ACS Physical Chemistry AuPub Date : 2025-05-08DOI: 10.1021/acsphyschemau.5c0002810.1021/acsphyschemau.5c00028
Karinna Mendanha, and , Guilherme Colherinhas*,
{"title":"Molecular Dynamics Simulations of Self-Assembled E2(SW)6E2 Peptide Nanofibers: Implications for Drug Delivery and Biomimetic Material Design","authors":"Karinna Mendanha, and , Guilherme Colherinhas*, ","doi":"10.1021/acsphyschemau.5c0002810.1021/acsphyschemau.5c00028","DOIUrl":"https://doi.org/10.1021/acsphyschemau.5c00028https://doi.org/10.1021/acsphyschemau.5c00028","url":null,"abstract":"<p >This work investigates the molecular dynamics of the peptide nanofiber E<sub>2</sub>(SW)<sub>6</sub>E<sub>2</sub>, a biomolecule/structure in an aqueous solution, characterized by hydrophilic and hydrophobic contrasts. Through classical molecular dynamics simulations, the study examines the energetic, structural, and dynamic properties of this nanofiber, with a focus on energetic and hydrogen bond (HB) interactions between peptides and peptide-water. Simulations of different fiber lengths indicate that larger models exhibit increased structural stability and longer HB lifetimes, contributing to enhanced fiber flexibility and integrity. Additionally, the analysis of the mass density profile along the nanofiber length reveals local decreases (but not zero) in mass density. The results further emphasize the potential of these structures for applications in ion and drug transport due to their hydrophobic core and hydrophilic surface. This work provides a comprehensive understanding of molecular interactions in self-assembled bionanomaterials in aqueous solutions.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"5 3","pages":"302–315 302–315"},"PeriodicalIF":3.7,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsphyschemau.5c00028","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144146620","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ACS Physical Chemistry AuPub Date : 2025-05-08eCollection Date: 2025-05-28DOI: 10.1021/acsphyschemau.5c00028
Karinna Mendanha, Guilherme Colherinhas
{"title":"Molecular Dynamics Simulations of Self-Assembled E<sub>2</sub>(SW)<sub>6</sub>E<sub>2</sub> Peptide Nanofibers: Implications for Drug Delivery and Biomimetic Material Design.","authors":"Karinna Mendanha, Guilherme Colherinhas","doi":"10.1021/acsphyschemau.5c00028","DOIUrl":"https://doi.org/10.1021/acsphyschemau.5c00028","url":null,"abstract":"<p><p>This work investigates the molecular dynamics of the peptide nanofiber E<sub>2</sub>(SW)<sub>6</sub>E<sub>2</sub>, a biomolecule/structure in an aqueous solution, characterized by hydrophilic and hydrophobic contrasts. Through classical molecular dynamics simulations, the study examines the energetic, structural, and dynamic properties of this nanofiber, with a focus on energetic and hydrogen bond (HB) interactions between peptides and peptide-water. Simulations of different fiber lengths indicate that larger models exhibit increased structural stability and longer HB lifetimes, contributing to enhanced fiber flexibility and integrity. Additionally, the analysis of the mass density profile along the nanofiber length reveals local decreases (but not zero) in mass density. The results further emphasize the potential of these structures for applications in ion and drug transport due to their hydrophobic core and hydrophilic surface. This work provides a comprehensive understanding of molecular interactions in self-assembled bionanomaterials in aqueous solutions.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"5 3","pages":"302-315"},"PeriodicalIF":3.7,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12123548/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144200233","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ACS Physical Chemistry AuPub Date : 2025-04-26eCollection Date: 2025-05-28DOI: 10.1021/acsphyschemau.5c00021
Clark Otey, Mukund Sharma, Jazmine Prana, Thomas M Czyszczon-Burton, Alejandro Hernandez, María Camarasa-Gómez, Daniel Hernangómez-Pérez, Michael S Inkpen
{"title":"Conductance Measurements of Polar Molecules in a Nonconducting Solvent.","authors":"Clark Otey, Mukund Sharma, Jazmine Prana, Thomas M Czyszczon-Burton, Alejandro Hernandez, María Camarasa-Gómez, Daniel Hernangómez-Pérez, Michael S Inkpen","doi":"10.1021/acsphyschemau.5c00021","DOIUrl":"https://doi.org/10.1021/acsphyschemau.5c00021","url":null,"abstract":"<p><p>Solution-based single-molecule conductance measurements of α,ω-bis-(carboxylic acids) are conveniently performed using a high-boiling-point nonconducting ethereal solvent. First-principles calculations support experimental observations that linear oligoalkanes exhibit the expected exponential decay of conductance with length, whereas junctions comprising cyclic bridge hydrocarbons of different lengths and/or structures exhibit a similar conductance.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"5 3","pages":"249-253"},"PeriodicalIF":3.7,"publicationDate":"2025-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12123542/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144200230","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ACS Physical Chemistry AuPub Date : 2025-04-26DOI: 10.1021/acsphyschemau.5c0002110.1021/acsphyschemau.5c00021
Clark Otey, Mukund Sharma, Jazmine Prana, Thomas M. Czyszczon-Burton, Alejandro Hernandez, María Camarasa-Gómez*, Daniel Hernangómez-Pérez* and Michael S. Inkpen*,
{"title":"Conductance Measurements of Polar Molecules in a Nonconducting Solvent","authors":"Clark Otey, Mukund Sharma, Jazmine Prana, Thomas M. Czyszczon-Burton, Alejandro Hernandez, María Camarasa-Gómez*, Daniel Hernangómez-Pérez* and Michael S. Inkpen*, ","doi":"10.1021/acsphyschemau.5c0002110.1021/acsphyschemau.5c00021","DOIUrl":"https://doi.org/10.1021/acsphyschemau.5c00021https://doi.org/10.1021/acsphyschemau.5c00021","url":null,"abstract":"<p >Solution-based single-molecule conductance measurements of α,ω-bis(carboxylic acids) are conveniently performed using a high-boiling-point nonconducting ethereal solvent. First-principles calculations support experimental observations that linear oligoalkanes exhibit the expected exponential decay of conductance with length, whereas junctions comprising cyclic bridge hydrocarbons of different lengths and/or structures exhibit a similar conductance.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"5 3","pages":"249–253 249–253"},"PeriodicalIF":3.7,"publicationDate":"2025-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsphyschemau.5c00021","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144146504","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ACS Physical Chemistry AuPub Date : 2025-03-26DOI: 10.1021/acsphyschemau.5c0001910.1021/acsphyschemau.5c00019
Gemma C. Solomon*, Tanja Cuk, Jin Z. Zhang and Shelley D. Minteer,
{"title":"How Can We Reduce the Barriers to Entering New Research Fields?","authors":"Gemma C. Solomon*, Tanja Cuk, Jin Z. Zhang and Shelley D. Minteer, ","doi":"10.1021/acsphyschemau.5c0001910.1021/acsphyschemau.5c00019","DOIUrl":"https://doi.org/10.1021/acsphyschemau.5c00019https://doi.org/10.1021/acsphyschemau.5c00019","url":null,"abstract":"","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"5 2","pages":"115–116 115–116"},"PeriodicalIF":3.7,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsphyschemau.5c00019","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143696494","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Gemma C Solomon, Tanja Cuk, Jin Z Zhang, Shelley D Minteer
{"title":"How Can We Reduce the Barriers to Entering New Research Fields?","authors":"Gemma C Solomon, Tanja Cuk, Jin Z Zhang, Shelley D Minteer","doi":"10.1021/acsphyschemau.5c00019","DOIUrl":"10.1021/acsphyschemau.5c00019","url":null,"abstract":"","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"5 2","pages":"115-116"},"PeriodicalIF":3.7,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11950842/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143754035","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ACS Physical Chemistry AuPub Date : 2025-03-10eCollection Date: 2025-03-26DOI: 10.1021/acsphyschemau.4c00103
Alexander J Menke, Joseph H Reibenspies, Casey J Patterson-Gardner, Alexander M Engstrom, R Scott Lokey, Eric E Simanek
{"title":"Choreoisosteres: Pseudoatom Variation in Macrocyclic Hinges Conserves Structure and Dynamics.","authors":"Alexander J Menke, Joseph H Reibenspies, Casey J Patterson-Gardner, Alexander M Engstrom, R Scott Lokey, Eric E Simanek","doi":"10.1021/acsphyschemau.4c00103","DOIUrl":"10.1021/acsphyschemau.4c00103","url":null,"abstract":"<p><p>Differing in pseudoatom, three macrocycles with isosteric substitutions (geminal dimethyl, cyclopropyl, cyclobutyl) can be described as choreoisosteres. Under ambient conditions, they share a dynamic hinge-like motion that can be described as fully revolute in solution. The barriers to hinging, Δ<i>G</i> <sup>‡</sup>, are identical within experimental error: Δ<i>G</i> <sup>‡</sup> = 14.2-15.2 kcal/mol as judged by variable-temperature <sup>13</sup>C NMR spectroscopy. Consistent with conserved dynamic behavior and isosterism, other physical properties including hydrophobicity and solution/membrane diffusion constants are amenable to prediction.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"5 2","pages":"134-138"},"PeriodicalIF":3.7,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11950847/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143754895","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ACS Physical Chemistry AuPub Date : 2025-03-10DOI: 10.1021/acsphyschemau.4c0010310.1021/acsphyschemau.4c00103
Alexander J. Menke, Joseph H. Reibenspies, Casey J. Patterson-Gardner, Alexander M. Engstrom, R. Scott Lokey and Eric E. Simanek*,
{"title":"Choreoisosteres: Pseudoatom Variation in Macrocyclic Hinges Conserves Structure and Dynamics","authors":"Alexander J. Menke, Joseph H. Reibenspies, Casey J. Patterson-Gardner, Alexander M. Engstrom, R. Scott Lokey and Eric E. Simanek*, ","doi":"10.1021/acsphyschemau.4c0010310.1021/acsphyschemau.4c00103","DOIUrl":"https://doi.org/10.1021/acsphyschemau.4c00103https://doi.org/10.1021/acsphyschemau.4c00103","url":null,"abstract":"<p >Differing in pseudoatom, three macrocycles with isosteric substitutions (geminal dimethyl, cyclopropyl, cyclobutyl) can be described as choreoisosteres. Under ambient conditions, they share a dynamic hinge-like motion that can be described as fully revolute in solution. The barriers to hinging, Δ<i>G</i><sup>‡</sup>, are identical within experimental error: Δ<i>G</i><sup>‡</sup> = 14.2–15.2 kcal/mol as judged by variable-temperature <sup>13</sup>C NMR spectroscopy. Consistent with conserved dynamic behavior and isosterism, other physical properties including hydrophobicity and solution/membrane diffusion constants are amenable to prediction.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"5 2","pages":"134–138 134–138"},"PeriodicalIF":3.7,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsphyschemau.4c00103","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143696517","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ACS Physical Chemistry AuPub Date : 2025-03-07eCollection Date: 2025-05-28DOI: 10.1021/acsphyschemau.5c00007
Guillaume P Laurent, Samuel L Leonard, Mita Halder, Damien B Culver, Peng Xu, Mark S Gordon, Frédéric A Perras
{"title":"Preferred Orientation of a Physisorbed Molecular Catalyst and Implications for Selectivity.","authors":"Guillaume P Laurent, Samuel L Leonard, Mita Halder, Damien B Culver, Peng Xu, Mark S Gordon, Frédéric A Perras","doi":"10.1021/acsphyschemau.5c00007","DOIUrl":"https://doi.org/10.1021/acsphyschemau.5c00007","url":null,"abstract":"<p><p>Confinement effects in stereoselective catalysis have been the topic of prolonged inquiry. Results have been largely mixed, with confinement having been reported to both enhance and degrade selectivity. Our ability to understand the surface's impact on catalytic mechanisms, and thus selectivity, has been severely hindered by the low level of details commonly seen in the structures of supported metal complexes. Recent developments in sensitivity-enhanced NMR are revealing not only the molecular structure of surface sites but also their configuration, orientation, and proximities to neighboring molecules. In studying [Rh-(cyclooctadiene)-((<i>S</i>)-(-)-2-aminomethyl-1-ethyl-pyrrolidine)]-CF<sub>3</sub>SO<sub>3</sub> noncovalently immobilized to silica, an enantioselective hydrogenation catalyst, we observed a strong preference for a particular orientation of the complex relative to the support surface. We discuss how preferential adsorption may help reduce the number of competing reaction pathways and, in turn, have outsized effects on selectivity.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"5 3","pages":"293-301"},"PeriodicalIF":3.7,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12123549/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144200235","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ACS Physical Chemistry AuPub Date : 2025-03-07DOI: 10.1021/acsphyschemau.5c0000710.1021/acsphyschemau.5c00007
Guillaume P. Laurent, Samuel L. Leonard, Mita Halder, Damien B. Culver, Peng Xu, Mark S. Gordon and Frédéric A. Perras*,
{"title":"Preferred Orientation of a Physisorbed Molecular Catalyst and Implications for Selectivity","authors":"Guillaume P. Laurent, Samuel L. Leonard, Mita Halder, Damien B. Culver, Peng Xu, Mark S. Gordon and Frédéric A. Perras*, ","doi":"10.1021/acsphyschemau.5c0000710.1021/acsphyschemau.5c00007","DOIUrl":"https://doi.org/10.1021/acsphyschemau.5c00007https://doi.org/10.1021/acsphyschemau.5c00007","url":null,"abstract":"<p >Confinement effects in stereoselective catalysis have been the topic of prolonged inquiry. Results have been largely mixed, with confinement having been reported to both enhance and degrade selectivity. Our ability to understand the surface’s impact on catalytic mechanisms, and thus selectivity, has been severely hindered by the low level of details commonly seen in the structures of supported metal complexes. Recent developments in sensitivity-enhanced NMR are revealing not only the molecular structure of surface sites but also their configuration, orientation, and proximities to neighboring molecules. In studying [Rh(cyclooctadiene)((<i>S</i>)-(−)-2-aminomethyl-1-ethyl-pyrrolidine)]CF<sub>3</sub>SO<sub>3</sub> noncovalently immobilized to silica, an enantioselective hydrogenation catalyst, we observed a strong preference for a particular orientation of the complex relative to the support surface. We discuss how preferential adsorption may help reduce the number of competing reaction pathways and, in turn, have outsized effects on selectivity.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"5 3","pages":"293–301 293–301"},"PeriodicalIF":3.7,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsphyschemau.5c00007","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144146487","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}