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Felsted RG, Graham TR, Zhao Y, Bazak JD, Nienhuis ET, Pauzauskie PJ, Joly AG, Pearce CI, Wang Z, Rosso KM. Anionic Effects on Concentrated Aqueous Lithium Ion Dynamics. J Phys Chem Lett 2024:5076-5087. [PMID: 38708887 DOI: 10.1021/acs.jpclett.4c00585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
The dynamics, orientational anisotropy, diffusivity, viscosity, and density were measured for concentrated lithium salt solutions, including lithium chloride (LiCl), lithium bromide (LiBr), lithium nitrite (LiNO2), and lithium nitrate (LiNO3), with methyl thiocyanate as an infrared vibrational probe molecule, using two-dimensional infrared spectroscopy (2D IR), nuclear magnetic resonance (NMR) spectroscopy, and viscometry. The 2D IR, NMR, and viscosity results show that LiNO2 exhibits longer correlation times, lower diffusivity, and nearly 4 times greater viscosity compared to those of the other lithium salt solutions of the same concentration, suggesting that nitrite anions may strongly facilitate structure formation via strengthening water-ion network interactions, directly impacting bulk solution properties at sufficiently high concentrations. Additionally, the LiNO2 and LiNO3 solutions show significantly weakened chemical interactions between the lithium cations and the methyl thiocyanate when compared with those of the lithium halide salts.
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Affiliation(s)
- Robert G Felsted
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Trent R Graham
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Yatong Zhao
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - J David Bazak
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Emily T Nienhuis
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Peter J Pauzauskie
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- Materials Science and Engineering Department, University of Washington, Seattle, Washington 98195, United States
| | - Alan G Joly
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Carolyn I Pearce
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington 99164, United States
| | - Zheming Wang
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Kevin M Rosso
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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2
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Roget SA, Carter-Fenk KA, Fayer MD. Water Dynamics and Structure of Highly Concentrated LiCl Solutions Investigated Using Ultrafast Infrared Spectroscopy. J Am Chem Soc 2022; 144:4233-4243. [PMID: 35226487 DOI: 10.1021/jacs.2c00616] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In highly concentrated salt solutions, the water hydrogen bond (H-bond) network is completely disrupted by the presence of ions. Water is forced to restructure as dictated by the water-ion and ion-ion interactions. Using ultrafast polarization-selective pump-probe (PSPP) spectroscopy measurements of the OD stretch of dilute HOD, we demonstrate that the limited water-water H-bonding present in concentrated lithium chloride solutions (up to four waters per ion pair) is, on average, stronger than that occurring in bulk water. Furthermore, information on the orientational dynamics and the angular restriction of water H-bonded to both water oxygens and chloride anions was obtained through analysis of the frequency-dependent anisotropy decays. It was found that, when the salt concentration increased, the water showed increasing restriction and slowing at frequencies correlated with strong H-bonding. The angular restriction of the water molecules and strengthening of water-water H-bonds are due to the formation of a water-ion network not present in bulk water and dilute salt solutions. The structural evolution of the ionic medium was also observed through spectral diffusion of the OD stretch using 2D IR spectroscopy. Compared to bulk water, there is significant slowing of the biexponential spectral diffusion dynamics. The slowest component of the spectral diffusion (13 ps) is virtually identical to the time for complete reorientation of HOD measured with the PSPP experiments. This result suggests that the slowest component of the spectral diffusion reflects rearrangement of water molecules in the water-ion network.
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Affiliation(s)
- Sean A Roget
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | | | - Michael D Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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3
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Yuan R, Fayer MD. Dynamics of Water Molecules and Ions in Concentrated Lithium Chloride Solutions Probed with Ultrafast 2D IR Spectroscopy. J Phys Chem B 2019; 123:7628-7639. [DOI: 10.1021/acs.jpcb.9b06038] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Rongfeng Yuan
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Michael D. Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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4
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Eckert PA, Kubarych KJ. Solvent Quality Controls Macromolecular Structural Dynamics of a Dendrimeric Hydrogenase Model. J Phys Chem B 2018; 122:12154-12163. [PMID: 30427195 DOI: 10.1021/acs.jpcb.8b07259] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We report a spectroscopic investigation of the ultrafast dynamics of the second-generation poly(aryl ether) dendritic hydrogenase model using two-dimensional infrared (2D-IR) spectroscopy to probe the metal carbonyl vibrations of the dendrimer and a reference small molecule, [Fe(μ-S)(CO)3]2. We find that the structural dynamics of the dendrimer are reflected in a slow phase of the spectral diffusion, which is absent from [Fe(μ-S)(CO)3]2, and we relate the slow phase to the quality of the solvent for poly(aryl ether) dendrimers. We observe a solvent-dependent modulation of the initial phase of vibrational relaxation of the carbonyl groups, which we attribute to an inhibition of solvent assistance in the intramolecular vibrational redistribution process for the dendrimer. There is also a clear solvent dependence of the vibrational frequencies of both the dendrimer and [Fe(μ-S)(CO)3]2. Our data represent the first 2D-IR study of a dendritic complex and provide insight into the solvent dependence of molecular conformation in solution and the ultrafast dynamics of moderately sized, conformationally mobile compounds.
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Affiliation(s)
- Peter A Eckert
- Department of Chemistry , University of Michigan , 930 N. University Avenue , Ann Arbor , Michigan 49109 , United States
| | - Kevin J Kubarych
- Department of Chemistry , University of Michigan , 930 N. University Avenue , Ann Arbor , Michigan 49109 , United States
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5
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Giammanco CH, Kramer PL, Yamada SA, Nishida J, Tamimi A, Fayer MD. Carbon dioxide in an ionic liquid: Structural and rotational dynamics. J Chem Phys 2016; 144:104506. [DOI: 10.1063/1.4943390] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Chiara H. Giammanco
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Patrick L. Kramer
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Steven A. Yamada
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Jun Nishida
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Amr Tamimi
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Michael D. Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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6
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Tamimi A, Fayer MD. Ionic Liquid Dynamics Measured with 2D IR and IR Pump–Probe Experiments on a Linear Anion and the Influence of Potassium Cations. J Phys Chem B 2016; 120:5842-54. [DOI: 10.1021/acs.jpcb.6b00409] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Amr Tamimi
- Department
of Chemistry Stanford University, Stanford, California 94305, United States
| | - Michael D. Fayer
- Department
of Chemistry Stanford University, Stanford, California 94305, United States
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7
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Kramer PL, Nishida J, Fayer MD. Separation of experimental 2D IR frequency-frequency correlation functions into structural and reorientation-induced contributions. J Chem Phys 2015; 143:124505. [DOI: 10.1063/1.4931402] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Patrick L. Kramer
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Jun Nishida
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Michael D. Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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9
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Kramer PL, Giammanco CH, Fayer MD. Dynamics of water, methanol, and ethanol in a room temperature ionic liquid. J Chem Phys 2015; 142:212408. [DOI: 10.1063/1.4914156] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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10
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Kramer PL, Nishida J, Giammanco CH, Tamimi A, Fayer MD. Observation and theory of reorientation-induced spectral diffusion in polarization-selective 2D IR spectroscopy. J Chem Phys 2015; 142:184505. [DOI: 10.1063/1.4920949] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Patrick L. Kramer
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Jun Nishida
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Chiara H. Giammanco
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Amr Tamimi
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Michael D. Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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11
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Giammanco CH, Kramer PL, Fayer MD. Dynamics of Dihydrogen Bonding in Aqueous Solutions of Sodium Borohydride. J Phys Chem B 2015; 119:3546-59. [DOI: 10.1021/jp512426y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chiara H. Giammanco
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Patrick L. Kramer
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Michael D. Fayer
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
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12
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Structural dynamics inside a functionalized metal-organic framework probed by ultrafast 2D IR spectroscopy. Proc Natl Acad Sci U S A 2014; 111:18442-7. [PMID: 25512539 DOI: 10.1073/pnas.1422194112] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The structural elasticity of metal-organic frameworks (MOFs) is a key property for their functionality. Here, we show that 2D IR spectroscopy with pulse-shaping techniques can probe the ultrafast structural fluctuations of MOFs. 2D IR data, obtained from a vibrational probe attached to the linkers of UiO-66 MOF in low concentration, revealed that the structural fluctuations have time constants of 7 and 670 ps with no solvent. Filling the MOF pores with dimethylformamide (DMF) slows the structural fluctuations by reducing the ability of the MOF to undergo deformations, and the dynamics of the DMF molecules are also greatly restricted. Methodology advances were required to remove the severe light scattering caused by the macroscopic-sized MOF particles, eliminate interfering oscillatory components from the 2D IR data, and address Förster vibrational excitation transfer.
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13
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Adamczyk K, Simpson N, Greetham GM, Gumiero A, Walsh MA, Towrie M, Parker AW, Hunt NT. Ultrafast infrared spectroscopy reveals water-mediated coherent dynamics in an enzyme active site. Chem Sci 2014; 6:505-516. [PMID: 28936306 PMCID: PMC5588449 DOI: 10.1039/c4sc02752c] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 10/22/2014] [Indexed: 11/24/2022] Open
Abstract
Ultrafast infrared spectroscopy provides insights into the dynamic nature of water in the active sites of catalase and peroxidase enzymes.
Understanding the impact of fast dynamics upon the chemical processes occurring within the active sites of proteins and enzymes is a key challenge that continues to attract significant interest, though direct experimental insight in the solution phase remains sparse. Similar gaps in our knowledge exist in understanding the role played by water, either as a solvent or as a structural/dynamic component of the active site. In order to investigate further the potential biological roles of water, we have employed ultrafast multidimensional infrared spectroscopy experiments that directly probe the structural and vibrational dynamics of NO bound to the ferric haem of the catalase enzyme from Corynebacterium glutamicum in both H2O and D2O. Despite catalases having what is believed to be a solvent-inaccessible active site, an isotopic dependence of the spectral diffusion and vibrational lifetime parameters of the NO stretching vibration are observed, indicating that water molecules interact directly with the haem ligand. Furthermore, IR pump–probe data feature oscillations originating from the preparation of a coherent superposition of low-frequency vibrational modes in the active site of catalase that are coupled to the haem ligand stretching vibration. Comparisons with an exemplar of the closely-related peroxidase enzyme family shows that they too exhibit solvent-dependent active-site dynamics, supporting the presence of interactions between the haem ligand and water molecules in the active sites of both catalases and peroxidases that may be linked to proton transfer events leading to the formation of the ferryl intermediate Compound I. In addition, a strong, water-mediated, hydrogen bonding structure is suggested to occur in catalase that is not replicated in peroxidase; an observation that may shed light on the origins of the different functions of the two enzymes.
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Affiliation(s)
- Katrin Adamczyk
- Department of Physics , University of Strathclyde , SUPA , 107 Rottenrow East , Glasgow , G4 0NG , UK .
| | - Niall Simpson
- Department of Physics , University of Strathclyde , SUPA , 107 Rottenrow East , Glasgow , G4 0NG , UK .
| | - Gregory M Greetham
- Central Laser Facility , Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford , Didcot, Oxon , OX11 0QX , UK
| | - Andrea Gumiero
- Diamond Light Source , Diamond House, Harwell Science and Innovation Campus , Didcot, Oxfordshire , OX11 0DE , UK
| | - Martin A Walsh
- Diamond Light Source , Diamond House, Harwell Science and Innovation Campus , Didcot, Oxfordshire , OX11 0DE , UK
| | - Michael Towrie
- Central Laser Facility , Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford , Didcot, Oxon , OX11 0QX , UK
| | - Anthony W Parker
- Central Laser Facility , Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford , Didcot, Oxon , OX11 0QX , UK
| | - Neil T Hunt
- Department of Physics , University of Strathclyde , SUPA , 107 Rottenrow East , Glasgow , G4 0NG , UK .
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14
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Kel O, Tamimi A, Fayer MD. The Influence of Cholesterol on Fast Dynamics Inside of Vesicle and Planar Phospholipid Bilayers Measured with 2D IR Spectroscopy. J Phys Chem B 2014; 119:8852-62. [DOI: 10.1021/jp503940k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Oksana Kel
- Department
of Chemistry, Stanford University, Stanford, California 94305-5080, United States
| | - Amr Tamimi
- Department
of Chemistry, Stanford University, Stanford, California 94305-5080, United States
| | - Michael D. Fayer
- Department
of Chemistry, Stanford University, Stanford, California 94305-5080, United States
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15
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pH-dependent picosecond structural dynamics in the distal pocket of nitrophorin 4 investigated by 2D IR spectroscopy. J Phys Chem B 2013; 117:15804-11. [PMID: 23885811 DOI: 10.1021/jp407052a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nitrophorin 4 (NP4) belongs to a family of pH-sensitive, nitric oxide (NO) transporter proteins that undergo a large structural change from a closed to an open conformation at high pH to allow for NO delivery. Measuring the pH-dependent structural dynamics in NP4-NO around the ligand binding site is crucial for developing a mechanistic understanding of NO binding and release. In this study, we use coherent two-dimensional infrared (2D IR) spectroscopy to measure picosecond structural dynamics sampled by the nitrosyl stretch in NP4-NO as a function of pH at room temperature. Our results show that both the closed and open conformers of the protein are present at low (pD 5.1) and high (pD 7.9) pH conditions. The closed and open conformers are characterized by two frequencies of the nitrosyl stretching vibration labeled A0 and A1, respectively. Analysis of the 2D IR line shapes reveals that at pD 5.1, the closed conformer experiences structural fluctuations arising from solvation dynamics on a ∼3 ps time scale. At pD 7.9, both the open and closed conformers exhibit fluctuations on a ∼1 ps time scale. At both pD conditions, the closed conformers maintain a static distribution of structures within the experimental time window of 100 ps. This is in contrast to the open conformer, which is able to interconvert among its substates on a ∼100 ps time scale. Our results directly measure the time scales of solvation dynamics in the distal pocket, the flexibility of the open conformation at high pH, and the rigidity of the closed conformers at both pH conditions. We discuss how the pH-dependent equilibrium structural fluctuations of the nitrosyl ligand measured in this study are related to the uptake and delivery of nitric oxide in NP4.
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16
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Kel O, Tamimi A, Thielges MC, Fayer MD. Ultrafast Structural Dynamics Inside Planar Phospholipid Multibilayer Model Cell Membranes Measured with 2D IR Spectroscopy. J Am Chem Soc 2013; 135:11063-74. [DOI: 10.1021/ja403675x] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Oksana Kel
- Department of Chemistry, Stanford University, Stanford, California 94305, United
States
| | - Amr Tamimi
- Department of Chemistry, Stanford University, Stanford, California 94305, United
States
| | - Megan C. Thielges
- Department of Chemistry, Stanford University, Stanford, California 94305, United
States
| | - Michael D. Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305, United
States
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17
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Brookes JF, Slenkamp KM, Lynch MS, Khalil M. Effect of solvent polarity on the vibrational dephasing dynamics of the nitrosyl stretch in an Fe(II) complex revealed by 2D IR spectroscopy. J Phys Chem A 2013; 117:6234-43. [PMID: 23480848 DOI: 10.1021/jp4005345] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The vibrational dephasing dynamics of the nitrosyl stretching vibration (ν(NO)) in sodium nitroprusside (SNP, Na2[Fe(CN)5NO]·2H2O) are investigated using two-dimensional infrared (2D IR) spectroscopy. The ν(NO) in SNP acts as a model system for the nitrosyl ligand found in metalloproteins which play an important role in the transportation and detection of nitric oxide (NO) in biological systems. We perform a 2D IR line shape study of the ν(NO) in the following solvents: water, deuterium oxide, methanol, ethanol, ethylene glycol, formamide, and dimethyl sulfoxide. The frequency of the ν(NO) exhibits a large vibrational solvatochromic shift of 52 cm(-1), ranging from 1884 cm(-1) in dimethyl sulfoxide to 1936 cm(-1) in water. The vibrational anharmonicity of the ν(NO) varies from 21 to 28 cm(-1) in the solvents used in this study. The frequency-frequency correlation functions (FFCFs) of the ν(NO) in SNP in each of the seven solvents are obtained by fitting the experimentally obtained 2D IR spectra using nonlinear response theory. The fits to the 2D IR line shape reveal that the spectral diffusion time scale of the ν(NO) in SNP varies from 0.8 to 4 ps and is negatively correlated with the empirical solvent polarity scales. We compare our results with the experimentally determined FFCFs of other charged vibrational probes in polar solvents and in the active sites of heme proteins. Our results suggest that the vibrational dephasing dynamics of the ν(NO) in SNP reflect the fluctuations of the nonhomogeneous electric field created by the polar solvents around the nitrosyl and cyanide ligands. The solute solvent interactions occurring at the trans-CN ligand are sensed through the π-back-bonding network along the Fe-NO bond in SNP.
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Affiliation(s)
- Jennifer F Brookes
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
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18
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Kumar SKK, Tamimi A, Fayer MD. Dynamics in the interior of AOT lamellae investigated with two-dimensional infrared spectroscopy. J Am Chem Soc 2013; 135:5118-26. [PMID: 23465101 DOI: 10.1021/ja312676e] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The dynamics inside the organic regions of aerosol-OT (AOT)/water mixtures in the lamellar mesophase, bicontinuous cubic (BC) phase, and in an analogous molecule without the charged sulfonate headgroup are investigated by observing spectral diffusion, orientational relaxation and population relaxation using ultrafast two-dimensional infrared (2D IR) vibrational echo spectroscopy and IR pump-probe experiments on the asymmetric CO stretch of a vibrational probe, tungsten hexacarbonyl (W(CO)6). The water layer thickness between the bilayer planes in the lamellar phase was varied. For comparison, the dynamics of W(CO)6 in the normal liquid bis(2-ethylhexyl) succinate (EHS), which is analogous to AOT but has no charged sulfonate headgroup, were also studied. The 2D IR experiments measure spectral diffusion, which results from the structural evolution of the system. Spectral diffusion is quantified by the frequency-frequency correlation function (FFCF). In addition to a homogeneous component, the FFCFs are biexponential decays with fast and slow time components of ∼12.5 and ∼150 ps in the lamellar phase. Both components of the FFCF are independent of the number of water molecules per headgroup for the lamellae, but they slow somewhat in the BC phase. The dynamics in the ordered phases are in sharp contrast to the dynamics in EHS, which displays fast and slow components of the FFCF of 5 and 80 ps, respectively. As the hydration level of AOT increases, vibrational lifetime decreases, suggesting some change in the local environment of W(CO)6 with water content.
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Affiliation(s)
- S K Karthick Kumar
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
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19
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Wong DB, Giammanco CH, Fenn EE, Fayer MD. Dynamics of Isolated Water Molecules in a Sea of Ions in a Room Temperature Ionic Liquid. J Phys Chem B 2013; 117:623-35. [DOI: 10.1021/jp310086s] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Daryl B. Wong
- Department of Chemistry, Stanford University, Stanford, California 94305, United
States
| | - Chiara H. Giammanco
- Department of Chemistry, Stanford University, Stanford, California 94305, United
States
| | - Emily E. Fenn
- Department of Chemistry, Stanford University, Stanford, California 94305, United
States
| | - Michael D. Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305, United
States
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20
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Chung JK, Thielges MC, Lynch SR, Fayer MD. Fast dynamics of HP35 for folded and urea-unfolded conditions. J Phys Chem B 2012; 116:11024-31. [PMID: 22909017 DOI: 10.1021/jp304058x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The changes in fast dynamics of HP35 with a double CN vibrational dynamics label (HP35-P(2)) as a function of the extent of denaturation by urea were investigated with two-dimensional infrared (2D IR) vibrational echo spectroscopy. Cyanophenylalanine (PheCN) replaces the native phenylalanine at two residues in the hydrophobic core of HP35, providing vibrational probes. NMR data show that HP35-P(2) maintains the native folded structure similar to wild type and that both PheCN residues share essentially the same environment within the peptide. A series of time-dependent 2D IR vibrational echo spectra were obtained for the folded peptide and the increasingly unfolded peptide. Analysis of the time dependence of the 2D spectra yields the system's spectral diffusion, which is caused by the sampling of accessible structures of the peptide under thermal equilibrium conditions. The structural dynamics become faster as the degree of unfolding is increased.
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Affiliation(s)
- Jean K Chung
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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21
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Bagchi S, Boxer SG, Fayer MD. Ribonuclease S dynamics measured using a nitrile label with 2D IR vibrational echo spectroscopy. J Phys Chem B 2012; 116:4034-42. [PMID: 22417088 PMCID: PMC3354990 DOI: 10.1021/jp2122856] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A nitrile-labeled amino acid, p-cyanophenylalanine, is introduced near the active site of the semisynthetic enzyme ribonuclease S to serve as a probe of protein dynamics and fluctuations. Ribonuclease S is the limited proteolysis product of subtilisin acting on ribonuclease A, and consists of a small fragment including amino acids 1-20, the S-peptide, and a larger fragment including residues 21-124, the S-protein. A series of two-dimensional vibrational echo experiments performed on the nitrile-labeled S-peptide and the RNase S are described. The time-dependent changes in the two-dimensional infrared vibrational echo line shapes are analyzed using the center line slope method to obtain the frequency-frequency correlation function (FFCF). The observations show that the nitrile probe in the S-peptide has dynamics that are similar to, but faster than, those of the single amino acid p-cyanophenylalanine in water. In contrast, the dynamics of the nitrile label when the peptide is bound to form ribonuclease S are dominated by homogeneous dephasing (motionally narrowed) contributions with only a small contribution from very fast inhomogeneous structural dynamics. The results provide insights into the nature of the structural dynamics of the ribonuclease S complex. The equilibrium dynamics of the nitrile labeled S-peptide and the ribonuclease S complex are also investigated by molecular dynamics simulations. The experimentally determined FFCFs are compared to the FFCFs obtained from the molecular dynamics simulations, thereby testing the capacity of simulations to determine the amplitudes and time scales of protein structural fluctuations on fast time scales under thermal equilibrium conditions.
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Affiliation(s)
- Sayan Bagchi
- Department of Chemistry, Stanford University, Stanford, California 94305
| | - Steven G. Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305
| | - M. D. Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305
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22
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Rosenfeld DE, Gengeliczki Z, Smith BJ, Stack TDP, Fayer MD. Structural Dynamics of a Catalytic Monolayer Probed by Ultrafast 2D IR Vibrational Echoes. Science 2011; 334:634-9. [DOI: 10.1126/science.1211350] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
| | - Zsolt Gengeliczki
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Brian J. Smith
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - T. D. P. Stack
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - M. D. Fayer
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
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23
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Eigner AA, Jones BH, Koprucki BW, Massari AM. Ground-State Structural Dynamics in Doped and Undoped Polyaniline Films Probed by Two-Dimensional Infrared Vibrational Echo Spectroscopy. J Phys Chem B 2011; 115:4583-91. [DOI: 10.1021/jp1113009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Audrey A. Eigner
- Department of Chemistry, University of Minnesota—Twin Cities, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Brynna H. Jones
- Department of Chemistry, University of Minnesota—Twin Cities, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Bryce W. Koprucki
- Department of Chemistry, University of Minnesota—Twin Cities, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Aaron M. Massari
- Department of Chemistry, University of Minnesota—Twin Cities, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
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24
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Bagchi S, Nebgen BT, Loring RF, Fayer MD. Dynamics of a myoglobin mutant enzyme: 2D IR vibrational echo experiments and simulations. J Am Chem Soc 2010; 132:18367-76. [PMID: 21142083 PMCID: PMC3033732 DOI: 10.1021/ja108491t] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Myoglobin (Mb) double mutant T67R/S92D displays peroxidase enzymatic activity in contrast to the wild type protein. The CO adduct of T67R/S92D shows two CO absorption bands corresponding to the A(1) and A(3) substates. The equilibrium protein dynamics for the two distinct substates of the Mb double mutant are investigated by using two-dimensional infrared (2D IR) vibrational echo spectroscopy and molecular dynamics (MD) simulations. The time-dependent changes in the 2D IR vibrational echo line shapes for both of the substates are analyzed using the center line slope (CLS) method to obtain the frequency-frequency correlation function (FFCF). The results for the double mutant are compared to those from the wild type Mb. The experimentally determined FFCF is compared to the FFCF obtained from molecular dynamics simulations, thereby testing the capacity of a force field to determine the amplitudes and time scales of protein structural fluctuations on fast time scales. The results provide insights into the nature of the energy landscape around the free energy minimum of the folded protein structure.
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Affiliation(s)
- Sayan Bagchi
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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25
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Kim S, Chung JK, Kwak K, Bowman SEJ, Bren KL, Bagchi B, Fayer MD. Native and unfolded cytochrome c--comparison of dynamics using 2D-IR vibrational echo spectroscopy. J Phys Chem B 2008; 112:10054-63. [PMID: 18646797 PMCID: PMC2671645 DOI: 10.1021/jp802246h] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Unfolded vs native CO-coordinated horse heart cytochrome c (h-cyt c) and a heme axial methionine mutant cyt c552 from Hydrogenobacter thermophilus ( Ht-M61A) are studied by IR absorption spectroscopy and ultrafast 2D-IR vibrational echo spectroscopy of the CO stretching mode. The unfolding is induced by guanidinium hydrochloride (GuHCl). The CO IR absorption spectra for both h-cyt c and Ht-M61A shift to the red as the GuHCl concentration is increased through the concentration region over which unfolding occurs. The spectra for the unfolded state are substantially broader than the spectra for the native proteins. A plot of the CO peak position vs GuHCl concentration produces a sigmoidal curve that overlays the concentration-dependent circular dichroism (CD) data of the CO-coordinated forms of both Ht-M61A and h-cyt c within experimental error. The coincidence of the CO peak shift curve with the CD curves demonstrates that the CO vibrational frequency is sensitive to the structural changes induced by the denaturant. 2D-IR vibrational echo experiments are performed on native Ht-M61A and on the protein in low- and high-concentration GuHCl solutions. The 2D-IR vibrational echo is sensitive to the global protein structural dynamics on time scales from subpicosecond to greater than 100 ps through the change in the shape of the 2D spectrum with time (spectral diffusion). At the high GuHCl concentration (5.1 M), at which Ht-M61A is essentially fully denatured as judged by CD, a very large reduction in dynamics is observed compared to the native protein within the approximately 100 ps time window of the experiment. The results suggest the denatured protein may be in a glassy-like state involving hydrophobic collapse around the heme.
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Affiliation(s)
- Seongheun Kim
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Jean K. Chung
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Kyungwon Kwak
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Sarah E. J. Bowman
- Department of Chemistry, University of Rochester, Rochester, NY 14627-0216
| | - Kara L. Bren
- Department of Chemistry, University of Rochester, Rochester, NY 14627-0216
| | - Biman Bagchi
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - M. D. Fayer
- Department of Chemistry, Stanford University, Stanford, CA 94305
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26
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Schmidt JR, Corcelli SA. Infrared absorption line shapes in the classical limit: A comparison of the classical dipole and fluctuating frequency approximations. J Chem Phys 2008; 128:184504. [DOI: 10.1063/1.2917349] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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27
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28
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Ishikawa H, Finkelstein IJ, Kim S, Kwak K, Chung JK, Wakasugi K, Massari AM, Fayer MD. Neuroglobin dynamics observed with ultrafast 2D-IR vibrational echo spectroscopy. Proc Natl Acad Sci U S A 2007; 104:16116-21. [PMID: 17916624 PMCID: PMC2042171 DOI: 10.1073/pnas.0707718104] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2007] [Indexed: 01/15/2023] Open
Abstract
Neuroglobin (Ngb), a protein in the globin family, is found in vertebrate brains. It binds oxygen reversibly. Compared with myoglobin (Mb), the amino acid sequence has limited similarity, but key residues around the heme and the classical globin fold are conserved in Ngb. The CO adduct of Ngb displays two CO absorption bands in the IR spectrum, referred to as N(3) (distal histidine in the pocket) and N(0) (distal histidine swung out of the pocket), which have absorption spectra that are almost identical with the Mb mutants L29F and H64V, respectively. The Mb mutants mimic the heme pocket structures of the corresponding Ngb conformers. The equilibrium protein dynamics for the CO adduct of Ngb are investigated by using ultrafast 2D-IR vibrational echo spectroscopy by observing the CO vibration's spectral diffusion (2D-IR spectra time dependence) and comparing the results with those for the Mb mutants. Although the heme pocket structure and the CO FTIR peak positions of Ngb are similar to those of the mutant Mb proteins, the 2D-IR results demonstrate that the fast structural fluctuations of Ngb are significantly slower than those of the mutant Mbs. The results may also provide some insights into the nature of the energy landscape in the vicinity of the folded protein free energy minimum.
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Affiliation(s)
- Haruto Ishikawa
- Department of Chemistry, Stanford University, Stanford, CA 94305; and
| | | | - Seongheun Kim
- Department of Chemistry, Stanford University, Stanford, CA 94305; and
| | - Kyungwon Kwak
- Department of Chemistry, Stanford University, Stanford, CA 94305; and
| | - Jean K. Chung
- Department of Chemistry, Stanford University, Stanford, CA 94305; and
| | - Keisuke Wakasugi
- Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Tokyo 153-8902, Japan
| | - Aaron M. Massari
- Department of Chemistry, Stanford University, Stanford, CA 94305; and
| | - Michael D. Fayer
- Department of Chemistry, Stanford University, Stanford, CA 94305; and
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29
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Li S, Schmidt JR, Corcelli SA, Lawrence CP, Skinner JL. Approaches for the calculation of vibrational frequencies in liquids: comparison to benchmarks for azide/water clusters. J Chem Phys 2007; 124:204110. [PMID: 16774322 DOI: 10.1063/1.2200690] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Ultrafast vibrational spectroscopy experiments, together with molecular-level theoretical interpretation, can provide important information about the structure and dynamics of complex condensed phase systems, including liquids. The theoretical challenge is to calculate the instantaneous vibrational frequencies of a molecule in contact with a molecular environment, accurately and quickly, and to this end a number of different methods have been developed. In this paper we critically analyze these different methods by comparing their results to accurate benchmark calculations on azide/water clusters. We also propose an optimized quantum mechanics/molecular mechanics method, which for this problem is superior to the other methods.
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Affiliation(s)
- Shuzhou Li
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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30
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Abstract
Spectrally resolved stimulated vibrational echo spectroscopy is used to investigate the dependence of fast protein dynamics on bulk solution viscosity at room temperature in four heme proteins: hemoglobin, myoglobin, a myoglobin mutant with the distal histidine replaced by a valine (H64V), and a cytochrome c552 mutant with the distal methionine replaced by an alanine (M61A). Fructose is added to increase the viscosity of the aqueous protein solutions over many orders of magnitude. The fast dynamics of the four globular proteins were found to be sensitive to solution viscosity and asymptotically approached the dynamical behavior that was previously observed in room temperature sugar glasses. The viscosity-dependent protein dynamics are analyzed in the context of a viscoelastic relaxation model that treats the protein as a deformable breathing sphere. The viscoelastic model is in qualitative agreement with the experimental data but does not capture sufficient system detail to offer a quantitative description of the underlying fluctuation amplitudes and relaxation rates. A calibration method based on the near-infrared spectrum of water overtones was constructed to accurately determine the viscosity of small volumes of protein solutions.
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31
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Finkelstein IJ, Goj A, McClain BL, Massari AM, Merchant KA, Loring RF, Fayer MD. Ultrafast dynamics of myoglobin without the distal histidine: stimulated vibrational echo experiments and molecular dynamics simulations. J Phys Chem B 2007; 109:16959-66. [PMID: 16853158 DOI: 10.1021/jp0517201] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Ultrafast protein dynamics of the CO adduct of a myoglobin mutant with the polar distal histidine replaced by a nonpolar valine (H64V) have been investigated by spectrally resolved infrared stimulated vibrational echo experiments and molecular dynamics (MD) simulations. In aqueous solution at room temperature, the vibrational dephasing rate of CO in the mutant is reduced by approximately 50% relative to the native protein. This finding confirms that the dephasing of the CO vibration in the native protein is sensitive to the interaction between the ligand and the distal histidine. The stimulated vibrational echo observable is calculated from MD simulations of H64V within a model in which vibrational dephasing is driven by electrostatic forces. In agreement with experiment, calculated vibrational echoes show slower dephasing for the mutant than for the native protein. However, vibrational echoes calculated for H64V do not show the quantitative agreement with measurements demonstrated previously for the native protein.
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Affiliation(s)
- Ilya J Finkelstein
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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32
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Finkelstein IJ, Ishikawa H, Kim S, Massari AM, Fayer MD. Substrate binding and protein conformational dynamics measured by 2D-IR vibrational echo spectroscopy. Proc Natl Acad Sci U S A 2007; 104:2637-42. [PMID: 17296942 PMCID: PMC1815234 DOI: 10.1073/pnas.0610027104] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2006] [Indexed: 11/18/2022] Open
Abstract
Enzyme structural dynamics play a pivotal role in substrate binding and biological function, but the influence of substrate binding on enzyme dynamics has not been examined on fast time scales. In this work, picosecond dynamics of horseradish peroxidase (HRP) isoenzyme C in the free form and when ligated to a variety of small organic molecule substrates is studied by using 2D-IR vibrational echo spectroscopy. Carbon monoxide bound at the heme active site of HRP serves as a spectroscopic marker that is sensitive to the structural dynamics of the protein. In the free form, HRP assumes two distinct spectroscopic conformations that undergo fluctuations on a tens-of-picoseconds time scale. After substrate binding, HRP is locked into a single conformation that exhibits reduced amplitudes and slower time-scale structural dynamics. The decrease in carbon monoxide frequency fluctuations is attributed to reduced dynamic freedom of the distal histidine and the distal arginine, which are key residues in modulating substrate binding affinity. It is suggested that dynamic quenching caused by substrate binding can cause the protein to be locked into a conformation suitable for downstream steps in the enzymatic cycle of HRP.
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Affiliation(s)
| | - Haruto Ishikawa
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Seongheun Kim
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Aaron M. Massari
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - M. D. Fayer
- Department of Chemistry, Stanford University, Stanford, CA 94305
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33
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Finkelstein IJ, Zheng J, Ishikawa H, Kim S, Kwak K, Fayer MD. Probing dynamics of complex molecular systems with ultrafast 2D IR vibrational echo spectroscopy. Phys Chem Chem Phys 2007; 9:1533-49. [PMID: 17429547 DOI: 10.1039/b618158a] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ultrafast 2D IR vibrational echo spectroscopy is described and a number of experimental examples are given. Details of the experimental method including the pulse sequence, heterodyne detection, and determination of the absorptive component of the 2D spectrum are outlined. As an initial example, the 2D spectrum of the stretching mode of CO bound to the protein myoglobin (MbCO) is presented. The time dependence of the 2D spectrum of MbCO, which is caused by protein structural evolution, is presented and its relationship to the frequency-frequency correlation function is described and used to make protein structural assignments based on comparisons to molecular dynamics simulations. The 2D vibrational echo experiments on the protein horseradish peroxidase are presented. The time dependence of the 2D spectra of the enzyme in the free form and with a substrate bound at the active site are compared and used to examine the influence of substrate binding on the protein's structural dynamics. The application of 2D vibrational echo spectroscopy to the study of chemical exchange under thermal equilibrium conditions is described. 2D vibrational echo chemical exchange spectroscopy is applied to the study of formation and dissociation of organic solute-solvent complexes and to the isomerization around a carbon-carbon single bond of an ethane derivative.
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34
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Mankoo PK, Keyes T. Classical Molecular Electrostatics: Recognition of Ligands in Proteins and the Vibrational Stark Effect. J Phys Chem B 2006; 110:25074-9. [PMID: 17149932 DOI: 10.1021/jp063971v] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
It is shown that classical electrostatics quantitatively describes both the binding of the diatomic ligands XO (X = C, N, O) to the heme group in myoglobin and the dependence of their vibrational frequencies upon an external field, the vibrational Stark effect. The key is a proper treatment of induced dipoles. The results suggest that ligand binding occurs via an "electrostatic bond", a generalization of the standard ionic bond to include induction, and, more generally, that classical electrostatics can replace quantum mechanics for a considerable simplification of some complex problems.
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Affiliation(s)
- Parminder K Mankoo
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
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35
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Meier C, Heitz MC. Laser control of vibrational excitation in carboxyhemoglobin: A quantum wave packet study. J Chem Phys 2005; 123:044504. [PMID: 16095366 DOI: 10.1063/1.1946737] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A coherent control algorithm is applied to obtain complex-shaped infrared laser pulses for the selective vibrational excitation of carbon monoxide at the active site of carbonmonoxyhemoglobin, modeled by the six-coordinated iron-porphyrin-imidazole-CO complex. The influence of the distal histidine is taken into account by an additional imidazole molecule. Density-functional theory is employed to calculate a multidimensional ground-state potential energy surface, and the vibrational dynamics as well as the laser interaction is described by quantum wave-packet calculations. At each instant in time, the optimal electric field is calculated and used for the subsequent quantum dynamics. The results presented show that the control scheme is applicable to complex systems and that it yields laser pulses with complex time-frequency structures, which, nevertheless, have a clear physical interpretation.
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Affiliation(s)
- Christoph Meier
- Laboratoire Collisions, Agrégats et Réactivité, UMR 5589, Institut de Recherche sur les Systèmes Atomiques et Moléculaires Complexes, Université Paul Sabatier, 118 Route de Narbonne, 31062 Toulouse, France.
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36
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Corcelli SA, Skinner JL. Infrared and Raman Line Shapes of Dilute HOD in Liquid H2O and D2O from 10 to 90 °C. J Phys Chem A 2005; 109:6154-65. [PMID: 16833955 DOI: 10.1021/jp0506540] [Citation(s) in RCA: 264] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A combined electronic structure/molecular dynamics approach was used to calculate infrared and isotropic Raman spectra for the OH or OD stretches of dilute HOD in D2O or H2O, respectively. The quantities needed to compute the infrared and Raman spectra were obtained from density functional theory calculations performed on clusters, generated from liquid-state configurations, containing an HOD molecule along with 4-9 solvent water molecules. The frequency, transition dipole, and isotropic transition polarizability were each empirically related to the electric field due to the solvent along the OH (or OD) bond, calculated on the H (or D) atom of interest. The frequency and transition dipole moment of the OH (or OD) stretch of the HOD molecule were found to be very sensitive to its instantaneous solvent environment, as opposed to the isotropic transition polarizability, which was found to be relatively insensitive to environment. Infrared and isotropic Raman spectra were computed within a molecular dynamics simulation by using the empirical relationships and semiclassical expressions for the line shapes. The line shapes agree well with experiment over a temperature range from 10 to 90 degrees C.
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Affiliation(s)
- S A Corcelli
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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37
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DeCamp MF, DeFlores L, McCracken JM, Tokmakoff A, Kwac K, Cho M. Amide I Vibrational Dynamics ofN-Methylacetamide in Polar Solvents: The Role of Electrostatic Interactions. J Phys Chem B 2005; 109:11016-26. [PMID: 16852342 DOI: 10.1021/jp050257p] [Citation(s) in RCA: 207] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The vibrational frequency of the amide I transition of peptides is known to be sensitive to the strength of its hydrogen bonding interactions. In an effort to account for interactions with hydrogen bonding solvents in terms of electrostatics, we study the vibrational dynamics of the amide I coordinate of N-methylacetamide in prototypical polar solvents: D2O, CDCl3, and DMSO-d6. These three solvents have varying hydrogen bonding strengths, and provide three distinct solvent environments for the amide group. The frequency-frequency correlation function, the orientational correlation function, and the vibrational relaxation rate of the amide I vibration in each solvent are retrieved by using three-pulse vibrational photon echoes, two-dimensional infrared spectroscopy, and pump-probe spectroscopy. Direct comparisons are made to molecular dynamics simulations. We find good quantitative agreement between the experimentally retrieved and simulated correlation functions over all time scales when the solute-solvent interactions are determined from the electrostatic potential between the solvent and the atomic sites of the amide group.
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Affiliation(s)
- M F DeCamp
- Department of Chemistry and George R. Harrison Spectroscopy Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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38
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Lawrence CP, Skinner JL. Quantum corrections in vibrational and electronic condensed phase spectroscopy: line shapes and echoes. Proc Natl Acad Sci U S A 2005; 102:6720-5. [PMID: 15849269 PMCID: PMC1100759 DOI: 10.1073/pnas.0408813102] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2004] [Indexed: 11/18/2022] Open
Abstract
Various linear and nonlinear vibrational and electronic spectroscopy experiments in liquids are usually analyzed within the second-cumulant approximation, and therefore the fundamental quantity of interest is the equilibrium time-correlation function of the fluctuating transition frequency. In the usual approach the "bath" variables responsible for the fluctuating frequency are treated classically, leading to a classical time-correlation function. Alternatively, sometimes a quantum correction appropriate for relatively high temperatures is included, which adds an imaginary part to the classical time-correlation function. This approach, although appealing, does not satisfy detailed balance. One can consider a similar correction, but where detailed balance is satisfied, by using the harmonic quantum correction factor. In this article, we compare these approaches for a model system and two realistic examples. Our conclusion is that for linear spectroscopy the classical result is usually adequate, whereas for nonlinear spectroscopy it can be more important to include quantum corrections.
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Affiliation(s)
- C P Lawrence
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA
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39
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Kühn O. Multidimensional vibrational quantum dynamics of CO–heme compounds: ultrafast IVR mediated Fe–CO bond-breaking after CO excitation? Chem Phys Lett 2005. [DOI: 10.1016/j.cplett.2004.12.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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40
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Demirdöven N, Cheatum CM, Chung HS, Khalil M, Knoester J, Tokmakoff A. Two-Dimensional Infrared Spectroscopy of Antiparallel β-Sheet Secondary Structure. J Am Chem Soc 2004; 126:7981-90. [PMID: 15212548 DOI: 10.1021/ja049811j] [Citation(s) in RCA: 223] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We investigate the sensitivity of femtosecond Fourier transform two-dimensional infrared spectroscopy to protein secondary structure with a study of antiparallel beta-sheets. The results show that 2D IR spectroscopy is more sensitive to structural differences between proteins than traditional infrared spectroscopy, providing an observable that allows comparison to quantitative models of protein vibrational spectroscopy. 2D IR correlation spectra of the amide I region of poly-l-lysine, concanavalin A, ribonuclease A, and lysozyme show cross-peaks between the IR-active transitions that are characteristic of amide I couplings for polypeptides in antiparallel hydrogen-bonding registry. For poly-l-lysine, the 2D IR spectrum contains the eight-peak structure expected for two dominant vibrations of an extended, ordered antiparallel beta-sheet. In the proteins with antiparallel beta-sheets, interference effects between the diagonal and cross-peaks arising from the sheets, combined with diagonally elongated resonances from additional amide transitions, lead to a characteristic "Z"-shaped pattern for the amide I region in the 2D IR spectrum. We discuss in detail how the number of strands in the sheet, the local configurational disorder in the sheet, the delocalization of the vibrational excitation, and the angle between transition dipole moments affect the position, splitting, amplitude, and line shape of the cross-peaks and diagonal peaks.
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Affiliation(s)
- Nurettin Demirdöven
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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41
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Hernanz A, Bratu I, Navarro R. IR Study on the Relaxation of the Phosphate Group of 5‘-dCMP in 2H2O and H2O Solutions. J Phys Chem B 2004. [DOI: 10.1021/jp030853o] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Antonio Hernanz
- Departamento de Ciencias y Técnicas Fisicoquímicas, Universidad Nacional de Educación a Distancia, Senda del Rey, 9, E-28040 Madrid, Spain, and National Institute for R & D of Isotopic and Molecular Technologies, P.O. Box 700, R-400293 Cluj-Napoca 5, Romania
| | - Ioan Bratu
- Departamento de Ciencias y Técnicas Fisicoquímicas, Universidad Nacional de Educación a Distancia, Senda del Rey, 9, E-28040 Madrid, Spain, and National Institute for R & D of Isotopic and Molecular Technologies, P.O. Box 700, R-400293 Cluj-Napoca 5, Romania
| | - Raquel Navarro
- Departamento de Ciencias y Técnicas Fisicoquímicas, Universidad Nacional de Educación a Distancia, Senda del Rey, 9, E-28040 Madrid, Spain, and National Institute for R & D of Isotopic and Molecular Technologies, P.O. Box 700, R-400293 Cluj-Napoca 5, Romania
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42
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Merchant KA, Noid WG, Thompson DE, Akiyama R, Loring RF, Fayer MD. Structural Assignments and Dynamics of the A Substates of MbCO: Spectrally Resolved Vibrational Echo Experiments and Molecular Dynamics Simulations. J Phys Chem B 2002. [DOI: 10.1021/jp026793o] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kusai A. Merchant
- Department of Chemistry, Stanford University, Stanford, California 94305, and Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853
| | - W. G. Noid
- Department of Chemistry, Stanford University, Stanford, California 94305, and Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853
| | - David E. Thompson
- Department of Chemistry, Stanford University, Stanford, California 94305, and Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853
| | - Ryo Akiyama
- Department of Chemistry, Stanford University, Stanford, California 94305, and Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853
| | - Roger F. Loring
- Department of Chemistry, Stanford University, Stanford, California 94305, and Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853
| | - M. D. Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305, and Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853
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43
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Merchant KA, Xu QH, Thompson DE, Fayer MD. Frequency Selected Ultrafast Infrared Vibrational Echo Studies of Liquids, Glasses, and Proteins. J Phys Chem A 2002. [DOI: 10.1021/jp021145q] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- K. A. Merchant
- Department of Chemistry, Stanford University, Stanford, California 94305
| | - Qing-Hua Xu
- Department of Chemistry, Stanford University, Stanford, California 94305
| | - David E. Thompson
- Department of Chemistry, Stanford University, Stanford, California 94305
| | - M. D. Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305
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44
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Xu QH, Fayer MD. Temperature-dependent vibrational dephasing: Comparison of liquid and glassy solvents using frequency-selected vibrational echoes. J Chem Phys 2002. [DOI: 10.1063/1.1492280] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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45
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Piryatinski A, Skinner JL. Determining Vibrational Solvation-Correlation Functions from Three-Pulse Infrared Photon Echoes. J Phys Chem B 2002. [DOI: 10.1021/jp0202542] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- A. Piryatinski
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706
| | - J. L. Skinner
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706
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Leitner DM. Temperature dependence of the pure vibrational dephasing rate in a heteropolymer. Chem Phys Lett 2002. [DOI: 10.1016/s0009-2614(02)00761-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Merchant KA, Thompson DE, Xu QH, Williams RB, Loring RF, Fayer MD. Myoglobin-CO conformational substate dynamics: 2D vibrational echoes and MD simulations. Biophys J 2002; 82:3277-88. [PMID: 12023251 PMCID: PMC1302116 DOI: 10.1016/s0006-3495(02)75669-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Two-dimensional (2D) infrared vibrational echoes were performed on horse heart carbonmonoxymyoglobin (MbCO) in water over a range of temperatures. The A(1) and A(3) conformational substates of MbCO are found to have different dephasing rates with different temperature dependences. A frequency-frequency correlation function derived from molecular dynamics simulations on MbCO at 298 K is used to calculate the vibrational echo decay. The calculated decay shows substantial agreement with the experimentally measured decays. The 2D vibrational echo probes protein dynamics and provides an observable that can be used to test structural assignments for the MbCO conformational substates.
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Affiliation(s)
- Kusai A Merchant
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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