1
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Roe J, Son JG, Park S, Seo J, Song T, Kim J, Oh SO, Jo Y, Lee Y, Shin YS, Jang H, Lee D, Yuk D, Seol JG, Kim YS, Cho S, Kim DS, Kim JY. Synergistic Buried Interface Regulation of Tin-Lead Perovskite Solar Cells via Co-Self-Assembled Monolayers. ACS NANO 2024. [PMID: 39172688 DOI: 10.1021/acsnano.4c06396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2024]
Abstract
Tin-lead (Sn-Pb) perovskite solar cells (PSCs) hold considerable potential for achieving efficiencies near the Shockley-Queisser (S-Q) limit. Notably, the inverted structure stands as the preferred fabrication method for the most efficient Sn-Pb PSCs. In this regard, it is imperative to implement a strategic customization of the hole selective layer to facilitate carrier extraction and refine the quality of perovskite films, which requires effective hole selectivity and favorable interactions with Sn-Pb perovskites. Herein, we propose the development of Co-Self-Assembled Monolayers (Co-SAM) by integrating both [2-(9H-carbazol-9-yl)ethyl]phosphonic acid (2PACz) and glycine at the buried contacts. The one-step deposition process employed in the fabrication of the Co-SAM ensures uniform coverage, resulting in a homogeneous surface potential. This is attributed to the molecular interactions occurring between 2PACz and glycine in the processing solution. Furthermore, the amine (-NH2) and ammonium (-NH3+) groups in glycine effectively passivate Sn4+ defects at the buried interface of Sn-Pb perovskite films, even under thermal stress. Consequently, the synergistic buried interface regulation of Co-SAM leads to a power conversion efficiency (PCE) of 23.46%, which outperforms devices modified with 2PACz or glycine alone. The Co-SAM-modified Sn-Pb PSC demonstrates enhanced thermal stability, maintaining 88% of its initial PCE under 65 °C thermal stress for 590 h.
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Affiliation(s)
- Jina Roe
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jung Geon Son
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Sujung Park
- Department of Semiconductor Physics and EHSRC, University of Ulsan, Ulsan 44610, Republic of Korea
| | - Jongdeuk Seo
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Taehee Song
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jaehyeong Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Si On Oh
- Graduate School of Carbon Neutrality, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Yeowon Jo
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Yeonjeong Lee
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Yun Seop Shin
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Graduate School of Carbon Neutrality, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Hyungsu Jang
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Dongmin Lee
- Graduate School of Carbon Neutrality, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Dohun Yuk
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jin Gyu Seol
- 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
| | - Shinuk Cho
- Department of Semiconductor Physics and EHSRC, University of Ulsan, Ulsan 44610, Republic of Korea
| | - Dong Suk Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Graduate School of Carbon Neutrality, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jin Young Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Graduate School of Carbon Neutrality, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
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2
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Sepulveda-Montaño LX, Galindo JF, Kuroda DG. A new computational methodology for the characterization of complex molecular environments using IR spectroscopy: bridging the gap between experiments and computations. Chem Sci 2024:d4sc03219e. [PMID: 39156932 PMCID: PMC11328912 DOI: 10.1039/d4sc03219e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Accepted: 08/08/2024] [Indexed: 08/20/2024] Open
Abstract
The molecular interactions and dynamics of complex liquid solutions are now routinely measured using IR and 2DIR spectroscopy. In particular, the use of the latter allows the determination of the frequency fluctuation correlation function (FFCF), while the former provides us with the average frequency. In turn, the FFCF can be used to quantify the vibrational dynamics of a molecule in a solution, and the center frequency provides details about the chemical environment, solvatochromism, of the vibrational mode. In simple solutions, the IR methodology can be used to unambiguously assign the interactions and dynamics observed by a molecule in solution. However, in complex environments with molecular heterogeneities, this assignment is not simple. Therefore, a method that allows for such an assignment is essential. Here, a parametrization free method, called Instantaneous Frequencies of Molecules or IFM, is presented. The IFM method, when coupled to classical molecular simulations, can predict the FFCF of a molecule in solutions. Here, N-methylacetamide (NMA) in seven different chemical environments, both simple and complex, is used to test this new method. The results show good agreement with experiments for the NMA solvatochromism and FFCF dynamics, including characteristic times and amplitudes of fluctuations. In addition, the new method shows equivalent or improved results when compared to conventional frequency maps. Overall, the use of the new method in conjunction with molecular dynamics simulations allows unlocking the full potential of IR spectroscopy to generate molecular maps from vibrational observables, capable of describing the interaction landscape of complex molecular systems.
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Affiliation(s)
| | - Johan F Galindo
- Department of Chemistry, Universidad Nacional de Colombia Sede Bogotá Bogotá 111321 Colombia
| | - Daniel G Kuroda
- Department of Chemistry, Louisiana State University Baton Rouge Louisiana 70803 USA
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3
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Li Z, Feng X, Yuan K, Zhang XX. Identification of Binding Sites in Copper(II)-Peptide Complexes Using Infrared Spectroscopy. J Phys Chem B 2024; 128:1884-1891. [PMID: 38378490 DOI: 10.1021/acs.jpcb.4c00029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Complex formation of the copper(II) ion (CuII) with histidine (H) and H-containing peptides plays a crucial role in various metallo-enzymatic reactions. To elucidate the nature of coordinate bonding in CuII complexes, Fourier-transform infrared spectroscopy and 2D IR spectroscopy were employed to investigate the coordination geometries of CuII with diglycine, l-histidylglycine (HG), glycyl-l-histidine (GH), and glycylglycyl-l-histidine. The coordination of CuII to different peptide groups, including the peptide N- and C-termini, the amide group, and the imidazole of the H side chain, exhibits distinct spectral features. The derived molecular structure of the CuII-HG complex based on these spectral features significantly differs from that of CuII-GH, suggesting a preference of the N-terminus and the steric hindrance of the H side chain in CuII chelation.
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Affiliation(s)
- Zhenghangcheng Li
- School of Physics, Dalian University of Technology, 2 Linggong Road, Dalian 116024, P. R. China
| | - Xueyu Feng
- School of Physics, Dalian University of Technology, 2 Linggong Road, Dalian 116024, P. R. China
| | - Kaijun Yuan
- State Key Laboratory of Molecular Reaction Dynamics and Dalian Coherent Light Source, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Xin-Xing Zhang
- School of Physics, Dalian University of Technology, 2 Linggong Road, Dalian 116024, P. R. China
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4
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Puro RL, Gray TP, Kapfunde TA, Richter-Addo GB, Raschke MB. Vibrational Coupling Infrared Nanocrystallography. NANO LETTERS 2024; 24:1909-1915. [PMID: 38315708 DOI: 10.1021/acs.nanolett.3c03958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Coupling between molecular vibrations leads to collective vibrational states with spectral features sensitive to local molecular order. This provides spectroscopic access to the low-frequency intermolecular energy landscape. In its nanospectroscopic implementation, this technique of vibrational coupling nanocrystallography (VCNC) offers information on molecular disorder and domain formation with nanometer spatial resolution. However, deriving local molecular order relies on prior knowledge of the transition dipole magnitude and crystal structure of the underlying ordered phase. Here we develop a quantitative model for VCNC by relating nano-FTIR collective vibrational spectra to the molecular crystal structure from X-ray crystallography. We experimentally validate our approach at the example of a metal organic porphyrin complex with a carbonyl ligand as the probe vibration. This framework establishes VCNC as a powerful tool for measuring low-energy molecular interactions, wave function delocalization, nanoscale disorder, and domain formation in a wide range of molecular systems.
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Affiliation(s)
- Richard L Puro
- Department of Physics and JILA, University of Colorado, Boulder, Colorado 80309, United States
| | - Thomas P Gray
- Department of Physics and JILA, University of Colorado, Boulder, Colorado 80309, United States
| | - Tsitsi A Kapfunde
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - George B Richter-Addo
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Markus B Raschke
- Department of Physics and JILA, University of Colorado, Boulder, Colorado 80309, United States
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5
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Baronio CM, Barth A. Refining protein amide I spectrum simulations with simple yet effective electrostatic models for local wavenumbers and dipole derivative magnitudes. Phys Chem Chem Phys 2024; 26:1166-1181. [PMID: 38099625 DOI: 10.1039/d3cp02018e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
Analysis of the amide I band of proteins is probably the most wide-spread application of bioanalytical infrared spectroscopy. Although highly desirable for a more detailed structural interpretation, a quantitative description of this absorption band is still difficult. This work optimized several electrostatic models with the aim to reproduce the effect of the protein environment on the intrinsic wavenumber of a local amide I oscillator. We considered the main secondary structures - α-helices, parallel and antiparallel β-sheets - with a maximum of 21 amide groups. The models were based on the electric potential and/or the electric field component along the CO bond at up to four atoms in an amide group. They were bench-marked by comparison to Hessian matrices reconstructed from density functional theory calculations at the BPW91, 6-31G** level. The performance of the electrostatic models depended on the charge set used to calculate the electric field and potential. Gromos and DSSP charge sets, used in common force fields, were not optimal for the better performing models. A good compromise between performance and the stability of model parameters was achieved by a model that considered the electric field at the positions of the oxygen, nitrogen, and hydrogen atoms of the considered amide group. The model describes also some aspects of the local conformation effect and performs similar on its own as in combination with an explicit implementation of the local conformation effect. It is better than a combination of a local hydrogen bonding model with the local conformation effect. Even though the short-range hydrogen bonding model performs worse, it captures important aspects of the local wavenumber sensitivity to the molecular surroundings. We improved also the description of the coupling between local amide I oscillators by developing an electrostatic model for the dependency of the dipole derivative magnitude on the protein environment.
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Affiliation(s)
- Cesare M Baronio
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
| | - Andreas Barth
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
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6
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Brüggemann J, Chekmeneva M, Wolter M, Jacob CR. Structural Dependence of Extended Amide III Vibrations in Two-Dimensional Infrared Spectra. J Phys Chem Lett 2023; 14:9257-9264. [PMID: 37812580 PMCID: PMC10591501 DOI: 10.1021/acs.jpclett.3c02662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 10/05/2023] [Indexed: 10/11/2023]
Abstract
Two-dimensional infrared (2D-IR) spectroscopy is a powerful experimental method for probing the structure and dynamics of proteins in aqueous solution. So far, most experimental studies have focused on the amide I vibrations, for which empirical vibrational exciton models provide a means of interpreting such experiments. However, such models are largely lacking for other regions of the vibrational spectrum. To close this gap, we employ an efficient quantum-chemical methodology for the calculation of 2D-IR spectra, which is based on anharmonic theoretical vibrational spectroscopy with localized modes. We apply this approach to explore the potential of 2D-IR spectroscopy in the extended amide III region. Using calculations for a dipeptide model as well as alanine polypeptides, we show that distinct 2D-IR cross-peaks in the extended amide III region can potentially be used to distinguish α-helix and β-strand structures. We propose that the extended amide III region could be a promising target for future 2D-IR experiments.
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Affiliation(s)
- Julia Brüggemann
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Maria Chekmeneva
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Mario Wolter
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Christoph R. Jacob
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry, Gaußstraße 17, 38106 Braunschweig, Germany
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7
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Torii H, Watanabe K. Asymmetry of the Electrostatic Environment as the Origin of the Symmetry Breaking Effect of the Nitrate Ion in Aqueous Solution. J Phys Chem B 2023; 127:6507-6515. [PMID: 37462156 DOI: 10.1021/acs.jpcb.3c01977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Elucidating the mechanism of how vibrational modes are affected by intermolecular interactions is important for a better understanding of the nature of the former as probes of the latter. Here, such an analysis is carried out for the N-O stretching modes of the nitrate ion interacting with water, with an emphasis on the symmetry breaking effect. On the basis of theoretical calculations on the structural, vibrational, and electrostatic properties of molecular clusters and spectral simulations for an aqueous solution, a transparent view is demonstrated on the mechanism that modulations of spatially local electrostatic environment give rise to structural and spectroscopic symmetry breaking effect. The electrostatic interaction model constructed here is a seven-parameter model; the use of a single electrostatic parameter, such as the electric field on a single atomic site, is found to be insufficient for quantitative evaluation. It is also shown that the frequency modulations of the N-O stretching modes in aqueous solution occur on a time scale much shorter than 0.1 ps.
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Affiliation(s)
- Hajime Torii
- Department of Applied Chemistry and Biochemical Engineering, Faculty of Engineering, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu 432-8561, Japan
- Department of Optoelectronics and Nanostructure Science, Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu 432-8561, Japan
| | - Kao Watanabe
- Department of Applied Chemistry and Biochemical Engineering, Faculty of Engineering, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu 432-8561, Japan
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8
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Banerjee S, Naik T, Ghosh A. Intermediate Antiparallel Fibrils in Aβ40 Dutch Mutant Aggregation: Insights from Nanoscale Infrared Spectroscopy. J Phys Chem B 2023; 127:5799-5807. [PMID: 37363988 PMCID: PMC10691422 DOI: 10.1021/acs.jpcb.3c01869] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Cerebral amyloid angiopathy (CAA), which involves amyloid deposition in blood vessels leading to fatal cerebral hemorrhage and recurring strokes, is present in the majority Alzheimer's disease (AD) cases. Familial mutations in the amyloid β peptide are correlated to higher risks of CAA and are mostly comprised of mutations at residues 22 and 23. While the structure of the wild-type Aβ peptide has been investigated in great detail, less is known about the structure of mutants involved in CAA and evolutions thereof. This is particularly true for mutations at residue 22, for which detailed molecular structures, as typically determined from Nuclear Magnetic Resonance (NMR) spectroscopy or electron microscopy, do not exist. In this report, we have used nanoscale infrared (IR) spectroscopy augmented with atomic force microscopy (AFM-IR) to investigate structural evolution of the Aβ Dutch mutant (E22Q) at the single aggregate level. We show that in the oligomeric stage, the structural ensemble is distinctly bimodal, with the two subtypes differing with respect to population of parallel β sheets. Fibrils on the other hand are structurally homogeneous, with early-stage fibrils distinctly antiparallel in character, which develop parallel β sheets upon maturation. Furthermore, the antiparallel structure is found to be a persistent feature across different stages of aggregation.
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Affiliation(s)
- Siddhartha Banerjee
- Department of Chemistry and Biochemistry, The University of Alabama, 1007E Shelby Hall, Tuscaloosa, Alabama 35487, United States
| | - Tanmayee Naik
- Department of Chemistry and Biochemistry, The University of Alabama, 1007E Shelby Hall, Tuscaloosa, Alabama 35487, United States
| | - Ayanjeet Ghosh
- Department of Chemistry and Biochemistry, The University of Alabama, 1007E Shelby Hall, Tuscaloosa, Alabama 35487, United States
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9
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Banerjee S, Naik T, Ghosh A. Intermediate antiparallel fibrils in Aβ40 Dutch mutant aggregation: nanoscale insights from AFM-IR. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.21.533667. [PMID: 36993390 PMCID: PMC10055286 DOI: 10.1101/2023.03.21.533667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Cerebral Amyloid Angiopathy (CAA), which involves amyloid deposition in blood vessels leading to fatal cerebral hemorrhage and recurring strokes, is present in the majority Alzheimer's disease cases. Familial mutations in the amyloid β peptide is correlated to higher risks of CAA, and are mostly comprised of mutations at residues 22 and 23. While the structure of the wild type Aβ peptide has been investigated in great detail, less is known about the structure of mutants involved in CAA and evolutions thereof. This is particularly true for mutations at residue 22, for which detailed molecular structures, as typically determined from Nuclear Magnetic Resonance (NMR) spectroscopy or electron microscopy, do not exist. In this report, we have used nanoscale infrared (IR) spectroscopy augmented with Atomic Force Microscopy (AFM-IR) to investigate structural evolution of the Aβ Dutch mutant (E22Q) at the single aggregate level. We show that that in the oligomeric stage, the structural ensemble is distinctly bimodal, with the two subtypes differing with respect to population of parallel β-sheets. Fibrils on the other hand are structurally homogeneous, with early-stage fibrils distinctly anti parallel in character, which develop parallel β-sheets upon maturation. Furthermore, the antiparallel structure is found to be a persistent feature across different stages of aggregation.
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10
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Brüggemann J, Wolter M, Jacob CR. Quantum-chemical calculation of two-dimensional infrared spectra using localized-mode VSCF/VCI. J Chem Phys 2022; 157:244107. [PMID: 36586972 DOI: 10.1063/5.0135273] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Computational protocols for the simulation of two-dimensional infrared (2D IR) spectroscopy usually rely on vibrational exciton models which require an empirical parameterization. Here, we present an efficient quantum-chemical protocol for predicting static 2D IR spectra that does not require any empirical parameters. For the calculation of anharmonic vibrational energy levels and transition dipole moments, we employ the localized-mode vibrational self-consistent field (L-VSCF)/vibrational configuration interaction (L-VCI) approach previously established for (linear) anharmonic theoretical vibrational spectroscopy [P. T. Panek and C. R. Jacob, ChemPhysChem 15, 3365-3377 (2014)]. We demonstrate that with an efficient expansion of the potential energy surface using anharmonic one-mode potentials and harmonic two-mode potentials, 2D IR spectra of metal carbonyl complexes and dipeptides can be predicted reliably. We further show how the close connection between L-VCI and vibrational exciton models can be exploited to extract the parameters of such models from those calculations. This provides a novel route to the fully quantum-chemical parameterization of vibrational exciton models for predicting 2D IR spectra.
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Affiliation(s)
- Julia Brüggemann
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Mario Wolter
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Christoph R Jacob
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
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11
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Strunge K, Madzharova F, Jensen F, Weidner T, Nagata Y. Theoretical Sum Frequency Generation Spectra of Protein Amide with Surface-Specific Velocity-Velocity Correlation Functions. J Phys Chem B 2022; 126:8571-8578. [PMID: 36194760 DOI: 10.1021/acs.jpcb.2c04321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Vibrational sum frequency generation (vSFG) spectroscopy is widely used to probe the protein structure at interfaces. Because protein vSFG spectra are complex, they can only provide detailed structural information if combined with computer simulations of protein molecular dynamics and spectra calculations. We show how vSFG spectra can be accurately modeled using a surface-specific velocity-velocity scheme based on ab initio normal modes. Our calculated vSFG spectra show excellent agreement with the experimental sum frequency spectrum of LTα14 peptide and provide insight into the origin of the characteristic α-helical amide I peak. Analysis indicates that the peak shape can be explained largely by two effects: (1) the uncoupled response of amide groups located on opposite sides of the α-helix will have different orientations with respect to the interface and therefore different local environments affecting the local mode vibrations and (2) vibrational splitting from nearest neighbor coupling evaluated as inter-residue vibrational correlation. The conclusion is consistent with frequency mapping techniques with an empirically based ensemble of peptide structures, thus showing how time correlation approaches and frequency mapping techniques can give independent yet complementary molecular descriptions of protein vSFG. These models reveal the sensitive relationship between protein structure and their amide I response, allowing exploitation of the complicated molecular vibrations and their interference to derive the structures of proteins under native conditions at interfaces.
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Affiliation(s)
- Kris Strunge
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Fani Madzharova
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Frank Jensen
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Tobias Weidner
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Yuki Nagata
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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12
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Role of the electrostatic interactions in the changes in the CN stretching frequency of benzonitrile interacting with hydrogen-bond donating molecules. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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13
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Tutorials in vibrational sum frequency generation spectroscopy. III. Collecting, processing, and analyzing vibrational sum frequency generation spectra. Biointerphases 2022; 17:041201. [PMID: 35931562 DOI: 10.1116/6.0001951] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In this Tutorial series, we aim to provide an accessible introduction to vibrational sum frequency generation (VSFG) spectroscopy, targeted toward people entering the VSFG world without a rigorous formal background in optical physics or nonlinear spectroscopy. In this article, we discuss in detail the processes of collecting and processing VSFG data, and user-friendly processing software (sfgtools) is provided for use by people new to the field. Some discussion of analyzing VSFG spectra is also given, specifically with a discussion of fitting homodyne VSFG spectra, and a discussion of what can be learned (both qualitatively and quantitatively) from VSFG spectra.
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14
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van Adrichem KE, Jansen TLC. AIM: A Mapping Program for Infrared Spectroscopy of Proteins. J Chem Theory Comput 2022; 18:3089-3098. [PMID: 35387451 PMCID: PMC9097285 DOI: 10.1021/acs.jctc.2c00113] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
Here, we present
a new analysis program, AIM, that allows extracting
the vibrational amide-I Hamiltonian using molecular dynamics trajectories
for protein infrared spectroscopy modeling. The constructed Hamiltonians
can be used as input for spectral calculations allowing the calculation
of infrared absorption spectra, vibrational circular dichroism, and
two-dimensional infrared spectra. These spectroscopies allow the study
of the structure and dynamics of proteins. We will explain the essence
of how AIM works and give examples of the information and spectra
that can be obtained with the program using the Trypsin Inhibitor
as an example. AIM is freely available from GitHub, and the package
contains a demonstration allowing easy introduction to the use of
the program.
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Affiliation(s)
- Kim E van Adrichem
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Thomas L C Jansen
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
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15
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Meuwly M. Atomistic Simulations for Reactions and Vibrational Spectroscopy in the Era of Machine Learning─ Quo Vadis?. J Phys Chem B 2022; 126:2155-2167. [PMID: 35286087 DOI: 10.1021/acs.jpcb.2c00212] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Atomistic simulations using accurate energy functions can provide molecular-level insight into functional motions of molecules in the gas and in the condensed phase. This Perspective delineates the present status of the field from the efforts of others and some of our own work and discusses open questions and future prospects. The combination of physics-based long-range representations using multipolar charge distributions and kernel representations for the bonded interactions is shown to provide realistic models for the exploration of the infrared spectroscopy of molecules in solution. For reactions, empirical models connecting dedicated energy functions for the reactant and product states allow statistically meaningful sampling of conformational space whereas machine-learned energy functions are superior in accuracy. The future combination of physics-based models with machine-learning techniques and integration into all-purpose molecular simulation software provides a unique opportunity to bring such dynamics simulations closer to reality.
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Affiliation(s)
- Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
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16
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Conformational ensembles of intrinsically disordered proteins and flexible multidomain proteins. Biochem Soc Trans 2022; 50:541-554. [PMID: 35129612 DOI: 10.1042/bst20210499] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 12/29/2022]
Abstract
Intrinsically disordered proteins (IDPs) and multidomain proteins with flexible linkers show a high level of structural heterogeneity and are best described by ensembles consisting of multiple conformations with associated thermodynamic weights. Determining conformational ensembles usually involves the integration of biophysical experiments and computational models. In this review, we discuss current approaches to determine conformational ensembles of IDPs and multidomain proteins, including the choice of biophysical experiments, computational models used to sample protein conformations, models to calculate experimental observables from protein structure, and methods to refine ensembles against experimental data. We also provide examples of recent applications of integrative conformational ensemble determination to study IDPs and multidomain proteins and suggest future directions for research in the field.
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17
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Chelius K, Wat JH, Phadkule A, Reppert M. Distinct electrostatic frequency tuning rates for amide I and amide I' vibrations. J Chem Phys 2021; 155:195101. [PMID: 34800962 DOI: 10.1063/5.0064518] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Amide I spectroscopy probes the backbone C=O stretch vibrations of peptides and proteins. Amide I spectra are often collected in deuterated water (D2O) since this provides a cleaner background in the amide I frequency range; such data are often referred to as amide I' spectra since deuteration induces changes in the mode structure, including a roughly ∼10 cm-1 redshift. For biological samples, however, deuteration is often not possible. As amide I frequency maps are increasingly applied to quantitative protein structural analysis, this raises the interesting challenge of drawing direct connections between amide I and amide I' data. We here analyze amide I and amide I' peak frequencies for a series of dipeptides and related compounds. Changes in protonation state induce large electrostatic shifts in the peak frequencies, allowing us to amass a sizable library of data points for direct amide I/amide I' comparison. While we find an excellent linear correlation between amide I and amide I' peak frequencies, the deuteration-induced shift is smaller for more red-shifted vibrations, indicating different electrostatic tuning rates in the two solvents. H2O/D2O shifts were negligible for proline-containing dipeptides that lack exchangeable amide hydrogens, indicating that the intrinsic properties of the solvent do not strongly influence the H/D shift. These findings indicate that the distinct tuning rates observed for the two vibrations arise from modifications to the intrinsic properties of the amide bond and provide (at least for solvated dipeptides) a simple, linear "map" for translating between amide I and amide I' frequencies.
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Affiliation(s)
- Kevin Chelius
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Jacob H Wat
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Amala Phadkule
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Mike Reppert
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
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18
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Mondal P, Cazade PA, Das AK, Bereau T, Meuwly M. Multipolar Force Fields for Amide-I Spectroscopy from Conformational Dynamics of the Alanine Trimer. J Phys Chem B 2021; 125:10928-10938. [PMID: 34559531 DOI: 10.1021/acs.jpcb.1c05423] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The dynamics and spectroscopy of N-methyl-acetamide (NMA) and trialanine in solution are characterized from molecular dynamics simulations using different energy functions, including a conventional point charge (PC)-based force field, one based on a multipolar (MTP) representation of the electrostatics, and a semiempirical DFT method. For the 1D infrared spectra, the frequency splitting between the two amide-I groups is 10 cm-1 from the PC, 13 cm-1 from the MTP, and 47 cm-1 from self-consistent charge density functional tight-binding (SCC-DFTB) simulations, compared with 25 cm-1 from experiment. The frequency trajectory required for the frequency fluctuation correlation function (FFCF) is determined from individual normal mode (INM) and full normal mode (FNM) analyses of the amide-I vibrations. The spectroscopy, time-zero magnitude of the FFCF C(t = 0), and the static component Δ02 from simulations using MTP and analysis based on FNM are all consistent with experiments for (Ala)3. Contrary to this, for the analysis excluding mode-mode coupling (INM), the FFCF decays to zero too rapidly and for simulations with a PC-based force field, the Δ02 is too small by a factor of two compared with experiments. Simulations with SCC-DFTB agree better with experiment for these observables than those from PC-based simulations. The conformational ensemble sampled from simulations using PCs is consistent with the literature (including PII, β, αR, and αL), whereas that covered by the MTP-based simulations is dominated by PII with some contributions from β and αR. This agrees with and confirms recently reported Bayesian-refined populations based on 1D infrared experiments. FNM analysis together with a MTP representation provides a meaningful model to correctly describe the dynamics of hydrated trialanine.
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Affiliation(s)
- Padmabati Mondal
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, Basel 4056, Switzerland
| | - Pierre-André Cazade
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, Basel 4056, Switzerland
| | - Akshaya K Das
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, Basel 4056, Switzerland
| | - Tristan Bereau
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, Basel 4056, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, Basel 4056, Switzerland.,Department of Chemistry, Brown University, Providence/RI 02912, United States
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19
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Confer MP, Holcombe BM, Foes AG, Holmquist JM, Walker SC, Deb S, Ghosh A. Label-Free Infrared Spectroscopic Imaging Reveals Heterogeneity of β-Sheet Aggregates in Alzheimer's Disease. J Phys Chem Lett 2021; 12:9662-9671. [PMID: 34590866 PMCID: PMC8933041 DOI: 10.1021/acs.jpclett.1c02306] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The aggregation of the amyloid beta (Aβ) protein into plaques is a pathological feature of Alzheimer's disease (AD). While amyloid aggregates have been extensively studied in vitro, their structural aspects and associated chemistry in the brain are not fully understood. In this report, we demonstrate, using infrared spectroscopic imaging, that Aβ plaques exhibit significant heterogeneities in terms of their secondary structure and phospholipid content. We show that the capabilities of discrete frequency infrared imaging (DFIR) are ideally suited for characterization of amyloid deposits in brain tissues and employ DFIR to identify nonplaque β-sheet aggregates distributed throughout brain tissues. We further demonstrate that phospholipid-rich β-sheet deposits exist outside of plaques in all diseased tissues, indicating their potential clinical significance. This is the very first application of DFIR toward a characterization of protein aggregates in an AD brain and provides a rapid, label-free approach that allows us to uncover β-sheet heterogeneities in the AD, which may be significant for targeted therapeutic strategies in the future.
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20
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Pinto SMV, Tasinato N, Barone V, Zanetti-Polzi L, Daidone I. A computational insight into the relationship between side chain IR line shapes and local environment in fibril-like structures. J Chem Phys 2021; 154:084105. [PMID: 33639764 DOI: 10.1063/5.0038913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Infrared spectroscopy is a widely used technique to characterize protein structures and protein mediated processes. While the amide I band provides information on proteins' secondary structure, amino acid side chains are used as infrared probes for the investigation of protein reactions and local properties. In this paper, we use a hybrid quantum mechanical/classical molecular dynamical approach based on the perturbed matrix method to compute the infrared band due to the C=O stretching mode of amide-containing side chains. We calculate, at first, the infrared band of zwitterionic glutamine in water and obtain results in very good agreement with the experimental data. Then, we compute the signal arising from glutamine side chains in a microcrystal of the yeast prion Sup35-derived peptide, GNNQQNY, with a fibrillar structure. The infrared bands obtained by selective isotopic labeling of the two glutamine residues, Q4 and Q5, of each peptide were experimentally used to investigate the local hydration in the fibrillar microcrystal. The experimental spectra of the two glutamine residues, which experience different hydration environments, feature different spectral signals that are well reproduced by the corresponding calculated spectra. In addition, the analysis of the simulated spectra clarifies the molecular origin of the experimentally observed spectroscopic differences that arise from the different local electric field experienced by the two glutamine residues, which is, in turn, determined by a different hydrogen bonding pattern.
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Affiliation(s)
- Sandra M V Pinto
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Nicola Tasinato
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | | | - Isabella Daidone
- Department of Physical and Chemical Sciences, University of L'Aquila, Via Vetoio, I-67100 L'Aquila, Italy
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21
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Zhang X, Chen X, Kuroda DG. Computing the frequency fluctuation dynamics of highly coupled vibrational transitions using neural networks. J Chem Phys 2021; 154:164514. [PMID: 33940799 DOI: 10.1063/5.0044911] [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 description of frequency fluctuations for highly coupled vibrational transitions has been a challenging problem in physical chemistry. In particular, the complexity of their vibrational Hamiltonian does not allow us to directly derive the time evolution of vibrational frequencies for these systems. In this paper, we present a new approach to this problem by exploiting the artificial neural network to describe the vibrational frequencies without relying on the deconstruction of the vibrational Hamiltonian. To this end, we first explored the use of the methodology to predict the frequency fluctuations of the amide I mode of N-methylacetamide in water. The results show good performance compared with the previous experimental and theoretical results. In the second part, the neural network approach is used to investigate the frequency fluctuations of the highly coupled carbonyl stretch modes for the organic carbonates in the solvation shell of the lithium ion. In this case, the frequency fluctuation predicted by the neural networks shows a good agreement with the experimental results, which suggests that this model can be used to describe the dynamics of the frequency in highly coupled transitions.
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Affiliation(s)
- Xiaoliu Zhang
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Xiaobing Chen
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Daniel G Kuroda
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA
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22
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Feng CJ, Sinitskiy A, Pande V, Tokmakoff A. Computational IR Spectroscopy of Insulin Dimer Structure and Conformational Heterogeneity. J Phys Chem B 2021; 125:4620-4633. [PMID: 33929849 DOI: 10.1021/acs.jpcb.1c00399] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
We have investigated the structure and conformational dynamics of insulin dimer using a Markov state model (MSM) built from extensive unbiased atomistic molecular dynamics simulations and performed infrared spectral simulations of the insulin MSM to describe how structural variation within the dimer can be experimentally resolved. Our model reveals two significant conformations to the dimer: a dominant native state consistent with other experimental structures of the dimer and a twisted state with a structure that appears to reflect a ∼55° clockwise rotation of the native dimer interface. The twisted state primarily influences the contacts involving the C-terminus of insulin's B chain, shifting the registry of its intermolecular hydrogen bonds and reorganizing its side-chain packing. The MSM kinetics predict that these configurations exchange on a 14 μs time scale, largely passing through two Markov states with a solvated dimer interface. Computational amide I spectroscopy of site-specifically 13C18O labeled amides indicates that the native and twisted conformation can be distinguished through a series of single and dual labels involving the B24F, B25F, and B26Y residues. Additional structural heterogeneity and disorder is observed within the native and twisted states, and amide I spectroscopy can also be used to gain insight into this variation. This study will provide important interpretive tools for IR spectroscopic investigations of insulin structure and transient IR kinetics experiments studying the conformational dynamics of insulin dimer.
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Affiliation(s)
- Chi-Jui Feng
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, United States
| | - Anton Sinitskiy
- Department of Bioengineering, Stanford University, Stanford, California 94305, United States
| | - Vijay Pande
- Department of Bioengineering, Stanford University, Stanford, California 94305, United States
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, United States
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23
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Edington SC, Liu S, Baiz CR. Infrared spectroscopy probes ion binding geometries. Methods Enzymol 2021; 651:157-191. [PMID: 33888203 DOI: 10.1016/bs.mie.2020.12.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Infrared (IR) spectroscopy is a well-established technique for probing the structure, behavior, and surroundings of molecules in their native environments. Its characteristics-most specifically high structural sensitivity, ready applicability to aqueous samples, and broad availability-make it a valuable enzymological technique, particularly for the interrogation of ion binding sites. While IR spectroscopy of the "garden variety" (steady state at room temperature with wild-type proteins) is versatile and powerful in its own right, the combination of IR spectroscopy with specialized experimental schemes for leveraging ultrafast time resolution, protein labeling, and other enhancements further extends this utility. This book chapter provides the fundamental physical background and literature context essential for harnessing IR spectroscopy in the general context of enzymology with specific focus on interrogation of ion binding. Studies of lanthanide ions binding to calmodulin are highlighted as illustrative examples of this process. Appropriate sample preparation, data collection, and spectral interpretation are discussed from a detail-oriented and practical perspective with the goal of facilitating the reader's rapid progression from reading words in a book to collecting and analyzing their own data in the lab.
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Affiliation(s)
- Sean C Edington
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - Stephanie Liu
- Department of Chemistry, The University of Texas at Austin, Austin, TX, United States
| | - Carlos R Baiz
- Department of Chemistry, The University of Texas at Austin, Austin, TX, United States.
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24
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Salehi SM, Koner D, Meuwly M. Dynamics and Infrared Spectrocopy of Monomeric and Dimeric Wild Type and Mutant Insulin. J Phys Chem B 2020; 124:11882-11894. [PMID: 33245663 DOI: 10.1021/acs.jpcb.0c08048] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The infrared spectroscopy and dynamics of -CO labels in wild type and mutant insulin monomer and dimer are characterized from molecular dynamics simulations using validated force fields. It is found that the spectroscopy of monomeric and dimeric forms in the region of the amide-I vibration differs for residues B24-B26 and D24-D26, which are involved in dimerization of the hormone. Also, the spectroscopic signatures change for mutations at position B24 from phenylalanine, which is conserved in many organisms and is known to play a central role in insulin aggregation, to alanine or glycine. Using three different methods to determine the frequency trajectories (solving the nuclear Schrödinger equation on an effective 1-dimensional potential energy curve, using instantaneous normal modes, and using parametrized frequency maps) leads to the same overall conclusions. The spectroscopic response of monomeric WT and mutant insulin differs from that of their respective dimers, and the spectroscopy of the two monomers in the dimer is also not identical. For the WT and F24A and F24G monomers, spectroscopic shifts are found to be ∼20 cm-1 for residues (B24-B26) located at the dimerization interface. Although the crystal structure of the dimer is that of a symmetric homodimer, dynamically the two monomers are not equivalent on the nanosecond time scale. Together with earlier work on the thermodynamic stability of the WT and the same mutants, it is concluded that combining computational and experimental infrared spectroscopy provides a potentially powerful way to characterize the aggregation state and dimerization energy of modified insulins.
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Affiliation(s)
- Seyedeh Maryam Salehi
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Debasish Koner
- 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
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25
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Zhang S, Andrews B, Schweitzer-Stenner R, Urbanc B. Intrinsic Conformational Dynamics of Alanine in Water/Ethanol Mixtures: An Experiment-Driven Molecular Dynamics Study. J Phys Chem B 2020; 124:11600-11616. [PMID: 33300341 DOI: 10.1021/acs.jpcb.0c08245] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In vitro, cationic glycylalanylglycine (GAG) forms a hydrogel in binary mixtures of water and ethanol. In water, alanine residue is known for its high polyproline II (pPII) content. Spectroscopic data, including three J-coupling constants and amide I' profiles, indicate that addition of 42% ethanol to water significantly reduces the pPII content of alanine residue in GAG. Here, experiment-based Gaussian Ramachandran distributions of alanine in GAG at different ethanol fractions are examined and three MD force fields are evaluated with respect to their ability to capture these ethanol-induced conformational changes. MD simulations on monomeric GAG in eight different water/ethanol mixtures within Amber ff14SB, OPLS-AA/M, and CHARMM36m reveal that only Amber ff14SB partially captures the ethanol-induced conformational changes of alanine residue in monomeric GAG when 42% ethanol is added to water. MD simulations of 200 mM GAG ensembles in pure water and in the aqueous solution with 42% ethanol showcase the ability of CHARMM36m to capture the effect of ethanol on the average pPII content of alanine in GAG and provide a plausible explanation for this effect, which may stem from an increased propensity of GAG to form oligomers in the presence of ethanol.
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Affiliation(s)
- Shuting Zhang
- Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Brian Andrews
- Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | | | - Brigita Urbanc
- Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, United States
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26
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Zhao J, Wang J. Specific and non-specific interactions between metal cations and zwitterionic alanine tripeptide in saline solutions reported by the symmetric carboxylate stretching and amide-II vibrations. Phys Chem Chem Phys 2020; 22:25042-25053. [PMID: 33112337 DOI: 10.1039/d0cp04247a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The "specific" interaction between metal cations (Na+, Ca2+, Mg2+, and Zn2+) and the charged COO- group, and the "non-specific" interaction between these cations and the peptide backbone of a zwitterionic trialanine (Ala3) in aqueous solutions were examined in detail, using linear infrared (IR) absorptions of the COO- symmetric stretching and the amide-II (mainly the C-N stretching) modes as IR probes. Different IR spectral changes in peak positions and intensities of the two IR probes clearly demonstrate their sensitivities to nearby cation distributions in distance and population. Quantum chemistry calculations and molecular dynamics simulations were used to describe the cation-peptide interaction picture. These combined results suggest that Na+ and Ca2+ tend to bind to the COO- group in the bidentate form, while Mg2+ and Zn2+ tend to bind to the COO- group in the pseudo-bridging form. The results also show that while all three divalent cations indirectly interact with the peptide backbone with large population, Ca2+ and Mg2+ can be sometimes distributed very close to the backbone. Such a non-specific cation interaction can be moderately sensed by the C-N stretching of the amide-II mode when cations approach the polar amide C[double bond, length as m-dash]O group, and is also influenced by the NH3+ charge group located at the N-terminus. The results suggest that the experimentally observed complication of the Hofmeister cation series shall be understood as a combined specific and non-specific cation-peptide interactions.
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Affiliation(s)
- Juan Zhao
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.
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27
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Biswas S, Mallik BS. Probing the vibrational dynamics of amide bands of N-methylformamide, N, N-dimethylacetamide, and N-methylacetamide in water. COMPUT THEOR CHEM 2020. [DOI: 10.1016/j.comptc.2020.113001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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28
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Biswas S, Mallik BS. Solvent-mediated dynamics and stretching profile of amide modes: QM/MM simulations of N-methylacetamide in ionic and various molecular liquids. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.114202] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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29
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Baiz CR, Błasiak B, Bredenbeck J, Cho M, Choi JH, Corcelli SA, Dijkstra AG, Feng CJ, Garrett-Roe S, Ge NH, Hanson-Heine MWD, Hirst JD, Jansen TLC, Kwac K, Kubarych KJ, Londergan CH, Maekawa H, Reppert M, Saito S, Roy S, Skinner JL, Stock G, Straub JE, Thielges MC, Tominaga K, Tokmakoff A, Torii H, Wang L, Webb LJ, Zanni MT. Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction. Chem Rev 2020; 120:7152-7218. [PMID: 32598850 PMCID: PMC7710120 DOI: 10.1021/acs.chemrev.9b00813] [Citation(s) in RCA: 173] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Vibrational spectroscopy is an essential tool in chemical analyses, biological assays, and studies of functional materials. Over the past decade, various coherent nonlinear vibrational spectroscopic techniques have been developed and enabled researchers to study time-correlations of the fluctuating frequencies that are directly related to solute-solvent dynamics, dynamical changes in molecular conformations and local electrostatic environments, chemical and biochemical reactions, protein structural dynamics and functions, characteristic processes of functional materials, and so on. In order to gain incisive and quantitative information on the local electrostatic environment, molecular conformation, protein structure and interprotein contacts, ligand binding kinetics, and electric and optical properties of functional materials, a variety of vibrational probes have been developed and site-specifically incorporated into molecular, biological, and material systems for time-resolved vibrational spectroscopic investigation. However, still, an all-encompassing theory that describes the vibrational solvatochromism, electrochromism, and dynamic fluctuation of vibrational frequencies has not been completely established mainly due to the intrinsic complexity of intermolecular interactions in condensed phases. In particular, the amount of data obtained from the linear and nonlinear vibrational spectroscopic experiments has been rapidly increasing, but the lack of a quantitative method to interpret these measurements has been one major obstacle in broadening the applications of these methods. Among various theoretical models, one of the most successful approaches is a semiempirical model generally referred to as the vibrational spectroscopic map that is based on a rigorous theory of intermolecular interactions. Recently, genetic algorithm, neural network, and machine learning approaches have been applied to the development of vibrational solvatochromism theory. In this review, we provide comprehensive descriptions of the theoretical foundation and various examples showing its extraordinary successes in the interpretations of experimental observations. In addition, a brief introduction to a newly created repository Web site (http://frequencymap.org) for vibrational spectroscopic maps is presented. We anticipate that a combination of the vibrational frequency map approach and state-of-the-art multidimensional vibrational spectroscopy will be one of the most fruitful ways to study the structure and dynamics of chemical, biological, and functional molecular systems in the future.
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Affiliation(s)
- Carlos R. Baiz
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, U.S.A
| | - Bartosz Błasiak
- Department of Physical and Quantum Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Jens Bredenbeck
- Johann Wolfgang Goethe-University, Institute of Biophysics, Max-von-Laue-Str. 1, 60438, Frankfurt am Main, Germany
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Seoul 02841, Republic of Korea
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Jun-Ho Choi
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Steven A. Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, U.S.A
| | - Arend G. Dijkstra
- School of Chemistry and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, U.K
| | - Chi-Jui Feng
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, U.S.A
| | - Sean Garrett-Roe
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, U.S.A
| | - Nien-Hui Ge
- Department of Chemistry, University of California at Irvine, Irvine, CA 92697-2025, U.S.A
| | - Magnus W. D. Hanson-Heine
- School of Chemistry, University of Nottingham, Nottingham, University Park, Nottingham, NG7 2RD, U.K
| | - Jonathan D. Hirst
- School of Chemistry, University of Nottingham, Nottingham, University Park, Nottingham, NG7 2RD, U.K
| | - Thomas L. C. Jansen
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Kijeong Kwac
- Center for Molecular Spectroscopy and Dynamics, Seoul 02841, Republic of Korea
| | - Kevin J. Kubarych
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, U.S.A
| | - Casey H. Londergan
- Department of Chemistry, Haverford College, Haverford, Pennsylvania 19041, U.S.A
| | - Hiroaki Maekawa
- Department of Chemistry, University of California at Irvine, Irvine, CA 92697-2025, U.S.A
| | - Mike Reppert
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Shinji Saito
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Myodaiji, Okazaki, 444-8585, Japan
| | - Santanu Roy
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6110, U.S.A
| | - James L. Skinner
- Institute for Molecular Engineering, University of Chicago, Chicago, IL 60637, U.S.A
| | - Gerhard Stock
- Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, 79104 Freiburg, Germany
| | - John E. Straub
- Department of Chemistry, Boston University, Boston, MA 02215, U.S.A
| | - Megan C. Thielges
- Department of Chemistry, Indiana University, 800 East Kirkwood, Bloomington, Indiana 47405, U.S.A
| | - Keisuke Tominaga
- Molecular Photoscience Research Center, Kobe University, Nada, Kobe 657-0013, Japan
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, U.S.A
| | - Hajime Torii
- Department of Applied Chemistry and Biochemical Engineering, Faculty of Engineering, and Department of Optoelectronics and Nanostructure Science, Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-Ku, Hamamatsu 432-8561, Japan
| | - Lu Wang
- Department of Chemistry and Chemical Biology, Institute for Quantitative Biomedicine, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ 08854, U.S.A
| | - Lauren J. Webb
- Department of Chemistry, The University of Texas at Austin, 105 E. 24th Street, STOP A5300, Austin, Texas 78712, U.S.A
| | - Martin T. Zanni
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706-1396, U.S.A
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30
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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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31
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Kwac K, Cho M. Machine learning approach for describing vibrational solvatochromism. J Chem Phys 2020; 152:174101. [DOI: 10.1063/5.0005591] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Kijeong Kwac
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, South Korea
- Department of Chemistry, Korea University, Seoul 02841, South Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, South Korea
- Department of Chemistry, Korea University, Seoul 02841, South Korea
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32
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Abstract
Infrared difference spectroscopy probes vibrational changes of proteins upon their perturbation. Compared with other spectroscopic methods, it stands out by its sensitivity to the protonation state, H-bonding, and the conformation of different groups in proteins, including the peptide backbone, amino acid side chains, internal water molecules, or cofactors. In particular, the detection of protonation and H-bonding changes in a time-resolved manner, not easily obtained by other techniques, is one of the most successful applications of IR difference spectroscopy. The present review deals with the use of perturbations designed to specifically change the protein between two (or more) functionally relevant states, a strategy often referred to as reaction-induced IR difference spectroscopy. In the first half of this contribution, I review the technique of reaction-induced IR difference spectroscopy of proteins, with special emphasis given to the preparation of suitable samples and their characterization, strategies for the perturbation of proteins, and methodologies for time-resolved measurements (from nanoseconds to minutes). The second half of this contribution focuses on the spectral interpretation. It starts by reviewing how changes in H-bonding, medium polarity, and vibrational coupling affect vibrational frequencies, intensities, and bandwidths. It is followed by band assignments, a crucial aspect mostly performed with the help of isotopic labeling and site-directed mutagenesis, and complemented by integration and interpretation of the results in the context of the studied protein, an aspect increasingly supported by spectral calculations. Selected examples from the literature, predominately but not exclusively from retinal proteins, are used to illustrate the topics covered in this review.
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33
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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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Abstract
Dimethyl sulfoxide (DMSO) water mixtures have been widely studied due to their unique concentration-dependent bulk properties. Here, we present an empirical spectroscopic map for the sulfinyl (S=O) stretching mode. The model can be used to interpret infrared (IR) absorption and ultrafast two-dimensional infrared (2D IR) spectra and quantify hydrogen bond populations and lifetimes by directly connecting spectroscopic measurements with structures and dynamics from molecular dynamics simulations. The electrostatic map is directly parameterized against experimental absorption spectra in the S=O stretching region (980-1100 cm-1) of dilute DMSO in water. A comparison of center peak frequencies shows that the map performs well across the entire DMSO concentration range, accurately reproducing the ∼10 cm-1 red-shift per hydrogen bond observed in the experiments. We further benchmark the map by comparing experimental and simulated 2D IR spectra generated by direct numerical integration of the Schrödinger equation. We expect that this empirical frequency map will provide a quantitative platform for investigating intermolecular interactions, microscopic heterogeneity, and ultrafast dynamics in complex liquid mixtures containing DMSO.
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Affiliation(s)
- Kwang-Im Oh
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78705, USA
| | - Carlos R Baiz
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78705, USA
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35
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Kwac K, Cho M. Differential evolution algorithm approach for describing vibrational solvatochromism. J Chem Phys 2019; 151:134112. [PMID: 31594319 DOI: 10.1063/1.5120777] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We model the solvation-induced vibrational frequency shifts of the amide I and amide II modes of N-methylacetamide in water and the nitrile stretch mode of acetonitrile in water by expressing the frequency shift as a polynomial function expanded by the inverse power of interatomic distances. The coefficients of the polynomial are optimized to minimize the deviation between the predicted frequency shifts and those calculated with quantum chemistry methods. Here, we show that a differential evolution algorithm combined with singular value decomposition is useful to find the optimum set of coefficients of polynomial terms. The differential evolution optimization shows that only a few terms in the polynomial are dominant in the contribution to the vibrational frequency shifts. We anticipate that the present work paves the way for further developing different genetic algorithms and machine learning schemes for their applications to vibrational spectroscopic studies.
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Affiliation(s)
- Kijeong Kwac
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, South Korea and Department of Chemistry, Korea University, Seoul 02841, South Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, South Korea and Department of Chemistry, Korea University, Seoul 02841, South Korea
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36
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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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37
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Kananenka AA, Yao K, Corcelli SA, Skinner JL. Machine Learning for Vibrational Spectroscopic Maps. J Chem Theory Comput 2019; 15:6850-6858. [DOI: 10.1021/acs.jctc.9b00698] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Alexei A. Kananenka
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, United States
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716, United States
| | - Kun Yao
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Steven A. Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - J. L. Skinner
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, United States
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38
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Feng CJ, Dhayalan B, Tokmakoff A. Refinement of Peptide Conformational Ensembles by 2D IR Spectroscopy: Application to Ala‒Ala‒Ala. Biophys J 2019; 114:2820-2832. [PMID: 29925019 DOI: 10.1016/j.bpj.2018.05.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 04/27/2018] [Accepted: 05/02/2018] [Indexed: 10/28/2022] Open
Abstract
Characterizing ensembles of intrinsically disordered proteins is experimentally challenging because of the ill-conditioned nature of ensemble determination with limited data and the intrinsic fast dynamics of the conformational ensemble. Amide I two-dimensional infrared (2D IR) spectroscopy has picosecond time resolution to freeze structural ensembles as needed for probing disordered-protein ensembles and conformational dynamics. Also, developments in amide I computational spectroscopy now allow a quantitative and direct prediction of amide I spectra based on conformational distributions drawn from molecular dynamics simulations, providing a route to ensemble refinement against experimental spectra. We performed a Bayesian ensemble refinement method on Ala-Ala-Ala against isotope-edited Fourier-transform infrared spectroscopy and 2D IR spectroscopy and tested potential factors affecting the quality of ensemble refinements. We found that isotope-edited 2D IR spectroscopy provides a stringent constraint on Ala-Ala-Ala conformations and returns consistent conformational ensembles with the dominant ppII conformer across varying prior distributions from many molecular dynamics force fields and water models. The dominant factor influencing ensemble refinements is the systematic frequency uncertainty from spectroscopic maps. However, the uncertainty of conformer populations can be significantly reduced by incorporating 2D IR spectra in addition to traditional Fourier-transform infrared spectra. Bayesian ensemble refinement against isotope-edited 2D IR spectroscopy thus provides a route to probe equilibrium-complex protein ensembles and potentially nonequilibrium conformational dynamics.
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Affiliation(s)
- Chi-Jui Feng
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois
| | - Balamurugan Dhayalan
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois.
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39
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Yu Y, Shi L. Vibrational solvatochromism of the ester carbonyl vibration of PCBM in organic solutions. J Chem Phys 2019. [DOI: 10.1063/1.5111046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Affiliation(s)
- Yue Yu
- School of Natural Sciences, University of California, Merced, California 95343, USA
| | - Liang Shi
- School of Natural Sciences, University of California, Merced, California 95343, USA
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40
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Theoretical analysis and modeling of the electrostatic responses of the vibrational and NMR spectroscopic properties of the cyanide anion. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.04.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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41
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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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42
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Jansen TLC, Saito S, Jeon J, Cho M. Theory of coherent two-dimensional vibrational spectroscopy. J Chem Phys 2019; 150:100901. [DOI: 10.1063/1.5083966] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Thomas la Cour Jansen
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Shinji Saito
- Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan and The Graduate University for Advanced Studies, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Jonggu Jeon
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, South Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, South Korea
- Department of Chemistry, Korea University, Seoul 02841, South Korea
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43
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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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44
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Frederix PWJM, Patmanidis I, Marrink SJ. Molecular simulations of self-assembling bio-inspired supramolecular systems and their connection to experiments. Chem Soc Rev 2018; 47:3470-3489. [PMID: 29688238 PMCID: PMC5961611 DOI: 10.1039/c8cs00040a] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Indexed: 01/01/2023]
Abstract
In bionanotechnology, the field of creating functional materials consisting of bio-inspired molecules, the function and shape of a nanostructure only appear through the assembly of many small molecules together. The large number of building blocks required to define a nanostructure combined with the many degrees of freedom in packing small molecules has long precluded molecular simulations, but recent advances in computational hardware as well as software have made classical simulations available to this strongly expanding field. Here, we review the state of the art in simulations of self-assembling bio-inspired supramolecular systems. We will first discuss progress in force fields, simulation protocols and enhanced sampling techniques using recent examples. Secondly, we will focus on efforts to enable the comparison of experimentally accessible observables and computational results. Experimental quantities that can be measured by microscopy, spectroscopy and scattering can be linked to simulation output either directly or indirectly, via quantum mechanical or semi-empirical techniques. Overall, we aim to provide an overview of the various computational approaches to understand not only the molecular architecture of nanostructures, but also the mechanism of their formation.
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Affiliation(s)
- Pim W. J. M. Frederix
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Groningen , The Netherlands . ;
| | - Ilias Patmanidis
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Groningen , The Netherlands . ;
| | - Siewert J. Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Groningen , The Netherlands . ;
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45
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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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46
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Levina E, Penkov NV, Rodionova NN, Tarasov SA, Barykina DV, Vener MV. Hydration of the Carboxylate Group in Anti-Inflammatory Drugs: ATR-IR and Computational Studies of Aqueous Solution of Sodium Diclofenac. ACS OMEGA 2018; 3:302-313. [PMID: 30023777 PMCID: PMC6044930 DOI: 10.1021/acsomega.7b01034] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 12/27/2017] [Indexed: 05/12/2023]
Abstract
Diclofenac (active ingredient of Voltaren) has a significant, multifaceted role in medicine, pharmacy, and biochemistry. Its physical properties and impact on biomolecular structures still attract essential scientific interest. However, its interaction with water has not been described yet at the molecular level. In the present study, we shed light on the interaction between the steric hindrance (the intramolecular N-H···O bond, etc.) carboxylate group (-CO2-) with water. Aqueous solution of sodium declofenac is investigated using attenuated total reflection-infrared (ATR-IR) and computational approaches, i.e., classical molecular dynamics (MD) simulations and density functional theory (DFT). Our coupled classical MD simulations, DFT calculations, and ATR-IR spectroscopy results indicated that the -CO2- group of the diclofenac anion undergoes strong specific interactions with the water molecules. The combined experimental and theoretical techniques provide significant insights into the spectroscopic manifestation of these interactions and the structure of the hydration shell of the -CO2- group. Moreover, the developed methodology for the theoretical analysis of the ATR-IR spectrum could serve as a template for the future IR/Raman studies of the strong interaction between the steric hindrance -CO2- group of bioactive molecules with the water molecules in dilute aqueous solutions.
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Affiliation(s)
- Elena
O. Levina
- Department
of Molecular and Chemical Physics, Moscow
Institute of Physics and Technology, 7 Institutskiy per., 141700 Dolgoprudny, Russia
| | - Nikita V. Penkov
- Department
of Methods of Optical and Spectral Analysis, Institute of Cell Biophysics, Russian Academy of Sciences, 3 Institutskaya Street, 142292 Pushchino, Russia
| | - Natalia N. Rodionova
- OOO
“NPF” Materia Medica Holding, 47-1 Trifonovskaya Street, 129272 Moscow, Russia
| | - Sergey A. Tarasov
- OOO
“NPF” Materia Medica Holding, 47-1 Trifonovskaya Street, 129272 Moscow, Russia
| | - Daria V. Barykina
- OOO
“NPF” Materia Medica Holding, 47-1 Trifonovskaya Street, 129272 Moscow, Russia
| | - Mikhail V. Vener
- Department
of Quantum Chemistry, Mendeleev University
of Chemical Technology, 9 Miusskaya Square, 125047 Moscow, Russia
- E-mail:
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47
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Jansen TLC. Simple Quantum Dynamics with Thermalization. J Phys Chem A 2018; 122:172-183. [PMID: 29199829 PMCID: PMC5770886 DOI: 10.1021/acs.jpca.7b10380] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 12/04/2017] [Indexed: 02/05/2023]
Abstract
In this paper, we introduce two simple quantum dynamics methods. One is based on the popular surface-hopping method, and the other is based on rescaling of the propagation on the bath ground-state potential surface. The first method is special, as it avoids specific feedback from the simulated quantum system to the bath and can be applied for precalculated classical trajectories. It is based on the equipartition theorem to determine if hops between different potential energy surfaces are allowed. By comparing with the formally exact Hierarchical Equations Of Motion approach for four model systems we find that the method generally approximates the quantum dynamics toward thermal equilibrium very well. The second method is based on rescaling of the nonadiabatic coupling and also neglect the effect of the state of the quantum system on the bath. By the nature of the approximations, they cannot reproduce the effect of bath relaxation following excitation. However, the methods are both computationally more tractable than the conventional fewest switches surface hopping, and we foresee that the methods will be powerful for simulations of quantum dynamics in systems with complex bath dynamics, where the system-bath coupling is not too strong compared to the thermal energy.
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Affiliation(s)
- Thomas L. C. Jansen
- Zernike Institute for Advanced
Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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48
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Torii H. Strategy for Modeling the Electrostatic Responses of the Spectroscopic Properties of Proteins. J Phys Chem B 2017; 122:154-164. [PMID: 29192780 DOI: 10.1021/acs.jpcb.7b10791] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
For better understanding and more efficient use of the spectroscopic probes (vibrational and NMR) of the local electrostatic situations inside proteins, appropriate modeling of the properties of those probes is essential. The present study is devoted to examining the strategy for constructing such models. A more well-founded derivation than the ones in previous studies is given in constructing the models. Theoretical analyses are conducted on two representative example cases related to proteins, i.e., the peptide group of the main chains and the CO and NO ligands to the Fe2+ ion of heme, with careful treatment of the behavior of electrons in the electrostatic responses and with verification of consistency with observable quantities. It is shown that, for the stretching frequencies and NMR chemical shifts, it is possible to construct reasonable electrostatic interaction models that encompass the situations of hydration and uniform electric field environment and thus are applicable also to the cases of nonuniform electrostatic situations, which are highly expected for inside of proteins.
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Affiliation(s)
- Hajime Torii
- Department of Chemistry, Faculty of Education and Department of Optoelectronics and Nanostructure Science, Graduate School of Science and Technology, Shizuoka University , 836 Ohya, Shizuoka 422-8529, Japan
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49
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Lomont JP, Ostrander JS, Ho JJ, Petti MK, Zanni MT. Not All β-Sheets Are the Same: Amyloid Infrared Spectra, Transition Dipole Strengths, and Couplings Investigated by 2D IR Spectroscopy. J Phys Chem B 2017; 121:8935-8945. [PMID: 28851219 DOI: 10.1021/acs.jpcb.7b06826] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report the transition dipole strengths and frequencies of the amyloid β-sheet amide I mode for the aggregated proteins amyloid-β1-40, calcitonin, α-synuclein, and glucagon. According to standard vibrational coupling models for proteins, the frequencies of canonical β-sheets are set by their size and structural and environmental disorder, which determines the delocalization length of the vibrational excitons. The larger the delocalization the lower the frequency of the main infrared-allowed transition, A⊥. The models also predict an accompanying increase in transition dipole strength. For the proteins measured here, we find no correlation between transition dipole strengths and amyloid β-sheet transition frequency. To understand this observation, we have extracted from the protein data bank crystal structures of amyloid peptides from which we calculate the amide I vibrational couplings, and we use these in a model β-sheet Hamiltonian to simulate amyloid vibrational spectra. We find that the variations in amyloid β-sheet structures (e.g., dihedral angles, interstrand distances, and orientations) create significant differences in the average values for interstrand and nearest neighbor couplings, and that those variations encompass the variation in measured A⊥ frequencies. We also find that off-diagonal disorder about the average values explains the range of transition dipole strengths observed experimentally. Thus, we conclude that the lack of correlation between transition dipole-strength and frequency is caused by variations in amyloid β-sheet structure. Taken together, these results indicate that the amide I frequency is very sensitive to amyloid β-sheet structure, the β-sheets of these 4 proteins are not identical, and the assumption that frequency of amyloids scales with β-sheet size cannot be adopted without an accompanying measurement of transition dipole strengths.
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Affiliation(s)
- Justin P Lomont
- Department of Chemistry, University of Wisconsin-Madison , Madison, WI 53706, United States
| | - Joshua S Ostrander
- Department of Chemistry, University of Wisconsin-Madison , Madison, WI 53706, United States
| | - Jia-Jung Ho
- Department of Chemistry, University of Wisconsin-Madison , Madison, WI 53706, United States
| | - Megan K Petti
- Department of Chemistry, University of Wisconsin-Madison , Madison, WI 53706, United States
| | - Martin T Zanni
- Department of Chemistry, University of Wisconsin-Madison , Madison, WI 53706, United States
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Feng CJ, Tokmakoff A. The dynamics of peptide-water interactions in dialanine: An ultrafast amide I 2D IR and computational spectroscopy study. J Chem Phys 2017; 147:085101. [PMID: 28863528 PMCID: PMC5593305 DOI: 10.1063/1.4991871] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 08/09/2017] [Indexed: 11/14/2022] Open
Abstract
We present a joint experimental and computational study of the dynamic interactions of dialanine (Ala-Ala) with water, comparing the results of ultrafast 2D IR and infrared transient absorption spectroscopy of its amide I vibration with spectra modeled from molecular dynamics (MD) simulations. The experimental data are analyzed to describe vibrational frequency fluctuations, vibrational energy relaxation, and chemical exchange processes. The origin of these processes in the same underlying fluctuating forces allows a common description in terms of the fluctuations and conformational dynamics of the peptide and associated solvent. By comparing computational spectroscopy from MD simulations with multiple force fields and water models, we describe how the dynamics of water hydrogen bond fluctuations and switching processes act as a source of friction that governs the dephasing and vibrational relaxation, and provide a description of coupled water and peptide motions that give rise to spectroscopic exchange processes.
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Affiliation(s)
- Chi-Jui Feng
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, USA
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, USA
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