The Journal of Physical Chemistry B最新文献

Probing Bioinorganic Electron Spin Decoherence Mechanisms with an Fe₂S₂ Metalloprotein. 用 Fe2S2 金属蛋白探测生物无机电子自旋退相干机制

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2024-10-11 DOI: 10.1021/acs.jpcb.4c06186

Christian A Totoiu, Alec H Follmer, Paul H Oyala, Ryan G Hadt

{"title":"Probing Bioinorganic Electron Spin Decoherence Mechanisms with an Fe2S2 Metalloprotein.","authors":"Christian A Totoiu, Alec H Follmer, Paul H Oyala, Ryan G Hadt","doi":"10.1021/acs.jpcb.4c06186","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c06186","url":null,"abstract":"Recent efforts have sought to develop paramagnetic molecular quantum bits (qubits) as a means to store and manipulate quantum information. Emerging structure-property relationships have shed light on electron spin decoherence mechanisms. While insights within molecular quantum information science have derived from synthetic systems, biomolecular platforms would allow for the study of decoherence phenomena in more complex chemical environments and further leverage molecular biology and protein engineering approaches. Here we have employed the exchange-coupled ST = 1/2 Fe2S2 active site of putidaredoxin, an electron transfer metalloprotein, as a platform for fundamental mechanistic studies of electron spin decoherence toward spin-based biological quantum sensing. At low temperatures, decoherence rates were anisotropic, reflecting a hyperfine-dominated decoherence mechanism, standing in contrast to the anisotropy of molecular systems observed previously. This mechanism provided a pathway for probing spatial effects on decoherence, such as protein vs solvent contributions. Furthermore, we demonstrated spatial sensitivity to single point mutations via site-directed mutagenesis and temporal sensitivity for monitoring solvent isotope exchange. Thus, this study demonstrates a step toward the design and construction of biomolecular quantum sensors.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142405742","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}

引用次数: 0

Absorption of Polypropylene in Dipalmitoylphosphatidylcholine Membranes: The Role of Molecular Weight and Initial Configuration of Polymer Chains. 聚丙烯在二棕榈酰磷脂酰胆碱膜中的吸收：分子量和聚合物链初始构型的作用。

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2024-10-10 Epub Date: 2024-09-25 DOI: 10.1021/acs.jpcb.4c05035

Isabella Munafò, Dino Costa, Giuseppe Milano, Gianmarco Munaò

{"title":"Absorption of Polypropylene in Dipalmitoylphosphatidylcholine Membranes: The Role of Molecular Weight and Initial Configuration of Polymer Chains.","authors":"Isabella Munafò, Dino Costa, Giuseppe Milano, Gianmarco Munaò","doi":"10.1021/acs.jpcb.4c05035","DOIUrl":"10.1021/acs.jpcb.4c05035","url":null,"abstract":"We study by molecular dynamics simulations the absorption of polypropylene (PP) chains within a dipalmitoylphosphatidylcholine (DPPC) lipid membrane in aqueous solvent. DPPC represents the most abundant phospholipid in biological membranes, while PP is one of the most common synthetic polymers diffused in the anthropic environment. By following in detail the absorption process, and the corresponding structural modification undergone by the membrane, we show how the initial configuration and the PP molecular weight determine the overall behavior of the system. Specifically, if PP chains initially lie on the DPPC surface, they are fully absorbed; likewise, polymers initially included within the membrane cannot escape from. On the other hand, if polymers are placed sufficiently apart from the membrane, they have time to join together and coalesce into a few nanoparticles. At contact, such nanoparticles may completely dissolve (for low molecular weight) and then be absorbed. For high molecular weight, not all of them dissolve, and therefore the system attains a condition in which some of the chains are absorbed, while others form a residual nanoparticle staying outside (but in contact with) the membrane. Such a state─albeit energetically unfavorable with respect to a condition in which all PP chains are absorbed─remains stable, at the least over a substantial simulation time, extending in our study up to 1.6 μs. The tendency for polymers to spontaneously form aggregates, which then prefer to stay in contact with the membrane, is further corroborated by calculation of the DPPC-nanoparticle potential of mean force.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142337385","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}

引用次数: 0

Chromophore Structural Change during the Photocycle of a Light-Driven Cl^- Pump from Mastigocladopsis repens: A Cryogenic Raman Study. 来自 Mastigocladopsis repens 的光驱动 Cl- 泵在光周期中的发色团结构变化：低温拉曼研究。

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2024-10-10 Epub Date: 2024-10-01 DOI: 10.1021/acs.jpcb.4c04136

Kana Miyazaki, Takashi Kikukawa, Masashi Unno, Tomotsumi Fujisawa

{"title":"Chromophore Structural Change during the Photocycle of a Light-Driven Cl- Pump from Mastigocladopsis repens: A Cryogenic Raman Study.","authors":"Kana Miyazaki, Takashi Kikukawa, Masashi Unno, Tomotsumi Fujisawa","doi":"10.1021/acs.jpcb.4c04136","DOIUrl":"10.1021/acs.jpcb.4c04136","url":null,"abstract":"Microbial rhodopsins are the most widely distributed photoreceptors that bind a retinal Schiff base chromophore. Among them, a light-driven Cl- pump discovered from Mastigocladopsis repens (MrHR) is distinctive in that it has the structural features of both H+ and Cl- pumps. While the photocycle has been characterized by light-induced changes of the absorption spectrum, the structural changes of the retinal chromophore remain largely unknown. In this study, we examined the chromophore structural changes of MrHR by using cryogenic Raman spectroscopy. We observed five photointermediates─K, L, N1, N2, and MrHR'─that show distinct vibrational spectra, indicating atypical chromophore structures, e.g., small distortion in the K intermediate and Schiff base configurational change in the MrHR' intermediate. Based on the Raman spectra of two N intermediates (N1 and N2), we propose that N1 is the Cl--bound state and N2 is the Cl--unbound state, which are responsible for the Cl- release and uptake, respectively, to achieve Cl- pumping.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142337388","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}

引用次数: 0

Clathrin-Mediated Endocytosis of Multiple Nanoparticles Tends to Be Less Cooperative: A Computational Study. Clathrin 介导的多个纳米颗粒的内吞合作性趋于降低：计算研究

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2024-10-10 Epub Date: 2024-10-01 DOI: 10.1021/acs.jpcb.4c05025

Ye Li, Yezhuo Zhang, Zhun Zhang, Man Zhang, Xinhui Niu, Xinyi Mao, Tongtao Yue, Xianren Zhang

{"title":"Clathrin-Mediated Endocytosis of Multiple Nanoparticles Tends to Be Less Cooperative: A Computational Study.","authors":"Ye Li, Yezhuo Zhang, Zhun Zhang, Man Zhang, Xinhui Niu, Xinyi Mao, Tongtao Yue, Xianren Zhang","doi":"10.1021/acs.jpcb.4c05025","DOIUrl":"10.1021/acs.jpcb.4c05025","url":null,"abstract":"The internalization of nanoparticles is of great significance for their biological applications. Clathrin-mediated endocytosis (CME) is one of the main endocytic pathways. However, there is still a lack of a fundamental understanding regarding the internalization of multiple nanoparticles via CME. Therefore, in this study, we conducted computational investigations to uncover detailed molecular mechanisms and kinetic pathways for differently shaped nanoparticles in the presence of clathrin. Particular focus is given to understanding the CME of multiple-nanoparticle systems. We found that unlike receptor-mediated endocytosis, multiple nanoparticles did not get cooperatively wrapped by the membrane but tended to undergo independent endocytosis in the presence of clathrin. To further investigate the endocytosis mechanism, we studied the effects of clathrins, nanoparticle shape, nanoparticle size, nanoparticle arrangement, and membrane surface tension. The self-assembly of clathrin prefers independent endocytosis for multiple nanoparticles. Besides, the cooperative behavior is weak with increasing nanoparticle-shape anisotropy. However, when the membrane tension is reduced, the endocytosis pathway for multiple nanoparticles is cooperative endocytosis. Moreover, we found that the self-assembly of clathrins reduces the critical size of nanoparticles to undergo cooperative wrapping by the cell membrane. Our results provide valuable insights into the molecular mechanisms of multiple nanoparticles through CME and offer useful guidance for the design of nanoparticles as drug/gene delivery carriers.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142337389","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}

引用次数: 0

Deciphering the Interdomain Coupling in a Gram-Negative Bacterial Membrane Insertase. 解密革兰氏阴性细菌膜插入酶的域间耦合。

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2024-10-10 Epub Date: 2024-09-27 DOI: 10.1021/acs.jpcb.4c02824

Adithya Polasa, Shadi A Badiee, Mahmoud Moradi

{"title":"Deciphering the Interdomain Coupling in a Gram-Negative Bacterial Membrane Insertase.","authors":"Adithya Polasa, Shadi A Badiee, Mahmoud Moradi","doi":"10.1021/acs.jpcb.4c02824","DOIUrl":"10.1021/acs.jpcb.4c02824","url":null,"abstract":"YidC is a membrane protein that plays an important role in inserting newly generated proteins into lipid membranes. The Sec-dependent complex is responsible for inserting proteins into the lipid bilayer in bacteria. YidC facilitates the insertion and folding of membrane proteins, both in conjunction with the Sec complex and independently. Additionally, YidC acts as a chaperone during the folding of proteins. Multiple investigations have conclusively shown that Gram-positive bacterial YidC has Sec-independent insertion mechanisms. Through the use of microsecond-level all-atom molecular dynamics (MD) simulations, we have carried out an in-depth investigation of the YidC protein originating from Gram-negative bacteria. This research sheds light on the significance of multiple domains of the YidC structure at a detailed molecular level by utilizing equilibrium MD simulations. Specifically, multiple models of YidC embedded in the lipid bilayer were constructed to characterize the critical role of the C2 loop and the periplasmic domain (PD) present in Gram-negative YidC, which is absent in its Gram-positive counterpart. Based on our results, the C2 loop plays a role in the overall stabilization of the protein, most notably in the transmembrane (TM) region, and it also has an allosteric influence on the PD region. We have found critical inter- and intradomain interactions that contribute to the stability of the protein and its function. Finally, our study provides a hypothetical Sec-independent insertion mechanism for Gram-negative bacterial YidC.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142337391","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}

引用次数: 0

Final E₅ to E₈ Steps in the Nitrogenase Mechanism for Nitrogen Fixation. 固氮酶固氮机制的最后 E5 至 E8 步骤。

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2024-10-10 Epub Date: 2024-09-30 DOI: 10.1021/acs.jpcb.4c04331

Per E M Siegbahn

引用次数: 0

Investigating Different Dynamic pHP1α States in Their KCl-Mediated Liquid-Liquid Phase Separation (LLPS) Using Solid-State NMR (SSNMR) and Molecular Dynamic (MD) Simulations. 利用固态核磁共振 (SSNMR) 和分子动力学 (MD) 模拟研究 pHP1α 在其 KCl 介导的液-液相分离 (LLPS) 中的不同动态状态。

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2024-10-10 DOI: 10.1021/acs.jpcb.4c03749

Sze Yuet Chin, Yinglu Chen, Lei Zhao, Xinyi Liu, Choon-Peng Chng, Aghil Soman, Lars Nordenskiöld, Changjin Huang, Xiangyan Shi, Kai Xue

{"title":"Investigating Different Dynamic pHP1α States in Their KCl-Mediated Liquid-Liquid Phase Separation (LLPS) Using Solid-State NMR (SSNMR) and Molecular Dynamic (MD) Simulations.","authors":"Sze Yuet Chin, Yinglu Chen, Lei Zhao, Xinyi Liu, Choon-Peng Chng, Aghil Soman, Lars Nordenskiöld, Changjin Huang, Xiangyan Shi, Kai Xue","doi":"10.1021/acs.jpcb.4c03749","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c03749","url":null,"abstract":"Chromatin phase separation is dynamically regulated by many factors, such as post-translational modifications and effector proteins, and plays a critical role in genomic activities. The liquid-liquid phase separation (LLPS) of chromatin and/or effector proteins has been observed both in vitro and in vivo. However, the underlying mechanisms are largely unknown, and elucidating the physicochemical properties of the phase-separated complexes remains technically challenging. In this study, we detected dynamic, viscous, and intermediate components within the phosphorylated heterochromatin protein 1α (pHP1α) phase-separated system by using modified solid-state NMR (SSNMR) pulse sequences. The basis of these sequences relies on the different time scale of motion detected by heteronuclear Overhauser effect (hetNOE), scalar coupling-based, and dipolar coupling-based transfer schemes in NMR. In comparison to commonly utilized scalar coupling-based methods for studying the dynamic components in phase-separated systems, hetNOE offers more direct insight into molecular dynamics. NMR signals from the three different states in the protein gel were selectively excited and individually studied. Combined with molecular dynamics (MD) simulations, our findings indicate that at low KCl concentration (30 mM), the protein gel displays reduced molecular motion. Conversely, an increase in molecular motion was observed at a high KCl concentration (150 mM), which we attribute to the resultant intermolecular electrostatic interactions regulated by KCl.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142386431","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}

引用次数: 0

Exploring Unusual Confined Chemistry: Excited-State Proton Transfer Reaction in Supported Liquid Membrane with Deep Eutectic Solvents. 探索非同寻常的封闭化学：深共晶溶剂支撑液膜中的受激态质子转移反应。

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2024-10-10 Epub Date: 2024-09-28 DOI: 10.1021/acs.jpcb.4c03517

Sangeeta, Arnab Sil, Vikash Singh, Renu Bhati, Biswajit Guchhait

{"title":"Exploring Unusual Confined Chemistry: Excited-State Proton Transfer Reaction in Supported Liquid Membrane with Deep Eutectic Solvents.","authors":"Sangeeta, Arnab Sil, Vikash Singh, Renu Bhati, Biswajit Guchhait","doi":"10.1021/acs.jpcb.4c03517","DOIUrl":"10.1021/acs.jpcb.4c03517","url":null,"abstract":"Supported liquid membrane (SLM) incorporating ionic liquids (ILs) or deep eutectic solvents (DESs) offers a promising method for ion and (bio)chemical separations and CO2 capture. However, a molecular understanding of whether chemical reactions occur in these confined media is crucial. We report excited-state proton transfer (ESPT) reaction of a photoacid, HPTS, in various DES-based SLMs (pore size ∼280 nm) using steady-state and time-resolved fluorescence spectroscopy. Our findings reveal that, while the ESPT is unfavorable in bulk DESs, it occurs substantially in SLM-containing DESs. Time-resolved area normalized emission spectra (TRANES) show that ESPT time ranges from 2.6 to 7.5 ns and is greatly affected by changes in DES constituents. The results suggest that HPTS interacts with ordered DES structures formed by long-range interfacial effects in membrane pores, making it suitable for ESPT. Furthermore, it is found that the dynamics of solvent relaxation in confined DESs are significantly slower than in bulk liquids. This observation, together with a large red-edge excitation shift, supports the impact of long-range interfacial effects on the DES structure inside membrane pores. Given the task-specific properties of DESs, the incorporation of these solvents into SLM pores can be a useful strategy for investigating new chemical processes.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142337396","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}

引用次数: 0

How Unnatural Amino Acids in Antimicrobial Peptides Change Interactions with Lipid Model Membranes. 抗菌肽中的非天然氨基酸如何改变与脂质模型膜的相互作用？

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2024-10-10 Epub Date: 2024-09-27 DOI: 10.1021/acs.jpcb.4c04152

Saheli Mitra, Mei-Tung Chen, Francisca Stedman, Jedidiah Hernandez, Grace Kumble, Xi Kang, Churan Zhang, Grace Tang, Ian Daugherty, Wanqing Liu, Jeremy Ocloo, Kevin Raphael Klucznik, Alexander Anzhi Li, Frank Heinrich, Berthony Deslouches, Stephanie Tristram-Nagle

{"title":"How Unnatural Amino Acids in Antimicrobial Peptides Change Interactions with Lipid Model Membranes.","authors":"Saheli Mitra, Mei-Tung Chen, Francisca Stedman, Jedidiah Hernandez, Grace Kumble, Xi Kang, Churan Zhang, Grace Tang, Ian Daugherty, Wanqing Liu, Jeremy Ocloo, Kevin Raphael Klucznik, Alexander Anzhi Li, Frank Heinrich, Berthony Deslouches, Stephanie Tristram-Nagle","doi":"10.1021/acs.jpcb.4c04152","DOIUrl":"10.1021/acs.jpcb.4c04152","url":null,"abstract":"This study investigates the potential of antimicrobial peptides (AMPs) as alternatives to combat antibiotic resistance, with a focus on two AMPs containing unnatural amino acids (UAAs), E2-53R (16 AAs) and LE-54R (14 AAs). In both peptides, valine is replaced by norvaline (Nva), and tryptophan is replaced by 1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid (Tic). Microbiological studies reveal their potent activity against both Gram-negative (G(-)) and Gram-positive (G(+)) bacteria without any toxicity to eukaryotic cells at test concentrations up to 32 μM. Circular dichroism (CD) spectroscopy indicates that these peptides maintain α-helical structures when interacting with G(-) and G(+) lipid model membranes (LMMs), a feature linked to their efficacy. X-ray diffuse scattering (XDS) demonstrates a softening of G(-), G(+) and eukaryotic (Euk33) LMMs and a nonmonotonic decrease in chain order as a potential determinant for bacterial membrane destabilization. Additionally, XDS finds a significant link between both peptides' interfacial location in G(-) and G(+) LMMs and their efficacy. Neutron reflectometry (NR) confirms the AMP locations determined using XDS. Lack of toxicity in eukaryotic cells may be related to their loss of α-helicity and their hydrocarbon location in Euk33 LMMs. Both AMPs with UAAs offer a novel strategy to wipe out antibiotic-resistant strains while maintaining human cells. These findings are compared with previously published data on E2-35, which consists of the natural amino acids arginine, tryptophan, and valine.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142337398","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}

引用次数: 0

Large Scale Simulations of Photosynthetic Antenna Systems: Interplay of Cooperativity and Disorder. 光合天线系统的大规模模拟：合作与无序的相互作用。

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2024-10-10 Epub Date: 2024-10-01 DOI: 10.1021/acs.jpcb.4c02406

Alessia Valzelli, Alice Boschetti, Francesco Mattiotti, Armin Kargol, Coleman Green, Fausto Borgonovi, G Luca Celardo

{"title":"Large Scale Simulations of Photosynthetic Antenna Systems: Interplay of Cooperativity and Disorder.","authors":"Alessia Valzelli, Alice Boschetti, Francesco Mattiotti, Armin Kargol, Coleman Green, Fausto Borgonovi, G Luca Celardo","doi":"10.1021/acs.jpcb.4c02406","DOIUrl":"10.1021/acs.jpcb.4c02406","url":null,"abstract":"Large-scale simulations of light-matter interaction in natural photosynthetic antenna complexes containing more than one hundred thousands of chlorophyll molecules, comparable with natural size, have been performed. Photosynthetic antenna complexes present in Green sulfur bacteria and Purple bacteria have been analyzed using a radiative non-Hermitian Hamiltonian, well-known in the field of quantum optics, instead of the widely used dipole-dipole Frenkel Hamiltonian. This approach allows us to study ensembles of emitters beyond the small volume limit (system size much smaller than the absorbed wavelength), where the Frenkel Hamiltonian fails. When analyzed on a large scale, such structures display superradiant states much brighter than their single components. An analysis of the robustness to static disorder and dynamical (thermal) noise shows that exciton coherence in the whole photosynthetic complex is larger than the coherence found in its parts. This provides evidence that the photosynthetic complex as a whole plays a predominant role in sustaining coherences in the system even at room temperature. Our results allow a better understanding of natural photosynthetic antennae and could drive experiments to verify how the response to electromagnetic radiation depends on the size of the photosynthetic antenna.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142337401","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}

引用次数: 0