1
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Bardaud JX, Hayakawa Y, Takayanagi H, Hirata K, Ishiuchi SI, Fujii M, Gloaguen E. Water-Induced Dissociative Mechanism of Carboxylate and Divalent Calcium Ions Revealed by IR Laser Spectroscopy. J Phys Chem Lett 2024; 15:9295-9300. [PMID: 39235303 DOI: 10.1021/acs.jpclett.4c01803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2024]
Abstract
The dissociation of carboxylate and divalent calcium ions is investigated at the molecular level in microsolvation experiments by gradually increasing the number of water molecules around the ions. IR photodissociation (IRPD) laser spectroscopy of H2-tagged (Ca2+, AcO-)(H2O)n=8-21 clusters in the ν(CO2-) spectral range combined with RI-B97-D3-BJ-abc/TZVPPD frequency calculations is used to identify the type of ion pairs involved in this process. These results reveal that the ion dissociation follows a multistep mechanism involving in particular pseudobridged monodentate contact ion pairs (CIPs), which are found to be the first intermediate species formed from bidentate CIPs along the ion dissociation path. Altogether, structural assignments suggest a sequence of simple reactions in the first coordination shell of the carboxylate group, leading us to propose two possible dissociation paths. The appearance threshold of monodentate structures is measured at n = 10, with that of solvent-shared ion pairs (SIPs) being potentially at n = 18. By showing in detail how solvation progressively takes over from the ionic interaction in shaping these supramolecular structures, this study can serve as a reference for solving ion-pairing/dissociation problems.
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Affiliation(s)
- Jean-Xavier Bardaud
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91400 Orsay, France
| | - Yurika Hayakawa
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Hikaru Takayanagi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Keisuke Hirata
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Shun-Ichi Ishiuchi
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
- IRFI/IPWR, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Masaaki Fujii
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
- IRFI/IPWR, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
- Research and Development Initiative, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan
| | - Eric Gloaguen
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91400 Orsay, France
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2
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Wang M, Sadhukhan T, Lewis NHC, Wang M, He X, Yan G, Ying D, Hoenig E, Han Y, Peng G, Lee OS, Shi F, Tiede DM, Zhou H, Tokmakoff A, Schatz GC, Liu C. Anomalously enhanced ion transport and uptake in functionalized angstrom-scale two-dimensional channels. Proc Natl Acad Sci U S A 2024; 121:e2313616121. [PMID: 38165939 PMCID: PMC10786305 DOI: 10.1073/pnas.2313616121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 12/01/2023] [Indexed: 01/04/2024] Open
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.
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Affiliation(s)
- Mingzhan Wang
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL60637
| | - Tumpa Sadhukhan
- Department of Chemistry, Northwestern University, Evanston, IL60208
- Department of Chemistry, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu603203, India
| | - Nicholas H. C. Lewis
- Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, University of Chicago, Chicago, IL60637
| | - Maoyu Wang
- X-Ray Science Division, Advanced Photon Source, Argonne National Laboratory, Lemont, IL60439
| | - Xiang He
- Advanced Materials for Energy-Water Systems Energy Frontier Research Center and Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, IL60439
| | - Gangbin Yan
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL60637
| | - Dongchen Ying
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL60637
| | - Eli Hoenig
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL60637
| | - Yu Han
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL60637
| | - Guiming Peng
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL60637
| | - One-Sun Lee
- Department of Chemistry, Northwestern University, Evanston, IL60208
| | - Fengyuan Shi
- Electron Microscopy Core, University of Illinois Chicago, Chicago, IL60607
| | - David M. Tiede
- Advanced Materials for Energy-Water Systems Energy Frontier Research Center and Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, IL60439
| | - Hua Zhou
- X-Ray Science Division, Advanced Photon Source, Argonne National Laboratory, Lemont, IL60439
| | - Andrei Tokmakoff
- Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, University of Chicago, Chicago, IL60637
| | - George C. Schatz
- Department of Chemistry, Northwestern University, Evanston, IL60208
| | - Chong Liu
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL60637
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3
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Foreman MM, Stanton JF, Weber JM. Relation Between Bond Angle and Carbon-Oxygen Stretching Frequencies in CO 2-Containing Compounds. J Phys Chem A 2023; 127:9717-9722. [PMID: 37944122 DOI: 10.1021/acs.jpca.3c05082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
The symmetric (νs) and antisymmetric (νas) O-C-O stretching modes of CO2-containing compounds encode structural information that can be difficult to decipher, due to the sensitivity of these spectral features to small shifts in charge distribution and structure, as well as the anharmonicities of these two vibrational modes. In this work, we discuss the relation between the frequency of these modes and the geometry of the O-C-O group, showing that the splitting between νs and νas (Δνas-s = νas - νs) can be predicted based only on the O-C-O bond angle obtained from quantum chemical calculations with reasonable accuracy (±46 cm-1, R2 = 0.994). The relationship is shown to hold for the infrared spectra of a variety of CO2-containing molecules measured in vacuo. The origins of this model are discussed in the framework of elementary mode analysis.
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Affiliation(s)
- Madison M Foreman
- JILA and Department of Chemistry, University of Colorado-Boulder, 440 UCB, Boulder, Colorado 80309-0440, United States
| | - John F Stanton
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - J Mathias Weber
- JILA and Department of Chemistry, University of Colorado-Boulder, 440 UCB, Boulder, Colorado 80309-0440, United States
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4
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Takayanagi H, Bardaud JX, Hirata K, Brenner V, Gloaguen E, Ishiuchi SI, Fujii M. Stepwise hydration of [CH 3COOMg] + studied by cold ion trap infrared spectroscopy: insights into interactions in the magnesium channel selection filters. Phys Chem Chem Phys 2023; 25:23923-23928. [PMID: 37642502 DOI: 10.1039/d3cp00992k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
The magnesium channel controls Mg2+ concentration in the cell and plays an indispensable role in biological functions. The crystal structure of the Magnesium Transport E channel suggested that Mg2+ hydrated by 6 water molecules is transported through a selection filter consisting of COO- groups on two Asp residues. This Mg2+ motion implies successive pairing with -OOC-R and dissociation mediated by water molecules. For another divalent ion, however, it is known that RCOO-⋯Ca2+ cannot be separated even with 12 water molecules. From this discrepancy, we probe the structure of Mg2+(CH3COO-)(H2O)4-17 clusters by measuring the infrared spectra and monitoring the vibrational frequencies of COO- with the help of quantum chemistry calculations. The hydration by (H2O)6 is not enough to induce ion separation, and partially-separated or separated pairs are formed from 10 water molecules at least. These results suggest that the ion separation between Mg2+ and carboxylate ions in the selection-filter of the MgtE channel not only results from water molecules in their first hydration shell, but also from additional factors including water molecules and protein groups in the second solvation shell of Mg2+.
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Affiliation(s)
- Hikaru Takayanagi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan.
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan
| | - Jean-Xavier Bardaud
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay, Bât 522, Gif-sur-Yvette 91191, France.
| | - Keisuke Hirata
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan.
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Valérie Brenner
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay, Bât 522, Gif-sur-Yvette 91191, France.
| | - Eric Gloaguen
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay, Bât 522, Gif-sur-Yvette 91191, France.
| | - Shun-Ichi Ishiuchi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan.
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Masaaki Fujii
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan.
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan
- IRFI/IPWR, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan
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5
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Mohamed A, Edington SC, Secor M, Breton JR, Hammes-Schiffer S, Johnson MA. Spectroscopic Characterization of the Divalent Metal Docking Motif to Isolated Cyanobenzoate: Direct Observation of Tridentate Binding to ortho-Cyanobenzoate and Implications for the CN Response. J Phys Chem A 2023; 127:1413-1421. [PMID: 36748882 DOI: 10.1021/acs.jpca.2c07658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Cryogenic ion vibrational spectra of D2-tagged cyanobenzoate (CBA) derivatives are obtained and analyzed to characterize the intrinsic spectroscopic responses of the -CO2- headgroup to its location on the ring in both the isolated anions and the cationic complexes with divalent metal ions, M2+ (M = Mg, Ca, Sr). The benzonitrile functionality establishes the different ring isomers (para, meta, ortho) according to the location of the carboxylate and provides an additional reporter on the molecular response to the proximal charge center. The aromatic carboxylates display shifts slightly smaller than those observed for a related aliphatic system upon metal ion complexation. Although the CBA anions display very similar band patterns for all three ring positions, upon complexation with metal ions, the ortho isomer yields dramatically different spectral responses in both the -CO2- moiety and the CN group. This behavior is traced to the emergence of a tridentate binding motif unique to the ortho isomer in which the metal ions bind to both the oxygen atoms of the carboxylate group and the N atom of the cyano group. In that configuration, the -CO2- moiety is oriented perpendicular to the phenyl ring, and the CN stretching fundamental is both strong and red-shifted relative to its behavior in the isolated neutral. The behaviors of the metal-bound ortho complexes occur in contrast to the usual blue shifts associated with "Lewis" type binding of metal ions end-on to -CN. The origins of these spectroscopic features are analyzed with the aid of electronic structure calculations, which also explore differences expected for complexation of monovalent cations to the ortho carboxylate. The resulting insights have implications for understanding the balance between electrostatic and steric interactions at metal binding sites in chemical and biological systems.
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Affiliation(s)
- Ahmed Mohamed
- Sterling Chemistry Laboratory Department of Chemistry, Yale University, New Haven, Connecticut 06512, United States
| | - Sean C Edington
- Sterling Chemistry Laboratory Department of Chemistry, Yale University, New Haven, Connecticut 06512, United States
| | - Maxim Secor
- Sterling Chemistry Laboratory Department of Chemistry, Yale University, New Haven, Connecticut 06512, United States
| | - James R Breton
- Sterling Chemistry Laboratory Department of Chemistry, Yale University, New Haven, Connecticut 06512, United States
| | - Sharon Hammes-Schiffer
- Sterling Chemistry Laboratory Department of Chemistry, Yale University, New Haven, Connecticut 06512, United States
| | - Mark A Johnson
- Sterling Chemistry Laboratory Department of Chemistry, Yale University, New Haven, Connecticut 06512, United States
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6
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Donon J, Bardaud JX, Brenner V, Ishiuchi SI, Fujii M, Gloaguen E. Stepwise dissociation of ion pairs by water molecules: cation-dependent separation mechanisms between carboxylate and alkali-earth metal ions. Phys Chem Chem Phys 2022; 24:12121-12125. [PMID: 35545953 DOI: 10.1039/d2cp01158a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Microhydrated H2-tagged ion pairs (Ca2+, AcO-)(H2O)n=0-8 and (Ba2+, AcO-)(H2O)n=0-5 are investigated by IR photodissociation laser spectroscopy and DFT-D frequency calculations. The detailed picture of the first steps of ion dissociation reveals two mechanisms, where water molecules promote dissociation either directly or indirectly depending on the nature of the cation.
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Affiliation(s)
- Jeremy Donon
- LIDYL, CEA, CNRS, Université Paris Saclay CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France.
| | - Jean-Xavier Bardaud
- LIDYL, CEA, CNRS, Université Paris Saclay CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France.
| | - Valérie Brenner
- LIDYL, CEA, CNRS, Université Paris Saclay CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France.
| | - Shun-Ichi Ishiuchi
- Laboratory for Chemistry and Life Science, Tokyo Institute of Technology, Yokohama 226-8503, Japan.
| | - Masaaki Fujii
- Laboratory for Chemistry and Life Science, Tokyo Institute of Technology, Yokohama 226-8503, Japan.
| | - Eric Gloaguen
- LIDYL, CEA, CNRS, Université Paris Saclay CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France.
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7
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Mitra S, Denton JK, Kelleher PJ, Johnson MA, Guasco TL, Choi TH, Jordan KD. Water Network Shape-Dependence of Local Interactions with the Microhydrated -NO 2- and -CO 2- Anionic Head Groups by Cold Ion Vibrational Spectroscopy. J Phys Chem A 2022; 126:2471-2479. [PMID: 35418229 DOI: 10.1021/acs.jpca.2c00721] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report the structural evolutions of water networks and solvatochromic response of the CH3NO2- radical anion in the OH and CH stretching regions by analysis of the vibrational spectra displayed by cryogenically cooled CH3NO2-·(H2O)n=1-6 clusters. The OH stretching bands evolve with a surprisingly large discontinuity at n = 6, which features the emergence of an intense, strongly red-shifted band along with a weaker feature that appears in the region assigned to a free OH fundamental. Very similar behavior is displayed by the perdeuterated carboxylate clusters, RCO2-·(H2O)n=5-7 (R = CD3CD2), indicating that this behavior is a general feature in the microhydration of the triatomic anionic domain and not associated with CH oscillators. Electronic structure calculations trace this behavior to the formation of a "book" isomer of the water hexamer that adopts a configuration in which one of the water molecules resides in an acceptor-acceptor-donor (AAD) (A = acceptor, D = donor) H-bonding site. Excitation of the bound OH in the AAD site explores the local network topology best suited to stabilize an incipient -XO2H-OH-(H2O)2 intracluster proton-transfer reaction. These systems thus provide particularly clear examples where the network shape controls the potential energy landscape that governs water network-mediated, intracluster proton transfer. The CH stretching bands of the CH3NO2-·(H2O)n=1-6 clusters also exhibit strong solvatochromic shifts, but in this case, they smoothly blue-shift with increasing hydration with no discontinuity at n = 6. This behavior is analyzed in the context of the solute-ion polarizability response and partial charge transfer to the water networks.
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Affiliation(s)
- Sayoni Mitra
- Sterling Chemistry Laboratory, Yale University, P.O. Box 208107, New Haven, Connecticut 06520, United States
| | - Joanna K Denton
- Sterling Chemistry Laboratory, Yale University, P.O. Box 208107, New Haven, Connecticut 06520, United States
| | - Patrick J Kelleher
- Sterling Chemistry Laboratory, Yale University, P.O. Box 208107, New Haven, Connecticut 06520, United States
| | - Mark A Johnson
- Sterling Chemistry Laboratory, Yale University, P.O. Box 208107, New Haven, Connecticut 06520, United States
| | - Timothy L Guasco
- Department of Chemistry, Millikin University, Decatur, Illinois 62522, United States
| | - Tae Hoon Choi
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Kenneth D Jordan
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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8
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Donon J, Habka S, Very T, Charnay-Pouget F, Mons M, Aitken DJ, Brenner V, Gloaguen E. Ion Pair Supramolecular Structure Identified by ATR-FTIR Spectroscopy and Simulations in Explicit Solvent*. Chemphyschem 2021; 22:2442-2455. [PMID: 34637180 DOI: 10.1002/cphc.202100565] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/17/2021] [Indexed: 11/12/2022]
Abstract
The present work uses ATR-FTIR spectroscopy assisted by simulations in explicit solvent and frequency calculations to investigate the supramolecular structure of carboxylate alkali-metal ion pairs in aqueous solutions. ATR-FTIR spectra in the 0.25-4.0 M concentration range displayed cation-specific behaviors, which enabled the measurement of the appearance concentration thresholds of contact ion pairs between 1.9 and 2.6 M depending on the cation. Conformational explorations performed using a non-local optimization method associated to a polarizable force-field (AMOEBA), followed by high quantum chemistry level (RI-B97-D3/dhf-TZVPP) optimizations, mode-dependent scaled harmonic frequency calculations and electron density analyses, were used to identify the main supramolecular structures contributing to the experimental spectra. A thorough analysis enables us to reveal the mechanisms responsible for the spectroscopic sensitivity of the carboxylate group and the respective role played by the cation and the water molecules, highlighting the necessity of combining advanced experimental and theoretical techniques to provide a fair and accurate description of ion pairing.
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Affiliation(s)
- Jeremy Donon
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay, Bât 522, 91191, Gif-sur-Yvette, France
| | - Sana Habka
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay, Bât 522, 91191, Gif-sur-Yvette, France
| | - Thibaut Very
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay, Bât 522, 91191, Gif-sur-Yvette, France.,IDRIS-CNRS, Campus Universitaire d'Orsay, BP 167, 91403, Orsay cedex, France
| | - Florence Charnay-Pouget
- ICMMO, CNRS, Université Paris Sud, Université Paris Saclay, UMR 8182, Bât. 420, 15 rue Georges Clémenceau, 91405, Orsay cedex, France.,Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF, 63000, Clermont-Ferrand, France
| | - Michel Mons
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay, Bât 522, 91191, Gif-sur-Yvette, France
| | - David J Aitken
- ICMMO, CNRS, Université Paris Sud, Université Paris Saclay, UMR 8182, Bât. 420, 15 rue Georges Clémenceau, 91405, Orsay cedex, France
| | - Valérie Brenner
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay, Bât 522, 91191, Gif-sur-Yvette, France
| | - Eric Gloaguen
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay, Bât 522, 91191, Gif-sur-Yvette, France
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9
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Kwasigroch B, Khuu T, Perez EH, Denton JK, Schneider EK, Straßner A, Theisen M, Kruppa SV, Weis P, Kappes MM, Riehn C, Johnson MA, Niedner-Schatteburg G. On the Hydrogen Oxalate Binding Motifs onto Dinuclear Cu and Ag Metal Phosphine Complexes. Chemistry 2021; 27:15136-15146. [PMID: 34632659 PMCID: PMC8597048 DOI: 10.1002/chem.202102768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Indexed: 11/23/2022]
Abstract
We report the binding geometries of the isomers that are formed when the hydrogen oxalate ((CO2)2H=HOx) anion attaches to dinuclear coinage metal phosphine complexes of the form [M1M2dcpm2(HOx)]+ with M=Cu, Ag and dcpm=bis(dicyclohexylphosphino)methane, abbreviated [MM]+. These structures are established by comparison of isomer‐selective experimental vibrational band patterns displayed by the cryogenically cooled and N2‐tagged cations with DFT calculations of the predicted spectra for various local minima. Two isomeric classes are identified that feature either attachment of the carboxylate oxygen atoms to the two metal centers (end‐on docking) or attachment of oxygen atoms on different carbon atoms asymmetrically to the metal ions (side‐on docking). Within each class, there are additional isomeric variations according to the orientation of the OH group. This behavior indicates that HOx undergoes strong and directional coordination to [CuCu]+ but adopts a more flexible coordination to [AgAg]+. Infrared spectra of the bare ions, fragmentation thresholds and ion mobility measurements are reported to explore the behaviors of the complexes at ambient temperature.
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Affiliation(s)
- Björn Kwasigroch
- Department of Chemistry, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 52, 67663, Kaiserslautern, Germany
| | - Thien Khuu
- Sterling Chemistry Laboratory, Yale University, 225 Prospect Str., New Haven, Connecticut, 06520, USA
| | - Evan H Perez
- Sterling Chemistry Laboratory, Yale University, 225 Prospect Str., New Haven, Connecticut, 06520, USA
| | - Joanna K Denton
- Sterling Chemistry Laboratory, Yale University, 225 Prospect Str., New Haven, Connecticut, 06520, USA
| | - Erik K Schneider
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber Weg 2, 76131, Karlsruhe, Germany
| | - Annika Straßner
- Department of Chemistry, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 52, 67663, Kaiserslautern, Germany
| | - Marvin Theisen
- Department of Chemistry, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 52, 67663, Kaiserslautern, Germany
| | - Sebastian V Kruppa
- Department of Chemistry, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 52, 67663, Kaiserslautern, Germany
| | - Patrick Weis
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber Weg 2, 76131, Karlsruhe, Germany
| | - Manfred M Kappes
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber Weg 2, 76131, Karlsruhe, Germany.,Institute for Nanotechnology, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Christoph Riehn
- Department of Chemistry, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 52, 67663, Kaiserslautern, Germany.,Research Center OPTIMAS, Erwin-Schrödinger Str. 46, 67663, Kaiserslautern, Germany
| | - Mark A Johnson
- Sterling Chemistry Laboratory, Yale University, 225 Prospect Str., New Haven, Connecticut, 06520, USA
| | - Gereon Niedner-Schatteburg
- Department of Chemistry, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 52, 67663, Kaiserslautern, Germany.,Research Center OPTIMAS, Erwin-Schrödinger Str. 46, 67663, Kaiserslautern, Germany
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10
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Vazquez de Vasquez MG, Wellen Rudd BA, Baer MD, Beasley EE, Allen HC. Role of Hydration in Magnesium versus Calcium Ion Pairing with Carboxylate: Solution and the Aqueous Interface. J Phys Chem B 2021; 125:11308-11319. [PMID: 34601874 DOI: 10.1021/acs.jpcb.1c06108] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The binding of group II metal cations such as Ca2+ and Mg2+ has been largely categorized as electrostatic or ionic using carboxylate symmetric and asymmetric stretching frequency assignments that have been historically used with little regard for the solvation environment of aqueous solutions. However, given the importance of these cations and their binding mechanisms related to biological function and in revealing surface enrichment factors for ocean to marine aerosol transfer, it is imperative that a deeper understanding be sought to include hydration effects. Here, infrared reflection-absorption and Raman spectra for surface and solution phase carboxylate binding information, respectively, are compared against bare (unbound) carboxylate and bidentate Zn2+:carboxylate spectral signatures. Spectral non-coincidence effect analysis, temperature studies, and spectral and potential of mean force calculations result in a concise interpretation of binding motifs that include the role of mediating water molecules, that is, contact and solvent-shared ion pairs. Calcium directly binds to the carboxylate group in contact ion pairs where magnesium rarely does. Moreover, we reveal the dominance of the solvent-shared ion pair of magnesium with carboxylate at the air-water interface and in solution.
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Affiliation(s)
| | - Bethany A Wellen Rudd
- Department of Chemistry, Ohio Wesleyan University, Delaware, Ohio 43015, United States
| | - Marcel D Baer
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Emma E Beasley
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Heather C Allen
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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11
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Liu S, Featherston ER, Cotruvo JA, Baiz CR. Lanthanide-dependent coordination interactions in lanmodulin: a 2D IR and molecular dynamics simulations study. Phys Chem Chem Phys 2021; 23:21690-21700. [PMID: 34581354 DOI: 10.1039/d1cp03628a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The biological importance of lanthanides, and the early lanthanides (La3+-Nd3+) in particular, has only recently been recognized, and the structural principles underlying selective binding of lanthanide ions in biology are not yet well established. Lanmodulin (LanM) is a novel protein that displays unprecedented affinity and selectivity for lanthanides over most other metal ions, with an uncommon preference for the early lanthanides. Its utilization of EF-hand motifs to bind lanthanides, rather than the Ca2+ typically recognized by these motifs in other proteins, has led it to be used as a model system to understand selective lanthanide recognition. Two-dimensional infrared (2D IR) spectroscopy combined with molecular dynamics simulations were used to investigate LanM's selectivity mechanisms by characterizing local binding site geometries upon coordination of early and late lanthanides as well as calcium. These studies focused on the protein's uniquely conserved proline residues in the second position of each EF-hand binding loop. We found that these prolines constrain the EF-hands for strong coordination of early lanthanides. Substitution of this proline results in a more flexible binding site to accommodate a larger range of ions but also results in less compact coordination geometries and greater disorder within the binding site. Finally, we identify the conserved glycine in the sixth position of each EF-hand as a mediator of local binding site conformation and global secondary structure. Uncovering fundamental structure-function relationships in LanM informs the development of synthetic biology technologies targeting lanthanides in industrial applications.
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Affiliation(s)
- Stephanie Liu
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA.
| | - Emily R Featherston
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA.
| | - Joseph A Cotruvo
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA.
| | - Carlos R Baiz
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA.
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12
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Foreman MM, Hirsch RJ, Weber JM. Effects of Formate Binding to a Bipyridine-Based Cobalt-4N Complex. J Phys Chem A 2021; 125:7297-7302. [PMID: 34396777 DOI: 10.1021/acs.jpca.1c06037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report the vibrational spectrum of a metal-organic complex consisting of a Co center surrounded by two bipyridine-based ligands and explore the change of the spectrum upon addition of a formate ligand to the complex. We assign the spectra using density functional theory. The infrared response encodes the binding motif of the formate to the metal, and the calculated charge distributions highlight the ability of the organic ligand framework to act as charge reservoirs modulating the redox properties of the metal center.
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Affiliation(s)
- Madison M Foreman
- JILA and Department of Chemistry, University of Colorado Boulder, 440 UCB, Boulder, Colorado 80309-0440, United States
| | - Rebecca J Hirsch
- JILA and Department of Chemistry, University of Colorado Boulder, 440 UCB, Boulder, Colorado 80309-0440, United States
| | - J Mathias Weber
- JILA and Department of Chemistry, University of Colorado Boulder, 440 UCB, Boulder, Colorado 80309-0440, United States
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13
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Edington SC, Liu S, Baiz CR. Infrared spectroscopy probes ion binding geometries. Methods Enzymol 2021; 651:157-191. [PMID: 33888203 DOI: 10.1016/bs.mie.2020.12.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Infrared (IR) spectroscopy is a well-established technique for probing the structure, behavior, and surroundings of molecules in their native environments. Its characteristics-most specifically high structural sensitivity, ready applicability to aqueous samples, and broad availability-make it a valuable enzymological technique, particularly for the interrogation of ion binding sites. While IR spectroscopy of the "garden variety" (steady state at room temperature with wild-type proteins) is versatile and powerful in its own right, the combination of IR spectroscopy with specialized experimental schemes for leveraging ultrafast time resolution, protein labeling, and other enhancements further extends this utility. This book chapter provides the fundamental physical background and literature context essential for harnessing IR spectroscopy in the general context of enzymology with specific focus on interrogation of ion binding. Studies of lanthanide ions binding to calmodulin are highlighted as illustrative examples of this process. Appropriate sample preparation, data collection, and spectral interpretation are discussed from a detail-oriented and practical perspective with the goal of facilitating the reader's rapid progression from reading words in a book to collecting and analyzing their own data in the lab.
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Affiliation(s)
- Sean C Edington
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - Stephanie Liu
- Department of Chemistry, The University of Texas at Austin, Austin, TX, United States
| | - Carlos R Baiz
- Department of Chemistry, The University of Texas at Austin, Austin, TX, United States.
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14
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Bai S, Kubelka J, Piri M. A positively charged calcite surface model for molecular dynamics studies of wettability alteration. J Colloid Interface Sci 2020; 569:128-139. [PMID: 32105900 DOI: 10.1016/j.jcis.2020.02.037] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/06/2020] [Accepted: 02/11/2020] [Indexed: 11/29/2022]
Abstract
A new model for a positively charged calcite surface was developed to allow realistic molecular dynamics studies of wettability alteration on carbonate rocks. The surface charge was introduced in a manner consistent with the underlying calcite geochemistry and with the conclusions of recent quantum mechanical studies. The simulations using the new surface model demonstrate that the experimentally observed wettability behavior of calcite is represented correctly. In particular, the model surface became oil-wet due to the adsorption of the carboxylate species. Furthermore, the oil-wet conditions were reversed more effectively by a cationic surfactant than by an anionic one, in agreement with the majority of experimental observations. Finally, with simulated smart water, the well-documented wettability alteration abilities of Ca2+ and SO42- could be explained by the formation of ion-pairs and competitive adsorption onto the surface, respectively. The simulation results with the new surface model conceptually agree with the electric double layer expansion being the predominant mechanism for the low salinity effect in oil recovery enhancement. The proposed calcite surface model will benefit future simulation studies on the wettability characteristics of carbonate rocks, and facilitate the design and optimizations of chemical agents and formulations to enhance the oil recovery from carbonate reservoirs.
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Affiliation(s)
- Shixun Bai
- Center of Innovation for Flow through Porous Media, Department of Petroleum Engineering, University of Wyoming, Laramie, WY 82071, United States
| | - Jan Kubelka
- Center of Innovation for Flow through Porous Media, Department of Petroleum Engineering, University of Wyoming, Laramie, WY 82071, United States.
| | - Mohammad Piri
- Center of Innovation for Flow through Porous Media, Department of Petroleum Engineering, University of Wyoming, Laramie, WY 82071, United States
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15
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Mitra S, Duong CH, McCaslin LM, Gerber RB, Johnson MA. Isomer-specific cryogenic ion vibrational spectroscopy of the D 2 tagged Cs +(HNO 3)(H 2O) n=0-2 complexes: ion-driven enhancement of the acidic H-bond to water. Phys Chem Chem Phys 2020; 22:4501-4507. [PMID: 32068217 DOI: 10.1039/c9cp06689f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report how the binary HNO3(H2O) interaction is modified upon complexation with a nearby Cs+ ion. Isomer-selective IR photodissociation spectra of the D2-tagged, ternary Cs+(HNO3)H2O cation confirms that two structural isomers are generated in the cryogenic ion source. In one of these, both HNO3 and H2O are directly coordinated to the ion, while in the other, the water molecule is attached to the OH group of the acid, which in turn binds to Cs+ with its -NO2 group. The acidic OH stretching fundamental in the latter isomer displays a ∼300 cm-1 red-shift relative to that in the neutral H-bonded van der Waals complex, HNO3(H2O). This behavior is analyzed with the aid of electronic structure calculations and discussed in the context of the increased effective acidity of HNO3 in the presence of the cation.
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Affiliation(s)
- Sayoni Mitra
- Sterling Chemistry Laboratory, Yale University, New Haven, CT, USA.
| | - Chinh H Duong
- Sterling Chemistry Laboratory, Yale University, New Haven, CT, USA.
| | - Laura M McCaslin
- Department of Chemistry, University of California Irvine, Irvine, CA, USA. and Institute of Chemistry and the Fritz-Haber Center for Molecular Dynamics, The Hebrew University, Jerusalem, Israel
| | - R Benny Gerber
- Department of Chemistry, University of California Irvine, Irvine, CA, USA. and Institute of Chemistry and the Fritz-Haber Center for Molecular Dynamics, The Hebrew University, Jerusalem, Israel
| | - Mark A Johnson
- Sterling Chemistry Laboratory, Yale University, New Haven, CT, USA.
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16
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Denton JK, Kelleher PJ, Johnson MA, Baer MD, Kathmann SM, Mundy CJ, Wellen Rudd BA, Allen HC, Choi TH, Jordan KD. Molecular-level origin of the carboxylate head group response to divalent metal ion complexation at the air-water interface. Proc Natl Acad Sci U S A 2019; 116:14874-14880. [PMID: 31278149 PMCID: PMC6660762 DOI: 10.1073/pnas.1818600116] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We exploit gas-phase cluster ion techniques to provide insight into the local interactions underlying divalent metal ion-driven changes in the spectra of carboxylic acids at the air-water interface. This information clarifies the experimental findings that the CO stretching bands of long-chain acids appear at very similar energies when the head group is deprotonated by high subphase pH or exposed to relatively high concentrations of Ca2+ metal ions. To this end, we report the evolution of the vibrational spectra of size-selected [Ca2+·RCO2-]+·(H2O) n=0to12 and RCO2-·(H2O) n=0to14 cluster ions toward the features observed at the air-water interface. Surprisingly, not only does stepwise hydration of the RCO2- anion and the [Ca2+·RCO2-]+ contact ion pair yield solvatochromic responses in opposite directions, but in both cases, the responses of the 2 (symmetric and asymmetric stretching) CO bands to hydration are opposite to each other. The result is that both CO bands evolve toward their interfacial asymptotes from opposite directions. Simulations of the [Ca2+·RCO2-]+·(H2O) n clusters indicate that the metal ion remains directly bound to the head group in a contact ion pair motif as the asymmetric CO stretch converges at the interfacial value by n = 12. This establishes that direct metal complexation or deprotonation can account for the interfacial behavior. We discuss these effects in the context of a model that invokes the water network-dependent local electric field along the C-C bond that connects the head group to the hydrocarbon tail as the key microscopic parameter that is correlated with the observed trends.
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Affiliation(s)
- Joanna K Denton
- Sterling Chemistry Laboratory, Yale University, New Haven, CT 06520
| | | | - Mark A Johnson
- Sterling Chemistry Laboratory, Yale University, New Haven, CT 06520;
| | - Marcel D Baer
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352
| | - Shawn M Kathmann
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352
| | - Christopher J Mundy
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195
| | - Bethany A Wellen Rudd
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH 43210
- Department of Chemistry, Ohio Wesleyan University, Delaware, OH 43015
| | - Heather C Allen
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH 43210
| | - Tae Hoon Choi
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260
| | - Kenneth D Jordan
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, PA 15260
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17
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Edington SC, Halling DB, Bennett SM, Middendorf TR, Aldrich RW, Baiz CR. Non-Additive Effects of Binding Site Mutations in Calmodulin. Biochemistry 2019; 58:2730-2739. [PMID: 31124357 DOI: 10.1021/acs.biochem.9b00096] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Despite decades of research on ion-sensing proteins, gaps persist in the understanding of ion binding affinity and selectivity even in well-studied proteins such as calmodulin. Site-directed mutagenesis is a powerful and popular tool for addressing outstanding questions about biological ion binding and is employed to selectively deactivate binding sites and insert chromophores at advantageous positions within ion binding structures. However, even apparently nonperturbative mutations can distort the binding dynamics they are employed to measure. We use Fourier transform infrared (FTIR) and ultrafast two-dimensional infrared (2D IR) spectroscopy of the carboxylate asymmetric stretching mode in calmodulin as a mutation- and label-independent probe of the conformational perturbations induced in calmodulin's binding sites by two classes of mutation, tryptophan insertion and carboxylate side-chain deletion, commonly used to study ion binding in proteins. Our results show that these mutations not only affect ion binding but also induce changes in calmodulin's conformational landscape along coordinates not probed by vibrational spectroscopy, remaining invisible without additional perturbation of binding site structure. Comparison of FTIR line shapes with 2D IR diagonal slices provides a clear example of how nonlinear spectroscopy produces well-resolved line shapes, refining otherwise featureless spectral envelopes into more informative vibrational spectra of proteins.
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Affiliation(s)
- Sean C Edington
- Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - D Brent Halling
- Department of Neuroscience , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Suzanna M Bennett
- Department of Neuroscience , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Thomas R Middendorf
- Department of Neuroscience , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Richard W Aldrich
- Department of Neuroscience , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Carlos R Baiz
- Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
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18
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Habka S, Very T, Donon J, Vaquero-Vara V, Tardivel B, Charnay-Pouget F, Mons M, Aitken DJ, Brenner V, Gloaguen E. Identification of ion pairs in solution by IR spectroscopy: crucial contributions of gas phase data and simulations. Phys Chem Chem Phys 2019; 21:12798-12805. [PMID: 30977483 DOI: 10.1039/c9cp00700h] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In a context where structure elucidation of ion pairs in solution remains a contemporary challenge, this work explores an original approach where accurate gas phase spectroscopic data are used to refine high level quantum chemistry calculations of ion pairs in solution, resulting in an unprecedented level of accuracy in vibrational frequency prediction. First, gas phase studies focus on a series of isolated contact ion pairs (M+, Ph-CH2-COO-, with M = Li, Na, K, Rb, Cs) for which conformer-selective IR spectra in the CO2- stretch region are recorded. These experiments reveal the interactions at play in isolated contact ion pairs, and provide vibrational frequencies enabling us to assess the accuracy of the theoretical approach used, i.e., mode-dependent scaled harmonic frequency calculations at the RI-B97-D3/dhf-TZVPP level. This level of calculation is then employed on large water clusters embedding either a free acetate ion or its contact or solvent-shared pairs with a sodium cation in order to simulate the individual vibrational spectra of these species in solution. This study shows that the stretching modes of carboxylate are sensitive to both solvent-shared and contact ion pair formation. FTIR spectra of solutions of increasing concentrations indeed reveal several spectral changes consistent with the presence of specific types of solvent-shared and contact ion pairs. By providing relevant guidelines for the interpretation of solution phase IR spectra, this work illustrates the potential of the approach for the elucidation of supramolecular structures in electrolyte solutions.
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Affiliation(s)
- Sana Habka
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France.
| | - Thibaut Very
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France.
| | - Jeremy Donon
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France.
| | - Vanesa Vaquero-Vara
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France.
| | - Benjamin Tardivel
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France.
| | - Florence Charnay-Pouget
- ICMMO, CNRS, Université Paris Sud, Université Paris Saclay, UMR 8182, Bât. 420, 15 rue Georges Clémenceau, 91405 Orsay cedex, France
| | - Michel Mons
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France.
| | - David J Aitken
- ICMMO, CNRS, Université Paris Sud, Université Paris Saclay, UMR 8182, Bât. 420, 15 rue Georges Clémenceau, 91405 Orsay cedex, France
| | - Valérie Brenner
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France.
| | - Eric Gloaguen
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France.
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19
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Valentine ML, Cardenas AE, Elber R, Baiz CR. Physiological Calcium Concentrations Slow Dynamics at the Lipid-Water Interface. Biophys J 2018; 115:1541-1551. [PMID: 30269885 PMCID: PMC6260210 DOI: 10.1016/j.bpj.2018.08.044] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 08/20/2018] [Accepted: 08/27/2018] [Indexed: 02/07/2023] Open
Abstract
Phospholipids can interact strongly with ions at physiological concentrations, and these interactions can alter membrane properties. Here, we describe the effects of calcium ions on the dynamics in phospholipid membranes. We used a combination of time-resolved ultrafast two-dimensional infrared spectroscopy and molecular dynamics simulations. We found that millimolar Ca2+ concentrations lead to slower fluctuations in the local environment at the lipid-water interface of membranes with phosphatidylserine. The effect was only observed in bilayers containing anionic phosphatidylserine; membranes composed of only zwitterionic phosphatidylcholine did not experience a slowdown. Local water dynamics were measured using the ester groups as label-free probes and were found to be up to 50% slower with 2.5 mM Ca2+. Molecular dynamics simulations show that Ca2+ primarily binds to the carboxylate group of phosphatidylserines. These findings have implications for apoptotic and diseased cells in which phosphatidylserine is exposed to extracellular calcium and for the biophysical effects of divalent cations on lipid bilayers.
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Affiliation(s)
- Mason L Valentine
- Department of Chemistry, University of Texas at Austin, Austin, Texas
| | - Alfredo E Cardenas
- Department of Chemistry, University of Texas at Austin, Austin, Texas; Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas
| | - Ron Elber
- Department of Chemistry, University of Texas at Austin, Austin, Texas; Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas
| | - Carlos R Baiz
- Department of Chemistry, University of Texas at Austin, Austin, Texas.
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20
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Menges FS, Zeng HJ, Kelleher PJ, Gorlova O, Johnson MA, Niemann T, Strate A, Ludwig R. Structural Motifs in Cold Ternary Ion Complexes of Hydroxyl-Functionalized Ionic Liquids: Isolating the Role of Cation-Cation Interactions. J Phys Chem Lett 2018; 9:2979-2984. [PMID: 29750531 DOI: 10.1021/acs.jpclett.8b01130] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We address the competition between intermolecular forces underlying the recent observation that ionic liquids (ILs) with a hydroxyl-functionalized cation can form domains with attractive interactions between the nominally repulsive positively charged constituents. Here we show that this behavior is present even in the isolated ternary (HEMIm+)2NTf2- complex (HEMIm+ = 1-(2-hydroxyethyl)-3-methylimidazolium) cooled to about 35 K in a photodissociation mass spectrometer. Of the three isomers isolated by double resonance techniques, one is identified to exhibit direct contact between the cations. This linkage involves a cooperative H-bond wherein the OH group on one cation binds to the OH group on the other, which then attaches to the basic N atom of the anion. Formation of this motif comes at the expense of the usually dominant interaction of the acidic C(2)H group on the Im ring with molecular anions, as evidenced by isomer-dependent shifts in the C(2)H vibrational fundamentals.
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Affiliation(s)
- Fabian S Menges
- Sterling Chemistry Laboratory , Yale University , New Haven , Connecticut 06520 , United States
| | - Helen J Zeng
- Sterling Chemistry Laboratory , Yale University , New Haven , Connecticut 06520 , United States
| | - Patrick J Kelleher
- Sterling Chemistry Laboratory , Yale University , New Haven , Connecticut 06520 , United States
| | - Olga Gorlova
- Sterling Chemistry Laboratory , Yale University , New Haven , Connecticut 06520 , United States
| | - Mark A Johnson
- Sterling Chemistry Laboratory , Yale University , New Haven , Connecticut 06520 , United States
| | - Thomas Niemann
- Department of Chemistry , University of Rostock , 18059 Rostock , Germany
- Leibniz-Institut für Katalyse e.V. , Albert-Einstein-Strasse 29a , 18059 Rostock , Germany
| | - Anne Strate
- Department of Chemistry , University of Rostock , 18059 Rostock , Germany
- Leibniz-Institut für Katalyse e.V. , Albert-Einstein-Strasse 29a , 18059 Rostock , Germany
| | - Ralf Ludwig
- Department of Chemistry , University of Rostock , 18059 Rostock , Germany
- Leibniz-Institut für Katalyse e.V. , Albert-Einstein-Strasse 29a , 18059 Rostock , Germany
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21
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Cao W, Hewage D, Yang DS. Spectroscopy and formation of lanthanum-hydrocarbon radicals formed by association and carbon-carbon bond cleavage of isoprene. J Chem Phys 2018; 148:194302. [PMID: 30307187 DOI: 10.1063/1.5026899] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
La atom reaction with isoprene is carried out in a laser-vaporization molecular beam source. The reaction yields an adduct as the major product and C-C cleaved and dehydrogenated species as the minor ones. La(C5H8), La(C2H2), and La(C3H4) are characterized with mass-analyzed threshold ionization (MATI) spectroscopy and quantum chemical computations. The MATI spectra of all three species exhibit a strong origin band and several weak vibronic bands corresponding to La-ligand stretch and ligand-based bend excitations. La(C5H8) is a five-membered metallacycle, whereas La(C2H2) and La(C3H4) are three-membered rings. All three metallacycles prefer a doublet ground state with a La 6s1-based valence electron configuration and a singlet ion. The five-membered metallacycle is formed through La addition and isoprene isomerization, whereas the two three-membered rings are produced by La addition and insertion, hydrogen migration, and carbon-carbon bond cleavage.
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Affiliation(s)
- Wenjin Cao
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, USA
| | - Dilrukshi Hewage
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, USA
| | - Dong-Sheng Yang
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, USA
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22
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Dodson LG, Thompson MC, Weber JM. Characterization of Intermediate Oxidation States in CO2Activation. Annu Rev Phys Chem 2018; 69:231-252. [DOI: 10.1146/annurev-physchem-050317-021122] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Leah G. Dodson
- JILA and NIST, University of Colorado, Boulder, Colorado 80309-0440, USA
| | - Michael C. Thompson
- JILA and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0440, USA;,
| | - J. Mathias Weber
- JILA and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0440, USA;,
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23
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Coordination to lanthanide ions distorts binding site conformation in calmodulin. Proc Natl Acad Sci U S A 2018; 115:E3126-E3134. [PMID: 29545272 DOI: 10.1073/pnas.1722042115] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The Ca2+-sensing protein calmodulin (CaM) is a popular model of biological ion binding since it is both experimentally tractable and essential to survival in all eukaryotic cells. CaM modulates hundreds of target proteins and is sensitive to complex patterns of Ca2+ exposure, indicating that it functions as a sophisticated dynamic transducer rather than a simple on/off switch. Many details of this transduction function are not well understood. Fourier transform infrared (FTIR) spectroscopy, ultrafast 2D infrared (2D IR) spectroscopy, and electronic structure calculations were used to probe interactions between bound metal ions (Ca2+ and several trivalent lanthanide ions) and the carboxylate groups in CaM's EF-hand ion-coordinating sites. Since Tb3+ is commonly used as a luminescent Ca2+ analog in studies of protein-ion binding, it is important to characterize distinctions between the coordination of Ca2+ and the lanthanides in CaM. Although functional assays indicate that Tb3+ fully activates many Ca2+-dependent proteins, our FTIR spectra indicate that Tb3+, La3+, and Lu3+ disrupt the bidentate coordination geometry characteristic of the CaM binding sites' strongly conserved position 12 glutamate residue. The 2D IR spectra indicate that, relative to the Ca2+-bound form, lanthanide-bound CaM exhibits greater conformational flexibility and larger structural fluctuations within its binding sites. Time-dependent 2D IR lineshapes indicate that binding sites in Ca2+-CaM occupy well-defined configurations, whereas binding sites in lanthanide-bound-CaM are more disordered. Overall, the results show that binding to lanthanide ions significantly alters the conformation and dynamics of CaM's binding sites.
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24
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Wellen Rudd BA, Vidalis AS, Allen HC. Thermodynamic versus non-equilibrium stability of palmitic acid monolayers in calcium-enriched sea spray aerosol proxy systems. Phys Chem Chem Phys 2018; 20:16320-16332. [DOI: 10.1039/c8cp01188e] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Calcium ions bind to palmitic acid monolayers at the air–aqueous interface resulting in changes of both thermodynamic and non-equilibrium stability.
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Affiliation(s)
| | - Andrew S. Vidalis
- Department of Chemistry & Biochemistry
- The Ohio State University
- Columbus
- USA
| | - Heather C. Allen
- Department of Chemistry & Biochemistry
- The Ohio State University
- Columbus
- USA
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25
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Ukmar-Godec T, Bertinetti L, Dunlop JWC, Godec A, Grabiger MA, Masic A, Nguyen H, Zlotnikov I, Zaslansky P, Faivre D. Materials Nanoarchitecturing via Cation-Mediated Protein Assembly: Making Limpet Teeth without Mineral. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2017; 29:1701171. [PMID: 28485089 DOI: 10.1002/adma.201701171] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 04/06/2017] [Indexed: 06/07/2023]
Abstract
Teeth are designed to deliver high forces while withstanding the generated stresses. Aside from isolated mineral-free exception (e.g., marine polychaetes and squids), minerals are thought to be indispensable for tooth-hardening and durability. Here, the unmineralized teeth of the giant keyhole limpet (Megathura crenulata) are shown to attain a stiffness, which is twofold higher than any known organic biogenic structures. In these teeth, protein and chitin fibers establish a stiff compact outer shell enclosing a less compact core. The stiffness and its gradients emerge from a concerted interaction across multiple length-scales: packing of hydrophobic proteins and folding into secondary structures mediated by Ca2+ and Mg2+ together with a strong spatial control in the local fiber orientation. These results integrating nanoindentation, acoustic microscopy, and finite-element modeling for probing the tooth's mechanical properties, spatially resolved small- and wide-angle X-ray scattering for probing the material ordering on the micrometer scale, and energy-dispersive X-ray scattering combined with confocal Raman microscopy to study structural features on the molecular scale, reveal a nanocomposite structure hierarchically assembled to form a versatile damage-tolerant protein-based tooth, with a stiffness similar to mineralized mammalian bone, but without any mineral.
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Affiliation(s)
- Tina Ukmar-Godec
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, Research Campus Golm, 14424, Potsdam, Germany
| | - Luca Bertinetti
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, Research Campus Golm, 14424, Potsdam, Germany
| | - John W C Dunlop
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, Research Campus Golm, 14424, Potsdam, Germany
| | - Aljaž Godec
- Mathematical Biophysics Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Michal A Grabiger
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, Research Campus Golm, 14424, Potsdam, Germany
| | - Admir Masic
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Huynh Nguyen
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, Research Campus Golm, 14424, Potsdam, Germany
| | - Igor Zlotnikov
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, 01307, Dresden, Germany
| | - Paul Zaslansky
- Charite, Julius Wolff Institute for Biomechanics and Musculoskeletal Regeneration, 13353, Berlin, Germany
| | - Damien Faivre
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, Research Campus Golm, 14424, Potsdam, Germany
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