1
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Bloino J, Jähnigen S, Merten C. After 50 Years of Vibrational Circular Dichroism Spectroscopy: Challenges and Opportunities of Increasingly Accurate and Complex Experiments and Computations. J Phys Chem Lett 2024:8813-8828. [PMID: 39167088 DOI: 10.1021/acs.jpclett.4c01700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
VCD research continues to thrive, driven by ongoing experimental and theoretical advances. Modern studies deal with increasingly complex samples featuring weak intermolecular interactions and shallow potential energy surfaces. Likewise, the combination of VCD measurements with, for instance, cryo-spectroscopic techniques has significantly increased their sensitivity. The extent to which such modern measurements enhance the informative value of VCD depends significantly on the quality of the theoretical models, which must adequately account for anharmonicity, solvation and molecular dynamics. We herein discuss how experimental advancements engage in a stimulating interplay with recent theoretical developments, pursuing either the static or the dynamic computational route. Both paths have their own strengths and limitations, each addressing fundamentally different problems. We give an outlook on future challenges of VCD research, including the possibility to combine static and dynamic approaches to obtain a full picture of the sample.
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Affiliation(s)
- Julien Bloino
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Sascha Jähnigen
- Freie Universität Berlin, Institut für Chemie und Biochemie, Arnimallee 22, 14195 Berlin, Germany
| | - Christian Merten
- Ruhr-Universität Bochum, Fakultät für Chemie und Biochemie, Universitätsstraße 150, 44801 Bochum, Germany
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2
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Taniguchi T, Agbo DO, Yang Q, Kapitán J, Wu T, Oyama S, Akai S, Sawama Y, Bouř P. Raman optical activity study of deuterated sugars: deuterium labelling as a tool for structural analysis. Phys Chem Chem Phys 2024; 26:21568-21574. [PMID: 39082369 DOI: 10.1039/d4cp02406k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
Structural analyses using Raman optical activity (ROA) spectroscopy conventionally rely on vibrational signals in the fingerprint region ranging from 100 to 1800 cm-1. Use of deuterium labelling to observe ROA signals in the C-D stretching region provides additional information about a local structure of large molecular systems. So far, the potential of C-D stretching ROA signals for structural analysis has rarely been explored. In the present work, we synthesized model deuterated glucose monosaccharides and studied their ROA properties by employing molecular dynamics and density functional theory to interpret the spectra. A good agreement between the simulated and experimental spectra is achieved when the proper conformer ratios are considered. This shows the usefulness of ROA spectroscopy assisted by deuterium labelling for stereochemical and conformational analysis.
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Affiliation(s)
- Tohru Taniguchi
- Frontier Research Center for Advanced Material and Life Science, Faculty of Advanced Life Science, Hokkaido University, North 21 West 11, Sapporo 001-0021, Japan.
| | - Davidson Obinna Agbo
- Frontier Research Center for Advanced Material and Life Science, Faculty of Advanced Life Science, Hokkaido University, North 21 West 11, Sapporo 001-0021, Japan.
| | - Qin Yang
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic
| | - Josef Kapitán
- Department of Optics, Palacký University Olomouc, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Tao Wu
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic
| | - Shuki Oyama
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Shuji Akai
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yoshinari Sawama
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic
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3
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Bagdžiūnas G. Can Chirality Answer Whether We Are Alone? Chirality 2024; 36:e23708. [PMID: 39054794 DOI: 10.1002/chir.23708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 07/09/2024] [Accepted: 07/12/2024] [Indexed: 07/27/2024]
Abstract
Detecting biosignatures of life in extraterrestrial environments remains one of the primary objectives of scientific inquiry. Currently, both remote and direct detection methods are primarily aimed at identifying key molecular classes fundamental to terrestrial biology. However, a more universally applicable spectroscopic approach could involve searching for homochiral molecules. Thus, this perspective delves into the significance of homochirality as a critical factor in the origin of life. Without homochirality, the formation of self-recognizing and self-replicating complex molecules would be hindered. The various hypotheses concerning the origin of homochiral molecules have been explored and analyzed within this context. This perspective emphasizes the potential for discovering extraterrestrial microscopic life through the detection of homochiral molecules using chirodetecting methods such as chromatography and chiroptical spectroscopy or circular polarimetry as a promising remote technique. This discussion highlights the importance of homochirality in the broader search for life beyond Earth and underscores the need for innovative methodologies and instrumentation in astrobiological research. These techniques can be an effective method for detecting homochirality on future planetary missions.
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Affiliation(s)
- Gintautas Bagdžiūnas
- Group of Supramolecular Analysis, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Vilnius, Lithuania
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4
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Sato H, Inoué S, Yoshida J, Kawamura I, Koshoubu J, Yamagishi A. Microscopic vibrational circular dichroism on the forewings of a European hornet: heterogenous sequences of protein domains with different secondary structures. Phys Chem Chem Phys 2024; 26:17918-17922. [PMID: 38888259 DOI: 10.1039/d4cp01827c] [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: 06/20/2024]
Abstract
We developed a microscopic scanning for vibrational circular dichroism (VCD) spectroscopy in which a quantum cascade laser is equipped with a highly focused infrared light source to attain a spatial resolution of 100 μm. This system was applied to the forewing of a European hornet to reveal how the protein domains are organised. Two-dimensional patterns were obtained from the VCD signals with steps of 100 μm. We scanned the 1500-1740 cm-1 wavenumber range, which covers amide I and II absorptions. Zone sequenced α-helical and β-sheet domains within an area of 200 μm2 in membranes close to where two veins cross. The sign of the VCD signal at 1650 cm-1 changed from positive to negative when probed along the zone axis, intermediated by the absence of VCD activity. The significance of this zone is discussed from the viewpoint of the mechanical properties required for flying motion. These features are unattainable using conventional FTIR (Fourier transform infrared) or FT-VCD methods with a spatial resolution of ∼10 mm2.
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Affiliation(s)
- Hisako Sato
- Faculty of Science, Ehime University, 1 2-5, Bunkyo-cho, Matsuyama, 790-8577, Japan.
| | - Sayako Inoué
- Geodynamics Research Center, Ehime University, Matsuyama 790-8577, Japan
| | - Jun Yoshida
- Department of Chemistry, College of Humanities & Sciences, Nihon University, Setagaya-ku, Tokyo 156-8550, Japan
| | - Izuru Kawamura
- Graduate School of Engineering Science, Yokohama National University Yokohama, 240-8501, Japan
| | - Jun Koshoubu
- JASCO Corporation, Ishikawa 2967-5, Hachioji Tokyo, 192-8537, Japan
| | - Akihiko Yamagishi
- Faculty of Medicine, Toho University, 2 5-21-16 Oomori-nishi, Ota-ku, Tokyo, 143-8540, Japan
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5
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Cheeseman JR, Frisch MJ, Keiderling TA. Increased accuracy of vibrational circular dichroism calculations for isotopically labeled helical peptides. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 313:124097. [PMID: 38457873 DOI: 10.1016/j.saa.2024.124097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/11/2024] [Accepted: 02/27/2024] [Indexed: 03/10/2024]
Abstract
Vibrational circular dichroism (VCD) spectra have been computed with qualitatively correct sign patterns for α-helical peptides using various methods, ranging from empirical models to ab initio quantum mechanical computations. However, some details, such as deuteration effects and isotope substitution shifts and sign patterns for the resultant amide I' band shape, have remained a predictive challenge. Fully optimized computations for a 25-residue Ala-rich peptide, including implicit solvent corrections and explicit side chains that experimentally stabilize these model helical peptides in water, have been carried out using density functional theory (DFT). These fully minimized structures show minor changes in the (ϕ,ψ) torsions at the termini and yield an extra negative band to the low energy side of the characteristic amide I' couplet VCD, in agreement with experiments. Additionally, these calculations give the right sign and relative intensity patterns, as compared to experimental results, for several 13C=O substituted variants. The differences from previously reported computations that used ideal helical structures and vacuum conditions imply that inclusion of distorted termini and solvent effects can have an impact on the final detailed spectral patterns. Inclusion of side chains in these calculations had very little effect on the computed amide I' IR and VCD. Tests of constrained geometries, varying dielectric, and different functionals indicate that each can affect the band shapes, particularly for the 12C=O components, but these aspects do not fully explain the difference from previous spectral simulations. Inclusion of long-range amide coupling, as obtained from DFT computation of the full structure, or transfer of parameters from a somewhat longer peptide model, rather than shorter model, seems to be more important for the final detailed band shape under isotopic substitution. However, these corrections can also induce other changes, suggesting that previously reported, limited calculations may have been qualitatively useful due to a balance of errors. This may also explain the success of simple empirical IR models.
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Affiliation(s)
- James R Cheeseman
- Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, CT 06492, USA
| | - Michael J Frisch
- Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, CT 06492, USA
| | - Timothy A Keiderling
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607, USA.
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6
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Liu Y, Hao A, Xing P. Ultrasensitive Solvatochirochromism of Single Benzene Chromophores. Chemistry 2024; 30:e202400059. [PMID: 38409631 DOI: 10.1002/chem.202400059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 02/28/2024]
Abstract
Solvents influence the structure, aggregation and folding behaviors of solvatochromic compounds. Ultrasensitive solvent mediated chiroptical response is conducive to the fabrication of molecular platform for sensing and recognition, which however, remains great challenges in conceptual or applicable design. Here we report a cysteine-based single benzene chromophore system that shows ultrasensitivity to solvents. Compared to the ratiometrically responsive systems, the chiroptical activities could be triggered or inverted depending on the substituents of chiral entities with an ultralow solvent volume fraction (<1 vol %). One drop of dipolar solvents shall significantly induce the emergence or inversion of chiroptical signals in bulky phases. Based on the experimental and computational studies, the ultrasensitivity is contributed to the intimate interplay between solvents and chiral compounds that anchors the specific chiral conformation. It illustrates that structurally simple organic compounds without aggregation or folding behaviors possess pronounced solvatochiroptical properties, which sheds light on the next-generation of chiroptical sensors and switches.
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Affiliation(s)
- Yiping Liu
- Key Laboratory of Colloid and Interface Chemistry of Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, 250100, Jinan, People's Republic of China
| | - Aiyou Hao
- Key Laboratory of Colloid and Interface Chemistry of Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, 250100, Jinan, People's Republic of China
| | - Pengyao Xing
- Key Laboratory of Colloid and Interface Chemistry of Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, 250100, Jinan, People's Republic of China
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7
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Adhikari S, Efremova MV, Spaeth P, Koopmans B, Lavrijsen R, Orrit M. Single-Particle Photothermal Circular Dichroism and Photothermal Magnetic Circular Dichroism Microscopy. NANO LETTERS 2024; 24:5093-5103. [PMID: 38578845 PMCID: PMC11066954 DOI: 10.1021/acs.nanolett.4c00448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 04/02/2024] [Accepted: 04/02/2024] [Indexed: 04/07/2024]
Abstract
Recent advances in single-particle photothermal circular dichroism (PT CD) and photothermal magnetic circular dichroism (PT MCD) microscopy have shown strong promise for diverse applications in chirality and magnetism. Photothermal circular dichroism microscopy measures direct differential absorption of left- and right-circularly polarized light by a chiral nanoobject and thus can measure a pure circular dichroism signal, which is free from the contribution of circular birefringence and linear dichroism. Photothermal magnetic circular dichroism, which is based on the polar magneto-optical Kerr effect, can probe the magnetic properties of a single nanoparticle (of sizes down to 20 nm) optically. Single-particle measurements enable studies of the spatiotemporal heterogeneity of magnetism at the nanoscale. Both PT CD and PT MCD have already found applications in chiral plasmonics and magnetic nanomaterials. Most importantly, the advent of these microscopic techniques opens possibilities for many novel applications in biology and nanomaterial science.
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Affiliation(s)
- Subhasis Adhikari
- Huygens-Kamerlingh
Onnes Laboratory, Leiden University, 2300 RA Leiden, The Netherlands
| | - Maria V. Efremova
- Department
of Applied Physics and Science Education, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Patrick Spaeth
- Department
of Sustainable Energy Materials, AMOLF; Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Bert Koopmans
- Department
of Applied Physics and Science Education, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Reinoud Lavrijsen
- Department
of Applied Physics and Science Education, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Michel Orrit
- Huygens-Kamerlingh
Onnes Laboratory, Leiden University, 2300 RA Leiden, The Netherlands
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8
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Rouquet E, Dupont J, Lepere V, Garcia GA, Nahon L, Zehnacker A. Conformer-Selective Photoelectron Circular Dichroism. Angew Chem Int Ed Engl 2024; 63:e202401423. [PMID: 38442011 DOI: 10.1002/anie.202401423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 03/04/2024] [Accepted: 03/05/2024] [Indexed: 03/07/2024]
Abstract
Conformational flexibility and chirality both play a key role in molecular recognition. It is therefore very useful to develop spectroscopic methods that simultaneously probe both properties. It has been theoretically predicted that photoelectron circular dichroism (PECD) should be very sensitive to conformational isomerism. However, experimental proof has been less forthcoming and only exists for a very few favorable cases. Here, we present a new PECD scheme based on resonance-enhanced two-photon ionization (RE2PI) using UV/Vis nanosecond laser excitations. The spectral resolution obtained thereby guarantees conformer-selectivity by inducing resonant conformer-specific ππ* S1←S0 transitions. We apply this experimental scheme to the study of chiral 1-indanol, which exists in two conformers linked by a ring inversion and defined by the position of the hydroxyl group, namely axial and equatorial. We show that the PECD of the equatorial and axial forms considerably differ in sign, magnitude and shape. We also discuss the influence of the total ionization energy, vibronic excitation of intermediate and final states, and relative polarization of the excitation and ionization lasers. Conformer-specificity adds a new dimension to the applications of PECD in analytical chemistry addressing now the general case of floppy systems.
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Affiliation(s)
- Etienne Rouquet
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405, Orsay, France
- Synchrotron Soleil, L'Orme des Merisiers, St. Aubin BP48, F-91192, Gif sur Yvette, France
| | - Jennifer Dupont
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405, Orsay, France
| | - Valeria Lepere
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405, Orsay, France
| | - Gustavo A Garcia
- Synchrotron Soleil, L'Orme des Merisiers, St. Aubin BP48, F-91192, Gif sur Yvette, France
| | - Laurent Nahon
- Synchrotron Soleil, L'Orme des Merisiers, St. Aubin BP48, F-91192, Gif sur Yvette, France
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405, Orsay, France
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9
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Bowles J, Jähnigen S, Agostini F, Vuilleumier R, Zehnacker A, Calvo F, Clavaguéra C. Vibrational Circular Dichroism Spectroscopy with a Classical Polarizable Force Field: Alanine in the Gas and Condensed Phases. Chemphyschem 2024; 25:e202300982. [PMID: 38318765 DOI: 10.1002/cphc.202300982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/07/2024]
Abstract
Polarizable force fields are an essential component for the chemically accurate modeling of complex molecular systems with a significant degree of fluxionality, beyond harmonic or perturbative approximations. In this contribution we examine the performance of such an approach for the vibrational spectroscopy of the alanine amino acid, in the gas and condensed phases, from the Fourier transform of appropriate time correlation functions generated along molecular dynamics (MD) trajectories. While the infrared (IR) spectrum only requires the electric dipole moment, the vibrational circular dichroism (VCD) spectrum further requires knowledge of the magnetic dipole moment, for which we provide relevant expressions to be used with polarizable force fields. The AMOEBA force field was employed here to model alanine in the neutral and zwitterionic isolated forms, solvated by water or nitrogen, and as a crystal. Within this framework, comparison of the electric and magnetic dipole moments to those obtained with nuclear velocity perturbation theory based on density-functional theory for the same MD trajectories are found to agree well with one another. The statistical convergence of the IR and VCD spectra is examined and found to be more demanding in the latter case. Comparisons with experimental frequencies are also provided for the condensed phases.
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Affiliation(s)
- Jessica Bowles
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, 91405, Orsay, France
| | - Sascha Jähnigen
- PASTEUR Laboratory, Département de Chimie, Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Federica Agostini
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, 91405, Orsay, France
| | - Rodolphe Vuilleumier
- PASTEUR Laboratory, Département de Chimie, Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Anne Zehnacker
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay UMR8214, 91405, Orsay, France
| | - Florent Calvo
- Université Grenoble Alpes, CNRS, LIPhy, 38000, Grenoble, France
| | - Carine Clavaguéra
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, 91405, Orsay, France
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10
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Fusè M, Mazzeo G, Longhi G, Abbate S, Yang Q, Bloino J. Scaling-up VPT2: A feasible route to include anharmonic correction on large molecules. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 311:123969. [PMID: 38330757 DOI: 10.1016/j.saa.2024.123969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 01/18/2024] [Accepted: 01/24/2024] [Indexed: 02/10/2024]
Abstract
Vibrational analysis plays a crucial role in the investigation of molecular systems. Though methodologies like second-order vibrational perturbation theory (VPT2) have paved the way to more accurate simulations, the computational cost remains a difficult barrier to overcome when the molecular size increases. Building upon recent advances in the identification of resonances, we propose an approach making anharmonic simulations possible for large-size systems, typically unreachable by standard means. This relies on the fact that, often, only portions of the whole spectra are of actual interest. Therefore, the anharmonic corrections can be included selectively on subsets of normal modes directly related to the regions of interest. Starting from the VPT2 equations, we evaluate rigorously and systematically the impact of the truncated anharmonic treatment onto simulations. The limit and feasibility of the reduced-dimensionality approach are detailed, starting on a smaller model system. The methodology is then challenged on the IR absorption and vibrational circular dichroism spectra of an organometallic complex in three different spectral ranges.
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Affiliation(s)
- Marco Fusè
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Viale Europa 11, 25123, Brescia, Italy.
| | - Giuseppe Mazzeo
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Viale Europa 11, 25123, Brescia, Italy
| | - Giovanna Longhi
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Viale Europa 11, 25123, Brescia, Italy; Istituto Nazionale di Ottica (INO), CNR, Research Unit of Brescia, c/o CSMT, VIA Branze 45, 25123, Brescia, Italy
| | - Sergio Abbate
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Viale Europa 11, 25123, Brescia, Italy; Istituto Nazionale di Ottica (INO), CNR, Research Unit of Brescia, c/o CSMT, VIA Branze 45, 25123, Brescia, Italy
| | - Qin Yang
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 542/2, 160 00, Prague, Czech Republic
| | - Julien Bloino
- Scuola Normale Superiore, Piazza dei Cavalieri, 56125, Pisa, Italy.
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11
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Sato H, Koshoubu J, Inoué S, Kawamura I, Yamagishi A. Multidimensional vibrational circular dichroism for insect wings: Comparison of species. Chirality 2024; 36:e23655. [PMID: 38419363 DOI: 10.1002/chir.23655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/16/2024] [Accepted: 02/02/2024] [Indexed: 03/02/2024]
Abstract
This study reports the microscopic measurements of vibrational circular dichroism (VCD) on four different insect wings using a quantum cascade laser VCD system equipped with microscopic scanning capabilities (named multi-dimensional VCD [MultiD-VCD]). Wing samples, including (i) beetle, Anomala albopilosa (female), (ii) European hornet, Verspa crabro flavofasciata Cameron, 1903 (female), (iii) tiny dragonfly, Nannophya pygmae Rambur, 1842 (male), and (iv) dragonfly, Symetrum gracile Oguma, 1915 (male), were used in this study. Two-dimensional patterns of VCD signals (~10 mm × 10 mm) were obtained at a spatial resolution of 100 μm. Measurements covered the absorption peaks assigned to amides I and II in the range of 1500-1740 cm-1 . The measurements were based on the enhancement of VCD signals for the stereoregular linkage of peptide groups. The patterns were remarkably dependent on the species. In samples (i) and (ii), the wings comprised segregated domains of protein aggregates of different secondary structures. The size of each microdomain was approximately 100 μm. In contrast, no clear VCD spectra were detected in samples (iii) and (iv). One possible reason was that the chain of stereoregular polypeptides was too short to achieve VCD enhancement in samples (iii) and (iv). Notably, the unique features were only observed in the VCD spectra because the IR spectra were nearly the same among the species. The VCD results hinted at the connection of protein microscopic structures with the wing flapping mechanisms of each species.
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Affiliation(s)
- Hisako Sato
- Faculty of Science, Ehime University, Matsuyama, Japan
| | | | - Sayako Inoué
- Geodynamics Research Center, Ehime University, Matsuyama, Japan
| | - Izuru Kawamura
- Graduate School of Engineering Science, Yokohama National University, Yokohama, Japan
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12
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Fusè M, Mazzeo G, Abbate S, Ruzziconi R, Bloino J, Longhi G. Mid-IR and CH stretching vibrational circular dichroism spectroscopy to distinguish various sources of chirality: The case of quinophaneoxazoline based ruthenium(II) complexes. Chirality 2024; 36:e23649. [PMID: 38409881 DOI: 10.1002/chir.23649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/13/2024] [Accepted: 01/15/2024] [Indexed: 02/28/2024]
Abstract
Five diastereomers of ruthenium(II) complexes based on quinolinophaneoxazoline ligands were investigated by vibrational circular dichroism (VCD) in the mid-IR and CH stretching regions. Diastereomers differ in three sources of chirality: the planar chirality of the quinolinophane moiety, the central chirality of an asymmetric carbon atom of the oxazoline ring, and the chirality of the ruthenium atom. VCD, allied to DFT calculations, has been found to be effective in disentangling the various forms of chirality. In particular, a VCD band is identified in the CH stretching region directly connected to the chirality of the metal. The analysis of the calculated VCD spectra is carried out by partitioning the complexes into fragments. The anharmonic analysis is also performed with a recently proposed reduced-dimensionality approach: such treatment is particularly important when examining spectroscopic regions highly perturbed by resonances, like the CH stretching region.
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Affiliation(s)
- Marco Fusè
- Dipartimento di Medicina Molecolare e Traslazionale (DMMT), Università di Brescia, Brescia, Italy
| | - Giuseppe Mazzeo
- Dipartimento di Medicina Molecolare e Traslazionale (DMMT), Università di Brescia, Brescia, Italy
| | - Sergio Abbate
- Dipartimento di Medicina Molecolare e Traslazionale (DMMT), Università di Brescia, Brescia, Italy
- Istituto Nazionale di Ottica (INO), CNR, Research Unit Brescia, Brescia, Italy
| | - Renzo Ruzziconi
- Dipartimento di Chimica Biologia e Biotecnologie, Università di Perugia, Perugia, Italy
| | - Julien Bloino
- Scuola Normale Superiore, Piazza dei Cavalieri, Pisa, Italy
| | - Giovanna Longhi
- Dipartimento di Medicina Molecolare e Traslazionale (DMMT), Università di Brescia, Brescia, Italy
- Istituto Nazionale di Ottica (INO), CNR, Research Unit Brescia, Brescia, Italy
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13
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O'Neill N, Lima TA, Furlan Ferreira F, Alvarez NJ, Schweitzer-Stenner R. Determining the nanostructure and main axis of gly-his-gly fibrils using the amide I' bands in FTIR, VCD, and Raman spectra. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 306:123584. [PMID: 37956526 DOI: 10.1016/j.saa.2023.123584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/29/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023]
Abstract
The zwitterionic tripeptide glycyl-histidine-glycine (GHG) has been shown to self-assemble into visible crystalline fibrils that form a gel-supporting network with a very high storage modulus. Here we elaborate on the theory and experimental setup behind our novel approach employed to determining the main fibril axis for these gel-forming fibrils by simulating the amide I band profile for infrared absorption (IR), vibrational circular dichroism (VCD), and visible Raman scattering. We also highlight that combining these three vibrational spectroscopies can help in validating structures that are solved using powder x-ray diffraction analysis (PXRD). The PXRD analysis yielded a GHG fibril unit cell with P21 symmetry containing two peptide monomers and two water molecules. The monomers adopt a conformation reminiscent of the distorted polyproline II conformation obtained for tri-lysine in aqueous solution. Stabilization occurs primarily through peptide-peptide intermolecular hydrogen bond interactions, while the role of water in peptide hydration is minimal. The comparison of simulated and experimental amide I' band profiles suggests that the xz plane of the crystal unit cell is being predominantly probed in the experimental IR and VCD spectra, with the x axis of the unit cell pointing in the direction of the main fibril axis. The monomer peptide in the unit cell interacts with six adjacent peptides forming hydrophobic channels by edge-to-face and parallel-displaced ππstacking in the y direction. These cores are further stabilized by a plethora of intermolecular interactions in the x and z directions. Our result suggests that the hydrophobic xz-surfaces would be a good target for the adsorption of hydrophobic drugs.
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Affiliation(s)
- Nichole O'Neill
- Department of Chemistry, Drexel University, Philadelphia, PA 19104, USA; Department of Chemical and Biological Engineering, Drexel University, Philadelphia, PA 19104, USA
| | - Thamires A Lima
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, PA 19104, USA
| | - Fabio Furlan Ferreira
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP 09210-580, Brazil
| | - Nicolas J Alvarez
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, PA 19104, USA.
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14
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Osifová Z, Kalvoda T, Galgonek J, Culka M, Vondrášek J, Bouř P, Bednárová L, Andrushchenko V, Dračínský M, Rulíšek L. What are the minimal folding seeds in proteins? Experimental and theoretical assessment of secondary structure propensities of small peptide fragments. Chem Sci 2024; 15:594-608. [PMID: 38179543 PMCID: PMC10763034 DOI: 10.1039/d3sc04960d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 11/22/2023] [Indexed: 01/06/2024] Open
Abstract
Certain peptide sequences, some of them as short as amino acid triplets, are significantly overpopulated in specific secondary structure motifs in folded protein structures. For example, 74% of the EAM triplet is found in α-helices, and only 3% occurs in the extended parts of proteins (typically β-sheets). In contrast, other triplets (such as VIV and IYI) appear almost exclusively in extended parts (79% and 69%, respectively). In order to determine whether such preferences are structurally encoded in a particular peptide fragment or appear only at the level of a complex protein structure, NMR, VCD, and ECD experiments were carried out on selected tripeptides: EAM (denoted as pro-'α-helical' in proteins), KAM(α), ALA(α), DIC(α), EKF(α), IYI(pro-β-sheet or more generally, pro-extended), and VIV(β), and the reference α-helical CATWEAMEKCK undecapeptide. The experimental data were in very good agreement with extensive quantum mechanical conformational sampling. Altogether, we clearly showed that the pro-helical vs. pro-extended propensities start to emerge already at the level of tripeptides and can be fully developed at longer sequences. We postulate that certain short peptide sequences can be considered minimal "folding seeds". Admittedly, the inherent secondary structure propensity can be overruled by the large intramolecular interaction energies within the folded and compact protein structures. Still, the correlation of experimental and computational data presented herein suggests that the secondary structure propensity should be considered as one of the key factors that may lead to understanding the underlying physico-chemical principles of protein structure and folding from the first principles.
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Affiliation(s)
- Zuzana Osifová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2, 160 00, Praha 6 Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University Hlavova 2030 Prague 128 00 Czech Republic
| | - Tadeáš Kalvoda
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2, 160 00, Praha 6 Czech Republic
| | - Jakub Galgonek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2, 160 00, Praha 6 Czech Republic
| | - Martin Culka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2, 160 00, Praha 6 Czech Republic
| | - Jiří Vondrášek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2, 160 00, Praha 6 Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2, 160 00, Praha 6 Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2, 160 00, Praha 6 Czech Republic
| | - Valery Andrushchenko
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2, 160 00, Praha 6 Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2, 160 00, Praha 6 Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2, 160 00, Praha 6 Czech Republic
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15
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Puente AR, Polavarapu PL. Influence of microsolvation on vibrational circular dichroism spectra in dimethyl sulfoxide solvent: A Bottom-Up approach using Quantum cluster growth. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 303:123231. [PMID: 37562213 DOI: 10.1016/j.saa.2023.123231] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/09/2023] [Accepted: 08/01/2023] [Indexed: 08/12/2023]
Abstract
Chiroptical spectroscopic measurements serve as routine methods to assign the absolute configuration of chiral compounds and interpret their conformational behavior in solution. One common challenge is the use of strongly hydrogen-bonding solvents, which can significantly bias the conformational ensemble and affect the vibrational circular dichroism (VCD) active bands in solution. One such solvent is dimethyl sulfoxide (DMSO)-an excellent solvent for stubborn compounds-that must be explicitly considered in VCD analysis. Explicit consideration of solvent remains a critical challenge in chiroptical spectroscopy due to the need to explore solute-solvent conformational space and the computational expense in modeling these clusters. Interested in the recent development of the Quantum Cluster Growth (QCG) program by the Grimme lab, we set out to model and interpret previously reported VCD spectra for several molecules using their efficient program. Our purposes are two-fold: (1) to investigate the applicability of the QCG program to the problem of reproducing VCD spectra in DMSO solvent and (2) to identify limitations in using this approach. We find that we can conveniently model and analyze the VCD spectra of investigated molecules in DMSO. However, the final set of conformers used for VCD calculations are functional dependent and different sets of conformers can provide satisfactory quantitative agreement between experimental and predicted VCD spectra. We hope that this study provides guidance for future chiroptical studies in the challenging DMSO solvent.
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Affiliation(s)
- Andrew R Puente
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
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16
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Grassin C, Pollok CH, Kreienborg NM, Merten C. Matrix effects in MI-VCD spectra of two chiral oxiranes and their potential microscopic origin. Phys Chem Chem Phys 2023; 25:31995-32001. [PMID: 37975701 DOI: 10.1039/d3cp05023h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Combining vibrational circular dichroism (VCD) spectroscopy with the matrix isolation (MI) technique opens up interesting possibilities to study chiral molecules. MI involves the isolation of guest species in inert solid matrices at cryogenic temperatures. Hence, MI-VCD measures are solid-state VCD measurements, and as such, can suffer from mostly birefringance-related artefacts in the same way as common solid-state VCD measurements. In this contribution, we demonstrate that the sample preparation condition have tremendous impact on the quality and reliability of the recorded MI-VCD spectra. While MI-IR spectra are basically blind to these artefacts, the variation of deposition temperatures and host flow rates seem to control whether high quality MI-VCD spectra are obtained or if depolarization effects lead to completely obscured spectra. For two selected examples, styrene oxide (SO) and 1-phenyl propylene oxide (PPO), we discuss how the various experimental conditions may lead to the aforementioned effects and give a microscopic description of their origin.
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Affiliation(s)
- Corentin Grassin
- Ruhr Universität Bochum, Fakultät für Chemie und Biochemie, Organische Chemie II, Universitätsstraße 150, 44801, Bochum, Germany.
| | - Corina H Pollok
- Ruhr Universität Bochum, Fakultät für Chemie und Biochemie, Organische Chemie II, Universitätsstraße 150, 44801, Bochum, Germany.
| | - Nora M Kreienborg
- Ruhr Universität Bochum, Fakultät für Chemie und Biochemie, Organische Chemie II, Universitätsstraße 150, 44801, Bochum, Germany.
| | - Christian Merten
- Ruhr Universität Bochum, Fakultät für Chemie und Biochemie, Organische Chemie II, Universitätsstraße 150, 44801, Bochum, Germany.
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17
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Yang Q, Bloino J, Šestáková H, Šebestík J, Kessler J, Hudecová J, Kapitán J, Bouř P. Combination of Resonance and Non-Resonance Chiral Raman Scattering in a Cobalt(III) Complex. Angew Chem Int Ed Engl 2023; 62:e202312521. [PMID: 37728178 DOI: 10.1002/anie.202312521] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 09/18/2023] [Accepted: 09/20/2023] [Indexed: 09/21/2023]
Abstract
Resonance Raman optical activity (RROA) spectra with high sensitivity reveal details on molecular structure, chirality, and excited electronic properties. Despite the difficulty of the measurements, the recorded data for the Co(III) complex with S,S-N,N-ethylenediaminedisuccinic acid are of exceptional quality and, coupled with the theory, spectacularly document the molecular behavior in resonance. This includes a huge enhancement of the chiral scattering, contribution of the antisymmetric polarizabilities to the signal, and the Herzberg-Teller effect significantly shaping the spectra. The chiral component is by about one order of magnitude bigger than for an analogous aluminum complex. The band assignment and intensity profile were confirmed by simulations based on density functional and vibronic theories. The resonance was attributed to the S0 →S3 transition, with the strongest signal enhancement of Raman and ROA spectral bands below about 800 cm-1 . For higher wavenumbers, other excited electronic states contribute to the scattering in a less resonant way. RROA spectroscopy thus appears as a unique tool to study the structure and electronic states of absorbing molecules in analytical chemistry, biology, and material science.
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Affiliation(s)
- Qin Yang
- Institute of Organic Chemistry and Biochemistry Academy of Sciences, Flemingovo náměstí 2, 16610, Prague, Czech Republic
| | - Julien Bloino
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - Hana Šestáková
- Institute of Organic Chemistry and Biochemistry Academy of Sciences, Flemingovo náměstí 2, 16610, Prague, Czech Republic
- University of Chemistry and Technology, Technická 5, 16628, Prague 6, Czech Republic
| | - Jaroslav Šebestík
- Institute of Organic Chemistry and Biochemistry Academy of Sciences, Flemingovo náměstí 2, 16610, Prague, Czech Republic
| | - Jiří Kessler
- Institute of Organic Chemistry and Biochemistry Academy of Sciences, Flemingovo náměstí 2, 16610, Prague, Czech Republic
| | - Jana Hudecová
- Department of Optics, Palacký University Olomouc, 17. listopadu 12, 77146, Olomouc, Czech Republic
| | - Josef Kapitán
- Department of Optics, Palacký University Olomouc, 17. listopadu 12, 77146, Olomouc, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry Academy of Sciences, Flemingovo náměstí 2, 16610, Prague, Czech Republic
- University of Chemistry and Technology, Technická 5, 16628, Prague 6, Czech Republic
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18
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Taniguchi T, Agbo DO. Vibrational circular dichroism spectroscopy in the C-D, XY, and XYZ stretching region. Phys Chem Chem Phys 2023; 25:28567-28575. [PMID: 37861094 DOI: 10.1039/d3cp04287a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Vibrational circular dichroism (VCD) spectroscopy is a powerful technique for structural analysis of chiral molecules, but information available from VCD spectra of large molecular systems can be limited by severe overlap of vibrational bands. While common chiral molecules do not absorb in the 1900-2400 cm-1 region, observation of VCD signals in this spectrally-isolated region is possible for molecules containing C-D, XY, and XYZ chromophores. Thus, a strategic introduction of these chromophores to a target molecule may produce VCD signals informative for molecular structures. VCD spectroscopy in the 1900-2400 cm-1 region is a rather unexplored research field and its basic properties remain to be investigated. This perspective article discusses insight obtained so far on the usefulness and physicochemical aspects of VCD spectroscopy in this region with briefly summarizing previous experimental VCD studies including classic examples as well as our recent results. We show that anharmonic effects such as overtones and combination bands often complicate VCD patterns. On the other hand, some molecules exhibit characteristic VCD signals that can be well interpreted by harmonic DFT spectral calculations for structural analysis. This article also discusses several examples of the use of this region for studying solute-solvent interactions and for VCD signal augmentation.
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Affiliation(s)
- Tohru Taniguchi
- Frontier Research Center for Advanced Material and Life Science, Faculty of Advanced Life Science, Hokkaido University, North 21 West 11, Sapporo 001-0021, Japan.
| | - Davidson Obinna Agbo
- Graduate School of Life Science, Hokkaido University, North 21 West 11, Sapporo 001-0021, Japan
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19
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Wu T, Pelc R, Bouř P. Molecular Properties of 3d and 4f Coordination Compounds Deciphered by Raman Optical Activity Spectroscopy. Chempluschem 2023; 88:e202300385. [PMID: 37665573 DOI: 10.1002/cplu.202300385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/31/2023] [Accepted: 09/04/2023] [Indexed: 09/05/2023]
Abstract
Molecular properties of coordination compounds can be efficiently studied by vibrational spectroscopy. The scope of Raman spectroscopy has been greatly enhanced by the introduction of Raman optical activity (ROA) sensitive to chirality. The present review describes some of its recent applications to study the coordination compounds. 3d and 4f metal complexes often absorb the excitation light, or exhibit luminescence. Therefore, effects caused in ROA spectra by electronic circular dichroism (ECD) and circularly polarized luminescence (CPL) must be taken into consideration.In 3d metal complexes ECD and circularly-polarized Raman scattering compete with the resonance ROA (RROA) signal. Pure RROA spectrum can thus be obtained by subtracting the so-called ECD-Raman component. CPL is frequently encountered in 4f systems. While it can mask the ROA spectra, it is useful to study molecular structure. These electronic effects can be reduced by using near-infrared excitation although vibrational ROA signal is much weaker compared to the usual green laser excitation scenario. The ROA methodology is thus complex, but capable of providing unique information about the molecules of interests and their interaction with light.
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Affiliation(s)
- Tao Wu
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague, Czech Republic
| | - Radek Pelc
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague, Czech Republic
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20
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Batista JM, Nicu VP. Simplified and enhanced VCD analysis of cyclic peptides guided by artificial intelligence. Phys Chem Chem Phys 2023; 25:22111-22116. [PMID: 37560904 DOI: 10.1039/d3cp01986a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
Cyclic peptides are privileged structures in medicinal chemistry; however, their solution-state structure characterization is difficult. Vibrational circular dichroism (VCD) spectroscopy is a powerful alternative to NMR, but requires challenging calculations. We present a VCD approach guided by a genetic algorithm, which is simple, more effective, and has a higher conformer resolution.
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Affiliation(s)
- João M Batista
- Federal University of São Paulo, Institute of Science and Technology, R. Talim 330, 12231-280, São José dos Campos-SP, Brazil.
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21
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Michaelis M, Cupellini L, Mensch C, Perry CC, Delle Piane M, Colombi Ciacchi L. Tidying up the conformational ensemble of a disordered peptide by computational prediction of spectroscopic fingerprints. Chem Sci 2023; 14:8483-8496. [PMID: 37592980 PMCID: PMC10430726 DOI: 10.1039/d3sc02202a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 07/15/2023] [Indexed: 08/19/2023] Open
Abstract
The most advanced structure prediction methods are powerless in exploring the conformational ensemble of disordered peptides and proteins and for this reason the "protein folding problem" remains unsolved. We present a novel methodology that enables the accurate prediction of spectroscopic fingerprints (circular dichroism, infrared, Raman, and Raman optical activity), and by this allows for "tidying up" the conformational ensembles of disordered peptides and disordered regions in proteins. This concept is elaborated for and applied to a dodecapeptide, whose spectroscopic fingerprint is measured and theoretically predicted by means of enhanced-sampling molecular dynamics coupled with quantum mechanical calculations. Following this approach, we demonstrate that peptides lacking a clear propensity for ordered secondary-structure motifs are not randomly, but only conditionally disordered. This means that their conformational landscape, or phase-space, can be well represented by a basis-set of conformers including about 10 to 100 structures. The implications of this finding have profound consequences both for the interpretation of experimental electronic and vibrational spectral features of peptides in solution and for the theoretical prediction of these features using accurate and computationally expensive techniques. The here-derived methods and conclusions are expected to fundamentally impact the rationalization of so-far elusive structure-spectra relationships for disordered peptides and proteins, towards improved and versatile structure prediction methods.
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Affiliation(s)
- Monika Michaelis
- Hybrid Materials Interfaces Group, Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, University of Bremen Am Fallturm 1 Bremen 28359 Germany
- Biomolecular and Materials Interface Research Group, Interdisciplinary Biomedical Research Centre, School of Science and Technology, Nottingham Trent University Clifton Lane Nottingham NG11 8NS UK
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, University of Pisa Via G. Moruzzi 13 Pisa I-56124 Italy
| | - Carl Mensch
- Molecular Spectroscopy Research Group, Department of Chemistry, University of Antwerp Groenenborgerlaan 171 Antwerp 2020 Belgium
| | - Carole C Perry
- Biomolecular and Materials Interface Research Group, Interdisciplinary Biomedical Research Centre, School of Science and Technology, Nottingham Trent University Clifton Lane Nottingham NG11 8NS UK
| | - Massimo Delle Piane
- Hybrid Materials Interfaces Group, Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, University of Bremen Am Fallturm 1 Bremen 28359 Germany
- Department of Applied Science and Technology, Politecnico di Torino Corso Duca degli Abruzzi 24 Torino 10129 Italy
| | - Lucio Colombi Ciacchi
- Hybrid Materials Interfaces Group, Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, University of Bremen Am Fallturm 1 Bremen 28359 Germany
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22
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Liu TH, Okuno M. Characterization of Secondary Structures of Model Polypeptides in Solutions with Hyper-Raman Spectroscopy. J Phys Chem B 2023. [PMID: 37468171 DOI: 10.1021/acs.jpcb.3c02101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
Characterization of the secondary structures of two model polypeptides, poly-l-lysine and poly-l-glutamic acid in aqueous solutions has been demonstrated by hyper-Raman (HR) spectroscopy for the first time. Complementary to infrared (IR) and visible Raman spectroscopy, HR spectroscopy gives the amide I, II, and III bands originating from the polypeptide backbones and the CCH3 symmetric bending mode, enabling us to distinguish different conformations. The α-helix gives the broad and weak amide III band, while the β-sheet and the random coil show similar spectral patterns with different relative intensities between the amide I and II bands. HR spectra from aqueous solutions of the α-helix and the random coil of poly-l-ornithine also possess these spectral features. The HR spectra are analogous to UV resonance Raman (UVRR) spectra, indicating the signal enhancement due to the electronic resonance effect via the π-π* transition. In contrast, the vibrational frequencies of the amide I band in the HR spectra are much higher than those in the IR, visible Raman, and UVRR spectra, suggesting the non-coincidence between HR, IR, and Raman bands. Our finding suggests that HR spectroscopy is promising to provide complementary information on the secondary structures of polypeptides in aqueous solutions as a spectral approach differing from existing vibrational spectroscopic methods.
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Affiliation(s)
- Tsung-Han Liu
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Meguro, Tokyo 153-8902, Japan
| | - Masanari Okuno
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Meguro, Tokyo 153-8902, Japan
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23
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Vermeyen T, Cunha A, Bultinck P, Herrebout W. Impact of conformation and intramolecular interactions on vibrational circular dichroism spectra identified with machine learning. Commun Chem 2023; 6:148. [PMID: 37438485 DOI: 10.1038/s42004-023-00944-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 06/29/2023] [Indexed: 07/14/2023] Open
Abstract
Vibrational Circular Dichroism (VCD) spectra often differ strongly from one conformer to another, even within the same absolute configuration of a molecule. Simulated molecular VCD spectra typically require expensive quantum chemical calculations for all conformers to generate a Boltzmann averaged total spectrum. This paper reports whether machine learning (ML) can partly replace these quantum chemical calculations by capturing the intricate connection between a conformer geometry and its VCD spectrum. Three hypotheses concerning the added value of ML are tested. First, it is shown that for a single stereoisomer, ML can predict the VCD spectrum of a conformer from solely the conformer geometry. Second, it is found that the ML approach results in important time savings. Third, the ML model produced is unfortunately hardly transferable from one stereoisomer to another.
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Affiliation(s)
- Tom Vermeyen
- Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, Antwerpen, 2020, Belgium.
- Department of Chemistry, Ghent University, Krijgslaan 281, Gent, 9000, Belgium.
| | - Ana Cunha
- Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, Antwerpen, 2020, Belgium
| | - Patrick Bultinck
- Department of Chemistry, Ghent University, Krijgslaan 281, Gent, 9000, Belgium.
| | - Wouter Herrebout
- Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, Antwerpen, 2020, Belgium
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24
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Přáda Brichtová E, Krupová M, Bouř P, Lindo V, Gomes Dos Santos A, Jackson SE. Glucagon-like peptide 1 aggregates into low-molecular-weight oligomers off-pathway to fibrillation. Biophys J 2023; 122:2475-2488. [PMID: 37138517 PMCID: PMC10323027 DOI: 10.1016/j.bpj.2023.04.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 01/04/2023] [Accepted: 04/27/2023] [Indexed: 05/05/2023] Open
Abstract
The physical stability of peptide-based drugs is of great interest to the pharmaceutical industry. Glucagon-like peptide 1 (GLP-1) is a 31-amino acid peptide hormone, the analogs of which are frequently used in the treatment of type 2 diabetes. We investigated the physical stability of GLP-1 and its C-terminal amide derivative, GLP-1-Am, both of which aggregate into amyloid fibrils. While off-pathway oligomers have been proposed to explain the unusual aggregation kinetics observed previously for GLP-1 under specific conditions, these oligomers have not been studied in any detail. Such states are important as they may represent potential sources of cytotoxicity and immunogenicity. Here, we identified and isolated stable, low-molecular-weight oligomers of GLP-1 and GLP-1-Am, using size-exclusion chromatography. Under the conditions studied, isolated oligomers were shown to be resistant to fibrillation or dissociation. These oligomers contain between two and five polypeptide chains and they have a highly disordered structure as indicated by a variety of spectroscopic techniques. They are highly stable with respect to time, temperature, or agitation despite their noncovalent character, which was established using liquid chromatography-mass spectrometry and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. These results provide evidence of stable, low-molecular-weight oligomers that are formed by an off-pathway mechanism which competes with amyloid fibril formation.
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Affiliation(s)
- Eva Přáda Brichtová
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Monika Krupová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Prague 6, Czech Republic; Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, Tromsø, Norway
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Prague 6, Czech Republic
| | - Viv Lindo
- AstraZeneca, Cambridge, United Kingdom
| | | | - Sophie E Jackson
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom.
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25
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Abstract
ConspectusChirality is ubiquitous in the universe and in living creatures over detectable length scales from the subatomic to the galactic, as exemplified in the two extremes by subatomic particles (neutrinos) and spiral galaxies. Between them are living creatures that display multiple levels of chirality emerging from hierarchically assembled asymmetric building blocks. Not too far from the bottom of this pyramid are the foundational building blocks with chiral atomic centers on sp3 carbon atoms exemplified by l-amino acids and d-sugars that are self-assembled into higher-order structures with increasing dimensions forming highly complex, amazingly functional, and energy-efficient living systems. The organization and materials employed in their construction inspired scientists to replicate complex living systems via the self-assembly of chiral components. Multiple studies pointed to unexpected and unique electromagnetic properties of chiral structures with nanoscale and microscale dimensions, including giant circular dichroism and collective circularly polarized scattering that their constituent units did not possess.To address the wide variety of chiral geometries observed in continuous materials, singular particles, and their complex systems, multiple analytic techniques are needed. Simultaneously, their spectroscopic properties create a pathway to multiple applications. For example, mirror-asymmetric vibrations at chiral centers formed by sp3 carbon atoms lead to optical activity for the infrared (IR) wavelength regions. At the same time, understanding the optical activity in, for example, the IR region enables biomedical applications because multiple modalities of biomedical imaging and vibrational optical activity (VOA) of biomolecules are known for IR range. In turn, VOA can be realized in both absorption and emission modalities due to large magnetic transition moments, as vibrational circular dichroism (VCD) or Raman optical activity (ROA) spectroscopy. In addition to the VOA, in the range of longer wavelengths, lattice vibrational mode or phononic behavior occurs in chiral crystals and nanoassemblies, which can be readily detected by terahertz circular dichroism (TCD) spectroscopy. Meanwhile, chiral self-assembly can induce circularly polarized light emission (CPLE) regardless of the existence of chirality in coassembled fluorophores. The CPLE from self-assembled chiral materials is particularly interesting because the CPLE can originate from both circularly polarized luminescence and circularly polarized scattering (CPS). Furthermore, because self-assembled nanostructures often exhibit stronger optical activity than their building blocks owing to dimension and resonance effects, the optical activity of single assembled nanostructures can be investigated by using microscopic technology combined with chiral optics. Here, we describe the state of the art for spectroscopic methods for the comprehensive analysis of chiral nanomaterials at various photon wavelengths, addressed with special attention given to new tools emerging both for materials with self-organized hierarchical chirality and single-particle spectroscopy.
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Affiliation(s)
- Junyoung Kwon
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Ki Hyun Park
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Won Jin Choi
- Physical and Life Sciences, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
- Department of Materials Science and Engineering, Department of Chemical Engineering, and Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Nicholas A Kotov
- Department of Materials Science and Engineering, Department of Chemical Engineering, and Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jihyeon Yeom
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
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26
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Krekic S, Mero M, Kuhl M, Balasubramanian K, Dér A, Heiner Z. Photoactive Yellow Protein Adsorption at Hydrated Polyethyleneimine and Poly-l-Glutamic Acid Interfaces. Molecules 2023; 28:molecules28104077. [PMID: 37241818 DOI: 10.3390/molecules28104077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/07/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Chiral and achiral vibrational sum-frequency generation (VSFG) spectroscopy was performed in the 1400-1700 and 2800-3800 cm-1 range to study the interfacial structure of photoactive yellow protein (PYP) adsorbed on polyethyleneimine (PEI) and poly-l-glutamic acid (PGA) surfaces. Nanometer-thick polyelectrolyte layers served as the substrate for PYP adsorption, with 6.5-pair layers providing the most homogeneous surfaces. When the topmost material was PGA, it acquired a random coil structure with a small number of β2-fibrils. Upon adsorption on oppositely charged surfaces, PYP yielded similar achiral spectra. However, the VSFG signal intensity increased for PGA surfaces with a concomitant redshift of the chiral Cα-H and N-H stretching bands, suggesting increased adsorption for PGA compared to PEI. At low wavenumbers, both the backbone and the side chains of PYP induced drastic changes to all measured chiral and achiral VSFG spectra. Decreasing ambient humidity led to the loss of tertiary structure with a re-orientation of α-helixes, evidenced by a strongly blue-shifted chiral amide I band of the β-sheet structure with a shoulder at 1654 cm-1. Our observations indicate that chiral VSFG spectroscopy is not only capable of determining the main type of secondary structure of PYP, i.e., β-scaffold, but is also sensitive to tertiary protein structure.
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Affiliation(s)
- Szilvia Krekic
- School of Analytical Sciences Adlershof, Humboldt-Universität zu Berlin, 12489 Berlin, Germany
- Institute of Biophysics, Biological Research Centre, 6726 Szeged, Hungary
- Doctoral School of Multidisciplinary Medical Sciences, University of Szeged, 6720 Szeged, Hungary
| | - Mark Mero
- Max Born Institute for Nonlinear Optics and Short Pulse Spectroscopy, 12489 Berlin, Germany
| | - Michel Kuhl
- School of Analytical Sciences Adlershof, Humboldt-Universität zu Berlin, 12489 Berlin, Germany
- Department of Chemistry and IRIS Adlershof, Humboldt-Universität zu Berlin, 12489 Berlin, Germany
| | - Kannan Balasubramanian
- School of Analytical Sciences Adlershof, Humboldt-Universität zu Berlin, 12489 Berlin, Germany
- Department of Chemistry and IRIS Adlershof, Humboldt-Universität zu Berlin, 12489 Berlin, Germany
| | - András Dér
- Institute of Biophysics, Biological Research Centre, 6726 Szeged, Hungary
| | - Zsuzsanna Heiner
- School of Analytical Sciences Adlershof, Humboldt-Universität zu Berlin, 12489 Berlin, Germany
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27
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Mukherjee S, Shanmugam G. A Novel Surfactant with Short Hydrophobic Head and Long Hydrophilic Tail Generates Vesicles with Unique Structural Feature. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2206906. [PMID: 36799147 DOI: 10.1002/smll.202206906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/20/2023] [Indexed: 05/11/2023]
Abstract
Surfactant molecules typically have a long hydrophobic tail and a short hydrophilic head group. It remains unexplored if surfactants can have a short hydrophobic head group and a long hydrophilic tail. Designing such surfactants is a challenge as a lengthy hydrophilic tail would completely solubilize the molecules. In this context, herein, the Fmoc-functionalized Gly-Pro-Hyp (GPO) tripeptide repeat-based molecule (Fm-GPO) with fluorenyl moiety as a short hydrophobic head and peptide as a long hydrophilic tail is demonstrated as a reverse surfactant at physiological pH, for the first time. π-π stacking of the fluorenyl moieties and intermolecular hydrogen bonding between the peptide chains with extended polyproline-II structure promoted the self-assembly into spherical vesicles with a unique feature of a large hydrophilic area in the interior and exterior of the bilayer. The current Fm-GPO system offers a new class of surfactants with unique features that can aid in the design of drug-loaded vehicles, which can be target-specific as the peptide chain can be manipulated with different functional ultra-short peptide sequences.
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Affiliation(s)
- Smriti Mukherjee
- Organic & Bioorganic Chemistry Laboratory, Council of Scientific and Industrial Research (CSIR) - Central Leather Research Institute (CLRI), Adyar, Chennai, 600020, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Ganesh Shanmugam
- Organic & Bioorganic Chemistry Laboratory, Council of Scientific and Industrial Research (CSIR) - Central Leather Research Institute (CLRI), Adyar, Chennai, 600020, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
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28
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Buzzaccaro S, Ruzzi V, Gelain F, Piazza R. A Light Scattering Investigation of Enzymatic Gelation in Self-Assembling Peptides. Gels 2023; 9:gels9040347. [PMID: 37102959 PMCID: PMC10137429 DOI: 10.3390/gels9040347] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/08/2023] [Accepted: 04/13/2023] [Indexed: 04/28/2023] Open
Abstract
Self-assembling peptides (SAPs) have been increasingly studied as hydrogel-former gelators because they can create biocompatible environments. A common strategy to trigger gelation, is to use a pH variation, but most methods result in a change in pH that is too rapid, leading to gels with hardly reproducible properties. Here, we use the urea-urease reaction to tune gel properties, by a slow and uniform pH increase. We were able to produce very homogeneous and transparent gels at several SAP concentrations, ranging from c=1g/L to c=10g/L. In addition, by exploiting such a pH control strategy, and combining photon correlation imaging with dynamic light scattering measurements, we managed to unravel the mechanism by which gelation occurs in solutions of (LDLK)3-based SAPs. We found that, in diluted and concentrated solutions, gelation follows different pathways. This leads to gels with different microscopic dynamics and capability of trapping nanoparticles. At high concentrations, a strong gel is formed, made of relatively thick and rigid branches that firmly entrap nanoparticles. By contrast, the gel formed in dilute conditions is weaker, characterized by entanglements and crosslinks of very thin and flexible filaments. The gel is still able to entrap nanoparticles, but their motion is not completely arrested. These different gel morphologies can potentially be exploited for controlled multiple drug release.
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Affiliation(s)
- Stefano Buzzaccaro
- Department of Chemistry, Materials Science, and Chemical Engineering (CMIC), Politecnico di Milano, Edificio 6, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Vincenzo Ruzzi
- Department of Chemistry, Materials Science, and Chemical Engineering (CMIC), Politecnico di Milano, Edificio 6, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Fabrizio Gelain
- Unità di Ingegneria Tissutale, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy
- Center for Nanomedicine and Tissue Engineering, ASST GOM Niguarda, 20162 Milano, Italy
| | - Roberto Piazza
- Department of Chemistry, Materials Science, and Chemical Engineering (CMIC), Politecnico di Milano, Edificio 6, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
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29
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Wang Y, Liu Y, Ren C, Ma R, Xu Z, Zhao B. A Charge-Transfer-Induced Strategy for Enantioselective Discrimination by Potential-Regulated Surface-Enhanced Raman Scattering Spectroscopy. BIOSENSORS 2023; 13:bios13040471. [PMID: 37185546 PMCID: PMC10136649 DOI: 10.3390/bios13040471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 03/31/2023] [Accepted: 04/07/2023] [Indexed: 05/17/2023]
Abstract
A simple and efficient enantioselective discrimination method, especially the chirality-label-free discrimination method, for the recognition of chiral small molecules with high resolution and wide applicability has been urgently desired. Herein, achiral Au/p-aminothiophenol (PATP) substrates were prepared to link the enantiomers via coupling reactions for constructing the enantioselective discrimination system. The resultant Au/PATP/enantiomer systems displayed charge-transfer (CT)-induced surface-enhanced Raman scattering (SERS) spectra that offered distinguishable information for the systems with different chirality. The differentiated spectral signal can be amplified by regulating the applied electrode potential, leading to great enantioselective discrimination performance. Moreover, the relationship between the discrimination performance and the potential-regulated CT process was revealed by SERS, which enabled an accurate and effective enantiomeric determination for various chiral molecules, including aromatic and aliphatic small molecules. The aliphatic molecule with the shorter chain was discriminated with a higher resolution, since the longer-chain molecule in the discrimination system may cause a change in the molecular electronic structure of the PATP. In addition, the aromatic chiral molecule can be distinguished easier than the aliphatic molecules, which means that the generation of the conjugation of electrons in the aromatic molecule-involved enantiomeric systems facilitates CT-induced SERS discrimination. Our work provides guidance for the design and development of an effective enantioselective discrimination strategy with high discrimination performance in diverse application fields.
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Affiliation(s)
- Yue Wang
- Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Yucong Liu
- Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Chunyu Ren
- Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Ruofei Ma
- Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Zhangrun Xu
- Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Bing Zhao
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130012, China
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30
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Guselnikova O, Elashnikov R, Svorcik V, Kartau M, Gilroy C, Gadegaard N, Kadodwala M, Karimullah AS, Lyutakov O. Coupling of plasmonic hot spots with shurikens for superchiral SERS-based enantiomer recognition. NANOSCALE HORIZONS 2023; 8:499-508. [PMID: 36752733 DOI: 10.1039/d3nh00008g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Detection of enantiomers is a challenging problem in drug development as well as environmental and food quality monitoring where traditional optical detection methods suffer from low signals and sensitivity. Application of surface enhanced Raman scattering (SERS) for enantiomeric discrimination is a powerful approach for the analysis of optically active small organic or large biomolecules. In this work, we proposed the coupling of disposable chiral plasmonic shurikens supporting the chiral near-field distribution with SERS active silver nanoclusters for enantio-selective sensing. As a result of the plasmonic coupling, significant difference in SERS response of optically active analytes is observed. The observations are studied by numerical simulations and it is hypothesized that the silver particles are being excited by superchiral fields generated at the surface inducing additional polarizations in the probe molecules. The plasmon coupling phenomena was found to be extremely sensitive to slight variations in shuriken geometry, silver nanostructured layer parameters, and SERS excitation wavelength(s). Designed structures were able to discriminate cysteine enantiomers at concentrations in the nanomolar range and probe biomolecular chirality, using a common Raman spectrometer within several minutes. The combination of disposable plasmonic substrates with specific near-field polarization can make the SERS enantiomer discrimination a commonly available technique using standard Raman spectrometers.
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Affiliation(s)
- Olga Guselnikova
- Department of Solid State Engineering, University of Chemistry and Technology, 16628 Prague, Czech Republic.
- Research School of Chemistry and Applied Biomedical Sciences, Tomsk Polytechnic University, Tomsk, 634050, Russian Federation.
| | - Roman Elashnikov
- Department of Solid State Engineering, University of Chemistry and Technology, 16628 Prague, Czech Republic.
| | - Vaclav Svorcik
- Department of Solid State Engineering, University of Chemistry and Technology, 16628 Prague, Czech Republic.
| | - Martin Kartau
- School of Chemistry, Joseph Black Building, University of Glasgow, Glasgow, G12 8QQ, UK.
| | - Cameron Gilroy
- School of Chemistry, Joseph Black Building, University of Glasgow, Glasgow, G12 8QQ, UK.
| | - Nikolaj Gadegaard
- James Watt School of Engineering, University of Glasgow, Rankine Building, Glasgow, G12 8LT, UK
| | - Malcolm Kadodwala
- School of Chemistry, Joseph Black Building, University of Glasgow, Glasgow, G12 8QQ, UK.
| | - Affar S Karimullah
- School of Chemistry, Joseph Black Building, University of Glasgow, Glasgow, G12 8QQ, UK.
| | - Oleksiy Lyutakov
- Department of Solid State Engineering, University of Chemistry and Technology, 16628 Prague, Czech Republic.
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31
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Effects of Dimerization, Dendrimerization, and Chirality in p-BthTX-I Peptide Analogs on the Antibacterial Activity and Enzymatic Inhibition of the SARS-CoV-2 PL pro Protein. Pharmaceutics 2023; 15:pharmaceutics15020436. [PMID: 36839758 PMCID: PMC9964244 DOI: 10.3390/pharmaceutics15020436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/18/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
Recent studies have shown that the peptide [des-Cys11,Lys12,Lys13-(p-BthTX-I)2K] (p-Bth) is a p-BthTX-I analog that shows enhanced antimicrobial activity, stability and hemolytic activity, and is easy to obtain compared to the wild-type sequence. This molecule also inhibits SARS-CoV-2 viral infection in Vero cells, acting on SARS-CoV-2 PLpro enzymatic activity. Thus, the present study aimed to assess the effects of structural modifications to p-Bth, such as dimerization, dendrimerization and chirality, on the antibacterial activity and inhibitory properties of PLpro. The results showed that the dimerization or dendrimerization of p-Bth was essential for antibacterial activity, as the monomeric structure led to a total loss of, or significant reduction in, bacterial activities. The dimers and tetramers obtained using branched lysine proved to be prominent compounds with antibacterial activity against Gram-positive and Gram-negative bacteria. In addition, hemolysis rates were below 10% at the corresponding concentrations. Conversely, the inhibitory activity of the PLpro of SARS-CoV-2 was similar in the monomeric, dimeric and tetrameric forms of p-Bth. Our findings indicate the importance of the dimerization and dendrimerization of this important class of antimicrobial peptides, which shows great potential for antimicrobial and antiviral drug-discovery campaigns.
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32
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Jähnigen S, Le Barbu-Debus K, Guillot R, Vuilleumier R, Zehnacker A. How Crystal Symmetry Dictates Non-Local Vibrational Circular Dichroism in the Solid State. Angew Chem Int Ed Engl 2023; 62:e202215599. [PMID: 36441537 PMCID: PMC10107176 DOI: 10.1002/anie.202215599] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 11/28/2022] [Accepted: 11/28/2022] [Indexed: 11/29/2022]
Abstract
Solid-State Vibrational Circular Dichroism (VCD) can be used to determine the absolute structure of chiral crystals, but its interpretation remains a challenge in modern spectroscopy. In this work, we investigate the effect of a twofold screw axis on the solid-state VCD spectrum in a combined experimental and theoretical analysis of P21 crystals of (S)-(+)-1-indanol. Even though the space group is achiral, a single proper symmetry operation has an important impact on the VCD spectrum, which reflects the supramolecular chirality of the crystal. Distinguishing between contributions originating from molecular chirality and from chiral crystal packing, we find that while IR absorption hardly depends on the symmetry of the space group, the situation is different for VCD, where completely new non-local patterns emerge. Understanding the two underlying mechanisms, namely gauge transport and direct coupling, will help to use VCD to distinguish polymorphic forms.
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Affiliation(s)
- Sascha Jähnigen
- PASTEUR, Département de Chimie, Ecole Normale Supérieure, CNRS, PSL University, Sorbonne Université, 75005, Paris, France
| | - Katia Le Barbu-Debus
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, 91405, Orsay, France
| | - Régis Guillot
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), CNRS, Université Paris-Saclay, 91405, Orsay, France
| | - Rodolphe Vuilleumier
- PASTEUR, Département de Chimie, Ecole Normale Supérieure, CNRS, PSL University, Sorbonne Université, 75005, Paris, France
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, 91405, Orsay, France
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33
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Yang Q, Bloino J. An Effective and Automated Processing of Resonances in Vibrational Perturbation Theory Applied to Spectroscopy. J Phys Chem A 2022; 126:9276-9302. [DOI: 10.1021/acs.jpca.2c06460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Affiliation(s)
- Qin Yang
- Faculty of Science, Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126Pisa, Italy
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610Prague, Czech Republic
| | - Julien Bloino
- Faculty of Science, Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126Pisa, Italy
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34
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Adhikari S, Orrit M. Optically Probing the Chirality of Single Plasmonic Nanostructures and of Single Molecules: Potential and Obstacles. ACS PHOTONICS 2022; 9:3486-3497. [PMID: 36411819 PMCID: PMC9673138 DOI: 10.1021/acsphotonics.2c01205] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 10/07/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
Circular dichroism (CD) is a standard method for the analysis of biomolecular conformation. It is very reliable when applied to molecules, but requires relatively large amounts of solution. Plasmonics offer the perspective of enhancement of CD signals, which would extend CD spectrometry to smaller amounts of molecules and to weaker chiral signals. However, plasmonic enhancement comes at the cost of additional complications: averaging over all orientations is no longer possible or reliable, linear dichroism leaks into CD signals because of experimental imperfections, scattering and its interference with the incident beam must be taken into account, and the interaction between chiral molecules and possibly chiral plasmonic structures considerably complicates the interpretation of measured signals. This Perspective aims to explore the motivations and problems of plasmonic chirality and to re-evaluate present and future solutions.
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35
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Isolation and structural characterization of antioxidant peptides from horse bone marrow protein hydrolysates. JOURNAL OF FOOD MEASUREMENT AND CHARACTERIZATION 2022. [DOI: 10.1007/s11694-022-01638-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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36
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Galimberti DR. Vibrational Circular Dichroism from DFT Molecular Dynamics: The AWV Method. J Chem Theory Comput 2022; 18:6217-6230. [PMID: 36112978 PMCID: PMC9558311 DOI: 10.1021/acs.jctc.2c00736] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The paper illustrates the Activity Weighted Velocities
(AWV) methodology
to compute Vibrational Circular Dichroism (VCD) anharmonic spectra
from Density Functional Theory (DFT) molecular dynamics. AWV calculates
the spectra by the Fourier Transform of the time correlation functions
of velocities, weighted by specific observables: the Atomic Polar
Tensors (APTs) and the Atomic Axial Tensors (AATs). Indeed, AWV shows
to correctly reproduce the experimental spectra for systems in the
gas and liquid phases, both in the case of weakly and strongly interacting
systems. The comparison with the experimental spectra is striking
especially in the fingerprint region, as demonstrated by the three
benchmark systems discussed: (1S)-Fenchone in the
gas phase, (S)-(−)-Propylene oxide in the
liquid phase, and (R)-(−)-2-butanol in the
liquid phase. The time evolution of APTs and AATs can be adequately
described by a linear combination of the tensors of a small set of
appropriate reference structures, strongly reducing the computational
cost without compromising accuracy. Additionally, AWV allows the partition
of the spectral signal in its molecular components without any expensive
postprocessing and any localization of the charge density or the wave
function.
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Affiliation(s)
- Daria Ruth Galimberti
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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37
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Eikås KDR, Beerepoot MTP, Ruud K. A Computational Protocol for Vibrational Circular Dichroism Spectra of Cyclic Oligopeptides. J Phys Chem A 2022; 126:5458-5471. [PMID: 35930395 PMCID: PMC9393892 DOI: 10.1021/acs.jpca.2c02953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cyclic peptides are a promising class of compounds for next-generation antibiotics as they may provide new ways of limiting antibiotic resistance development. Although their cyclic structure will introduce some rigidity, their conformational space is large and they usually have multiple chiral centers that give rise to a wide range of possible stereoisomers. Chiroptical spectroscopies such as vibrational circular dichroism (VCD) are used to assign stereochemistry and discriminate enantiomers of chiral molecules, often in combination with electronic structure methods. The reliable determination of the absolute configuration of cyclic peptides will require robust computational methods than can identify all significant conformers and their relative population and reliably assign their stereochemistry from their chiroptical spectra by comparison with ab initio calculated spectra. We here present a computational protocol for the accurate calculation of the VCD spectra of a series of flexible cyclic oligopeptides. The protocol builds on the Conformer-Rotamer Ensemble Sampling Tool (CREST) developed by Grimme and co-workers ( Phys. Chem. Chem. Phys. 2020, 22, 7169-7192 and J. Chem. Theory. Comput. 2019, 15, 2847-2862) in combination with postoptimizations using B3LYP and moderately sized basis sets. Our recommended computational protocol for the computation of VCD spectra of cyclic oligopeptides consists of three steps: (1) conformational sampling with CREST and tight-binding density functional theory (xTB); (2) energy ranking based on single-point energy calculations as well as geometry optimization and VCD calculations of conformers that are within 2.5 kcal/mol of the most stable conformer using B3LYP/6-31+G*/CPCM; and (3) VCD spectra generation based on Boltzmann weighting with Gibbs free energies. Our protocol provides a feasible basis for generating VCD spectra also for larger cyclic peptides of biological/pharmaceutical interest and can thus be used to investigate promising compounds for next-generation antibiotics.
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Affiliation(s)
- Karolina Di Remigio Eikås
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Maarten T P Beerepoot
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Kenneth Ruud
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, 9037 Tromsø, Norway.,Norwegian Defence Research Establishment, P.O. Box 25, 2027 Kjeller, Norway
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38
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Dupont J, Guillot R, Lepère V, Zehnacker A. Jet-cooled laser spectroscopy and solid-state vibrational circular dichroism of the cyclo-(Tyr-Phe) diketopiperazine dipeptide. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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39
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Xu J, Xue Y, Jian X, Zhao Y, Dai Z, Xu J, Gao Z, Mei Y, Song YY. Understanding of chiral site-dependent enantioselective identification on a plasmon-free semiconductor based SERS substrate. Chem Sci 2022; 13:6550-6557. [PMID: 35756506 PMCID: PMC9172570 DOI: 10.1039/d2sc01938h] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/10/2022] [Indexed: 12/19/2022] Open
Abstract
Chiral differentiation is an important topic in diverse fields ranging from pharmaceutics to chiral synthesis. The improvement of sensitivity and the elucidation of the mechanism of chiral recognition are still the two main challenges. Herein, a plasmon-free semiconductive surface-enhanced Raman spectroscopy (SERS) substrate with sensitive chiral recognition ability is proposed for the discrimination of enantiomers. A homochiral environment is constructed by typical π–π stacking between l-tryptophan (l-Trp) and phenyl rings on well-aligned TiO2 nanotubes (TiO2 NTs). Using 3,4-dihydroxyphenylalanine (DOPA) enantiomers as the targets and the chelating interaction of Fe3+–DOPA for the onsite growth of Prussian blue (PB), the enantioselectivity difference between l-DOPA and d-DOPA on the homochiral substrate can be directly monitored from PB signals in the Raman-silent region. By combining the experimental results with molecular dynamic (MD) simulations, it is found that satisfactory enantioselective identification not only requires a homochiral surface but also largely depends on the chiral center environment-differentiated hydrogen-bond formation availability. An intelligent enantioselective identification strategy is designed to demonstrate that both enantioselectivity and stereoselectivity are crucial factors for chiral sensing.![]()
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Affiliation(s)
- Jing Xu
- College of Sciences, Northeastern University Shenyang 110819 China
| | - Yuanfei Xue
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University Shanghai 200062 China .,NYU-ECNU Center for Computational Chemistry at NYU Shanghai Shanghai 200062 China.,Collaborative Innovation Center of Extreme Optics, Shanxi University Taiyuan Shanxi 030006 China
| | - Xiaoxia Jian
- College of Sciences, Northeastern University Shenyang 110819 China
| | - Yue Zhao
- College of Sciences, Northeastern University Shenyang 110819 China
| | - Zhenqing Dai
- College of Sciences, Northeastern University Shenyang 110819 China
| | - Jingwen Xu
- College of Sciences, Northeastern University Shenyang 110819 China
| | - Zhida Gao
- College of Sciences, Northeastern University Shenyang 110819 China
| | - Ye Mei
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University Shanghai 200062 China .,NYU-ECNU Center for Computational Chemistry at NYU Shanghai Shanghai 200062 China.,Collaborative Innovation Center of Extreme Optics, Shanxi University Taiyuan Shanxi 030006 China
| | - Yan-Yan Song
- College of Sciences, Northeastern University Shenyang 110819 China
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40
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Mangiavacchi F, Mazzeo G, Graziani MC, Marini F, Drabowicz J, Wielgus E, Sancineto L, Longhi G, Vivani R, Abbate S, Santi C. A Vibrational and Electronic Circular Dichroism Study of Chiral Seleno Compounds Prepared from a Novel Naphthol based Diselenide. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
| | - Giuseppe Mazzeo
- Brescia University Department of Molecular and Translational Medicine ITALY
| | - Maria Chiara Graziani
- University of Perugia: Universita degli Studi di Perugia Scienze Farmaceutiche ITALY
| | - Francesca Marini
- University of Perugia: Universita degli Studi di Perugia Scienze Farmaceutiche ITALY
| | - Józef Drabowicz
- Polish Academy of Sciences Centre of Molecular and Macromolecular Studies: Polska Akademia Nauk Centrum Badan Molekularnych i Makromolekularnych Organic Chemistry POLAND
| | - Ewelina Wielgus
- Centre of Molecular and Macromolecular Studies PAS: Polska Akademia Nauk Centrum Badan Molekularnych i Makromolekularnych Structural Chemistry POLAND
| | - Luca Sancineto
- University of Perugia: Universita degli Studi di Perugia Scienze Farmaceutiche ITALY
| | - Giovanna Longhi
- Brescia University Department of Molecular and Translational Medicine ITALY
| | - Riccardo Vivani
- University of Perugia: Universita degli Studi di Perugia Scienze Farmaceutiche ITALY
| | - Sergio Abbate
- Brescia University Department of Molecular and Translational Medicine ITALY
| | - Claudio Santi
- University of Perugia: Universita degli Studi di Perugia Scienze Farmaceutiche Via del Liceo 06100 Perugia ITALY
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41
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Tang H, Rosenmann D, Czaplewski DA, Yang X, Gao J. Dual-band selective circular dichroism in mid-infrared chiral metasurfaces. OPTICS EXPRESS 2022; 30:20063-20075. [PMID: 36221765 DOI: 10.1364/oe.457218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 05/12/2022] [Indexed: 06/16/2023]
Abstract
Most chiral metamaterials and metasurfaces are designed to operate in a single wavelength band and with a certain circular dichroism (CD) value. Here, mid-infrared chiral metasurface absorbers with selective CD in dual-wavelength bands are designed and demonstrated. The dual-band CD selectivity and tunability in the chiral metasurface absorbers are enabled by the unique design of a unit cell with two coupled rectangular bars. It is shown that the sign of CD in each wavelength band can be independently controlled and flipped by simply adjusting the geometric parameters, the width and the length, of the vertical rectangular bars. The mechanism of the dual-band CD selection in the chiral metasurface absorber is further revealed by studying the electric field and magnetic field distributions of the antibonding and bonding modes supported in the coupled bars under circularly polarized incident light. Furthermore, the chiral resonance wavelength can be continuously increased by scaling up the geometric parameters of the metasurface unit cell. The demonstrated results will contribute to the advance of future mid-infrared applications such as chiral molecular sensing, thermophotovoltaics, and optical communication.
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42
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Morgante P, Ludowieg HD, Autschbach J. Comparative Study of Vibrational Raman Optical Activity with Different Time-Dependent Density Functional Approximations: The VROA36 Database. J Phys Chem A 2022; 126:2909-2927. [PMID: 35512708 DOI: 10.1021/acs.jpca.2c00951] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A new database, VROA36, is introduced to investigate the performance of computational approaches for vibrational Raman optical activity (VROA) calculations. The database is composed of 36 molecules with known experimental VROA spectra. It includes 93 conformers. Normal modes calculated with B3LYP-D3(BJ)/def2-TZVP are used to compute the VROA spectra with four functionals, B3LYP-D3(BJ), ωB97X-D, M11, and optimally tuned LC-PBE, as well as several basis sets. SimROA indices and frequency scaling factors are used to compare calculated spectra with each other and with experimental data. The four functionals perform equally well independently of the basis set and usually achieve good agreement with the experimental data. For molecules in near- or at-resonance conditions, the inclusion of a complex (damped) linear response approach is important to obtain physically meaningful VROA intensities. The use of any of the tested functional approximations with the def2-SVPD Gaussian-type basis set, or a basis of similar flexibility, can be recommended for efficient and reliable theoretical VROA studies.
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Affiliation(s)
- Pierpaolo Morgante
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260-3000, United States
| | - Herbert D Ludowieg
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260-3000, United States
| | - Jochen Autschbach
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260-3000, United States
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43
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Zapata Trujillo JC, McKemmish LK. Meta‐analysis of uniform scaling factors for harmonic frequency calculations. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1584] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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44
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Aerts R, Bogaerts J, Herrebout W, Johannessen C. Insights in the vibrational optical activity spectra of the antibiotic vancomycin in DMSO. Phys Chem Chem Phys 2022; 24:9619-9625. [PMID: 35403645 DOI: 10.1039/d2cp00746k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Vibrational circular dichroism (VCD) and Raman optical activity (ROA) are two spectroscopic techniques that are sensitive towards the conformational behaviour of molecules, and are often complementary herein. In this work we pursue the determination of the conformational ensemble of the antibiotic glycopeptide vancomycin in DMSO through comparison of experimental and computational spectra, both for VCD and ROA. ROA is found to be highly suitable for the task, identifying an ensemble that strongly resembles the NMR conformation. In the case of VCD, however, a too high sensitivity of the intensities with respect to minor conformational changes hampers a reliable conformational analysis. Whence attempting to improve the match between the VCD experiment and calculations by any means - e.g., by inducing minor conformational changes or including solvent effects in the calculations - we show that there is the risk of going down the rabbit hole. In conclusion, this work contributes to the broader understanding of where, when and how VCD and ROA can be deployed as techniques for conformational analysis.
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Affiliation(s)
- Roy Aerts
- Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium.
| | - Jonathan Bogaerts
- Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium.
| | - Wouter Herrebout
- Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium.
| | - Christian Johannessen
- Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium.
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45
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Zhou S, Bian J, Chen P, Xie M, Chao J, Hu W, Lu Y, Zhang W. Polarization-dispersive imaging spectrometer for scattering circular dichroism spectroscopy of single chiral nanostructures. LIGHT, SCIENCE & APPLICATIONS 2022; 11:64. [PMID: 35304873 PMCID: PMC8933428 DOI: 10.1038/s41377-022-00755-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 02/21/2022] [Accepted: 02/27/2022] [Indexed: 05/29/2023]
Abstract
Circular dichroism spectroscopy is one of the most important tools in nanoscopic chiroptics. However, there is lack of simple, fast and reliable method for measuring the circular dichroism responses of single nanostructures. To tackle this issue, we report a polarization-dispersive imaging spectrometer which is capable of measuring the scattering circular dichroism response of a single chiral nanostructure with a single shot. Using this technique, we studied the scattering circular dichroism spectra of a model system, the vertically coupled plasmonic nanorod pair. Both experimental and theoretical results indicate that the polarization-dispersive spectrometer measures the imaginary part of nonlocal susceptibility of the structure. We further applied the technique to 3-dimensional Au nanorod structures assembled on DNA origami templates together with correlated scanning electron microscopic measurements. Rich chiroptical phenomena were unveiled at the single nanostructure level.
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Affiliation(s)
- Shuang Zhou
- College of Engineering and Applied Sciences, MOE Key Laboratory of Intelligent Optical Sensing and Manipulation, Nanjing university, Nanjing, 210023, China
| | - Jie Bian
- College of Engineering and Applied Sciences, MOE Key Laboratory of Intelligent Optical Sensing and Manipulation, Nanjing university, Nanjing, 210023, China.
- State Key Laboratory of Analytical Chemistry for Life Science, and Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, 210093, China.
| | - Peng Chen
- College of Engineering and Applied Sciences, MOE Key Laboratory of Intelligent Optical Sensing and Manipulation, Nanjing university, Nanjing, 210023, China
| | - Mo Xie
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
| | - Jie Chao
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
| | - Wei Hu
- College of Engineering and Applied Sciences, MOE Key Laboratory of Intelligent Optical Sensing and Manipulation, Nanjing university, Nanjing, 210023, China
| | - Yanqing Lu
- College of Engineering and Applied Sciences, MOE Key Laboratory of Intelligent Optical Sensing and Manipulation, Nanjing university, Nanjing, 210023, China
| | - Weihua Zhang
- College of Engineering and Applied Sciences, MOE Key Laboratory of Intelligent Optical Sensing and Manipulation, Nanjing university, Nanjing, 210023, China.
- State Key Laboratory of Analytical Chemistry for Life Science, and Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, 210093, China.
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46
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Dupont J, Lepère V, Zehnacker A, Hartweg S, Garcia GA, Nahon L. Photoelectron Circular Dichroism as a Signature of Subtle Conformational Changes: The Case of Ring Inversion in 1-Indanol. J Phys Chem Lett 2022; 13:2313-2320. [PMID: 35245057 DOI: 10.1021/acs.jpclett.2c00074] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Chirality plays a fundamental role in the molecular recognition processes. Molecular flexibility is also crucial in molecular recognition, allowing the interacting molecules to adjust their structures and hence optimize the interaction. Methods probing simultaneously chirality and molecular conformation are therefore crucially needed. Taking advantage of a possible control in the gas phase of the conformational distribution between the equatorial and axial conformers resulting from a ring inversion in jet-cooled 1-indanol, we demonstrate here the sensitivity of valence-shell photoelectron circular dichroism (PECD) to both chirality and subtle conformational changes, in a case where the photoelectron spectra of the two conformers are identical. For the highest occupied orbital, we observe a dramatic inversion of the PECD-induced photoelectron asymmetries, while the photoionization cross-section and usual anisotropy (β) parameter are completely insensitive to conformational isomerism. Such a sensitivity is a major asset for the ongoing developments of PECD-based techniques as a sensitive chiral (bio)chemical analytical tool in the gas phase.
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Affiliation(s)
- Jennifer Dupont
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405 Orsay, France
| | - Valéria Lepère
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405 Orsay, France
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405 Orsay, France
| | - Sebastian Hartweg
- Synchrotron Soleil, L'Orme des Merisiers, St. Aubin BP48, F-91192 Gif sur Yvette, France
| | - Gustavo A Garcia
- Synchrotron Soleil, L'Orme des Merisiers, St. Aubin BP48, F-91192 Gif sur Yvette, France
| | - Laurent Nahon
- Synchrotron Soleil, L'Orme des Merisiers, St. Aubin BP48, F-91192 Gif sur Yvette, France
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47
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Noble BB, Todorova N, Yarovsky I. Electromagnetic bioeffects: a multiscale molecular simulation perspective. Phys Chem Chem Phys 2022; 24:6327-6348. [PMID: 35245928 DOI: 10.1039/d1cp05510k] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Electromagnetic bioeffects remain an enigma from both the experimental and theoretical perspectives despite the ubiquitous presence of related technologies in contemporary life. Multiscale computational modelling can provide valuable insights into biochemical systems and predict how they will be perturbed by external stimuli. At a microscopic level, it can be used to determine what (sub)molecular scale reactions various stimuli might induce; at a macroscopic level, it can be used to examine how these changes affect dynamic behaviour of essential molecules within the crowded biomolecular milieu in living tissues. In this review, we summarise and evaluate recent computational studies that examined the impact of externally applied electric and electromagnetic fields on biologically relevant molecular systems. First, we briefly outline the various methodological approaches that have been employed to study static and oscillating field effects across different time and length scales. The practical value of such modelling is then illustrated through representative case-studies that showcase the diverse effects of electric and electromagnetic field on the main physiological solvent - water, and the essential biomolecules - DNA, proteins, lipids, as well as some novel biomedically relevant nanomaterials. The implications and relevance of the theoretical multiscale modelling to practical applications in therapeutic medicine are also discussed. Finally, we summarise ongoing challenges and potential opportunities for theoretical modelling to advance the current understanding of electromagnetic bioeffects for their modulation and/or beneficial exploitation in biomedicine and industry.
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Affiliation(s)
- Benjamin B Noble
- School of Engineering, RMIT University, GPO Box 2476, Melbourne, Australia. .,Australian Centre for Electromagnetic Bioeffects Research, Australia
| | - Nevena Todorova
- School of Engineering, RMIT University, GPO Box 2476, Melbourne, Australia. .,Australian Centre for Electromagnetic Bioeffects Research, Australia
| | - Irene Yarovsky
- School of Engineering, RMIT University, GPO Box 2476, Melbourne, Australia. .,Australian Centre for Electromagnetic Bioeffects Research, Australia
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48
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Saemi Yokomichi MA, Leite Silva HR, Eivazian Vianna Nogueira Brandao L, Festozo Vicente E, Batista Junior JM. Conformational preferences induced by cyclization in orbitides: a vibrational CD study. Org Biomol Chem 2022; 20:1306-1314. [DOI: 10.1039/d1ob02170b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Orbitides are bioactive head-to-tail natural cyclic peptides from plant species. Their bioactivity is intrinsically related to the main conformations adopted in solution, whose correct characterization represents an important bottleneck for...
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49
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Sato H, Aisawa S, Ida H, Shimizu M, Watanabe K, Koshoubu J, Yoshida J, Kawamura I. Two-dimensional Imaging of a Model Pharmaceutical Dosage Tablet Using a Scanning Vibrational Circular Dichroism System. CHEM LETT 2021. [DOI: 10.1246/cl.210635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Hisako Sato
- Graduate School of Science and Engineering, Ehime University, Matsuyama 790-8577, Japan
| | - Sumio Aisawa
- Department of Chemistry and Biological Sciences, Faculty of Science and Engineering, Iwate University, 4-3-5 Ueda, Morioka, 020-8551, Japan
| | - Honoka Ida
- Department of Chemistry and Biological Sciences, Faculty of Science and Engineering, Iwate University, 4-3-5 Ueda, Morioka, 020-8551, Japan
| | | | | | - Jun Koshoubu
- JASCO Corporation, Hachioji, Tokyo, 192-8537, Japan
| | - Jun Yoshida
- Department of Chemistry, College of Humanities & Sciences, Nihon University, Setagaya-ku, Tokyo 156-8550, Japan
| | - Izuru Kawamura
- Graduate School of Engineering Science, Yokohama National University, Hodogaya-ku, Yokohama 240-8501, Japan
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50
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Mazzeo G, Cimmino A, Longhi G, Masi M, Evidente A, Abbate S. The Assignment of the Absolute Configuration of Non-Cyclic Sesquiterpenes by Vibrational and Electronic Circular Dichroism: The Example of Chiliadenus lopadusanus Metabolites. Biomolecules 2021; 11:biom11121902. [PMID: 34944545 PMCID: PMC8699476 DOI: 10.3390/biom11121902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/10/2021] [Accepted: 12/16/2021] [Indexed: 11/16/2022] Open
Abstract
9-Hydroxynerolidol, 9-oxonerolidol, and chiliadenol B are three farnesane-type sesquiterpenoids isolated from Chiliadenus lopadusanus that have shown an interesting activity against human pathogens as Gram+ and Gram- bacteria resistant to antibiotics. However, the absolute configuration (AC) of these interesting sesquiterpenes has not been assigned so far. Vibrational and electronic circular dichroism spectra have been recorded and correlations are pointed out for the three compounds. Density functional theory (DFT) calculations are used in conjunction with Mosher's method of investigation to assign AC. Statistical analysis is considered to quantitatively define the choice of AC from VCD spectra.
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Affiliation(s)
- Giuseppe Mazzeo
- Dipartimento di Medicina Molecolare e Traslazionale, Università degli Studi di Brescia, Viale Europa 11, 25123 Brescia, Italy; (G.M.); (G.L.)
| | - Alessio Cimmino
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario Monte Sant’Angelo, 80126 Napoli, Italy; (A.C.); (M.M.); (A.E.)
| | - Giovanna Longhi
- Dipartimento di Medicina Molecolare e Traslazionale, Università degli Studi di Brescia, Viale Europa 11, 25123 Brescia, Italy; (G.M.); (G.L.)
| | - Marco Masi
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario Monte Sant’Angelo, 80126 Napoli, Italy; (A.C.); (M.M.); (A.E.)
| | - Antonio Evidente
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario Monte Sant’Angelo, 80126 Napoli, Italy; (A.C.); (M.M.); (A.E.)
| | - Sergio Abbate
- Dipartimento di Medicina Molecolare e Traslazionale, Università degli Studi di Brescia, Viale Europa 11, 25123 Brescia, Italy; (G.M.); (G.L.)
- Correspondence: ; Tel.: +39-030-3717415
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