1
|
Donaldson PM, Greetham GM, Middleton CT, Luther BM, Zanni MT, Hamm P, Krummel AT. Breaking Barriers in Ultrafast Spectroscopy and Imaging Using 100 kHz Amplified Yb-Laser Systems. Acc Chem Res 2023; 56:2062-2071. [PMID: 37429010 PMCID: PMC10809409 DOI: 10.1021/acs.accounts.3c00152] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Indexed: 07/12/2023]
Abstract
ConspectusUltrafast spectroscopy and imaging have become tools utilized by a broad range of scientists involved in materials, energy, biological, and chemical sciences. Commercialization of ultrafast spectrometers including transient absorption spectrometers, vibrational sum frequency generation spectrometers, and even multidimensional spectrometers have put these advanced spectroscopy measurements into the hands of practitioners originally outside the field of ultrafast spectroscopy. There is now a technology shift occurring in ultrafast spectroscopy, made possible by new Yb-based lasers, that is opening exciting new experiments in the chemical and physical sciences. Amplified Yb-based lasers are not only more compact and efficient than their predecessors but also, most importantly, operate at many times the repetition rate with improved noise characteristics in comparison to the previous generation of Ti:sapphire amplifier technologies. Taken together, these attributes are enabling new experiments, generating improvements to long-standing techniques, and affording the transformation of spectroscopies to microscopies. This Account aims to show that the shift to 100 kHz lasers is a transformative step in nonlinear spectroscopy and imaging, much like the dramatic expansion that occurred with the commercialization of Ti:sapphire laser systems in the 1990s. The impact of this technology will be felt across a great swath of scientific communities. We first describe the technology landscape of amplified Yb-based laser systems used in conjunction with 100 kHz spectrometers operating with shot-to-shot pulse shaping and detection. We also identify the range of different parametric conversion and supercontinuum techniques which now provide a path to making pulses of light optimal for ultrafast spectroscopy. Second, we describe specific instances from our laboratories of how the amplified Yb-based light sources and spectrometers are transformative. For multiple probe time-resolved infrared and transient 2D IR spectroscopy, the gain in temporal span and signal-to-noise enables dynamical spectroscopy measurements from femtoseconds to seconds. These gains widen the applicability of time-resolved infrared techniques across a range of topics in photochemistry, photocatalysis, and photobiology as well as lower the technical barriers to implementation in a laboratory. For 2D visible spectroscopy and microscopy with white light, as well as 2D IR imaging, the high repetition rates of these new Yb-based light sources allow one to spatially map 2D spectra while maintaining high signal-to-noise in the data. To illustrate the gains, we provide examples of imaging applications in the study of photovoltaic materials and spectroelectrochemistry.
Collapse
Affiliation(s)
- Paul M. Donaldson
- Central
Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0QX, United Kingdom
| | - Greg M. Greetham
- Central
Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0QX, United Kingdom
| | - Chris T. Middleton
- PhaseTech
Spectroscopy, Inc., 4916
East Broadway, Suite 125, Madison, Wisconsin 53716, United States
| | - Bradley M. Luther
- Colorado
State University, Department of Chemistry, 200 W. Lake Street, Fort Collins, Colorado 80523, United States
| | - Martin T. Zanni
- University
of Wisconsin, Department of Chemistry, Room 8361, 1101 University Ave., Madison, Wisconsin 53706, United States
| | - Peter Hamm
- University
of Zurich, Department of Chemistry, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Amber T. Krummel
- Colorado
State University, Department of Chemistry, 200 W. Lake Street, Fort Collins, Colorado 80523, United States
| |
Collapse
|
2
|
Meng W, Peng HC, Liu Y, Stelling A, Wang L. Modeling the Infrared Spectroscopy of Oligonucleotides with 13C Isotope Labels. J Phys Chem B 2023; 127:2351-2361. [PMID: 36898003 DOI: 10.1021/acs.jpcb.2c08915] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
The carbonyl stretching modes have been widely used in linear and two-dimensional infrared (IR) spectroscopy to probe the conformation, interaction, and biological functions of nucleic acids. However, due to their universal appearance in nucleobases, the IR absorption bands of nucleic acids are often highly congested in the 1600-1800 cm-1 region. Following the fruitful applications in proteins, 13C isotope labels have been introduced to the IR measurements of oligonucleotides to reveal their site-specific structural fluctuations and hydrogen bonding conditions. In this work, we combine recently developed frequency and coupling maps to develop a theoretical strategy that models the IR spectra of oligonucleotides with 13C labels directly from molecular dynamics simulations. We apply the theoretical method to nucleoside 5'-monophosphates and DNA double helices and demonstrate how elements of the vibrational Hamiltonian determine the spectral features and their changes upon isotope labeling. Using the double helices as examples, we show that the calculated IR spectra are in good agreement with experiments and the 13C isotope labeling technique can potentially be applied to characterize the stacking configurations and secondary structures of nucleic acids.
Collapse
Affiliation(s)
- Wenting Meng
- Department of Chemistry and Chemical Biology, Institute for Quantitative Biomedicine, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Hao-Che Peng
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Yuanhao Liu
- Department of Statistics, Institute for Quantitative Biomedicine, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Allison Stelling
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Lu Wang
- Department of Chemistry and Chemical Biology, Institute for Quantitative Biomedicine, Rutgers University, Piscataway, New Jersey 08854, United States
| |
Collapse
|
3
|
Kraka E, Quintano M, La Force HW, Antonio JJ, Freindorf M. The Local Vibrational Mode Theory and Its Place in the Vibrational Spectroscopy Arena. J Phys Chem A 2022; 126:8781-8798. [DOI: 10.1021/acs.jpca.2c05962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, Texas75275-0314, United States
| | - Mateus Quintano
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, Texas75275-0314, United States
| | - Hunter W. La Force
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, Texas75275-0314, United States
| | - Juliana J. Antonio
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, Texas75275-0314, United States
| | - Marek Freindorf
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, Texas75275-0314, United States
| |
Collapse
|
4
|
Fingerhut BP. The mutual interactions of RNA, counterions and water - quantifying the electrostatics at the phosphate-water interface. Chem Commun (Camb) 2021; 57:12880-12897. [PMID: 34816825 PMCID: PMC8640580 DOI: 10.1039/d1cc05367a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/01/2021] [Indexed: 11/25/2022]
Abstract
The structure and dynamics of polyanionic biomolecules, like RNA, are decisively determined by their electric interactions with the water molecules and the counterions in the environment. The solvation dynamics of the biomolecules involves a subtle balance of non-covalent and many-body interactions with structural fluctuations due to thermal motion occurring in a femto- to subnanosecond time range. This complex fluctuating many particle scenario is crucial in defining the properties of biological interfaces with far reaching significance for the folding of RNA structures and for facilitating RNA-protein interactions. Given the inherent complexity, suited model systems, carefully calibrated and benchmarked by experiments, are required to quantify the relevant interactions of RNA with the aqueous environment. In this feature article we summarize our recent progress in the understanding of the electrostatics at the biological interface of double stranded RNA (dsRNA) and transfer RNA (tRNA). Dimethyl phosphate (DMP) is introduced as a viable and rigorously accessible model system allowing the interaction strength with water molecules and counterions, their relevant fluctuation timescales and the spatial reach of interactions to be established. We find strong (up to ≈90 MV cm-1) interfacial electric fields with fluctuations extending up to ≈20 THz and demonstrate how the asymmetric stretching vibration νAS(PO2)- of the polarizable phosphate group can serve as the most sensitive probe for interfacial interactions, establishing a rigorous link between simulations and experiment. The approach allows for the direct interfacial observation of interactions of biologically relevant Mg2+ counterions with phosphate groups in contact pair geometries via the rise of a new absorption band imposed by exchange repulsion interactions at short interatomic distances. The systematic extension to RNA provides microscopic insights into the changes of the hydration structure that accompany the temperature induced melting of the dsRNA double helix and quantify the ionic interactions in the folded tRNA. The results show that pairs of negatively charged phosphate groups and Mg2+ ions represent a key structural feature of RNA embedded in water. They highlight the importance of binding motifs made of contact pairs in the electrostatic stabilization of RNA structures that have a strong impact on the surface potential and enable the fine tuning of the local electrostatic properties which are expected to be relevant for mediating the interactions between biomolecules.
Collapse
|
5
|
Fick RJ, Liu AY, Nussbaumer F, Kreutz C, Rangadurai A, Xu Y, Sommer RD, Shi H, Scheiner S, Stelling AL. Probing the Hydrogen-Bonding Environment of Individual Bases in DNA Duplexes with Isotope-Edited Infrared Spectroscopy. J Phys Chem B 2021; 125:7613-7627. [PMID: 34236202 PMCID: PMC8311644 DOI: 10.1021/acs.jpcb.1c01351] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
![]()
Measuring the strength
of the hydrogen bonds between DNA base pairs
is of vital importance for understanding how our genetic code is physically
accessed and recognized in cells, particularly during replication
and transcription. Therefore, it is important to develop probes for
these key hydrogen bonds (H-bonds) that dictate events critical to
cellular function, such as the localized melting of DNA. The vibrations
of carbonyl bonds are well-known probes of their H-bonding environment,
and their signals can be observed with infrared (IR) spectroscopy.
Yet, pinpointing a single bond of interest in the complex IR spectrum
of DNA is challenging due to the large number of carbonyl signals
that overlap with each other. Here, we develop a method using isotope
editing and infrared (IR) spectroscopy to isolate IR signals from
the thymine (T) C2=O carbonyl. We use solvatochromatic studies
to show that the TC2=O signal’s position in the IR spectrum
is sensitive to the H-bonding capacity of the solvent. Our results
indicate that C2=O of a single T base within DNA duplexes experiences
weak H-bonding interactions. This finding is consistent with the existence
of a third, noncanonical CH···O H-bond between adenine
and thymine in both Watson–Crick and Hoogsteen base pairs in
DNA.
Collapse
Affiliation(s)
- Robert J Fick
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Amy Y Liu
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, United States
| | - Felix Nussbaumer
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck 6020, Austria
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck 6020, Austria
| | - Atul Rangadurai
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, United States
| | - Yu Xu
- Department of Chemistry, Duke University, Durham, North Carolina 27710, United States
| | - Roger D Sommer
- Molecular Education, Technology, and Research Innovation Center, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Honglue Shi
- Department of Chemistry, Duke University, Durham, North Carolina 27710, United States
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Allison L Stelling
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States.,Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, United States
| |
Collapse
|
6
|
Elsaesser T, Schauss J, Kundu A, Fingerhut BP. Phosphate Vibrations Probe Electric Fields in Hydrated Biomolecules: Spectroscopy, Dynamics, and Interactions. J Phys Chem B 2021; 125:3899-3908. [PMID: 33834783 PMCID: PMC8154594 DOI: 10.1021/acs.jpcb.1c01502] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Electric interactions
have a strong impact on the structure and
dynamics of biomolecules in their native water environment. Given
the variety of water arrangements in hydration shells and the femto-
to subnanosecond time range of structural fluctuations, there is a
strong quest for sensitive noninvasive probes of local electric fields.
The stretching vibrations of phosphate groups, in particular the asymmetric
(PO2)− stretching vibration νAS(PO2)−, allow for a quantitative
mapping of dynamic electric fields in aqueous environments via a field-induced
redshift of their transition frequencies and concomitant changes of
vibrational line shapes. We present a systematic study of νAS(PO2)− excitations in molecular
systems of increasing complexity, including dimethyl phosphate (DMP),
short DNA and RNA duplex structures, and transfer RNA (tRNA) in water.
A combination of linear infrared absorption, two-dimensional infrared
(2D-IR) spectroscopy, and molecular dynamics (MD) simulations gives
quantitative insight in electric-field tuning rates of vibrational
frequencies, electric field and fluctuation amplitudes, and molecular
interaction geometries. Beyond neat water environments, the formation
of contact ion pairs of phosphate groups with Mg2+ ions
is demonstrated via frequency upshifts of the νAS(PO2)− vibration, resulting in a distinct
vibrational band. The frequency positions of contact geometries are
determined by an interplay of attractive electric and repulsive exchange
interactions.
Collapse
Affiliation(s)
- Thomas Elsaesser
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin 12489, Germany
| | - Jakob Schauss
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin 12489, Germany
| | - Achintya Kundu
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin 12489, Germany
| | - Benjamin P Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin 12489, Germany
| |
Collapse
|
7
|
Affiliation(s)
- Peter Hamm
- Department of Chemistry, University of Zurich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland
| |
Collapse
|
8
|
Kundu A, Schauss J, Fingerhut BP, Elsaesser T. Change of Hydration Patterns upon RNA Melting Probed by Excitations of Phosphate Backbone Vibrations. J Phys Chem B 2020; 124:2132-2138. [PMID: 32101008 DOI: 10.1021/acs.jpcb.0c01474] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The water hydration shell has a decisive impact on the structural and functional properties of RNA. Changes of the RNA structure upon melting and in biochemical processes are accompanied by a change of hydration patterns, a process that is barely characterized. To discern hydration geometries around the backbone phosphate groups of an RNA double helix at the molecular level, we combine two-dimensional infrared spectroscopy of phosphate vibrations with theoretical simulations. There are three distinct coexisting hydration motifs of the RNA A-helix: an ordered chain-like arrangement of water molecules with links between neighboring phosphate groups, separate local hydration shells of up to six water molecules, and hydrated phosphate/counterion contact pairs. RNA disordering upon melting is connected with a transition from predominantly ordered water structures to local hydration shells around phosphate units. Structural fluctuations are dominated by librational water motions occurring on a 300 fs time scale, without exchange between hydration motifs.
Collapse
Affiliation(s)
- Achintya Kundu
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin 12489, Germany
| | - Jakob Schauss
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin 12489, Germany
| | - Benjamin P Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin 12489, Germany
| | - Thomas Elsaesser
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin 12489, Germany
| |
Collapse
|
9
|
Jiang Y, Wang L. Modeling the vibrational couplings of nucleobases. J Chem Phys 2020; 152:084114. [PMID: 32113367 PMCID: PMC7046491 DOI: 10.1063/1.5141858] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 02/06/2020] [Indexed: 12/11/2022] Open
Abstract
Vibrational spectroscopy, in particular infrared spectroscopy, has been widely used to probe the three-dimensional structures and conformational dynamics of nucleic acids. As commonly used chromophores, the C=O and C=C stretch modes in the nucleobases exhibit distinct spectral features for different base pairing and stacking configurations. To elucidate the origin of their structural sensitivity, in this work, we develop transition charge coupling (TCC) models that allow one to efficiently calculate the interactions or couplings between the C=O and C=C chromophores based on the geometric arrangements of the nucleobases. To evaluate their performances, we apply the TCC models to DNA and RNA oligonucleotides with a variety of secondary and tertiary structures and demonstrate that the predicted couplings are in quantitative agreement with the reference values. We further elucidate how the interactions between the paired and stacked bases give rise to characteristic IR absorption peaks and show that the TCC models provide more reliable predictions of the coupling constants as compared to the transition dipole coupling scheme. The TCC models, together with our recently developed through-bond coupling constants and vibrational frequency maps, provide an effective theoretical strategy to model the vibrational Hamiltonian, and hence the vibrational spectra of nucleic acids in the base carbonyl stretch region directly from atomistic molecular simulations.
Collapse
Affiliation(s)
- Yaoyukun Jiang
- Department of Chemistry and Chemical Biology, Institute for Quantitative Biomedicine, Rutgers University, 174 Frelinghuysen Road, Piscataway, New Jersey 08854, USA
| | - Lu Wang
- Department of Chemistry and Chemical Biology, Institute for Quantitative Biomedicine, Rutgers University, 174 Frelinghuysen Road, Piscataway, New Jersey 08854, USA
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
|
12
|
Fritzsch R, Donaldson PM, Greetham GM, Towrie M, Parker AW, Baker MJ, Hunt NT. Rapid Screening of DNA–Ligand Complexes via 2D-IR Spectroscopy and ANOVA–PCA. Anal Chem 2018; 90:2732-2740. [DOI: 10.1021/acs.analchem.7b04727] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Robby Fritzsch
- Department
of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow G4 0NG, U.K
| | - Paul M. Donaldson
- STFC
Central Laser Facility, Research Complex at Harwell, Rutherford Appleton
Laboratory, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX, U.K
| | - Gregory M. Greetham
- STFC
Central Laser Facility, Research Complex at Harwell, Rutherford Appleton
Laboratory, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX, U.K
| | - Michael Towrie
- STFC
Central Laser Facility, Research Complex at Harwell, Rutherford Appleton
Laboratory, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX, U.K
| | - Anthony W. Parker
- STFC
Central Laser Facility, Research Complex at Harwell, Rutherford Appleton
Laboratory, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX, U.K
| | - Matthew J. Baker
- WestCHEM,
Department of Pure and Applied Chemistry, Technology and Innovation
Centre, University of Strathclyde, 99 George Street, Glasgow G1 1RD, U.K
| | - Neil T. Hunt
- Department
of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow G4 0NG, U.K
| |
Collapse
|
13
|
Yang F, Dong X, Feng M, Zhao J, Wang J. Central-metal effect on intramolecular vibrational energy transfer of M(CO) 5Br (M = Mn, Re) probed by two-dimensional infrared spectroscopy. Phys Chem Chem Phys 2018; 20:3637-3647. [PMID: 29340363 DOI: 10.1039/c7cp05117d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Vibrational energy transfer in transition metal complexes with flexible structures in condensed phases is of central importance to catalytical chemistry processes. In this work, two molecules with different metal atoms, M(CO)5Br (where M = Mn, Re), were used as model systems, and their axial and radial carbonyl stretching modes as infrared probes. The central-metal effect on intramolecular vibrational energy redistribution (IVR) in M(CO)5Br was investigated in polar and nonpolar solvents. The linear infrared (IR) peak splitting between carbonyl vibrations increases as the metal atom changes from Mn to Re. The waiting-time dependent two-dimensional infrared diagonal- and off-diagonal peak amplitudes reveal a faster IVR process in Re(CO)5Br than in Mn(CO)5Br. With the aid of density functional theory (DFT) calculations, the central-metal effect on IVR time linearly correlates with the vibrational coupling strength between the two involved modes. In addition, the polar solvent is found to accelerate the IVR process by affecting the anharmonic vibrational potentials of a solute vibration mode.
Collapse
Affiliation(s)
- Fan Yang
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.
| | | | | | | | | |
Collapse
|
14
|
Dong X, Yang F, Zhao J, Wang J. Efficient Intramolecular Vibrational Excitonic Energy Transfer in Ru3(CO)12 Cluster Revealed by Two-Dimensional Infrared Spectroscopy. J Phys Chem B 2018; 122:1296-1305. [DOI: 10.1021/acs.jpcb.7b10067] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xueqian Dong
- Beijing
National Laboratory for Molecular Sciences; Molecular Reaction Dynamics
Laboratory, CAS Research/Education Center for Excellence in Molecular
Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Fan Yang
- Beijing
National Laboratory for Molecular Sciences; Molecular Reaction Dynamics
Laboratory, CAS Research/Education Center for Excellence in Molecular
Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Juan Zhao
- Beijing
National Laboratory for Molecular Sciences; Molecular Reaction Dynamics
Laboratory, CAS Research/Education Center for Excellence in Molecular
Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jianping Wang
- Beijing
National Laboratory for Molecular Sciences; Molecular Reaction Dynamics
Laboratory, CAS Research/Education Center for Excellence in Molecular
Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| |
Collapse
|
15
|
Donaldson P, Greetham G, Shaw D, Parker A, Towrie M. A 100 kHz Pulse Shaping 2D-IR Spectrometer Based on Dual Yb:KGW Amplifiers. J Phys Chem A 2018; 122:780-787. [DOI: 10.1021/acs.jpca.7b10259] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- P.M. Donaldson
- Central
Laser Facility, Science and Technology Facilities Council, Research
Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0QX, U.K
| | - G.M. Greetham
- Central
Laser Facility, Science and Technology Facilities Council, Research
Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0QX, U.K
| | - D.J. Shaw
- Central
Laser Facility, Science and Technology Facilities Council, Research
Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0QX, U.K
- Department
of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow, G4 0NG, U.K
| | - A.W. Parker
- Central
Laser Facility, Science and Technology Facilities Council, Research
Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0QX, U.K
| | - M. Towrie
- Central
Laser Facility, Science and Technology Facilities Council, Research
Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0QX, U.K
| |
Collapse
|
16
|
Wang J. Ultrafast two-dimensional infrared spectroscopy for molecular structures and dynamics with expanding wavelength range and increasing sensitivities: from experimental and computational perspectives. INT REV PHYS CHEM 2017. [DOI: 10.1080/0144235x.2017.1321856] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Jianping Wang
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, The Chinese Academy of Sciences, Beijing, P.R. China
- College of Chemistry, University of Chinese Academy of Sciences, Beijing, P.R. China
| |
Collapse
|
17
|
Ramakers LAI, Hithell G, May JJ, Greetham GM, Donaldson PM, Towrie M, Parker AW, Burley GA, Hunt NT. 2D-IR Spectroscopy Shows that Optimized DNA Minor Groove Binding of Hoechst33258 Follows an Induced Fit Model. J Phys Chem B 2017; 121:1295-1303. [PMID: 28102674 DOI: 10.1021/acs.jpcb.7b00345] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The induced fit binding model describes a conformational change occurring when a small molecule binds to its biomacromolecular target. The result is enhanced noncovalent interactions between the ligand and biomolecule. Induced fit is well-established for small molecule-protein interactions, but its relevance to small molecule-DNA binding is less clear. We investigate the molecular determinants of Hoechst33258 binding to its preferred A-tract sequence relative to a suboptimal alternating A-T sequence. Results from two-dimensional infrared spectroscopy, which is sensitive to H-bonding and molecular structure changes, show that Hoechst33258 binding results in loss of the minor groove spine of hydration in both sequences, but an additional perturbation of the base propeller twists occurs in the A-tract binding region. This induced fit maximizes favorable ligand-DNA enthalpic contributions in the optimal binding case and demonstrates that controlling the molecular details that induce subtle changes in DNA structure may hold the key to designing next-generation DNA-binding molecules.
Collapse
Affiliation(s)
- Lennart A I Ramakers
- Department of Physics, University of Strathclyde, SUPA , 107 Rottenrow East, Glasgow G4 0NG, United Kingdon
| | - Gordon Hithell
- Department of Physics, University of Strathclyde, SUPA , 107 Rottenrow East, Glasgow G4 0NG, United Kingdon
| | - John J May
- Department of Pure and Applied Chemistry, WestCHEM, University of Strathclyde , 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Gregory M Greetham
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory , Harwell, Oxford OX11 0QX, United Kingdom
| | - Paul M Donaldson
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory , Harwell, Oxford OX11 0QX, United Kingdom
| | - Michael Towrie
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory , Harwell, Oxford OX11 0QX, United Kingdom
| | - Anthony W Parker
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory , Harwell, Oxford OX11 0QX, United Kingdom
| | - Glenn A Burley
- Department of Pure and Applied Chemistry, WestCHEM, University of Strathclyde , 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Neil T Hunt
- Department of Physics, University of Strathclyde, SUPA , 107 Rottenrow East, Glasgow G4 0NG, United Kingdon
| |
Collapse
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
Fingerhut BP, Costard R, Elsaesser T. Predominance of short range Coulomb forces in phosphate-water interactions—a theoretical analysis. J Chem Phys 2016. [DOI: 10.1063/1.4962755] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Benjamin P. Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| | - Rene Costard
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| | - Thomas Elsaesser
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| |
Collapse
|