ACS Physical Chemistry Au最新文献

{"title":"Two-Dimensional Infrared Spectroscopy Resolves the Vibrational Landscape in Donor-Bridge-Acceptor Complexes with Site-Specific Isotopic Labeling.","authors":"James D Shipp, Ricardo J Fernández-Terán, Alexander J Auty, Heather Carson, Andrew J Sadler, Michael Towrie, Igor V Sazanovich, Paul M Donaldson, Anthony J H M Meijer, Julia A Weinstein","doi":"10.1021/acsphyschemau.4c00073","DOIUrl":"10.1021/acsphyschemau.4c00073","url":null,"abstract":"<p><p>Donor-bridge-acceptor complexes (D-B-A) are important model systems for understanding of light-induced processes. Here, we apply two-color two-dimensional infrared (2D-IR) spectroscopy to D-B-A complexes with a <i>trans</i>-Pt(II) acetylide bridge (D-C≡C-Pt-C≡C-A) to uncover the mechanism of vibrational energy redistribution (IVR). Site-selective ¹³C isotopic labeling of the bridge is used to decouple the acetylide modes positioned on either side of the Pt-center. Decoupling of the D-acetylide- from the A-acetylide- enables site-specific investigation of vibrational energy transfer (VET) rates, dynamic anharmonicities, and spectral diffusion. Surprisingly, the asymmetrically labeled D-B-A still undergoes intramolecular IVR between acetylide groups even though they are decoupled and positioned across a heavy atom usually perceived as a \"vibrational bottleneck\". Further, the rate of population transfer from the bridge to the acceptor was both site-specific and distance dependent. We show that vibrational excitation of the acetylide modes is transferred to ligand-centered modes on a subpicosecond time scale, followed by VET to solvent modes on the time scale of a few picoseconds. We also show that isotopic substitution does not affect the rate of spectral diffusion, indicating that changes in the vibrational dynamics are not a result of differences in local environment around the acetylides. Oscillations imprinted on the decay of the vibrationally excited acceptor-localized carbonyl modes show they enter a coherent superposition of states after excitation that dephases over 1-2 ps, and thus cannot be treated as independent in the 2D-IR spectra. These findings elucidate the vibrational landscape governing IR-mediated electron transfer and illustrate the power of isotopic labeling combined with multidimensional IR spectroscopy to disentangle vibrational energy propagation pathways in complex systems.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"4 6","pages":"761-772"},"PeriodicalIF":3.7,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11613348/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142781018","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}

{"title":"Unveiling the Photoactivation Mechanism of BLUF Photoreceptor Protein through Hybrid Quantum Mechanics/Molecular Mechanics Free-Energy Calculation","authors":"Masahiko Taguchi,&nbsp;Shun Sakuraba,&nbsp;Justin Chan and Hidetoshi Kono*,&nbsp;","doi":"10.1021/acsphyschemau.4c0004010.1021/acsphyschemau.4c00040","DOIUrl":"https://doi.org/10.1021/acsphyschemau.4c00040https://doi.org/10.1021/acsphyschemau.4c00040","url":null,"abstract":"<p >OaPAC is a photoactivated enzyme that forms a homodimer. The two blue-light using flavin (BLUF) photoreceptor domains are connected to the catalytic domains with long coiled-coil C-terminal helices. Upon photoreception, reorganization of the hydrogen bonding network between Tyr6, Gln48, and the chromophore in the BLUF domain and keto–enol tautomerization of Gln48 are thought to occur. However, the quantitative energetics of the photoisomerization reaction and how the BLUF domain’s structural change propagates toward the catalytic domain are still unknown. We evaluate the free-energy differences among the dark-state and two different light-state structures by the free-energy perturbation calculations combined with QM/MM free-energy optimizations. Furthermore, we performed long-time MD simulations for the free-energetically optimized dark- and light-state structures to clarify the differences in protein dynamics upon photoisomerization. The free-energy difference between the two optimized light-state structures was estimated at ∼4.7 kcal/mol. The free-energetically optimized light-state structure indicates that the chemically unstable enol tautomer of Gln48 in the light state is stabilized by forming a strong hydrogen bonding network with the chromophore and Tyr6. In addition, the components of free-energy difference between the dark- and light-state structures show that the energy upon photoreception is stored in the environment rather than the internal photoreceived region, suggesting a mechanism to keep the photoactivated signaling state with the chemically unstable enol tautomer of Gln48. In the light state, a fluctuation of Trp90 near the C-terminal helix becomes large, which causes subsequent structural changes in the BLUF core and the C-terminal helix. We also identified residue pairs with significant differences concerning residue-wise contact maps between the dark and light states.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"4 6","pages":"647–659 647–659"},"PeriodicalIF":3.7,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsphyschemau.4c00040","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142713631","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}

{"title":"Two-Dimensional Infrared Spectroscopy Resolves the Vibrational Landscape in Donor–Bridge–Acceptor Complexes with Site-Specific Isotopic Labeling","authors":"James D. Shipp*,&nbsp;Ricardo J. Fernández-Terán*,&nbsp;Alexander J. Auty,&nbsp;Heather Carson,&nbsp;Andrew J. Sadler,&nbsp;Michael Towrie,&nbsp;Igor V. Sazanovich,&nbsp;Paul M. Donaldson,&nbsp;Anthony J. H. M. Meijer and Julia A. Weinstein*,&nbsp;","doi":"10.1021/acsphyschemau.4c0007310.1021/acsphyschemau.4c00073","DOIUrl":"https://doi.org/10.1021/acsphyschemau.4c00073https://doi.org/10.1021/acsphyschemau.4c00073","url":null,"abstract":"<p >Donor–bridge–acceptor complexes (D–B–A) are important model systems for understanding of light-induced processes. Here, we apply two-color two-dimensional infrared (2D-IR) spectroscopy to D–B–A complexes with a <i>trans</i>-Pt(II) acetylide bridge (D–C≡C–Pt–C≡C–A) to uncover the mechanism of vibrational energy redistribution (IVR). Site-selective ¹³C isotopic labeling of the bridge is used to decouple the acetylide modes positioned on either side of the Pt-center. Decoupling of the D-acetylide- from the A-acetylide- enables site-specific investigation of vibrational energy transfer (VET) rates, dynamic anharmonicities, and spectral diffusion. Surprisingly, the asymmetrically labeled D–B–A still undergoes intramolecular IVR between acetylide groups even though they are decoupled and positioned across a heavy atom usually perceived as a “vibrational bottleneck”. Further, the rate of population transfer from the bridge to the acceptor was both site-specific and distance dependent. We show that vibrational excitation of the acetylide modes is transferred to ligand-centered modes on a subpicosecond time scale, followed by VET to solvent modes on the time scale of a few picoseconds. We also show that isotopic substitution does not affect the rate of spectral diffusion, indicating that changes in the vibrational dynamics are not a result of differences in local environment around the acetylides. Oscillations imprinted on the decay of the vibrationally excited acceptor-localized carbonyl modes show they enter a coherent superposition of states after excitation that dephases over 1–2 ps, and thus cannot be treated as independent in the 2D-IR spectra. These findings elucidate the vibrational landscape governing IR-mediated electron transfer and illustrate the power of isotopic labeling combined with multidimensional IR spectroscopy to disentangle vibrational energy propagation pathways in complex systems.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"4 6","pages":"761–772 761–772"},"PeriodicalIF":3.7,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsphyschemau.4c00073","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142713632","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}

{"title":"Unveiling the Photoactivation Mechanism of BLUF Photoreceptor Protein through Hybrid Quantum Mechanics/Molecular Mechanics Free-Energy Calculation.","authors":"Masahiko Taguchi, Shun Sakuraba, Justin Chan, Hidetoshi Kono","doi":"10.1021/acsphyschemau.4c00040","DOIUrl":"10.1021/acsphyschemau.4c00040","url":null,"abstract":"<p><p>OaPAC is a photoactivated enzyme that forms a homodimer. The two blue-light using flavin (BLUF) photoreceptor domains are connected to the catalytic domains with long coiled-coil C-terminal helices. Upon photoreception, reorganization of the hydrogen bonding network between Tyr6, Gln48, and the chromophore in the BLUF domain and keto-enol tautomerization of Gln48 are thought to occur. However, the quantitative energetics of the photoisomerization reaction and how the BLUF domain's structural change propagates toward the catalytic domain are still unknown. We evaluate the free-energy differences among the dark-state and two different light-state structures by the free-energy perturbation calculations combined with QM/MM free-energy optimizations. Furthermore, we performed long-time MD simulations for the free-energetically optimized dark- and light-state structures to clarify the differences in protein dynamics upon photoisomerization. The free-energy difference between the two optimized light-state structures was estimated at ∼4.7 kcal/mol. The free-energetically optimized light-state structure indicates that the chemically unstable enol tautomer of Gln48 in the light state is stabilized by forming a strong hydrogen bonding network with the chromophore and Tyr6. In addition, the components of free-energy difference between the dark- and light-state structures show that the energy upon photoreception is stored in the environment rather than the internal photoreceived region, suggesting a mechanism to keep the photoactivated signaling state with the chemically unstable enol tautomer of Gln48. In the light state, a fluctuation of Trp90 near the C-terminal helix becomes large, which causes subsequent structural changes in the BLUF core and the C-terminal helix. We also identified residue pairs with significant differences concerning residue-wise contact maps between the dark and light states.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"4 6","pages":"647-659"},"PeriodicalIF":3.7,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11613238/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142781198","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}

{"title":"Evaluating the Fluorescence Quenching of Troxerutin for Commercial UV Sunscreen Filters.","authors":"Jack Dalton, Natércia D N Rodrigues, Daniel Berndt, Vasilios G Stavros","doi":"10.1021/acsphyschemau.4c00070","DOIUrl":"10.1021/acsphyschemau.4c00070","url":null,"abstract":"<p><p>2-Phenylbenzimidazole-5-sulfonic acid (PBSA) and disodium phenyl dibenzimidazole tetrasulfonate (DPDT) are commercially available ultraviolet (UV) sunscreen filters that are known to undergo radiative relaxation following the absorption of UV light. The release of high-energy photons from this relaxation can be detrimental to human health; therefore, fluorescence quenchers need to be incorporated in commercial sunscreen formulations containing PBSA or DPDT. Troxerutin is a fluorescence quencher utilized for DPDT commercially. Here, its ability to quench the fluorescence of both PBSA and DPDT is evaluated using a dual-pronged approach by breaking down the multicomponent problem into its constituent parts. First, PBSA and DPDT's femtosecond to nanosecond photodynamics are uncovered in solution and on the surface of a human skin mimic to ascertain a benchmark. Second, these results are compared to their photodynamics in the presence of troxerutin. A significant reduction in the fluorescence lifetime is observed for both PBSA and DPDT on a human skin mimic with the addition of troxerutin, which is attributed to a Dexter energy transfer (DET) or Förster resonance energy transfer (FRET) quenching mechanism. This finding demonstrates the hitherto unseen fluorescence quenching mechanism of troxerutin on a human skin mimic and its role in quenching the fluorescence of commercial UV sunscreen filters through a DET or FRET mechanism.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"4 6","pages":"750-760"},"PeriodicalIF":3.7,"publicationDate":"2024-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11613208/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142780745","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}

{"title":"Evaluating the Fluorescence Quenching of Troxerutin for Commercial UV Sunscreen Filters","authors":"Jack Dalton,&nbsp;Natércia d. N. Rodrigues,&nbsp;Daniel Berndt and Vasilios G. Stavros*,&nbsp;","doi":"10.1021/acsphyschemau.4c0007010.1021/acsphyschemau.4c00070","DOIUrl":"https://doi.org/10.1021/acsphyschemau.4c00070https://doi.org/10.1021/acsphyschemau.4c00070","url":null,"abstract":"<p >2-Phenylbenzimidazole-5-sulfonic acid (PBSA) and disodium phenyl dibenzimidazole tetrasulfonate (DPDT) are commercially available ultraviolet (UV) sunscreen filters that are known to undergo radiative relaxation following the absorption of UV light. The release of high-energy photons from this relaxation can be detrimental to human health; therefore, fluorescence quenchers need to be incorporated in commercial sunscreen formulations containing PBSA or DPDT. Troxerutin is a fluorescence quencher utilized for DPDT commercially. Here, its ability to quench the fluorescence of both PBSA and DPDT is evaluated using a dual-pronged approach by breaking down the multicomponent problem into its constituent parts. First, PBSA and DPDT’s femtosecond to nanosecond photodynamics are uncovered in solution and on the surface of a human skin mimic to ascertain a benchmark. Second, these results are compared to their photodynamics in the presence of troxerutin. A significant reduction in the fluorescence lifetime is observed for both PBSA and DPDT on a human skin mimic with the addition of troxerutin, which is attributed to a Dexter energy transfer (DET) or Förster resonance energy transfer (FRET) quenching mechanism. This finding demonstrates the hitherto unseen fluorescence quenching mechanism of troxerutin on a human skin mimic and its role in quenching the fluorescence of commercial UV sunscreen filters through a DET or FRET mechanism.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"4 6","pages":"750–760 750–760"},"PeriodicalIF":3.7,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsphyschemau.4c00070","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142719580","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}

{"title":"Visions for the Future of Physical Chemistry.","authors":"Gemma C Solomon, Jin Zhong Zhang, Tanja Cuk","doi":"10.1021/acsphyschemau.4c00086","DOIUrl":"10.1021/acsphyschemau.4c00086","url":null,"abstract":"","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"4 6","pages":"575-580"},"PeriodicalIF":3.7,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11613332/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142781201","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}

{"title":"Visions for the Future of Physical Chemistry","authors":"Gemma C. Solomon*,&nbsp;Jin Zhong Zhang* and Tanja Cuk*,&nbsp;","doi":"10.1021/acsphyschemau.4c0008610.1021/acsphyschemau.4c00086","DOIUrl":"https://doi.org/10.1021/acsphyschemau.4c00086https://doi.org/10.1021/acsphyschemau.4c00086","url":null,"abstract":"","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"4 6","pages":"575–580 575–580"},"PeriodicalIF":3.7,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsphyschemau.4c00086","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142713586","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}

{"title":"Amino Acid Residue-Specific Ramachandran Distributions Derived from a Simple Mean Field Potential.","authors":"Brian Andrews","doi":"10.1021/acsphyschemau.4c00064","DOIUrl":"10.1021/acsphyschemau.4c00064","url":null,"abstract":"<p><p>Protein dynamics in the unfolded state, in the context of early stage protein folding or intrinsically disordered proteins (IDPs), is not well understood. The discovery of IDPs, and their sequence-dependent dynamics, has led to many computational and experimental investigations regarding the conformational preferences of short oligopeptides and individual amino acid residues in the unfolded state. As proteins consist of sequences of amino acid residues, characterizing the intrinsic conformational preferences of the individual residues in the unfolded state is crucial for understanding the emergent conformations of peptides and proteins. While advances have been made in understanding conformational preferences, the atomistic mechanisms driving these preferences remain unresolved. In this work, we show that the distributions of atomic overlaps between backbone and side chain atoms in Ramachandran space are unique for amino acid residue mimetic structures alanine, valine, leucine, and isoleucine in Ramachandran space indicating unique intrapeptide energy landscapes for each residue. We then construct a mean field potential consisting of only an empirical peptide backbone-water and average intrapeptide Lennard-Jones contributions to explore their influence on the conformational preferences. With this fairly simple model, we were able to produce Ramachandran distributions that qualitatively agree with previously reported experimental and computational predictions about the conformational preferences of these amino acid residues in the unfolded state in water. Our results indicate these conformational preferences are the result of the balance between pPII-stabilizing backbone-water interactions and repulsive side chain-backbone interactions where the latter will depend uniquely on the atomic makeup and geometry of the side chain.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"4 6","pages":"707-719"},"PeriodicalIF":3.7,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11613349/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142780691","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}

{"title":"Amino Acid Residue-Specific Ramachandran Distributions Derived from a Simple Mean Field Potential","authors":"Brian Andrews*,&nbsp;","doi":"10.1021/acsphyschemau.4c0006410.1021/acsphyschemau.4c00064","DOIUrl":"https://doi.org/10.1021/acsphyschemau.4c00064https://doi.org/10.1021/acsphyschemau.4c00064","url":null,"abstract":"<p >Protein dynamics in the unfolded state, in the context of early stage protein folding or intrinsically disordered proteins (IDPs), is not well understood. The discovery of IDPs, and their sequence-dependent dynamics, has led to many computational and experimental investigations regarding the conformational preferences of short oligopeptides and individual amino acid residues in the unfolded state. As proteins consist of sequences of amino acid residues, characterizing the intrinsic conformational preferences of the individual residues in the unfolded state is crucial for understanding the emergent conformations of peptides and proteins. While advances have been made in understanding conformational preferences, the atomistic mechanisms driving these preferences remain unresolved. In this work, we show that the distributions of atomic overlaps between backbone and side chain atoms in Ramachandran space are unique for amino acid residue mimetic structures alanine, valine, leucine, and isoleucine in Ramachandran space indicating unique intrapeptide energy landscapes for each residue. We then construct a mean field potential consisting of only an empirical peptide backbone–water and average intrapeptide Lennard-Jones contributions to explore their influence on the conformational preferences. With this fairly simple model, we were able to produce Ramachandran distributions that qualitatively agree with previously reported experimental and computational predictions about the conformational preferences of these amino acid residues in the unfolded state in water. Our results indicate these conformational preferences are the result of the balance between pPII-stabilizing backbone–water interactions and repulsive side chain–backbone interactions where the latter will depend uniquely on the atomic makeup and geometry of the side chain.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"4 6","pages":"707–719 707–719"},"PeriodicalIF":3.7,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsphyschemau.4c00064","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142719531","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}