1
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Naranjo C, Doncel-Giménez A, Gómez R, Aragó J, Ortí E, Sánchez L. Solvent-dependent self-assembly of N-annulated perylene diimides. From dimers to supramolecular polymers. Chem Sci 2023; 14:9900-9909. [PMID: 37736635 PMCID: PMC10510848 DOI: 10.1039/d3sc03372d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 08/28/2023] [Indexed: 09/23/2023] Open
Abstract
The synthesis and self-assembling features of the N-annulated perylene diimide (NPBI) 1 in different solvents are reported. Compound 1 possesses two chiral linkers, derived from (S)-(+)-alaninol, that connect the central aromatic NPBI segment and the peripheral trialkoxybenzamide units. The Ala-based linker has been demonstrated to strongly favor the formation of intramolecularly H-bonded seven-membered pseudocycles. NPBI 1 shows a strong tendency to self-assemble even in a good solvent like CHCl3 and the formation of chiral dimers is detected in this good solvent. Both experimental techniques and theoretical calculations reveal that the intramolecular H-bonded pseudocycles are very robust and the formation of chiral dimers is driven by the π-stacking of two units of the NPBI core. Unexpectedly, an efficient transfer of the asymmetry of the point chirality at the linker to the aromatic moiety is observed in the molecularly dissolved state. Changing the solvent to more apolar methylcyclohexane modifies the self-assembly process and the formation of chiral supramolecular polymers is detected. The supramolecular polymerization of 1 is demonstrated to follow an isodesmic mechanism unlike previous referable systems. In the formation of the supramolecular polymers of 1, the combination of experimental and computational data indicates that the H-bonded pseudocycles are also present in the aggregated state and the rope-like, columnar aggregates formed by the self-assembly of 1 rely on the π-stacking of the NPBI backbones.
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Affiliation(s)
- Cristina Naranjo
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid 28040 Madrid Spain
| | - Azahara Doncel-Giménez
- Instituto de Ciencia Molecular (ICMol), Universidad de Valencia C/Catedrático José Beltrán, 2 46980 Paterna Spain
| | - Rafael Gómez
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid 28040 Madrid Spain
| | - Juan Aragó
- Instituto de Ciencia Molecular (ICMol), Universidad de Valencia C/Catedrático José Beltrán, 2 46980 Paterna Spain
| | - Enrique Ortí
- Instituto de Ciencia Molecular (ICMol), Universidad de Valencia C/Catedrático José Beltrán, 2 46980 Paterna Spain
| | - Luis Sánchez
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid 28040 Madrid Spain
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2
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Serec K, Babić SD, Tomić S. Magnesium ions reversibly bind to DNA double stranded helix in thin films. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 268:120663. [PMID: 34875504 DOI: 10.1016/j.saa.2021.120663] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 11/08/2021] [Accepted: 11/23/2021] [Indexed: 06/13/2023]
Abstract
Effects of magnesium (Mg2+) ions on the stability and structural properties of double-stranded DNA are vitally important for DNA folding and functional behavior. Complementing our previous study on highly hydrated thin films of DNA with sodium counterions, with no buffer (pH ≈ 6) and surrounded with Mg2+ cations, here we use Fourier transform infrared spectroscopy and band shape analysis to explore in detail the vibrational signatures of DNA-magnesium interaction in the case when DNA charges are neutralized solely by Mg2+ cations, hereafter called MgDNA. Ion atmosphere has been controlled by the magnesium to phosphate molar concentration ratio r which varied between 0.0067 and 10. For r = 0 we find that spectral features in the base region remain similar as in DNA, whereas changes in the backbone region indicate that the B conformation becomes fully stabilized. With increasing r a pronounced structural reshaping occurs in the phosphate backbone region indicating a blue shift of the asymmetric band, while the symmetric band does not show any displacement in frequency. The band shape analysis of overlapping peaks in the respective phosphate regions demonstrates that the number of constituent modes as well as their positions in frequency do not change, whereas their intensities and bandwidths display disparate changes. The results reflect a variety of local environments at the DNA backbone due to a heterogeneous ion atmosphere with randomly distributed magnesium ions and local patterns of hydrogen bonds which change with increasing r. Remarkably, after crowded r = 10 ion atmosphere is depleted, Mg induced spectral changes vanish and structural features of MgDNA (r ≈ 0) are fully restored. Overall results strongly suggest that in MgDNA on highly hydrated thin films the hydrogen-base pairing remains preserved and that Mg2+ ions, similar to sodium ions, retain their mobility and interact with double helix via water-mediated electrostatic forces.
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Affiliation(s)
- Kristina Serec
- Department of Physics and Biophysics, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia; Centre of Excellence in Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, 10000 Zagreb, Croatia.
| | - Sanja Dolanski Babić
- Department of Physics and Biophysics, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia; Centre of Excellence in Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, 10000 Zagreb, Croatia
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3
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Fingerhut BP, Schauss J, Kundu A, Elsaesser T. Contact pairs of RNA with magnesium ions-electrostatics beyond the Poisson-Boltzmann equation. Biophys J 2021; 120:5322-5332. [PMID: 34715079 PMCID: PMC8715182 DOI: 10.1016/j.bpj.2021.10.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/24/2021] [Accepted: 10/22/2021] [Indexed: 11/18/2022] Open
Abstract
The electrostatic interaction of RNA with its aqueous environment is most relevant for defining macromolecular structure and biological function. The attractive interaction of phosphate groups in the RNA backbone with ions in the water environment leads to the accumulation of positively charged ions in the first few hydration layers around RNA. Electrostatics of this ion atmosphere and the resulting ion concentration profiles have been described by solutions of the nonlinear Poisson-Boltzmann equation and atomistic molecular dynamics (MD) simulations. Much less is known on contact pairs of RNA phosphate groups with ions at the RNA surface, regarding their abundance, molecular geometry, and role in defining RNA structure. Here, we present a combined theoretical and experimental study of interactions of a short RNA duplex with magnesium (Mg2+) ions. MD simulations covering a microsecond time range give detailed hydration geometries as well as electrostatics and spatial arrangements of phosphate-Mg2+ pairs, including both pairs in direct contact and separated by a single water layer. The theoretical predictions are benchmarked by linear infrared absorption and nonlinear two-dimensional infrared spectra of the asymmetric phosphate stretch vibration which probes both local interaction geometries and electric fields. Contact pairs of phosphate groups and Mg2+ ions are identified via their impact on the vibrational frequency position and line shape. A quantitative analysis of infrared spectra for a range of Mg2+-excess concentrations and comparison with fluorescence titration measurements shows that on average 20-30% of the Mg2+ ions interacting with the RNA duplex form contact pairs. The experimental and MD results are in good agreement. In contrast, calculations based on the nonlinear Poisson-Boltzmann equation fail in describing the ion arrangement, molecular electrostatic potential, and local electric field strengths correctly. Our results underline the importance of local electric field mapping and molecular-level simulations to correctly account for the electrostatics at the RNA-water interface.
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4
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Fingerhut BP. The mutual interactions of RNA, counterions and water - quantifying the electrostatics at the phosphate-water interface. Chem Commun (Camb) 2021; 57:12880-12897. [PMID: 34816825 PMCID: PMC8640580 DOI: 10.1039/d1cc05367a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/01/2021] [Indexed: 11/25/2022]
Abstract
The structure and dynamics of polyanionic biomolecules, like RNA, are decisively determined by their electric interactions with the water molecules and the counterions in the environment. The solvation dynamics of the biomolecules involves a subtle balance of non-covalent and many-body interactions with structural fluctuations due to thermal motion occurring in a femto- to subnanosecond time range. This complex fluctuating many particle scenario is crucial in defining the properties of biological interfaces with far reaching significance for the folding of RNA structures and for facilitating RNA-protein interactions. Given the inherent complexity, suited model systems, carefully calibrated and benchmarked by experiments, are required to quantify the relevant interactions of RNA with the aqueous environment. In this feature article we summarize our recent progress in the understanding of the electrostatics at the biological interface of double stranded RNA (dsRNA) and transfer RNA (tRNA). Dimethyl phosphate (DMP) is introduced as a viable and rigorously accessible model system allowing the interaction strength with water molecules and counterions, their relevant fluctuation timescales and the spatial reach of interactions to be established. We find strong (up to ≈90 MV cm-1) interfacial electric fields with fluctuations extending up to ≈20 THz and demonstrate how the asymmetric stretching vibration νAS(PO2)- of the polarizable phosphate group can serve as the most sensitive probe for interfacial interactions, establishing a rigorous link between simulations and experiment. The approach allows for the direct interfacial observation of interactions of biologically relevant Mg2+ counterions with phosphate groups in contact pair geometries via the rise of a new absorption band imposed by exchange repulsion interactions at short interatomic distances. The systematic extension to RNA provides microscopic insights into the changes of the hydration structure that accompany the temperature induced melting of the dsRNA double helix and quantify the ionic interactions in the folded tRNA. The results show that pairs of negatively charged phosphate groups and Mg2+ ions represent a key structural feature of RNA embedded in water. They highlight the importance of binding motifs made of contact pairs in the electrostatic stabilization of RNA structures that have a strong impact on the surface potential and enable the fine tuning of the local electrostatic properties which are expected to be relevant for mediating the interactions between biomolecules.
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5
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Singh AK, Wen C, Cheng S, Vinh NQ. Long-range DNA-water interactions. Biophys J 2021; 120:4966-4979. [PMID: 34687717 DOI: 10.1016/j.bpj.2021.10.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 09/14/2021] [Accepted: 10/18/2021] [Indexed: 11/18/2022] Open
Abstract
DNA functions only in aqueous environments and adopts different conformations depending on the hydration level. The dynamics of hydration water and hydrated DNA leads to rotating and oscillating dipoles that, in turn, give rise to a strong megahertz to terahertz absorption. Investigating the impact of hydration on DNA dynamics and the spectral features of water molecules influenced by DNA, however, is extremely challenging because of the strong absorption of water in the megahertz to terahertz frequency range. In response, we have employed a high-precision megahertz to terahertz dielectric spectrometer, assisted by molecular dynamics simulations, to investigate the dynamics of water molecules within the hydration shells of DNA as well as the collective vibrational motions of hydrated DNA, which are vital to DNA conformation and functionality. Our results reveal that the dynamics of water molecules in a DNA solution is heterogeneous, exhibiting a hierarchy of four distinct relaxation times ranging from ∼8 ps to 1 ns, and the hydration structure of a DNA chain can extend to as far as ∼18 Å from its surface. The low-frequency collective vibrational modes of hydrated DNA have been identified and found to be sensitive to environmental conditions including temperature and hydration level. The results reveal critical information on hydrated DNA dynamics and DNA-water interfaces, which impact the biochemical functions and reactivity of DNA.
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Affiliation(s)
- Abhishek K Singh
- Department of Physics and Center for Soft Matter and Biological Physics, Blacksburg, Virginia
| | - Chengyuan Wen
- Department of Physics and Center for Soft Matter and Biological Physics, Blacksburg, Virginia
| | - Shengfeng Cheng
- Department of Physics and Center for Soft Matter and Biological Physics, Blacksburg, Virginia; Macromolecules Innovation Institute, Blacksburg, Virginia; Department of Mechanical Engineering, Virginia Tech, Blacksburg, Virginia
| | - Nguyen Q Vinh
- Department of Physics and Center for Soft Matter and Biological Physics, Blacksburg, Virginia; Macromolecules Innovation Institute, Blacksburg, Virginia; Department of Mechanical Engineering, Virginia Tech, Blacksburg, Virginia.
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6
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Gera R, Bakker HJ, Franklin-Mergarejo R, Morzan UN, Falciani G, Bergamasco L, Versluis J, Sen I, Dante S, Chiavazzo E, Hassanali AA. Emergence of Electric Fields at the Water-C12E6 Surfactant Interface. J Am Chem Soc 2021; 143:15103-15112. [PMID: 34498857 DOI: 10.1021/jacs.1c05112] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We study the properties of the interface of water and the surfactant hexaethylene glycol monododecyl ether (C12E6) with a combination of heterodyne-detected vibrational sum frequency generation (HD-VSFG), Kelvin-probe measurements, and molecular dynamics (MD) simulations. We observe that the addition of the hydrogen-bonding surfactant C12E6, close to the critical micelle concentration (CMC), induces a drastic enhancement in the hydrogen bond strength of the water molecules close to the interface, as well as a flip in their net orientation. The mutual orientation of the water and C12E6 molecules leads to the emergence of a broad (∼3 nm) interface with a large electric field of ∼1 V/nm, as evidenced by the Kelvin-probe measurements and MD simulations. Our findings may open the door for the design of novel electric-field-tuned catalytic and light-harvesting systems anchored at the water-surfactant-air interface.
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Affiliation(s)
- Rahul Gera
- AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Huib J Bakker
- AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | | | - Uriel N Morzan
- International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
| | - Gabriele Falciani
- Energy Department, Politecnico di Torino, Corso Duca degli Abruzzi 24, Torino 10129, Italy
| | - Luca Bergamasco
- Energy Department, Politecnico di Torino, Corso Duca degli Abruzzi 24, Torino 10129, Italy
| | - Jan Versluis
- AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Indraneel Sen
- Uppsala University, Laegerhyddsvaegen 1, 751 20 Uppsala, Sweden
| | - Silvia Dante
- Materials Characterization Facility, Italian Institute of Technology, 16163 Genoa, Italy
| | - Eliodoro Chiavazzo
- Energy Department, Politecnico di Torino, Corso Duca degli Abruzzi 24, Torino 10129, Italy
| | - Ali A Hassanali
- International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
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7
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Elsaesser T, Schauss J, Kundu A, Fingerhut BP. Phosphate Vibrations Probe Electric Fields in Hydrated Biomolecules: Spectroscopy, Dynamics, and Interactions. J Phys Chem B 2021; 125:3899-3908. [PMID: 33834783 PMCID: PMC8154594 DOI: 10.1021/acs.jpcb.1c01502] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Electric interactions
have a strong impact on the structure and
dynamics of biomolecules in their native water environment. Given
the variety of water arrangements in hydration shells and the femto-
to subnanosecond time range of structural fluctuations, there is a
strong quest for sensitive noninvasive probes of local electric fields.
The stretching vibrations of phosphate groups, in particular the asymmetric
(PO2)− stretching vibration νAS(PO2)−, allow for a quantitative
mapping of dynamic electric fields in aqueous environments via a field-induced
redshift of their transition frequencies and concomitant changes of
vibrational line shapes. We present a systematic study of νAS(PO2)− excitations in molecular
systems of increasing complexity, including dimethyl phosphate (DMP),
short DNA and RNA duplex structures, and transfer RNA (tRNA) in water.
A combination of linear infrared absorption, two-dimensional infrared
(2D-IR) spectroscopy, and molecular dynamics (MD) simulations gives
quantitative insight in electric-field tuning rates of vibrational
frequencies, electric field and fluctuation amplitudes, and molecular
interaction geometries. Beyond neat water environments, the formation
of contact ion pairs of phosphate groups with Mg2+ ions
is demonstrated via frequency upshifts of the νAS(PO2)− vibration, resulting in a distinct
vibrational band. The frequency positions of contact geometries are
determined by an interplay of attractive electric and repulsive exchange
interactions.
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Affiliation(s)
- Thomas Elsaesser
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin 12489, Germany
| | - Jakob Schauss
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin 12489, Germany
| | - Achintya Kundu
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin 12489, Germany
| | - Benjamin P Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin 12489, Germany
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8
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Vishnubhotla R, Montgomery CB, Steffens KL, Semancik S. Conformational Changes of Immobilized Polythymine due to External Stressors Studied with Temperature-Controlled Electrochemical Microdevices. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:2607-2618. [PMID: 33595321 PMCID: PMC9278808 DOI: 10.1021/acs.langmuir.0c03219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Conformational changes of single-stranded DNA (ssDNA) play an important role in a DNA strand's ability to bind to target ligands. A variety of factors can influence conformation, including temperature, ionic strength, pH, buffer cation valency, strand length, and sequence. To better understand the effects of these factors on immobilized DNA structures, we employ temperature-controlled electrochemical microsensors to study the effects of salt concentration and temperature variation on the conformation and motion of polythymine (polyT) strands of varying lengths (10, 20, 50 nucleotides). PolyT strands were tethered to a gold working electrode at the proximal end through a thiol linker via covalent bonding between the Au electrode and sulfur link, which can tend to decompose between a temperature range of 60 and 90 °C. The strands were also modified with an electrochemically active methylene blue (MB) moiety at the distal end. Electron transfer (eT) was measured by square wave voltammetry (SWV) and used to infer information pertaining to the average distance between the MB and the working electrode. We observe changes in DNA flexibility due to varying ionic strength, while the effects of increased DNA thermal motion are tracked for elevated temperatures. This work elucidates the behavior of ssDNA in the presence of a phosphate-buffered saline at NaCl concentrations ranging from 20 to 1000 mmol/L through a temperature range of 10-50 °C in 1° increments, well below the decomposition temperature range. The results lay the groundwork for studies on more complex DNA strands in conjunction with different chemical and physical conditions.
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9
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Competition between chiral solvents and chiral monomers in the helical bias of supramolecular polymers. Nat Chem 2021; 13:200-207. [PMID: 33257888 DOI: 10.1038/s41557-020-00583-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 10/19/2020] [Indexed: 01/30/2023]
Abstract
Solute-solvent interactions are key for the assembly and proper functioning of biomacromolecules and play important roles in many fields of organic and polymer chemistry. Despite numerous reports describing the effects of (chiral) solvents on helical conformations of (supramolecular) polymers, the combination of chiral solvents and chiral monomers is unexplored. Here we report diastereomeric differences in the supramolecular polymerization of enantiomers of chiral triphenylene-2,6,10-tricarboxamides in chiral chlorinated solvents. Competition between the preferences induced by the stereocentres of the assembled monomers and those present in the solvent molecules results in unforeseen temperature-dependent solvation effects. By combining experiments and mathematical modelling, we show that the observed differences between enantiomers originate from the combined additive entropic effects of stereocentres present in the monomer and in the solvent. Remarkably, copolymerizations show that the chiral solvent can bias the copolymer helicity and thereby overrule the helical preference of the monomers. Our results highlight the importance of cumulative solvation effects in supramolecular polymerizations.
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10
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Schauss J, Kundu A, Fingerhut BP, Elsaesser T. Magnesium Contact Ions Stabilize the Tertiary Structure of Transfer RNA: Electrostatics Mapped by Two-Dimensional Infrared Spectra and Theoretical Simulations. J Phys Chem B 2021; 125:740-747. [PMID: 33284610 PMCID: PMC7848891 DOI: 10.1021/acs.jpcb.0c08966] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
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Ions interacting with hydrated RNA
play a central role in defining
its secondary and tertiary structure. While spatial arrangements of
ions, water molecules, and phosphate groups have been inferred from
X-ray studies, the role of electrostatic and other noncovalent interactions
in stabilizing compact folded RNA structures is not fully understood
at the molecular level. Here, we demonstrate that contact ion pairs
of magnesium (Mg2+) and phosphate groups embedded in local
water shells stabilize the tertiary equilibrium structure of transfer
RNA (tRNA). Employing dialyzed tRNAPhe from yeast and tRNA
from Escherichia coli, we follow the
population of Mg2+ sites close to phosphate groups of the
ribose-phosphodiester backbone step by step, combining linear and
nonlinear infrared spectroscopy of phosphate vibrations with molecular
dynamics simulations and ab initio vibrational frequency calculations.
The formation of up to six Mg2+/phosphate contact pairs
per tRNA and local field-induced reorientations of water molecules
balance the phosphate–phosphate repulsion in nonhelical parts
of tRNA, thus stabilizing the folded structure electrostatically.
Such geometries display limited sub-picosecond fluctuations in the
arrangement of water molecules and ion residence times longer than
1 μs. At higher Mg2+ excess, the number of contact
ion pairs per tRNA saturates around 6 and weakly interacting ions
prevail. Our results suggest a predominance of contact ion pairs over
long-range coupling of the ion atmosphere and the biomolecule in defining
and stabilizing the tertiary structure of tRNA.
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Affiliation(s)
- Jakob Schauss
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin 12489, Germany
| | - Achintya Kundu
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin 12489, Germany
| | - Benjamin P Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin 12489, Germany
| | - Thomas Elsaesser
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin 12489, Germany
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11
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Tenuzzo L, Camisasca G, Gallo P. Protein-Water and Water-Water Long-Time Relaxations in Protein Hydration Water upon Cooling-A Close Look through Density Correlation Functions. Molecules 2020; 25:molecules25194570. [PMID: 33036320 PMCID: PMC7583983 DOI: 10.3390/molecules25194570] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/29/2020] [Accepted: 09/30/2020] [Indexed: 11/16/2022] Open
Abstract
We report results on the translational dynamics of the hydration water of the lysozyme protein upon cooling obtained by means of molecular dynamics simulations. The self van Hove functions and the mean square displacements of hydration water show two different temperature activated relaxation mechanisms, determining two dynamic regimes where transient trapping of the molecules is followed by hopping phenomena to allow to the structural relaxations. The two caging and hopping regimes are different in their nature. The low-temperature hopping regime has a time scale of tenths of nanoseconds and a length scale on the order of 2–3 water shells. This is connected to the nearest-neighbours cage effect and restricted to the supercooling, it is absent at high temperature and it is the mechanism to escape from the cage also present in bulk water. The second hopping regime is active at high temperatures, on the nanoseconds time scale and over distances of nanometers. This regime is connected to water displacements driven by the protein motion and it is observed very clearly at high temperatures and for temperatures higher than the protein dynamical transition. Below this temperature, the suppression of protein fluctuations largely increases the time-scale of the protein-related hopping phenomena at least over 100 ns. These protein-related hopping phenomena permit the detection of translational motions of hydration water molecules longly persistent in the hydration shell of the protein.
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12
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Kundu A, Schauss J, Fingerhut BP, Elsaesser T. Change of Hydration Patterns upon RNA Melting Probed by Excitations of Phosphate Backbone Vibrations. J Phys Chem B 2020; 124:2132-2138. [PMID: 32101008 DOI: 10.1021/acs.jpcb.0c01474] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The water hydration shell has a decisive impact on the structural and functional properties of RNA. Changes of the RNA structure upon melting and in biochemical processes are accompanied by a change of hydration patterns, a process that is barely characterized. To discern hydration geometries around the backbone phosphate groups of an RNA double helix at the molecular level, we combine two-dimensional infrared spectroscopy of phosphate vibrations with theoretical simulations. There are three distinct coexisting hydration motifs of the RNA A-helix: an ordered chain-like arrangement of water molecules with links between neighboring phosphate groups, separate local hydration shells of up to six water molecules, and hydrated phosphate/counterion contact pairs. RNA disordering upon melting is connected with a transition from predominantly ordered water structures to local hydration shells around phosphate units. Structural fluctuations are dominated by librational water motions occurring on a 300 fs time scale, without exchange between hydration motifs.
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Affiliation(s)
- Achintya Kundu
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin 12489, Germany
| | - Jakob Schauss
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin 12489, Germany
| | - Benjamin P Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin 12489, Germany
| | - Thomas Elsaesser
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin 12489, Germany
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13
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Madrigal EA, Taylor JK, Raghu G, West RM. Cross-linking of DNA monolayers by cisplatin examined using electrostatic denaturation. J Electroanal Chem (Lausanne) 2020. [DOI: 10.1016/j.jelechem.2019.113762] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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14
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Schauss J, Kundu A, Fingerhut BP, Elsaesser T. Contact Ion Pairs of Phosphate Groups in Water: Two-Dimensional Infrared Spectroscopy of Dimethyl Phosphate and ab Initio Simulations. J Phys Chem Lett 2019; 10:6281-6286. [PMID: 31560211 DOI: 10.1021/acs.jpclett.9b02157] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The interaction of phosphate groups with ions in an aqueous environment has a strong impact on the structure and folding processes of DNA and RNA. The dynamic variety of ionic arrangements, including both contact pairs and water separated ions, and the molecular coupling mechanisms are far from being understood. In a combined experimental and theoretical approach, we address the properties of contact ion pairs of the prototypical system dimethyl phosphate with Na+, Ca2+, and Mg2+ ions in water. Linear and femtosecond two-dimensional infrared (2D-IR) spectroscopy of the asymmetric (PO2)- stretching vibration separates and characterizes the different species via their blue-shifted vibrational signatures and 2D-IR line shapes. Phosphate-magnesium contact pairs stand out as the most compact geometry while the contact pairs with Ca2+ and Na+ display a wider structural variation. Microscopic density functional theory simulations rationalize the observed frequency shifts and reveal distinct differences between the contact geometries.
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Affiliation(s)
- Jakob Schauss
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , Berlin 12489 , Germany
| | - Achintya Kundu
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , Berlin 12489 , Germany
| | - Benjamin P Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , Berlin 12489 , Germany
| | - Thomas Elsaesser
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , Berlin 12489 , Germany
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15
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Sheu SY, Liu YC, Zhou JK, Schlag EW, Yang DY. Surface Topography Effects of Globular Biomolecules on Hydration Water. J Phys Chem B 2019; 123:6917-6932. [PMID: 31282162 DOI: 10.1021/acs.jpcb.9b03734] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Hydration water serves as a microscopic manifestation of structural stability and functions of biomolecules. To develop bio-nanomaterials in applications, it is important to study how the surface topography and heterogeneity of biomolecules result in their diversity of the hydration dynamics and energetics. We here performed molecular dynamics simulations combined with the steered molecular dynamics and umbrella sampling to investigate the dynamics and escape process associated with the free energy change of water molecules close to a globular biomolecule, i.e., hemoglobin (Hb) and G-quadruplex DNA (GDNA). The residence time, power of long-time tail, and dipole relaxation time were found to display drastic changes within the averaged hydration shell of 3.0-5.0 Å. Compared with bulk water, in the inner hydration shell, the water dipole moment displays a slower relaxation process and is more oriented toward GDNA than toward Hb, forming a hedgehog-like structure when it surrounds GDNA. In particular, a spine water structure is observed in the GDNA narrow groove. The water isotope effect not only prolongs the dynamic time scales of libration motion in the inner hydration shell and the dipole relaxation processes in the bulk but also strengthens the DNA spine water structure. The potential of the mean force profile reflects the integrity of the hydration shell structure and enables us to obtain detailed insights into the structures formed by water, such as the caged H-bond network and the edge bridge structures; it also reveals that local hydration shell free energy (LHSFE) depends on H-bond rupture processes and ranges from 0.2 to 4.2 kcal/mol. Our results demonstrate that the surface topography of a biomolecule influences the integrity of the hydration shell structure and LHSFE. Our studies are able to identify various further applications in the areas of microfluid devices and nano-dewetting on bioinspired surfaces.
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Affiliation(s)
- Sheh-Yi Sheu
- Department of Life Sciences and Institute of Genome Sciences , National Yang-Ming University , Taipei 112 , Taiwan.,Institute of Biomedical Informatics , National Yang-Ming University , Taipei 112 , Taiwan
| | - Yu-Cheng Liu
- Institute of Biomedical Informatics , National Yang-Ming University , Taipei 112 , Taiwan
| | - Jia-Kai Zhou
- Department of Life Sciences and Institute of Genome Sciences , National Yang-Ming University , Taipei 112 , Taiwan
| | - Edward W Schlag
- Institut für Physikalische und Theoretische Chemie , TU-München , Lichtenbergstr. 4 , 85748 Garching , Germany
| | - Dah-Yen Yang
- Institute of Atomic and Molecular Sciences , Academia Sinica , Taipei 106 , Taiwan
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16
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Teng X, Hwang W. Effect of Methylation on Local Mechanics and Hydration Structure of DNA. Biophys J 2019; 114:1791-1803. [PMID: 29694859 DOI: 10.1016/j.bpj.2018.03.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 03/03/2018] [Accepted: 03/14/2018] [Indexed: 12/31/2022] Open
Abstract
Cytosine methylation affects mechanical properties of DNA and potentially alters the hydration fingerprint for recognition by proteins. The atomistic origin for these effects is not well understood, and we address this via all-atom molecular dynamics simulations. We find that the stiffness of the methylated dinucleotide step changes marginally, whereas the neighboring steps become stiffer. Stiffening is further enhanced for consecutively methylated steps, providing a mechanistic origin for the effect of hypermethylation. Steric interactions between the added methyl groups and the nonpolar groups of the neighboring nucleotides are responsible for the stiffening in most cases. By constructing hydration maps, we found that methylation also alters the surface hydration structure in distinct ways. Its resistance to deformation may contribute to the stiffening of DNA for deformational modes lacking steric interactions. These results highlight the sequence- and deformational-mode-dependent effects of cytosine methylation.
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Affiliation(s)
- Xiaojing Teng
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas
| | - Wonmuk Hwang
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas; Department of Materials Science & Engineering, Texas A&M University, College Station, Texas; School of Computational Sciences, Korea Institute for Advanced Study, Seoul, Korea.
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17
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Kundu A, Dahms F, Fingerhut BP, Nibbering ETJ, Pines E, Elsaesser T. Hydrated Excess Protons in Acetonitrile/Water Mixtures: Solvation Species and Ultrafast Proton Motions. J Phys Chem Lett 2019; 10:2287-2294. [PMID: 30999753 DOI: 10.1021/acs.jpclett.9b00756] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The solvation structure of protons in aqueous media is highly relevant to electric properties and to proton transport in liquids and membranes. At ambient temperature, polar liquids display structural fluctuations on femto- to picosecond time scales with a direct impact on proton solvation. We use two-dimensional infrared (2D-IR) spectroscopy to follow proton dynamics in acetonitrile/water mixtures with the Zundel cation H5O2+ prepared in neat acetonitrile as a benchmark. The 2D-IR spectra of the proton transfer mode of H5O2+ demonstrate stochastic large-amplitude motions in the double-minimum proton potential, driven by fluctuating electric fields. In all cases, the excess proton is embedded in a water dimer, forming an H5O2+ complex as the major solvation species. This observation is rationalized by quantum mechanics/molecular mechanics molecular dynamics simulations including up to four water molecules embedded in acetonitrile. The Zundel motif interacts with its closest water neighbor in an H7O3+ unit without persistent proton localization.
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Affiliation(s)
- Achintya Kundu
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , Berlin 12489 , Germany
| | - Fabian Dahms
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , Berlin 12489 , Germany
| | - Benjamin P Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , Berlin 12489 , Germany
| | - Erik T J Nibbering
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , Berlin 12489 , Germany
| | - Ehud Pines
- Department of Chemistry , Ben Gurion University of the Negev , Beer-Sheva 84105 , Israel
| | - Thomas Elsaesser
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , Berlin 12489 , Germany
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18
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Schauss J, Dahms F, Fingerhut BP, Elsaesser T. Phosphate-Magnesium Ion Interactions in Water Probed by Ultrafast Two-Dimensional Infrared Spectroscopy. J Phys Chem Lett 2019; 10:238-243. [PMID: 30599134 DOI: 10.1021/acs.jpclett.8b03568] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Electric interactions between ions and ionic molecular groups in aqueous solution play a fundamental role in chemistry and biology. While Mg2+ ions are known to strongly affect the structure and folding dynamics of biomolecules, the relevance of different solvation geometries and the underlying interactions are mainly unresolved. We study dynamics and couplings between the hydrated Mg2+ and the dimethylphosphate anion, an established model system for the DNA and RNA backbone. The asymmetric (PO2-) stretching vibration serves as a sensitive noninvasive probe of phosphate-ion interactions. Femtosecond two-dimensional infrared (2D-IR) spectroscopy directly maps Mg2+ ions in contact with the phosphate groups via a distinct blue-shifted signature in the 2D spectrum. Data for different Mg2+ concentrations are analyzed by microscopic density functional theory modeling of cluster geometries and associated spectroscopic features, providing spatial assignments of the observed 2D-IR signatures. Phosphate-ion interactions arising from electrostatic Coulomb forces and exchange repulsion are the predominant origin of the observed frequency shifts.
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Affiliation(s)
- Jakob Schauss
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , Berlin 12489 , Germany
| | - Fabian Dahms
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , Berlin 12489 , Germany
| | - Benjamin P Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , Berlin 12489 , Germany
| | - Thomas Elsaesser
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , Berlin 12489 , Germany
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19
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Fingerhut BP, Bruening EM, Schauss J, Siebert T, Elsaesser T. Interactions of RNA and Water probed by 2D-IR Spectroscopy. EPJ WEB OF CONFERENCES 2019. [DOI: 10.1051/epjconf/201920510003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Combined experimental-theoretical investigation of ultrafast hydration dynamics of an A-form RNA double helix in water reveals an ordered arrangement of water molecules and provides boundary conditions for the ion atmosphere around the polyanionic RNA.
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20
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21
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Bruening EM, Schauss J, Siebert T, Fingerhut BP, Elsaesser T. Vibrational Dynamics and Couplings of the Hydrated RNA Backbone: A Two-Dimensional Infrared Study. J Phys Chem Lett 2018; 9:583-587. [PMID: 29337564 DOI: 10.1021/acs.jpclett.7b03314] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The equilibrium structure of the RNA sugar-phosphate backbone and its hydration shell is distinctly different from hydrated DNA. Applying femtosecond two-dimensional infrared (2D-IR) spectroscopy in a range from 950 to 1300 cm-1, we elucidate the character, dynamics, and couplings of backbone modes of a double-stranded RNA A-helix geometry in its aqueous environment. The 2D-IR spectra display a greater number of backbone modes than for DNA, with distinctly different lineshapes of diagonal peaks. Phosphate-ribose interactions and local hydration structures are reflected in the complex coupling pattern of RNA modes. Interactions with the fluctuating water shell give rise to spectral diffusion on a 300 fs time scale, leading to a quasi-homogeneous line shape of the symmetric (PO2)- stretching mode of the strongly hydrated phosphate groups. The RNA results are benchmarked by 2D-IR spectra of DNA oligomers in water and analyzed by molecular dynamics and quantum mechanical molecular mechanics simulations.
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Affiliation(s)
- Eva M Bruening
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , Max-Born-Str. 2a, D-12489 Berlin, Germany
| | - Jakob Schauss
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , Max-Born-Str. 2a, D-12489 Berlin, Germany
| | - Torsten Siebert
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , Max-Born-Str. 2a, D-12489 Berlin, Germany
| | - Benjamin P Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , Max-Born-Str. 2a, D-12489 Berlin, Germany
| | - Thomas Elsaesser
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , Max-Born-Str. 2a, D-12489 Berlin, Germany
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22
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Kowalewski M, Fingerhut BP, Dorfman KE, Bennett K, Mukamel S. Simulating Coherent Multidimensional Spectroscopy of Nonadiabatic Molecular Processes: From the Infrared to the X-ray Regime. Chem Rev 2017; 117:12165-12226. [DOI: 10.1021/acs.chemrev.7b00081] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Markus Kowalewski
- Department
of Chemistry and Department of Physics and Astronomy, University of California, Irvine, California 92697-2025, United States
| | - Benjamin P. Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| | - Konstantin E. Dorfman
- State
Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Kochise Bennett
- Department
of Chemistry and Department of Physics and Astronomy, University of California, Irvine, California 92697-2025, United States
| | - Shaul Mukamel
- Department
of Chemistry and Department of Physics and Astronomy, University of California, Irvine, California 92697-2025, United States
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23
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Youssef M, Van Vliet KJ, Yildiz B. Polarizing Oxygen Vacancies in Insulating Metal Oxides under a High Electric Field. PHYSICAL REVIEW LETTERS 2017; 119:126002. [PMID: 29341632 DOI: 10.1103/physrevlett.119.126002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Indexed: 06/07/2023]
Abstract
We demonstrate a thermodynamic formulation to quantify defect formation energetics in an insulator under a high electric field. As a model system, we analyzed neutral oxygen vacancies (color centers) in alkaline-earth-metal binary oxides using density functional theory, Berry phase calculations, and maximally localized Wannier functions. The work of polarization lowers the field-dependent electric Gibbs energy of formation of this defect. This is attributed mainly to the ease of polarizing the two electrons trapped in the vacant site, and secondarily to the defect induced reduction in bond stiffness and softening of phonon modes. The formulation and analysis have implications for understanding the behavior of insulating oxides in electronic, magnetic, catalytic, and electrocaloric devices under a high electric field.
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Affiliation(s)
- Mostafa Youssef
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Krystyn J Van Vliet
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Bilge Yildiz
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
- Department of Nuclear Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
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24
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Folpini G, Reimann K, Woerner M, Elsaesser T, Hoja J, Tkatchenko A. Strong Local-Field Enhancement of the Nonlinear Soft-Mode Response in a Molecular Crystal. PHYSICAL REVIEW LETTERS 2017; 119:097404. [PMID: 28949583 DOI: 10.1103/physrevlett.119.097404] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Indexed: 05/29/2023]
Abstract
The nonlinear response of soft-mode excitations in polycrystalline acetylsalicylic acid (aspirin) is studied with two-dimensional terahertz spectroscopy. We demonstrate that the correlation of CH_{3} rotational modes with collective oscillations of π electrons drives the system into the nonperturbative regime of light-matter interaction, even for a moderate strength of the THz driving field on the order of 50 kV/cm. Nonlinear absorption around 1.1 THz leads to a blueshifted coherent emission at 1.7 THz, revealing the dynamic breakup of the strong electron-phonon correlations. The observed behavior is reproduced by theoretical calculations including dynamic local-field correlations.
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Affiliation(s)
- Giulia Folpini
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, 12489 Berlin, Germany
| | - Klaus Reimann
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, 12489 Berlin, Germany
| | - Michael Woerner
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, 12489 Berlin, Germany
| | - Thomas Elsaesser
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, 12489 Berlin, Germany
| | - Johannes Hoja
- Physics and Materials Science Research Unit, University of Luxembourg, L-1511 Luxembourg, Luxembourg and Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Alexandre Tkatchenko
- Physics and Materials Science Research Unit, University of Luxembourg, L-1511 Luxembourg, Luxembourg and Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
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25
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Abstract
The structure and function of biomolecules are strongly influenced by their hydration shells. Structural fluctuations and molecular excitations of hydrating water molecules cover a broad range in space and time, from individual water molecules to larger pools and from femtosecond to microsecond time scales. Recent progress in theory and molecular dynamics simulations as well as in ultrafast vibrational spectroscopy has led to new and detailed insight into fluctuations of water structure, elementary water motions, electric fields at hydrated biointerfaces, and processes of vibrational relaxation and energy dissipation. Here, we review recent advances in both theory and experiment, focusing on hydrated DNA, proteins, and phospholipids, and compare dynamics in the hydration shells to bulk water.
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Affiliation(s)
- Damien Laage
- École
Normale Supérieure, PSL Research University, UPMC Univ Paris
06, CNRS, Département de Chimie,
PASTEUR, 24 rue Lhomond, 75005 Paris, France
- Sorbonne
Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
| | - Thomas Elsaesser
- Max-Born-Institut
für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| | - James T. Hynes
- École
Normale Supérieure, PSL Research University, UPMC Univ Paris
06, CNRS, Département de Chimie,
PASTEUR, 24 rue Lhomond, 75005 Paris, France
- Sorbonne
Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
- Department
of Chemistry and Biochemistry, University
of Colorado, Boulder, Colorado 80309, United
States
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26
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Liu Y, Guchhait B, Siebert T, Fingerhut BP, Elsaesser T. Molecular couplings and energy exchange between DNA and water mapped by femtosecond infrared spectroscopy of backbone vibrations. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:044015. [PMID: 28405593 PMCID: PMC5384856 DOI: 10.1063/1.4980075] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 03/31/2017] [Indexed: 05/15/2023]
Abstract
Molecular couplings between DNA and water together with the accompanying processes of energy exchange are mapped via the ultrafast response of DNA backbone vibrations after OH stretch excitation of the water shell. Native salmon testes DNA is studied in femtosecond pump-probe experiments under conditions of full hydration and at a reduced hydration level with two water layers around the double helix. Independent of their local hydration patterns, all backbone vibrations in the frequency range from 940 to 1120 cm-1 display a quasi-instantaneous reshaping of the spectral envelopes of their fundamental absorption bands upon excitation of the water shell. The subsequent reshaping kinetics encompass a one-picosecond component, reflecting the formation of a hot ground state of the water shell, and a slower contribution on a time scale of tens of picoseconds. Such results are benchmarked by measurements with resonant excitation of the backbone modes, resulting in distinctly different absorption changes. We assign the fast changes of DNA absorption after OH stretch excitation to structural changes in the water shell which couple to DNA through the local electric fields. The second slower process is attributed to a flow of excess energy from the water shell into DNA, establishing a common heated ground state in the molecular ensemble. This interpretation is supported by theoretical calculations of the electric fields exerted by the water shell at different temperatures.
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Affiliation(s)
- Yingliang Liu
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , 12489 Berlin, Germany
| | - Biswajit Guchhait
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , 12489 Berlin, Germany
| | - Torsten Siebert
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , 12489 Berlin, Germany
| | - Benjamin P Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , 12489 Berlin, Germany
| | - Thomas Elsaesser
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , 12489 Berlin, Germany
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27
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Laage D, Elsaesser T, Hynes JT. Perspective: Structure and ultrafast dynamics of biomolecular hydration shells. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:044018. [PMID: 28470026 PMCID: PMC5398927 DOI: 10.1063/1.4981019] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 03/31/2017] [Indexed: 05/25/2023]
Abstract
The structure and function of biomolecules can be strongly influenced by their hydration shells. A key challenge is thus to determine the extent to which these shells differ from bulk water, since the structural fluctuations and molecular excitations of hydrating water molecules within these shells can cover a broad range in both space and time. Recent progress in theory, molecular dynamics simulations, and ultrafast vibrational spectroscopy has led to new and detailed insight into the fluctuations of water structure, elementary water motions, and electric fields at hydrated biointerfaces. Here, we discuss some central aspects of these advances, focusing on elementary molecular mechanisms and processes of hydration on a femto- to picosecond time scale, with some special attention given to several issues subject to debate.
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Affiliation(s)
- Damien Laage
- Ecole Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Départment de Chimie, PASTEUR, 24 rue Lhomond, 75005 Paris, France
| | - Thomas Elsaesser
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, 12489 Berlin, Germany
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28
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Yang J, Youssef M, Yildiz B. Predicting point defect equilibria across oxide hetero-interfaces: model system of ZrO2/Cr2O3. Phys Chem Chem Phys 2017; 19:3869-3883. [DOI: 10.1039/c6cp04997d] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We present a multi-scale model to predict defect redistribution both in interface core and space charge layer across oxide/oxide hetero-interfaces.
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Affiliation(s)
- Jing Yang
- Laboratory for Electrochemical Interfaces
- Massachusetts Institute of Technology
- Cambridge
- USA
- Department of Materials Science and Engineering
| | - Mostafa Youssef
- Laboratory for Electrochemical Interfaces
- Massachusetts Institute of Technology
- Cambridge
- USA
- Department of Materials Science and Engineering
| | - Bilge Yildiz
- Laboratory for Electrochemical Interfaces
- Massachusetts Institute of Technology
- Cambridge
- USA
- Department of Materials Science and Engineering
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29
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Fingerhut BP, Costard R, Elsaesser T. Predominance of short range Coulomb forces in phosphate-water interactions—a theoretical analysis. J Chem Phys 2016. [DOI: 10.1063/1.4962755] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Benjamin P. Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| | - Rene Costard
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| | - Thomas Elsaesser
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
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