ACS Physical Chemistry Au最新文献_第5页

Visions for the Future of Physical Chemistry. 展望物理化学的未来。

IF 3.7

ACS Physical Chemistry Au Pub Date : 2024-10-22 eCollection Date: 2024-11-27 DOI: 10.1021/acsphyschemau.4c00086

Gemma C Solomon, Jin Zhong Zhang, Tanja Cuk

引用次数: 0

Visions for the Future of Physical Chemistry 物理化学的未来愿景

IF 3.7

ACS Physical Chemistry Au Pub Date : 2024-10-22 DOI: 10.1021/acsphyschemau.4c0008610.1021/acsphyschemau.4c00086

Gemma C. Solomon*, Jin Zhong Zhang* and Tanja Cuk*,

引用次数: 0

Amino Acid Residue-Specific Ramachandran Distributions Derived from a Simple Mean Field Potential. 由简单平均场势导出的氨基酸残基特异性Ramachandran分布。

IF 3.7

ACS Physical Chemistry Au Pub Date : 2024-10-21 eCollection Date: 2024-11-27 DOI: 10.1021/acsphyschemau.4c00064

Brian Andrews

{"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":"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.","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}

引用次数: 0

Amino Acid Residue-Specific Ramachandran Distributions Derived from a Simple Mean Field Potential 从简单平均场势推导出氨基酸残基特异性拉马钱德兰分布

IF 3.7

ACS Physical Chemistry Au Pub Date : 2024-10-21 DOI: 10.1021/acsphyschemau.4c0006410.1021/acsphyschemau.4c00064

Brian Andrews*,

{"title":"Amino Acid Residue-Specific Ramachandran Distributions Derived from a Simple Mean Field Potential","authors":"Brian Andrews*, ","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":"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.","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}

引用次数: 0

Insights into the Structural, Thermal/Dilatometric, and Optical Properties of Dy³⁺-Doped Phosphate Glasses for Lighting Applications. 照明应用中Dy3+掺杂磷酸盐玻璃的结构、热/膨胀和光学性质的见解。

IF 3.7

ACS Physical Chemistry Au Pub Date : 2024-10-21 eCollection Date: 2024-11-27 DOI: 10.1021/acsphyschemau.4c00066

José A Jiménez, Vinod Hedge, C S Dwaraka Viswanath, Richard Amesimenu

{"title":"Insights into the Structural, Thermal/Dilatometric, and Optical Properties of Dy3+-Doped Phosphate Glasses for Lighting Applications.","authors":"José A Jiménez, Vinod Hedge, C S Dwaraka Viswanath, Richard Amesimenu","doi":"10.1021/acsphyschemau.4c00066","DOIUrl":"10.1021/acsphyschemau.4c00066","url":null,"abstract":"Dysprosium-doped glasses are of interest for applications in light-emitting devices, yet the full range of effects of Dy3+ ions on glass properties is not fully understood. In this work, phosphate glasses with 50P2O5-(50 - x)BaO-xDy2O3 (0 ≤ x ≤ 4.0 mol %) nominal compositions were prepared by melting and the impact of Dy3+ ions on glass physical, structural, thermo-mechanical, and optical properties was evaluated. Following refractive index, density, and X-ray diffraction characterizations, the glasses were studied comprehensively through Raman spectroscopy, X-ray photoelectron spectroscopy, dilatometry, optical absorption, and photoluminescence (PL) spectroscopy. The thorough investigation and data analyses shed light on the Dy3+-driven structural and thermal properties reported here for the first time. The thermal expansion behavior was put in context with the reported data for other lanthanides and analyzed in the framework of the high ionic field strengths, leading to tighter glass networks. Further, a detailed analysis of the absorption, PL, and emission decay curves was carried out, providing insights into the origin of the optical behavior. Supported is the hypothesis that the cross-relaxation channels between Dy3+ ions taking place at low concentrations are responsible for the decrease in the decay times while the PL attractive for lighting applications still improves. Conversely, high Dy3+ concentrations facilitate the emission quenching proceeding via an electric dipole-dipole interaction likely incorporating the resonant excitation migration pathway for Dy3+-Dy3+ mean distances shorter than ∼15 Å.","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"4 6","pages":"720-735"},"PeriodicalIF":3.7,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11613285/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142781062","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}

引用次数: 0

Insights into the Structural, Thermal/Dilatometric, and Optical Properties of Dy3+-Doped Phosphate Glasses for Lighting Applications 洞察用于照明应用的掺杂 Dy3+ 磷酸盐玻璃的结构、热/散热和光学特性

IF 3.7

ACS Physical Chemistry Au Pub Date : 2024-10-21 DOI: 10.1021/acsphyschemau.4c0006610.1021/acsphyschemau.4c00066

José A. Jiménez*, Vinod Hedge, C. S. Dwaraka Viswanath and Richard Amesimenu,

{"title":"Insights into the Structural, Thermal/Dilatometric, and Optical Properties of Dy3+-Doped Phosphate Glasses for Lighting Applications","authors":"José A. Jiménez*, Vinod Hedge, C. S. Dwaraka Viswanath and Richard Amesimenu, ","doi":"10.1021/acsphyschemau.4c0006610.1021/acsphyschemau.4c00066","DOIUrl":"https://doi.org/10.1021/acsphyschemau.4c00066https://doi.org/10.1021/acsphyschemau.4c00066","url":null,"abstract":"Dysprosium-doped glasses are of interest for applications in light-emitting devices, yet the full range of effects of Dy3+ ions on glass properties is not fully understood. In this work, phosphate glasses with 50P2O5-(50 – x)BaO-xDy2O3 (0 ≤ x ≤ 4.0 mol %) nominal compositions were prepared by melting and the impact of Dy3+ ions on glass physical, structural, thermo-mechanical, and optical properties was evaluated. Following refractive index, density, and X-ray diffraction characterizations, the glasses were studied comprehensively through Raman spectroscopy, X-ray photoelectron spectroscopy, dilatometry, optical absorption, and photoluminescence (PL) spectroscopy. The thorough investigation and data analyses shed light on the Dy3+-driven structural and thermal properties reported here for the first time. The thermal expansion behavior was put in context with the reported data for other lanthanides and analyzed in the framework of the high ionic field strengths, leading to tighter glass networks. Further, a detailed analysis of the absorption, PL, and emission decay curves was carried out, providing insights into the origin of the optical behavior. Supported is the hypothesis that the cross-relaxation channels between Dy3+ ions taking place at low concentrations are responsible for the decrease in the decay times while the PL attractive for lighting applications still improves. Conversely, high Dy3+ concentrations facilitate the emission quenching proceeding via an electric dipole–dipole interaction likely incorporating the resonant excitation migration pathway for Dy3+–Dy3+ mean distances shorter than ∼15 Å.","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"4 6","pages":"720–735 720–735"},"PeriodicalIF":3.7,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsphyschemau.4c00066","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142719533","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}

引用次数: 0

Atomistic Multiscale Modeling of Colloidal Plasmonic Nanoparticles. 胶体等离子体纳米粒子的原子多尺度模拟。

IF 3.7

ACS Physical Chemistry Au Pub Date : 2024-10-17 eCollection Date: 2024-11-27 DOI: 10.1021/acsphyschemau.4c00052

Luca Nicoli, Sveva Sodomaco, Piero Lafiosca, Tommaso Giovannini, Chiara Cappelli

引用次数: 0

Atomistic Multiscale Modeling of Colloidal Plasmonic Nanoparticles 胶体质子纳米粒子的原子多尺度建模

IF 3.7

ACS Physical Chemistry Au Pub Date : 2024-10-17 DOI: 10.1021/acsphyschemau.4c0005210.1021/acsphyschemau.4c00052

Luca Nicoli, Sveva Sodomaco, Piero Lafiosca, Tommaso Giovannini* and Chiara Cappelli*,

{"title":"Atomistic Multiscale Modeling of Colloidal Plasmonic Nanoparticles","authors":"Luca Nicoli, Sveva Sodomaco, Piero Lafiosca, Tommaso Giovannini* and Chiara Cappelli*, ","doi":"10.1021/acsphyschemau.4c0005210.1021/acsphyschemau.4c00052","DOIUrl":"https://doi.org/10.1021/acsphyschemau.4c00052https://doi.org/10.1021/acsphyschemau.4c00052","url":null,"abstract":"A novel fully atomistic multiscale classical approach to model the optical response of solvated real-size plasmonic nanoparticles (NPs) is presented. The model is based on the coupling of the Frequency Dependent Fluctuating Charges and Fluctuating Dipoles (ωFQFμ), specifically designed to describe plasmonic substrates, and the polarizable Fluctuating Charges (FQ) classical force field to model the solvating environment. The resulting ωFQFμ/FQ approach accounts for the interactions between the radiation and the NP, as well as with the surrounding solvent molecules, by incorporating mutual interactions between the plasmonic substrate and solvent. ωFQFμ/FQ is validated against reference TD-DFTB/FQ calculations, demonstrating remarkable accuracy, particularly in reproducing plasmon resonance frequency shifts for structures below the quantum-size limit. The flexibility and reliability of the approach are also demonstrated by simulating the optical response of homogeneous and bimetallic NPs dissolved in pure solvents and solvent mixtures.","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"4 6","pages":"669–678 669–678"},"PeriodicalIF":3.7,"publicationDate":"2024-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsphyschemau.4c00052","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142719364","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}

引用次数: 0

Thermodynamics of Anion Binding by (Thio)ureido-calix[4]arene Derivatives in Acetonitrile. （硫）脲杯[4]芳烃衍生物在乙腈中的阴离子结合热力学。

IF 3.7

ACS Physical Chemistry Au Pub Date : 2024-10-15 eCollection Date: 2024-11-27 DOI: 10.1021/acsphyschemau.4c00077

Marija Cvetnić, Nikola Cindro, Nikola Bregović, Vladislav Tomišić

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引用次数: 0

Thermodynamics of Anion Binding by (Thio)ureido-calix[4]arene Derivatives in Acetonitrile (硫)脲基萼片[4]炔衍生物在乙腈中与阴离子结合的热力学研究

IF 3.7

ACS Physical Chemistry Au Pub Date : 2024-10-15 DOI: 10.1021/acsphyschemau.4c0007710.1021/acsphyschemau.4c00077

Marija Cvetnić, Nikola Cindro, Nikola Bregović* and Vladislav Tomišić,

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引用次数: 0