{"title":"Phases and Architectures in Metal/Metal Oxide Systems Driven by Strong Metal–Support Interactions","authors":"Jordi Morales-Vidal, Zan Lian, Thaylan Pinheiro Araújo, Sharon Mitchell, Javier Pérez-Ramírez, Núria López","doi":"10.1021/acsphyschemau.5c00138","DOIUrl":"10.1021/acsphyschemau.5c00138","url":null,"abstract":"<p>Metal oxide supported metal catalysts are widely appliedin industrialprocesses. Many of these materials dynamically evolve under reducingatmospheres, leading to metal nanoparticles partially or fully encapsulatedby metal oxide shells, impacting catalytic performance. This phenomenonis known as strong metal–support interaction (SMSI) and isthermodynamically driven. However, understanding the metal/metal oxideinterfaces derived from the broad and flexible compositional spaceand the large structural changes in SMSI structures is difficult tomonitor experimentally. Here, we use density functional theory togetherwith machine learning interatomic potentials and global minima optimizationto investigate SMSI by building a set of interfaces between commoncatalytic metals (Ni, Pd, Pt) and reducible metal oxides (r-TiO<sub>2</sub>, CeO<sub>2</sub>, In<sub>2</sub>O<sub>3</sub>) at differentreduction levels. Phase diversity arises from the competition betweenthe formation of different metal oxides or binary alloys, while thelocal properties of the suboxide layers are responsible for the finalarchitecture and composition determining the electronic propertiesof the material. Two descriptors related to the competition betweenalloy and oxide formation are proposed to elucidate the phase diversity.Our work provides a systematic approach to advance the design of SMSI-basedcatalytic materials by offering insights into the atomic-level architectureof the metal/metal oxide interfaces.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"6 2","pages":"340–347"},"PeriodicalIF":4.8,"publicationDate":"2026-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147575594","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ACS Physical Chemistry AuPub Date : 2026-03-25Epub Date: 2026-01-08DOI: 10.1021/acsphyschemau.5c00141
Jelto Neirynck, Sander Geerinckx, Sven M. J. Rogge
{"title":"Challenges and Best Practices in Modeling Anisotropic Stresses in Soft Polymorphic Materials","authors":"Jelto Neirynck, Sander Geerinckx, Sven M. J. Rogge","doi":"10.1021/acsphyschemau.5c00141","DOIUrl":"10.1021/acsphyschemau.5c00141","url":null,"abstract":"<p>Soft polymorphic materials, such as metal–organicframeworks(MOFs) and covalent organic frameworks (COFs), often display distinctanisotropy. Yet, their phase transition behavior has been predominantlycharacterized under isotropic stimuli, such as temperature or pressurevariations, up to now. In this work, we employed the Cauchystat toinvestigate how MIL-53(Al) and COF-5, two prototypical soft porouscrystals, respond to anisotropic stresses instead. For MIL-53(Al),we showed that normal stresses induce a phase transition already atstresses below the critical hydrostatic pressure, depending on thedirectionality of the applied stress. For COF-5, we determined thecritical shear stress needed to induce a layer instability, leadingto delamination. In both cases, we highlighted the importance of selectingadequate values of the Cauchystat control parameters to obtain accuratepredictions. Based on these insights, we formulated best practicesto simulate phase transitions in soft porous crystals under nonhydrostaticloadings, which is required for, e.g., nanosensors and -dampers.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"6 2","pages":"356–366"},"PeriodicalIF":4.8,"publicationDate":"2026-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147575628","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ACS Physical Chemistry AuPub Date : 2026-03-25Epub Date: 2026-01-27DOI: 10.1021/acsphyschemau.5c00145
Hyojung Kim, Sung Man Park, Chan Ho Kwon
{"title":"Ionization-Induced Electronic and Vibronic Structure of 3,5-Difluoropyridine Probed by VUV-MATI Spectroscopy","authors":"Hyojung Kim, Sung Man Park, Chan Ho Kwon","doi":"10.1021/acsphyschemau.5c00145","DOIUrl":"10.1021/acsphyschemau.5c00145","url":null,"abstract":"<p>Fluorinated pyridines, particularly difluoropyridines,exhibitposition-dependent electronic properties arising from the interplayof inductive, resonance, and hyperconjugative effects introduced byfluorine substitution. In this study, the ionization-induced electronicand structural characteristics of 3,5-difluoropyridine (3,5-DFP)<span></span>apreviously uncharacterized meta–meta disubstituted isomer<span></span>wereinvestigated using high-resolution vacuum ultraviolet mass-analyzedthreshold ionization spectroscopy in conjunction with quantum-chemicalcalculations. The adiabatic ionization energy was determined to be9.6829 ± 0.0004 eV, indicating an intermediate degree of electronicstabilization between the 2,3- and 2,5-isomers. Natural bond orbitalanalysis showed that the π-type HOMO of 3,5-DFP experiencesmoderate delocalization over the aromatic framework, whereas the σ-typeHOMO–1 exhibits minimal interaction with the fluorine substituents,resulting in reduced stabilization. Franck–Condon analysisand vibrational spectroscopy revealed distinct ionization-driven geometricdistortions dominated by ring-bending and stretching modes. The smallD<sub>0</sub>–D<sub>1</sub> energy separation (0.185 eV) supportsassignment of the 44 cm<sup>–1</sup> feature as the 0–0transition of the D<sub>1</sub> state, yielding a second adiabaticionization energy of 9.6884 ± 0.0004 eV. These results demonstratehow fluorine substitution patterns regulate orbital ordering, structuralrelaxation, and vibronic coupling in pyridine cations. By elucidatingthe effects of meta–meta fluorination, this work fills a criticalgap in difluoropyridine chemistry and provides fundamental insightrelevant to the precision design of functional aromatic moleculesfor applications in materials science, catalysis, and pharmaceuticalchemistry.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"6 2","pages":"367–377"},"PeriodicalIF":4.8,"publicationDate":"2026-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147575664","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ACS Physical Chemistry AuPub Date : 2026-03-25Epub Date: 2026-01-15DOI: 10.1021/acsphyschemau.5c00085
Zhongrui Li, Yue Wang, Ran Yan, Ke Yuan, Udo Becker
{"title":"Relativistic Modeling of K- and L‑Shell Decay in Sulfur Ions across Oxidation States","authors":"Zhongrui Li, Yue Wang, Ran Yan, Ke Yuan, Udo Becker","doi":"10.1021/acsphyschemau.5c00085","DOIUrl":"10.1021/acsphyschemau.5c00085","url":null,"abstract":"<p>Core-hole decay processes in sulfur ions from S<sup>2–</sup> to S<sup>+6</sup> were systematically investigated by using relativisticquantum electrodynamics. Fine-structure wave functions were generatedvia multiconfiguration Dirac–Fock methods to model decay pathways,including Auger and radiative channels. Auger processes were treatedusing configuration interaction, with Auger transition rates calculatedthrough distorted-wave and isolated-resonance approximations. Radiativedecay rates were determined for multipoles using relaxed-orbital oscillatorstrengths. The simulations reveal that Auger electron kinetic energiesdecrease monotonically with increasing oxidation state, while Augertransition intensities vary sensitively with ionization state. Thesevariations are driven by changes in electronic configuration, whichmodulate Coulomb and Breit interactions, thereby altering energy gapsand intensity ratios across transitions. While radiative decay remainsweak in all sulfur ionization states due to the low atomic number,K-shell decay exhibits a significantly higher radiative contributionthan L-shell decay. Additionally, higher ionization leads to a slightreduction in the Auger-to-fluorescence decay ratio. Notably, spin–orbitcoupling in 2p core–shells exerts a pronounced influence onAuger transition probabilities and X-ray fluorescence yields, thoughits impact diminishes with increasing ionization.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"6 2","pages":"259–271"},"PeriodicalIF":4.8,"publicationDate":"2026-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147575614","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ACS Physical Chemistry AuPub Date : 2026-03-25Epub Date: 2025-12-17DOI: 10.1021/acsphyschemau.5c00087
Farizal Hakiki, Muhamad Raihan Al Fikri, Veni Dwi Amelia Putri, Indra Gunawan, Witta Kartika Restu, Muslim Abdurrahman
{"title":"Chemical EOR with Methyl Ester Sulfonate: Achieving Residual Oil Saturation via 2–4-Order Capillary Number Increase","authors":"Farizal Hakiki, Muhamad Raihan Al Fikri, Veni Dwi Amelia Putri, Indra Gunawan, Witta Kartika Restu, Muslim Abdurrahman","doi":"10.1021/acsphyschemau.5c00087","DOIUrl":"10.1021/acsphyschemau.5c00087","url":null,"abstract":"<p>This study extends the application of methyl ester sulfonate(MES),a biodegradable, anionic surfactant derived from renewable resources,for chemically enhanced oil recovery (EOR) in high-salinity (up to700 mM NaCl) and high-temperature (80 °C) conditions. MES isdemonstrated to reduce oil–water interfacial tension to lowvalues (∼0.02 mN/m at 80 °C), alter sandstone wettabilityto preferentially water-wet, and form stable Winsor III microemulsions.We highlight a key advancement by systematically compiling and comparingpublished capillary desaturation data, showing that increasing thecapillary number by a factor of 10<sup>2</sup>–10<sup>4</sup> enables the system to approach irreducible water or residual oilsaturation. Our experimental results align with this trend, whereMES significantly increases capillary numbers through synergisticeffects of interfacial tension reduction and wettability alteration.Zeta potential measurements confirm colloidal stability across a broadconcentration and salinity range, while thermal analysis supportsMES stability up to 90 °C. Spontaneous imbibition tests showoil recovery exceeding 28% under optimized salinity, further validatingthe MES efficacy. This work not only expands the operational envelopeof MES for chemical EOR but also reinforces the mechanistic link betweenthe capillary number scaling and residual oil displacement. By integratinglab-scale results with a broad data set from the literature, thisstudy delivers a compelling foundation for deploying MES in field-scaleEOR operations, particularly in mature reservoirs where sustainableand cost-effective solutions are critical.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"6 2","pages":"272–285"},"PeriodicalIF":4.8,"publicationDate":"2026-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147575612","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ACS Physical Chemistry AuPub Date : 2026-03-25Epub Date: 2026-03-01DOI: 10.1021/acsphyschemau.5c00121
Lara Williams, Luc Schmitt, Andreas Scherer, Mykhailo Azarkh
{"title":"SOQS: Superposition of Quantum States for Selective Detection of Dipolar Frequency Multiples in Pulsed EPR Spectroscopy","authors":"Lara Williams, Luc Schmitt, Andreas Scherer, Mykhailo Azarkh","doi":"10.1021/acsphyschemau.5c00121","DOIUrl":"10.1021/acsphyschemau.5c00121","url":null,"abstract":"<p>Pulsedelectron paramagnetic resonance (EPR) spectroscopyprovidesa means for determining nanometer-range distance distributions betweenparamagnetic centers. The method relies on the measurement of dipolarcoupling frequencies, while the lowest resolved dipolar frequencysets the upper limit for distance determination. We explore the possibilityof increasing the upper distance limit by accessing the dipolar frequencymultiples from the selective excitation of transitions with Δ<em>M<sub>S</sub></em> > 1. Such transitions arise from the superpositionof quantum states (SOQS) and provide up to four times the dipolarfrequency, and up to 60% increase in the upper distance limit. Thishas been demonstrated through spin dynamics calculations for the tripletstate of a xanthene chromophore and experimentally for NV<sup>–</sup> centers in diamond. Future steps toward the practical applicationare discussed.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"6 2","pages":"324–333"},"PeriodicalIF":4.8,"publicationDate":"2026-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147575647","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ACS Physical Chemistry AuPub Date : 2026-03-25Epub Date: 2026-03-01DOI: 10.1021/acsphyschemau.5c00148
Yi Cheng
{"title":"The Htrs–Ttrs Function of Phase Transition Enthalpy for Chemical Elements and Inorganic and Organic Compounds","authors":"Yi Cheng","doi":"10.1021/acsphyschemau.5c00148","DOIUrl":"10.1021/acsphyschemau.5c00148","url":null,"abstract":"<p>The periodic tableof chemical elements has undergone over a centuryof development and has made indelible contributions to the fieldsof physics and chemical science. Exploring the relationship betweenthe structure and properties of elements and establishing mathematicalmodels of their physical properties has always been a goal that scientistshave pursued tirelessly. For example, can the relationships betweenmelting points (<em>T<sub>f</sub></em>), boiling points (<em>T<sub>b</sub></em>), and enthalpies (<em>H<sub>v</sub></em> or <em>H<sub>f</sub></em>) of various elements be unifiedinto a single mathematical function? Does the phase transition temperatureof an element necessarily increase with its atomic number? Does thephase transition enthalpy also increase accordingly? The valence electronnumber of an element is a significant characteristic value in itsperiodicity, and elements with the same valence electron number formthe same groups. Connecting the <em>H</em><sub><em>trs</em></sub>/<em>T</em><sub><em>trs</em></sub> points ofelements in the same group yields a <em>H</em><sub><em>trs</em></sub>–<em>T</em><sub><em>trs</em></sub> curve and function. Research has revealed that the <em>H</em><sub><em>trs</em></sub>–<em>T</em><sub><em>trs</em></sub> functions of elements in the samegroup can all be unified into a single quadratic trinomial: <em>H<sub>trs</sub></em> = <em>aT<sub>trs</sub></em><sup>2</sup> + <em>bT<sub>trs</sub></em> + <em>c</em>,with a correlation coefficient <em>R</em><sup><em>2</em></sup> ≈ 1. This quadratic trinomial is an increasing function;therefore, the phase transition enthalpy of elements in the same groupincreases with the rise in phase transition temperature. Based onthis quadratic trinomial and the phase transition temperatures ofelements, the phase transition enthalpy of homologous elements canbe predicted, or the phase transition temperature can be retrodictedfrom known phase transition enthalpy. In addition, this method canalso be used to correct the known phase transition temperatures orenthalpies of the elements. Further work has found that many inorganicand organic compounds also exhibit the characteristics of <em>H</em><sub><em>trs</em></sub>–<em>T</em><sub><em>trs</em></sub>. The concept of <em>H</em><sub><em>trs</em></sub>–<em>T</em><sub><em>trs</em></sub> function will provide new fundamental data andresearch approaches for thermodynamics, material structure, condensedmatter physics, quantum mechanics, inorganic chemistry, and organicchemistry.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"6 2","pages":"378–387"},"PeriodicalIF":4.8,"publicationDate":"2026-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147575656","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ACS Physical Chemistry AuPub Date : 2026-03-25Epub Date: 2026-01-12DOI: 10.1021/acsphyschemau.5c00098
Luís Gustavo Teixeira Alves Duarte, Iker Lamas, Dominik Bäuerle, Saeed Shareef, Renato D. Cunha, Carles Curutchet, Mariano Curti, Elisabet Romero
{"title":"Unraveling Charge-Transfer States and Their Ultrafast Dynamics in Artificial Light-Harvesting Complexes","authors":"Luís Gustavo Teixeira Alves Duarte, Iker Lamas, Dominik Bäuerle, Saeed Shareef, Renato D. Cunha, Carles Curutchet, Mariano Curti, Elisabet Romero","doi":"10.1021/acsphyschemau.5c00098","DOIUrl":"10.1021/acsphyschemau.5c00098","url":null,"abstract":"<p>Photosynthesis relieson highly organized pigment–proteincomplexes in order to store sunlight energy as biochemical energy.These complexes capture light with remarkable efficiency and are responsiblefor ultrafast charge separation within a finely tuned energy landscapeprovided by the protein environments, producing one of nature’smost sophisticated energy conversion systems. Inspired by nature, <em>de novo</em> designed proteins have been proven to be versatileplatforms to emulate the function of natural light-harvesting complexesand reaction centers. With Stark and ultrafast transient absorptionspectroscopies, we explored the exciton and charge-transfer (CT) mixing,as well as the excited-state dynamics, of a chlorophyll <em>a</em> analogue (Zn-pheophorbide <em>a</em>) in dimers formed within4-α-helix bundles whose design was previously guided by moleculardynamics simulations. Due to dimerization, we observe an increasein the CT character of the excitonically coupled dimers’ excitedstate in comparison to monomeric ZnP. Furthermore, additional nonradiativerelaxation pathways, together with the formation of transient speciesabsent in monomeric systems, were observed for the dimers. We demonstratethat <em>de novo</em> designed proteins can replicate keyfeatures of photosynthetic energy conversion, serving as tunable scaffoldsfor optimizing light-harvesting processes. Ultimately, these systemshave promising applications including photovoltaic cells and biomedicaltreatments based on sustainable materials.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"6 2","pages":"286–300"},"PeriodicalIF":4.8,"publicationDate":"2026-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147575585","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ACS Physical Chemistry AuPub Date : 2026-03-25Epub Date: 2026-02-26DOI: 10.1021/acsphyschemau.5c00134
Alan Almeida, Ana Clara das Neves, Paula Brandão, Mariem Masmoudi, Luis Ghivelder, Clebson Cruz, Mario Reis
{"title":"Magnetic Anisotropy and Spin Coupling in a Cobalt(II) Dimer with Bioinspired Bridges","authors":"Alan Almeida, Ana Clara das Neves, Paula Brandão, Mariem Masmoudi, Luis Ghivelder, Clebson Cruz, Mario Reis","doi":"10.1021/acsphyschemau.5c00134","DOIUrl":"10.1021/acsphyschemau.5c00134","url":null,"abstract":"<p>Cobalt(II) metalcomplexes constitute a versatile platformforinvestigating how coordination geometry and spin–orbit couplingdetermine their magnetic properties. Although numerous cobalt(II)coordination complexes have been reported in recent literature, onlya limited number exhibit comprehensive and quantitatively reliablemagnetic characterization. In this work, we investigate the magneticproperties of the hexacoordinated cobalt dimer [Co<sub>2</sub>(μ-L1H)<sub>2</sub>(μ-H<sub>2</sub>O)<sub>2</sub>(H<sub>2</sub>O)<sub>4</sub>]4NO<sub>3</sub>·2H<sub>2</sub>O, where L1H denotes the adeninebridging ligand. The hexacoordinated environment stabilizes a high-spin <em>S</em> = 3/2 configuration for both Co(II) centers, resultingin strong spin–orbit coupling and significant zero-field splitting,described by axial (<em>D</em>) and rhombic (<em>E</em>) anisotropy parameters. Fits to magnetic susceptibility and magnetizationdata reveal antiferromagnetic coupling between the Co(II) ions, witha ratio of <em>E</em>/<em>D</em> ≈ 1/4 and <em>D</em>/<em>k</em><sub>B</sub> = 89 K, evidencing pronouncedmagnetic anisotropy in the system. This behavior is further supportedby anisotropic Landé factors <em>g</em><sub><em>x</em></sub> = <em>g</em><sub><em>y</em></sub> = 2.5 and <em>g</em><sub><em>z</em></sub> = 2.4,consistent with easy-plane magnetic anisotropy.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"6 2","pages":"334–339"},"PeriodicalIF":4.8,"publicationDate":"2026-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147575589","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ACS Physical Chemistry AuPub Date : 2026-03-25Epub Date: 2026-01-23DOI: 10.1021/acsphyschemau.5c00120
Alejandro Feito, Eduardo Pedraza, Estefania Cuesta, Alejandro Castro, Antonio Rey, Ignacio Sanchez-Burgos, Rosana Collepardo-Guevara, Andrés R. Tejedor, Jorge R. Espinosa
{"title":"Determination of Nucleotide–Nucleotide and Nucleotide–Amino Acid Binding Interactions from All-Atom Potential-of-Mean-Force Calculations","authors":"Alejandro Feito, Eduardo Pedraza, Estefania Cuesta, Alejandro Castro, Antonio Rey, Ignacio Sanchez-Burgos, Rosana Collepardo-Guevara, Andrés R. Tejedor, Jorge R. Espinosa","doi":"10.1021/acsphyschemau.5c00120","DOIUrl":"10.1021/acsphyschemau.5c00120","url":null,"abstract":"<p>Biomolecular condensates emerge from multivalent interactionsbetweenproteins and nucleic acids and are frequently modeled by using coarse-grainedmolecular dynamics simulations. The parametrization of these modelscritically depends on atomistic data describing the underlying molecularinteractions. In this work, we employ all-atom molecular dynamicssimulations and potential-of-mean-force (PMF) calculations to investigatethe landscape of interactions between RNA nucleotides and proteinamino acids. We begin by characterizing nucleotide–nucleotidebinding modes through canonical base-pairing analysis, observing notableagreement in the predictions from both the AMBER03ws and CHARMM36force fields. Further rationalization of different nucleotide–nucleotideinteraction modes involves the calculation of PMFs for ribose–ribose,phosphate–phosphate, and RNA tertiary interactions such asG-quadruplex formation. We also examine the effect of salt concentrationon these interactions, finding a reduction in electrostatic self-repulsionfor phosphate–phosphate binding upon increasing the ionic strength.Expanding our analysis to amino acids, we first benchmark the performanceof both AMBER03ws and a99SB-disp force fields for describing pairwiseamino acid interactions, and then, we evaluate different nucleotide–aminoacid binding profiles. Our findings reveal a subset of amino acids<span></span>Lysand Arg (positively charged), Asp and Glu (negatively charged), andGln, Ser, and Asn (polar residues)<span></span>that consistently engagewith the nitrogenous bases of different nucleotides. Such bindingis primarily mediated by hydrogen bonding and, in some cases, cation−πinteractions. Furthermore, we identify strong π–πstacking interactions with aromatic residues and phosphate–Argcontacts as key contributors to condensate cohesion in RNA–proteincondensates. Our comprehensive analysis provides a detailed libraryof nucleotide–amino acid interactions, offering quantitativeinsights to inform coarse-grained model parametrization and deepeningour understanding of condensate self-assembly, nucleic acid recognition,and phase-separation regulation at the submolecular scale.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"6 2","pages":"308–323"},"PeriodicalIF":4.8,"publicationDate":"2026-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147575633","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}