Solomon Owiredu, Aleah Berkebile, Grace Carr, Tashinga Chigodora, Juan Martinez Soto, Nicole McGuire, Duran Lee, Samuel A. Oluwole, J. S. Raaj Vellore Winfred, Christian Agatemor
{"title":"Structure and Solvent Effects on Nonconventional Fluorescence in Choline–Carboxylic Acid Ionic Liquids Hybrid Solvents","authors":"Solomon Owiredu, Aleah Berkebile, Grace Carr, Tashinga Chigodora, Juan Martinez Soto, Nicole McGuire, Duran Lee, Samuel A. Oluwole, J. S. Raaj Vellore Winfred, Christian Agatemor","doi":"10.1021/acs.jpcb.6c05016","DOIUrl":"https://doi.org/10.1021/acs.jpcb.6c05016","url":null,"abstract":"<p>The molecular parametersthat influence emissive-state formationand excited-state relaxation in nonconventional fluorophores remainpoorly understood. Here, we use structurally related choline–carboxylicacid ionic liquids (ILs) derived from valeric acid (CAVA), levulinicacid (CALE), and 4-pentenoic acid (CAPE) to investigate how the structure,composition, and solvent environment of the carboxylic acid influencenonconventional fluorescence. CAVA exhibits negligible fluorescence,whereas CALE and CAPE display pronounced and composition-dependentemission in aqueous solution. Increasing the choline:carboxylic acidratio from 1:1 to 1:4 enhances the observed fluorescence intensityin both emissive series, while replacing the carbonyl-containing levulinicacid with alkenyl-containing 4-pentenoic acid markedly alters theemission profile, excitation dependence, and excited-state dynamics.SAXS reveals no detectable nanoscale aggregation associated with fluorescenceenhancement, while viscosity and <sup>1</sup>H NMR measurements showcomposition-dependent changes in bulk and local intermolecular environments.Neither properties nor differences in excitationlight absorption consistentlytrack the fluorescence behavior across CALE and CAPE. Solvent- andexcitation-dependent fluorescence, ultrafast transient absorption,and time-resolved fluorescence measurements reveal excitation-dependentemission, sub-picosecond spectral evolution, and biexponential nanoseconddecay, consistent with a complex excited-state landscape. Together,these results demonstrate that carboxylic acid structure, composition,and solvent environment substantially influence the photophysicalbehavior of these ILs and establish choline–carboxylic acidILs as a useful platform for investigating structure–photophysicsrelationships in nonconventional fluorescence.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"130 38","pages":"10001–10014"},"PeriodicalIF":3.2,"publicationDate":"2026-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149022670","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Structural Dynamics and Optical Spectra of the Phycobiliprotein PC612 Complex","authors":"Dongyu Lyu, Sayan Maity, Ulrich Kleinekathöfer","doi":"10.1021/acs.jpcb.6c03535","DOIUrl":"https://doi.org/10.1021/acs.jpcb.6c03535","url":null,"abstract":"<p>Phycocyanin 612 (PC612) is a light-harvesting complexfound incryptophyte algae, characterized by its distinct open structure andflexible protein conformation, allowing the algae to survive in low-lightaqueous environments. Although cryptophyte algae are known to showa diverse range of spectroscopic properties, the complex electronicstructures and photophysical properties of their pigment molecules,known as bilins, are not yet fully understood, particularly in termsof how the surrounding protein environment influences them. In thisstudy, we performed quantum mechanics/molecular mechanics simulationswith excited-state calculations utilizing a numerically efficientdensity functional tight-binding method to examine the structuraldynamics and optical features of bilin molecules within an open-formPC612 complex. Our results indicate that the protein matrix significantlycontrols the fluctuations of excitation energies and excitonic couplingsof the pigment network. Very different from (bacterio)chlorophyll-containingsystems, thermal fluctuations induced by the environment have a minimaleffect on the pigment spectral densities due to similar electron densitydistributions in the ground and excited states. The computed absorptionspectra, calculated at different temperatures, are in reasonable agreementwith the experimental counterparts, accurately predicting the relativepeak positions and confirming the validity of our findings.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"130 38","pages":"9792–9804"},"PeriodicalIF":3.2,"publicationDate":"2026-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149027933","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Mechanisms of Stability of the Metaphase Spindle and Associated Proteins Regulating Microtubule Flux","authors":"Yao Wang, Yu-Ru Liu, Peng-Ye Wang, Ping Xie","doi":"10.1021/acs.jpcb.6c04388","DOIUrl":"https://doi.org/10.1021/acs.jpcb.6c04388","url":null,"abstract":"<p>How the metaphase spindle in higher eukaryotes maintainsstabilityin the presence of poleward microtubule (MT) flux is a confusing issue.Here, we present a model for the spindle by incorporating augmin-mediatedMT connections and MT crosslinking by NuMA proteins. On the basisof the model, we study computationally the dynamics of the spindlefor the wild-type case and for the case with depletion, inhibition,or overexpression of various associated proteins such as kinesin-8KIF18A, CLASP, NuMA, kinesin-4 KIF4A, augmin complex, kinesin-13 MCAK,kinesin-13 KIF2A, and kinesin-5, as well as with addition of the MT-targetingagent BAL27862. The numerical results are consistent with the availableexperimental data. We explain the mechanism of the stability of thespindle, namely, the mechanism of how each MT maintains a constantlength, how antiparallel MT overlaps maintain their constant lengths,how each MT maintains on average a fixed position relative to anotherone despite having different flux rates, and how the spindle lengthis kept constant. The mechanisms of different associated proteinsregulating differentially the MT flux rate, antiparallel MT overlaplength, spindle length, and interkinetochore distance are explained.Moreover, our model explains well various other puzzling experimentalresults such as those showing that the normal MT flux was still presentdespite MT minus ends being detached from the spindle poles and theMT depolymerization at spindle poles being inhibited.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"130 38","pages":"9876–9885"},"PeriodicalIF":3.2,"publicationDate":"2026-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149027911","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Roman Golovchak, Liudmila Loghina, Joshua Rye, Emmabeth Parrish Vaughn, Andriy Kovalskiy, Keira Scott, Calleway Schmidt, Roman Jambor, Miroslav Vlcek
{"title":"Photochromism of Dihydroazulene Embedded in Solid Polymer Matrices","authors":"Roman Golovchak, Liudmila Loghina, Joshua Rye, Emmabeth Parrish Vaughn, Andriy Kovalskiy, Keira Scott, Calleway Schmidt, Roman Jambor, Miroslav Vlcek","doi":"10.1021/acs.jpcb.6c04116","DOIUrl":"https://doi.org/10.1021/acs.jpcb.6c04116","url":null,"abstract":"<p>Photochromic dihydroazulene/vinylheptafulvene systemshave beenextensively investigated in solution, whereas their behavior in solidpolymer matrices remains much less understood despite their relevancefor photonic and optically responsive devices. Here, a phenyl-substituteddihydroazulene derivative (Ph-DHA) was embedded in nine opticallytransparent polymer matrices that differ in polarity, chemical functionality,rigidity, and segmental mobility. The resulting films were examinedby in situ optical transmission measurements under continuous 365nm irradiation and during subsequent thermal recovery. UV exposureinduced pronounced coloration of all films, accompanied by a red shiftof the optical absorption edge from approximately 2.7–2.9 eVto 1.8–1.9 eV, indicating formation of the photoinduced vinylheptafulveneform in the solid state. The initial photoinduced changes in absorbancefollowed a stretched exponential time dependence with the stretchexponent <em>β</em> approaching unity (pure exponential).The minimal time constants (fastest responses) were observed in the460–500 nm spectral region. Thermal recovery at elevated temperatureswas also adequately described by a stretched exponential functionbut with greater <em>β</em> variation (0.6–1.0).The characteristic relaxation times showed weaker spectral dependenceand generally decreased upon heating. No simple correlation betweenthe kinetic parameters and any single polymer property, such as polarity,molecular weight, or chemical functionality, was observed. Instead,the results suggest that a broad distribution of local microenvironmentsand relaxation pathways within the polymer host governs the rate ofphotochromic response of Ph-DHA in solid films. This systematic comparisondemonstrates that Ph-DHA retains robust and thermally reversible photochromismacross chemically diverse solid polymer matrices and provides a phenomenologicalbasis for designing polymer-based photoresponsive films.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"130 38","pages":"10076–10086"},"PeriodicalIF":3.2,"publicationDate":"2026-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149022827","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Igor Yu. Gotlib, Alina S. Koneva, Petr A. Korchak, Evgenia A. Safonova, Andrey V. Petrov, Alexey I. Victorov
{"title":"Glycine and Sodium Glycinate in Water: Experiment and Molecular Dynamics with Different Model Parameters","authors":"Igor Yu. Gotlib, Alina S. Koneva, Petr A. Korchak, Evgenia A. Safonova, Andrey V. Petrov, Alexey I. Victorov","doi":"10.1021/acs.jpcb.6c03325","DOIUrl":"https://doi.org/10.1021/acs.jpcb.6c03325","url":null,"abstract":"<p>Amino acids play a fundamental role in biological processesandhave various practical applications. Specifically, they have beenconsidered as promising agents for the preparation of environmentallyfriendly deep eutectic solvents. To understand the physicochemicalbehavior of amino acids and their salts on a molecular level, atomisticmolecular dynamics (MD) is quite helpful. In this work, glycine andsodium glycinate aqueous solutions were simulated with short-rangeinteractions described by the OPLS-AA force field, using differentatomic charge sets for the glycine zwitterion (GLZ) and the glycinateanion (GLA), and different model potentials for Na<sup>+</sup>. Diffusionin those solutions was measured by the PGSTE NMR method at 298.15K. A comparison of the MD results with these and other available experimentaldata shows that to obtain a satisfactory agreement with experiment,one should adjust the model atomic charges in GLZ or GLA as well asthe interaction parameters for sodium ions, so that the solute associativityis reproduced properly. For both systems, CNDO charges combined withthe Joung–Cheatham model for Na<sup>+</sup> work relativelywell. MD predicts that in aqueous solutions, GLA anions are less clusterizedthan GLZ zwitterions, which agrees with the experimental fact thatsodium glycinate is much more soluble than glycine.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"130 38","pages":"9929–9942"},"PeriodicalIF":3.2,"publicationDate":"2026-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149022668","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Atomic-Scale Resolution of Ion Transport Behavior in a Flexible Polymer Electrolyte under Tensile/Compressive Strain and Electric Fields","authors":"Zongyuan Chen, Minyue Yan, Xin Wang, Xun Zhu, Yang Yang, Qiang Liao","doi":"10.1021/acs.jpcb.6c02697","DOIUrl":"https://doi.org/10.1021/acs.jpcb.6c02697","url":null,"abstract":"<p>Polymer electrolytes, due to their excellent flexibilityand efficiention-transport properties, are considered as the promising electrolytematerials for flexible power devices. However, the ion-transport mechanismsunder mechanical strain and electric field remain insufficiently understood.In this work, molecular dynamics simulation is employed to constructmodels of un-cross-linked polyacrylamide-based polymer electrolytescontaining 6 M potassium hydroxide and investigate the ion transportbehavior under tensile/compressive strain and electric fields. Theionic conductivity of 93.90 mS·cm<sup>–1</sup> decreasesto 80.12 mS·cm<sup>–1</sup> due to a tensile strain of100% and it increases to 104.05 mS·cm<sup>–1</sup> asa result of applied compressive strain, which show a tension inhibitionand compression promotion trend. Under applied electric fields, thecompressive strain plays crucial roles on the sensitivity of ion transportto the electric field across different strain modes. The work providesthe atomic-level insight for designing high-performance polymer electrolytesin a practical electric-stress-coupled environment.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"130 38","pages":"10034–10046"},"PeriodicalIF":3.2,"publicationDate":"2026-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149022764","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Hari O. S. Yadav, Ritika Chauhan, An-Tsung Kuo, Mayank Dixit
{"title":"Unraveling the Hydration Behavior of Poly(2-Methoxyethyl Acrylate) and Its Model Monomer via Molecular Dynamics Simulations","authors":"Hari O. S. Yadav, Ritika Chauhan, An-Tsung Kuo, Mayank Dixit","doi":"10.1021/acs.jpcb.6c03247","DOIUrl":"https://doi.org/10.1021/acs.jpcb.6c03247","url":null,"abstract":"<p>Thehydration behavior of polymeric materials is governed by asubtle interplay between local chemical functionality and polymerbackbone connectivity. In this work, we investigate the hydrationbehavior of poly(2-methoxyethyl acrylate) (PMEA) and its monomericanalogue, 2-methoxyethyl acetate (MEA), using molecular dynamics simulations.MEA is examined at infinite dilution and at water contents rangingfrom 40 to 9 wt %, and the hydration behavior across this hydrationrange is compared with that of PMEA at 9 wt % water to assess thedegree of similarity and to isolate the role of the collective effectsassociated with the polymer architecture. Hydration behavior is analyzedusing a range of structural and dynamical metrics. Structural analysesreveal that at 9 wt % water, MEA and PMEA exhibit similar local hydrationstructures around their various oxygen sites, indicating comparableshort-range coordination. In contrast, dynamical properties show pronounceddifferences: water in PMEA displays significantly slower translationalmotion, longer residence times near polymer oxygen sites, and markedlyprolonged hydrogen-bond dynamics compared to MEA at the same hydrationlevel. The results demonstrate that, despite similar local hydrationstructures, the polymer architecture imposes strong dynamical constraintson interfacial water, resulting in a clear decoupling between localhydration structure and interfacial water dynamics. The study providesmolecular-level insight into the distinctive hydration behavior ofPMEA and highlights the importance of considering hydration dynamicsalongside local hydration structure.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"130 38","pages":"10047–10060"},"PeriodicalIF":3.2,"publicationDate":"2026-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149027875","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Impact of Anticancer Polymers on Model Cancerous Membranes: Molecular-Level Insight from Computer Simulations","authors":"Andrey A. Gurtovenko, Victor M. Nazarychev","doi":"10.1021/acs.jpcb.6c03563","DOIUrl":"https://doi.org/10.1021/acs.jpcb.6c03563","url":null,"abstract":"<p>Anticancer polymers represent a novel, promising classof therapeuticalagents aimed to combat emerging multidrug resistance. Here, we employatomic-scale computer simulations to explore for the first time themolecular-level impact of anticancer polymers on model cancerous membranes.To this end, we focused on methacrylate-based random copolymers withproven anticancer activity. Our computational findings show that phosphatidylserinelipids on the surface of cancerous membranes serve as the primarytargets for protonated amine groups of anticancer polymers. Adsorptionof cationic anticancer polymers induces the lateral ordering and clusteringof anionic phosphatidylserines in line with existing experimentaldata. Embedding polymers into the membrane results in an expansionof the membrane, which is accompanied by a drop in its thickness andby disordering of lipid acyl chains. Within the membrane, anticancerpolymers adopt a comb-like conformation with the backbones being buriedin the hydrophobic membrane core and the protonated side groups beingbound to lipid phosphate groups. The polymer-induced thinning of themembrane turns out to depend non-monotonically on polymer hydrophobicity.This highlights the importance of a balance between the overall chargeand the hydrophobicity of polymers for promoting anticancer activity.Although spontaneous pore formation was shown to be beyond the timescales accessible through atomic-scale simulations, membrane thinningcan be considered a first step toward the nucleation of transmembranepores and subsequent membrane collapse. Our electroporation testsshowed that the membrane became more prone to poration upon adsorptionof anticancer polymers. All in all, our computational findings providevaluable microscopic information for further optimization of anticancerpolymeric agents.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"130 38","pages":"9816–9825"},"PeriodicalIF":3.2,"publicationDate":"2026-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149027942","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Kano N. Toyoizumi, Yuichi Fujita, Seiji Akimoto, Ryo Nagao
{"title":"Altered Excitation-Energy Transfer in the Dark-Adapted Leptolyngbya boryana Variant dg211","authors":"Kano N. Toyoizumi, Yuichi Fujita, Seiji Akimoto, Ryo Nagao","doi":"10.1021/acs.jpcb.6c03891","DOIUrl":"https://doi.org/10.1021/acs.jpcb.6c03891","url":null,"abstract":"<p>Dark-heterotrophic growth allows photosynthetic pigment–proteincomplexes to be examined when photosynthetic energy conversion isnot required for growth. A dark-adapted variant, dg211, of <em>Leptolyngbya boryana</em> has been reported to exhibitaltered carotenoid composition, but its effect on excitation-energytransfer remains unclear. Here, we analyzed light-grown wild-type(WT-light) and dg211 (dg211-light), and dark-grown dg211 (dg211-dark)cells using immunoblotting, pigment analysis, absorption spectroscopy,77 K steady-state and time-resolved fluorescence spectroscopy, andfluorescence decay-associated spectra. <em>β</em>-Carotenewas detected in the WT-light and dg211-light cells but not in thedg211-dark cells, although chlorophyll <em>a</em> and phycobilisome-relatedspectral features were retained. In the dg211-dark cells, D1 accumulationwas markedly reduced, whereas PsaA/B remained detectable. PSII-delayedfluorescence disappeared, while PSI-associated 729–730 nm fluorescencepersisted, indicating a severe depletion of functional PSII reaction-centerunits with retention of PSI-associated features. Pronounced 687 nmnanosecond fluorescence was attributed mainly to prolonged excitation-energyretention in phycobilisome-related emitting states. These findingsreveal substantial reorganization of photosynthetic excitation-energytransfer in dark-grown dg211.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"130 38","pages":"9843–9850"},"PeriodicalIF":3.2,"publicationDate":"2026-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149027912","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Mutation-Dependent Conformational Dynamics and Dual-Mode Afatinib Binding in EGFR Exon 19 Variants","authors":"Kousik K. Bhanja, Rajesh Ghosh, Niladri Patra","doi":"10.1021/acs.jpcb.6c03491","DOIUrl":"https://doi.org/10.1021/acs.jpcb.6c03491","url":null,"abstract":"<p>Exon 19 mutations in the epidermal growth factor receptor(EGFR)kinase domain, including the common ΔE746-A750 deletion andthe less frequent L747P substitution, are clinically important driversof non-small cell lung cancer (NSCLC). Although these mutations occurwithin the β3-αC region, how they alter EGFR conformationaldynamics and influence the response to the covalent inhibitor afatinibremains incompletely understood. Here, we investigated mutation-dependentchanges in EGFR conformational ensembles, dual-mode of afatinib binding,and Cys797-mediated covalent reaction energetics in wild-type, ΔE746-A750,and L747P kinase domains. We find that both mutations preferentiallystabilize active-like kinase conformations but do so through distinctstructural mechanisms. The ΔE746-A750 deletion produces greaterP-loop and ATP-pocket conformational heterogeneity, whereas L747Prestricts αC-helix and activation-loop dynamics and more stronglystabilizes the active-like ensemble. Afatinib binding disrupts theK745-E762 interaction and alters the αC-helix conformation whilethe pre-formed covalent state samples αC-out configurationsthat increase accessibility of an αC-adjacent pocket that isless accessible in the apo state. Alchemical calculations furtherreveal mutation- and protonation-state-dependent differences in theconditional noncovalent binding free energy of afatinib. QM/MM calculationsof Cys797-afatinib bond formation reveal mutation-dependent differencesin the calculated reaction barrier, with L747P showing a lower barrierthan ΔE746-A750 within the employed QM/MM model. Together, theseresults show that EGFR exon 19 mutations reshape the conformationallandscape and local structural environment of the kinase, therebyinfluencing afatinib binding and the energetic environment of covalentbond formation. These findings provide a structural framework forunderstanding how distinct EGFR mutations can produce different responsesto covalent kinase inhibition.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"130 38","pages":"9776–9791"},"PeriodicalIF":3.2,"publicationDate":"2026-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149027878","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}