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Wang Y, Li YX, Cseh L, Chen YX, Yang SG, Zeng X, Liu F, Hu W, Ungar G. Enantiomers Self-Sort into Separate Counter-Twisted Ribbons of the Fddd Liquid Crystal─Antiferrochirality and Parachirality. J Am Chem Soc 2023; 145:17443-17460. [PMID: 37523689 PMCID: PMC10416214 DOI: 10.1021/jacs.3c06164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Indexed: 08/02/2023]
Abstract
The recently discovered orthorhombic liquid crystal (LC) phase of symmetry Fddd is proving to be widespread. In this work, a chiral hydroxybutyrate linkage is inserted into the molecular core of hexacatenar rodlike compounds, containing a thienylfluorenone fluorophore. In addition to more usual tools, the methods used include grazing-incidence X-ray scattering, modulated differential scanning calorimetry (DSC), flash DSC with rates up to 6000 K/s, and chiro-optical spectroscopies using Mueller matrix method, plus conformational mapping. Although pure R and S enantiomers form only a strongly chiral hexagonal columnar LC phase (Colh*), the racemic mixture forms a highly ordered Fddd phase with 4 right- and 4 left-handed twisted ribbon-like columns traversing its large unit cell. In that structure, the two enantiomers locally deracemize and self-sort into the columns of their preferred chirality. The twisted ribbons in Fddd, with a 7.54 nm pitch, consist of stacked rafts, each containing ∼2 side-by-side molecules, the successive rafts rotated by 17°. In contrast, an analogous achiral compound forms only the columnar phase. The multiple methods used gave a comprehensive picture and helped in-depth understanding not only of the Fddd phase but also of the "parachiral" Colh* in pure enantiomers with irregular helicity, whose chirality is compared to the magnetization of a paramagnet in a field. Unusual short-range ordering effects are also described. An explanation of these phenomena is proposed based on conformational analysis. Surprisingly, the isotropic-columnar transition is extremely fast, completing within ∼20 ms. A clear effect of phase on UV-vis absorption and emission is observed.
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Affiliation(s)
- Yan Wang
- Shaanxi
International Research Centre for Soft Matter, State Key Laboratory
for Mechanical Behaviour of Materials, Xi’an
Jiaotong University, Xi’an 710049, China
| | - Ya-Xin Li
- School
of Chemistry and Chemical Engineering, Henan
University of Technology, Zhengzhou 450001, China
| | - Liliana Cseh
- Romanian
Academy, Coriolan Dragulescu Institute of Chemistry, Timisoara 300223, Romania
| | - Yong-Xuan Chen
- State
Key Laboratory of Coordinate Chemistry, School of Chemistry and Chemical
Engineering, Nanjing University, Nanjing 210093, China
| | - Shu-Gui Yang
- Shaanxi
International Research Centre for Soft Matter, State Key Laboratory
for Mechanical Behaviour of Materials, Xi’an
Jiaotong University, Xi’an 710049, China
| | - Xiangbing Zeng
- Department
of Materials Science and Engineering, University
of Sheffield, Sheffield S1 3JD, U.K.
| | - Feng Liu
- Shaanxi
International Research Centre for Soft Matter, State Key Laboratory
for Mechanical Behaviour of Materials, Xi’an
Jiaotong University, Xi’an 710049, China
| | - Wenbing Hu
- State
Key Laboratory of Coordinate Chemistry, School of Chemistry and Chemical
Engineering, Nanjing University, Nanjing 210093, China
| | - Goran Ungar
- Shaanxi
International Research Centre for Soft Matter, State Key Laboratory
for Mechanical Behaviour of Materials, Xi’an
Jiaotong University, Xi’an 710049, China
- Department
of Materials Science and Engineering, University
of Sheffield, Sheffield S1 3JD, U.K.
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Li YX, Gao HF, Zhang RB, Gabana K, Chang Q, Gehring GA, Cheng XH, Zeng XB, Ungar G. A case of antiferrochirality in a liquid crystal phase of counter-rotating staircases. Nat Commun 2022; 13:384. [PMID: 35046396 PMCID: PMC8770800 DOI: 10.1038/s41467-022-28024-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 12/16/2021] [Indexed: 11/25/2022] Open
Abstract
Helical structures continue to inspire, prompted by examples such as DNA double-helix and alpha-helix in proteins. Most synthetic polymers also crystallize as helices, which relieves steric clashes by twisting, while keeping the molecules straight for their ordered packing. In columnar liquid crystals, which often display useful optoelectronic properties, overall helical chirality can be induced by inclusion of chiral chemical groups or dopants; these bias molecular twist to either left or right, analogous to a magnetic field aligning the spins in a paramagnet. In this work, however, we show that liquid-crystalline columns with long-range helical order can form by spontaneous self-assembly of straight- or bent-rod molecules without inclusion of any chiral moiety. A complex lattice with Fddd symmetry and 8 columns per unit cell (4 right-, 4 left-handed) characterizes this "antiferrochiral" structure. In selected compounds it allows close packing of their fluorescent groups reducing their bandgap and giving them promising light-emitting properties.
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Affiliation(s)
- Ya-Xin Li
- State Key Laboratory for Mechanical Behaviour of Materials, Shaanxi International Research Centre for Soft Matter, Xi'an Jiaotong University, 710049, Xi'an, P. R. China
- Department of Materials Science and Engineering, University of Sheffield, Sheffield, S1 3JD, UK
- School of Chemistry and Chemical Engineering, Henan University of Technology, 450001, Zhengzhou, P. R. China
| | - Hong-Fei Gao
- Key Laboratory of Medicinal Chemistry from Natural Resources, Ministry of Education, Yunnan University, Kunming, P. R. China
| | - Rui-Bin Zhang
- Department of Materials Science and Engineering, University of Sheffield, Sheffield, S1 3JD, UK
| | - Kutlwano Gabana
- Department of Physics and Astronomy, University of Sheffield, Sheffield, E1 2C, UK
| | - Qing Chang
- Key Laboratory of Medicinal Chemistry from Natural Resources, Ministry of Education, Yunnan University, Kunming, P. R. China
| | - Gillian A Gehring
- Department of Physics and Astronomy, University of Sheffield, Sheffield, E1 2C, UK
| | - Xiao-Hong Cheng
- Key Laboratory of Medicinal Chemistry from Natural Resources, Ministry of Education, Yunnan University, Kunming, P. R. China.
- School of Chemistry and Chemical Engineering, Yangtze Normal University, Fuling, P. R. China.
| | - Xiang-Bing Zeng
- Department of Materials Science and Engineering, University of Sheffield, Sheffield, S1 3JD, UK.
| | - Goran Ungar
- State Key Laboratory for Mechanical Behaviour of Materials, Shaanxi International Research Centre for Soft Matter, Xi'an Jiaotong University, 710049, Xi'an, P. R. China.
- Department of Materials Science and Engineering, University of Sheffield, Sheffield, S1 3JD, UK.
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Kuzmanic A, Pannu NS, Zagrovic B. X-ray refinement significantly underestimates the level of microscopic heterogeneity in biomolecular crystals. Nat Commun 2015; 5:3220. [PMID: 24504120 PMCID: PMC3926004 DOI: 10.1038/ncomms4220] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 01/07/2014] [Indexed: 11/09/2022] Open
Abstract
Biomolecular X-ray structures typically provide a static, time- and ensemble-averaged view of molecular ensembles in crystals. In the absence of rigid-body motions and lattice defects, B-factors are thought to accurately reflect the structural heterogeneity of such ensembles. In order to study the effects of averaging on B-factors, we employ molecular dynamics simulations to controllably manipulate microscopic heterogeneity of a crystal containing 216 copies of villin headpiece. Using average structure factors derived from simulation, we analyse how well this heterogeneity is captured by high-resolution molecular-replacement-based model refinement. We find that both isotropic and anisotropic refined B-factors often significantly deviate from their actual values known from simulation: even at high 1.0 Å resolution and Rfree of 5.9%, B-factors of some well-resolved atoms underestimate their actual values even sixfold. Our results suggest that conformational averaging and inadequate treatment of correlated motion considerably influence estimation of microscopic heterogeneity via B-factors, and invite caution in their interpretation.
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Affiliation(s)
- Antonija Kuzmanic
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Navraj S Pannu
- Biophysical Structural Chemistry, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
| | - Bojan Zagrovic
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
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Tschierske C, Ungar G. Mirror Symmetry Breaking by Chirality Synchronisation in Liquids and Liquid Crystals of Achiral Molecules. Chemphyschem 2015; 17:9-26. [DOI: 10.1002/cphc.201500601] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Indexed: 01/05/2023]
Affiliation(s)
- Carsten Tschierske
- Institute of Chemistry, Organic Chemistry; Martin Luther University Halle-Wittenberg; Kurt-Mothes Str. 2 06120 Halle/Saale Germany
| | - Goran Ungar
- Department of Physics; Zhejiang Sci-Tech University; Xiasha College Park 310018 Hangzhou China
- Department of Materials Science and Engineering; University of Sheffield; Sheffield S1 3JD Sheffield UK
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Kruschel D, Zagrovic B. Conformational averaging in structural biology: issues, challenges and computational solutions. MOLECULAR BIOSYSTEMS 2009; 5:1606-16. [PMID: 20023721 DOI: 10.1039/b917186j] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Most experimental methods in structural biology provide time- and ensemble-averaged signals and, consequently, molecular structures based on such signals often exhibit only idealized, average features. Second, most experimental signals are only indirectly related to real, molecular geometries, and solving a structure typically involves a complicated procedure, which may not always result in a unique solution. To what extent do such conformationally-averaged, non-linear experimental signals and structural models derived from them accurately represent the underlying microscopic reality? Are there some structural motifs that are actually artificially more likely to be "seen" in an experiment simply due to the averaging artifact? Finally, what are the practical consequences of ignoring the averaging effects when it comes to functional and mechanistic implications that we try to glean from experimentally-based structural models? In this review, we critically address the work that has been aimed at studying such questions. We summarize the details of experimental methods typically used in structural biology (most notably nuclear magnetic resonance, X-ray crystallography and different types of spectroscopy), discuss their individual susceptibility to conformational (motional) averaging, and review several theoretical approaches, most importantly molecular dynamics simulations that are increasingly being used to aid experimentalists in interpreting structural biology experiments.
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Affiliation(s)
- Daniela Kruschel
- Laboratory of Computational Biophysics, Mediterranean Institute for Life Sciences, Mestrovicevo setaliste bb, Split, HR-21000, Croatia
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Müller CL, Sbalzarini IF, van Gunsteren WF, Zagrović B, Hünenberger PH. In the eye of the beholder: Inhomogeneous distribution of high-resolution shapes within the random-walk ensemble. J Chem Phys 2009; 130:214904. [PMID: 19508095 DOI: 10.1063/1.3140090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The concept of high-resolution shapes (also referred to as folds or states, depending on the context) of a polymer chain plays a central role in polymer science, structural biology, bioinformatics, and biopolymer dynamics. However, although the idea of shape is intuitively very useful, there is no unambiguous mathematical definition for this concept. In the present work, the distributions of high-resolution shapes within the ideal random-walk ensembles with N=3,...,6 beads (or up to N=10 for some properties) are investigated using a systematic (grid-based) approach based on a simple working definition of shapes relying on the root-mean-square atomic positional deviation as a metric (i.e., to define the distance between pairs of structures) and a single cutoff criterion for the shape assignment. Although the random-walk ensemble appears to represent the paramount of homogeneity and randomness, this analysis reveals that the distribution of shapes within this ensemble, i.e., in the total absence of interatomic interactions characteristic of a specific polymer (beyond the generic connectivity constraint), is significantly inhomogeneous. In particular, a specific (densest) shape occurs with a local probability that is 1.28, 1.79, 2.94, and 10.05 times (N=3,...,6) higher than the corresponding average over all possible shapes (these results can tentatively be extrapolated to a factor as large as about 10(28) for N=100). The qualitative results of this analysis lead to a few rather counterintuitive suggestions, namely, that, e.g., (i) a fold classification analysis applied to the random-walk ensemble would lead to the identification of random-walk "folds;" (ii) a clustering analysis applied to the random-walk ensemble would also lead to the identification random-walk "states" and associated relative free energies; and (iii) a random-walk ensemble of polymer chains could lead to well-defined diffraction patterns in hypothetical fiber or crystal diffraction experiments. The inhomogeneous nature of the shape probability distribution identified here for random walks may represent a significant underlying baseline effect in the analysis of real polymer chain ensembles (i.e., in the presence of specific interatomic interactions). As a consequence, a part of what is called a polymer shape may actually reside just "in the eye of the beholder" rather than in the nature of the interactions between the constituting atoms, and the corresponding observation-related bias should be taken into account when drawing conclusions from shape analyses as applied to real structural ensembles.
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Affiliation(s)
- Christian L Müller
- Institute of Computational Science and Swiss Institute of Bioinformatics, ETH Zürich, Switzerland
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