301
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Loukova GV, Vasiliev VP, Milov AA, Smirnov VA, Minkin VI. Unraveling electronic properties of an organometallic solute: Lippert-Mataga and quantum-chemical extensive study. J Photochem Photobiol A Chem 2016. [DOI: 10.1016/j.jphotochem.2016.04.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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302
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Haldar T, Kashid SM, Deb P, Kesh S, Bagchi S. Pick and Choose the Spectroscopic Method to Calibrate the Local Electric Field inside Proteins. J Phys Chem Lett 2016; 7:2456-2460. [PMID: 27295386 DOI: 10.1021/acs.jpclett.6b00852] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Electrostatic interactions in proteins play a crucial role in determining the structure-function relation in biomolecules. In recent years, fluorescent probes have been extensively employed to interrogate the polarity in biological cavities through dielectric constants or semiempirical polarity scales. A choice of multiple spectroscopic methods, not limited by fluorophores, along with a molecular level description of electrostatics involving solute-solvent interactions, would allow more flexibility to pick and choose the experimental technique to determine the local electrostatics within protein interiors. In this work we report that ultraviolet/visible-absorption, infrared-absorption, or (13)C NMR can be used to calibrate the local electric field in both hydrogen bonded and non-hydrogen bonded protein environments. The local electric field at the binding site of a serum protein has been determined using the absorption wavelength as well as the carbonyl stretching frequency of its natural steroid substrate, testosterone. Excellent agreement is observed in the results obtained from two independent spectroscopic techniques.
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Affiliation(s)
- Tapas Haldar
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 411008, India
| | - Somnath M Kashid
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 411008, India
| | - Pranab Deb
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 411008, India
| | - Sandeep Kesh
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 411008, India
| | - Sayan Bagchi
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 411008, India
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303
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Dinpajooh M, Matyushov DV. Dielectric constant of water in the interface. J Chem Phys 2016; 145:014504. [DOI: 10.1063/1.4955203] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Mohammadhasan Dinpajooh
- Department of Physics and School of Molecular Sciences, Arizona State University, P.O. Box 871504, Tempe, Arizona 85287, USA
| | - Dmitry V. Matyushov
- Department of Physics and School of Molecular Sciences, Arizona State University, P.O. Box 871504, Tempe, Arizona 85287, USA
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304
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Dahms F, Costard R, Pines E, Fingerhut BP, Nibbering ETJ, Elsaesser T. The Hydrated Excess Proton in the Zundel Cation H5
O2
+
: The Role of Ultrafast Solvent Fluctuations. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602523] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Fabian Dahms
- Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie; Max Born Strasse 2A 12489 Berlin Germany
| | - Rene Costard
- Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie; Max Born Strasse 2A 12489 Berlin Germany
| | - Ehud Pines
- Department of Chemistry; Ben Gurion University of the Negev; P.O.B. 653 Beersheva 84105 Israel
| | - Benjamin P. Fingerhut
- Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie; Max Born Strasse 2A 12489 Berlin Germany
| | - Erik T. J. Nibbering
- Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie; Max Born Strasse 2A 12489 Berlin Germany
| | - Thomas Elsaesser
- Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie; Max Born Strasse 2A 12489 Berlin Germany
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305
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Dahms F, Costard R, Pines E, Fingerhut BP, Nibbering ETJ, Elsaesser T. The Hydrated Excess Proton in the Zundel Cation H5 O2 (+) : The Role of Ultrafast Solvent Fluctuations. Angew Chem Int Ed Engl 2016; 55:10600-5. [PMID: 27374368 DOI: 10.1002/anie.201602523] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Indexed: 11/05/2022]
Abstract
The nature of the excess proton in liquid water has remained elusive after decades of extensive research. In view of ultrafast structural fluctuations of bulk water scrambling the structural motifs of excess protons in water, we selectively probe prototypical protonated water solvates in acetonitrile on the femtosecond time scale. Focusing on the Zundel cation H5 O2 (+) prepared in room-temperature acetonitrile, we unravel the distinct character of its vibrational absorption continuum and separate it from OH stretching and bending excitations in transient pump-probe spectra. The infrared absorption continuum originates from a strong ultrafast frequency modulation of the H(+) transfer vibration and its combination and overtones. Vibrational lifetimes of H5 O2 (+) are found to be in the sub-100 fs range, much shorter than those of unprotonated water. Theoretical results support a picture of proton hydration where fluctuating electrical interactions with the solvent and stochastic thermal excitations of low-frequency modes continuously modify the proton binding site while affecting its motions.
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Affiliation(s)
- Fabian Dahms
- Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max Born Strasse 2A, 12489, Berlin, Germany
| | - Rene Costard
- Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max Born Strasse 2A, 12489, Berlin, Germany
| | - Ehud Pines
- Department of Chemistry, Ben Gurion University of the Negev, P.O.B. 653, Beersheva, 84105, Israel
| | - Benjamin P Fingerhut
- Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max Born Strasse 2A, 12489, Berlin, Germany
| | - Erik T J Nibbering
- Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max Born Strasse 2A, 12489, Berlin, Germany.
| | - Thomas Elsaesser
- Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max Born Strasse 2A, 12489, Berlin, Germany.
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306
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Imoto S, Kibies P, Rosin C, Winter R, Kast SM, Marx D. Toward Extreme Biophysics: Deciphering the Infrared Response of Biomolecular Solutions at High Pressures. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602757] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Sho Imoto
- Lehrstuhl für Theoretische Chemie; Ruhr-Universität Bochum; 44780 Bochum Germany
| | - Patrick Kibies
- Physikalische Chemie III; Technische Universität Dortmund; 44227 Dortmund Germany
| | - Christopher Rosin
- Physikalische Chemie I; Technische Universität Dortmund; 44227 Dortmund Germany
| | - Roland Winter
- Physikalische Chemie I; Technische Universität Dortmund; 44227 Dortmund Germany
| | - Stefan M. Kast
- Physikalische Chemie III; Technische Universität Dortmund; 44227 Dortmund Germany
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie; Ruhr-Universität Bochum; 44780 Bochum Germany
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307
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Imoto S, Kibies P, Rosin C, Winter R, Kast SM, Marx D. Toward Extreme Biophysics: Deciphering the Infrared Response of Biomolecular Solutions at High Pressures. Angew Chem Int Ed Engl 2016; 55:9534-8. [DOI: 10.1002/anie.201602757] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 05/18/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Sho Imoto
- Lehrstuhl für Theoretische Chemie; Ruhr-Universität Bochum; 44780 Bochum Germany
| | - Patrick Kibies
- Physikalische Chemie III; Technische Universität Dortmund; 44227 Dortmund Germany
| | - Christopher Rosin
- Physikalische Chemie I; Technische Universität Dortmund; 44227 Dortmund Germany
| | - Roland Winter
- Physikalische Chemie I; Technische Universität Dortmund; 44227 Dortmund Germany
| | - Stefan M. Kast
- Physikalische Chemie III; Technische Universität Dortmund; 44227 Dortmund Germany
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie; Ruhr-Universität Bochum; 44780 Bochum Germany
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308
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Sen S, Boda M, Venkat Lata S, Naresh Patwari G. Internal electric fields in small water clusters [(H2O)n; n = 2-6]. Phys Chem Chem Phys 2016; 18:16730-7. [PMID: 27270616 DOI: 10.1039/c6cp02803a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The electric field experienced by a water molecule within a water cluster depends on its position relative to the rest of the water molecules. The stabilization energies and the red-shifts in the donor O-H stretching vibrations in the water clusters increase with the cluster size concomitant with the increase in the electric field experienced by the donor O-H of a particular water molecule due to the hydrogen bonding network. The red-shifts in O-H stretching frequencies show a spread of about ±100 cm(-1) against the corresponding electric fields. Deviations from linearity were marked in the region of 100-160 MV cm(-1), which can be attributed to the strain in the hydrogen bonding network, especially for structures with DDAA and DDA motifs. The linear Stark effect holds up to 200 MV cm(-1) of internal electric field for the average red-shifts in the O-H stretching frequencies, with a Stark tuning rate of 2.4 cm(-1) (MV cm(-1))(-1), suggesting the validity of the classical model in small water clusters.
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Affiliation(s)
- Saumik Sen
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - Manjusha Boda
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - S Venkat Lata
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - G Naresh Patwari
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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309
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Haldar T, Bagchi S. Electrostatic Interactions Are Key to C═O n-π* Shifts: An Experimental Proof. J Phys Chem Lett 2016; 7:2270-2275. [PMID: 27249517 DOI: 10.1021/acs.jpclett.6b01052] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Carbonyl n-π* transitions are known to undergo blue shift in polar and hydrogen-bonding solvents. Using semiempirical expressions, previous studies hypothesized several factors like change in dipole moment and hydrogen-bond strength upon excitation to cause the blue shift. Theoretically, ground-state electrostatics has been predicted to be the key to the observed shifts, however, an experimental proof has been lacking. Our experimental results demonstrate a consistent linear correlation between IR (ground-state phenomenon) and n-π* frequency shifts (involves both ground and excited electronic-states) of carbonyls in hydrogen-bonded and non-hydrogen-bonded environments. The carbonyl hydrogen-bonding status is experimentally verified from deviation in n-π*/fluorescence correlation. The IR/n-π* correlation validates the key role of electrostatic stabilization of the ground state toward n-π* shifts and demonstrates the electrostatic nature of carbonyl hydrogen bonds. n-π* shifts show linear sensitivity to calculated electrostatic fields on carbonyls. Our results portray the potential for n-π* absorption to estimate local polarity in biomolecules and to probe chemical reactions involving carbonyl activation/stabilization.
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Affiliation(s)
- Tapas Haldar
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 411008, India
| | - Sayan Bagchi
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 411008, India
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310
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Dey A, Mondal SI, Sen S, Patwari GN. Spectroscopic and Ab Initio Investigation of C−H⋅⋅⋅N Hydrogen-Bonded Complexes of Fluorophenylacetylenes: Frequency Shifts and Correlations. Chemphyschem 2016; 17:2509-15. [PMID: 27146197 DOI: 10.1002/cphc.201600343] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Arghya Dey
- Department of Chemistry; Indian Institute of Technology Bombay; Powai, Mumbai - 400076 India
| | - Sohidul Islam Mondal
- Department of Chemistry; Indian Institute of Technology Bombay; Powai, Mumbai - 400076 India
| | - Saumik Sen
- Department of Chemistry; Indian Institute of Technology Bombay; Powai, Mumbai - 400076 India
| | - G. Naresh Patwari
- Department of Chemistry; Indian Institute of Technology Bombay; Powai, Mumbai - 400076 India
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311
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Poynton FE, Hall JP, Keane PM, Schwarz C, Sazanovich IV, Towrie M, Gunnlaugsson T, Cardin CJ, Cardin DJ, Quinn SJ, Long C, Kelly JM. Direct observation by time-resolved infrared spectroscopy of the bright and the dark excited states of the [Ru(phen) 2(dppz)] 2+ light-switch compound in solution and when bound to DNA. Chem Sci 2016; 7:3075-3084. [PMID: 29997799 PMCID: PMC6005197 DOI: 10.1039/c5sc04514b] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 01/26/2016] [Indexed: 02/01/2023] Open
Abstract
The [Ru(phen)2(dppz)]2+ complex (1) is non-emissive in water but is highly luminescent in organic solvents or when bound to DNA, making it a useful probe for DNA binding. To date, a complete mechanistic explanation for this "light-switch" effect is still lacking. With this in mind we have undertaken an ultrafast time resolved infrared (TRIR) study of 1 and directly observe marker bands between 1280-1450 cm-1, which characterise both the emissive "bright" and the non-emissive "dark" excited states of the complex, in CD3CN and D2O respectively. These characteristic spectral features are present in the [Ru(dppz)3]2+ solvent light-switch complex but absent in [Ru(phen)3]2+, which is luminescent in both solvents. DFT calculations show that the vibrational modes responsible for these characteristic bands are predominantly localised on the dppz ligand. Moreover, they reveal that certain vibrational modes of the "dark" excited state couple with vibrational modes of two coordinating water molecules, and through these to the bulk solvent, thus providing a new insight into the mechanism of the light-switch effect. We also demonstrate that the marker bands for the "bright" state are observed for both Λ- and Δ-enantiomers of 1 when bound to DNA and that photo-excitation of the complex induces perturbation of the guanine and cytosine carbonyl bands. This perturbation is shown to be stronger for the Λ-enantiomer, demonstrating the different binding site properties of the two enantiomers and the ability of this technique to determine the identity and nature of the binding site of such intercalators.
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Affiliation(s)
- Fergus E Poynton
- School of Chemistry , Trinity College Dublin , The University of Dublin , Dublin 2 , Ireland .
- Trinity Biomedical Sciences Institute (TBSI) , Trinity College Dublin , The University of Dublin , Dublin 2 , Ireland
| | - James P Hall
- Department of Chemistry , University of Reading , Reading RG6 6AD , UK
- Diamond Light Source , Harwell Science and Innovation Campus , Didcot , Oxfordshire OX11 0QX , UK
| | - Páraic M Keane
- School of Chemistry , Trinity College Dublin , The University of Dublin , Dublin 2 , Ireland .
- Department of Chemistry , University of Reading , Reading RG6 6AD , UK
| | - Christine Schwarz
- Department of Chemistry , University of Reading , Reading RG6 6AD , UK
| | - Igor V Sazanovich
- Central Laser Facility , Research Complex at Harwell , STFC Rutherford Appleton Laboratory , Oxfordshire OX11 0QX , UK
| | - Michael Towrie
- Central Laser Facility , Research Complex at Harwell , STFC Rutherford Appleton Laboratory , Oxfordshire OX11 0QX , UK
| | - Thorfinnur Gunnlaugsson
- School of Chemistry , Trinity College Dublin , The University of Dublin , Dublin 2 , Ireland .
- Trinity Biomedical Sciences Institute (TBSI) , Trinity College Dublin , The University of Dublin , Dublin 2 , Ireland
| | | | - David J Cardin
- Department of Chemistry , University of Reading , Reading RG6 6AD , UK
| | - Susan J Quinn
- School of Chemistry , University College Dublin , Dublin 4 , Ireland
| | - Conor Long
- The School of Chemical Sciences , Dublin City University , Dublin 9 , Ireland .
| | - John M Kelly
- School of Chemistry , Trinity College Dublin , The University of Dublin , Dublin 2 , Ireland .
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312
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Deb P, Haldar T, Kashid SM, Banerjee S, Chakrabarty S, Bagchi S. Correlating Nitrile IR Frequencies to Local Electrostatics Quantifies Noncovalent Interactions of Peptides and Proteins. J Phys Chem B 2016; 120:4034-46. [DOI: 10.1021/acs.jpcb.6b02732] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pranab Deb
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Tapas Haldar
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Somnath M Kashid
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Subhrashis Banerjee
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Suman Chakrabarty
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Sayan Bagchi
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
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313
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List NH, Jensen HJA, Kongsted J. Local electric fields and molecular properties in heterogeneous environments through polarizable embedding. Phys Chem Chem Phys 2016; 18:10070-80. [PMID: 27007060 DOI: 10.1039/c6cp00669h] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In spectroscopies, the local field experienced by a molecule embedded in an environment will be different from the externally applied electromagnetic field, and this difference may significantly alter the response and transition properties of the molecule. The polarizable embedding (PE) model has previously been developed to model the local field contribution stemming from the direct molecule-environment coupling of the electromagnetic response properties of molecules in solution as well as in heterogeneous environments, such as proteins. Here we present an extension of this approach to address the additional effective external field effect, i.e., the manifestations of the environment polarization induced by the external field, which allows for the calculation of properties defined in terms of the external field. Within a response framework, we report calculations of the one- and two-photon absorption (1PA and 2PA, respectively) properties of PRODAN-methanol clusters as well as the fluorescent protein DsRed. Our results demonstrate the necessity of accounting for both the dynamical reaction field and effective external field contributions to the local field in order to reproduce full quantum chemical reference calculations. For the lowest π→π* transition in DsRed, inclusion of effective external field effects gives rise to a 1.9- and 3.5-fold reduction in the 1PA and 2PA cross-sections, respectively. The effective external field is, however, strongly influenced by the heterogeneity of the protein matrix, and the resulting effect can lead to either screening or enhancement depending on the nature of the transition under consideration.
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314
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Wolke CT, Fournier JA, Miliordos E, Kathmann SM, Xantheas SS, Johnson MA. Isotopomer-selective spectra of a single intact H2O molecule in the Cs+(D2O)5H2O isotopologue: Going beyond pattern recognition to harvest the structural information encoded in vibrational spectra. J Chem Phys 2016; 144:074305. [DOI: 10.1063/1.4941285] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Conrad T. Wolke
- Sterling Chemistry Laboratory, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
| | - Joseph A. Fournier
- Sterling Chemistry Laboratory, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
| | - Evangelos Miliordos
- Physical Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, Richland, Washington 99352, USA
| | - Shawn M. Kathmann
- Physical Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, Richland, Washington 99352, USA
| | - Sotiris S. Xantheas
- Physical Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, Richland, Washington 99352, USA
| | - Mark A. Johnson
- Sterling Chemistry Laboratory, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
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315
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Hack J, Grills DC, Miller JR, Mani T. Identification of Ion-Pair Structures in Solution by Vibrational Stark Effects. J Phys Chem B 2016; 120:1149-57. [PMID: 26807492 DOI: 10.1021/acs.jpcb.5b11893] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ion pairing is a fundamental consideration in many areas of chemistry and has implications in a wide range of sciences and technologies that include batteries and organic photovoltaics. Ions in solution are known to inhabit multiple possible states, including free ions (FI), contact ion pairs (CIP), and solvent-separated ion pairs (SSIP). However, in solutions of organic radicals and nonmetal electrolytes, it is often difficult to distinguish between these states. In the first part of this work, we report evidence for the formation of SSIPs in low-polarity solvents and distinct measurements of CIP, SSIP, and FI, by using the ν(C≡N) infrared (IR) band of a nitrile-substituted fluorene radical anion. Use of time-resolved IR detection following pulse radiolysis allowed us to unambiguously assign the peak of the FI. In the presence of nonmetal electrolytes, two distinct red-shifted peaks were observed and assigned to the CIP and SSIP. The assignments are interpreted in the framework of the vibrational Stark effect (VSE) and are supported by (1) the solvent dependence of ion-pair populations, (2) the observation of a cryptand-separated sodium ion pair that mimics the formation of SSIPs, and (3) electronic structure calculations. In the second part of this work, we show that a blue-shift of the ν(C≡N) IR band due to the VSE can be induced in a nitrile-substituted fluorene radical anion by covalently tethering it to a metal-chelating ligand that forms an intramolecular ion pair upon reduction and complexation with sodium ion. This adds support to the conclusion that the shift in IR absorptions by ion pairing originates from the VSE. These results combined show that we can identify ion-pair structures by using the VSE, including the existence of SSIPs in a low-polarity solvent.
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Affiliation(s)
- John Hack
- Chemistry Department, Brookhaven National Laboratory , Upton, New York 11973-5000, United States.,Chemical Engineering Department, University of Virginia , 102 Engineers' Way, PO Box 400741, Charlottesville, Virginia 22904-4741, United States
| | - David C Grills
- Chemistry Department, Brookhaven National Laboratory , Upton, New York 11973-5000, United States
| | - John R Miller
- Chemistry Department, Brookhaven National Laboratory , Upton, New York 11973-5000, United States
| | - Tomoyasu Mani
- Chemistry Department, Brookhaven National Laboratory , Upton, New York 11973-5000, United States
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316
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Sevinc PC, Dhital B, Govind Rao V, Wang Y, Lu HP. Probing Electric Field Effect on Covalent Interactions at a Molecule–Semiconductor Interface. J Am Chem Soc 2016; 138:1536-42. [PMID: 26735967 DOI: 10.1021/jacs.5b10253] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Papatya C. Sevinc
- Department of Chemistry and
Center for Photochemical Sciences, Bowling Green State University, Bowling
Green, Ohio 43403, United States
| | - Bharat Dhital
- Department of Chemistry and
Center for Photochemical Sciences, Bowling Green State University, Bowling
Green, Ohio 43403, United States
| | - Vishal Govind Rao
- Department of Chemistry and
Center for Photochemical Sciences, Bowling Green State University, Bowling
Green, Ohio 43403, United States
| | - Yuanmin Wang
- Department of Chemistry and
Center for Photochemical Sciences, Bowling Green State University, Bowling
Green, Ohio 43403, United States
| | - H. Peter Lu
- Department of Chemistry and
Center for Photochemical Sciences, Bowling Green State University, Bowling
Green, Ohio 43403, United States
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317
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Błasiak B, Ritchie AW, Webb LJ, Cho M. Vibrational solvatochromism of nitrile infrared probes: beyond the vibrational Stark dipole approach. Phys Chem Chem Phys 2016; 18:18094-111. [DOI: 10.1039/c6cp01578f] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Systematic probing of local environments around biopolymers is important for understanding their functions.
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Affiliation(s)
- Bartosz Błasiak
- Center of Molecular Spectroscopy and Dynamics
- Institute of Basic Science (IBS)
- Seoul 02841
- Republic of Korea
- Department of Chemistry
| | - Andrew W. Ritchie
- Department of Chemistry
- Center for Nano- and Molecular Science and Technology, and Institute for Cell and Molecular Biology
- The University of Texas at Austin
- Austin
- USA
| | - Lauren J. Webb
- Department of Chemistry
- Center for Nano- and Molecular Science and Technology, and Institute for Cell and Molecular Biology
- The University of Texas at Austin
- Austin
- USA
| | - Minhaeng Cho
- Center of Molecular Spectroscopy and Dynamics
- Institute of Basic Science (IBS)
- Seoul 02841
- Republic of Korea
- Department of Chemistry
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318
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List NH, Olsen JMH, Kongsted J. Excited states in large molecular systems through polarizable embedding. Phys Chem Chem Phys 2016; 18:20234-50. [DOI: 10.1039/c6cp03834d] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using the polarizable embedding model enables rational design of light-sensitive functional biological materials.
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Affiliation(s)
- Nanna Holmgaard List
- Department of Physics, Chemistry and Pharmacy
- University of Southern Denmark
- 5230 Odense M
- Denmark
| | | | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy
- University of Southern Denmark
- 5230 Odense M
- Denmark
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319
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Monitoring one-electron photo-oxidation of guanine in DNA crystals using ultrafast infrared spectroscopy. Nat Chem 2015; 7:961-7. [PMID: 26587711 DOI: 10.1038/nchem.2369] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 09/04/2015] [Indexed: 12/19/2022]
Abstract
To understand the molecular origins of diseases caused by ultraviolet and visible light, and also to develop photodynamic therapy, it is important to resolve the mechanism of photoinduced DNA damage. Damage to DNA bound to a photosensitizer molecule frequently proceeds by one-electron photo-oxidation of guanine, but the precise dynamics of this process are sensitive to the location and the orientation of the photosensitizer, which are very difficult to define in solution. To overcome this, ultrafast time-resolved infrared (TRIR) spectroscopy was performed on photoexcited ruthenium polypyridyl-DNA crystals, the atomic structure of which was determined by X-ray crystallography. By combining the X-ray and TRIR data we are able to define both the geometry of the reaction site and the rates of individual steps in a reversible photoinduced electron-transfer process. This allows us to propose an individual guanine as the reaction site and, intriguingly, reveals that the dynamics in the crystal state are quite similar to those observed in the solvent medium.
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320
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Ritchie AW, Webb LJ. Understanding and Manipulating Electrostatic Fields at the Protein-Protein Interface Using Vibrational Spectroscopy and Continuum Electrostatics Calculations. J Phys Chem B 2015; 119:13945-57. [PMID: 26375183 DOI: 10.1021/acs.jpcb.5b06888] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Biological function emerges in large part from the interactions of biomacromolecules in the complex and dynamic environment of the living cell. For this reason, macromolecular interactions in biological systems are now a major focus of interest throughout the biochemical and biophysical communities. The affinity and specificity of macromolecular interactions are the result of both structural and electrostatic factors. Significant advances have been made in characterizing structural features of stable protein-protein interfaces through the techniques of modern structural biology, but much less is understood about how electrostatic factors promote and stabilize specific functional macromolecular interactions over all possible choices presented to a given molecule in a crowded environment. In this Feature Article, we describe how vibrational Stark effect (VSE) spectroscopy is being applied to measure electrostatic fields at protein-protein interfaces, focusing on measurements of guanosine triphosphate (GTP)-binding proteins of the Ras superfamily binding with structurally related but functionally distinct downstream effector proteins. In VSE spectroscopy, spectral shifts of a probe oscillator's energy are related directly to that probe's local electrostatic environment. By performing this experiment repeatedly throughout a protein-protein interface, an experimental map of measured electrostatic fields generated at that interface is determined. These data can be used to rationalize selective binding of similarly structured proteins in both in vitro and in vivo environments. Furthermore, these data can be used to compare to computational predictions of electrostatic fields to explore the level of simulation detail that is necessary to accurately predict our experimental findings.
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Affiliation(s)
- Andrew W Ritchie
- Department of Chemistry, Center for Nano- and Molecular Science and Technology, and Institute for Cell and Molecular Biology, The University of Texas at Austin , 105 East 24th Street STOP A5300, Austin, Texas 78712, United States
| | - Lauren J Webb
- Department of Chemistry, Center for Nano- and Molecular Science and Technology, and Institute for Cell and Molecular Biology, The University of Texas at Austin , 105 East 24th Street STOP A5300, Austin, Texas 78712, United States
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321
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Bobone S, De Zotti M, Bortolotti A, Biondi B, Ballano G, Palleschi A, Toniolo C, Formaggio F, Stella L. The fluorescence and infrared absorption probepara-cyanophenylalanine: Effect of labeling on the behavior of different membrane-interacting peptides. Biopolymers 2015; 104:521-32. [DOI: 10.1002/bip.22674] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 04/30/2015] [Accepted: 05/04/2015] [Indexed: 12/18/2022]
Affiliation(s)
- Sara Bobone
- Department of Chemical Sciences and Technologies; University of Rome Tor Vergata; 00133 Rome Italy
| | - Marta De Zotti
- Department of Chemistry; University of Padova; 35131 Padova Italy
| | - Annalisa Bortolotti
- Department of Chemical Sciences and Technologies; University of Rome Tor Vergata; 00133 Rome Italy
| | - Barbara Biondi
- Institute of Biomolecular Chemistry, Padova Unit, CNR; 35131 Padova Italy
| | - Gema Ballano
- Department of Chemistry; University of Padova; 35131 Padova Italy
| | - Antonio Palleschi
- Department of Chemical Sciences and Technologies; University of Rome Tor Vergata; 00133 Rome Italy
| | - Claudio Toniolo
- Department of Chemistry; University of Padova; 35131 Padova Italy
- Institute of Biomolecular Chemistry, Padova Unit, CNR; 35131 Padova Italy
| | - Fernando Formaggio
- Department of Chemistry; University of Padova; 35131 Padova Italy
- Institute of Biomolecular Chemistry, Padova Unit, CNR; 35131 Padova Italy
| | - Lorenzo Stella
- Department of Chemical Sciences and Technologies; University of Rome Tor Vergata; 00133 Rome Italy
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322
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Voinov MA, Smirnov AI. Ionizable Nitroxides for Studying Local Electrostatic Properties of Lipid Bilayers and Protein Systems by EPR. Methods Enzymol 2015; 564:191-217. [PMID: 26477252 PMCID: PMC5008871 DOI: 10.1016/bs.mie.2015.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Electrostatic interactions are known to play a major role in the myriad of biochemical and biophysical processes. Here, we describe biophysical methods to probe local electrostatic potentials of proteins and lipid bilayer systems that are based on an observation of reversible protonation of nitroxides by electron paramagnetic resonance (EPR). Two types of probes are described: (1) methanethiosulfonate derivatives of protonatable nitroxides for highly specific covalent modification of the cysteine's sulfhydryl groups and (2) spin-labeled phospholipids with a protonatable nitroxide tethered to the polar head group. The probes of both types report on their ionization state through changes in magnetic parameters and degree of rotational averaging, thus, allowing the electrostatic contribution to the interfacial pKa of the nitroxide, and, therefore, the local electrostatic potential to be determined. Due to their small molecular volume, these probes cause a minimal perturbation to the protein or lipid system. Covalent attachment secures the position of the reporter nitroxides. Experimental procedures to characterize and calibrate these probes by EPR, and also the methods to analyze the EPR spectra by simulations are outlined. The ionizable nitroxide labels and the nitroxide-labeled phospholipids described so far cover an exceptionally wide range of ca. 2.5-7.0 pH units, making them suitable to study a broad range of biophysical phenomena, especially at the negatively charged lipid bilayer surfaces. The rationale for selecting proper electrostatically neutral interface for probe calibration, and examples of lipid bilayer surface potential studies, are also described.
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Affiliation(s)
- Maxim A Voinov
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina, USA
| | - Alex I Smirnov
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina, USA.
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323
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Fried SD, Boxer SG. BIOPHYSICS. Response to Comments on "Extreme electric fields power catalysis in the active site of ketosteroid isomerase". Science 2015; 349:936. [PMID: 26315428 DOI: 10.1126/science.aab1627] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 07/24/2015] [Indexed: 01/28/2023]
Abstract
Natarajan et al. and Chen and Savidge comment that comparing the electric field in ketosteroid isomerase's (KSI's) active site to zero overestimates the catalytic effect of KSI's electric field because the reference reaction occurs in water, which itself exerts a sizable electrostatic field. To compensate, Natarajan et al. argue that additional catalytic weight arises from positioning of the general base, whereas Chen and Savidge propose a separate contribution from desolvation of the general base. We note that the former claim is not well supported by published results, and the latter claim is intriguing but lacks experimental basis. We also take the opportunity to clarify some of the more conceptually subtle aspects of electrostatic catalysis.
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Affiliation(s)
- Stephen D Fried
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA.
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324
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Zhang N, Wang XR, Yuan YX, Wang HF, Xu MM, Ren ZG, Yao JL, Gu RA. Probing double layer structure at Au/[BMIm]BF4 interface by molecular length-dependent SERS Stark effect. J Electroanal Chem (Lausanne) 2015. [DOI: 10.1016/j.jelechem.2015.05.041] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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325
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Lasne J, Rosu-Finsen A, Cassidy A, McCoustra MRS, Field D. Spontaneously electrical solids in a new light. Phys Chem Chem Phys 2015. [DOI: 10.1039/c5cp03174e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Reflection–absorption infrared spectroscopy (RAIRS) of nitrous oxide (N2O) thin films is shown to provide an independent means of observing the spontelectric state; the first new structural phase of matter, with unique electrical properties, to have emerged in decades.
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Affiliation(s)
- Jérôme Lasne
- Institute of Chemical Sciences
- Heriot-Watt University
- Riccarton
- UK
| | | | - Andrew Cassidy
- Department of Physics and Astronomy
- Aarhus University
- DK-8000 Aarhus C
- Denmark
| | | | - David Field
- Department of Physics and Astronomy
- Aarhus University
- DK-8000 Aarhus C
- Denmark
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