1
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Erastova V, Evans IR, Glossop WN, Guryel S, Hodgkinson P, Kerr HE, Oganesyan VS, Softley LK, Wickins HM, Wilson MR. Unravelling Guest Dynamics in Crystalline Molecular Organics Using 2H Solid-State NMR and Molecular Dynamics Simulation. J Am Chem Soc 2024; 146:18360-18369. [PMID: 38935813 PMCID: PMC11240262 DOI: 10.1021/jacs.4c03246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/30/2024] [Accepted: 05/30/2024] [Indexed: 06/29/2024]
Abstract
2H solid-state NMR and atomistic molecular dynamics (MD) simulations are used to understand the disorder of guest solvent molecules in two cocrystal solvates of the pharmaceutical furosemide. Traditional approaches to interpreting the NMR data fail to provide a coherent model of molecular behavior and indeed give misleading kinetic data. In contrast, the direct prediction of the NMR properties from MD simulation trajectories allows the NMR data to be correctly interpreted in terms of combined jump-type and libration-type motions. Time-independent component analysis of the MD trajectories provides additional insights, particularly for motions that are invisible to NMR. This allows a coherent picture of the dynamics of molecules restricted in molecular-sized cavities to be determined.
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Affiliation(s)
- Valentina Erastova
- Department
of Chemistry, Durham University, Stockton Road, Durham DH1 3LE, U.K.
- Department
of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster
Road, Edinburgh EH9 3FJ, U.K.
| | - Ivana R. Evans
- Department
of Chemistry, Durham University, Stockton Road, Durham DH1 3LE, U.K.
| | - William N. Glossop
- Department
of Chemistry, Durham University, Stockton Road, Durham DH1 3LE, U.K.
| | - Songül Guryel
- Department
of Chemistry, Durham University, Stockton Road, Durham DH1 3LE, U.K.
| | - Paul Hodgkinson
- Department
of Chemistry, Durham University, Stockton Road, Durham DH1 3LE, U.K.
| | - Hannah E. Kerr
- Department
of Chemistry, Durham University, Stockton Road, Durham DH1 3LE, U.K.
| | | | - Lorna K. Softley
- Department
of Chemistry, Durham University, Stockton Road, Durham DH1 3LE, U.K.
| | - Helen M. Wickins
- Department
of Chemistry, Durham University, Stockton Road, Durham DH1 3LE, U.K.
| | - Mark R. Wilson
- Department
of Chemistry, Durham University, Stockton Road, Durham DH1 3LE, U.K.
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2
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Mitra S, Sharma VK, Ghosh SK. Effects of ionic liquids on biomembranes: A review on recent biophysical studies. Chem Phys Lipids 2023; 256:105336. [PMID: 37586678 DOI: 10.1016/j.chemphyslip.2023.105336] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/05/2023] [Accepted: 08/11/2023] [Indexed: 08/18/2023]
Abstract
Ionic liquids (ILs) have been emerged as a versatile class of compounds that can be easily tuned to achieve desirable properties for various applications. The ability of ILs to interact with biomembranes has attracted significant interest, as they have been shown to modulate membrane properties in ways that may have implications for various biological processes. This review provides an overview of recent studies that have investigated the interaction between ILs and biomembranes. We discuss the effects of ILs on the physical and chemical properties of biomembranes, including changes in membrane fluidity, permeability, and stability. We also explore the mechanisms underlying the interaction of ILs with biomembranes, such as electrostatic interactions, hydrogen bonding, and van der Waals forces. Additionally, we discuss the future prospects of this field.
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Affiliation(s)
- Saheli Mitra
- Department of Physics, School of Natural Sciences, Shiv Nadar Institution of Eminence, NH 91, Tehsil Dadri, G. B. Nagar, Uttar Pradesh 201314, India.
| | - Veerendra K Sharma
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India.
| | - Sajal K Ghosh
- Department of Physics, School of Natural Sciences, Shiv Nadar Institution of Eminence, NH 91, Tehsil Dadri, G. B. Nagar, Uttar Pradesh 201314, India.
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3
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Kaser SJ, Christoff-Tempesta T, Uliassi LD, Cho Y, Ortony JH. Domain-Specific Phase Transitions in a Supramolecular Nanostructure. J Am Chem Soc 2022; 144:17841-17847. [PMID: 36125359 DOI: 10.1021/jacs.2c05908] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Understanding thermal phase behavior within nanomaterials can inform their rational design for medical technologies like drug delivery systems and vaccines, as well as for energy technologies and catalysis. This study resolves thermal phases of discrete domains within a supramolecular aramid amphiphile (AA) nanoribbon. Dynamics are characterized by X-band EPR spectroscopy of spin labels positioned at specific sites through the nanoribbon cross-section. The fitting of the electron paramagnetic resonance (EPR) line shapes reveals distinct conformational dynamics, with fastest dynamics at the surface water layer, intermediate dynamics within the flexible cationic head group domain, and slowest dynamics in the interior aramid domain. Measurement of conformational mobility as a function of temperature reveals first- and second-order phase transitions, with melting transitions observed in the surface and head group domains and a temperature-insensitive crystalline phase in the aramid domain. Arrhenius analysis yields activation energies of diffusion at each site. This work demonstrates that distinct thermal phase behaviors between adjacent nanodomains within a supramolecular nanostructure may be resolved and illustrates the utility of EPR spectroscopy for thermal phase characterization of nanostructures.
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Affiliation(s)
- Samuel J Kaser
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts02139, United States
| | - Ty Christoff-Tempesta
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts02139, United States
| | - Linnaea D Uliassi
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts02139, United States
| | - Yukio Cho
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts02139, United States
| | - Julia H Ortony
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts02139, United States
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4
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Molecular Simulation Approaches to the Study of Thermotropic and Lyotropic Liquid Crystals. CRYSTALS 2022. [DOI: 10.3390/cryst12050685] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Over the last decade, the availability of computer time, together with new algorithms capable of exploiting parallel computer architectures, has opened up many possibilities in molecularly modelling liquid crystalline systems. This perspective article points to recent progress in modelling both thermotropic and lyotropic systems. For thermotropic nematics, the advent of improved molecular force fields can provide predictions for nematic clearing temperatures within a 10 K range. Such studies also provide valuable insights into the structure of more complex phases, where molecular organisation may be challenging to probe experimentally. Developments in coarse-grained models for thermotropics are discussed in the context of understanding the complex interplay of molecular packing, microphase separation and local interactions, and in developing methods for the calculation of material properties for thermotropics. We discuss progress towards the calculation of elastic constants, rotational viscosity coefficients, flexoelectric coefficients and helical twisting powers. The article also covers developments in modelling micelles, conventional lyotropic phases, lyotropic phase diagrams, and chromonic liquid crystals. For the latter, atomistic simulations have been particularly productive in clarifying the nature of the self-assembled aggregates in dilute solution. The development of effective coarse-grained models for chromonics is discussed in detail, including models that have demonstrated the formation of the chromonic N and M phases.
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5
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Byra N, Krukowski S, Sadlo J, Kolodziejski W. Composites Containing Nanohydroxyapatites and a Stable TEMPO Radical: Preparation and Characterization Using Spectrophotometry, EPR and 1H MAS NMR. MATERIALS 2022; 15:ma15062043. [PMID: 35329493 PMCID: PMC8952365 DOI: 10.3390/ma15062043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/05/2022] [Accepted: 03/08/2022] [Indexed: 02/01/2023]
Abstract
Hydroxyapatite is the main constituent of mammalian hard tissues. Basic applications of synthetic hydroxyapatites include bone and dental implantology and drug delivery systems. The study of hydroxyapatite surface properties could give greater insight into the processes of bone mineralization and degradation. Nitroxide radicals are stable radicals that exhibit anticancer and antioxidative properties and are often used as spin probes to study the dynamics of complex biological systems. In this work, we attempted to adsorb the stable 2,2,6,6-tetramethylpiperidine-1-oxyl radical (TEMPO) on two hydroxyapatites (HAs) differing in specific surface area and the degree of hydration. The adsorption was carried out from cyclohexane, 1-chlorobutane and water. The solutions after adsorption were studied spectrophotometrically, while the obtained composites were characterized via NMR and EPR spectroscopy. The results show that it is possible to reproducibly obtain fairly stable composites, where the main factors influencing the adsorbed amount of the radical are solvent polarity and specific surface area of hydroxyapatite. The Langmuir isotherm was determined to be the most suitable adsorption model. The analysis of EPR and NMR spectra allowed us to determine the distribution of the TEMPO molecules on the hydroxyapatite surface, as well as a probable adsorption mechanism. The HA/TEMPO composites could potentially be used to study certain properties of hydroxyapatite surfaces with EPR spectroscopy. They could also be used as fillers after hard tissue surgery, as well as metal-free MRI contrasts.
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Affiliation(s)
- Natalia Byra
- Department of Analytical Chemistry, Medical University of Warsaw, Banacha 1, 02-097 Warsaw, Poland; (S.K.); (W.K.)
- Correspondence:
| | - Sylwester Krukowski
- Department of Analytical Chemistry, Medical University of Warsaw, Banacha 1, 02-097 Warsaw, Poland; (S.K.); (W.K.)
| | - Jaroslaw Sadlo
- Institute of Nuclear Chemistry and Technology, Dorodna 16, 03-195 Warsaw, Poland;
| | - Waclaw Kolodziejski
- Department of Analytical Chemistry, Medical University of Warsaw, Banacha 1, 02-097 Warsaw, Poland; (S.K.); (W.K.)
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6
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Del Frate G, Macchiagodena M, Akhunzada MJ, D'Autilia F, Catte A, Bhattacharjee N, Barone V, Cardarelli F, Brancato G. Probing Liquid-Ordered and Disordered Phases in Lipid Model Membranes: A Combined Theoretical and Spectroscopic Study of a Fluorescent Molecular Rotor. J Phys Chem B 2022; 126:480-491. [PMID: 35001625 PMCID: PMC8785181 DOI: 10.1021/acs.jpcb.1c08324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
An integrated theoretical/experimental
strategy has been applied
to the study of environmental effects on the spectroscopic parameters
of 4-(diphenylamino)phtalonitrile (DPAP), a fluorescent molecular
rotor. The computational part starts from the development of an effective
force field for the first excited electronic state of DPAP and proceeds
through molecular dynamics simulations in solvents of different polarities
toward the evaluation of Stokes shifts by quantum mechanics/molecular
mechanics (QM/MM) approaches. The trends of the computed results closely
parallel the available experimental results thus giving confidence
to the interpretation of new experimental studies of the photophysics
of DPAP in lipid bilayers. In this context, results show unambiguously
that both flexible dihedral angles and global rotations are significantly
retarded in a cholesterol/DPPC lipid matrix with respect to the DOPC
matrix, thus confirming the sensitivity of DPAP to probe different
environments and, therefore, its applicability as a probe for detecting
different structures and levels of plasma membrane organization.
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Affiliation(s)
| | | | | | - Francesca D'Autilia
- Center for Nanotechnology Innovation@NEST (CNI@NEST), Piazza San Silvestro 12, I-56127 Pisa, Italy
| | - Andrea Catte
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | | | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Istituto Nazionale di Fisica Nucleare(INFN), Largo Pontecorvo 3, I-56 127 Pisa, Italy.,Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase (CSGI), Via della Lastruccia 3, I-50 019 Sesto Fiorentino, Florence, Italy
| | | | - Giuseppe Brancato
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Istituto Nazionale di Fisica Nucleare(INFN), Largo Pontecorvo 3, I-56 127 Pisa, Italy.,Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase (CSGI), Via della Lastruccia 3, I-50 019 Sesto Fiorentino, Florence, Italy
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Golysheva EA, Dzuba SA. Lipid chain mobility and packing in DOPC bilayers at cryogenic temperatures. Chem Phys Lipids 2019; 226:104817. [PMID: 31525380 DOI: 10.1016/j.chemphyslip.2019.104817] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/07/2019] [Accepted: 09/03/2019] [Indexed: 11/30/2022]
Abstract
Low-temperature molecular mobility and packing in biological tissues are important for their survival upon cryopreservation. Electron paramagnetic resonance (EPR) in its pulsed version of electron spin echo (ESE) allows studying stochastic librations of spin-labeled molecules, the type of motion which dominates at low temperatures. These librations are characterized by the parameter <α2>τc where <α2> is the mean squared angular amplitude and τc is the correlation time for the motion. This parameter is known to be larger for higher temperature and for looser intermolecular structure. In this work, ESE data for the bilayers comprised of doubly-unsaturated DOPC (dioleoyl-glycero-phosphocholine) lipids and mono-unsaturated POPC (palmitoyl-oleoyl-glycero-phosphocholine) lipids with spin-labeled stearic acids added were obtained in the temperature range between 80 and 210 K; the results were compared also with the previously obtained data for fully-saturated DPPC (dipalmitoyl-glycero-phosphocholine) lipid bilayers [J. Phys. Chem. B2014, 118, 12,478-12,485; Appl. Magn. Reson. 2018, 49, 1369-1383]. It turned out that for DOPC bilayers the <α2>τc values are of intermediate magnitude between those for POPC and DPPC bilayers, which implies an intermediate density of lipid packing. A possible explanation of this result could be rearrangement at cryogenic temperatures of the DOPC lipid tails, with their terminal segments folding cooperatively. This interpretation is also in agreement with the known thermodynamic properties of gel-fluid transition for DOPC bilayer.
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Affiliation(s)
- Elena A Golysheva
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk, 630090, Russian Federation; Department of Physics, Novosibirsk State University, Novosibirsk, 630090, Russian Federation
| | - Sergei A Dzuba
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk, 630090, Russian Federation; Department of Physics, Novosibirsk State University, Novosibirsk, 630090, Russian Federation.
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8
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Catte A, White GF, Wilson MR, Oganesyan VS. Direct Prediction of EPR Spectra from Lipid Bilayers: Understanding Structure and Dynamics in Biological Membranes. Chemphyschem 2018; 19:2183-2193. [PMID: 29858887 PMCID: PMC6175124 DOI: 10.1002/cphc.201800386] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Indexed: 11/16/2022]
Abstract
Of the many biophysical techniques now being brought to bear on studies of membranes, electron paramagnetic resonance (EPR) of nitroxide spin probes was the first to provide information about both mobility and ordering in lipid membranes. Here, we report the first prediction of variable temperature EPR spectra of model lipid bilayers in the presence and absence of cholesterol from the results of large scale fully atomistic molecular dynamics (MD) simulations. Three types of structurally different spin probes were employed in order to study different parts of the bilayer. Our results demonstrate very good agreement with experiment and thus confirm the accuracy of the latest lipid force fields. The atomic resolution of the simulations allows the interpretation of the molecular motions and interactions in terms of their impact on the sensitive EPR line shapes. Direct versus indirect effects of cholesterol on the dynamics of spin probes are analysed. Given the complexity of structural organisation in lipid bilayers, the advantage of using a combined MD-EPR simulation approach is two-fold. Firstly, prediction of EPR line shapes directly from MD trajectories of actual phospholipid structures allows unambiguous interpretation of EPR spectra of biological membranes in terms of complex motions. Secondly, such an approach provides an ultimate test bed for the up-to-date MD simulation models employed in the studies of biological membranes, an area that currently attracts great attention.
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Affiliation(s)
- Andrea Catte
- School of ChemistryUniversity of East AngliaNorwichNR4 7TJUK
| | - Gaye F. White
- School of ChemistryUniversity of East AngliaNorwichNR4 7TJUK
| | - Mark R. Wilson
- Department of ChemistryDurham University, Lower MountjoySouth RoadDurhamDH1 3 LEUK
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