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Koyakkat M, Ishida T, Fujita K, Shirota H. Low-Frequency Spectra of Hydrated Ionic Liquids with Kosmotropic and Chaotropic Anions. J Phys Chem B 2024; 128:4171-4182. [PMID: 38640467 DOI: 10.1021/acs.jpcb.4c01255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2024]
Abstract
In this study, we investigated the water concentration dependence of the intermolecular vibrations of two hydrated ionic liquids (ILs), cholinium dihydrogen phosphate ([ch][dhp]) and cholinium bromide ([ch]Br), using femtosecond Raman-induced Kerr effect spectroscopy (fs-RIKES). The anions of the former and latter hydrated ILs are kosmotropic and chaotropic, respectively. We found that the spectral peak of ∼50 cm-1 shifted to the low-frequency side in hydrated [ch][dhp], indicating the weakening of its intermolecular interactions. In contrast, no change in the peak frequency of the low-frequency band at ∼50 cm-1 was observed with increasing water concentration in hydrated [ch]Br. The vibrational density of states (VDOS) spectra generated from molecular dynamics (MD) simulations were in qualitative agreement with the experimental results. Decomposition analysis of the VDOS spectra for each component revealed that the red shift of the low-frequency band in the hydrated [ch][dhp] upon water addition was essentially due to the contributions of anions and water rather than that of the cholinium cation. We also found from the low-frequency spectra of the two hydrated ILs that they differed in the concentration dependence of the 180 cm-1 band, which is assigned as a hindered translational motion of water molecules combined to form O···O stretching motions. From the relationship between the peak frequency of the low-frequency band and the bulk parameter, which is the square root of the surface tension divided by the density, we found that the peak frequency in the hydrated IL with kosmotropic [dhp]- depends on the bulk parameter, similar to the case for an aqueous solution of the typical deep eutectic solvent reline. However, the peak frequency of the hydrated IL with chaotropic Br- is constant with the bulk parameter.
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Affiliation(s)
- Maharoof Koyakkat
- Department of Chemistry, Chiba University, 1-33 Yayoi, Inage-ku, Chiba 263-8522, Japan
| | - Tateki Ishida
- Institute for Molecular Science and Research Center for Computational Science, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
| | - Kyoko Fujita
- Department of Pathophysiology, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Hideaki Shirota
- Department of Chemistry, Chiba University, 1-33 Yayoi, Inage-ku, Chiba 263-8522, Japan
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2
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Jalilvand S, Mousavi H. Vibration spectra of DNA and RNA segments. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2024; 53:95-109. [PMID: 38265690 DOI: 10.1007/s00249-023-01699-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/17/2023] [Accepted: 12/23/2023] [Indexed: 01/25/2024]
Abstract
The dispersion curves and density of states are used to analyze the vibrational characteristics of DNA and RNA segments. This is done using a harmonic Hamiltonian and the Green's function technique. Two configurations of DNA and RNA, finite and cyclic, have been investigated and compared to their infinite counterparts. For the DNA molecule, three models, including a fishbone model, a ldder model, and a fishbone ladder model, have been employed, while the RNA molecule has been represented using a half fishbone model. To enhance the realism of DNA and RNA simulations, the unit cells within each infinite system as well as the length of the finite and cyclic cases are gradually enlarged. The connections between the sub-sites have been modeled using linear springs, where the stiffness of the vertical springs exhibits random variations throughout the length of the DNA and RNA models. Shorter DNA and RNA segments exhibit additional peaks in their density of states, resulting in more bands in dispersion curves. This indicates that as the number of building blocks grows in these segments, their curves resemble those of infinite systems. These findings have practical implications for studying the vibration characteristics of similar macro-systems.
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Affiliation(s)
| | - Hamze Mousavi
- Department of Physics, Razi University, Kermanshah, Iran.
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3
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Li Y, Xu L, Ouyang J, Lei J, Hu J, Xing X, Chen P, Li J, Zhong C, Yang B, Li H. Harmonic and anharmonic studies on THz spectra of two vanillin polymorphs. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 309:123869. [PMID: 38198992 DOI: 10.1016/j.saa.2024.123869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/05/2023] [Accepted: 01/05/2024] [Indexed: 01/12/2024]
Abstract
Polymorphism commonly exists in organic molecular crystals. The fingerprint features in low-frequency vibrational range are important information reflecting different intermolecular interactions of polymorphs. Interpreting these features is very helpful to understand vibrational property of polymorphs and reveal the thermodynamic stability. In this work, the low-frequency vibrations of form I and II of vanillin are investigated using terahertz time-domain spectroscopy. Static DFT calculation and ab initio molecular dynamics (AIMD) are employed to interpret their low-frequency vibrations of both forms in harmonic and anharmonic ways, respectively. Their low-frequency vibration characteristics in harmonic calculations are discussed, and anharmonic mode couplings between OH bond stretch and the stretching and bending motion of hydrogen bonds are uncovered. Moreover, the thermodynamic energies including electronic potential energy and vibrational/kinetic energy arising from nuclear motions are calculated. The result reveals that the stability order of the two forms is mainly dependent on their electric potential energy difference.
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Affiliation(s)
- Yin Li
- School of Physics and Materials Science, Nanchang University, Xuefu Avenue 999, Nanchang City 330031, China.
| | - Li Xu
- School of Chemistry, Biology and Materials Science, East China University of Technology, Guanglan Avenue 418, Nanchang City 330013, China
| | - Jinbo Ouyang
- School of Chemistry, Biology and Materials Science, East China University of Technology, Guanglan Avenue 418, Nanchang City 330013, China.
| | - Jiangtao Lei
- Institute of Space Science and Technology, Nanchang University, Xuefu Avenue 999, Nanchang City 330031, China
| | - Jun Hu
- School of Mechatronics & Vehicle Engineering, East China Jiaotong University, Nanchang, Jiangxi 330013, China
| | - Xiaohong Xing
- School of Chemistry, Biology and Materials Science, East China University of Technology, Guanglan Avenue 418, Nanchang City 330013, China
| | - Peng Chen
- School of Chemistry, Biology and Materials Science, East China University of Technology, Guanglan Avenue 418, Nanchang City 330013, China
| | - Jiaqing Li
- School of Physics and Materials Science, Nanchang University, Xuefu Avenue 999, Nanchang City 330031, China
| | - Changqing Zhong
- School of Physics and Materials Science, Nanchang University, Xuefu Avenue 999, Nanchang City 330031, China
| | - Bo Yang
- School of Physics and Materials Science, Nanchang University, Xuefu Avenue 999, Nanchang City 330031, China
| | - Heng Li
- Fujian Provincial Key Laboratory of Semiconductors and Applications, Collaborative Innovation Center for Optoelectronic Semiconductors and Efficient Devices, Department of Physics, Xiamen University, Xiamen 361005, China; Jiujiang Research Institute, Xiamen University, Jiujiang 332000, China
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4
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González-Jiménez M, Liao Z, Williams EL, Wynne K. Lifting Hofmeister's Curse: Impact of Cations on Diffusion, Hydrogen Bonding, and Clustering of Water. J Am Chem Soc 2024; 146:368-376. [PMID: 38124370 PMCID: PMC10786029 DOI: 10.1021/jacs.3c09421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023]
Abstract
Water plays a role in the stability, reactivity, and dynamics of the solutes that it contains. The presence of ions alters this capacity by changing the dynamics and structure of water. However, our understanding of how and to what extent this occurs is still incomplete. Here, a study of the low-frequency Raman spectra of aqueous solutions of various cations by using optical Kerr-effect spectroscopy is presented. This technique allows for the measurement of the changes that ions cause in both the diffusive dynamics and the vibrations of the hydrogen-bond structure of water. It is found that when salts are added, some of the water molecules become part of the ion solvation layers, while the rest retain the same diffusional properties as those of pure water. The slowing of the dynamics of the water molecules in the solvation shell of each ion was found to depend on its charge density at infinite dilution conditions and on its position in the Hofmeister series at higher concentrations. It is also observed that all cations weaken the hydrogen-bond structure of the solution and that this weakening depends only on the size of the cation. Finally, evidence is found that ions tend to form amorphous aggregates, even at very dilute concentrations. This work provides a novel approach to water dynamics that can be used to better study the mechanisms of solute nucleation and crystallization, the structural stability of biomolecules, and the dynamic properties of complex solutions, such as water-in-salt electrolytes.
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Affiliation(s)
| | - Zhiyu Liao
- School of Chemistry, University of Glasgow, Glasgow G12 8QQ, U.K.
| | | | - Klaas Wynne
- School of Chemistry, University of Glasgow, Glasgow G12 8QQ, U.K.
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5
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Kabir A, Bhattarai M, Rasmussen KØ, Shehu A, Usheva A, Bishop AR, Alexandrov B. Examining DNA breathing with pyDNA-EPBD. Bioinformatics 2023; 39:btad699. [PMID: 37991847 PMCID: PMC10681863 DOI: 10.1093/bioinformatics/btad699] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/23/2023] [Accepted: 11/21/2023] [Indexed: 11/24/2023] Open
Abstract
MOTIVATION The two strands of the DNA double helix locally and spontaneously separate and recombine in living cells due to the inherent thermal DNA motion. This dynamics results in transient openings in the double helix and is referred to as "DNA breathing" or "DNA bubbles." The propensity to form local transient openings is important in a wide range of biological processes, such as transcription, replication, and transcription factors binding. However, the modeling and computer simulation of these phenomena, have remained a challenge due to the complex interplay of numerous factors, such as, temperature, salt content, DNA sequence, hydrogen bonding, base stacking, and others. RESULTS We present pyDNA-EPBD, a parallel software implementation of the Extended Peyrard-Bishop-Dauxois (EPBD) nonlinear DNA model that allows us to describe some features of DNA dynamics in detail. The pyDNA-EPBD generates genomic scale profiles of average base-pair openings, base flipping probability, DNA bubble probability, and calculations of the characteristically dynamic length indicating the number of base pairs statistically significantly affected by a single point mutation using the Markov Chain Monte Carlo algorithm. AVAILABILITY AND IMPLEMENTATION pyDNA-EPBD is supported across most operating systems and is freely available at https://github.com/lanl/pyDNA_EPBD. Extensive documentation can be found at https://lanl.github.io/pyDNA_EPBD/.
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Affiliation(s)
- Anowarul Kabir
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87544, United States
- Department of Computer Science, George Mason University, Fairfax, VA 22030, United States
| | - Manish Bhattarai
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87544, United States
| | - Kim Ø Rasmussen
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87544, United States
| | - Amarda Shehu
- Department of Computer Science, George Mason University, Fairfax, VA 22030, United States
| | - Anny Usheva
- Department of Surgery, Brown University, Providence, RI 02912, United States
| | - Alan R Bishop
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87544, United States
| | - Boian Alexandrov
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87544, United States
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6
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Kabir A, Bhattarai M, Rasmussen KØ, Shehu A, Usheva A, Bishop AR, Alexandrov BS. Examining DNA Breathing with pyDNA-EPBD. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.09.557010. [PMID: 37745370 PMCID: PMC10515784 DOI: 10.1101/2023.09.09.557010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Motivation The two strands of the DNA double helix locally and spontaneously separate and recombine in living cells due to the inherent thermal DNA motion.This dynamics results in transient openings in the double helix and is referred to as "DNA breathing" or "DNA bubbles." The propensity to form local transient openings is important in a wide range of biological processes, such as transcription, replication, and transcription factors binding. However, the modeling and computer simulation of these phenomena, have remained a challenge due to the complex interplay of numerous factors, such as, temperature, salt content, DNA sequence, hydrogen bonding, base stacking, and others. Results We present pyDNA-EPBD, a parallel software implementation of the Extended Peyrard-Bishop- Dauxois (EPBD) nonlinear DNA model that allows us to describe some features of DNA dynamics in detail. The pyDNA-EPBD generates genomic scale profiles of average base-pair openings, base flipping probability, DNA bubble probability, and calculations of the characteristically dynamic length indicating the number of base pairs statistically significantly affected by a single point mutation using the Markov Chain Monte Carlo (MCMC) algorithm.
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Affiliation(s)
- Anowarul Kabir
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87544, NM, 87102
- George Mason University, 4400 University Dr, Fairfax, VA 22030
| | - Manish Bhattarai
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87544, NM, 87102
| | - Kim Ø. Rasmussen
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87544, NM, 87102
| | - Amarda Shehu
- George Mason University, 4400 University Dr, Fairfax, VA 22030
| | - Anny Usheva
- Brown University, 69 Brown St Box 1822, Providence, RI 02912
| | - Alan R Bishop
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87544, NM, 87102
| | - Boian S Alexandrov
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87544, NM, 87102
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7
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Shirota H, Rajbangshi J, Koyakkat M, Baksi A, Cao M, Biswas R. Low-frequency spectra of reline and its mixtures with water: A comparative study based on femtosecond Raman-induced Kerr effect spectroscopy and molecular dynamics simulations. J Photochem Photobiol A Chem 2023. [DOI: 10.1016/j.jphotochem.2022.114504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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8
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Choi WJ, Lee SH, Park BC, Kotov NA. Terahertz Circular Dichroism Spectroscopy of Molecular Assemblies and Nanostructures. J Am Chem Soc 2022; 144:22789-22804. [DOI: 10.1021/jacs.2c04817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Won Jin Choi
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
- Physical and Life Sciences, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Sang Hyun Lee
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Bum Chul Park
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Nicholas A. Kotov
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Macromolecular Science and Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
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9
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Wang L, Zhao Z, Du M, Qin H, Ako RT, Sriram S. Tuning symmetry-protected quasi bound state in the continuum using terahertz meta-atoms of rotational and reflectional symmetry. OPTICS EXPRESS 2022; 30:23631-23639. [PMID: 36225039 DOI: 10.1364/oe.454739] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/18/2022] [Indexed: 06/16/2023]
Abstract
Conventionally, a symmetry-protected quasi bound state of the continuum (BIC) becomes achievable by breaking the C2 symmetry of meta-atoms. Our work exhibits a novel approach to achieving dual band quasi-BIC by breaking the C2v symmetry into Cs symmetry. Also, we show that a single band quasi-BIC can be achieved by breaking the C2v symmetry into C2 symmetry. Our metasurface of C2v symmetry is composed of double gaps split ring resonator (DSRR), and it degrades to C2 symmetry when the double gaps are displaced in opposite directions. One band quasi-BIC can be observed occurring at around 0.36 and 0.61 THz respectively with the metasurface excited by x- and y-polarized terahertz radiation, respectively. A couple of dark dipole oscillator dominates the quasi-BIC at 0.36 THz, while a quadruple-like oscillator dominates the quasi-BIC at 0.61 THz. The damping ratio and coupling coefficients of the above single quasi-BIC are close to the orthogonal polarization of the incident terahertz wave. However, the metasurface of the DSRR array degrades down to Cs symmetry when the double gaps are displaced in the same directions. A dual band quasi-BIC (0.23 THz and 0.62 THz) is found to be sensitive to the y-polarized terahertz radiation. It is found that the inductive-capacitive (LC) resonance results in quasi-BIC at 0.23 THz, while a quadrupole-like oscillation results in quasi-BIC at 0.62 THz. The quasi-BIC at 0.62 THz has a higher coupling coefficient and lower damping ratio than quasi-BIC at 0.23 THz in a metasurface of Cs symmetry. The realization of the above locally symmetric breaking on the quasi-BIC of terahertz metasurfaces is helpful for the innovation of multi-band terahertz biosensors.
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10
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Shirota H, Yanase K, Ogura T, Sato T. Intermolecular Dynamics and Structure in Aqueous Lidocaine Hydrochloride Solutions. J Phys Chem B 2022; 126:1787-1798. [PMID: 35170970 DOI: 10.1021/acs.jpcb.1c10504] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We investigated the intermolecular dynamics and static structure in the aqueous solutions of lidocaine hydrochloride (LDHCl) in the concentration range of [LDHCl] = 0-2.00 M using femtosecond Raman-induced Kerr effect spectroscopy (fs-RIKES), small- and wide-angle X-ray scattering (SWAXS), and dynamic light scattering (DLS). For the fs-RIKES experiments, the concentration dependence of the difference low-frequency spectra of the aqueous LDHCl solutions relative to the neat water, which was mainly due to the intermolecular vibrations, was characterized using an exponential function with a characteristic concentration of ∼1 M. For the SWAXS experiments, we observed a manifestation of an excess scattering component centered within a range of 8-10 nm-1 in the aqueous LDHCl solutions. The results of Fourier inversion and further deconvolution analyses unambiguously demonstrated that lidocaines assemble into a nanometer-sized micelle-like structure with the innermost core (∼0.3 nm) and outer shell (∼0.5 nm), respectively. The DLS experiments also found nanometer-sized aggregates and further indicated evidence of the clusters of the aggregates. The results of viscosities, densities, and surface tensions of the solutions and the quantum chemistry calculations supported the unique features of the microscopic intermolecular interaction and the micelle-like aggregation.
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Affiliation(s)
- Hideaki Shirota
- Department of Chemistry, Chiba University, 1-33 Yayoi, Inage-ku, Chiba 263-8522, Japan
| | - Keiichi Yanase
- Department of Chemistry and Materials, Faculty of Textile Science and Technology, Shinshu University, 3-15-1 Tokida, Ueda, Nagano 386-8567, Japan
| | - Taiki Ogura
- Department of Chemistry and Materials, Faculty of Textile Science and Technology, Shinshu University, 3-15-1 Tokida, Ueda, Nagano 386-8567, Japan
| | - Takaaki Sato
- Department of Chemistry and Materials, Faculty of Textile Science and Technology, Shinshu University, 3-15-1 Tokida, Ueda, Nagano 386-8567, Japan
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11
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Polok K, Subba N, Gadomski W, Sen P. Search for the origin of synergistic solvation in methanol/chloroform mixture using optical Kerr effect spectroscopy. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.117013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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12
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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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Ando M, Shirota H. Low-Frequency Spectra of 1-Methyl-3-octylimidazolium Tetrafluoroborate Mixtures with Poly(ethylene glycol) by Femtosecond Raman-Induced Kerr Effect Spectroscopy. J Phys Chem B 2021; 125:12006-12019. [PMID: 34694116 DOI: 10.1021/acs.jpcb.1c07079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This is the first report on low-frequency spectra of ionic liquid (IL)/polymer mixtures using femtosecond Raman-induced Kerr effect spectroscopy. We studied mixtures of 1-methyl-3-octylimidazolium tetrafluoroborate ([MOIm][BF4]) and poly(ethylene glycol) (PEG) with Mn = 400 (PEG400) at various concentrations. To elucidate the unique features of the IL/polymer mixture system, mixtures of PEG400 with a molecular liquid, 1-octhylimidazole (OIm), which is a neutral analog of the cation, were also studied. In addition, mixtures of [MOIm][BF4] with ethylene glycol (EG) and poly(ethylene glycol) with Mn = 4000 (PEG4000) were also investigated. The first moments of broad low-frequency spectra, mainly due to intermolecular vibrations for the [MOIm][BF4]/PEG400 and OIm/PEG400, increased slightly with increasing concentration of PEG400, indicating that microscopic intermolecular interactions, in general, are slightly enhanced. We also compared the [MOIm][BF4] mixtures with EG, PEG400, and PEG4000 at concentrations of 5 and 10 wt % PEG or EG. The low-frequency spectra of samples with the same concentrations were quite similar, but a comparison of the normalized spectra showed that the spectral intensity in the low-frequency region below ∼50 cm-1 of the [MOIm][BF4] mixtures with PEG400 and PEG4000 is somewhat lower than that of the [MOIm][BF4] mixtures with EG. Although the effect of the polymer is small compared to other polymer solution systems, this feature is attributed to a suppression of translational motion in the mixtures of [MOIm][BF4] with PEG compared to the mixtures of [MOIm][BF4] with EG due to the greater mass of PEG than EG. Density, surface tension, viscosity, and electrical conductivity were also estimated. From Walden plots, it was found that the [MOIm][BF4]/PEG4000 system showed more ideal electrical conductive behavior than the [MOIm][BF4]/PEG400 and [MOIm][BF4]/EG systems.
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Affiliation(s)
- Masatoshi Ando
- Department of Chemistry, Chiba University, 1-33 Yayoi, Inage-ku, Chiba 263-8522, Japan
| | - Hideaki Shirota
- Department of Chemistry, Chiba University, 1-33 Yayoi, Inage-ku, Chiba 263-8522, Japan
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14
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Pan Z, Huang J, Zhuang W. Protein-Ligand Binding Molecular Details Revealed by Terahertz Optical Kerr Spectroscopy: A Simulation Study. JACS AU 2021; 1:1788-1797. [PMID: 34723281 PMCID: PMC8549111 DOI: 10.1021/jacsau.1c00356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Indexed: 06/13/2023]
Abstract
Picosecond fast motions and their involvement in the biochemical processes such as protein-ligand binding has engaged significant attention. Terahertz optical Kerr spectroscopy (OKE) has the superior potential to probe these fast motions directly. Application of OKE in protein-ligand binding study is, however, limited by the difficulty of quantitative atomistic interpretation, and the calculation of Kerr spectrum for entire solvated protein complex was considered not yet feasible, due to the lack of one consistent polarizable model for both configuration sampling and polarizability calculation. Here, we analyzed the biochemical relevance of OKE to the lysozyme-triacetylchitotriose binding based on the first OKE simulation using one consistent Drude polarizable model. An analytical multipole and induced dipole scheme was employed to calculate the off-diagonal Drude polarizability more efficiently and accurately. Further theoretical analysis revealed how the subtle twisting and stiffening of aromatic protein residues' spatial arrangement as well as the confinement of small water clusters between ligand and protein cavity due to the ligand binding can be examined using Kerr spectroscopy. Comparison between the signals of bound complex and that of uncorrelated protein/ligand demonstrated that binding action alone has reflection in the OKE spectrum. Our study indicated OKE as a powerful terahertz probe for protein-ligand binding chemistry and dynamics.
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Affiliation(s)
- Zhijun Pan
- State
Key Laboratory of Structural Chemistry, Fujian Institute of Research
on the Structure of Matter, Chinese Academy
of Sciences, Fuzhou, Fujian 35000, China
- Shenzhen
Bay Laboratory, Guangming
District, Shenzhen 518107, China
| | - Jing Huang
- Westlake
Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural
Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
| | - Wei Zhuang
- State
Key Laboratory of Structural Chemistry, Fujian Institute of Research
on the Structure of Matter, Chinese Academy
of Sciences, Fuzhou, Fujian 35000, China
- Institute
of Urban Environment, Chinese Academy of
Sciences, XiaMen, Fujian 361021, China
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15
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Hillebrand M, Kalosakas G, Bishop AR, Skokos C. Bubble lifetimes in DNA gene promoters and their mutations affecting transcription. J Chem Phys 2021; 155:095101. [PMID: 34496591 DOI: 10.1063/5.0060335] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Relative lifetimes of inherent double stranded DNA openings with lengths up to ten base pairs are presented for different gene promoters and corresponding mutants that either increase or decrease transcriptional activity in the framework of the Peyrard-Bishop-Dauxois model. Extensive microcanonical simulations are used with energies corresponding to physiological temperature. The bubble lifetime profiles along the DNA sequences demonstrate a significant reduction of the average lifetime at the mutation sites when the mutated promoter decreases transcription, while a corresponding enhancement of the bubble lifetime is observed in the case of mutations leading to increased transcription. The relative difference in bubble lifetimes between the mutated and wild type promoters at the position of mutation varies from 20% to more than 30% as the bubble length decreases.
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Affiliation(s)
- M Hillebrand
- Nonlinear Dynamics and Chaos Group, Department of Mathematics and Applied Mathematics, University of Cape Town, Rondebosch 7701, South Africa
| | - G Kalosakas
- Department of Materials Science, University of Patras, GR-26504 Rio, Greece
| | - A R Bishop
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Ch Skokos
- Nonlinear Dynamics and Chaos Group, Department of Mathematics and Applied Mathematics, University of Cape Town, Rondebosch 7701, South Africa
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16
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González-Jiménez M, Ramakrishnan G, Tukachev NV, Senn HM, Wynne K. Low-frequency vibrational modes in G-quadruplexes reveal the mechanical properties of nucleic acids. Phys Chem Chem Phys 2021; 23:13250-13260. [PMID: 34095914 PMCID: PMC8207511 DOI: 10.1039/d0cp05404f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Low-frequency vibrations play an essential role in biomolecular processes involving DNA such as gene expression, charge transfer, drug intercalation, and DNA–protein recognition. However, understanding the vibrational basis of these mechanisms relies on theoretical models due to the lack of experimental evidence. Here we present the low-frequency vibrational spectra of G-quadruplexes (structures formed by four strands of DNA) and B-DNA characterized using femtosecond optical Kerr-effect spectroscopy. Contrary to expectation, we found that G-quadruplexes show several strongly underdamped delocalized phonon-like modes that have the potential to contribute to the biology of the DNA at the atomic level. In addition, G-quadruplexes present modes at a higher frequency than B-DNA demonstrating that changes in the stiffness of the molecule alter its gigahertz to terahertz vibrational profile. Low-frequency vibrations play an essential role in biomolecular processes involving DNA such as gene expression, charge transfer, drug intercalation, and DNA–protein recognition.![]()
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17
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Lee Y, Kim JG, Lee SJ, Muniyappan S, Kim TW, Ki H, Kim H, Jo J, Yun SR, Lee H, Lee KW, Kim SO, Cammarata M, Ihee H. Ultrafast coherent motion and helix rearrangement of homodimeric hemoglobin visualized with femtosecond X-ray solution scattering. Nat Commun 2021; 12:3677. [PMID: 34135339 PMCID: PMC8209046 DOI: 10.1038/s41467-021-23947-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/27/2021] [Indexed: 11/17/2022] Open
Abstract
Ultrafast motion of molecules, particularly the coherent motion, has been intensively investigated as a key factor guiding the reaction pathways. Recently, X-ray free-electron lasers (XFELs) have been utilized to elucidate the ultrafast motion of molecules. However, the studies on proteins using XFELs have been typically limited to the crystalline phase, and proteins in solution have rarely been investigated. Here we applied femtosecond time-resolved X-ray solution scattering (fs-TRXSS) and a structure refinement method to visualize the ultrafast motion of a protein. We succeeded in revealing detailed ultrafast structural changes of homodimeric hemoglobin involving the coherent motion. In addition to the motion of the protein itself, the time-dependent change of electron density of the hydration shell was tracked. Besides, the analysis on the fs-TRXSS data of myoglobin allows for observing the effect of the oligomeric state on the ultrafast coherent motion. Femtosecond time-resolved X-ray solution scattering (fs-TRXSS) measurements provide information on the structural dynamics of proteins in solution. Here, the authors present a structure refinement method for the analysis of fs-TRXSS data and use it to characterise the ultrafast structural changes of homodimeric haemoglobin.
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Affiliation(s)
- Yunbeom Lee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Jong Goo Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Sang Jin Lee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Srinivasan Muniyappan
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Tae Wu Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Hosung Ki
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Hanui Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Junbeom Jo
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - So Ri Yun
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Hyosub Lee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Kyung Won Lee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Seong Ok Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | | | - Hyotcherl Ihee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea. .,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea.
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18
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Zhu Z, Zhang J, Song Y, Chang C, Ren G, Shen J, Zhang Z, Ji T, Chen M, Zhao H. Broadband terahertz signatures and vibrations of dopamine. Analyst 2021; 145:6006-6013. [PMID: 32756617 DOI: 10.1039/d0an00771d] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Dopamine (DA) is an essential neurotransmitter and hormone of the nervous system, its structural and conformational properties play critical roles in biological functions and signal transmission processes. Although this neuroactive molecule has been studied extensively, the low-frequency vibration features that are closely related to the conformation and molecular interactions in the terahertz (THz) band still remain unclear. In this study, a broadband THz time-domain spectroscopy (THz-TDS) system in the frequency band of 0.5-18 THz was used to characterize the unique THz fingerprint of DA. In addition, density functional theory (DFT) calculations were performed to analyze the vibrational properties of DA. The results suggest that each THz resonant absorption peak of DA corresponds to specific vibrational modes, and the collective vibration also exists in the broadband THz range. Moreover, the interactions between the DA ligand and the D2 and D3 receptors were investigated by docking, and the simulated THz spectra were obtained. The results indicate the dominant role of hydrogen bonding interactions and the specificity of molecular conformation. This work may help to understand the resonance coupling between THz electromagnetic waves and neurotransmitters.
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Affiliation(s)
- Zhongjie Zhu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.
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19
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Tokunaga Y, Tanaka M, Iida H, Kinoshita M, Tojima Y, Takeuchi K, Imashimizu M. Nonthermal excitation effects mediated by sub-terahertz radiation on hydrogen exchange in ubiquitin. Biophys J 2021; 120:2386-2393. [PMID: 33894216 PMCID: PMC8390810 DOI: 10.1016/j.bpj.2021.04.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/23/2021] [Accepted: 04/16/2021] [Indexed: 11/28/2022] Open
Abstract
Water dynamics in the hydration layers of biomolecules play crucial roles in a wide range of biological functions. A hydrated protein contains multiple components of diffusional and vibrational dynamics of water and protein, which may be coupled at ∼0.1-THz frequency (10-ps timescale) at room temperature. However, the microscopic description of biomolecular functions based on various modes of protein-water-coupled motions remains elusive. A novel approach for perturbing the hydration dynamics in the subterahertz frequency range and probing them at the atomic level is therefore warranted. In this study, we investigated the effect of klystron-based, intense 0.1-THz excitation on the slow dynamics of ubiquitin using NMR-based measurements of hydrogen-deuterium exchange. We demonstrated that the subterahertz irradiation accelerated the hydrogen-deuterium exchange of the amides located in the interior of the protein and hydrophobic surfaces while decelerating this exchange in the amides located in the surface loop and short 310 helix regions. This subterahertz-radiation-induced effect was qualitatively contradictory to the increased-temperature-induced effect. Our results suggest that the heterogeneous water dynamics occurring at the protein-water interface include components that are nonthermally excited by the subterahertz radiation. Such subterahertz-excited components may be linked to the slow function-related dynamics of the protein.
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Affiliation(s)
- Yuji Tokunaga
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Masahito Tanaka
- Research Institute for Measurement and Analytical Instrumentation, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Hitoshi Iida
- Research Institute for Physical Measurement, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Moto Kinoshita
- Research Institute for Physical Measurement, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Yuya Tojima
- Research Institute for Physical Measurement, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Koh Takeuchi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Masahiko Imashimizu
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan.
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20
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Serdyukov DS, Goryachkovskaya TN, Mescheryakova IA, Kuznetsov SA, Popik VM, Peltek SE. Fluorescent bacterial biosensor E. coli/pTdcR-TurboYFP sensitive to terahertz radiation. BIOMEDICAL OPTICS EXPRESS 2021; 12:705-721. [PMID: 33680537 PMCID: PMC7901329 DOI: 10.1364/boe.412074] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 05/05/2023]
Abstract
A fluorescent biosensor E. coli/pTdcR-TurboYFP sensitive to terahertz (THz) radiation was developed via transformation of Escherichia coli (E. coli) cells with plasmid, in which the promotor of the tdcR gene controls the expression of yellow fluorescent protein TurboYFP. The biosensor was exposed to THz radiation in various vessels and nutrient media. The threshold and dynamics of fluorescence were found to depend on irradiation conditions. Heat shock or chemical stress yielded the absence of fluorescence induction. The biosensor is applicable to studying influence of THz radiation on the activity of tdcR promotor that is involved in the transport and metabolism of threonine and serine in E. coli.
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Affiliation(s)
- Danil S. Serdyukov
- Laboratory of Molecular Biotechnologies of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, 630090, Russia
- Kurchatov Genomics Center of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, 630090, Russia
- Institute of Laser Physics of the Siberian Branch of the Russian Academy of Sciences, 15B Lavrentiev Aven., Novosibirsk, 630090, Russia
| | - Tatiana N. Goryachkovskaya
- Laboratory of Molecular Biotechnologies of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, 630090, Russia
- Kurchatov Genomics Center of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, 630090, Russia
| | - Irina A. Mescheryakova
- Laboratory of Molecular Biotechnologies of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, 630090, Russia
- Kurchatov Genomics Center of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, 630090, Russia
| | - Sergei A. Kuznetsov
- Physics Department of Novosibirsk State University, 2 Pirogov Str., Novosibirsk, 630090, Russia
- Technological Design Institute of Applied Microelectronics — Novosibirsk Branch of Rzhanov Institute of Semiconductor Physics of the Siberian Branch of the Russian Academy of Sciences, 2/1 Lavrentiev Aven., Novosibirsk, 630090, Russia
| | - Vasiliy M. Popik
- Budker Institute of Nuclear Physics of the Siberian Branch of the Russian Academy of Sciences, 11 Lavrentiev Aven., Novosibirsk, 630090, Russia
| | - Sergey E. Peltek
- Laboratory of Molecular Biotechnologies of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, 630090, Russia
- Kurchatov Genomics Center of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, 630090, Russia
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21
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Imashimizu M, Tanaka M, Hoshina H. Gre factors prevent thermal and mechanical stresses induced by terahertz irradiation during transcription. Genes Cells 2020; 26:56-64. [PMID: 33247986 DOI: 10.1111/gtc.12822] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/18/2020] [Accepted: 11/21/2020] [Indexed: 11/29/2022]
Abstract
During transcription in cells, the transcription complex consisting of RNA polymerase, DNA and nascent RNA is exposed to fluctuating temperature and pressure. However, little is known about the mechanism of transcriptional homeostasis under fluctuating physical parameters. In this study, we generated these fluctuating parameters using pulsed local heating and acoustic waves in the reaction system of transcription by Escherichia coli RNA polymerase, using a terahertz free-electron laser. We demonstrated that transcription processes, including abortive initiation and elongation pausing, and the fidelity of elongation are significantly affected by the laser-based local perturbations. We also found that all these functional alternations in the transcription process are almost completely mitigated by the presence of Gre proteins. It is well known that Gre proteins enhance RNA cleavage of polymerase by binding to the pore structure termed secondary channel. Recently, the chaperone activities have also been proposed for Gre proteins, yet the details directly associated with transcription are largely unknown. Our finding indicates that Gre proteins are necessary for maintaining transcriptional homeostasis under thermal and mechanical stresses.
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Affiliation(s)
- Masahiko Imashimizu
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Masahito Tanaka
- Research Institute for Measurement and Analytical Instrumentation, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Hiromichi Hoshina
- Terahertz Sensing and Imaging Team, Center for Advanced Photonics, RIKEN, Sendai, Miyagi, Japan
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22
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Maciá E. Base-Pairs' Correlated Oscillation Effects on the Charge Transfer in Double-Helix B-DNA Molecules. MATERIALS (BASEL, SWITZERLAND) 2020; 13:E5119. [PMID: 33202814 PMCID: PMC7697525 DOI: 10.3390/ma13225119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/09/2020] [Accepted: 11/09/2020] [Indexed: 05/12/2023]
Abstract
By introducing a suitable renormalization process, the charge carrier and phonon dynamics of a double-stranded helical DNA molecule are expressed in terms of an effective Hamiltonian describing a linear chain, where the renormalized transfer integrals explicitly depend on the relative orientations of the Watson-Crick base pairs, and the renormalized on-site energies are related to the electronic parameters of consecutive base pairs along the helix axis, as well as to the low-frequency phonons' dispersion relation. The existence of synchronized collective oscillations enhancing the π-π orbital overlapping among different base pairs is disclosed from the study of the obtained analytical dynamical equations. The role of these phonon-correlated, long-range oscillation effects on the charge transfer properties of double-stranded DNA homopolymers is discussed in terms of the resulting band structure.
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Affiliation(s)
- Enrique Maciá
- Departamento de Física de Materiales, Facultad CC. Físicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
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23
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Peralta M, Feijoo S, Varela S, Mujica V, Medina E. Coherence preservation and electron-phonon interaction in electron transfer in DNA. J Chem Phys 2020; 153:165102. [PMID: 33138441 DOI: 10.1063/5.0023775] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We analyze the influence of electron-phonon (e-ph) interaction in a model for electron transfer (ET) processes in DNA in terms of the envelope function approach for spinless electrons. We are specifically concerned with the effect of e-ph interaction on the coherence of the ET process and how to model the interaction of DNA with phonon reservoirs of biological relevance. We assume that the electron bearing orbitals are half filled and derive the physics of e-ph coupling in the vicinity in reciprocal space. We find that at half filling, the acoustical modes are decoupled to ET at first order, while optical modes are predominant. The latter are associated with inter-strand vibrational modes in consistency with previous studies involving polaron models of ET. Coupling to acoustic modes depends on electron doping of DNA, while optical modes are always coupled within our model. Our results yield e-ph coupling consistent with estimates in the literature, and we conclude that large polarons are the main result of such e-ph interactions. This scenario will have strong consequences on decoherence of ET under physiological conditions due to relative isolation from thermal equilibration of the ET mechanism.
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Affiliation(s)
- Mayra Peralta
- Yachay Tech University, School of Physical Sciences and Nanotechnology, 100119 Urcuqui, Ecuador
| | - Steven Feijoo
- Yachay Tech University, School of Physical Sciences and Nanotechnology, 100119 Urcuqui, Ecuador
| | - Solmar Varela
- Yachay Tech University, School of Physical Sciences and Nanotechnology, 100119 Urcuqui, Ecuador
| | - Vladimiro Mujica
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, USA and Ikerbasque Foundation and Donostia International Physics Center (DIPC), Manuel de Lardizabal Pasealekua 4, 20018 Donostia, Euskadi, Spain
| | - Ernesto Medina
- Yachay Tech University, School of Physical Sciences and Nanotechnology, 100119 Urcuqui, Ecuador
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24
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Hadži S, Lah J. Origin of heat capacity increment in DNA folding: The hydration effect. Biochim Biophys Acta Gen Subj 2020; 1865:129774. [PMID: 33164852 DOI: 10.1016/j.bbagen.2020.129774] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 10/09/2020] [Accepted: 10/20/2020] [Indexed: 02/03/2023]
Abstract
BACKGROUND Understanding DNA folding thermodynamics is crucial for prediction of DNA thermal stability. It is now well established that DNA folding is accompanied by a decrease of the heat capacity ∆cp, F, however its molecular origin is not understood. In analogy to protein folding it has been assumed that this is due to dehydration of DNA constituents, however no evidence exists to support this conclusion. METHODS Here we analyze partial molar heat capacity of nucleic bases and nucleosides in aqueous solutions obtained from calorimetric experiments and calculate the hydration heat capacity contribution ∆cphyd. RESULTS We present hydration heat capacity contributions of DNA constituents and show that they correlate with the solvent accessible surface area. The average contribution for nucleic base dehydration is +0.56 J mol-1 K-1 Å-2 and can be used to estimate the ∆cp, F contribution for DNA folding. CONCLUSIONS We show that dehydration is one of the major sources contributing to the observed ∆cp, F increment in DNA folding. Other possible sources contributing to the overall ∆cp, F should be significant but appear to compensate each other to high degree. The calculated ∆cphyd for duplexes and noncanonical DNA structures agree excellently with the overall experimental ∆cp, F values. By contrast, empirical parametrizations developed for proteins result in poor ∆cphyd predictions and should not be applied to DNA folding. GENERAL SIGNIFICANCE Heat capacity is one of the main thermodynamic quantities that strongly affects thermal stability of macromolecules. At the molecular level the heat capacity in DNA folding stems from removal of water from nucleobases.
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Affiliation(s)
- S Hadži
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia.
| | - J Lah
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia.
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25
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Farrell A, González-Jiménez M, Ramakrishnan G, Wynne K. Low-Frequency (Gigahertz to Terahertz) Depolarized Raman Scattering Off n-Alkanes, Cycloalkanes, and Six-Membered Rings: A Physical Interpretation. J Phys Chem B 2020; 124:7611-7624. [PMID: 32790389 PMCID: PMC7476039 DOI: 10.1021/acs.jpcb.0c03769] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 08/06/2020] [Indexed: 11/29/2022]
Abstract
Molecular liquids have long been known to undergo various distinct intermolecular motions, from fast librations and cage-rattling oscillations to slow orientational and translational diffusion. However, their resultant gigahertz to terahertz spectra are far from simple, appearing as broad shapeless bands that span many orders of magnitude of frequency, making meaningful interpretation troublesome. Ad hoc spectral line shape fitting has become a notoriously fine art in the field; a unified approach to handling such spectra is long overdue. Here we apply ultrafast optical Kerr-effect (OKE) spectroscopy to study the intermolecular dynamics of room-temperature n-alkanes, cycloalkanes, and six-carbon rings, as well as liquid methane and propane. This work provides stress tests and converges upon an experimentally robust model across simple molecular series and range of temperatures, providing a blueprint for the interpretation of the dynamics of van der Waals liquids. This will enable the interpretation of low-frequency spectra of more complex liquids.
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Affiliation(s)
- Andrew
J. Farrell
- School of Chemistry, University
of Glasgow, Glasgow G12 8QQ, United Kingdom
| | | | | | - Klaas Wynne
- School of Chemistry, University
of Glasgow, Glasgow G12 8QQ, United Kingdom
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26
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Ando M, Kawano M, Tashiro A, Takamuku T, Shirota H. Low-Frequency Spectra of 1-Methyl-3-octylimidazolium Tetrafluoroborate Mixtures with Methanol, Acetonitrile, and Dimethyl Sulfoxide: A Combined Study of Femtosecond Raman-Induced Kerr Effect Spectroscopy and Molecular Dynamics Simulations. J Phys Chem B 2020; 124:7857-7871. [DOI: 10.1021/acs.jpcb.0c04870] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Masatoshi Ando
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi, Inage-ku, Chiba 263-8522, Japan
| | - Masahiro Kawano
- Department of Chemistry and Applied Chemistry, Graduate School of Science and Engineering, Saga University, Honjo-machi, Saga 840-8502, Japan
| | - Atsuya Tashiro
- Department of Chemistry and Applied Chemistry, Graduate School of Science and Engineering, Saga University, Honjo-machi, Saga 840-8502, Japan
| | - Toshiyuki Takamuku
- Faculty of Science and Engineering, Saga University, Honjo-machi, Saga 840-8502, Japan
| | - Hideaki Shirota
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi, Inage-ku, Chiba 263-8522, Japan
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27
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Gabriele VR, Shvonski A, Hoffman CS, Giersig M, Herczynski A, Naughton MJ, Kempa K. Towards spectrally selective catastrophic response. Phys Rev E 2020; 101:062415. [PMID: 32688591 DOI: 10.1103/physreve.101.062415] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 05/28/2020] [Indexed: 11/07/2022]
Abstract
We study the large-amplitude response of classical molecules to electromagnetic radiation, showing the universality of the transition from linear to nonlinear response and breakup at sufficiently large amplitudes. We demonstrate that a range of models, from the simple harmonic oscillator to the successful Peyrard-Bishop-Dauxois type models of DNA, which include realistic effects of the environment (including damping and dephasing due to thermal fluctuations), lead to characteristic universal behavior: formation of domains of dissociation in driving force amplitude-frequency space, characterized by the presence of local boundary minima. We demonstrate that by simply following the progression of the resonance maxima in this space, while gradually increasing intensity of the radiation, one must necessarily arrive at one of these minima, i.e., a point where the ultrahigh spectral selectivity is retained. We show that this universal property, applicable to other oscillatory systems, is a consequence of the fact that these models belong to the fold catastrophe universality class of Thom's catastrophe theory. This in turn implies that for most biostructures, including DNA, high spectral sensitivity near the onset of the denaturation processes can be expected. Such spectrally selective molecular denaturation could find important applications in biology and medicine.
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Affiliation(s)
- V R Gabriele
- Department of Physics, Boston College, Chestnut Hill, Massachusetts 02467, USA
| | - A Shvonski
- Department of Physics, Boston College, Chestnut Hill, Massachusetts 02467, USA.,Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - C S Hoffman
- Department of Biology, Boston College, Chestnut Hill, Massachusetts 02467, USA
| | - M Giersig
- Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany.,International Academy of Optoelectronics at Zhaoqing, South China Normal University, 526238 Guangdong, People's Republic of China
| | - A Herczynski
- Department of Physics, Boston College, Chestnut Hill, Massachusetts 02467, USA
| | - M J Naughton
- Department of Physics, Boston College, Chestnut Hill, Massachusetts 02467, USA
| | - K Kempa
- Department of Physics, Boston College, Chestnut Hill, Massachusetts 02467, USA
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28
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Lane PD, Reichenbach J, Farrell AJ, Ramakers LAI, Adamczyk K, Hunt NT, Wynne K. Experimental observation of nanophase segregation in aqueous salt solutions around the predicted liquid-liquid transition in water. Phys Chem Chem Phys 2020; 22:9438-9447. [PMID: 32314750 DOI: 10.1039/c9cp06082k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The liquid-liquid transition in supercooled liquid water, predicted to occur around 220 K, is controversial due to the difficulty of studying it caused by competition from ice crystallization (the so-called "no man's land"). In aqueous solutions, it has been predicted to give rise to phase separation on a nanometer scale between a solute-rich high-density phase and a water-rich low-density phase. Here we report direct experimental evidence for the formation of a nanosegregated phase in eutectic aqueous solutions of LiCl and LiSCN where the presence of crystalline water can be experimentally excluded. Femtosecond infrared and Raman spectroscopies are used to determine the temperature-dependent structuring of water, the solvation of the SCN- anion, and the size of the phase segregated domains.
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Affiliation(s)
- Paul D Lane
- Department of Physics, SUPA, University of Strathclyde, Glasgow, UK.
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29
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Shirota H, Moriyama K. Low-Frequency Vibrational Motions of Polystyrene in Carbon Tetrachloride: Comparison with Model Monomer and Dependence on Concentration and Molecular Weight. J Phys Chem B 2020; 124:2006-2016. [PMID: 32073847 DOI: 10.1021/acs.jpcb.9b10672] [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
In this study, the low-frequency vibrational dynamics of polystyrene (PS) in CCl4 was investigated by femtosecond Raman-induced Kerr effect spectroscopy. Ethylbenzene (EBz) was also investigated as a model monomer of the polymer to elucidate the unique dynamical features of PS in solution. The broadened low-frequency spectrum of the PS/CCl4 in the frequency region below 150 cm-1 is significantly different from that of the EBz/CCl4. Difference spectra between the PS or EBz solutions and neat CCl4, normalized to an internal vibrational mode of CCl4, clearly show a much lower spectral intensity for the PS/CCl4 than the EBz/CCl4 in the low-frequency region below ca. 20 cm-1. This indicates that translational motions are suppressed in the PS/CCl4 compared to the EBz/CCl4. Moreover, the high-frequency motion at ca. 70 cm-1, mainly due to phenyl ring librations, occurs at higher frequency in PS (78 cm-1) than EBz (65 cm-1). In addition, the results of concentration-dependent experiments show that the first moment (M1) of the low-frequency difference spectra of both PS/CCl4 and EBz/CCl4 is almost independent of the concentration. The molecular weight dependence of the low-frequency spectrum in the PS/CCl4 shows that the M1 value of the low-frequency spectral band of PS shifts to higher frequencies when the molecular weight of PS increases up to Mw = ∼1000, which corresponds approximately to the decamer, and then remains constant upon further increasing the molecular weight.
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Affiliation(s)
- Hideaki Shirota
- Department of Chemistry, Chiba University, 1-33 Yayoi, Inage-ku, Chiba 263-8522, Japan
| | - Katsuhiko Moriyama
- Department of Chemistry, Chiba University, 1-33 Yayoi, Inage-ku, Chiba 263-8522, Japan
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30
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Magdău IB, Mead GJ, Blake GA, Miller TF. Interpretation of the THz-THz-Raman Spectrum of Bromoform. J Phys Chem A 2019; 123:7278-7287. [DOI: 10.1021/acs.jpca.9b05165] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ioan B. Magdău
- Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Griffin J. Mead
- Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Geoffrey A. Blake
- Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
- Division of Geological & Planetary Sciences, California Institute of Technology, Pasadena, California 91125, United States
| | - Thomas F. Miller
- Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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31
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Fritzsch R, Greetham GM, Clark IP, Minnes L, Towrie M, Parker AW, Hunt NT. Monitoring Base-Specific Dynamics during Melting of DNA-Ligand Complexes Using Temperature-Jump Time-Resolved Infrared Spectroscopy. J Phys Chem B 2019; 123:6188-6199. [PMID: 31268327 DOI: 10.1021/acs.jpcb.9b04354] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Ultrafast time-resolved infrared spectroscopy employing nanosecond temperature-jump initiation has been used to study the melting of double-stranded (ds)DNA oligomers in the presence and absence of minor groove-binding ligand Hoechst 33258. Ligand binding to ds(5'-GCAAATTTCC-3'), which binds Hoechst 33258 in the central A-tract region with nanomolar affinity, causes a dramatic increase in the timescales for strand melting from 30 to ∼250 μs. Ligand binding also suppresses premelting disruption of the dsDNA structure, which takes place on 100 ns timescales and includes end-fraying. In contrast, ligand binding to the ds(5'-GCATATATCC-3') sequence, which exhibits an order of magnitude lower affinity for Hoechst 33258 than the A-tract motif, leads to an increase by only a factor of 5 in melting timescales and reduced suppression of premelting sequence perturbation and end-fraying. These results demonstrate a dynamic impact of the minor groove ligand on the dsDNA structure that correlates with binding strength and thermodynamic stabilization of the duplex. Moreover, the ability of the ligand to influence base pairs distant from the binding site has potential implications for allosteric communication mechanisms in dsDNA.
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Affiliation(s)
- Robby Fritzsch
- Department of Physics, SUPA , University of Strathclyde , Glasgow G4 0NG , U.K
| | - Gregory M Greetham
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus, Didcot OX11 0QX , U.K
| | - Ian P Clark
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus, Didcot OX11 0QX , U.K
| | - Lucy Minnes
- Department of Physics, SUPA , University of Strathclyde , Glasgow G4 0NG , U.K
| | - Michael Towrie
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus, Didcot OX11 0QX , U.K
| | - Anthony W Parker
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus, Didcot OX11 0QX , U.K
| | - Neil T Hunt
- Department of Chemistry and York Biomedical Research Institute , University of York , Heslington, York YO10 5DD , U.K
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32
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Batista de Carvalho ALM, Mamede AP, Dopplapudi A, Garcia Sakai V, Doherty J, Frogley M, Cinque G, Gardner P, Gianolio D, Batista de Carvalho LAE, Marques MPM. Anticancer drug impact on DNA – a study by neutron spectroscopy coupled with synchrotron-based FTIR and EXAFS. Phys Chem Chem Phys 2019; 21:4162-4175. [DOI: 10.1039/c8cp05881d] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Complementary information on drug–DNA interplay has been achieved for Pt/Pd anticancer agents, by a combined QENS, SR-FTIR-ATR and EXAFS approach.
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Affiliation(s)
| | - Adriana P. Mamede
- Química-Física Molecular
- Department of Chemistry
- University of Coimbra
- 3004-535 Coimbra
- Portugal
| | - Asha Dopplapudi
- ISIS Facility
- STFC Rutherford Appleton Laboratory
- Chilton
- Didcot
- UK
| | | | - James Doherty
- Diamond Light Source
- Harwell Science and Innovation Campus
- Chilton
- Didcot
- UK
| | - Mark Frogley
- Diamond Light Source
- Harwell Science and Innovation Campus
- Chilton
- Didcot
- UK
| | - Gianfelice Cinque
- Diamond Light Source
- Harwell Science and Innovation Campus
- Chilton
- Didcot
- UK
| | - Peter Gardner
- Manchester Institute of Biotechnology
- University of Manchester
- Manchester
- UK
| | - Diego Gianolio
- Diamond Light Source
- Harwell Science and Innovation Campus
- Chilton
- Didcot
- UK
| | | | - M. Paula M. Marques
- Química-Física Molecular
- Department of Chemistry
- University of Coimbra
- 3004-535 Coimbra
- Portugal
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33
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34
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Reichenbach J, Wynne K. Frustration vs Prenucleation: Understanding the Surprising Stability of Supersaturated Sodium Thiosulfate Solutions. J Phys Chem B 2018; 122:7590-7596. [DOI: 10.1021/acs.jpcb.8b04112] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
| | - Klaas Wynne
- School of Chemistry, University of Glasgow, Glasgow G12 8QQ, U.K
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35
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Hand K, Yates E. Terahertz: dictating the frequency of life. Do macromolecular vibrational modes impose thermal limitations on terrestrial life? J R Soc Interface 2018; 14:rsif.2017.0673. [PMID: 29142018 DOI: 10.1098/rsif.2017.0673] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 10/25/2017] [Indexed: 11/12/2022] Open
Abstract
Conditions on exoplanets include elevated temperatures and pressures. The response of carbon-based biological macromolecules to such conditions is then relevant to the viability of life. The capacity of proteins and ribozymes to catalyse reactions or bind receptors, and nucleic acids to convey information, depends on them sampling different conformational states. These are determined by macromolecular vibrational states, or phonon modes, accessible using terahertz (THz: 1012Hz) absorption spectroscopy. THz spectra of biological macromolecules exhibit broad absorption at approximately 6 THz (equating to approx. 280 K) corresponding to dense transitions between phonon modes. There are also troughs at approximately 10 THz (approx. 500 K) implying diminishing numbers of available conformational states at higher temperatures; hence, fewer routes by which biochemical processes can be realized, as equilibrium is approached. Could this conformational bottleneck hinder the operation of biological macromolecules at higher temperatures? We suggest that the troughs at approximately 10 THz in absorbance spectra indicate that the hydrogen bonds, charge interactions and geometry of biological macromolecules associated with terrestrial life impose fundamental vibrational properties that could limit the upper temperature at which they may function.
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Affiliation(s)
- Kieran Hand
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Edwin Yates
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
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36
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Ruggiero MT, Zhang W, Bond AD, Mittleman DM, Zeitler JA. Uncovering the Connection Between Low-Frequency Dynamics and Phase Transformation Phenomena in Molecular Solids. PHYSICAL REVIEW LETTERS 2018; 120:196002. [PMID: 29799217 DOI: 10.1103/physrevlett.120.196002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Indexed: 06/08/2023]
Abstract
The low-frequency motions of molecules in the condensed phase have been shown to be vital to a large number of physical properties and processes. However, in the case of disordered systems, it is often difficult to elucidate the atomic-level details surrounding these phenomena. In this work, we have performed an extensive experimental and computational study on the molecular solid camphor, which exhibits a rich and complex structure-dynamics relationship, and undergoes an order-disorder transition near ambient conditions. The combination of x-ray diffraction, variable temperature and pressure terahertz time-domain spectroscopy, ab initio molecular dynamics, and periodic density functional theory calculations enables a complete picture of the phase transition to be obtained, inclusive of mechanistic, structural, and thermodynamic phenomena. Additionally, the low-frequency vibrations of a disordered solid are characterized for the first time with atomic-level precision, uncovering a clear link between such motions and the phase transformation. Overall, this combination of methods allows for significant details to be obtained for disordered solids and the associated transformations, providing a framework that can be directly applied for a wide range of similar systems.
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Affiliation(s)
- Michael T Ruggiero
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, United Kingdom
- Present Address: Department of Chemistry, University of Vermont, 82 University Place, Burlington, Vermont 05405, USA
| | - Wei Zhang
- School of Engineering, Brown University, Providence, Rhode Island 02912, USA
| | - Andrew D Bond
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Daniel M Mittleman
- School of Engineering, Brown University, Providence, Rhode Island 02912, USA
| | - J Axel Zeitler
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, United Kingdom
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37
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Roy P, Jha A, Yasarapudi VB, Ram T, Puttaraju B, Patil S, Dasgupta J. Ultrafast bridge planarization in donor-π-acceptor copolymers drives intramolecular charge transfer. Nat Commun 2017; 8:1716. [PMID: 29170455 PMCID: PMC5700982 DOI: 10.1038/s41467-017-01928-z] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Accepted: 10/24/2017] [Indexed: 11/09/2022] Open
Abstract
Donor-π-acceptor conjugated polymers form the material basis for high power conversion efficiencies in organic solar cells. Large dipole moment change upon photoexcitation via intramolecular charge transfer in donor-π-acceptor backbone is conjectured to facilitate efficient charge-carrier generation. However, the primary structural changes that drive ultrafast charge transfer step have remained elusive thereby limiting a rational structure-function correlation for such copolymers. Here we use structure-sensitive femtosecond stimulated Raman spectroscopy to demonstrate that π-bridge torsion forms the primary reaction coordinate for intramolecular charge transfer in donor-π-acceptor copolymers. Resonance-selective Raman snapshots of exciton relaxation reveal rich vibrational dynamics of the bridge modes associated with backbone planarization within 400 fs, leading to hot intramolecular charge transfer state formation while subsequent cooling dynamics of backbone-centric modes probe the charge transfer relaxation. Our work establishes a phenomenological gating role of bridge torsions in determining the fundamental timescale and energy of photogenerated carriers, and therefore opens up dynamics-based guidelines for fabricating energy-efficient organic photovoltaics.
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Affiliation(s)
- Palas Roy
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, 400005, India
| | - Ajay Jha
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, 400005, India
| | - Vineeth B Yasarapudi
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, 400005, India
| | - Thulasi Ram
- Department of Nuclear and Atomic Physics, Tata Institute of Fundamental Research, Mumbai, 400005, India
| | - Boregowda Puttaraju
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, 560012, India
| | - Satish Patil
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, 560012, India
| | - Jyotishman Dasgupta
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, 400005, India.
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38
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Sensale S, Peng Z, Chang HC. Kinetic theory for DNA melting with vibrational entropy. J Chem Phys 2017; 147:135101. [PMID: 28987107 DOI: 10.1063/1.4996174] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
By treating DNA as a vibrating nonlinear lattice, an activated kinetic theory for DNA melting is developed to capture the breakage of the hydrogen bonds and subsequent softening of torsional and bending vibration modes. With a coarse-grained lattice model, we identify a key bending mode with GHz frequency that replaces the hydrogen vibration modes as the dominant out-of-phase phonon vibration at the transition state. By associating its bending modulus to a universal in-phase bending vibration modulus at equilibrium, we can hence estimate the entropic change in the out-of-phase vibration from near-equilibrium all-atom simulations. This and estimates of torsional and bending entropy changes lead to the first predictive and sequence-dependent theory with good quantitative agreement with experimental data for the activation energy of melting of short DNA molecules without intermediate hairpin structures.
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Affiliation(s)
- Sebastian Sensale
- Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, Indiana 46556-5637, USA
| | - Zhangli Peng
- Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, Indiana 46556-5637, USA
| | - Hsueh-Chia Chang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556-5637, USA
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39
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Alexandrov LB, Rasmussen KØ, Bishop AR, Alexandrov BS. Evaluating the role of coherent delocalized phonon-like modes in DNA cyclization. Sci Rep 2017; 7:9731. [PMID: 28851939 PMCID: PMC5575098 DOI: 10.1038/s41598-017-09537-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 07/27/2017] [Indexed: 12/11/2022] Open
Abstract
The innate flexibility of a DNA sequence is quantified by the Jacobson-Stockmayer's J-factor, which measures the propensity for DNA loop formation. Recent studies of ultra-short DNA sequences revealed a discrepancy of up to six orders of magnitude between experimentally measured and theoretically predicted J-factors. These large differences suggest that, in addition to the elastic moduli of the double helix, other factors contribute to loop formation. Here, we develop a new theoretical model that explores how coherent delocalized phonon-like modes in DNA provide single-stranded "flexible hinges" to assist in loop formation. We combine the Czapla-Swigon-Olson structural model of DNA with our extended Peyrard-Bishop-Dauxois model and, without changing any of the parameters of the two models, apply this new computational framework to 86 experimentally characterized DNA sequences. Our results demonstrate that the new computational framework can predict J-factors within an order of magnitude of experimental measurements for most ultra-short DNA sequences, while continuing to accurately describe the J-factors of longer sequences. Further, we demonstrate that our computational framework can be used to describe the cyclization of DNA sequences that contain a base pair mismatch. Overall, our results support the conclusion that coherent delocalized phonon-like modes play an important role in DNA cyclization.
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Affiliation(s)
- Ludmil B Alexandrov
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87545, United States of America
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM, 87102, USA
| | - Kim Ø Rasmussen
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87545, United States of America
| | - Alan R Bishop
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87545, United States of America
| | - Boian S Alexandrov
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87545, United States of America.
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM, 87102, USA.
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40
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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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41
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Ramakrishnan G, González-Jiménez M, Lapthorn AJ, Wynne K. Spectrum of Slow and Super-Slow (Picosecond to Nanosecond) Water Dynamics around Organic and Biological Solutes. J Phys Chem Lett 2017; 8:2964-2970. [PMID: 28612605 DOI: 10.1021/acs.jpclett.7b01127] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Water dynamics in the solvation shell of solutes plays a very important role in the interaction of biomolecules and in chemical reaction dynamics. However, a selective spectroscopic study of the solvation shell is difficult because of the interference of the solute dynamics. Here we report on the observation of heavily slowed down water dynamics in the solvation shell of different solutes by measuring the low-frequency spectrum of solvation water, free from the contribution of the solute. A slowdown factor of ∼50 is observed even for relatively low concentrations of the solute. We go on to show that the effect can be generalized to different solutes including proteins.
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Affiliation(s)
| | | | - Adrian J Lapthorn
- School of Chemistry, WestCHEM, University of Glasgow , Glasgow G12 8QQ, United Kingdom
| | - Klaas Wynne
- School of Chemistry, WestCHEM, University of Glasgow , Glasgow G12 8QQ, United Kingdom
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42
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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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43
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Reichenbach J, Ruddell SA, González-Jiménez M, Lemes J, Turton DA, France DJ, Wynne K. Phonon-like Hydrogen-Bond Modes in Protic Ionic Liquids. J Am Chem Soc 2017; 139:7160-7163. [PMID: 28511538 DOI: 10.1021/jacs.7b03036] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Gigahertz- to terahertz-frequency infrared and Raman spectra contain a wealth of information concerning the structure, intermolecular forces, and dynamics of ionic liquids. However, these spectra generally have a large number of contributions ranging from slow diffusional modes to underdamped librations and intramolecular vibrational modes. This makes it difficult to isolate effects such as the role of Coulombic and hydrogen-bonding interactions. We have applied far-infrared and ultrafast optical Kerr effect spectroscopies on carefully selected ions with a greater or lesser degree of symmetry in order to isolate spectral signals of interest. This has allowed us to demonstrate the presence of longitudinal and transverse optical phonon modes and a great similarity of alkylammonium-based protic ionic liquids to liquid water. The data show that such phonon modes will be present in all ionic liquids, requiring a reinterpretation of their spectra.
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Affiliation(s)
- Judith Reichenbach
- School of Chemistry, WestCHEM, University of Glasgow , Glasgow G12 8QQ, U.K
| | - Stuart A Ruddell
- School of Chemistry, WestCHEM, University of Glasgow , Glasgow G12 8QQ, U.K
| | | | - Julio Lemes
- School of Chemistry, WestCHEM, University of Glasgow , Glasgow G12 8QQ, U.K
| | - David A Turton
- School of Chemistry, WestCHEM, University of Glasgow , Glasgow G12 8QQ, U.K
| | - David J France
- School of Chemistry, WestCHEM, University of Glasgow , Glasgow G12 8QQ, U.K
| | - Klaas Wynne
- School of Chemistry, WestCHEM, University of Glasgow , Glasgow G12 8QQ, U.K
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44
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Dhumal NR, Kiefer J, Turton D, Wynne K, Kim HJ. Dielectric Relaxation of the Ionic Liquid 1-Ethyl-3-methylimidazolium Ethyl Sulfate: Microwave and Far-IR Properties. J Phys Chem B 2017; 121:4845-4852. [DOI: 10.1021/acs.jpcb.7b00160] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nilesh R. Dhumal
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Johannes Kiefer
- Technische
Thermodynamik, Universität Bremen, 28359 Bremen, Germany
| | - David Turton
- School
of Chemistry, University of Glasgow, Glasgow G12 8QQ, U.K
| | - Klaas Wynne
- School
of Chemistry, University of Glasgow, Glasgow G12 8QQ, U.K
| | - Hyung J. Kim
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
- School
of Computational Sciences, Korea Institute for Advanced Study, Seoul 02455, Korea
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45
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Kakinuma S, Ishida T, Shirota H. Femtosecond Raman-Induced Kerr Effect Study of Temperature-Dependent Intermolecular Dynamics in Imidazolium-Based Ionic Liquids: Effects of Anion Species and Cation Alkyl Groups. J Phys Chem B 2017; 121:250-264. [DOI: 10.1021/acs.jpcb.6b11009] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Tateki Ishida
- Department
of Theoretical and Computational Molecular Science, Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
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46
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Hithell G, González-Jiménez M, Greetham GM, Donaldson PM, Towrie M, Parker AW, Burley GA, Wynne K, Hunt NT. Ultrafast 2D-IR and optical Kerr effect spectroscopy reveal the impact of duplex melting on the structural dynamics of DNA. Phys Chem Chem Phys 2017; 19:10333-10342. [DOI: 10.1039/c7cp00054e] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Changes in the structural and solvation dynamics of DNA upon duplex melting are observed by 2D-IR and optical Kerr-effect spectroscopies.
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Affiliation(s)
- Gordon Hithell
- Department of Physics, University of Strathclyde, SUPA
- Glasgow
- UK
| | | | - Gregory M. Greetham
- STFC Central Laser Facility, Research Complex at Harwell, Harwell Science and Innovation Campus
- Didcot
- UK
| | - Paul M. Donaldson
- STFC Central Laser Facility, Research Complex at Harwell, Harwell Science and Innovation Campus
- Didcot
- UK
| | - Michael Towrie
- STFC Central Laser Facility, Research Complex at Harwell, Harwell Science and Innovation Campus
- Didcot
- UK
| | - Anthony W. Parker
- STFC Central Laser Facility, Research Complex at Harwell, Harwell Science and Innovation Campus
- Didcot
- UK
| | - Glenn A. Burley
- Department of Pure and Applied Chemistry, WestCHEM, University of Strathclyde, 295 Cathedral Street
- Glasgow
- UK
| | - Klaas Wynne
- School of Chemistry, WestCHEM, University of Glasgow
- Glasgow
- UK
| | - Neil T. Hunt
- Department of Physics, University of Strathclyde, SUPA
- Glasgow
- UK
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47
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El Khoury Y, Hellwig P. Far infrared spectroscopy of hydrogen bonding collective motions in complex molecular systems. Chem Commun (Camb) 2017; 53:8389-8399. [DOI: 10.1039/c7cc03496b] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Far infrared spectroscopy as a tool for the study of inter and intramolecular interactions in complex molecular structures.
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Affiliation(s)
- Youssef El Khoury
- Laboratoire de Bioélectrochimie et Spectroscopie
- UMR 7140
- CMC
- Université de Strasbourg CNRS
- Strasbourg
| | - Petra Hellwig
- Laboratoire de Bioélectrochimie et Spectroscopie
- UMR 7140
- CMC
- Université de Strasbourg CNRS
- Strasbourg
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48
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Ruggiero MT, Krynski M, Kissi EO, Sibik J, Markl D, Tan NY, Arslanov D, van der Zande W, Redlich B, Korter TM, Grohganz H, Löbmann K, Rades T, Elliott SR, Zeitler JA. The significance of the amorphous potential energy landscape for dictating glassy dynamics and driving solid-state crystallisation. Phys Chem Chem Phys 2017; 19:30039-30047. [DOI: 10.1039/c7cp06664c] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We show clear evidence for a theory proposing that the shape and structure of the PES is the fundamental factor underlying the dynamics at temperatures below the glass transition.
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49
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Ruggiero MT, Axel Zeitler J, Korter TM. Concomitant polymorphism and the martensitic-like transformation of an organic crystal. Phys Chem Chem Phys 2017; 19:28502-28506. [DOI: 10.1039/c7cp04666a] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Terahertz vibrational spectroscopy and solid-state density functional theory together reveal the true nature of a pseudo-continuous crystalline polymorphic phase transition.
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Affiliation(s)
- Michael T. Ruggiero
- Department of Chemistry
- Syracuse University
- Syracuse
- USA
- Department of Chemical Engineering and Biotechnology, University of Cambridge
| | - J. Axel Zeitler
- Department of Chemical Engineering and Biotechnology, University of Cambridge
- Cambridge
- UK
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