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Khuu T, Rana A, Edington SC, Yang N, McCoy AB, Johnson MA. Observation of Slow Eigen-Zundel Interconversion in H +(H 2O) 6 Clusters upon Isomer-Selective Vibrational Excitation and Buffer Gas Cooling in a Cryogenic Ion Trap. J Am Soc Mass Spectrom 2023; 34:737-744. [PMID: 36972483 DOI: 10.1021/jasms.3c00007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The formation of isomers when trapping floppy cluster ions in a temperature-controlled ion trap is a generally observed phenomenon. This involves collisional quenching of the ions initially formed at high temperature by buffer gas cooling until their internal energies fall below the barriers in the potential energy surface that separate them. Here we explore the kinetics at play in the case of the two isomers adopted by the H+(H2O)6 cluster ion that differ in the proton accommodation motif. One of these is most like the Eigen cation with a tricoordinated hydronium motif (denoted E), and the other is most like the Zundel ion with the proton equally shared between two water molecules (denoted Z). After initial cooling to about 20 K in the radiofrequency (Paul) trap, the relative populations of these two spectroscopically distinct isomers are abruptly changed through isomer-selective photoexcitation of bands in the OH stretching region with a pulsed (∼6 ns) infrared laser while the ions are in the trap. We then monitor the relaxation of the vibrationally excited clusters and reformation of the two cold isomers by recording infrared photodissociation spectra with a second IR laser as a function of delay time from the initial excitation. The latter spectra are obtained after ejecting the trapped ions into a time-of-flight photofragmentation mass spectrometer, thus enabling long (∼0.1 s) delay times. Excitation of the Z isomer is observed to display long-lived vibrationally excited states that are collisionally cooled on a ms time scale, some of which quench into the E isomer. These excited E species then display spontaneous interconversion to the Z form on a ∼10 ms time scale. These qualitative observations set the stage for a series of experimental measurements that can provide quantitative benchmarks for theoretical simulations of cluster dynamics and the potential energy surfaces that underlie them.
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Affiliation(s)
- Thien Khuu
- Sterling Chemistry Laboratory, Yale University, New Haven, Connecticut 06520, United States
| | - Abhijit Rana
- Sterling Chemistry Laboratory, Yale University, New Haven, Connecticut 06520, United States
| | - Sean C Edington
- Sterling Chemistry Laboratory, Yale University, New Haven, Connecticut 06520, United States
| | - Nan Yang
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Anne B McCoy
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Mark A Johnson
- Sterling Chemistry Laboratory, Yale University, New Haven, Connecticut 06520, United States
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Harville PA, Edington SC, Moss OC, Huang M, McCoy AB, Johnson MA. High-resolution vibrational predissociation spectroscopy of I − · H 2O by single-mode CW infrared excitation in a 3D cryogenic ion trap. Mol Phys 2023. [DOI: 10.1080/00268976.2023.2174784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Affiliation(s)
- Payten A. Harville
- Department of Chemistry, Yale University, New Haven, Connecticut, United States of America
| | - Sean C. Edington
- Department of Chemistry, Yale University, New Haven, Connecticut, United States of America
| | - Olivia C. Moss
- Department of Chemistry, Yale University, New Haven, Connecticut, United States of America
| | - Meng Huang
- Department of Chemistry and Cherry Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia, United States of America
| | - Anne B. McCoy
- Department of Chemistry, University of Washington, Seattle, Washington, United States of America
| | - Mark A. Johnson
- Department of Chemistry, Yale University, New Haven, Connecticut, United States of America
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Stropoli SJ, Khuu T, Messinger JP, Karimova NV, Boyer MA, Zakai I, Mitra S, Lachowicz AL, Yang N, Edington SC, Gerber RB, McCoy AB, Johnson MA. Preparation and Characterization of the Halogen-Bonding Motif in the Isolated Cl -·IOH Complex with Cryogenic Ion Vibrational Spectroscopy. J Phys Chem Lett 2022; 13:2750-2756. [PMID: 35315676 DOI: 10.1021/acs.jpclett.2c00218] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In the presence of a halide ion, hypohalous acids can adopt two binding motifs upon formation of the ion-molecule complexes [XHOY]- (X, Y = Cl, Br, I): a hydrogen (HB) bond to the acid OH group and a halogen (XB) bond between the anion and the acid halogen. Here we isolate the X-bonded Cl-·IOH ion-molecule complex by collisions of I-·(H2O)n clusters with HOCl vapor and measure its vibrational spectrum by IR photodissociation of the H2-tagged complex. Anharmonic analysis of its vibrational band pattern reveals that formation of the XB complex results in dramatic lowering of the HOI bending fundamental frequency and elongation of the O-I bond (by 168 cm-1 and 0.13 Å, respectively, relative to isolated HOI). The frequency of the O-I stretch (estimated 436 cm-1) is also encoded in the spectrum by the weak v = 0 → 2 overtone transition at 872 cm-1.
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Affiliation(s)
- Santino J Stropoli
- Sterling Chemistry Laboratory, Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Thien Khuu
- Sterling Chemistry Laboratory, Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Joseph P Messinger
- Sterling Chemistry Laboratory, Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Natalia V Karimova
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Mark A Boyer
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Itai Zakai
- Institute of Chemistry and the Fritz-Haber Center for Molecular Dynamics, The Hebrew University, Jerusalem 91905, Israel
| | - Sayoni Mitra
- Sterling Chemistry Laboratory, Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Anton L Lachowicz
- Sterling Chemistry Laboratory, Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Nan Yang
- Sterling Chemistry Laboratory, Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Sean C Edington
- Sterling Chemistry Laboratory, Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - R Benny Gerber
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
- Institute of Chemistry and the Fritz-Haber Center for Molecular Dynamics, The Hebrew University, Jerusalem 91905, Israel
| | - Anne B McCoy
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Mark A Johnson
- Sterling Chemistry Laboratory, Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
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Edington SC, Perez EH, Charboneau DJ, Menges FS, Hazari N, Johnson MA. Chemical Reduction of Ni II Cyclam and Characterization of Isolated Ni I Cyclam with Cryogenic Vibrational Spectroscopy and Inert-Gas-Mediated High-Resolution Mass Spectrometry. J Phys Chem A 2021; 125:6715-6721. [PMID: 34324319 DOI: 10.1021/acs.jpca.1c05016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
NiII cyclam (cyclam = 1,4,8,11-tetraazacyclotetradecane) is an efficient catalyst for the selective reduction of CO2 to CO. A crucial elementary step in the proposed catalytic cycle is the coordination of CO2 to a NiI cyclam intermediate. Isolation and spectroscopic characterization of this labile NiI species without solvent has proven to be challenging, however, and only partial IR spectra have previously been reported using multiple photon fragmentation of ions generated by gas-phase electron transfer to the NiII cyclam dication at 300 K. Here, we report a chemical reduction method that efficiently prepares NiI cyclam in solution. This enables the NiI complex to be transferred into a cryogenic photofragmentation mass spectrometer using inert-gas-mediated electrospray ionization. The vibrational spectra of the 30 K ion using both H2 and N2 messenger tagging over the range 800-4000 cm-1 were then measured. The resulting spectra were analyzed with the aid of electronic structure calculations, which show strong method dependence in predicted band positions and small molecule activation. The conformational changes of the cyclam ligand induced by binding of the open shell NiI cation were compared with those caused by the spherical, closed-shell LiI cation, which has a similar ionic radius. We also report the vibrational spectrum of a NiI cyclam complex with a strongly bound O2 ligand. The cyclam ligand supporting this species exhibits a large conformational change compared to the complexes with weakly bound N2 and H2, which is likely due to significant charge transfer from Ni to the coordinated O2.
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Affiliation(s)
- Sean C Edington
- Sterling Chemistry Laboratory, Chemistry Department, Yale University, New Haven, Connecticut 06520, United States
| | - Evan H Perez
- Sterling Chemistry Laboratory, Chemistry Department, Yale University, New Haven, Connecticut 06520, United States
| | - David J Charboneau
- Sterling Chemistry Laboratory, Chemistry Department, Yale University, New Haven, Connecticut 06520, United States
| | - Fabian S Menges
- Sterling Chemistry Laboratory, Chemistry Department, Yale University, New Haven, Connecticut 06520, United States
| | - Nilay Hazari
- Sterling Chemistry Laboratory, Chemistry Department, Yale University, New Haven, Connecticut 06520, United States
| | - Mark A Johnson
- Sterling Chemistry Laboratory, Chemistry Department, Yale University, New Haven, Connecticut 06520, United States
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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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Menges FS, Perez EH, Edington SC, Duong CH, Yang N, Johnson MA. Integration of High-Resolution Mass Spectrometry with Cryogenic Ion Vibrational Spectroscopy. J Am Soc Mass Spectrom 2019; 30:1551-1557. [PMID: 31183838 PMCID: PMC6813835 DOI: 10.1007/s13361-019-02238-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 04/23/2019] [Accepted: 04/24/2019] [Indexed: 05/07/2023]
Abstract
We describe an instrumental configuration for the structural characterization of fragment ions generated by collisional dissociation of peptide ions in the typical MS2 scheme widely used for peptide sequencing. Structures are determined by comparing the vibrational band patterns displayed by cryogenically cooled ions with calculated spectra for candidate structural isomers. These spectra were obtained in a linear action mode by photodissociation of weakly bound D2 molecules. This is accomplished by interfacing a Thermo Fisher Scientific Orbitrap Velos Pro to a cryogenic, triple focusing time-of-flight photofragmentation mass spectrometer (the Yale TOF spectrometer). The interface involves replacement of the Orbitrap's higher-energy collisional dissociation cell with a voltage-gated aperture that maintains the commercial instrument's standard capabilities while enabling bidirectional transfer of ions between the high-resolution FT analyzer and external ion sources. The performance of this hybrid instrument is demonstrated by its application to the a1, y1 and z1 fragment ions generated by CID of a prototypical dipeptide precursor, protonated L-phenylalanyl-L-tyrosine (H+-Phe-Tyr-OH or FY-H+). The structure of the unusual z1 ion, nominally formed after NH3 is ejected from the protonated tyrosine (y1) product, is identified as the cyclopropane-based product is tentatively identified as a cyclopropane-based product.
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Affiliation(s)
- Fabian S Menges
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
| | - Evan H Perez
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
| | - Sean C Edington
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
| | - Chinh H Duong
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
| | - Nan Yang
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
| | - Mark A Johnson
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA.
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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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Affiliation(s)
- Sean C. Edington
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Carlos R. Baiz
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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Affiliation(s)
- Sean C. Edington
- Department
of Chemistry, University of Texas at Austin, 105 E. 24th St. Stop A5300, Austin, Texas 78712-1224, United States
| | - Jennifer C. Flanagan
- Department
of Chemistry, University of Texas at Austin, 105 E. 24th St. Stop A5300, Austin, Texas 78712-1224, United States
| | - Carlos R. Baiz
- Department
of Chemistry, University of Texas at Austin, 105 E. 24th St. Stop A5300, Austin, Texas 78712-1224, United States
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