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3. Coordinate‐based simulation of pair distance distribution functions for small and large molecular assemblies: implementation and applications.

Author

Zuo, Xiaobing and Tiede, David M.

Subjects
*TOBACCO mosaic virus, *NANOSTRUCTURED materials, *DISTRIBUTION (Probability theory), *MOLECULAR structure, *BIOMATERIALS
Abstract

X‐ray scattering has become a major tool in the structural characterization of nanoscale materials. Thanks to the widely available experimental and computational atomic models, coordinate‐based X‐ray scattering simulation has played a crucial role in data interpretation in the past two decades. However, simulation of real‐space pair distance distribution functions (PDDFs) from small‐ and wide‐angle X‐ray scattering, SAXS/WAXS, has been relatively less exploited. This study presents a comparison of PDDF simulation methods, which are applied to molecular structures that range in size from β‐cyclodextrin [1 kDa molecular weight (MW), 66 non‐hydrogen atoms] to the satellite tobacco mosaic virus capsid (1.1 MDa MW, 81960 non‐hydrogen atoms). The results demonstrate the power of interpretation of experimental SAXS/WAXS from the real‐space view, particularly by providing a more intuitive method for understanding of partial structure contributions. Furthermore, the computational efficiency of PDDF simulation algorithms makes them attractive as approaches for the analysis of large nanoscale materials and biological assemblies. The simulation methods demonstrated in this article have been implemented in stand‐alone software, SolX 3.0, which is available to download from https://12idb.xray.aps.anl.gov/solx.html. [ABSTRACT FROM AUTHOR]

Published
2024
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5. Proton-Responsive Ligands Promote CO2Capture and Accelerate Catalytic CO2/HCO2–Interconversion

Author

Barlow, Jeffrey M., Gupta, Nikita, Glusac, Ksenija D., Tiede, David M., and Kaphan, David M.

Abstract

The synthesis and investigation of [Rh(DHMPE)2][BF4] (1) are reported. 1features proton-responsive 1,2-bis[(dihydroxymethyl)phosphino]ethane (DHMPE) ligands, which readily capture CO2from atmospheric sources upon deprotonation. The protonation state of the DHMPE ligand was observed to have a significant impact on the catalytic reactivity of 1with CO2. Deprotonation and CO2binding to 1result in a ∼10-fold rate enhancement in catalytic degenerate CO2reduction with formate, monitored by 12C/13C isotope exchange between H12CO2–and 13CO2. Studies performed using a similar complex lacking the hydroxyl ligand functionality ([Rh(DEPE)2][BF4] where DEPE = 1,2-bis(diethylphosphino)ethane) do not show the same rate enhancements when base is added. Based upon the cation-dependent activity of the catalyst, Eyring analysis, and cation sequestration experiments, CO2binding to 1is proposed to facilitate preorganization of formate/CO2in the transition state via ligand-based encapsulation of Na+or K+cations to lower the activation energy and increase the observed catalytic rate. Incorporation of proton-responsive DHMPE ligands provides a unique approach to accelerate the kinetics of catalytic CO2reduction to formate.

Published
2024
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6. Anomalously enhanced ion transport and uptake in functionalized angstrom-scale two-dimensional channels

Author

Wang, Mingzhan, primary, Sadhukhan, Tumpa, additional, Lewis, Nicholas H. C., additional, Wang, Maoyu, additional, He, Xiang, additional, Yan, Gangbin, additional, Ying, Dongchen, additional, Hoenig, Eli, additional, Han, Yu, additional, Peng, Guiming, additional, Lee, One-Sun, additional, Shi, Fengyuan, additional, Tiede, David M., additional, Zhou, Hua, additional, Tokmakoff, Andrei, additional, Schatz, George C., additional, and Liu, Chong, additional

Published
2024
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10. Comparing Photosynthetic and Photovoltaic Efficiencies and Recognizing the Potential for Improvement

Author

Blankenship, Robert E, Tiede, David M, Barber, James, Brudvig, Gary W, Fleming, Graham, Ghirardi, Maria, Gunner, MR, Junge, Wolfgang, Kramer, David M, Melis, Anastasios, Moore, Thomas A, Moser, Christopher C, Nocera, Daniel G, Nozik, Arthur J, Ort, Donald R, Parson, William W, Prince, Roger C, and Sayre, Richard T

Subjects
Plant Biology, Biological Sciences, Chemical Sciences, Affordable and Clean Energy, Biomass, Electricity, Electrolysis, Hydrogen, Photosynthesis, Plant Development, Plants, Solar Energy, Sunlight, Synthetic Biology, General Science & Technology
Abstract

Comparing photosynthetic and photovoltaic efficiencies is not a simple issue. Although both processes harvest the energy in sunlight, they operate in distinctly different ways and produce different types of products: biomass or chemical fuels in the case of natural photosynthesis and nonstored electrical current in the case of photovoltaics. In order to find common ground for evaluating energy-conversion efficiency, we compare natural photosynthesis with present technologies for photovoltaic-driven electrolysis of water to produce hydrogen. Photovoltaic-driven electrolysis is the more efficient process when measured on an annual basis, yet short-term yields for photosynthetic conversion under optimal conditions come within a factor of 2 or 3 of the photovoltaic benchmark. We consider opportunities in which the frontiers of synthetic biology might be used to enhance natural photosynthesis for improved solar energy conversion efficiency.

Published
2011

12. Anomalously enhanced ion transport and uptake in functionalized angstrom-scale two-dimensional channels.

Author

Mingzhan Wang, Sadhukhan, Tumpa, Lewis, Nicholas H. C., Maoyu Wang, Xiang He, Gangbin Yan, Dongchen Ying, Hoenig, Eli, Yu Han, Guiming Peng, One-Sun Lee, Fengyuan Shi, Tiede, David M., Hua Zhou, Tokmakoff, Andrei, Schatz, George C., and Chong Liu

Subjects
ION channels, FUNCTIONAL groups, FILMMAKING, IONS
Abstract

Emulating angstrom-scale dynamics of the highly selective biological ion channels is a challenging task. Recent work on angstrom-scale artificial channels has expanded our understanding of ion transport and uptake mechanisms under confinement. However, the role of chemical environment in such channels is still not well understood. Here, we report the anomalously enhanced transport and uptake of ions under confined MoS2-based channels that are ~five angstroms in size. The ion uptake preference in the MoS2-based channels can be changed by the selection of surface functional groups and ion uptake sequence due to the interplay between kinetic and thermodynamic factors that depend on whether the ions are mixed or not prior to uptake. Our work offers a holistic picture of ion transport in 2D confinement and highlights ion interplay in this regime. [ABSTRACT FROM AUTHOR]

Published
2024
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31. Experimental Verification of Ir 5d Orbital States and Atomic Structures in Highly Active Amorphous Iridium Oxide Catalysts

Author

Kwon, Gihan, primary, Chang, Seo Hyoung, additional, Heo, Jin Eun, additional, Lee, Kyeong Jun, additional, Kim, Jin-Kwang, additional, Cho, Byeong-Gwan, additional, Koo, Tae Yeong, additional, Kim, B. J., additional, Kim, Chanseok, additional, Lee, Jun Hee, additional, Bak, Seong-Min, additional, Beyer, Kevin A., additional, Zhong, Hui, additional, Koch, Robert J., additional, Hwang, Sooyeon, additional, Utschig, Lisa M., additional, Huang, Xiaojing, additional, Hu, Gongfang, additional, Brudvig, Gary W., additional, Tiede, David M., additional, and Kim, Jungho, additional

Published
2021
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33. Advanced Materials for Energy-Water Systems: The Central Role of Water/Solid Interfaces in Adsorption, Reactivity, and Transport

Author

Barry, Edward, primary, Burns, Raelyn, additional, Chen, Wei, additional, De Hoe, Guilhem X., additional, De Oca, Joan Manuel Montes, additional, de Pablo, Juan J., additional, Dombrowski, James, additional, Elam, Jeffrey W., additional, Felts, Alanna M., additional, Galli, Giulia, additional, Hack, John, additional, He, Qiming, additional, He, Xiang, additional, Hoenig, Eli, additional, Iscen, Aysenur, additional, Kash, Benjamin, additional, Kung, Harold H., additional, Lewis, Nicholas H. C., additional, Liu, Chong, additional, Ma, Xinyou, additional, Mane, Anil, additional, Martinson, Alex B. F., additional, Mulfort, Karen L., additional, Murphy, Julia, additional, Mølhave, Kristian, additional, Nealey, Paul, additional, Qiao, Yijun, additional, Rozyyev, Vepa, additional, Schatz, George C., additional, Sibener, Steven J., additional, Talapin, Dmitri, additional, Tiede, David M., additional, Tirrell, Matthew V., additional, Tokmakoff, Andrei, additional, Voth, Gregory A., additional, Wang, Zhongyang, additional, Ye, Zifan, additional, Yesibolati, Murat, additional, Zaluzec, Nestor J., additional, and Darling, Seth B., additional

Published
2021
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34. Advanced Materials for Energy-Water Systems: The Central Role of Water/Solid Interfaces in Adsorption, Reactivity, and Transport

Author

Barry, Edward, Burns, Raelyn, Chen, Wei, De Hoe, Guilhem X., De Oca, Joan Manuel Montes, De Pablo, Juan J., Dombrowski, James, Elam, Jeffrey W., Felts, Alanna M., Galli, Giulia, Hack, John, He, Qiming, He, Xiang, Hoenig, Eli, Iscen, Aysenur, Kash, Benjamin, Kung, Harold H., Lewis, Nicholas H.C., Liu, Chong, Ma, Xinyou, Mane, Anil, Martinson, Alex B.F., Mulfort, Karen L., Murphy, Julia, Mølhave, Kristian, Nealey, Paul, Qiao, Yijun, Rozyyev, Vepa, Schatz, George C., Sibener, Steven J., Talapin, Dmitri, Tiede, David M., Tirrell, Matthew V., Tokmakoff, Andrei, Voth, Gregory A., Wang, Zhongyang, Ye, Zifan, Yesibolati, Murat, Zaluzec, Nestor J., Darling, Seth B., Barry, Edward, Burns, Raelyn, Chen, Wei, De Hoe, Guilhem X., De Oca, Joan Manuel Montes, De Pablo, Juan J., Dombrowski, James, Elam, Jeffrey W., Felts, Alanna M., Galli, Giulia, Hack, John, He, Qiming, He, Xiang, Hoenig, Eli, Iscen, Aysenur, Kash, Benjamin, Kung, Harold H., Lewis, Nicholas H.C., Liu, Chong, Ma, Xinyou, Mane, Anil, Martinson, Alex B.F., Mulfort, Karen L., Murphy, Julia, Mølhave, Kristian, Nealey, Paul, Qiao, Yijun, Rozyyev, Vepa, Schatz, George C., Sibener, Steven J., Talapin, Dmitri, Tiede, David M., Tirrell, Matthew V., Tokmakoff, Andrei, Voth, Gregory A., Wang, Zhongyang, Ye, Zifan, Yesibolati, Murat, Zaluzec, Nestor J., and Darling, Seth B.

Abstract

The structure, chemistry, and charge of interfaces between materials and aqueous fluids play a central role in determining properties and performance of numerous water systems. Sensors, membranes, sorbents, and heterogeneous catalysts almost uniformly rely on specific interactions between their surfaces and components dissolved or suspended in the water - and often the water molecules themselves - to detect and mitigate contaminants. Deleterious processes in these systems such as fouling, scaling (inorganic deposits), and corrosion are also governed by interfacial phenomena. Despite the importance of these interfaces, much remains to be learned about their multiscale interactions. Developing a deeper understanding of the molecular- and mesoscale phenomena at water/solid interfaces will be essential to driving innovation to address grand challenges in supplying sufficient fit-for-purpose water in the future. In this Review, we examine the current state of knowledge surrounding adsorption, reactivity, and transport in several key classes of water/solid interfaces, drawing on a synergistic combination of theory, simulation, and experiments, and provide an outlook for prioritizing strategic research directions.

Published
2021

38. Low-temperature interquinone electron transfer in photosynthetic reaction centers from Rhodobacter sphaeroides and Blastochloris viridis: Characterization of Q(sub B) (super -) states by high-frequency electron paramagnetic resonance (EPR) and electron-nuclear double resonance (ENDOR)

Author

Utschig, Lisa M., Thurnauer, Marion C., Tiede, david M., and Poluektov, Oleg G.

Subjects
Electron transport -- Analysis, Bacteria, Photosynthetic -- Genetic aspects, Proteins -- Structure, Proteins -- Analysis, Biological sciences, Chemistry
Abstract

Localized light-induced conformational changes around the reduced quinone acceptor (Q(sub B)(super -)) in Rhodobacter sphaeroides and Blastochloris viridis reaction centers are studied using high-frequency electron paramagnetic resonance (HF-EPR) techniques. No structural differences in the protein structure near Q(sub B)(super-) is observed with electron-nuclear double resonance (HF ENDOR) and the conclusion that the changes are present beyond the local environment is reached.

Published
2005

39. Self-assembly of supramolecular light-harvesting arrays from covalent multi-chromophore perylene-3,4:9,10-bis(dicarboximide) building blocks

Author

Ahrens, Michael J.; Sinks, Louise E., Rybtchinski, Boris; Liu, Wenhao, Jones, Brooks A.; Giaimo, Jovan M., Gusev, Alexy V.; Goshe, Andrew J., and Tiede, David M.; Wasielewski, Michael R.

Subjects
Light-emitting diodes -- Usage, Chromophores -- Research, Chromophores -- Chemical properties, Chemistry
Abstract

A method using functional covalent building blocks having structures designed to get particular self-assembly motifs to produce supramolecular photofunctional materials is studied. This system ensures that it optimizes energy and charge transport properties without resynthesizing the entire system, and this gives a high quality in both solar and light emitting diode applications.

Published
2004

40. Small-angle X-ray scattering studies of the manganese stabilizing subunit in photosystem II

Author

Svensson, Bengt, Tiede, David M., Barry, Bridgette A., Haber, Louis H., and Saykally, Richard J.

Subjects
Proteins -- Optical properties, Proteins -- Research, X-rays -- Usage, Chemicals, plastics and rubber industries
Abstract

Small-angle X-ray scattering studies (SAXS) are used to determine the size, shape, and oligomeric composition of the manganese stabilizing protein (MSP) of photosystem II. The SAXS study suggests that MSP is a monomeric, elongated prolate ellipsoid with dimensions, 112 x 23 x 23 angstrom(super 3) and an axial ratio of 4.8.

Published
2002

41. Protein conformations explored by difference high-angle solution X-ray scattering: oxidation state and temperature dependent changes in cytochrome C

Author

Tiede, David M., Zhang, Ruitian, and Seifert, Soenke

Subjects
Biochemistry -- Research, Oxidation-reduction reaction -- Physiological aspects, Proteins -- Physiological aspects, X-rays -- Scattering, Cytochrome c -- Physiological aspects, Solution (Chemistry) -- Physiological aspects, Biological sciences, Chemistry
Abstract

Research has been conducted on the protein conformation states. The use of the high-angle X-ray scattering in investigating these states in solution and the study of the oxidation state- and the temperature-dependent changes in cytochrome c solution scattering are described

Published
2002

43. Cu(sup)2+ site in photosynthetic bacterial reaction centers from Rhodobacter sphaeroides, Rhodobacter capsulatus, and Rhodopseudomonas viridis

Author

Utschig, Lisa M., Poluektov, Oleg, Schlesselman, Sandra L., Thurnauer, Marion C., and Tiede, David M.

Subjects
Bacteria, Photosynthetic -- Research, Binding sites (Biochemistry) -- Analysis, Copper -- Physiological aspects, Electron paramagnetic resonance spectroscopy -- Usage, Biological sciences, Chemistry
Abstract

Results demonstrate that the photosynthetic reaction centers of the three photosynthetic bacteria studied exhibit a structurally analogous copper binding site mediating electron transfer process modulation. Data further reveal that 2 or more histidine residues ligate the copper at the reaction center's surface.

Published
2001

45. Mimicking Natural Photosynthesis: Designing Ultrafast Photosensitized Electron Transfer into Multiheme Cytochrome Protein Nanowires

Author

Marzolf, Daniel R., primary, McKenzie, Aidan M., additional, O’Malley, Matthew C., additional, Ponomarenko, Nina S., additional, Swaim, Coleman M., additional, Brittain, Tyler J., additional, Simmons, Natalie L., additional, Pokkuluri, Phani Raj, additional, Mulfort, Karen L., additional, Tiede, David M., additional, and Kokhan, Oleksandr, additional

Published
2020
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46. Surface immobilized copper(i) diimine photosensitizers as molecular probes for elucidating the effects of confinement at interfaces for solar energy conversion

Author

Eberhart, Michael S., primary, Phelan, Brian T., additional, Niklas, Jens, additional, Sprague-Klein, Emily A., additional, Kaphan, David M., additional, Gosztola, David J., additional, Chen, Lin X., additional, Tiede, David M., additional, Poluektov, Oleg G., additional, and Mulfort, Karen L., additional

Published
2020
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48. Magnetic field-induced ordering of a polymer-grafted biomembrane-mimetic hydrogel

Author

Firestone, Millicent A., Tiede, David M., and Seifert, Sonke

Subjects
Anisotropy -- Research, Colloids -- Research, Magnetic induction (Electromagnetic induction) -- Research, Membranes (Biology) -- Research, Chemicals, plastics and rubber industries
Abstract

It has been demonstrated that a polymer-grafted biomembrane-mimetic hydrogel is macroscopically oriented by application of a moderate magnetic field. The field-induced anisotropy of the gel phase continues even following removal from the field.

Published
2000

49. EPR investigation of Cu (super)2+ -substituted photosynthetic bacterial reaction centers: evidence for histidine ligation at the surface metal site

Author

Utschig, Lisa M., Poluektov, Oleg, Tiede, David M., and Thurnauer, Marion C.

Subjects
Biochemistry -- Research, Electron paramagnetic resonance -- Analysis, Copper -- Research, Bacteria -- Research, Histidine -- Research, Proteins -- Research, Electron paramagnetic resonance spectroscopy -- Analysis, Biological sciences, Chemistry
Abstract

Research has been conducted on the bacterial photosynthetic reaction center (RC) protein. The probing of the metal site coordination environments on the RC protein with pulsed electron paramagnetic resonance spectroscopy is described.

Published
2000

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