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Xu R, Jiang Z, Yang Q, Bloino J, Biczysko M. Harmonic and anharmonic vibrational computations for biomolecular building blocks: Benchmarking DFT and basis sets by theoretical and experimental IR spectrum of glycine conformers. J Comput Chem 2024; 45:1846-1869. [PMID: 38682874 DOI: 10.1002/jcc.27377] [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: 02/12/2024] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 05/01/2024]
Abstract
Advanced vibrational spectroscopic experiments have reached a level of sophistication that can only be matched by numerical simulations in order to provide an unequivocal analysis, a crucial step to understand the structure-function relationship of biomolecules. While density functional theory (DFT) has become the standard method when targeting medium-size or larger systems, the problem of its reliability and accuracy are well-known and have been abundantly documented. To establish a reliable computational protocol, especially when accuracy is critical, a tailored benchmark is usually required. This is generally done over a short list of known candidates, with the basis set often fixed a priori. In this work, we present a systematic study of the performance of DFT-based hybrid and double-hybrid functionals in the prediction of vibrational energies and infrared intensities at the harmonic level and beyond, considering anharmonic effects through vibrational perturbation theory at the second order. The study is performed for the six-lowest energy glycine conformers, utilizing available "state-of-the-art" accurate theoretical and experimental data as reference. Focusing on the most intense fundamental vibrations in the mid-infrared range of glycine conformers, the role of the basis sets is also investigated considering the balance between computational cost and accuracy. Targeting larger systems, a broad range of hybrid schemes with different computational costs is also tested.
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Affiliation(s)
- Ruiqin Xu
- Department of Physics, College of Sciences, Shanghai University, Shanghai, China
| | | | - Qin Yang
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czechia
| | - Julien Bloino
- Classe di Scienze, Scuola Normale Superiore, Pisa, Italy
| | - Malgorzata Biczysko
- Department of Physics, College of Sciences, Shanghai University, Shanghai, China
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2
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Niu X, Wang Y, Liu Y, Yuan M, Zhang J, Li H, Wang K. Defect-engineered chiral metal-organic frameworks. Mikrochim Acta 2024; 191:458. [PMID: 38985164 DOI: 10.1007/s00604-024-06534-7] [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: 06/05/2024] [Accepted: 07/02/2024] [Indexed: 07/11/2024]
Abstract
Chirality has an important impact on chemical and biological research, as most active substances are chiral. In recent decades, metal-organic frameworks (MOFs), which are assembled from metal ions or clusters and organic linkers via metal-ligand bonding, have attracted considerable scientific interest due to their high crystallinity, exceptional porosity and tunable pore sizes, high modularity, and diverse functionalities. Since the discovery of the first functional chiral metal-organic frameworks (CMOFs), CMOFs have been involved in a variety of disciplines such as chemistry, physics, optics, medicine, and pharmacology. The introduction of defect engineering theory into CMOFs allows the construction of a class of defective CMOFs with high hydrothermal stability and multi-stage pore structure. The introduction of defects not only increases the active sites but also enlarges the pore sizes of the materials, which improves chiral recognition, separation, and catalytic reactions, and has been widely investigated in various fields. This review describes the design and synthesis of various defective CMOFs, their characterization, and applications. Finally, the development of the materials is summarized, and an outlook is given. This review should provide researchers with an insight into the design and study of complex defective CMOFs.
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Affiliation(s)
- Xiaohui Niu
- College of Petrochemical Technology, Lanzhou University of Technology, 730050, Lanzhou, People's Republic of China.
| | - Yuewei Wang
- College of Petrochemical Technology, Lanzhou University of Technology, 730050, Lanzhou, People's Republic of China
| | - Yongqi Liu
- College of Petrochemical Technology, Lanzhou University of Technology, 730050, Lanzhou, People's Republic of China
| | - Mei Yuan
- College of Petrochemical Technology, Lanzhou University of Technology, 730050, Lanzhou, People's Republic of China
| | - Jianying Zhang
- College of Petrochemical Technology, Lanzhou University of Technology, 730050, Lanzhou, People's Republic of China
| | - Hongxia Li
- College of Petrochemical Technology, Lanzhou University of Technology, 730050, Lanzhou, People's Republic of China
| | - Kunjie Wang
- College of Petrochemical Technology, Lanzhou University of Technology, 730050, Lanzhou, People's Republic of China.
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3
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Voeten RLC, Majeed HA, Bos TS, Somsen GW, Haselberg R. Investigating direct current potentials that affect native protein conformation during trapped ion mobility spectrometry-mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2024; 59:e5021. [PMID: 38605451 DOI: 10.1002/jms.5021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 10/13/2023] [Accepted: 03/06/2024] [Indexed: 04/13/2024]
Abstract
Trapped ion mobility spectrometry-time-of-flight mass spectrometry (TIMS-TOFMS) has emerged as a tool to study protein conformational states. In TIMS, gas-phase ions are guided across the IM stages by applying direct current (DC) potentials (D1-6), which, however, might induce changes in protein structures through collisional activation. To define conditions for native protein analysis, we evaluated the influence of these DC potentials using the metalloenzyme bovine carbonic anhydrase (BCA) as primary test compound. The variation of DC potentials did not change BCA-ion charge and heme content but affected (relative) charge-state intensities and adduct retention. Constructed extracted-ion mobilograms and corresponding collisional cross-section (CCS) profiles gave useful insights in (alterations of) protein conformational state. For BCA, the D3 and D6 potential (which are applied between the deflection transfer and funnel 1 [F1] and the accumulation exit and the start of the ramp, respectively) had most profound effects, showing multimodal CCS distributions at higher potentials indicating gradual unfolding. The other DC potentials only marginally altered the CCS profiles of BCA. To allow for more general conclusions, five additional proteins of diverse molecular weight and conformational stability were analyzed, and for the main protein charge states, CCS profiles were constructed. Principal component analysis (PCA) of the obtained data showed that D1 and D3 exhibit the highest degree of correlation with the ratio of folded and unfolded protein (F/U) as extracted from the mobilograms obtained per set D potential. The correlation of D6 with F/U and protein charge were similar, and D2, D4, and D5 showed an inverse correlation with F/U but were correlated with protein charge. Although DC boundary values for induced conformational changes appeared protein dependent, a set of DC values could be determined, which assured native analysis of most proteins.
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Affiliation(s)
- Robert L C Voeten
- Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Centre for Analytical Sciences Amsterdam (CASA), Amsterdam, The Netherlands
- TI-COAST, Amsterdam, The Netherlands
| | - Hany A Majeed
- Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Centre for Analytical Sciences Amsterdam (CASA), Amsterdam, The Netherlands
| | - Tijmen S Bos
- Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Centre for Analytical Sciences Amsterdam (CASA), Amsterdam, The Netherlands
| | - Govert W Somsen
- Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Centre for Analytical Sciences Amsterdam (CASA), Amsterdam, The Netherlands
| | - Rob Haselberg
- Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Centre for Analytical Sciences Amsterdam (CASA), Amsterdam, The Netherlands
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4
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Bashir S, Aiman A, Chaudhary AA, Khan N, Ahanger IA, Sami N, Almugri EA, Ali MA, Khan SUD, Shahid M, Basir SF, Hassan MI, Islam A. Probing protein aggregation through spectroscopic insights and multimodal approaches: A comprehensive review for counteracting neurodegenerative disorders. Heliyon 2024; 10:e27949. [PMID: 38689955 PMCID: PMC11059433 DOI: 10.1016/j.heliyon.2024.e27949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/01/2024] [Accepted: 03/08/2024] [Indexed: 05/02/2024] Open
Abstract
Aberrant accumulation of protein misfolding can cause aggregation and fibrillation and is one of the primary characteristic features of neurodegenerative diseases. Because they are disordered, misfolded, and aggregated proteins pose a significant setback in drug designing. The structural study of intermediate steps in these kinds of aggregated proteins will allow us to determine the conformational changes as well as the probable pathways encompassing various neurodegenerative disorders. The analysis of protein aggregates involved in neurodegenerative diseases relies on a diverse toolkit of biophysical techniques, encompassing both morphological and non-morphological methods. Additionally, Thioflavin T (ThT) assays and Circular Dichroism (CD) spectroscopy facilitate investigations into aggregation kinetics and secondary structure alterations. The collective application of these biophysical techniques empowers researchers to comprehensively unravel the intricate nature of protein aggregates associated with neurodegeneration. Furthermore, the topics covered in this review have summed up a handful of well-established techniques used for the structural analysis of protein aggregation. This multifaceted approach advances our fundamental understanding of the underlying mechanisms driving neurodegenerative diseases and informs potential therapeutic strategies.
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Affiliation(s)
- Sania Bashir
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Ayesha Aiman
- Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Anis Ahmad Chaudhary
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Nashrah Khan
- Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Ishfaq Ahmad Ahanger
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Neha Sami
- Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Eman Abdullah Almugri
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Mohamed A.M. Ali
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
- Department of Biochemistry, Faculty of Science, Ain Shams University, Abbassia, 11566, Cairo, Egypt
| | - Salah-Ud-Din Khan
- Department of Biochemistry, College of Medicine, Imam Mohammad Ibn Saud Islamic Universi-ty (IMSIU), Riyadh, 11623, Saudi Arabia
| | - Mohammad Shahid
- Department of Basic Medical Sciences, College of Medicine, Prince Sattam Bin Abdulaziz University, AlKharj, 11942, Saudi Arabia
| | - Seemi Farhat Basir
- Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
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Yang Y, Alshalalfeh M, Xu Y. Conformational distributions of tetrahydro-2-turoic acid in water at different pH values by their IR and vibrational circular dichroism spectra. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 307:123634. [PMID: 37976578 DOI: 10.1016/j.saa.2023.123634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 11/01/2023] [Accepted: 11/07/2023] [Indexed: 11/19/2023]
Abstract
Infrared (IR) and vibrational circular dichroism (VCD) spectra of tetrahydro-2-furoic acid (THFA) in aqueous solutions under several different pH conditions were recorded. To interpret the IR and VCD spectra of THFA obtained in highly acidic and basic aqueous solutions, extensive and systematic conformational searches were conducted to acquire the low-energy minima for both the neutral and deprotonated forms of THFA species, as well as their hydrated clusters. This was accomplished by using the conformer-rotamer ensemble sampling tool (CREST) with an implicit solvation model for water. The CREST candidates were further optimized at the B3LYP-D3BJ/def2-TZVP level of theory. The simulated VCD spectra of the neutral THFA conformers in the polarizable continuum model (PCM) of water alone exhibit little agreement with the experimental data under highly acidic conditions. Applying the clusters-in-a-liquid solvation model by considering the monohydrate THFA conformers in the PCM of water, significantly improved agreement with the experimental data. Similarly, the deprotonated THFA species solvated with one to four explicit water molecules in the PCM of water were considered. While the IR and VCD spectra of the deprotonated THFA monohydrate conformers offer the best agreement with the experimental data, other larger hydrated clusters, particularly the dihydrates, also contribute to the spectra. Through the synergistic combined experimental and theoretical approach used in the study, comprehensive conformational distributions of the predominant THFA species across various pH conditions were extracted.
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Affiliation(s)
- Yanqing Yang
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
| | - Mutasem Alshalalfeh
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
| | - Yunjie Xu
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada.
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6
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Rode JE, Łyczko K, Kaczorek D, Kawęcki R, Dobrowolski JC. VCD spectra of chiral naphthalene-1-carboxamides in the solid-state. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 310:123939. [PMID: 38301569 DOI: 10.1016/j.saa.2024.123939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 01/14/2024] [Accepted: 01/20/2024] [Indexed: 02/03/2024]
Abstract
The VCD spectra of chiral 2,3-dihydro-1H-benzo[de]isoquinolin-1-one (8-substituted naphthalene-1-carboxamide, BIQ) were studied in KBr pellets. The X-ray diffractometry revealed that the Me, Ph, and pClPh BIQs crystalize in the monoclinic P21, while nBu, pMePh, and oMeOPh BIQs in the orthorhombic P212121 space group. Only the Me-BIQ crystal exhibits the presence of cyclic amide dimers, while the others contain chains of the amid group hydrogen bonds. For all BIQs, except pMePh, the most intense IR band in the 1750-1550 cm-1 region is located at ca. 1680 cm-1 and is accompanied by two weak ones at ca. 1618 and 1590 cm-1. For the pMePh derivative, four almost equally intense IR bands at 1662, 1639, 1614, and 1588 cm-1 are observed. This region of the IR spectra of BIQs, but pMePh, is well reproduced by calculations based on BIQ monomers. On the other hand, the complex IR pattern of pMePh is computationally reproduced when larger crystal fragments, like octamers, are considered. Registration of the VCD spectra enabled recognizing the complexity of IR contours at ca. 1680 cm-1 by the corresponding VCD motives. For (i) Me, Ph and pClPh (R)-enantiomers, two (+)(-) bands were distinguished and for (ii) nBu and pMePh ones, one VCD band with right-side asymmetry was found. For (iii) oMeOPh the VCD pattern cannot be unambiguously assigned. Thus, the VCD spectra in the ν(C=O) range diverse the studied compounds. Among the set of molecules, pMePh has exceptional crystal geometry. Therefore, its most intense ν(C=O) band position and shape can be connected with the geometry of the hydrogen bonds, interactions, and crystal packing. Interpretation of the VCD spectra is based on linear and packed BIQ octamers. This cluster model can reproduce the main features of the solid-state VCD of BIQs.
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Affiliation(s)
- Joanna E Rode
- Institute of Nuclear Chemistry and Technology, 16 Dorodna Street 03-195, Warsaw, Poland.
| | - Krzysztof Łyczko
- Institute of Nuclear Chemistry and Technology, 16 Dorodna Street 03-195, Warsaw, Poland
| | - Dorota Kaczorek
- University of Siedlce, Faculty of Science, 3 Maja Street No 54 08-110, Siedlce, Poland
| | - Robert Kawęcki
- University of Siedlce, Faculty of Science, 3 Maja Street No 54 08-110, Siedlce, Poland
| | - Jan Cz Dobrowolski
- Institute of Nuclear Chemistry and Technology, 16 Dorodna Street 03-195, Warsaw, Poland
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7
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Khalid MI, Salem MSH, Takizawa S. Synthesis and Structural and Optical Behavior of Dehydrohelicene-Containing Polycyclic Compounds. Molecules 2024; 29:296. [PMID: 38257209 PMCID: PMC10819569 DOI: 10.3390/molecules29020296] [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: 11/30/2023] [Revised: 12/28/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
Dehydrohelicene-based molecules stand out as highly promising scaffolds and captivating chiroptical materials, characterized by their unique chirality. Their quasi-helical π-conjugated molecular architecture, featuring successively ortho-annulated aromatic rings, endows them with remarkable thermal stability and optical properties. Over the past decade, diverse approaches have emerged for synthesizing these scaffolds, reinvigorating this field, with anticipated increased attention in the coming years. This review provides a comprehensive overview of the historical evolution of dehydrohelicene chemistry since the pioneering work of Zander and Franke in 1969 and highlights recent advancements in the synthesis of various molecules incorporating dehydrohelicene motifs. We elucidate the intriguing structural features and optical merits of these molecules, occasionally drawing comparisons with their helicene or circulene analogs to underscore the significance of the bond between the helical termini.
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Affiliation(s)
- Md. Imrul Khalid
- SANKEN, Osaka University, Mihogaoka, Ibaraki-shi 567-0047, Osaka, Japan; (M.I.K.); (M.S.H.S.)
- Organic and Carbon Nanomaterials Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Mohamed S. H. Salem
- SANKEN, Osaka University, Mihogaoka, Ibaraki-shi 567-0047, Osaka, Japan; (M.I.K.); (M.S.H.S.)
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt
| | - Shinobu Takizawa
- SANKEN, Osaka University, Mihogaoka, Ibaraki-shi 567-0047, Osaka, Japan; (M.I.K.); (M.S.H.S.)
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Weng GG, Xu K, Hou T, Huang XD, Qin MF, Bao SS, Zheng LM. Enhancing the Circularly Polarized Luminescence of Europium Coordination Polymers by Doping a Chromophore Ligand into Superhelices. Inorg Chem 2023; 62:21044-21052. [PMID: 38051505 DOI: 10.1021/acs.inorgchem.3c02806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Lanthanide-based molecular materials showing efficient circularly polarized luminescence (CPL) activity with a high quantum yield are attractive due to their potential applications in data storage, optical sensors, and 3D displays. Herein we present an innovative method to achieve enhanced CPL activity and a high quantum yield by doping a chromophore ligand into a coordination polymer superhelix. A series of homochiral europium(III) phosphonates with a helical morphology were prepared with the molecular formula S-, R-[Eu(cyampH)3-3n(nempH)3n]·3H2O (S/R-Eu-n, n = 0-5%). The doping of chromophore ligand S- or R-nempH2 into superhelices of S/R-Eu-0% not only turned on the CPL activity with the dissymmetry factor |glum| on the order of 10-3 but also increased the quantum yield by about 14-fold. This work may shed light on the development of efficient CPL-active lanthanide-based coordination polymers for applications.
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Affiliation(s)
- Guo-Guo Weng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
- Key Laboratory of Jiangxi University for Functional Materials Chemistry, School of Chemistry and Chemical Engineering, Gannan Normal University, Ganzhou, Jiangxi 341000, P. R. China
| | - Kui Xu
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Ting Hou
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Xin-Da Huang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Ming-Feng Qin
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Song-Song Bao
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Li-Min Zheng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
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9
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Ye L, Li J, Richter FU, Jahani Y, Lu R, Lee BR, Tseng ML, Altug H. Dielectric Tetramer Nanoresonators Supporting Strong Superchiral Fields for Vibrational Circular Dichroism Spectroscopy. ACS PHOTONICS 2023; 10:4377-4384. [PMID: 38533249 PMCID: PMC10961839 DOI: 10.1021/acsphotonics.3c01186] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/15/2023] [Accepted: 10/20/2023] [Indexed: 03/28/2024]
Abstract
Chirality (C) is a fundamental property of objects, in terms of symmetry. It is extremely important to sense and distinguish chiral molecules in the fields of biochemistry, science, and medicine. Vibrational circular dichroism (VCD) spectroscopy, obtained from the differential absorption of left- and right- circularly polarized light (CPL) in the infrared range, is a promising technique for enantiomeric detection and separation. However, VCD signals are typically very weak for most small molecules. Dielectric metasurfaces are an emerging platform to enhance the sensitivity of VCD spectroscopy of chiral molecules via superchiral field manipulation. Here, we demonstrate a dielectric metasurface consisting of achiral germanium (Ge) tetramer nanoresonators that provide a proper and accessible high C enhancement (CE). We realize a maximum C enhancement (CE_max) with respect to the incident CPL (CE_max = Cmax/CRCP) of more than 750. The volume-averaged C enhancement (CE_ave = Cave/CRCP) is 148 in the 50 nm thick region above the sample surface and 215 in the central region of the structure. Especially, the corresponding CE_ave values are more than 89 and 183 even when a 50 nm thick chiral lossy molecular layer is coated on the metasurface. The metasurface benefits from geometrically achiral nanostructure design to eliminate intrinsic background chiral-optical signal from the substrate, which is useful in chiral sensing, enantioselectivity, and VCD spectroscopy applications in the mid-infrared range.
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Affiliation(s)
- Longfang Ye
- Institute
of Electromagnetics and Acoustics, School of Electronic Science and
Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Jingyan Li
- Institute
of Electromagnetics and Acoustics, School of Electronic Science and
Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Felix Ulrich Richter
- Laboratory
of Bionanophotonic Systems, Institute of Bioengineering, École Polytechnique Fédérale
de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Yasaman Jahani
- Laboratory
of Bionanophotonic Systems, Institute of Bioengineering, École Polytechnique Fédérale
de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Rui Lu
- Jiangsu
Key Laboratory of Chemical Pollution Control and Resources Reuse,
School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, People’s Republic of China
| | - Bo Ray Lee
- Institute
of Electronics, National Yang Ming Chiao
Tung University, Hsinchu 300, Taiwan
| | - Ming Lun Tseng
- Institute
of Electronics, National Yang Ming Chiao
Tung University, Hsinchu 300, Taiwan
| | - Hatice Altug
- Laboratory
of Bionanophotonic Systems, Institute of Bioengineering, École Polytechnique Fédérale
de Lausanne (EPFL), Lausanne 1015, Switzerland
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10
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Hermann DR, Ramer G, Riedlsperger L, Lendl B. Chiral Monitoring Across Both Enantiomeric Excess and Concentration Space: Leveraging Quantum Cascade Lasers for Sensitive Vibrational Circular Dichroism Spectroscopy. APPLIED SPECTROSCOPY 2023; 77:1362-1370. [PMID: 37847076 DOI: 10.1177/00037028231206186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
Recently, high-throughput quantum cascade laser-based vibrational circular dichroism (QCL-VCD) technology has reduced the measurement time for high-quality vibrational circular dichroism spectra from hours to a few minutes. This study evaluates QCL-VCD for chiral monitoring using flow-through measurement of a changing sample in a circulating loop. A balanced detection QCL-VCD system was applied to the enantiomeric pair R/S-1,1'-bi-2-naphthol in solution. Different mixtures of the two components were used to simulate a racemization process, collecting spectral data at a time resolution of 6 min, and over three concentration levels. The goal of this experimental setup was to evaluate QCL-VCD in terms of both molar and enantiomeric excess (EE) sensitivity at a time resolution relevant to chiral monitoring in chemical processes. Subsequent chemometric evaluation by partial least squares regression revealed a cross-validated prediction accuracy of 2.8% EE with a robust prediction also for the test data set (error = 3.5% EE). In addition, the data set was also treated with the least absolute shrinkage and selection operator (LASSO), which also achieved a robust prediction. Due to the operating principle of LASSO, the obtained coefficients constituted a few discrete spectral frequencies, which represent the most variance. This information can be used in the future for dedicated QCL-based instrument design, gaining a higher time resolution without sacrificing predictive capabilities.
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Affiliation(s)
- Daniel-Ralph Hermann
- Research Division of Environmental Analytics, Process Analytics and Sensors, Institute of Chemical Technologies and Analytics, TU Wien, Vienna, Austria
| | - Georg Ramer
- Research Division of Environmental Analytics, Process Analytics and Sensors, Institute of Chemical Technologies and Analytics, TU Wien, Vienna, Austria
| | - Lisa Riedlsperger
- Research Division of Environmental Analytics, Process Analytics and Sensors, Institute of Chemical Technologies and Analytics, TU Wien, Vienna, Austria
| | - Bernhard Lendl
- Research Division of Environmental Analytics, Process Analytics and Sensors, Institute of Chemical Technologies and Analytics, TU Wien, Vienna, Austria
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11
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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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12
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Nguyen DD, Kim I. Vibrational circular dichroism unveils hidden clues. LIGHT, SCIENCE & APPLICATIONS 2023; 12:210. [PMID: 37652916 PMCID: PMC10471598 DOI: 10.1038/s41377-023-01239-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Infrared chiral plasmonic metamaterials based on perpendicularly positioned nanorods enable surface-enhanced vibrational circular dichroism for more selective and sensitive identification of protein fingerprints and enantioselective sensing, which creates a new pathway for chemical or biomedical applications.
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Affiliation(s)
- Dang Du Nguyen
- Department of Biophysics, Institute of Quantum Biophysics, Sungkyunkwan University, Suwon, 16419, Republic of Korea
- Department of Intelligent Precision Healthcare Convergence, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Inki Kim
- Department of Biophysics, Institute of Quantum Biophysics, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
- Department of Intelligent Precision Healthcare Convergence, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
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13
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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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14
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Eikås KDR, Krupová M, Kristoffersen T, Beerepoot MTP, Ruud K. Can the absolute configuration of cyclic peptides be determined with vibrational circular dichroism? Phys Chem Chem Phys 2023; 25:14520-14529. [PMID: 37190985 DOI: 10.1039/d2cp04942b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Cyclic peptides show a wide range of biological activities, among others as antibacterial agents. These peptides are often large and flexible with multiple chiral centers. The determination of the stereochemistry of molecules with multiple chiral centers is a challenging and important task in drug development. Chiroptical spectroscopies such as vibrational circular dichroism (VCD) can distinguish between different stereoisomers. The absolute configuration (AC) of a stereoisomer can be determined by comparing its experimental spectra to computed spectra of stereoisomers with known AC. In this way, the AC of rigid molecules with up to seven chiral centers has been assigned (Bogaerts et al., Phys. Chem. Chem. Phys., 2020, 22, 18014). The question arises whether this is possible with more conformationally flexible molecules such as cyclic peptides. We here investigate to what extent the AC of cyclic peptides can be determined with VCD. More specifically, we investigate the maximum number of chiral centers a cyclic peptide can have in order to be able to unambiguously assign the AC with VCD. We present experimental and computed IR and VCD spectra for a series of eight tetrapeptides and hexapeptides with two, three and four chiral centers. We use our recently developed computational protocol with a conformational search based on sampling with meta-dynamics. We use visual inspection to compare the computed spectra of different stereoisomers with an experimental spectrum of the corresponding cyclic peptide with known AC. We find that the AC of the investigated cyclic peptides with two chiral centers can be unambiguously assigned with VCD. This is however not possible for all of the cyclic peptides with three chiral centers and for none of those with four chiral centers. At best, one can limit the number of possible stereoisomers in those cases. Our work shows that other techniques are needed to assign the AC of cyclic peptides with three or more chiral centers. Our study also constitutes a warning that the spectra of all stereoisomers should be computed before attempting to match to an experimental spectrum, to avoid an accidental erroneous match.
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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.
| | - Monika Krupová
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, 9037 Tromsø, Norway.
| | - Tone Kristoffersen
- 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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15
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Ditler E, Kumar C, Luber S. Vibrational circular dichroism spectra of natural products by means of the nuclear velocity perturbation theory. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 298:122769. [PMID: 37163900 DOI: 10.1016/j.saa.2023.122769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/24/2023] [Accepted: 04/18/2023] [Indexed: 05/12/2023]
Abstract
We present the application of the recently implemented nuclear velocity perturbation theory, using the combined Gaussian and plane waves approach in CP2K, to the vibrational circular dichroism (VCD) spectra of a set of natural products. Even though the calculations were carried out for isolated molecules in the gas-phase limit, neglecting inter-molecular interactions and anharmonic effects, the match between simulated and experimental spectra is reasonable. We also study the influence of different density functionals on the conformational search and the resulting VCD spectra via group coupling matrices (GCMs). The GCM analysis reveals that the VCD signal can in some cases arise from moieties which are close to each other and in other cases from moieties far from each other. Differences in spectra obtained using different exchange-correlation density functionals can be attributed to interaction terms between different moieties in the molecules changing their sign.
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Affiliation(s)
- Edward Ditler
- University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Chandan Kumar
- University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Sandra Luber
- University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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16
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Dual-comb optical activity spectroscopy for the analysis of vibrational optical activity induced by external magnetic field. Nat Commun 2023; 14:883. [PMID: 36797264 PMCID: PMC9935641 DOI: 10.1038/s41467-023-36509-w] [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: 07/10/2022] [Accepted: 02/03/2023] [Indexed: 02/18/2023] Open
Abstract
Optical activity (OA) spectroscopy is a powerful tool to characterize molecular chirality, explore the stereo-specific structure and study the solution-state conformation of biomolecules, which is widely utilized in the fields of molecular chirality, pharmaceutics and analytical chemistry. Due to the considerably weak effect, OA spectral analysis has high demands on measurement speed and sensitivity, especially for organic biomolecules. Moreover, gas-phase OA measurements require higher resolution to resolve Doppler-limited profiles. Here, we show the unmatched potential of dual-comb spectroscopy (DCS) in magnetic optical activity spectroscopy (MOAS) of gas-phase molecules with the resolution of hundred-MHz level and the high-speed measurement of sub-millisecond level. As a demonstration, we achieved the rapid, high-precision and high-resolution MOAS measurement of the nitrogen dioxide [Formula: see text]+[Formula: see text] band and the nitric oxide overtone band, which can be used to analyze fine structure of molecules. Besides, the preliminary demonstration of liquid-phase chiroptical activity (as weak as 10-5) has been achieved with several seconds of sampling time, which could become a routine approach enabling ultrafast dynamics analysis of chiral structural conformations.
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17
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Choi WJ, Lee SH, Park BC, Kotov NA. Terahertz Circular Dichroism Spectroscopy of Molecular Assemblies and Nanostructures. J Am Chem Soc 2022; 144:22789-22804. [DOI: 10.1021/jacs.2c04817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Won Jin Choi
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
- Physical and Life Sciences, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Sang Hyun Lee
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Bum Chul Park
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Nicholas A. Kotov
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Macromolecular Science and Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
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18
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Rizevsky S, Zhaliazka K, Matveyenka M, Quinn K, Kurouski D. Lipids reverse supramolecular chirality and reduce toxicity of amyloid fibrils. FEBS J 2022; 289:7537-7544. [PMID: 35736671 DOI: 10.1111/febs.16564] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/01/2022] [Accepted: 06/22/2022] [Indexed: 01/14/2023]
Abstract
Abrupt aggregation of misfolded proteins is a hallmark of many medical pathologies including diabetes type 2, Alzheimer and Parkinson diseases. This results in the formation of amyloid fibrils, protein aggregates with distinct supramolecular chirality. A growing body of evidence suggests that lipids can alter rates of protein aggregation. In this study, we investigated whether lipids could alter the supramolecular chirality of amyloid fibrils. We found that if present at the stage of protein aggregation, phospho- and sphingolipids uniquely reversed supramolecular chirality of insulin and lysozyme fibrils. Furthermore, amyloid fibrils with opposite supramolecular chirality exerted distinctly different cell toxicity. Specifically, insulin and lysozyme fibrils with reversed supramolecular chirality were less toxic to cells than the aggregates with normal supramolecular chirality. These findings point on the important role of lipids and supramolecular chirality of amyloid fibrils in the onset and progression of amyloid diseases.
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Affiliation(s)
- Stanislav Rizevsky
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA.,Department of Biotechnology, Binh Duong University, Thu Dau Mot, Vietnam
| | - Kiryl Zhaliazka
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Mikhail Matveyenka
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | | | - Dmitry Kurouski
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA.,Department of Biomedical Engineering, Texas A&M University, College Station, TX, USA
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19
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Hermann DR, Ramer G, Kitzler-Zeiler M, Lendl B. Quantum Cascade Laser-Based Vibrational Circular Dichroism Augmented by a Balanced Detection Scheme. Anal Chem 2022; 94:10384-10390. [PMID: 35833877 PMCID: PMC9330291 DOI: 10.1021/acs.analchem.2c01269] [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: 11/29/2022]
Abstract
![]()
Vibrational circular dichroism (VCD) constitutes a powerful
technique,
enabling the determination of the absolute configuration of molecules
without the need for specialized reagents. While delivering critical
information, VCD signals commonly are several orders of magnitude
weaker than classical absorbance signals, which so far necessitated
long measurement times to achieve acceptable signal-to-noise ratios
(SNRs) in VCD experiments. We present here an improved setup for the
measurement of VCD in the range between 5.6 and 6.5 μm. Employing
an external cavity quantum cascade laser (EC-QCL) as a high-power
light source, we collected spectra with competitive noise levels in
less than 5 min. The basis for this improvement was a balanced detection
module combined with an optical path catered to VCD measurements.
With the stabilization provided by the two-detector setup, noise originating
from the laser source could be suppressed effectively. Noise level
improvement up to a factor of 4 compared to the classical single detector
EC-QCL-VCD could be reported. Compared to commercial Fourier transform
infrared (FT-IR) instruments, the presented setup offers measurement
time reductions of a factor of at least 6, with comparable noise levels.
The applicability of the setup for qualitative and quantitative VCDs
was proven. With the comparatively high temporal resolution provided,
the monitoring of optically active processes will be possible in future
applications.
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Affiliation(s)
- Daniel R Hermann
- Institute of Chemical Technologies and Analytics, TU Wien, Getreidemarkt 9/164-UPA, 1060 Vienna, Austria
| | - Georg Ramer
- Institute of Chemical Technologies and Analytics, TU Wien, Getreidemarkt 9/164-UPA, 1060 Vienna, Austria
| | | | - Bernhard Lendl
- Institute of Chemical Technologies and Analytics, TU Wien, Getreidemarkt 9/164-UPA, 1060 Vienna, Austria
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20
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Ditler E, Zimmermann T, Kumar C, Luber S. Implementation of Nuclear Velocity Perturbation and Magnetic Field Perturbation Theory in CP2K and Their Application to Vibrational Circular Dichroism. J Chem Theory Comput 2022; 18:2448-2461. [PMID: 35363490 DOI: 10.1021/acs.jctc.2c00006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present the implementation of nuclear velocity perturbation theory (NVPT), using a pioneering combination of atom-centered (velocity-dependent) Gaussian basis functions and plane waves in the CP2K package. The atomic polar tensors (APTs) and atomic axial tensors (AATs) are evaluated in the velocity representation using efficient density functional perturbation theory. The presence of nonlocal pseudopotentials, the representation of potentials on numerical integration grids, and effects arising from the basis functions being centered on the atoms have been considered in the implementation. The Magnetic Field Perturbation Theory (MFPT) using gauge-including atomic orbitals is implemented in the same code and compared to the NVPT. Our implementation is the first to compare both approaches (MFPT and NVPT) in the same code. The implementation has been verified via sum rules and by investigating the gauge origin dependence of the AATs for a set of small molecules, oxirane, and fluoro-oxirane. We also present vibrational circular dichroism spectra that are related to the APTs and AATs, applying both theories.
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Affiliation(s)
- Edward Ditler
- Department of Chemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Tomáš Zimmermann
- Department of Chemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Chandan Kumar
- Department of Chemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Sandra Luber
- Department of Chemistry, University of Zurich, CH-8057 Zurich, Switzerland
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21
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Rizevsky S, Zhaliazka K, Dou T, Matveyenka M, Kurouski D. Characterization of Substrates and Surface-Enhancement in Atomic Force Microscopy Infrared Analysis of Amyloid Aggregates. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2022; 126:4157-4162. [PMID: 35719853 PMCID: PMC9205157 DOI: 10.1021/acs.jpcc.1c09643] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Atomic force microscopy infrared (AFM-IR) spectroscopy is an emerging analytical technique that can be used to probe the structural organization of specimens with nanometer spatial resolution. A growing body of evidence suggests that nanoscale structural analysis of very small (<10 nm) biological objects, such as viruses and amyloid aggregates, requires substrates that must fit strict criteria of low surface roughness and low IR background, simultaneously. In this study, we examine the suitability of a broad range of substrates commonly used in AFM and IR fields, and we determined that silicon, zinc sulfide, and calcium fluoride are the most ideal substrates for nanoscale imaging of amyloid oligomers, protein aggregates that are directly linked to the onset and progression of neurodegenerative diseases. Our data show that these substrates provide the lowest roughness and the lowest background in the 800-1800 cm-1 spectral window from all examined AFM and IR substrates. We also investigate a contribution of surface enhancement in AFM-IR by the direct comparison of signal intensities from oligomers located on silicon and gold-coated silicon surfaces. We found that metallization of such substrates provides a factor of ~7 enhancements to the IR signal and induces an equivalent enhancement of the sample background in the 950-1250 cm-1 spectral region.
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Affiliation(s)
- Stanislav Rizevsky
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States; Department of Biotechnology, Binh Duong University, Thu Dau Mot 820000, Vietnam
| | - Kiryl Zhaliazka
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Tianyi Dou
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Mikhail Matveyenka
- Department of Biochemistry and Biophysics, Texas A&M University College Station, Texas 77843, United States
| | - Dmitry Kurouski
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States; Department of Biomedical Engineering, Texas A&M University, College Station, Texas 77843, United States
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22
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Ren S, Liu C, Xu K, Jiang N, Hu F, Tan PH, Zheng H, Xu X, Shen C, Zhang J. Azimuth-Resolved Circular Dichroism of Metamaterials. J Phys Chem Lett 2022; 13:1697-1704. [PMID: 35156806 DOI: 10.1021/acs.jpclett.1c03944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Chiral optical metamaterials have attracted a great deal of attention due to their intriguing properties with respect to fundamental research and practical applications. For metamaterials with achiral structures, the system composed of metamaterials and obliquely incident light has extrinsic chirality and can produce circular dichroism (CD) effect. However, there have been few studies on the azimuth-dependent CD spectra of achiral metamaterials that have greatly improved our understanding of optical phenomena caused by external chirality. In this work, we experimentally studied the azimuth-dependent CD that originated from the extrinsic chirality of the metamaterials in an asymmetric-U shape and a U-bar-shape gold unit structure, separately. We explain the origin of the CD in the coupling of the macro-electric dipole and magnetic dipole, and the simulation results are in good agreement with the experiment. Our results provide a possible way to build an on-chip azimuth sensor based on azimuth-dependent CD spectra of metamaterials.
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Affiliation(s)
- Shuliang Ren
- State Key Laboratory of Superlattices and Microstructures, Institute of Semiconductors, Chinese Academy of Sciences, Beijing 100083, China
- Center of Materials Sciences and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Changji Liu
- Shaanxi Joint Lab of Graphene, State Key Lab Incubation Base of Photoelectric Technology and Functional Materials, International Collaborative Center on Photoelectric Technology and Nano Functional Materials, Institute of Photonics & Photon-Technology, Northwest University, Xi'an 710069, China
| | - Kaixuan Xu
- State Key Laboratory of Superlattices and Microstructures, Institute of Semiconductors, Chinese Academy of Sciences, Beijing 100083, China
- Center of Materials Sciences and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nai Jiang
- State Key Laboratory of Superlattices and Microstructures, Institute of Semiconductors, Chinese Academy of Sciences, Beijing 100083, China
- Center of Materials Sciences and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fangrong Hu
- Guangxi Colleges and Universities Key Laboratory of Optoelectronic Information Processing, Guilin University of Electronic Technology, Guilin 541004, China
| | - Ping-Heng Tan
- State Key Laboratory of Superlattices and Microstructures, Institute of Semiconductors, Chinese Academy of Sciences, Beijing 100083, China
- Center of Materials Sciences and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Houzhi Zheng
- State Key Laboratory of Superlattices and Microstructures, Institute of Semiconductors, Chinese Academy of Sciences, Beijing 100083, China
- Center of Materials Sciences and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinlong Xu
- Shaanxi Joint Lab of Graphene, State Key Lab Incubation Base of Photoelectric Technology and Functional Materials, International Collaborative Center on Photoelectric Technology and Nano Functional Materials, Institute of Photonics & Photon-Technology, Northwest University, Xi'an 710069, China
| | - Chao Shen
- State Key Laboratory of Superlattices and Microstructures, Institute of Semiconductors, Chinese Academy of Sciences, Beijing 100083, China
- Center of Materials Sciences and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Zhang
- State Key Laboratory of Superlattices and Microstructures, Institute of Semiconductors, Chinese Academy of Sciences, Beijing 100083, China
- Center of Materials Sciences and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Center of Excellence in Topological Quantum Computation, University of Chinese Academy of Sciences, Beijing 101408, China
- Beijing Academy of Quantum Information Sciences, Beijing 100193, China
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23
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Visheratina A, Kumar P, Kotov N. Engineering of inorganic nanostructures with hierarchy of chiral geometries at multiple scales. AIChE J 2021. [DOI: 10.1002/aic.17438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
| | - Prashant Kumar
- Biointerfaces Institute University of Michigan Ann Arbor Michigan USA
| | - Nicholas Kotov
- Biointerfaces Institute University of Michigan Ann Arbor Michigan USA
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24
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Yamagishi H, Sato H, Kawamura I. Vibrational circular dichroism of D-amino acid-containing peptide NdWFamide in the crystal form. Chirality 2021; 33:652-659. [PMID: 34313360 DOI: 10.1002/chir.23343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/02/2021] [Accepted: 07/08/2021] [Indexed: 01/31/2023]
Abstract
Microcrystals of l-Asn-d-Trp-l-Phe-NH2 (NdWFamide), a tripeptide derived from Aplysia kurodai that exhibits invertebrate cardiac activity, were evaluated by vibrational circular dichroism (VCD). The chirality of the tryptophan residue at the second position in NdWFamide was associated with the conformation and biological characteristics. The VCD spectrum of NdWFamide was a mirror image of its enantiomer; however, it was significantly different from that of its diastereomer, NWFamide, which is its precursor. The obtained VCD signals of NdWFamide were in good agreement with the VCD signals that were calculated based on the optimized aggregates of NdWFamide, which formed a helical-like backbone conformation. The evaluation of the VCD results revealed the conformation of NdWFamide in the crystalline state and succeeded in distinguishing its stereoisomers. Therefore, this study demonstrates VCD as a useful method for the structural analysis of naturally occurring d-amino acid-containing peptides.
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Affiliation(s)
- Hiroki Yamagishi
- Graduate School of Engineering Science, Yokohama National University, Yokohama, Japan
| | - Hisako Sato
- Graduate School of Science and Engineering, Ehime University, Matsuyama, Japan
| | - Izuru Kawamura
- Graduate School of Engineering Science, Yokohama National University, Yokohama, Japan
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25
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Gogoi A, Konwer S, Zhuo GY. Polarimetric Measurements of Surface Chirality Based on Linear and Nonlinear Light Scattering. Front Chem 2021; 8:611833. [PMID: 33644001 PMCID: PMC7902787 DOI: 10.3389/fchem.2020.611833] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 12/31/2020] [Indexed: 01/21/2023] Open
Abstract
A molecule, molecular aggregate, or protein that cannot be superimposed on its mirror image presents chirality. Most living systems are organized by chiral building blocks, such as amino acids, peptides, and carbohydrates, and any change in their molecular structure (i.e., handedness or helicity) alters the biochemical and pharmacological functions of the molecules, many of which take place at surfaces. Therefore, studying surface chirogenesis at the nanoscale is fundamentally important and derives various applications. For example, since proteins contain highly ordered secondary structures, the intrinsic chirality can be served as a signature to measure the dynamics of protein adsorption and protein conformational changes at biological surfaces. Furthermore, a better understanding of chiral recognition and separation at bio-nanointerfaces is helpful to standardize chiral drugs and monitor the synthesis of adsorbents with high precision. Thus, exploring the changes in surface chirality with polarized excitations would provide structural and biochemical information of the adsorbed molecules, which has led to the development of label-free and noninvasive measurement tools based on linear and nonlinear optical effects. In this review, the principles and selected applications of linear and nonlinear optical methods for quantifying surface chirality are introduced and compared, aiming to conceptualize new ideas to address critical issues in surface biochemistry.
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Affiliation(s)
- Ankur Gogoi
- Department of Physics, Jagannath Barooah College, Jorhat, India
| | - Surajit Konwer
- Department of Chemistry, Dibrugarh University, Dibrugarh, India
| | - Guan-Yu Zhuo
- Institute of New Drug Development, China Medical University, Taichung, Taiwan.,Integrative Stem Cell Center, China Medical University Hospital, Taichung, Taiwan
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Sakai T, Akagi Y, Suzuki H, Irie M, Nakamura T, Sato H, Kawamura I. Structural Characterization of a Cyclodextrin/l-menthol Inclusion Complex in the Solid-state by Solid-state NMR and Vibrational Circular Dichroism. ANAL SCI 2020; 36:1337-1343. [PMID: 32565526 DOI: 10.2116/analsci.20p120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Hydrophobic and volatile flavor molecules can be encapsulated inside cyclodextrins (CyDs). Inclusion complexes are frequently used in solid or dispersed states in preserved food and cosmetics. In this study, the solid-state structures of spray-dried inclusion complexes of l-menthol in α-CyD and β-CyD were analyzed using 13C solid-state NMR and vibrational circular dichroism (VCD). The NMR signals of l-menthol and CyDs were identified in the physical mixture and the l-menthol inclusion complex of α- and β-CyD. The NMR signal of the isopropyl-methyl group of menthol in the α-CyD inclusion complex exhibited a large low-field shift, which suggested a steric hindrance between menthol and α-CyD. VCD exhibited specific changes in the intensity of bands corresponding to C-C vibrations in α-CyD and O-C stretching vibrations in l-menthol. Our results indicated that l-menthol specifically fitted the narrow space within α-CyD. The combined solid-state NMR and VCD analysis provided structural insights into the flavor inclusion complex in the solid-state.
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Affiliation(s)
| | | | | | - Mitsuki Irie
- Graduate School of Engineering Science, Yokohama National University
| | | | - Hisako Sato
- Graduate School of Science and Engineering, Ehime University
| | - Izuru Kawamura
- Graduate School of Engineering Science, Yokohama National University
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27
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Albano G, Pescitelli G, Di Bari L. Chiroptical Properties in Thin Films of π-Conjugated Systems. Chem Rev 2020; 120:10145-10243. [PMID: 32892619 DOI: 10.1021/acs.chemrev.0c00195] [Citation(s) in RCA: 239] [Impact Index Per Article: 59.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chiral π-conjugated molecules provide new materials with outstanding features for current and perspective applications, especially in the field of optoelectronic devices. In thin films, processes such as charge conduction, light absorption, and emission are governed not only by the structure of the individual molecules but also by their supramolecular structures and intermolecular interactions to a large extent. Electronic circular dichroism, ECD, and its emission counterpart, circularly polarized luminescence, CPL, provide tools for studying aggregated states and the key properties to be sought for designing innovative devices. In this review, we shall present a comprehensive coverage of chiroptical properties measured on thin films of organic π-conjugated molecules. In the first part, we shall discuss some general concepts of ECD, CPL, and other chiroptical spectroscopies, with a focus on their applications to thin film samples. In the following, we will overview the existing literature on chiral π-conjugated systems whose thin films have been characterized by ECD and/or CPL, as well other chiroptical spectroscopies. Special emphasis will be put on systems with large dissymmetry factors (gabs and glum) and on the application of ECD and CPL to derive structural information on aggregated states.
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Affiliation(s)
- Gianluigi Albano
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe Moruzzi 13, 56124 Pisa, Italy
| | - Gennaro Pescitelli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe Moruzzi 13, 56124 Pisa, Italy
| | - Lorenzo Di Bari
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe Moruzzi 13, 56124 Pisa, Italy
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28
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Solid-state vibrational circular dichroism studies on the conformation of an amino acid molecule in crystalline state. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140439. [DOI: 10.1016/j.bbapap.2020.140439] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/18/2020] [Accepted: 04/29/2020] [Indexed: 11/20/2022]
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29
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Delarue Bizzini L, Bürgi T, Mayor M. The Enantiomers of Trinorbornane and Derivatives Thereof. Helv Chim Acta 2020. [DOI: 10.1002/hlca.202000019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
| | - Thomas Bürgi
- Department of Physical Chemistry University of Geneva 30 Quai Ernest-Ansermet CH-1211 Geneva Switzerland
| | - Marcel Mayor
- Department of Chemistry University of Basel St. Johanns-Ring 19 CH-4056 Basel Switzerland
- Institute for Nanotechnology (INT) Karlsruhe Institute of Technology (KIT) P. O. Box 3640 DE-76021 Karlsruhe Germany
- Lehn Institute of Functional Materials School of Chemistry Sun Yat-Sen University Guangzhou 510275 P. R. China
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30
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Keiderling TA. Structure of Condensed Phase Peptides: Insights from Vibrational Circular Dichroism and Raman Optical Activity Techniques. Chem Rev 2020; 120:3381-3419. [DOI: 10.1021/acs.chemrev.9b00636] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Timothy A. Keiderling
- Department of Chemistry, University of Illinois at Chicago 845 West Taylor Street m/c 111, Chicago, Illinois 60607-7061, United States
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31
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Nafie LA. Vibrational optical activity: From discovery and development to future challenges. Chirality 2020; 32:667-692. [DOI: 10.1002/chir.23191] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/21/2020] [Accepted: 01/23/2020] [Indexed: 12/13/2022]
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32
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Koenis MAJ, Visser O, Visscher L, Buma WJ, Nicu VP. GUI Implementation of VCDtools, A Program to Analyze Computed Vibrational Circular Dichroism Spectra. J Chem Inf Model 2020; 60:259-267. [PMID: 31830414 PMCID: PMC6988127 DOI: 10.1021/acs.jcim.9b00956] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
As
computing power increases, vibrational circular dichroism (VCD)
calculations on molecules of larger sizes and complexities become
possible. At the same time, the spectra resulting from these computations
become increasingly more cumbersome to analyze. Here, we describe
the GUI implementation into the Amsterdam Density Functional (ADF)
software package of VCDtools, a toolbox that provides a user-friendly
means to analyze VCD spectra. Key features are the use of the generalized
coupled oscillator analysis methods, as well as an easy visualization
of the atomic electric and magnetic transition dipole moments which
together provide detailed insight in the origin of the VCD intensity.
Using several prototypical examples we demonstrate the functionalities
of the program. In particular, we show how the spectra can be analyzed
to detect differences between theory and experiment arising from large-amplitude
motions or incorrect molecular structures and, most importantly, how
the program can be used to prevent incorrect enantiomeric assignments.
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Affiliation(s)
- Mark A J Koenis
- Van 't Hoff Institute for Molecular Sciences , University of Amsterdam , Science Park 904 , 1098 XH Amsterdam , The Netherlands
| | - Olivier Visser
- Software for Chemisty and Materials , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands
| | - Lucas Visscher
- Amsterdam Center for Multiscale Modeling, Section Theoretical Chemistry, Faculty of Sciences , Vrije Universiteit Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands
| | - Wybren J Buma
- Van 't Hoff Institute for Molecular Sciences , University of Amsterdam , Science Park 904 , 1098 XH Amsterdam , The Netherlands.,Institute for Molecules and Materials, FELIX Laboratory , Radboud University , Toernooiveld 7c , 6525 ED Nijmegen , The Netherlands
| | - Valentin P Nicu
- Department of Environmental Science, Physics, Physical Education and Sport , Lucian Blaga University of Sibiu , loan Ratiu Street, Number 7-9 , 550012 Sibiu , Romania
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33
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Polavarapu PL, Santoro E. Vibrational optical activity for structural characterization of natural products. Nat Prod Rep 2020; 37:1661-1699. [DOI: 10.1039/d0np00025f] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This review presents the recent progress towards elucidating the structures of chiral natural products and applications using vibrational optical activity (VOA) spectroscopy.
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34
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Scriba GK. Chiral recognition in separation sciences. Part I: Polysaccharide and cyclodextrin selectors. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.115639] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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35
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36
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He R, Mai B, Fan J, Jiang Y, Chen G, Guo D, Chen G, Yao X, Gao H, Zhang W. Identification, Quantification, and Stereoselective Degradation of Triazole Fungicide Cyproconazole in Two Matrixes through Chiral Liquid Chromatography-Tandem Mass Spectrometry. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:10782-10790. [PMID: 31490683 DOI: 10.1021/acs.jafc.9b03632] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Systematic investigation of cyproconazole, including absolute stereochemistry, fungicidal activity, quantification in two matrixes, and stereoselective degradation in cucumber, are conducted in this study. By virtue of vibrational circular dichroism (VCD) spectroscopy, absolute configurations of four stereoisomers were identified to be (2R,3R)-(+)-, (2R,3S)-(+)-, (2S,3S)-(-)-, and (2S,3R)-(-)-cyproconazoles. Then four stereoisomers exhibited stereoselective fungicidal activities against Fusarium graminearum Schw and Magnaporthe oryzae, and the order of fungicidal activity was (2S,3S)-(-)-stereoisomer > the stereoisomer mixture > (2S,3R)-(-)-stereoisomer > (2R,3R)-(+)-stereoisomer > (2R,3S)-(+)-stereoisomer. Moreover, chiral liquid chromatography-tandem mass spectrometry was used to identify and quantify cyproconazole stereoisomers in soil and cucumber matrixes. Good linearity (R2 ≥ 0.99) and recoveries (86.79-92.47%, RSD ≤ 3.94%) for them were achieved, individually. Furthermore, stereoselective degradation of four cyproconazole stereoisomers was observed in cucumber and the order of degradation rate was (2R,3R)-(+)-cyproconazole > (2S,3S)-(-)-cyproconazole > (2R,3S)-(+)-cyproconazole > (2S,3R)-(-)-cyproconazole. We envision that such systematic assessments of chiral fungicides at an enantiomeric level would provide valuable information in future studies involving enantioselective physiological, metabolic, and toxicological activities.
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Affiliation(s)
- Rujian He
- School of Chemistry and Environment , South China Normal University , Guangzhou 510006 , P.R. China
| | - Binliang Mai
- School of Chemistry and Environment , South China Normal University , Guangzhou 510006 , P.R. China
| | - Jun Fan
- School of Chemistry and Environment , South China Normal University , Guangzhou 510006 , P.R. China
| | - Ying Jiang
- School of Chemistry and Environment , South China Normal University , Guangzhou 510006 , P.R. China
| | - Gui Chen
- School of Chemistry and Environment , South China Normal University , Guangzhou 510006 , P.R. China
| | - Dong Guo
- Guangzhou Research & Creativity Biotechnology Co. Ltd. , Guangzhou 510663 , P.R. China
| | - Guodong Chen
- College of Pharmacy , Jinan University , Guangzhou 510632 , P.R. China
| | - Xinsheng Yao
- College of Pharmacy , Jinan University , Guangzhou 510632 , P.R. China
| | - Hao Gao
- College of Pharmacy , Jinan University , Guangzhou 510632 , P.R. China
| | - Weiguang Zhang
- School of Chemistry and Environment , South China Normal University , Guangzhou 510006 , P.R. China
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37
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A Comparative Study on Interactions of Antimicrobial Peptides L- and D-phenylseptin with 1,2-dimyristoyl-sn-glycero-3-phosphocholine. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9132601] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
L-phenylseptin (L-Phes) and D-phenylseptin (D-Phes) are amphibian antimicrobial peptides isolated from the skin secretion of Hypsiboas punctatus. In the N-termini, L-Phes and D-Phes contain three consecutive phenylalanine residues, l-Phe-l-Phe-l-Phe and l-Phe-d-Phe-l-Phe, respectively. They are known to exhibit antimicrobial activity against Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa, and Xanthomonas axonopodis pv. Glycines. However, their mechanism of action and the role of the D-amino acid residue have not been elucidated yet. In this study, the interactions of both peptides with 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) were investigated by means of quartz crystal microbalance, circular dichroism, vibrational circular dichroism, 31P solid-state NMR, and molecular dynamics simulation. Both peptides have similar binding constants to the DMPC lipid bilayers, in the order of 106 M−1, and form an α-helix structure in the DMPC lipid bilayers. Both the peptides induce similar changes in the dynamics of DMPC lipids. Thus, in spite of the difference in the conformations caused by the chirality at the N-terminus, the peptides showed similar behavior in the membrane-bound state, experimentally and computationally.
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38
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Kawamura I, Sato H. Solid-state vibrational circular dichroism studies of L- and D-serine. Anal Biochem 2019; 580:14-20. [PMID: 31153871 DOI: 10.1016/j.ab.2019.05.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 04/26/2019] [Accepted: 05/29/2019] [Indexed: 02/06/2023]
Abstract
d-Serine is considered a key endogenous substance involved in several enzymatic reactions in the human body. In this study, solid-state vibrational circular dichroism (VCD) measurements of enantiomeric serine were performed for spectroscopic distinction between d- and l-serine. The mirror-image VCD signals of the isomers in the KBr pellets were observed in the mid-infrared range of 1800-1250 cm-1. The calculated infrared (IR) and VCD spectra for the optimized serine structures were in good agreement with the corresponding observed spectra. In addition, the chemical shift values estimated from the shielding constants of the optimized structure of serine corresponded with the observed values in 13C and 15N solid-state nuclear magnetic resonance spectra, supporting the VCD assignments. Our results suggest the need for further study of VCD to develop a sensitive and high-resolution spectroscopic technique for the detection of d-amino acids.
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Affiliation(s)
- Izuru Kawamura
- Graduate School of Engineering, Yokohama National University, 240-8501, Yokohama, Japan.
| | - Hisako Sato
- (b)Graduate School of Science and Engineering, Ehime University, 790-8577, Matsuyama, Japan.
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39
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Abstract
A β-strand is a component of a β-sheet and is an important structural motif in biomolecules. An α-helix has clear helicity, while chirality of a β-strand had been discussed on the basis of molecular twists generated by forming hydrogen bonds in parallel or non-parallel β-sheets. Herein we describe handedness determination of two-fold helicity in a zig-zag β-strand structure. Left- (M) and right-handedness (P) of the two-fold helicity was defined by application of two concepts: tilt-chirality and multi-point approximation. We call the two-fold helicity in a β-strand, whose handedness has been unrecognized and unclarified, as hidden chirality. Such hidden chirality enables us to clarify precise chiral characteristics of biopolymers. It is also noteworthy that characterization of chirality of high dimensional structures like a β-strand and α-helix, referred to as high dimensional chirality (HDC) in the present study, will contribute to elucidation of the possible origins of chirality and homochirality in nature because such HDC originates from not only asymmetric centers but also conformations in a polypeptide chain.
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40
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Design and structural characterisation of monomeric water-soluble α-helix and β-hairpin peptides: State-of-the-art. Arch Biochem Biophys 2019; 661:149-167. [DOI: 10.1016/j.abb.2018.11.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/06/2018] [Accepted: 11/14/2018] [Indexed: 02/06/2023]
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41
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Li Z, Li L, Zheng Y, Chen C, Sun T. Diagnostic absolute configuration determination of clavulanate potassium: A comprehensive investigation of chiroptical spectroscopies and theoretical calculations. J Pharm Biomed Anal 2018; 160:351-359. [DOI: 10.1016/j.jpba.2018.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 07/12/2018] [Accepted: 08/05/2018] [Indexed: 10/28/2022]
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42
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Yan Y, Fan J, Guo D, Lin Y, Lai Y, Wang T, Gao H, Yao X, Zhang W. Lenalidomide, a blockbuster drug for the treatment of multiple myeloma: Semipreparative separation through supercritical fluid chromatography and vibrational circular dichroism spectroscopy. J Sep Sci 2018; 41:3840-3847. [DOI: 10.1002/jssc.201800519] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 07/16/2018] [Accepted: 08/06/2018] [Indexed: 01/22/2023]
Affiliation(s)
- Yilun Yan
- School of Chemistry and Environment; South China Normal University; Guangzhou P. R. China
| | - Jun Fan
- School of Chemistry and Environment; South China Normal University; Guangzhou P. R. China
| | - Dong Guo
- Guangdong YanJie Pharmatech Co. Ltd; Guangzhou P. R. China
| | - Yuemei Lin
- School of Chemistry and Environment; South China Normal University; Guangzhou P. R. China
| | - Yecai Lai
- Guangdong YanJie Pharmatech Co. Ltd; Guangzhou P. R. China
| | - Tai Wang
- Guangdong YanJie Pharmatech Co. Ltd; Guangzhou P. R. China
| | - Hao Gao
- College of Pharmacy; Jinan University; Guangzhou P. R. China
| | - Xinsheng Yao
- College of Pharmacy; Jinan University; Guangzhou P. R. China
| | - Weiguang Zhang
- School of Chemistry and Environment; South China Normal University; Guangzhou P. R. China
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43
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Jiang Y, Fan J, He R, Guo D, Wang T, Zhang H, Zhang W. High-fast enantioselective determination of prothioconazole in different matrices by supercritical fluid chromatography and vibrational circular dichroism spectroscopic study. Talanta 2018; 187:40-46. [DOI: 10.1016/j.talanta.2018.04.097] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 04/22/2018] [Accepted: 04/29/2018] [Indexed: 10/17/2022]
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44
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Xu W, Ni D, Yu S, Zhang T, Mu W. Insights into hydrolysis versus transfructosylation: Mutagenesis studies of a novel levansucrase from Brenneria sp. EniD312. Int J Biol Macromol 2018; 116:335-345. [DOI: 10.1016/j.ijbiomac.2018.05.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 04/21/2018] [Accepted: 05/04/2018] [Indexed: 10/16/2022]
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45
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Frederix PWJM, Patmanidis I, Marrink SJ. Molecular simulations of self-assembling bio-inspired supramolecular systems and their connection to experiments. Chem Soc Rev 2018; 47:3470-3489. [PMID: 29688238 PMCID: PMC5961611 DOI: 10.1039/c8cs00040a] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Indexed: 01/01/2023]
Abstract
In bionanotechnology, the field of creating functional materials consisting of bio-inspired molecules, the function and shape of a nanostructure only appear through the assembly of many small molecules together. The large number of building blocks required to define a nanostructure combined with the many degrees of freedom in packing small molecules has long precluded molecular simulations, but recent advances in computational hardware as well as software have made classical simulations available to this strongly expanding field. Here, we review the state of the art in simulations of self-assembling bio-inspired supramolecular systems. We will first discuss progress in force fields, simulation protocols and enhanced sampling techniques using recent examples. Secondly, we will focus on efforts to enable the comparison of experimentally accessible observables and computational results. Experimental quantities that can be measured by microscopy, spectroscopy and scattering can be linked to simulation output either directly or indirectly, via quantum mechanical or semi-empirical techniques. Overall, we aim to provide an overview of the various computational approaches to understand not only the molecular architecture of nanostructures, but also the mechanism of their formation.
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Affiliation(s)
- Pim W. J. M. Frederix
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Groningen , The Netherlands . ;
| | - Ilias Patmanidis
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Groningen , The Netherlands . ;
| | - Siewert J. Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Groningen , The Netherlands . ;
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