems based on basil extract significantly increased the survival of bacteria after storage at \u221225 \u00b0C, with the number of viable cells reaching (1.5\u20132.75) \u00d7 108 CFU\/mL. This effect was observed in comparison with control groups that used saline or sucrose. Fluorescent analysis of live\/dead cells confirmed the improvement in cell membrane preservation. At the same time, no signs of metabolic inhibition were detected. Taken together, the experimental and computational results support the hypothesis that the cryoprotective effect may involve complementary antioxidant and membrane-associated interactions. However, direct biophysical validation of the proposed membrane mechanism is still required. These results emphasize that polyphenol extracts are promising natural functional ingredients for improving the stability and shelf life of probiotic and starter cultures in food systems.<\/jats:p>","DOI":"10.3390\/molecules31152661","type":"journal-article","created":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T13:55:11Z","timestamp":1785419711000},"page":"2661","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Molecular Mechanisms of Basil (Ocimum basilicum L.) Polyphenol Extracts as Bio-Based Cryoprotectants for Streptococcus thermophilus: Chemical Profiling, DFT, Molecular Dynamics and Cell Viability"],"prefix":"10.3390","volume":"31","author":[{"given":"Valeria A.","family":"Pyanchenkova","sequence":"first","affiliation":[{"name":"Infochemistry Scientific Center, ITMO University, 9 Lomonosova Str., 191002 St. Petersburg, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vladislav S.","family":"Filozop","sequence":"additional","affiliation":[{"name":"Infochemistry Scientific Center, ITMO University, 9 Lomonosova Str., 191002 St. Petersburg, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mikhail O.","family":"Volodarskiy","sequence":"additional","affiliation":[{"name":"Infochemistry Scientific Center, ITMO University, 9 Lomonosova Str., 191002 St. Petersburg, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-8616-3543","authenticated-orcid":false,"given":"Dmitrii N.","family":"Borovikov","sequence":"additional","affiliation":[{"name":"Infochemistry Scientific Center, ITMO University, 9 Lomonosova Str., 191002 St. Petersburg, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8636-9858","authenticated-orcid":false,"given":"Olga L.","family":"Balabanova","sequence":"additional","affiliation":[{"name":"Saint-Petersburg Institute of Emergency Care Named After I.I. Dzhanelidze, 192242 St. Petersburg, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olga O.","family":"Osmak","sequence":"additional","affiliation":[{"name":"Infochemistry Scientific Center, ITMO University, 9 Lomonosova Str., 191002 St. Petersburg, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Semen S.","family":"Kazarin","sequence":"additional","affiliation":[{"name":"Infochemistry Scientific Center, ITMO University, 9 Lomonosova Str., 191002 St. Petersburg, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4156-7655","authenticated-orcid":false,"given":"Pavel V.","family":"Nesterov","sequence":"additional","affiliation":[{"name":"Infochemistry Scientific Center, ITMO University, 9 Lomonosova Str., 191002 St. Petersburg, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2272-2103","authenticated-orcid":false,"given":"Ivan V.","family":"Moskalenko","sequence":"additional","affiliation":[{"name":"Infochemistry Scientific Center, ITMO University, 9 Lomonosova Str., 191002 St. Petersburg, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8545-1051","authenticated-orcid":false,"given":"Mariia S.","family":"Ashikhmina","sequence":"additional","affiliation":[{"name":"Infochemistry Scientific Center, ITMO University, 9 Lomonosova Str., 191002 St. Petersburg, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ekaterina V.","family":"Skorb","sequence":"additional","affiliation":[{"name":"Infochemistry Scientific Center, ITMO University, 9 Lomonosova Str., 191002 St. Petersburg, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,7,30]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1016\/j.cryobiol.2023.02.003","article-title":"Use of Cryoprotectors and Antioxidants in Sturgeon Semen Cryopreservation","volume":"111","author":"Kolyada","year":"2023","journal-title":"Cryobiology"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"105164","DOI":"10.1016\/j.tifs.2025.105164","article-title":"Revolutionizing Cryopreservation: Bio-Based Cryoprotectants, Mechanisms, and Advanced Applications for Sustainable Pan-Food Systems","volume":"163","author":"Liu","year":"2025","journal-title":"Trends Food Sci. Technol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1862","DOI":"10.1038\/s41598-025-85509-x","article-title":"High Throughput Method for Simultaneous Screening of Membrane Permeability and Toxicity for Discovery of New Cryoprotective Agents","volume":"15","author":"Ahmadkhani","year":"2025","journal-title":"Sci. Rep."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"108545","DOI":"10.1016\/j.biotechadv.2025.108545","article-title":"Expanding the Cryoprotectant Toolbox in Biomedicine by Multifunctional Antifreeze Peptides","volume":"81","author":"Hemmati","year":"2025","journal-title":"Biotechnol. Adv."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1007\/s11626-025-01027-0","article-title":"Cryopreservation of Biological Materials: Applications and Economic Perspectives","volume":"62","author":"Aarattuthodi","year":"2025","journal-title":"Vitr. Cell. Dev. Biol. Anim."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1444","DOI":"10.1080\/07373937.2022.2155971","article-title":"Synergistic Combination of Cryoprotectants for High Freeze-Dried Survival Rate and Viable Cell Counts of Streptococcus thermophilus","volume":"41","author":"Di","year":"2023","journal-title":"Dry. Technol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1016\/j.jare.2022.05.002","article-title":"New Insight into the Mechanism by Which Antifreeze Peptides Regulate the Physiological Function of Streptococcus thermophilus Subjected to Freezing Stress","volume":"45","author":"Chen","year":"2023","journal-title":"J. Adv. Res."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"104811","DOI":"10.1016\/j.cryobiol.2023.104811","article-title":"Effect of Freeze-Dried Protectants on the Survival Rate and Fermentation Performance of Fermented Milk\u2019s Directed Vat Set Starters","volume":"114","author":"Tian","year":"2024","journal-title":"Cryobiology"},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Ros-Santaella, J.L., and Pintus, E. (2021). Plant Extracts as Alternative Additives for Sperm Preservation. Antioxidants, 10.","DOI":"10.3390\/antiox10050772"},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Goujet, H., Kaarouch, I., Malki, A., Mbaye, M.M., Cabry, R., Louanjli, N., Rhouda, T., and Benkhalifa, M. (2025). Effects of Essential Oils as Antioxidant and Cryoprotective Agents in Improving Frozen and Thawed Human Sperm Criteria. Antioxidants, 14.","DOI":"10.3390\/antiox14010075"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"624","DOI":"10.1021\/acs.langmuir.3c02808","article-title":"Optimization of Deep Eutectic Solvents Enables Green and Efficient Cryopreservation","volume":"40","author":"He","year":"2024","journal-title":"Langmuir"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"163002","DOI":"10.1016\/j.scitotenv.2023.163002","article-title":"Biobased Natural Deep Eutectic System as Versatile Solvents: Structure, Interaction and Advanced Applications","volume":"881","author":"Usmani","year":"2023","journal-title":"Sci. Total Environ."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Jahed, K.R., Saini, A.K., and Sherif, S.M. (2023). Coping with the Cold: Unveiling Cryoprotectants, Molecular Signaling Pathways, and Strategies for Cold Stress Resilience. Front. Plant Sci., 14.","DOI":"10.3389\/fpls.2023.1246093"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"2002425","DOI":"10.1002\/advs.202002425","article-title":"Ice Inhibition for Cryopreservation: Materials, Strategies, and Challenges","volume":"8","author":"Chang","year":"2021","journal-title":"Adv. Sci."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Wang, J., Wu, P., Dhital, S., Yu, A., and Chen, X.D. (2025). Impact of Freezing and Freeze Drying on Lactobacillus Rhamnosus GG Survival: Mechanisms of Cell Damage and the Role of Pre-Freezing Conditions and Cryoprotectants. Foods, 14.","DOI":"10.3390\/foods14101817"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1186\/s12951-025-03265-6","article-title":"Overcoming Ice: Cutting-Edge Materials and Advanced Strategies for Effective Cryopreservation of Biosample","volume":"23","author":"Huang","year":"2025","journal-title":"J. Nanobiotechnol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1016\/j.cryobiol.2019.11.002","article-title":"Natural Cryoprotectants Combinations of L-Proline and Trehalose for Red Blood Cells Cryopreservation","volume":"91","author":"Dou","year":"2019","journal-title":"Cryobiology"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1918","DOI":"10.1021\/acs.jafc.8b06514","article-title":"Cryoprotective Activity and Action Mechanism of Antifreeze Peptides Obtained from Tilapia Scales on Streptococcus thermophilus during Cold Stress","volume":"67","author":"Chen","year":"2019","journal-title":"J. Agric. Food Chem."},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Karonen, M. (2022). Insights into Polyphenol\u2013Lipid Interactions: Chemical Methods, Molecular Aspects and Their Effects on Membrane Structures. Plants, 11.","DOI":"10.3390\/plants11141809"},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Villala\u00edn, J. (2024). Localization and Aggregation of Honokiol in the Lipid Membrane. Antioxidants, 13.","DOI":"10.3390\/antiox13081025"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"5290","DOI":"10.1038\/s41598-020-62090-z","article-title":"Cold Stress Changes Antioxidant Defense System, Phenylpropanoid Contents and Expression of Genes Involved in Their Biosynthesis in Ocimum basilicum L.","volume":"10","author":"Rezaie","year":"2020","journal-title":"Sci. Rep."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"112805","DOI":"10.1016\/j.postharvbio.2024.112805","article-title":"Basil Postharvest Chilling Sensitivity Is Modulated by the Dynamics between Antioxidant Enzymes and Metabolites","volume":"211","author":"Rodeo","year":"2024","journal-title":"Postharvest Biol. Technol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"143581","DOI":"10.1016\/j.foodchem.2025.143581","article-title":"Basil Chilling Injury: Oxidative Stress or Energy Depletion?","volume":"477","author":"Larsen","year":"2025","journal-title":"Food Chem."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"158","DOI":"10.7455\/ijfs\/6.2.2017.a4","article-title":"Impact of Selected Polyphenolics on the Structural Properties of Model Lipid Membranes\u2014A Review","volume":"6","author":"Ulrih","year":"2017","journal-title":"Int. J. Food Stud."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1874","DOI":"10.1073\/pnas.1012516108","article-title":"Reconciliation of Opposing Views on Membrane-Sugar Interactions","volume":"108","author":"Andersen","year":"2011","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"6667","DOI":"10.1021\/jp402385d","article-title":"Molecular Dynamics Simulations of Membrane\u2013Sugar Interactions","volume":"117","author":"Kapla","year":"2013","journal-title":"J. Phys. Chem. B"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1256","DOI":"10.1016\/j.foodchem.2010.10.054","article-title":"Interactions of P-Coumaric, Caffeic and Ferulic Acids and Their Styrenes with Model Lipid Membranes","volume":"125","author":"Ota","year":"2011","journal-title":"Food Chem."},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Hughes, K., Le, T.B., Van Der Smissen, P., Tyteca, D., Mingeot-Leclercq, M.-P., and Quetin-Leclercq, J. (2023). The Antileishmanial Activity of Eugenol Associated with Lipid Storage Reduction Rather Than Membrane Properties Alterations. Molecules, 28.","DOI":"10.3390\/molecules28093871"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"114689","DOI":"10.1016\/j.molliq.2020.114689","article-title":"The Biophysical Interaction of Ferulic Acid with Liposomes as Biological Membrane Model: The Effect of the Lipid Bilayer Composition","volume":"324","author":"Andrade","year":"2021","journal-title":"J. Mol. Liq."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"2973","DOI":"10.1016\/j.bbamem.2011.08.011","article-title":"The Natural Antioxidant Rosmarinic Acid Spontaneously Penetrates Membranes to Inhibit Lipid Peroxidation In Situ","volume":"1808","author":"Fadel","year":"2011","journal-title":"Biochim. Biophys. Acta (BBA)\u2014Biomembr."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"2411","DOI":"10.1021\/jf0303924","article-title":"Antioxidant Effect of Ferulic Acid in Isolated Membranes and Intact Cells: Synergistic Interactions with \u03b1-Tocopherol, \u03b2-Carotene, and Ascorbic Acid","volume":"52","author":"Trombino","year":"2004","journal-title":"J. Agric. Food Chem."},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Bai, X., Li, X., Liu, X., Xing, Z., Su, R., Wang, Y., Xia, X., and Shi, C. (2022). Antibacterial Effect of Eugenol on Shigella Flexneri and Its Mechanism. Foods, 11.","DOI":"10.3390\/foods11172565"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1016\/j.ijantimicag.2012.05.015","article-title":"Use of Multiparameter Flow Cytometry to Determine the Effects of Monoterpenoids and Phenylpropanoids on Membrane Polarity and Permeability in Staphylococci and Enterococci","volume":"40","author":"Hammer","year":"2012","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1186\/s41021-024-00307-7","article-title":"Rosmarinic Acid, a Natural Polyphenol, Has a Potential pro-Oxidant Risk via NADH-Mediated Oxidative DNA Damage","volume":"46","author":"Kobayashi","year":"2024","journal-title":"Genes Environ."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"2606","DOI":"10.3168\/jds.2020-19110","article-title":"Polysaccharides Can Improve the Survival of Lactiplantibacillus Plantarum Subjected to Freeze-Drying","volume":"104","author":"Wang","year":"2021","journal-title":"J. Dairy Sci."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"115855","DOI":"10.1016\/j.foodres.2025.115855","article-title":"Plant-Based Oat Peptides as Cryoprotectants Mitigate Freezing Damage to Lactobacillus Bulgaricus CICC 22163","volume":"203","author":"Song","year":"2025","journal-title":"Food Res. Int."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"2776","DOI":"10.1021\/acsfoodscitech.4c00488","article-title":"Synergistic Antioxidant Activity in Deep Eutectic Solvents: Extracting and Enhancing Natural Products","volume":"4","author":"Kerry","year":"2024","journal-title":"ACS Food Sci. Technol."},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Aloisio, C., Razola-D\u00edaz, M.d.C., Aznar-Ramos, M.J., Longhi, M.R., Andreatta, A.E., and Verardo, V. (2023). Optimization of the Extraction Conditions of Bioactive Compounds from Ocimum basilicum Leaves Using Ultrasound-Assisted Extraction via a Sonotrode. Molecules, 28.","DOI":"10.3390\/molecules28135286"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"315","DOI":"10.2298\/APT1243315V","article-title":"Optimization of the Ocimum basilicum L. Extraction Process Regarding the Antioxidant Activity","volume":"43","author":"Vidovic","year":"2012","journal-title":"Acta Period. Technol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"e15534","DOI":"10.1111\/jfpp.15534","article-title":"Characteristic and Antioxidant Activity of Cladophora glomerata Ethanolic Extract as Affected by Prior Chlorophyll Removal and Drying Methods","volume":"46","author":"Yarnpakdee","year":"2022","journal-title":"J. Food Process. Preserv."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1016\/j.sajb.2023.04.029","article-title":"Solvent-Assisted Dechlorophyllization of Psidium Guajava Leaf Extract: Effects on the Polyphenol Content, Cytocompatibility, Antibacterial, Anti-Inflammatory, and Anticancer Activities","volume":"158","author":"Singh","year":"2023","journal-title":"S. Afr. J. Bot."},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"Aung, W.W., Panich, K., Watthanophas, S., Naridsirikul, S., Ponphaiboon, J., Krongrawa, W., Kulpicheswanich, P., Limmatvapirat, S., and Limmatvapirat, C. (2023). Preparation of Bioactive De-Chlorophyll Rhein-Rich Senna Alata Extract. Antibiotics, 12.","DOI":"10.3390\/antibiotics12010181"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"4217","DOI":"10.1007\/s11696-023-02771-x","article-title":"Optimization of Microwave-Enhanced Extraction Parameters to Recover Phenolic Compounds and Antioxidants from Corchorus Olitorius Leaves","volume":"77","author":"Alara","year":"2023","journal-title":"Chem. Pap."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1016\/j.sajb.2021.01.030","article-title":"Phenolic Contents and In Vitro Antioxidant, Anti-Tyrosinase, and Anti-Inflammatory Effects of Leaves and Roots Extracts of the Halophyte Limonium Delicatulum","volume":"139","author":"Bakhouche","year":"2021","journal-title":"S. Afr. J. Bot."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"113174","DOI":"10.1016\/j.comptc.2021.113174","article-title":"Theoretical Insights into the Direct Radical Scavenging Activities of 8-Hydroxyquinoline: Mechanistic, Thermodynamic and Kinetic Studies","volume":"1198","year":"2021","journal-title":"Comput. Theor. Chem."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"126646","DOI":"10.1016\/j.molliq.2024.126646","article-title":"Decomposition, Interpretation and Prediction of Various Ionic Liquid Solvation Parameters: Kamlet-Taft, Catal\u00e1n and Reichardt\u2019s ENT","volume":"417","author":"Sappl","year":"2025","journal-title":"J. Mol. Liq."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"102852","DOI":"10.1016\/j.apmt.2025.102852","article-title":"Sunlight-Driven Azobenzene-Based Thin Films for Smart Coating Applications","volume":"45","author":"Das","year":"2025","journal-title":"Appl. Mater. Today"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"129279","DOI":"10.1016\/j.ijbiomac.2024.129279","article-title":"Encapsulation of Probiotics in Freeze-Dried Calcium Alginate and \u03ba-Carrageenan Beads Using Definitive Screening Design: A Comprehensive Characterisation and In Vitro Digestion Study","volume":"258","author":"Premjit","year":"2024","journal-title":"Int. J. Biol. Macromol."},{"key":"ref_49","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_50","doi-asserted-by":"crossref","first-page":"9954","DOI":"10.1021\/jp003020w","article-title":"Structure and Dynamics of the TIP3P, SPC, and SPC\/E Water Models at 298 K","volume":"105","author":"Mark","year":"2001","journal-title":"J. Phys. Chem. A"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1002\/jcc.21367","article-title":"CHARMM General Force Field: A Force Field for Drug-like Molecules Compatible with the CHARMM All-atom Additive Biological Force Fields","volume":"31","author":"Vanommeslaeghe","year":"2010","journal-title":"J. Comput. Chem."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"1859","DOI":"10.1002\/jcc.20945","article-title":"CHARMM-GUI: A Web-based Graphical User Interface for CHARMM","volume":"29","author":"Jo","year":"2008","journal-title":"J. Comput. Chem."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"2135","DOI":"10.1002\/jcc.23354","article-title":"CHARMM36 All-Atom Additive Protein Force Field: Validation Based on Comparison to NMR Data","volume":"34","author":"Huang","year":"2013","journal-title":"J. Comput. Chem."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"10089","DOI":"10.1063\/1.464397","article-title":"Particle Mesh Ewald: An N\u22c5log(N) Method for Ewald Sums in Large Systems","volume":"98","author":"Darden","year":"1993","journal-title":"J. Chem. Phys."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1021\/ct700200b","article-title":"P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation","volume":"4","author":"Hess","year":"2008","journal-title":"J. Chem. Theory Comput."},{"key":"ref_56","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_57","doi-asserted-by":"crossref","first-page":"114107","DOI":"10.1063\/5.0020514","article-title":"Pressure Control Using Stochastic Cell Rescaling","volume":"153","author":"Bernetti","year":"2020","journal-title":"J. Chem. Phys."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"2319","DOI":"10.1002\/jcc.21787","article-title":"MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations","volume":"32","author":"Denning","year":"2011","journal-title":"J. Comput. Chem."}],"container-title":["Molecules"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1420-3049\/31\/15\/2661\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,1]],"date-time":"2026-08-01T04:36:53Z","timestamp":1785559013000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1420-3049\/31\/15\/2661"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,30]]},"references-count":58,"journal-issue":{"issue":"15","published-online":{"date-parts":[[2026,8]]}},"alternative-id":["molecules31152661"],"URL":"https:\/\/doi.org\/10.3390\/molecules31152661","relation":{},"ISSN":["1420-3049"],"issn-type":[{"value":"1420-3049","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,30]]}}}