51
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Hoffman DJ, Fayer MD. CLS Next Gen: Accurate Frequency–Frequency Correlation Functions from Center Line Slope Analysis of 2D Correlation Spectra Using Artificial Neural Networks. J Phys Chem A 2020; 124:5979-5992. [DOI: 10.1021/acs.jpca.0c04313] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- David J. Hoffman
- 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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52
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Chen X, Cui Y, Gobeze HB, Kuroda DG. Assessing the Location of Ionic and Molecular Solutes in a Molecularly Heterogeneous and Nonionic Deep Eutectic Solvent. J Phys Chem B 2020; 124:4762-4773. [PMID: 32421342 PMCID: PMC7304071 DOI: 10.1021/acs.jpcb.0c02482] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
Deep
eutectic solvents (DES) are emerging sustainable designer
solvents viewed as greener and better alternatives to ionic liquids.
Nonionic DESs possess unique properties such as viscosity and hydrophobicity
that make them desirable in microextraction applications such as oil-spill
remediation. This work builds upon a nonionic DES, NMA–LA DES,
previously designed by our group. The NMA–LA DES presents a
rich nanoscopic morphology that could be used to allocate solutes
of different polarities. In this work, the possibility of solvating
different solutes within the nanoscopically heterogeneous molecular
structure of the NMA–LA DES is investigated using ionic and
molecular solutes. In particular, the localized vibrational transitions
in these solutes are used as reporters of the DES molecular structure
via vibrational spectroscopy. The FTIR and 2DIR data suggest that
the ionic solute is confined in a polar and continuous domain formed
by NMA, clearly sensing the direct effect of the change in NMA concentration.
In the case of the molecular nonionic and polar solute, the data indicates
that the solute resides in the interface between the polar and nonpolar
domains. Finally, the results for the nonpolar and nonionic solute
(W(CO)6) are unexpected and less conclusive. Contrary to
its polarity, the data suggest that the W(CO)6 resides
within the NMA polar domain of the DES, probably by inducing a domain
restructuring in the solvent. However, the data are not conclusive
enough to discard the possibility that the restructuring comprises
not only the polar domain but also the interface. Overall, our results
demonstrate that the NMA–LA DES has nanoscopic domains with
affinity to particular molecular properties, such as polarity. Thus,
the presented results have a direct implication to separation science.
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Affiliation(s)
- Xiaobing Chen
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Yaowen Cui
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Habtom B Gobeze
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Daniel G Kuroda
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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53
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Flanagan JC, Cardenas AE, Baiz CR. Ultrafast Spectroscopy of Lipid-Water Interfaces: Transmembrane Crowding Drives H-Bond Dynamics. J Phys Chem Lett 2020; 11:4093-4098. [PMID: 32364385 DOI: 10.1021/acs.jpclett.0c00783] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Biology takes place in crowded, heterogeneous environments, and it is therefore essential to account for crowding effects in our understanding of biophysical processes at the molecular level. Comparable to the cytosol, proteins occupy approximately 30% of the plasma membrane surface; thus, crowding should have an effect on the local structure and dynamics at the lipid-water interface. Using a combination of ultrafast two-dimensional infrared spectroscopy and molecular dynamics simulations, we quantify the effects of membrane peptide concentration on the picosecond interfacial H-bond dynamics. The measurements reveal a nonmonotonic dependence of water orientation and dynamics as a function of transmembrane peptide:lipid ratio. We observe three dynamical regimes: a "pure lipid-like" regime at low peptide concentrations, a bulk-like region at intermediate peptide concentrations where dynamics are faster by ∼20% compared to those of the pure lipid bilayer, and a crowded regime where high peptide concentrations slow dynamics by ∼50%.
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54
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Baryiames CP, Baiz CR. Slow Oil, Slow Water: Long-Range Dynamic Coupling across a Liquid–Liquid Interface. J Am Chem Soc 2020; 142:8063-8067. [DOI: 10.1021/jacs.0c00817] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Christopher P. Baryiames
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Stop A5300, Austin, Texas 78712-1224, United States
| | - Carlos R. Baiz
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Stop A5300, Austin, Texas 78712-1224, United States
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55
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Dong X, Wang S, Yu P, Yang F, Zhao J, Wu LZ, Tung CH, Wang J. Ultrafast Vibrational Energy Transfer through the Covalent Bond and Intra- and Intermolecular Hydrogen Bonds in a Supramolecular Dimer by Two-Dimensional Infrared Spectroscopy. J Phys Chem B 2020; 124:544-555. [PMID: 31873023 DOI: 10.1021/acs.jpcb.9b10431] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this work, the structural fluctuations and vibrational energy transfer dynamics in a supramolecular homodimer model, which is composed of 2-(9-anthracene)ureido-6-(1-undecyl)-4[1H]-pyrimidinone (UPAn) with quadruple intermolecular and single intramolecular hydrogen bonds (HBs), have been examined using ultrafast two-dimensional infrared (2D IR) and steady-state IR spectroscopies. A less structurally fluctuating intermolecular HB is found between the pyrimidinone C═O and ureido N-H groups. However, a larger structurally fluctuating intramolecular HB is suggested by the equilibrium and dynamical line-shape measurements of the ureido C═O stretch. Further, dynamical time-dependent 2D IR diagonal and off-diagonal signals show that intra- and intermolecular vibrational energy transfer processes occur on the picosecond timescale, where the latter is more efficient due to intermolecular hydrogen bonding interaction and through-space interaction.
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Affiliation(s)
- Xueqian Dong
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Center for Excellence in Molecular Sciences , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , P. R. China.,University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Sumin Wang
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials , Technical Institute of Physics and Chemistry, Chinese Academy of Sciences , Beijing 100190 , P. R. China.,School of Materials and Chemical Engineering , Xi'an Technological University , Xi'an 710021 , P. R. China
| | - Pengyun Yu
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Center for Excellence in Molecular Sciences , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , P. R. China.,University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Fan Yang
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Center for Excellence in Molecular Sciences , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , P. R. China
| | - Juan Zhao
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Center for Excellence in Molecular Sciences , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , P. R. China.,University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Li-Zhu Wu
- University of Chinese Academy of Sciences , Beijing 100049 , P. R. China.,Key Laboratory of Photochemical Conversion and Optoelectronic Materials , Technical Institute of Physics and Chemistry, Chinese Academy of Sciences , Beijing 100190 , P. R. China
| | - Chen-Ho Tung
- University of Chinese Academy of Sciences , Beijing 100049 , P. R. China.,Key Laboratory of Photochemical Conversion and Optoelectronic Materials , Technical Institute of Physics and Chemistry, Chinese Academy of Sciences , Beijing 100190 , P. R. China
| | - Jianping Wang
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Center for Excellence in Molecular Sciences , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , P. R. China.,University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
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56
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Li X, Zhou D, Hao H, Chen H, Weng Y, Bian H. Vibrational Relaxation Dynamics of a Semiconductor Copper(I) Thiocyanate (CuSCN) Film as a Hole-Transporting Layer. J Phys Chem Lett 2020; 11:548-555. [PMID: 31884795 DOI: 10.1021/acs.jpclett.9b03480] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The semiconductor CuSCN film, which is typically used as the hole-transporting layer (HTL) in solar cell studies, has been investigated by Fourier transform infrared (FTIR) spectroscopy and ultrafast transient infrared (IR) spectroscopy. A sharp peak at 2175 cm-1 corresponding to the CN vibrational stretching mode in CuSCN was observed, and the peak frequency remained unchanged by varying the thickness of the CuSCN thin film. Vibrational relaxation measurements showed that the 0-1 and 1-2 transitions of CN stretching can be observed at 2175 and 2140 cm-1, respectively. The heat-induced absorption and bleaching peaks (2167 and 2175 cm-1) can be clearly seen at a waiting time of 40 ps. The vibrational relaxation of the CN stretching mode determined from the 1-2 transition exhibited a biexponential decay with time constants of 7.4 ± 0.5 (90%) and 158 ± 50 ps (10%). Importantly, the abnormal anisotropy decay of the CN stretching mode in the CuSCN thin film was also observed for the first time. A detailed analysis showed that the distinct anisotropy decay curve could be described using a triexponential decay function, which was explained by three different processes: resonance energy transfer (∼8 ps), a thermalization process (∼40 ps), and molecular rotation (∼150 ps). The time scale of the thermalization process caused by the vibrational relaxation in CuSCN is at a time scale of 40 ps, which is important for us to understand the thermally activated charge-transport property of the CuSCN film employed as the HTL. Further UV pump-IR probe measurement revealed that the carrier scattering and relaxation processes in the CuSCN film are strongly associated with the vibrational excitation and relaxation dynamics of the CN stretching mode. It is expected that the fundamental understanding of the vibrational relaxation dynamics of the CuSCN thin film should provide helpful insight to elucidate its role as the HTL in solar cell studies at the molecular level.
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Affiliation(s)
- Xiaoqian Li
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710119 , China
| | - Dexia Zhou
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710119 , China
| | - Hongxing Hao
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710119 , China
| | - Hailong Chen
- Beijing National Laboratory for Condensed Matter Physics, CAS Key Laboratory of Soft Matter Physics , Institute of Physics, Chinese Academy of Sciences , Beijing 100190 , China
| | - Yuxiang Weng
- Beijing National Laboratory for Condensed Matter Physics, CAS Key Laboratory of Soft Matter Physics , Institute of Physics, Chinese Academy of Sciences , Beijing 100190 , China
| | - Hongtao Bian
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710119 , China
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57
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Smith JW, Chen Q. Liquid-phase electron microscopy imaging of cellular and biomolecular systems. J Mater Chem B 2020; 8:8490-8506. [DOI: 10.1039/d0tb01300e] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Liquid-phase electron microscopy, a new method for real-time nanoscopic imaging in liquid, makes it possible to study cells or biomolecules with a singular combination of spatial and temporal resolution. We review the state of the art in biological research in this growing and promising field.
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Affiliation(s)
- John W. Smith
- Department of Materials Science and Engineering, University of Illinois at Urbana–Champaign
- Urbana
- USA
| | - Qian Chen
- Department of Materials Science and Engineering, University of Illinois at Urbana–Champaign
- Urbana
- USA
- Department of Chemistry
- University of Illinois at Urbana–Champaign
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58
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Vieira Pinto SM, Tasinato N, Barone V, Amadei A, Zanetti-Polzi L, Daidone I. Modeling amino-acid side chain infrared spectra: the case of carboxylic residues. Phys Chem Chem Phys 2020; 22:3008-3016. [DOI: 10.1039/c9cp04774c] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Infrared (IR) spectroscopy is commonly utilized for the investigation of protein structures and protein-mediated processes.
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Affiliation(s)
- Sandra Mónica Vieira Pinto
- Scuola Normale Superiore
- I-56126 Pisa
- Italy
- Department of Physical and Chemical Sciences
- University of L'Aquila
| | | | | | - Andrea Amadei
- Department of Chemical and Technological Sciences
- University of Rome “Tor Vergata
- I-00185 Rome
- Italy
| | - Laura Zanetti-Polzi
- Department of Physical and Chemical Sciences
- University of L'Aquila
- I-67010 L'Aquila
- Italy
- CNR Institute of Nanoscience
| | - Isabella Daidone
- Department of Physical and Chemical Sciences
- University of L'Aquila
- I-67010 L'Aquila
- Italy
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59
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Kuroi K, Kamijo M, Ueki M, Niwa Y, Hiramatsu H, Nakabayashi T. Time-resolved FTIR study on the structural switching of human galectin-1 by light-induced disulfide bond formation. Phys Chem Chem Phys 2020; 22:1137-1144. [DOI: 10.1039/c9cp04881b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The light-induced disulfide bond technique, which we have previously developed, has enabled the time-resolved measurement of the disulfide-induced conformational switching of the lectin protein human galectin-1.
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Affiliation(s)
- Kunisato Kuroi
- Graduate School of Pharmaceutical Sciences
- Tohoku University
- Sendai 980-8578
- Japan
- Faculty of Pharmaceutical Sciences
| | - Mana Kamijo
- Faculty of Pharmaceutical Sciences
- Tohoku University
- Sendai 980-8578
- Japan
| | - Mutsuki Ueki
- Faculty of Pharmaceutical Sciences
- Tohoku University
- Sendai 980-8578
- Japan
| | - Yusuke Niwa
- Graduate School of Pharmaceutical Sciences
- Tohoku University
- Sendai 980-8578
- Japan
| | - Hirotsugu Hiramatsu
- Department of Applied Chemistry and Institute of Molecular Science
- National Chiao Tung University
- Hsinchu 30010
- Taiwan
- Center for Emergent Functional Matter Science
| | - Takakazu Nakabayashi
- Graduate School of Pharmaceutical Sciences
- Tohoku University
- Sendai 980-8578
- Japan
- Faculty of Pharmaceutical Sciences
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60
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Seol JG, Kwon H, Jin GY, Moon J, Yi C, Kim YS. Scattering Elimination of Heterodyne-Detected Two-Dimensional Infrared Spectra Using Choppers and Shutters. J Phys Chem A 2019; 123:10837-10843. [DOI: 10.1021/acs.jpca.9b09219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jin Gyu Seol
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Hyejin Kwon
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Geun Young Jin
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Juran Moon
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Chairyoung Yi
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Yung Sam Kim
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
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61
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Chen X, Fulfer KD, Woodard KT, Kuroda DG. Structure and Dynamics of the Lithium-Ion Solvation Shell in Ureas. J Phys Chem B 2019; 123:9889-9898. [DOI: 10.1021/acs.jpcb.9b07623] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Xiaobing Chen
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Kristen D. Fulfer
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
- Chemistry Program, Centre College, Danville, Kentucky 40422, United States
| | - Kaylee T. Woodard
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Daniel G. Kuroda
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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62
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Flanagan JC, Baiz CR. Ultrafast pH-jump two-dimensional infrared spectroscopy. OPTICS LETTERS 2019; 44:4937-4940. [PMID: 31613233 DOI: 10.1364/ol.44.004937] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 09/17/2019] [Indexed: 06/10/2023]
Abstract
We present a pH-jump two-dimensional infrared (2D IR) spectrometer to probe pH-dependent conformational changes from nanoseconds to milliseconds. The design incorporates a nanosecond 355 nm source into a pulse-shaper-based 2D IR spectrometer to trigger dissociation of a caged proton prior to probing subsequent conformational changes with femtosecond 2D IR spectroscopy. We observe a blue shift in the amide I mode (C═O stretch) of diglycine induced by protonation of the terminal amine. This method combines the bond-specific structural sensitivity of ultrafast 2D IR with triggered conformational dynamics, providing structural access to multiscale biomolecular transformations such as protein folding.
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63
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Chatterjee S, Ghosh D, Haldar T, Deb P, Sakpal SS, Deshmukh SH, Kashid SM, Bagchi S. Hydrocarbon Chain-Length Dependence of Solvation Dynamics in Alcohol-Based Deep Eutectic Solvents: A Two-Dimensional Infrared Spectroscopic Investigation. J Phys Chem B 2019; 123:9355-9363. [DOI: 10.1021/acs.jpcb.9b08954] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Srijan Chatterjee
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Deborin Ghosh
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Tapas Haldar
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Pranab Deb
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sushil S. Sakpal
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Samadhan H. Deshmukh
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Somnath M. Kashid
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sayan Bagchi
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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64
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Baryiames CP, Teel M, Baiz CR. Interfacial H-Bond Dynamics in Reverse Micelles: The Role of Surfactant Heterogeneity. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:11463-11470. [PMID: 31407910 DOI: 10.1021/acs.langmuir.9b01693] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Characterizing the hydrogen bond structure and dynamics at surfactant interfaces is essential for understanding how microscopic interactions translate to bulk microemulsion properties. Heterogeneous blends containing tens or hundreds of surfactants are common in the industry, but the most fundamental studies have been carried out on micelles composed of a single surfactant species. Therefore, the effect of surfactant heterogeneity on the interfacial structure and dynamics remains poorly understood. Here, we use ultrafast two-dimensional infrared spectroscopy and molecular dynamics simulations to characterize sub-picosecond solvation dynamics as a function of the surfactant composition in ∼120 nm water-in-oil reverse micelles. We probe the ester carbonyl vibrations of nonionic sorbitan surfactants, which are located precisely at the interface between the polar and nonpolar regions, and as such, report on the interfacial water dynamics. We show a 7% increase in hydrogen bond populations together with a 37% slowdown of interfacial hydrogen bond dynamics in heterogeneous mixtures containing hundreds of species, compared to more uniform compositions. Simulations, which are in semiquantitative agreement with experiments, indicate that structural diversity leads to decreased packing efficiency, which in turn drives water further into the otherwise hydrophobic region. Interestingly, this increase in hydration is accompanied by a slowdown of dynamics, indicating that water molecules solvating surfactants are conformationally constrained. These studies demonstrate that the composition and heterogeneity are key factors in determining interfacial properties.
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Affiliation(s)
| | - Morgan Teel
- University of Texas at Austin , Austin 78712 , Texas , United States
| | - Carlos R Baiz
- University of Texas at Austin , Austin 78712 , Texas , United States
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65
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Williams IM, Qasim LN, Tran L, Scott A, Riley K, Dutta S. C-D Vibration at C2 Position of Imidazolium Cation as a Probe of the Ionic Liquid Microenvironment. J Phys Chem A 2019; 123:6342-6349. [PMID: 31257885 DOI: 10.1021/acs.jpca.9b02387] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Unlike molecular solvents, imidazolium-based ionic liquids are entirely made of ions with spatial heterogeneity. There is a need for spectroscopic probes that can assess the microenvironment near the cations of these complex liquids. In this manuscript, we describe simple chemical procedures to label the C2 position of imidazolium cation with a C-D vibrational probe and show, through linear and nonlinear vibrational spectroscopies, that this C-D stretching mode can be a useful analytical tool to assess both the solvent microenvironment and solute-solvent interactions in imidazolium-based ionic liquids from the cation point of view. It is expected that this C-D vibration probe on the cation will lead to the development of innovative experimental strategies that can provide a better understanding of such ionic liquids.
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Affiliation(s)
- Isis Marie Williams
- Department of Chemistry , Xavier University of Louisiana , New Orleans , Louisiana 70125 , United States
| | - Layla N Qasim
- Department of Chemistry , Tulane University , New Orleans , Louisiana 70118 , United States
| | - Ly Tran
- Department of Chemistry , Xavier University of Louisiana , New Orleans , Louisiana 70125 , United States
| | - Asia Scott
- Department of Chemistry , Xavier University of Louisiana , New Orleans , Louisiana 70125 , United States
| | - Kevin Riley
- Department of Chemistry , Xavier University of Louisiana , New Orleans , Louisiana 70125 , United States
| | - Samrat Dutta
- Department of Chemistry , Xavier University of Louisiana , New Orleans , Louisiana 70125 , United States
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66
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Abstract
AbstractThe dynamics of proteins in solution includes a variety of processes, such as backbone and side-chain fluctuations, interdomain motions, as well as global rotational and translational (i.e. center of mass) diffusion. Since protein dynamics is related to protein function and essential transport processes, a detailed mechanistic understanding and monitoring of protein dynamics in solution is highly desirable. The hierarchical character of protein dynamics requires experimental tools addressing a broad range of time- and length scales. We discuss how different techniques contribute to a comprehensive picture of protein dynamics, and focus in particular on results from neutron spectroscopy. We outline the underlying principles and review available instrumentation as well as related analysis frameworks.
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67
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Edington SC, Halling DB, Bennett SM, Middendorf TR, Aldrich RW, Baiz CR. Non-Additive Effects of Binding Site Mutations in Calmodulin. Biochemistry 2019; 58:2730-2739. [PMID: 31124357 DOI: 10.1021/acs.biochem.9b00096] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Despite decades of research on ion-sensing proteins, gaps persist in the understanding of ion binding affinity and selectivity even in well-studied proteins such as calmodulin. Site-directed mutagenesis is a powerful and popular tool for addressing outstanding questions about biological ion binding and is employed to selectively deactivate binding sites and insert chromophores at advantageous positions within ion binding structures. However, even apparently nonperturbative mutations can distort the binding dynamics they are employed to measure. We use Fourier transform infrared (FTIR) and ultrafast two-dimensional infrared (2D IR) spectroscopy of the carboxylate asymmetric stretching mode in calmodulin as a mutation- and label-independent probe of the conformational perturbations induced in calmodulin's binding sites by two classes of mutation, tryptophan insertion and carboxylate side-chain deletion, commonly used to study ion binding in proteins. Our results show that these mutations not only affect ion binding but also induce changes in calmodulin's conformational landscape along coordinates not probed by vibrational spectroscopy, remaining invisible without additional perturbation of binding site structure. Comparison of FTIR line shapes with 2D IR diagonal slices provides a clear example of how nonlinear spectroscopy produces well-resolved line shapes, refining otherwise featureless spectral envelopes into more informative vibrational spectra of proteins.
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Affiliation(s)
- Sean C Edington
- Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - D Brent Halling
- Department of Neuroscience , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Suzanna M Bennett
- Department of Neuroscience , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Thomas R Middendorf
- Department of Neuroscience , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Richard W Aldrich
- Department of Neuroscience , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Carlos R Baiz
- Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
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68
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Wei Q, Zhang M, Zhou D, Li X, Bian H, Fang Y. Ultrafast Hydrogen Bond Exchanging between Water and Anions in Concentrated Ionic Liquid Aqueous Solutions. J Phys Chem B 2019; 123:4766-4775. [PMID: 31082232 DOI: 10.1021/acs.jpcb.9b03504] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The mixtures of 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM]BF4) ionic liquids (ILs) and water as a function of IL concentrations have been investigated by Fourier transform infrared (FTIR) spectroscopy and ultrafast two-dimensional IR (2D IR) spectroscopy. FTIR spectra of the mixtures resolve two different types of water species, one interacting with the BF4- anions and the other associated with bulklike water molecules. These two water species are in a dynamic equilibrium through forming different hydrogen bonding configurations which are separated by more than 100 cm-1 in the IR spectra. The structural dynamics of the IL mixtures are further revealed by monitoring the vibrational relaxation dynamics of the OD stretching group of interfacial water molecules hydrogen bonded to BF4- anions. With the increase of the IL bulk concentration, vibrational population and rotational dynamics of the interfacial water molecules can be described by a biexponential decay function and are strongly dependent on the IL concentrations. Furthermore, the ultrafast hydrogen bond exchanging between water and BF4- anions in the ILs are also measured using 2D IR spectroscopy. The average hydrogen bond exchanging rate is determined to be 19 ± 4 ps, which is around 3 times slower than that in the NaBF4 electrolyte aqueous solution. The much slower hydrogen bond exchanging rate indicates that the local structure of ILs and water molecules are strongly mediated by the steric effect of the cationic group in the ILs, which is proposed to be responsible for the formation of the heterogeneous structure in the IL mixtures. By using SCN- as the anionic probe, the structural inhomogeneity in the IL solutions can be confirmed from the distinct rotational dynamics of the SCN-, which is segregated from the rotational dynamics of water molecules in the IL mixtures.
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Affiliation(s)
- Qianshun Wei
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710119 , China
| | - Miaomiao Zhang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710119 , China
| | - Dexia Zhou
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710119 , China
| | - Xiaoqian Li
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710119 , China
| | - Hongtao Bian
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710119 , China
| | - Yu Fang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710119 , China
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69
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Ghosh S, Wategaonkar S. C–H···O Hydrogen Bond Anchored Water Bridge in 1,2,4,5-Tetracyanobenzene-Water Clusters. J Phys Chem A 2019; 123:3851-3862. [DOI: 10.1021/acs.jpca.9b02238] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sanat Ghosh
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India
| | - Sanjay Wategaonkar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India
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70
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Cui Y, Rushing JC, Seifert S, Bedford NM, Kuroda DG. Molecularly Heterogeneous Structure of a Nonionic Deep Eutectic Solvent Composed of N-Methylacetamide and Lauric Acid. J Phys Chem B 2019; 123:3984-3993. [DOI: 10.1021/acs.jpcb.8b11732] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Yaowen Cui
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Jeramie C. Rushing
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Soenke Seifert
- X-ray Sciences Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Nicholas M. Bedford
- School of Chemical Engineering, University of New South Wales, Sydney, NSW 2052, Australia
| | - Daniel G. Kuroda
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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71
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Hoffman DJ, Fica-Contreras SM, Fayer MD. Fast dynamics of a hydrogen-bonding glass forming liquid: Chemical exchange-induced spectral diffusion in 2D IR spectroscopy. J Chem Phys 2019; 150:124507. [DOI: 10.1063/1.5088499] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- David J. Hoffman
- 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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72
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Site-Specific Peptide Probes Detect Buried Water in a Lipid Membrane. Biophys J 2019; 116:1692-1700. [PMID: 31000156 DOI: 10.1016/j.bpj.2019.03.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 03/05/2019] [Accepted: 03/06/2019] [Indexed: 01/08/2023] Open
Abstract
Transmembrane peptides contain polar residues in the interior of the membrane, which may alter the electrostatic environment and favor hydration in the otherwise nonpolar environment of the membrane core. Here, we demonstrate a general, nonperturbative strategy to probe hydration of the peptide backbone at specific depths within the bilayer using a combination of site-specific isotope labels, ultrafast two-dimensional infrared spectroscopy, and spectral modeling based on molecular dynamics simulations. Our results show that the amphiphilic pH-low insertion peptide supports a highly heterogeneous environment, with significant backbone hydration of nonpolar residues neighboring charged residues. For example, a leucine residue located as far as 1 nm into the hydrophobic bulk reports hydrogen-bonded populations as high as ∼20%. These findings indicate that the polar nature of these residues may facilitate the transport of water molecules into the hydrophobic core of the membrane.
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73
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Roberson MG, Smith DK, White SM, Wallace IS, Tucker MJ. Interspecies Bombolitins Exhibit Structural Diversity upon Membrane Binding, Leading to Cell Specificity. Biophys J 2019; 116:1064-1074. [PMID: 30824115 DOI: 10.1016/j.bpj.2019.02.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 02/07/2019] [Accepted: 02/08/2019] [Indexed: 02/05/2023] Open
Abstract
Bombolitins, a class of peptides produced by bees of the genus Bombus, target and disrupt cellular membranes, leading to lysis. Antimicrobial peptides exhibit various mechanisms of action resulting from the interplay between peptide structure, lipid composition, and cellular target membrane selectivity. Herein, two bombolitins displaying significant amino-acid-sequence similarity, BII and BL6, were assessed for antimicrobial activity as well as correlated dodecylphosphocholine (DPC) micelle binding and membrane-induced peptide conformational changes. Infrared and circular dichroism spectroscopies were used to assess the structure-function relationship of each bombolitin, and the results indicate that BII forms a rigid and helically ordered secondary structure upon binding to DPC micelles, whereas BL6 largely lacks secondary structural order. Moreover, the binding affinity of each peptide to DPC micelles was determined, revealing that BL6 displayed a difference in binding affinity by over two orders of magnitude. Further investigations into the growth-inhibitory activity of the two bombolitins were performed against Escherichia coli and Saccharomyces cerevisiae. Interestingly, BII specifically targeted S. cerevisiae, whereas BL6 more effectively inhibited E. coli growth. Overall, the antimicrobial selectivity and specificity of BII and BL6 are largely dependent on the primary as well as secondary structural content of the peptides and the membrane composition.
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Affiliation(s)
| | - Devin K Smith
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada
| | - Simon M White
- Department of Chemistry, University of Nevada, Reno, Reno, Nevada
| | - Ian S Wallace
- Department of Chemistry, University of Nevada, Reno, Reno, Nevada; Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada.
| | - Matthew J Tucker
- Department of Chemistry, University of Nevada, Reno, Reno, Nevada.
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74
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Petti MK, Ostrander JS, Saraswat V, Birdsall ER, Rich KL, Lomont JP, Arnold MS, Zanni MT. Enhancing the signal strength of surface sensitive 2D IR spectroscopy. J Chem Phys 2019; 150:024707. [PMID: 30646693 DOI: 10.1063/1.5065511] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Spectroscopic techniques that are capable of measuring surfaces and interfaces must overcome two technical challenges: one, the low coverage of molecules at the surface, and two, discerning between signals from the bulk and surface. We present surface enhanced attenuated reflection 2D infrared (SEAR 2D IR) spectroscopy, a method that combines localized surface plasmons with a reflection pump-probe geometry to achieve monolayer sensitivity. The method is demonstrated at 6 µm with the amide I band of a model peptide, a cysteine terminated α-helical peptide tethered to a gold surface. Using SEAR 2D IR spectroscopy, the signal from this sample is enhanced 20 000-times over a monolayer on a dielectric surface. Like attenuated total reflection IR spectroscopy, SEAR 2D IR spectroscopy can be applied to strongly absorbing solvents. We demonstrated this capability by solvating a peptide monolayer with H2O, which cannot normally be used when measuring the amide I band. SEAR 2D IR spectroscopy will be advantageous for studying chemical reactions at electrochemical surfaces, interfacial charge transfer in photovoltaics, and structural changes of transmembrane proteins in lipid membranes.
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Affiliation(s)
- Megan K Petti
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Joshua S Ostrander
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Vivek Saraswat
- Department of Materials Science and Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Erin R Birdsall
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Kacie L Rich
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Justin P Lomont
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Michael S Arnold
- Department of Materials Science and Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Martin T Zanni
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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75
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Okabe H, Miyata D, Nakabayashi T, Hiramatsu H. Evaluation of Dihedral Angles of Peptides Using IR Bands of Two Successive Isotope Labeled Residues. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2019. [DOI: 10.1246/bcsj.20180183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Hitomi Okabe
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Daisuke Miyata
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Takakazu Nakabayashi
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Hirotsugu Hiramatsu
- Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, Hsinchu 30010, Taiwan
- Center for Emergent Functional Matter Science, National Chiao Tung University, Hsinchu 30010, Taiwan
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76
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Vibrational Approach to the Dynamics and Structure of Protein Amyloids. Molecules 2019; 24:molecules24010186. [PMID: 30621325 PMCID: PMC6337179 DOI: 10.3390/molecules24010186] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 12/31/2018] [Accepted: 01/02/2019] [Indexed: 02/06/2023] Open
Abstract
Amyloid diseases, including neurodegenerative diseases such as Alzheimer’s and Parkinson’s, are linked to a poorly understood progression of protein misfolding and aggregation events that culminate in tissue-selective deposition and human pathology. Elucidation of the mechanistic details of protein aggregation and the structural features of the aggregates is critical for a comprehensive understanding of the mechanisms of protein oligomerization and fibrillization. Vibrational spectroscopies, such as Fourier transform infrared (FTIR) and Raman, are powerful tools that are sensitive to the secondary structure of proteins and have been widely used to investigate protein misfolding and aggregation. We address the application of the vibrational approaches in recent studies of conformational dynamics and structural characteristics of protein oligomers and amyloid fibrils. In particular, introduction of isotope labelled carbonyl into a peptide backbone, and incorporation of the extrinsic unnatural amino acids with vibrational moieties on the side chain, have greatly expanded the ability of vibrational spectroscopy to obtain site-specific structural and dynamic information. The applications of these methods in recent studies of protein aggregation are also reviewed.
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77
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Song Y, Konar A, Sechrist R, Roy VP, Duan R, Dziurgot J, Policht V, Matutes YA, Kubarych KJ, Ogilvie JP. Multispectral multidimensional spectrometer spanning the ultraviolet to the mid-infrared. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2019; 90:013108. [PMID: 30709236 DOI: 10.1063/1.5055244] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 11/29/2018] [Indexed: 06/09/2023]
Abstract
Multidimensional spectroscopy is the optical analog to nuclear magnetic resonance, probing dynamical processes with ultrafast time resolution. At optical frequencies, the technical challenges of multidimensional spectroscopy have hindered its progress until recently, where advances in laser sources and pulse-shaping have removed many obstacles to its implementation. Multidimensional spectroscopy in the visible and infrared (IR) regimes has already enabled respective advances in our understanding of photosynthesis and the structural rearrangements of liquid water. A frontier of ultrafast spectroscopy is to extend and combine multidimensional techniques and frequency ranges, which have been largely restricted to operating in the distinct visible or IR regimes. By employing two independent amplifiers seeded by a single oscillator, it is straightforward to span a wide range of time scales (femtoseconds to seconds), all of which are often relevant to the most important energy conversion and catalysis problems in chemistry, physics, and materials science. Complex condensed phase systems have optical transitions spanning the ultraviolet (UV) to the IR and exhibit dynamics relevant to function on time scales of femtoseconds to seconds and beyond. We describe the development of the Multispectral Multidimensional Nonlinear Spectrometer (MMDS) to enable studies of dynamical processes in atomic, molecular, and material systems spanning femtoseconds to seconds, from the UV to the IR regimes. The MMDS employs pulse-shaping methods to provide an easy-to-use instrument with an unprecedented spectral range that enables unique combination spectroscopies. We demonstrate the multispectral capabilities of the MMDS on several model systems.
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Affiliation(s)
- Yin Song
- Department of Physics, University of Michigan, 450 Church St., Ann Arbor, Michigan 48109, USA
| | - Arkaprabha Konar
- Department of Physics, University of Michigan, 450 Church St., Ann Arbor, Michigan 48109, USA
| | - Riley Sechrist
- Department of Physics, University of Michigan, 450 Church St., Ann Arbor, Michigan 48109, USA
| | - Ved Prakash Roy
- Department of Chemistry, University of Michigan, 930 N University Ave., Ann Arbor, Michigan 48109, USA
| | - Rong Duan
- Department of Chemistry, University of Michigan, 930 N University Ave., Ann Arbor, Michigan 48109, USA
| | - Jared Dziurgot
- Department of Physics, University of Michigan, 450 Church St., Ann Arbor, Michigan 48109, USA
| | - Veronica Policht
- Department of Physics, University of Michigan, 450 Church St., Ann Arbor, Michigan 48109, USA
| | - Yassel Acosta Matutes
- Department of Physics, University of Michigan, 450 Church St., Ann Arbor, Michigan 48109, USA
| | - Kevin J Kubarych
- Department of Chemistry, University of Michigan, 930 N University Ave., Ann Arbor, Michigan 48109, USA
| | - Jennifer P Ogilvie
- Department of Physics, University of Michigan, 450 Church St., Ann Arbor, Michigan 48109, USA
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78
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Liu Q, Zhang Y, Zhang Q, Wei Q, Zhou D, Wu G, Cai K, Yuan K, Bian H. Understanding the intramolecular vibrational energy transfer and structural dynamics of anionic ligands in a photo-catalytic CO 2reduction catalyst. Phys Chem Chem Phys 2019; 21:23026-23035. [DOI: 10.1039/c9cp05029a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The knowledge of intramolecular vibrational energy redistribution (IVR) and structural dynamics of rhenium photo-catalysts is essential for understanding the mechanism of the photo-catalytic process of CO2reduction.
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Affiliation(s)
- Qianchen Liu
- Key Laboratory of Applied Surface and Colloid Chemistry of Ministry of Education
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
- Xi'an
- China
| | - Yutong Zhang
- State Key Laboratory of Molecular Reaction Dynamics
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian
- China
| | - Qi Zhang
- State Key Laboratory of Molecular Reaction Dynamics
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian
- China
| | - Qianshun Wei
- Key Laboratory of Applied Surface and Colloid Chemistry of Ministry of Education
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
- Xi'an
- China
| | - Dexia Zhou
- Key Laboratory of Applied Surface and Colloid Chemistry of Ministry of Education
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
- Xi'an
- China
| | - Guorong Wu
- State Key Laboratory of Molecular Reaction Dynamics
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian
- China
| | - Kaicong Cai
- College of Chemistry and Materials Science
- Fujian Normal University
- Fuzhou
- China
| | - Kaijun Yuan
- State Key Laboratory of Molecular Reaction Dynamics
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian
- China
| | - Hongtao Bian
- Key Laboratory of Applied Surface and Colloid Chemistry of Ministry of Education
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
- Xi'an
- China
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79
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Baronio CM, Baldassarre M, Barth A. Insight into the internal structure of amyloid-β oligomers by isotope-edited Fourier transform infrared spectroscopy. Phys Chem Chem Phys 2019; 21:8587-8597. [DOI: 10.1039/c9cp00717b] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Isotope-edited infrared spectroscopy reveals the structural unit of amyloid-β oligomers.
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Affiliation(s)
| | | | - Andreas Barth
- Department of Biochemistry and Biophysics
- Stockholm University
- Sweden
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80
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LIU S, ZHANG X, GUO R, WEI Y, NODA I, OZAKI Y, XU Y, WU J. Design of a Novel Apparatus to Enrich Analytes via a Diffuse-Evaporation Process for HPLC-FTIR Analysis. ANAL SCI 2018; 34:1351-1356. [DOI: 10.2116/analsci.18p227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Shengnan LIU
- College of Chemistry and Material Science, Hebei Normal University
- College of Chemistry and Molecular Engineering, Peking University
| | - Xiaohua ZHANG
- College of Chemistry and Molecular Engineering, Peking University
| | - Ran GUO
- College of Chemistry and Molecular Engineering, Peking University
| | - Yongju WEI
- College of Chemistry and Material Science, Hebei Normal University
| | - Isao NODA
- College of Chemistry and Molecular Engineering, Peking University
- Department of Materials Science and Engineering, University of Delaware
| | - Yukihiro OZAKI
- College of Chemistry and Molecular Engineering, Peking University
- Department of Chemistry, School of Science and Technology, Kwansei Gakuin University
| | - Yizhuang XU
- College of Chemistry and Molecular Engineering, Peking University
| | - Jinguang WU
- College of Chemistry and Molecular Engineering, Peking University
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81
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Wei Q, Zhou D, Li X, Chen Y, Bian H. Structural Dynamics of Dimethyl Sulfoxide Aqueous Solutions Investigated by Ultrafast Infrared Spectroscopy: Using Thiocyanate Anion as a Local Vibrational Probe. J Phys Chem B 2018; 122:12131-12138. [DOI: 10.1021/acs.jpcb.8b10058] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Qianshun Wei
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an 710119, China
| | - Dexia Zhou
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an 710119, China
| | - Xiaoqian Li
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an 710119, China
| | - Yuwan Chen
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an 710119, China
| | - Hongtao Bian
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an 710119, China
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82
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Buchanan LE, Maj M, Dunkelberger EB, Cheng PN, Nowick JS, Zanni MT. Structural Polymorphs Suggest Competing Pathways for the Formation of Amyloid Fibrils That Diverge from a Common Intermediate Species. Biochemistry 2018; 57:6470-6478. [PMID: 30375231 DOI: 10.1021/acs.biochem.8b00997] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
It is now recognized that many amyloid-forming proteins can associate into multiple fibril structures. Here, we use two-dimensional infrared spectroscopy to study two fibril polymorphs formed by human islet amyloid polypeptide (hIAPP or amylin), which is associated with type 2 diabetes. The polymorphs exhibit different degrees of structural organization near the loop region of hIAPP fibrils. The relative populations of these polymorphs are systematically altered by the presence of macrocyclic peptides which template β-sheet formation at specific sections of the hIAPP sequence. These experiments are consistent with polymorphs that result from competing pathways for fibril formation and that the macrocycles bias hIAPP aggregation toward one pathway or the other. Another macrocyclic peptide that matches the loop region but extends the lag time leaves the relative populations of the polymorphs unaltered, suggesting that the branching point for structural divergence occurs after the lag phase, when the oligomers convert into seeds that template fibril formation. Thus, we conclude that the structures of the polymorphs stem from restricting oligomers along diverging folding pathways, which has implications for drug inhibition, cytotoxicity, and the free energy landscape of hIAPP aggregation.
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Affiliation(s)
- Lauren E Buchanan
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706-1396 , United States
| | - Michał Maj
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706-1396 , United States
| | - Emily B Dunkelberger
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706-1396 , United States
| | - Pin-Nan Cheng
- Department of Chemistry , University of California-Irvine , Irvine , California 92697-2025 , United States
| | - James S Nowick
- Department of Chemistry , University of California-Irvine , Irvine , California 92697-2025 , United States
| | - Martin T Zanni
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706-1396 , United States
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83
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Maiti KS. Ultrafast N–H vibrational dynamics of hydrogen-bonded cyclic amide reveal by 2DIR spectroscopy. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.10.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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84
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Deb P, Jin GY, Singh SK, Moon J, Kwon H, Das A, Bagchi S, Kim YS. Interconverting Hydrogen-Bonding and Weak n → π* Interactions in Aqueous Solution: A Direct Spectroscopic Evidence. J Phys Chem Lett 2018; 9:5425-5429. [PMID: 30149713 DOI: 10.1021/acs.jpclett.8b02398] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Molecular structure and function depend on myriad noncovalent interactions. However, the weak and transient nature of noncovalent interactions in solution makes them challenging to study. Information on weak interactions is typically derived from theory and indirect structural data. Solvent fluctuations, not revealed by structure analysis, further complicate the study of these interactions. Using 2D infrared spectroscopy, we show that the strong hydrogen bond and the weak n → π* interaction coexist and interconvert in aqueous solution. We found that the kinetics of these interconverting interactions becomes faster with increasing water content. This experimental observation provides a new perspective on the existence of weak noncovalent interactions in aqueous solution.
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Affiliation(s)
- Pranab Deb
- Physical and Materials Chemistry Division , CSIR-National Chemical Laboratory (CSIR-NCL) , Dr. Homi Bhabha Road , Pune 411008 , India
- Academy of Scientific & Innovative Research (AcSIR) , CSIR-National Chemical Laboratory (CSIR-NCL) , Dr. Homi Bhabha Road , Pune 411008 , India
| | - Geun Young Jin
- Department of Chemistry , Ulsan National Institute of Science and Technology (UNIST) , 50 UNIST-gil , Ulsan 44919 , Republic of Korea
- Department of NanoFusion Technology , Pusan National University , Busan 46241 , Republic of Korea
| | - Santosh K Singh
- Department of Chemistry , Indian Institute of Science Education and Research (IISER) , Dr. Homi Bhabha Road , Pune 411008 , India
| | - Juran Moon
- Department of Chemistry , Ulsan National Institute of Science and Technology (UNIST) , 50 UNIST-gil , Ulsan 44919 , Republic of Korea
| | - Hyejin Kwon
- Department of Chemistry , Ulsan National Institute of Science and Technology (UNIST) , 50 UNIST-gil , Ulsan 44919 , Republic of Korea
| | - Aloke Das
- Department of Chemistry , Indian Institute of Science Education and Research (IISER) , Dr. Homi Bhabha Road , Pune 411008 , India
| | - Sayan Bagchi
- Physical and Materials Chemistry Division , CSIR-National Chemical Laboratory (CSIR-NCL) , Dr. Homi Bhabha Road , Pune 411008 , India
- Academy of Scientific & Innovative Research (AcSIR) , CSIR-National Chemical Laboratory (CSIR-NCL) , Dr. Homi Bhabha Road , Pune 411008 , India
| | - Yung Sam Kim
- Department of Chemistry , Ulsan National Institute of Science and Technology (UNIST) , 50 UNIST-gil , Ulsan 44919 , Republic of Korea
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85
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Blaffert J, Haeri HH, Blech M, Hinderberger D, Garidel P. Spectroscopic methods for assessing the molecular origins of macroscopic solution properties of highly concentrated liquid protein solutions. Anal Biochem 2018; 561-562:70-88. [PMID: 30243977 DOI: 10.1016/j.ab.2018.09.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 09/08/2018] [Accepted: 09/17/2018] [Indexed: 01/14/2023]
Abstract
In cases of subcutaneous injection of therapeutic monoclonal antibodies, high protein concentrations (>50 mg/ml) are often required. During the development of these high concentration liquid formulations (HCLF), challenges such as aggregation, gelation, opalescence, phase separation, and high solution viscosities are more prone compared to low concentrated protein formulations. These properties can impair manufacturing processes, as well as protein stability and shelf life. To avoid such unfavourable solution properties, a detailed understanding about the nature of these properties and their driving forces are required. However, the fundamental mechanisms that lead to macroscopic solution properties, as above mentioned, are complex and not fully understood, yet. Established analytical methods for assessing the colloidal stability, i.e. the ability of a native protein to remain dispersed in solution, are restricted to dilute conditions and provide parameters such as the second osmotic virial coefficient, B22, and the diffusion interaction coefficient, kD. These parameters are routinely applied for qualitative estimations and identifications of proteins with challenging solution behaviours, such as high viscosities and aggregation, although the assays are prepared for low protein concentration conditions, typically between 0.1 and 20 mg/ml ("ideal" solution conditions). Quantitative analysis of samples of high protein concentration is difficult and it is hard to obtain information about the driving forces of such solution properties and corresponding protein-protein self-interactions. An advantage of using specific spectroscopic methods is the potential of directly analysing highly concentrated protein solutions at different solution conditions. This allows for collecting/gaining valuable information about the fundamental mechanisms of solution properties of the high protein concentration regime. In addition, the derived parameters might be more predictive as compared to the parameters originating from assays which are optimized for the low protein concentration range. The provided information includes structural data, molecular dynamics at various timescales and protein-solvent interactions, which can be obtained at molecular resolution. Herein, we provide an overview about spectroscopic techniques for analysing the origins of macroscopic solution behaviours in general, with a specific focus on pharmaceutically relevant high protein concentration and formulation conditions.
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Affiliation(s)
- Jacob Blaffert
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany
| | - Haleh Hashemi Haeri
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany
| | - Michaela Blech
- Boehringer Ingelheim Pharma GmbH & Co. KG, Protein Science, Birkerndorfer Str. 65, 88397, Biberach/Riß, Germany
| | - Dariush Hinderberger
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany
| | - Patrick Garidel
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany; Boehringer Ingelheim Pharma GmbH & Co. KG, Protein Science, Birkerndorfer Str. 65, 88397, Biberach/Riß, Germany.
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86
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87
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Hogle DG, Cunningham AR, Tucker MJ. Equilibrium versus Nonequilibrium Peptide Dynamics: Insights into Transient 2D IR Spectroscopy. J Phys Chem B 2018; 122:8783-8795. [PMID: 30040900 DOI: 10.1021/acs.jpcb.8b05063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Over the past two decades, two-dimensional infrared (2D IR) spectroscopy has evolved from the theoretical underpinnings of nonlinear spectroscopy as a means of investigating detailed molecular structure on an ultrafast time scale. The combined time and spectral resolution over which spectra can be collected on complex molecular systems has led to the precise structural resolution of dynamic species that have previously been impossible to directly observe through traditional methods. The adoption of 2D IR spectroscopy for the study of protein folding and peptide interactions has provided key details of how small changes in conformations can exert major influences on the activities of these complex molecular systems. Traditional 2D IR experiments are limited to molecules under equilibrium conditions, where small motions and fluctuations of these larger molecules often still lead to functionality. Utilizing techniques that allow the rapid initiation of chemical or structural changes in conjunction with 2D IR spectroscopy, i.e., transient 2D IR, a vast dynamic range becomes available to the spectroscopist uncovering structural content far from equilibrium. Furthermore, this allows the observation of reaction pathways of these macromolecules under quasi- and nonequilibrium conditions.
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Affiliation(s)
- David G Hogle
- Department of Chemistry , University of Nevada, Reno , 1664 North Virginia Street , Reno , Nevada 89557 , United States
| | - Amy R Cunningham
- Department of Chemistry , University of Nevada, Reno , 1664 North Virginia Street , Reno , Nevada 89557 , United States
| | - Matthew J Tucker
- Department of Chemistry , University of Nevada, Reno , 1664 North Virginia Street , Reno , Nevada 89557 , United States
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88
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Grafton AB, Cheatum CM. Two-dimensional infrared study of the C D and C O stretching vibrations in strongly hydrogen-bonded complexes. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.05.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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89
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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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90
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Lyutyy TV, Reva VV. Energy dissipation of rigid dipoles in a viscous fluid under the action of a time-periodic field: The influence of thermal bath and dipole interaction. Phys Rev E 2018; 97:052611. [PMID: 29906895 DOI: 10.1103/physreve.97.052611] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Indexed: 11/07/2022]
Abstract
Ferrofluid heating by an external alternating field is studied based on the rigid dipole model, where the magnetization of each particle in a fluid is supposed to be firmly fixed in the crystal lattice. Equations of motion, employing Newton's second law for rotational motion, the condition of rigid body rotation, and the assumption that the friction torque is proportional to angular velocity are used. This oversimplification permits us to expand the model easily: to take into account the thermal noise and interparticle interaction that allows us to estimate from unified positions the role of thermal activation and dipole interaction in the heating process. Our studies are conducted in three stages. The exact expressions for the average power loss of a single particle are obtained within the dynamical approximation. Then, in the stochastic case, the power loss of a single particle is estimated analytically using the Fokker-Planck equation and numerically using the effective Langevin equation. Finally, the power loss for the particle ensemble is obtained using the molecular dynamics method. Here, the local dipole fields are calculated approximately based on the Barnes-Hut algorithm. The revealed trends in the behavior of both a single particle and the particle ensemble suggest the way of choosing the conditions for obtaining the maximum heating efficiency. The competitiveness character of the interparticle interaction and thermal noise is investigated in detail. Two situations, when the thermal noise rectifies the power loss reduction caused by the interaction, are described. The first of them is related to the complete destruction of dense clusters at high noise intensity. The second one originates from the rare switching of the particles in clusters due to thermal activation, when the noise intensity is relatively weak. In this way, the constructive role of noise appears in the system.
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Affiliation(s)
- T V Lyutyy
- Sumy State University, 2 Rimsky-Korsakov Street, UA-40007 Sumy, Ukraine
| | - V V Reva
- Sumy State University, 2 Rimsky-Korsakov Street, UA-40007 Sumy, Ukraine
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91
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Roy S, Maiti KS. Structural sensitivity of CH vibrational band in methyl benzoate. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 196:289-294. [PMID: 29459159 DOI: 10.1016/j.saa.2018.02.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Accepted: 02/08/2018] [Indexed: 06/08/2023]
Abstract
The CH vibrational bands of methyl benzoate are studied to understand its coupling pattern with other vibrational bands of the biological molecule. This will facilitate to understand the biological structure and dynamics in spectroscopic as well as in microscopic study. Due to the congested spectroscopic pattern, near degeneracy, and strong anharmonicity of the CH stretch vibrations, assignment of the CH vibrational frequencies are often misleading. Anharmonic vibrational frequency calculation with multidimensional potential energy surface interprets the CH vibrational spectra more accurately. In this article we have presented the importance of multidimensional potential energy surface in anharmonic vibrational frequency calculation and discuss the unexpected red shift of asymmetric CH stretch vibration of methyl group. The CD stretch vibrational band which is splitted to double peaks due to the Fermi resonance is also discussed here.
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Affiliation(s)
- Susmita Roy
- Die Klinik und Poliklinik für Orthopädie und Sportorthopädie, Technische Universität München, Ismaninger Straße 22, München D81675, Germany
| | - Kiran Sankar Maiti
- Lehrstuhl für Experimental Physik, Ludwig-Maximilians-Universität München, Am Couombwall 1, Garching 85748, Germany; Max-Planck-Institut für Quantenoptik, Hans-Kopfermann-Straße 1, Garching 85748, Germany.
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92
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Cohn B, Prasad AK, Chuntonov L. Communication: Probing the interaction of infrared antenna arrays and molecular films with ultrafast quantum dynamics. J Chem Phys 2018; 148:131101. [DOI: 10.1063/1.5025600] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Bar Cohn
- Schulich Faculty of Chemistry, Solid State Institute, Technion–Israel Institute of Technology, Haifa 32000, Israel
| | - Amit K. Prasad
- Schulich Faculty of Chemistry, Solid State Institute, Technion–Israel Institute of Technology, Haifa 32000, Israel
| | - Lev Chuntonov
- Schulich Faculty of Chemistry, Solid State Institute, Technion–Israel Institute of Technology, Haifa 32000, Israel
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93
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Coordination to lanthanide ions distorts binding site conformation in calmodulin. Proc Natl Acad Sci U S A 2018; 115:E3126-E3134. [PMID: 29545272 DOI: 10.1073/pnas.1722042115] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The Ca2+-sensing protein calmodulin (CaM) is a popular model of biological ion binding since it is both experimentally tractable and essential to survival in all eukaryotic cells. CaM modulates hundreds of target proteins and is sensitive to complex patterns of Ca2+ exposure, indicating that it functions as a sophisticated dynamic transducer rather than a simple on/off switch. Many details of this transduction function are not well understood. Fourier transform infrared (FTIR) spectroscopy, ultrafast 2D infrared (2D IR) spectroscopy, and electronic structure calculations were used to probe interactions between bound metal ions (Ca2+ and several trivalent lanthanide ions) and the carboxylate groups in CaM's EF-hand ion-coordinating sites. Since Tb3+ is commonly used as a luminescent Ca2+ analog in studies of protein-ion binding, it is important to characterize distinctions between the coordination of Ca2+ and the lanthanides in CaM. Although functional assays indicate that Tb3+ fully activates many Ca2+-dependent proteins, our FTIR spectra indicate that Tb3+, La3+, and Lu3+ disrupt the bidentate coordination geometry characteristic of the CaM binding sites' strongly conserved position 12 glutamate residue. The 2D IR spectra indicate that, relative to the Ca2+-bound form, lanthanide-bound CaM exhibits greater conformational flexibility and larger structural fluctuations within its binding sites. Time-dependent 2D IR lineshapes indicate that binding sites in Ca2+-CaM occupy well-defined configurations, whereas binding sites in lanthanide-bound-CaM are more disordered. Overall, the results show that binding to lanthanide ions significantly alters the conformation and dynamics of CaM's binding sites.
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94
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Falvo C. Linear and non-linear infrared response of one-dimensional vibrational Holstein polarons in the anti-adiabatic limit: Optical and acoustical phonon models. J Chem Phys 2018; 148:074103. [PMID: 29471642 DOI: 10.1063/1.5001698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The theory of linear and non-linear infrared response of vibrational Holstein polarons in one-dimensional lattices is presented in order to identify the spectral signatures of self-trapping phenomena. Using a canonical transformation, the optical response is computed from the small polaron point of view which is valid in the anti-adiabatic limit. Two types of phonon baths are considered: optical phonons and acoustical phonons, and simple expressions are derived for the infrared response. It is shown that for the case of optical phonons, the linear response can directly probe the polaron density of states. The model is used to interpret the experimental spectrum of crystalline acetanilide in the C=O range. For the case of acoustical phonons, it is shown that two bound states can be observed in the two-dimensional infrared spectrum at low temperature. At high temperature, analysis of the time-dependence of the two-dimensional infrared spectrum indicates that bath mediated correlations slow down spectral diffusion. The model is used to interpret the experimental linear-spectroscopy of model α-helix and β-sheet polypeptides. This work shows that the Davydov Hamiltonian cannot explain the observations in the NH stretching range.
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Affiliation(s)
- Cyril Falvo
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405 Orsay, France and Univ. Grenoble Alpes, CNRS, LIPhy, 38000 Grenoble, France
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95
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Mondal P, Meuwly M. Vibrational Stark spectroscopy for assessing ligand-binding strengths in a protein. Phys Chem Chem Phys 2018; 19:16131-16143. [PMID: 28604854 DOI: 10.1039/c7cp01892d] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Nitrile groups are potentially useful spectroscopic probes in the infrared to characterize the binding and dynamics of ligands in proteins. This opens the possibility of locating and determining the binding mode of suitably labelled ligands in proteins based on optical spectroscopy, without the need for determining an X-ray structure. However, relating structure and spectroscopy requires means to accurately compute infrared spectra. This is investigated for benzonitrile (PhCN) in water, wild type (WT) and two lysozyme mutants in solution. The force field is validated by comparing with experimental data for benzonitrile in water which is the basis for computing the Stark shift and time scale for spectral diffusion of PhCN in WT and the L99A and L99G mutants of T4 lysozyme. The 1-d spectra for PhCN in WT and the two mutant proteins differ in their maximum absorption by up to 4 cm-1, which reflects the modified electrostatic environments in the three proteins. It is also tested whether extending from 1-d to 2-d infrared spectroscopy provides further discrimination in the ligand-binding modes. First, for PhCN in solution the frequency fluctuation correlation function (FFCF) decays to zero at short times whereas in the protein a pronounced static inhomogeneous component is found. Secondly, the decay time of the FFCF for the mutant to which PhCN binds most strongly has the longest decay time. It is demonstrated explicitly that the ligand-binding free energy with respect to the three protein variants correlates with the Stark shift. This makes 1-d infrared spectroscopy together with computations a valuable tool for characterizing binding modes and potentially binding locations in proteins.
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Affiliation(s)
- Padmabati Mondal
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056-Basel, Switzerland.
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96
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Rodgers JM, Abaskharon RM, Ding B, Chen J, Zhang W, Gai F. Fermi resonance as a means to determine the hydrogen-bonding status of two infrared probes. Phys Chem Chem Phys 2018; 19:16144-16150. [PMID: 28604875 DOI: 10.1039/c7cp02442h] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The C[double bond, length as m-dash]O/C[triple bond, length as m-dash]N stretching vibration arising from a carbonyl/nitrile functional group in various molecular systems has been frequently used to assess, for example, local hydrogen-bonding interactions, among other applications. However, in practice it is not always easy to ascertain whether the carbonyl or nitrile group in question is engaged in such interactions. Herein, we use 4-cyanoindole and cyclopentanone as models to show that, when a fundamental C[double bond, length as m-dash]O or C[triple bond, length as m-dash]N stretching mode is involved in Fermi resonance, the underlying vibrational coupling constant (W) is a convenient reporter of the hydrogen-bonding status of the corresponding carbonyl or nitrile group. Specifically, we find that for both groups a W value of 7.7 cm-1 or greater is indicative of their involvement in hydrogen-bonding interactions. Furthermore, we find that, as observed in similar studies, the Fermi resonance coupling leads to quantum beats in the two-dimensional infrared spectra of 4-cyanoindole in isopropanol, with a period of about 1.9 ps.
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Affiliation(s)
- Jeffrey M Rodgers
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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97
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Luo Y, Ma H, Sun Y, Che P, Nie X, Wang T, Xu J. Understanding and Measurement for the Binding Energy of Hydrogen bonds of Biomass-Derived Hydroxyl Compounds. J Phys Chem A 2018; 122:843-848. [DOI: 10.1021/acs.jpca.7b10637] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Yang Luo
- State
Key Laboratory of Catalysis, Dalian Institute of Chemical Physics,
Chinese Academy of Sciences, Dalian National Laboratory for Clean Energy, Dalian 116023, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Hong Ma
- State
Key Laboratory of Catalysis, Dalian Institute of Chemical Physics,
Chinese Academy of Sciences, Dalian National Laboratory for Clean Energy, Dalian 116023, P. R. China
| | - Yuxia Sun
- State
Key Laboratory of Catalysis, Dalian Institute of Chemical Physics,
Chinese Academy of Sciences, Dalian National Laboratory for Clean Energy, Dalian 116023, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Penghua Che
- State
Key Laboratory of Catalysis, Dalian Institute of Chemical Physics,
Chinese Academy of Sciences, Dalian National Laboratory for Clean Energy, Dalian 116023, P. R. China
| | - Xin Nie
- State
Key Laboratory of Catalysis, Dalian Institute of Chemical Physics,
Chinese Academy of Sciences, Dalian National Laboratory for Clean Energy, Dalian 116023, P. R. China
| | - Tianlong Wang
- State
Key Laboratory of Catalysis, Dalian Institute of Chemical Physics,
Chinese Academy of Sciences, Dalian National Laboratory for Clean Energy, Dalian 116023, P. R. China
| | - Jie Xu
- State
Key Laboratory of Catalysis, Dalian Institute of Chemical Physics,
Chinese Academy of Sciences, Dalian National Laboratory for Clean Energy, Dalian 116023, P. R. China
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98
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Yan C, Thomaz JE, Wang YL, Nishida J, Yuan R, Breen JP, Fayer MD. Ultrafast to Ultraslow Dynamics of a Langmuir Monolayer at the Air/Water Interface Observed with Reflection Enhanced 2D IR Spectroscopy. J Am Chem Soc 2017; 139:16518-16527. [DOI: 10.1021/jacs.7b06602] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Chang Yan
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Joseph E. Thomaz
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Yong-Lei Wang
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Jun Nishida
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Rongfeng Yuan
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - John P. Breen
- 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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99
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Antipov SV, Bhattacharyya S, El Hage K, Xu ZH, Meuwly M, Rothlisberger U, Vaníček J. Ultrafast dynamics induced by the interaction of molecules with electromagnetic fields: Several quantum, semiclassical, and classical approaches. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:061509. [PMID: 29376107 PMCID: PMC5758379 DOI: 10.1063/1.4996559] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 10/11/2017] [Indexed: 06/07/2023]
Abstract
Several strategies for simulating the ultrafast dynamics of molecules induced by interactions with electromagnetic fields are presented. After a brief overview of the theory of molecule-field interaction, we present several representative examples of quantum, semiclassical, and classical approaches to describe the ultrafast molecular dynamics, including the multiconfiguration time-dependent Hartree method, Bohmian dynamics, local control theory, semiclassical thawed Gaussian approximation, phase averaging, dephasing representation, molecular mechanics with proton transfer, and multipolar force fields. In addition to the general overview, some focus is given to the description of nuclear quantum effects and to the direct dynamics, in which the ab initio energies and forces acting on the nuclei are evaluated on the fly. Several practical applications, performed within the framework of the Swiss National Center of Competence in Research "Molecular Ultrafast Science and Technology," are presented: These include Bohmian dynamics description of the collision of H with H2, local control theory applied to the photoinduced ultrafast intramolecular proton transfer, semiclassical evaluation of vibrationally resolved electronic absorption, emission, photoelectron, and time-resolved stimulated emission spectra, infrared spectroscopy of H-bonding systems, and multipolar force fields applications in the condensed phase.
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Affiliation(s)
- Sergey V Antipov
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Swarnendu Bhattacharyya
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Krystel El Hage
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Zhen-Hao Xu
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Jiří Vaníček
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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100
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Kraack JP. Ultrafast structural molecular dynamics investigated with 2D infrared spectroscopy methods. Top Curr Chem (Cham) 2017; 375:86. [PMID: 29071445 DOI: 10.1007/s41061-017-0172-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 10/02/2017] [Indexed: 12/23/2022]
Abstract
Ultrafast, multi-dimensional infrared (IR) spectroscopy has been advanced in recent years to a versatile analytical tool with a broad range of applications to elucidate molecular structure on ultrafast timescales, and it can be used for samples in a many different environments. Following a short and general introduction on the benefits of 2D IR spectroscopy, the first part of this chapter contains a brief discussion on basic descriptions and conceptual considerations of 2D IR spectroscopy. Outstanding classical applications of 2D IR are used afterwards to highlight the strengths and basic applicability of the method. This includes the identification of vibrational coupling in molecules, characterization of spectral diffusion dynamics, chemical exchange of chemical bond formation and breaking, as well as dynamics of intra- and intermolecular energy transfer for molecules in bulk solution and thin films. In the second part, several important, recently developed variants and new applications of 2D IR spectroscopy are introduced. These methods focus on (i) applications to molecules under two- and three-dimensional confinement, (ii) the combination of 2D IR with electrochemistry, (iii) ultrafast 2D IR in conjunction with diffraction-limited microscopy, (iv) several variants of non-equilibrium 2D IR spectroscopy such as transient 2D IR and 3D IR, and (v) extensions of the pump and probe spectral regions for multi-dimensional vibrational spectroscopy towards mixed vibrational-electronic spectroscopies. In light of these examples, the important open scientific and conceptual questions with regard to intra- and intermolecular dynamics are highlighted. Such questions can be tackled with the existing arsenal of experimental variants of 2D IR spectroscopy to promote the understanding of fundamentally new aspects in chemistry, biology and materials science. The final part of the chapter introduces several concepts of currently performed technical developments, which aim at exploiting 2D IR spectroscopy as an analytical tool. Such developments embrace the combination of 2D IR spectroscopy and plasmonic spectroscopy for ultrasensitive analytics, merging 2D IR spectroscopy with ultra-high-resolution microscopy (nanoscopy), future variants of transient 2D IR methods, or 2D IR in conjunction with microfluidics. It is expected that these techniques will allow for groundbreaking research in many new areas of natural sciences.
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Affiliation(s)
- Jan Philip Kraack
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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