Pub Date : 2024-10-22DOI: 10.1021/acs.jpclett.4c02500
Yanli Liu, Qiushuang Xu, Li Wang, Aihua Gao, Quanjiang Li, Shenghui Chen, Yanliang Zhao, Meishan Wang, Jun Jiang, Chuanyi Jia
Solvent polarity control as an efficient methodology to regulate the chiroptical properties, including spectral shape, width, intensity, wavelength, etc., has emerged as a novel frontier in optical materials design. However, the underling relationship connecting polarity to the optical property remains unclear. Herein, using state-of-the-art computations and the FC|VG model, the solvent effect on the chiroptical properties of bora[6]helicene was accurately and systematically computed to shed light on this issue. It is found that the vibronic coupling is crucial in explaining the spectral shape, width, and relative intensity of different peaks. Moreover, the intensity and position of the emission (EMI) and circularly polarized luminescence (CPL) are closely related to the polarity of the solvent. Intriguingly, we got a series of good linear relationships between polarity and EMI|CPL (|r| ≥ 0.95). Thus, this parameter can be used as a potential descriptor to estimate the intensity and position of EMI|CPL, leading to new strategies for designing fully colored fluorescent materials.
{"title":"Rational Control of Maximum EMI/CPL Intensity and Wavelength of Bora[6]helicene via Polarity and Vibronic Effects.","authors":"Yanli Liu, Qiushuang Xu, Li Wang, Aihua Gao, Quanjiang Li, Shenghui Chen, Yanliang Zhao, Meishan Wang, Jun Jiang, Chuanyi Jia","doi":"10.1021/acs.jpclett.4c02500","DOIUrl":"https://doi.org/10.1021/acs.jpclett.4c02500","url":null,"abstract":"<p><p>Solvent polarity control as an efficient methodology to regulate the chiroptical properties, including spectral shape, width, intensity, wavelength, etc., has emerged as a novel frontier in optical materials design. However, the underling relationship connecting polarity to the optical property remains unclear. Herein, using state-of-the-art computations and the FC|VG model, the solvent effect on the chiroptical properties of bora[6]helicene was accurately and systematically computed to shed light on this issue. It is found that the vibronic coupling is crucial in explaining the spectral shape, width, and relative intensity of different peaks. Moreover, the intensity and position of the emission (EMI) and circularly polarized luminescence (CPL) are closely related to the polarity of the solvent. Intriguingly, we got a series of good linear relationships between polarity and EMI|CPL (|<i>r</i>| ≥ 0.95). Thus, this parameter can be used as a potential descriptor to estimate the intensity and position of EMI|CPL, leading to new strategies for designing fully colored fluorescent materials.</p>","PeriodicalId":62,"journal":{"name":"The Journal of Physical Chemistry Letters","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142453516","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}
Pub Date : 2024-10-22DOI: 10.1021/acs.jpclett.4c02676
Dongsheng Qiu, Waqar Ali Memon, Hanjian Lai, Yunpeng Wang, Heng Li, Nan Zheng, Feng He
Within the realm of organic solar cells (OSCs), designing new high-efficiency polymer donors remains a significant challenge. Achieving the right balance in polymer backbone planarity is crucial: excessive planarity can lead to undesirable aggregation, while insufficient planarity can hinder the charge transport efficiency. In this study, we designed and synthesized an imidazole-based acceptor (A) unit for the first time and then investigated the impact of backbone planarity on charge transport capacity and power conversion efficiency (PCE). Backbone planarity was precisely tuned by incorporating isomeric alkyl chains on the thiophene π-bridge, resulting in four distinct polymer donors: MZC8-F, MZC8-Cl, MZEH-F, and MZEH-Cl. The results showed that the steric hindrance from the EH-branched alkyl chain induced backbone distortion and caused a blue-shift in the absorption spectrum. MZEH-Cl, with its poor planarity and excessively low HOMO energy level, achieved a PCE of just 7.6%. Through careful modulation, MZC8-Cl emerged as the most efficient, with a remarkable PCE of 17.3%, setting a new benchmark for imidazole-based polymer donors. This study not only deepens the understanding of the role of polymer backbone planarity in photovoltaic performance but also lays the groundwork for developing high-efficiency polymer donors.
{"title":"Synergistic Design of Imidazole-Based Polymer Donors for Enhanced Organic Solar Cell Efficiency","authors":"Dongsheng Qiu, Waqar Ali Memon, Hanjian Lai, Yunpeng Wang, Heng Li, Nan Zheng, Feng He","doi":"10.1021/acs.jpclett.4c02676","DOIUrl":"https://doi.org/10.1021/acs.jpclett.4c02676","url":null,"abstract":"Within the realm of organic solar cells (OSCs), designing new high-efficiency polymer donors remains a significant challenge. Achieving the right balance in polymer backbone planarity is crucial: excessive planarity can lead to undesirable aggregation, while insufficient planarity can hinder the charge transport efficiency. In this study, we designed and synthesized an imidazole-based acceptor (A) unit for the first time and then investigated the impact of backbone planarity on charge transport capacity and power conversion efficiency (PCE). Backbone planarity was precisely tuned by incorporating isomeric alkyl chains on the thiophene π-bridge, resulting in four distinct polymer donors: MZC8-F, MZC8-Cl, MZEH-F, and MZEH-Cl. The results showed that the steric hindrance from the EH-branched alkyl chain induced backbone distortion and caused a blue-shift in the absorption spectrum. MZEH-Cl, with its poor planarity and excessively low HOMO energy level, achieved a PCE of just 7.6%. Through careful modulation, MZC8-Cl emerged as the most efficient, with a remarkable PCE of 17.3%, setting a new benchmark for imidazole-based polymer donors. This study not only deepens the understanding of the role of polymer backbone planarity in photovoltaic performance but also lays the groundwork for developing high-efficiency polymer donors.","PeriodicalId":62,"journal":{"name":"The Journal of Physical Chemistry Letters","volume":null,"pages":null},"PeriodicalIF":6.475,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142486592","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}
Pub Date : 2024-10-22DOI: 10.1021/acs.jpclett.4c02638
Shiyan Gong, Peng Wang, Yuxiang Mo
In this study, we present a precise determination of the bond dissociation energy of CO2 using state-to-state resolved threshold fragment yield spectra at a photoexcitation wavelength of around 92 nm. Our findings show that the bond dissociation energy of CO2, CO2 → CO + O, is 43976.12(15) cm-1 or 526.0714(18) kJ/mol. Furthermore, by incorporating our previously measured bond dissociation energies for CO and O2, we determined the dissociation energy of CO2 into C + O2 and the CO2 atomization energy (CO2 → C + O + O) to be 92309.73(21) and 133578.92(18) cm-1 or 1104.2699(25) and 1597.9592(22) kJ/mol, respectively. Thus, the bond dissociation energies of CO2 for all channels now have uncertainties of 0.2 cm-1 or 0.002 kJ/mol. These results serve as reference points for the enthalpies of C atom and CO and CO2 molecules and provide benchmarks for high-level ab initio quantum chemistry calculations.
{"title":"Bond Dissociation Energy of CO<sub>2</sub> with Spectroscopic Accuracy Using State-to-State Resolved Threshold Fragment Yield Spectra.","authors":"Shiyan Gong, Peng Wang, Yuxiang Mo","doi":"10.1021/acs.jpclett.4c02638","DOIUrl":"https://doi.org/10.1021/acs.jpclett.4c02638","url":null,"abstract":"<p><p>In this study, we present a precise determination of the bond dissociation energy of CO<sub>2</sub> using state-to-state resolved threshold fragment yield spectra at a photoexcitation wavelength of around 92 nm. Our findings show that the bond dissociation energy of CO<sub>2</sub>, CO<sub>2</sub> → CO + O, is 43976.12(15) cm<sup>-1</sup> or 526.0714(18) kJ/mol. Furthermore, by incorporating our previously measured bond dissociation energies for CO and O<sub>2</sub>, we determined the dissociation energy of CO<sub>2</sub> into C + O<sub>2</sub> and the CO<sub>2</sub> atomization energy (CO<sub>2</sub> → C + O + O) to be 92309.73(21) and 133578.92(18) cm<sup>-1</sup> or 1104.2699(25) and 1597.9592(22) kJ/mol, respectively. Thus, the bond dissociation energies of CO<sub>2</sub> for all channels now have uncertainties of 0.2 cm<sup>-1</sup> or 0.002 kJ/mol. These results serve as reference points for the enthalpies of C atom and CO and CO<sub>2</sub> molecules and provide benchmarks for high-level <i>ab initio</i> quantum chemistry calculations.</p>","PeriodicalId":62,"journal":{"name":"The Journal of Physical Chemistry Letters","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142453513","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}
Pub Date : 2024-10-22DOI: 10.1021/acs.jpclett.4c02679
Alexander P Fellows, Ben John, Martin Wolf, Martin Thämer
Ultrathin molecular films are widespread in both natural and industrial settings, where details of the molecular structure such as density, out-of-plane tilt angles, and in-plane directionality determine their physicochemical properties. Many of these films possess important molecular-to-macroscopic heterogeneity in these structural parameters, which have traditionally been difficult to characterize. Here, we show how extending sum-frequency generation (SFG) microscopy measurements to higher dimensionality by azimuthal-scanning can extract the spatial variation in the three-dimensional molecular structure at an interface. We extend the commonly applied theoretical assumptions used to analyze SFG signals to the study of systems possessing in-plane anisotropy. This theoretical framework is then applied to a phase-separated mixed lipid monolayer to investigate the variation in molecular density and 3D orientation across the chirally packed lipid domains. The results show little variation in out-of-plane structure but a distinct micron-scale region at the domain boundaries with a reduction in both density and in-plane ordering.
{"title":"Extracting the Heterogeneous 3D Structure of Molecular Films Using Higher Dimensional SFG Microscopy.","authors":"Alexander P Fellows, Ben John, Martin Wolf, Martin Thämer","doi":"10.1021/acs.jpclett.4c02679","DOIUrl":"https://doi.org/10.1021/acs.jpclett.4c02679","url":null,"abstract":"<p><p>Ultrathin molecular films are widespread in both natural and industrial settings, where details of the molecular structure such as density, out-of-plane tilt angles, and in-plane directionality determine their physicochemical properties. Many of these films possess important molecular-to-macroscopic heterogeneity in these structural parameters, which have traditionally been difficult to characterize. Here, we show how extending sum-frequency generation (SFG) microscopy measurements to higher dimensionality by azimuthal-scanning can extract the spatial variation in the three-dimensional molecular structure at an interface. We extend the commonly applied theoretical assumptions used to analyze SFG signals to the study of systems possessing in-plane anisotropy. This theoretical framework is then applied to a phase-separated mixed lipid monolayer to investigate the variation in molecular density and 3D orientation across the chirally packed lipid domains. The results show little variation in out-of-plane structure but a distinct micron-scale region at the domain boundaries with a reduction in both density and in-plane ordering.</p>","PeriodicalId":62,"journal":{"name":"The Journal of Physical Chemistry Letters","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142453515","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}
Pub Date : 2024-10-22DOI: 10.1021/acs.jpclett.4c02141
Emmanuel Odella, Jonathan H Fetherolf, Maxim Secor, Lydia DiPaola, Rodrigo E Dominguez, Edwin J Gonzalez, Anton Y Khmelnitskiy, Gerdenis Kodis, Thomas L Groy, Thomas A Moore, Sharon Hammes-Schiffer, Ana L Moore
Bioinspired benzimidazole-phenol constructs with an intramolecular hydrogen bond connecting the phenol and the benzimidazole have been synthesized to study both proton-coupled electron transfer (PCET) and excited-state intramolecular proton transfer (ESIPT) processes. Strategic incorporation of a methyl group disrupts the coplanarity between the aromatic units, causing a pronounced twist, weakening the intramolecular hydrogen bond, decreasing the phenol redox potential, reducing the chemical reversibility, and quenching the fluorescence emission. Infrared spectroelectrochemistry and transient absorption spectroscopy confirm the formation of the oxidized product upon PCET and probe excited-state relaxation mechanisms, respectively. Density functional theory calculations of redox potentials corroborate the experimental findings. Additionally, time-dependent density functional theory calculations uncover the fluorescence quenching mechanism, showing that the nonradiative twisted intramolecular charge transfer state responsible for fluorescence quenching is more energetically favorable in the methyl-substituted system. Incorporating groups causing steric hindrance expands the design of biomimetic systems capable of performing both PCET and ESIPT.
{"title":"When a Twist Makes a Difference: Exploring PCET and ESIPT on a Nonplanar Hydrogen-Bonded Donor-Acceptor System.","authors":"Emmanuel Odella, Jonathan H Fetherolf, Maxim Secor, Lydia DiPaola, Rodrigo E Dominguez, Edwin J Gonzalez, Anton Y Khmelnitskiy, Gerdenis Kodis, Thomas L Groy, Thomas A Moore, Sharon Hammes-Schiffer, Ana L Moore","doi":"10.1021/acs.jpclett.4c02141","DOIUrl":"https://doi.org/10.1021/acs.jpclett.4c02141","url":null,"abstract":"<p><p>Bioinspired benzimidazole-phenol constructs with an intramolecular hydrogen bond connecting the phenol and the benzimidazole have been synthesized to study both proton-coupled electron transfer (PCET) and excited-state intramolecular proton transfer (ESIPT) processes. Strategic incorporation of a methyl group disrupts the coplanarity between the aromatic units, causing a pronounced twist, weakening the intramolecular hydrogen bond, decreasing the phenol redox potential, reducing the chemical reversibility, and quenching the fluorescence emission. Infrared spectroelectrochemistry and transient absorption spectroscopy confirm the formation of the oxidized product upon PCET and probe excited-state relaxation mechanisms, respectively. Density functional theory calculations of redox potentials corroborate the experimental findings. Additionally, time-dependent density functional theory calculations uncover the fluorescence quenching mechanism, showing that the nonradiative twisted intramolecular charge transfer state responsible for fluorescence quenching is more energetically favorable in the methyl-substituted system. Incorporating groups causing steric hindrance expands the design of biomimetic systems capable of performing both PCET and ESIPT.</p>","PeriodicalId":62,"journal":{"name":"The Journal of Physical Chemistry Letters","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142453533","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}
Pub Date : 2024-10-22DOI: 10.1021/acs.jpclett.4c02497
Steven D E Fried, Srijit Mukherjee, Yuezhi Mao, Steven G Boxer
NAD(P)H cofactors are found in all forms of life and are essential for electron and hydrogen atom transfer. The linear response of a carbon-deuterium (C-D) vibration based on the vibrational Stark effect can facilitate measurements of electric fields for critical biological reactions including cofactor-mediated hydride transfer. We find both inter- and intramolecular electric fields influence the C-D frequency in NAD(P)H and nicotinamide-like models where the reactive C4-hydrogen has been deuterated. Hence, the C-D frequency can report both environmental electrostatics and conformational changes of the nicotinamide ring. Conformation-dependent effects are mediated through space as electrostatic effects, rather than through-bond. A Stark tuning rate of ∼0.57 cm-1/(MV/cm) was determined using both experimental and computational approaches, including vibrational solvatochromism, molecular dynamics simulations, and in silico Stark calculations. The vibrational probe's Stark tuning rate is shown to be robust and suitable for measuring fields along hydride transfer reaction coordinates in enzymes.
{"title":"Environment- and Conformation-Induced Frequency Shifts of C-D Vibrational Stark Probes in NAD(P)H Cofactors.","authors":"Steven D E Fried, Srijit Mukherjee, Yuezhi Mao, Steven G Boxer","doi":"10.1021/acs.jpclett.4c02497","DOIUrl":"https://doi.org/10.1021/acs.jpclett.4c02497","url":null,"abstract":"<p><p>NAD(P)H cofactors are found in all forms of life and are essential for electron and hydrogen atom transfer. The linear response of a carbon-deuterium (C-D) vibration based on the vibrational Stark effect can facilitate measurements of electric fields for critical biological reactions including cofactor-mediated hydride transfer. We find both inter- and intramolecular electric fields influence the C-D frequency in NAD(P)H and nicotinamide-like models where the reactive C4-hydrogen has been deuterated. Hence, the C-D frequency can report both environmental electrostatics and conformational changes of the nicotinamide ring. Conformation-dependent effects are mediated through space as electrostatic effects, rather than through-bond. A Stark tuning rate of ∼0.57 cm<sup>-1</sup>/(MV/cm) was determined using both experimental and computational approaches, including vibrational solvatochromism, molecular dynamics simulations, and <i>in silico</i> Stark calculations. The vibrational probe's Stark tuning rate is shown to be robust and suitable for measuring fields along hydride transfer reaction coordinates in enzymes.</p>","PeriodicalId":62,"journal":{"name":"The Journal of Physical Chemistry Letters","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142453514","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}
Pub Date : 2024-10-21DOI: 10.1021/acs.jpclett.4c02426
Yilian Xi, Hanqing Shi, Jingwei Zhang, Heping Li, Ningyan Cheng, Hang Xu, Jiaqi Liu, Keren Li, Huaiming Guo, Haifeng Feng, Jianfeng Wang, Weichang Hao, Yi Du
Discoveries of above-room-temperature intrinsic ferromagnetism in two-dimensional (2D) van der Waals (vdW) materials offer a platform for studying fundamental 2D magnetism and spintronic devices, especially the recently discovered above-room-temperature 2D vdW Fe3GaTe2 (FGaT). However, the magnetic mechanism in FGaT remains elusive. Here, a detailed investigation using magnetic force microscopy on the thickness-dependent magnetic behavior of FGaT single crystals is reported. The Heisenberg exchange interaction constant (J) at room temperature is determined to be 1.32836 × 10–12 J/m. Our study combining angle-resolved photoemission spectroscopy and density functional theory suggests that the high Curie temperature in FGaT is attributed to the shift of the localized Fe d band toward the Fermi level as well as the enhanced magnetic exchange effect due to the strong itinerant ability of Fe. This work sheds light on the understanding of magnetism in FGaT and provides a promising platform to investigate the mechanisms of 2D magnetic materials.
{"title":"Large Magnetic Anisotropy in van der Waals Ferromagnet Fe3GaTe2 above Room Temperature","authors":"Yilian Xi, Hanqing Shi, Jingwei Zhang, Heping Li, Ningyan Cheng, Hang Xu, Jiaqi Liu, Keren Li, Huaiming Guo, Haifeng Feng, Jianfeng Wang, Weichang Hao, Yi Du","doi":"10.1021/acs.jpclett.4c02426","DOIUrl":"https://doi.org/10.1021/acs.jpclett.4c02426","url":null,"abstract":"Discoveries of above-room-temperature intrinsic ferromagnetism in two-dimensional (2D) van der Waals (vdW) materials offer a platform for studying fundamental 2D magnetism and spintronic devices, especially the recently discovered above-room-temperature 2D vdW Fe<sub>3</sub>GaTe<sub>2</sub> (FGaT). However, the magnetic mechanism in FGaT remains elusive. Here, a detailed investigation using magnetic force microscopy on the thickness-dependent magnetic behavior of FGaT single crystals is reported. The Heisenberg exchange interaction constant (<i>J</i>) at room temperature is determined to be 1.32836 × 10<sup>–12</sup> J/m. Our study combining angle-resolved photoemission spectroscopy and density functional theory suggests that the high Curie temperature in FGaT is attributed to the shift of the localized Fe <i>d</i> band toward the Fermi level as well as the enhanced magnetic exchange effect due to the strong itinerant ability of Fe. This work sheds light on the understanding of magnetism in FGaT and provides a promising platform to investigate the mechanisms of 2D magnetic materials.","PeriodicalId":62,"journal":{"name":"The Journal of Physical Chemistry Letters","volume":null,"pages":null},"PeriodicalIF":6.475,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142452016","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}
Pub Date : 2024-10-21DOI: 10.1021/acs.jpclett.4c02654
Vysakh Ramachandran, William Brown, Christopher Gayvert, Davit A. Potoyan
Liquid–liquid phase separation of proteins and nucleic acids into condensate phases is a versatile mechanism for ensuring the compartmentalization of cellular biochemistry. RNA molecules play critical roles in these condensates, particularly in transcriptional regulation and stress responses, exhibiting a wide range of thermodynamic and dynamic behaviors. However, deciphering the molecular grammar that governs the stability and dynamics of protein–RNA condensates remains challenging due to the multicomponent and heterogeneous nature of condensates. In this study, we employ atomistic simulations of 20 distinct mixtures containing minimal RNA and peptide fragments which allows us to dissect the phase-separating affinities of all 20 amino acids in the presence of RNA. Our findings elucidate chemically specific interactions, hydration profiles, and ionic effects that synergistically promote or suppress protein–RNA phase separation. We map a ternary phase diagram of interactions, identifying four distinct groups of residues that promote, maintain, suppress, and disrupt protein–RNA clusters.
{"title":"Nucleoprotein Phase-Separation Affinities Revealed via Atomistic Simulations of Short Peptide and RNA Fragments","authors":"Vysakh Ramachandran, William Brown, Christopher Gayvert, Davit A. Potoyan","doi":"10.1021/acs.jpclett.4c02654","DOIUrl":"https://doi.org/10.1021/acs.jpclett.4c02654","url":null,"abstract":"Liquid–liquid phase separation of proteins and nucleic acids into condensate phases is a versatile mechanism for ensuring the compartmentalization of cellular biochemistry. RNA molecules play critical roles in these condensates, particularly in transcriptional regulation and stress responses, exhibiting a wide range of thermodynamic and dynamic behaviors. However, deciphering the molecular grammar that governs the stability and dynamics of protein–RNA condensates remains challenging due to the multicomponent and heterogeneous nature of condensates. In this study, we employ atomistic simulations of 20 distinct mixtures containing minimal RNA and peptide fragments which allows us to dissect the phase-separating affinities of all 20 amino acids in the presence of RNA. Our findings elucidate chemically specific interactions, hydration profiles, and ionic effects that synergistically promote or suppress protein–RNA phase separation. We map a ternary phase diagram of interactions, identifying four distinct groups of residues that promote, maintain, suppress, and disrupt protein–RNA clusters.","PeriodicalId":62,"journal":{"name":"The Journal of Physical Chemistry Letters","volume":null,"pages":null},"PeriodicalIF":6.475,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142452014","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}
Pub Date : 2024-10-21DOI: 10.1021/acs.jpclett.4c02598
Xingyue Guan, Yunqiang Bian, Zilong Guo, Jian Zhang, Yi Cao, Wenfei Li, Wei Wang
Catch-bonds, whereby noncovalent ligand–receptor interactions are counterintuitively reinforced by tensile forces, play a major role in cell adhesion under mechanical stress. A basic prerequisite for catch-bond formation, as implicated in classic catch-bond models, is that force-induced remodeling of the ligand binding interface occurs prior to bond rupture. However, what strategy receptor proteins utilize to meet such specific kinetic control remains elusive. Here we report a bidirectional allostery mechanism of catch-bond formation based on theoretical and molecular dynamics simulation studies. Binding of ligand allosterically reduces the threshold force for unlocking of otherwise stably folded force-sensing element (i.e., forward allostery), so that a much smaller tensile force can trigger the conformational switching of receptor protein to high binding-strength state via backward allosteric coupling before bond rupture. Such bidirectional allostery fulfills the specific kinetic control required by catch-bond formation and is likely to be commonly utilized in cell adhesion. The essential thermodynamic and kinetic features of receptor proteins essential for catch-bond formation were identified.
{"title":"Bidirectional Allostery Mechanism in Catch-Bond Formation of CD44 Mediated Cell Adhesion","authors":"Xingyue Guan, Yunqiang Bian, Zilong Guo, Jian Zhang, Yi Cao, Wenfei Li, Wei Wang","doi":"10.1021/acs.jpclett.4c02598","DOIUrl":"https://doi.org/10.1021/acs.jpclett.4c02598","url":null,"abstract":"Catch-bonds, whereby noncovalent ligand–receptor interactions are counterintuitively reinforced by tensile forces, play a major role in cell adhesion under mechanical stress. A basic prerequisite for catch-bond formation, as implicated in classic catch-bond models, is that force-induced remodeling of the ligand binding interface occurs prior to bond rupture. However, what strategy receptor proteins utilize to meet such specific kinetic control remains elusive. Here we report a bidirectional allostery mechanism of catch-bond formation based on theoretical and molecular dynamics simulation studies. Binding of ligand allosterically reduces the threshold force for unlocking of otherwise stably folded force-sensing element (i.e., forward allostery), so that a much smaller tensile force can trigger the conformational switching of receptor protein to high binding-strength state via backward allosteric coupling before bond rupture. Such bidirectional allostery fulfills the specific kinetic control required by catch-bond formation and is likely to be commonly utilized in cell adhesion. The essential thermodynamic and kinetic features of receptor proteins essential for catch-bond formation were identified.","PeriodicalId":62,"journal":{"name":"The Journal of Physical Chemistry Letters","volume":null,"pages":null},"PeriodicalIF":6.475,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142452029","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}
Pub Date : 2024-10-21DOI: 10.1021/acs.jpclett.4c01796
Rafael Neri Prystaj Colombo, Steffane Q. Nascimento, Frank Nelson Crespilho
For a long time, the prevailing view in the scientific community was that proteins, being complex macromolecules composed of amino acid chains linked by peptide bonds, adopt folded structure with insulating or semiconducting properties, with high bandgaps. However, recent discoveries of unexpectedly high conductance levels, reaching values in the range of dozens of nanosiemens (nS) in proteins, have challenged this conventional understanding. In this study, we used scanning tunneling microscopy (STM) to explore the single-entity conductance properties of enzymatic channels, focusing on bilirubin oxidase (BOD) as a model metalloprotein. By immobilizing BOD on a conductive carbon surface, we discern its preferred orientation, facilitating the formation of electronic and ionic channels. These channels show efficient electron transport (ETp), with apparent conductance up to the 15 nS range. Notably, these conductance pathways are localized, minimizing electron transport barriers due to solvents and ions, underscoring BOD’s redox versatility. Furthermore, electron transfer (ET) within the BOD occurs via preferential pathways. The alignment of the conductance channels with hydrophilicity maps, molecular vacancies, and regions accessible to electrolytes explains the observed conductance values. Additionally, BOD exhibits redox activity, with its active center playing a critical role in the ETp process. These findings significantly advance our understanding of the intricate mechanisms that govern ETp processes in proteins, offering new insights into the conductance of metalloproteins.
{"title":"Conductance Channels in a Single-Entity Enzyme","authors":"Rafael Neri Prystaj Colombo, Steffane Q. Nascimento, Frank Nelson Crespilho","doi":"10.1021/acs.jpclett.4c01796","DOIUrl":"https://doi.org/10.1021/acs.jpclett.4c01796","url":null,"abstract":"For a long time, the prevailing view in the scientific community was that proteins, being complex macromolecules composed of amino acid chains linked by peptide bonds, adopt folded structure with insulating or semiconducting properties, with high bandgaps. However, recent discoveries of unexpectedly high conductance levels, reaching values in the range of dozens of nanosiemens (nS) in proteins, have challenged this conventional understanding. In this study, we used scanning tunneling microscopy (STM) to explore the single-entity conductance properties of enzymatic channels, focusing on bilirubin oxidase (BOD) as a model metalloprotein. By immobilizing BOD on a conductive carbon surface, we discern its preferred orientation, facilitating the formation of electronic and ionic channels. These channels show efficient electron transport (ETp), with apparent conductance up to the 15 nS range. Notably, these conductance pathways are localized, minimizing electron transport barriers due to solvents and ions, underscoring BOD’s redox versatility. Furthermore, electron transfer (ET) within the BOD occurs via preferential pathways. The alignment of the conductance channels with hydrophilicity maps, molecular vacancies, and regions accessible to electrolytes explains the observed conductance values. Additionally, BOD exhibits redox activity, with its active center playing a critical role in the ETp process. These findings significantly advance our understanding of the intricate mechanisms that govern ETp processes in proteins, offering new insights into the conductance of metalloproteins.","PeriodicalId":62,"journal":{"name":"The Journal of Physical Chemistry Letters","volume":null,"pages":null},"PeriodicalIF":6.475,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142452090","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}