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Pem B, Brkljača Z, Philippe A, Schaumann GE, Vazdar M, Bakarić D. FTIR spectroscopy and molecular level insight of diluted aqueous solutions of acetic acid. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 302:123135. [PMID: 37454436 DOI: 10.1016/j.saa.2023.123135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 06/27/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023]
Abstract
Aqueous solutions of acetic acid (AA) have been intensively explored for decades with a particular attention addressed to the hydrogen bond network generated by COOH group at different concentrations. In majority of studies conducted so far the envelope originated from νCO is decomposed into two bands assigned to differently hydrated monomers: the one presumably to AA···H2O, and another one to AA···(H2O)2. In order to examine if species other than the mentioned monomers produce this spectral signature, we performed computational and FTIR spectroscopic study of AA in aqueous solutions. Dilute solutions of deuterated acetic acid (CD3COOD) in D2O and in C2Cl4 as a reference were prepared (c0 = 0.001, 0.01 and 0.1 mol dm-3) as well as of deuterated sodium acetate (CD3COONa) in D2O. CD3COOD in 0.1 mol dm-3 solution in D2O displays a feature that separated in two signals with maxima at 1706 cm-1 and 1687 cm-1. A combined DFT and molecular dynamics study performed in this work showed the assignation of those spectral bands to be a more complex problem than previously thought, with syn-anti isomerism and hydration contributing to the experimentally observed broad νCO envelope.
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Affiliation(s)
- Barbara Pem
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Zlatko Brkljača
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia; Selvita d.o.o. Prilaz baruna Filipovića 29, 10000 Zagreb, Croatia
| | - Allan Philippe
- University of Koblenz-Landau, iES Landau-Institute for Environmental Sciences, Group of Environmental and Soil Chemistry, Fortstraße 7, D-76829 Landau, Germany
| | - Gabriele E Schaumann
- University of Koblenz-Landau, iES Landau-Institute for Environmental Sciences, Group of Environmental and Soil Chemistry, Fortstraße 7, D-76829 Landau, Germany
| | - Mario Vazdar
- Department of Mathematics, Informatics and Cybernetics, University of Chemistry and Technology, 166 28 Prague, Czech Republic
| | - Danijela Bakarić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia; University of Koblenz-Landau, iES Landau-Institute for Environmental Sciences, Group of Environmental and Soil Chemistry, Fortstraße 7, D-76829 Landau, Germany.
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2
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Li N, Zhang F. THz-PCR Based on Resonant Coupling between Middle Infrared and DNA Carbonyl Vibrations. ACS APPLIED MATERIALS & INTERFACES 2023; 15:8224-8231. [PMID: 36724344 DOI: 10.1021/acsami.2c22413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The carbonyl groups of deoxyribonucleotide can resonantly couple with 53 THz middle infrared, which can highly transmit water without ionization-based damage to DNA molecules. Herein, we predict that vibrational coupling with THz irradiation could lower down the hybridization landscape of nucleic acids and thus affect DNA replication. Using polymerase chain reaction (PCR) as a measure, we found that THz shining can reduce the denature temperature of DNA duplexes by about 3 °C, which allows one to conduct PCR at lower temperature, facilitating long-time amplification reaction without losing enzymatic fidelity, i.e., normal PCR should be carried out at denaturing temperature ∼4 °C higher than the melting temperature (Tm), but THz-PCR only requires temperature ∼1 °C higher than Tm due to the nonthermal effect of THz shining. Moreover, the melting time can also be shortened to 1/5 due to the enhanced vibration coupling with 53 THz irradiation. We proposed THz-PCR as an innovated DNA amplification technique with ultrahigh specificity and sensitivity and also successfully demonstrated its advantages in forensic detections.
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Affiliation(s)
- Na Li
- Quantum Biophotonic Lab, Key Laboratory of Optical Technology and Instrument for Medicine, Ministry of Education, School of Optical-Electrical and Computer Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Feng Zhang
- Quantum Biophotonic Lab, Key Laboratory of Optical Technology and Instrument for Medicine, Ministry of Education, School of Optical-Electrical and Computer Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, China
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3
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Hanes AT, Grieco C, Lalisse RF, Hadad CM, Kohler B. Vibrational relaxation by methylated xanthines in solution: Insights from 2D IR spectroscopy and calculations. J Chem Phys 2023; 158:044302. [PMID: 36725522 DOI: 10.1063/5.0135412] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Two-dimensional infrared (2D IR) spectroscopy, infrared pump-infrared probe spectroscopy, and density functional theory calculations were used to study vibrational relaxation by ring and carbonyl stretching modes in a series of methylated xanthine derivatives in acetonitrile and deuterium oxide (heavy water). Isotropic signals from the excited symmetric and asymmetric carbonyl stretch modes decay biexponentially in both solvents. Coherent energy transfer between the symmetric and asymmetric carbonyl stretching modes gives rise to a quantum beat in the time-dependent anisotropy signals. The damping time of the coherent oscillation agrees with the fast decay component of the carbonyl bleach recovery signals, indicating that this time constant reflects intramolecular vibrational redistribution (IVR) to other solute modes. Despite their similar frequencies, the excited ring modes decay monoexponentially with a time constant that matches the slow decay component of the carbonyl modes. The slow decay times, which are faster in heavy water than in acetonitrile, approximately match the ones observed in previous UV pump-IR probe measurements on the same compounds. The slow component is assigned to intermolecular energy transfer to solvent bath modes from low-frequency solute modes, which are populated by IVR and are anharmonically coupled to the carbonyl and ring stretch modes. 2D IR measurements indicate that the carbonyl stretching modes are weakly coupled to the delocalized ring modes, resulting in slow exchange that cannot explain the common solvent-dependence. IVR is suggested to occur at different rates for the carbonyl vs ring modes due to differences in mode-specific couplings and not to differences in the density of accessible states.
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Affiliation(s)
- Alex T Hanes
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, USA
| | - Christopher Grieco
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, USA
| | - Remy F Lalisse
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, USA
| | - Christopher M Hadad
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, USA
| | - Bern Kohler
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, USA
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4
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Edington SC, Halling DB, Bennett SM, Middendorf TR, Aldrich RW, Baiz CR. Non-Additive Effects of Binding Site Mutations in Calmodulin. Biochemistry 2019; 58:2730-2739. [PMID: 31124357 DOI: 10.1021/acs.biochem.9b00096] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Despite decades of research on ion-sensing proteins, gaps persist in the understanding of ion binding affinity and selectivity even in well-studied proteins such as calmodulin. Site-directed mutagenesis is a powerful and popular tool for addressing outstanding questions about biological ion binding and is employed to selectively deactivate binding sites and insert chromophores at advantageous positions within ion binding structures. However, even apparently nonperturbative mutations can distort the binding dynamics they are employed to measure. We use Fourier transform infrared (FTIR) and ultrafast two-dimensional infrared (2D IR) spectroscopy of the carboxylate asymmetric stretching mode in calmodulin as a mutation- and label-independent probe of the conformational perturbations induced in calmodulin's binding sites by two classes of mutation, tryptophan insertion and carboxylate side-chain deletion, commonly used to study ion binding in proteins. Our results show that these mutations not only affect ion binding but also induce changes in calmodulin's conformational landscape along coordinates not probed by vibrational spectroscopy, remaining invisible without additional perturbation of binding site structure. Comparison of FTIR line shapes with 2D IR diagonal slices provides a clear example of how nonlinear spectroscopy produces well-resolved line shapes, refining otherwise featureless spectral envelopes into more informative vibrational spectra of proteins.
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Affiliation(s)
- Sean C Edington
- Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - D Brent Halling
- Department of Neuroscience , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Suzanna M Bennett
- Department of Neuroscience , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Thomas R Middendorf
- Department of Neuroscience , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Richard W Aldrich
- Department of Neuroscience , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Carlos R Baiz
- Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
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5
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Grafton AB, Cheatum CM. Two-dimensional infrared study of the C D and C O stretching vibrations in strongly hydrogen-bonded complexes. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.05.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Affiliation(s)
- Sean C. Edington
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Carlos R. Baiz
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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7
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Okuda M, Ohta K, Tominaga K. Rotational Dynamics of Solutes with Multiple Single Bond Axes Studied by Infrared Pump-Probe Spectroscopy. J Phys Chem A 2018; 122:946-954. [PMID: 29278912 DOI: 10.1021/acs.jpca.7b09939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To investigate the relationship between the structural degrees of freedom around a vibrational probe and the rotational relaxation process of a solute in solution, we studied the anisotropy decays of three different N3-derivatized amino acids in primary alcohol solutions. By performing polarization-controlled IR pump-probe measurements, we reveal that the anisotropy decays of the vibrational probe molecules in 1-alcohol solutions possess two decay components, at subpicosecond and picosecond time scales. On the basis of results showing that the fast relaxation component is insensitive to the vibrational probe molecule, we suggest that the anisotropy decay of the N3 group on a subpicosecond time scale results from a local, small-amplitude fluctuation of the flexible vibrational probe, which does not depend on the details of its molecular structure. However, the slow relaxation component depends on the solute: with longer alkyl chains attached to the N3 group, the anisotropy decay of the slow component is faster. Consequently, we conclude that the slow relaxation component corresponds to the reorientational motion of the N3 group correlated with other intramolecular rotational motions (e.g., rotational motions of the neighboring alkyl chain). Our experimental results provide important insight into understanding the rotational dynamics of solutes with multiple single bond axes in solution.
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Affiliation(s)
- Masaki Okuda
- Molecular Photoscience Research Center and ‡Graduate School of Science, Kobe University , Rokkodai-cho 1-1, Nada, Kobe 657-8501, Japan
| | - Kaoru Ohta
- Molecular Photoscience Research Center and ‡Graduate School of Science, Kobe University , Rokkodai-cho 1-1, Nada, Kobe 657-8501, Japan
| | - Keisuke Tominaga
- Molecular Photoscience Research Center and ‡Graduate School of Science, Kobe University , Rokkodai-cho 1-1, Nada, Kobe 657-8501, Japan
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8
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Nummert V, Piirsalu M, Vahur S, Toom L, Leito I, Koppel IA. Effects of neutral and charged substituents on the infrared carbonyl stretching frequencies in phenyl and alkyl benzoates in DMSO. J PHYS ORG CHEM 2017. [DOI: 10.1002/poc.3608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Vilve Nummert
- Institute of Chemistry; University of Tartu; Ravila 14a 50411 Tartu Estonia
| | - Mare Piirsalu
- Institute of Chemistry; University of Tartu; Ravila 14a 50411 Tartu Estonia
| | - Signe Vahur
- Institute of Chemistry; University of Tartu; Ravila 14a 50411 Tartu Estonia
| | - Lauri Toom
- Institute of Technology; University of Tartu; Nooruse 1 50411 Tartu Estonia
| | - Ivo Leito
- Institute of Chemistry; University of Tartu; Ravila 14a 50411 Tartu Estonia
| | - Ilmar A. Koppel
- Institute of Chemistry; University of Tartu; Ravila 14a 50411 Tartu Estonia
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9
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Okuda M, Ohta K, Tominaga K. Comparison of vibrational dynamics between non-ionic and ionic vibrational probes in water: Experimental study with two-dimensional infrared and infrared pump-probe spectroscopies. J Chem Phys 2016. [DOI: 10.1063/1.4962344] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Affiliation(s)
- Masaki Okuda
- Graduate School of Science, Kobe University, Rokkodai-cho 1-1, Nada, Kobe 657-8501, Japan
| | - Kaoru Ohta
- Moleuclar Photoscience Research Center, Kobe University, Rokkodai-cho 1-1, Nada, Kobe 657-8501, Japan
| | - Keisuke Tominaga
- Graduate School of Science, Kobe University, Rokkodai-cho 1-1, Nada, Kobe 657-8501, Japan
- Moleuclar Photoscience Research Center, Kobe University, Rokkodai-cho 1-1, Nada, Kobe 657-8501, Japan
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10
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Okuda M, Ohta K, Tominaga K. Vibrational dynamics of azide-derivatized amino acids studied by nonlinear infrared spectroscopy. J Chem Phys 2015; 142:212418. [DOI: 10.1063/1.4917032] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Affiliation(s)
- Masaki Okuda
- Graduate School of Science, Kobe University, Rokkodai-cho 1-1, Nada. Kobe 657-8501, Japan
| | - Kaoru Ohta
- Moleuclar Photoscience Research Center, Kobe University, Rokkodai-cho 1-1, Nada. Kobe 657-8501, Japan
| | - Keisuke Tominaga
- Graduate School of Science, Kobe University, Rokkodai-cho 1-1, Nada. Kobe 657-8501, Japan
- Moleuclar Photoscience Research Center, Kobe University, Rokkodai-cho 1-1, Nada. Kobe 657-8501, Japan
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11
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Saharay M, Kirkpatrick RJ. Ab initio and metadynamics studies on the role of essential functional groups in biomineralization of calcium carbonate and environmental situations. Phys Chem Chem Phys 2014; 16:26843-54. [PMID: 25375213 DOI: 10.1039/c4cp03904a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The interactions of proteins, polysaccharides and other biomolecules with Ca(2+), CO3(2-), and water are central to the understanding of biomineralization and crystallization of calcium carbonate (CaCO3), and their association with the natural organic matter (NOM) in the environment. A molecular-level investigation of how such interactions and thermodynamic forces drive the nucleation and growth of crystalline CaCO3 in living organisms remains elusive. This paper presents ab initio and metadynamics studies of the interactions of Ca(2+), CO3(2-), and water with the essential amino acids/functional groups, e.g. arginine/NH2(+), aspartate or glutamate/COO(-), aspartic or glutamic acid/COOH, and serine/OH, of protein/organic molecules that are likely to be critical to the biomineralization of CaCO3. These functional groups were modeled as guanidinium (Gdm(+)), acetate (AcO(-)), acetic acid (AcOH), and ethanol (EtOH) molecules, respectively. The Gdm(+)-Ca(2+)-CO3(2-) and AcO(-)-Ca(2+)-CO3(2-) systems were found to form stable ion-complexes irrespective of the presence of near neighbor water molecules. The strong electrostatic interactions of these functional groups with their counter-ions significantly affect the fundamental vibrational frequencies of the functional groups, mainly the NH2 stretching (str.) and degenerate (deg.) scissors modes of Gdm(+) and -C=OO, CC, and CO str. modes of AcO(-). The free-energy calculations reveal that EtOH forms weakly bound molecular complexes with the Ca(2+)-CO3(2-) ion pairs in water. However, the interaction strength of EtOH with crystalline CaCO3 can increase significantly due to combined effect of H-bond and electron donor acceptor (EDA) type of interactions. These results indicate that -NH2(+) and -COO(-) bearing molecules serve as potential nucleation sites promoting crystallization of CaCO3 phases while -OH bearing molecules are likely to control the morphology of the crystalline phases by attaching to the growing crystal surfaces.
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Affiliation(s)
- Moumita Saharay
- Center for Modelling Simulation and Design, University of Hyderabad, Hyderabad 500046, Telangana, India.
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Banno M, Kotani A, Ohta K, Tominaga K. Solute–Solvent Interactions of Benzonitrile in Solutions Studied by Sub-Picosecond Infrared Pump–Probe Spectroscopy. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2014. [DOI: 10.1246/bcsj.20130226] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
| | - Ayumi Kotani
- Department of Chemistry, Graduate School of Science, Kobe University
| | - Kaoru Ohta
- Molecular Photoscience Research Center, Kobe University
| | - Keisuke Tominaga
- Molecular Photoscience Research Center, Kobe University
- Department of Chemistry, Graduate School of Science, Kobe University
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13
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Yamaguchi S, Banno M, Ohta K, Tominaga K. Frequency Dependence of Vibrational Energy Relaxation and Spectral Diffusion of the N–H Stretching Band of Pyrrole–Base Complexes in Solution. J Phys Chem A 2013; 117:6323-31. [DOI: 10.1021/jp401461k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sayuri Yamaguchi
- Graduate
School of Science and ‡Molecular Photoscience Research Center, Kobe University, Nada, Kobe, Japan
| | - Motohiro Banno
- Graduate
School of Science and ‡Molecular Photoscience Research Center, Kobe University, Nada, Kobe, Japan
| | - Kaoru Ohta
- Graduate
School of Science and ‡Molecular Photoscience Research Center, Kobe University, Nada, Kobe, Japan
| | - Keisuke Tominaga
- Graduate
School of Science and ‡Molecular Photoscience Research Center, Kobe University, Nada, Kobe, Japan
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14
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Car–Parrinello simulation of the vibrational spectra of strong hydrogen bonds with isotopic substitution effects: Application to oxalic acid dihydrate. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2012.12.035] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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15
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Banno M, Ohta K, Tominaga K. Vibrational dynamics of acetate in D2O studied by infrared pump-probe spectroscopy. Phys Chem Chem Phys 2012; 14:6359-66. [PMID: 22358129 DOI: 10.1039/c2cp23647h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Solute-solvent interactions between acetate and D(2)O were investigated by vibrational spectroscopic methods. The vibrational dynamics of the COO asymmetric stretching mode in D(2)O was observed by time-resolved infrared (IR) pump-probe spectroscopy. The pump-probe signal contained both decay and oscillatory components. The time dependence of the decay component could be explained by a double exponential function with time constants of 200 fs and 2.6 ps, which are the same for both the COO asymmetric and symmetric stretching modes. The Fourier spectrum of the oscillatory component contained a band around 80 cm(-1), which suggests that the COO asymmetric stretching mode couples to a low-frequency vibrational mode with a wavenumber of 80 cm(-1). Based on quantum chemistry calculations, we propose that a bridged complex comprising an acetate ion and one D(2)O molecule, in which the two oxygen atoms in the acetate anion form hydrogen bonds with the two deuterium atoms in D(2)O, is the most stable structure. The 80 cm(-1) low-frequency mode was assigned to the asymmetric stretching vibration of the hydrogen bond in the bridged complex.
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Affiliation(s)
- Motohiro Banno
- Molecular Photoscience Research Center, Kobe University, Nada, Kobe 657-8501, Japan
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Heisler IA, Mazur K, Yamaguchi S, Tominaga K, Meech SR. Measuring acetic acid dimer modes by ultrafast time-domain Raman spectroscopy. Phys Chem Chem Phys 2011; 13:15573-9. [PMID: 21625711 DOI: 10.1039/c1cp20990f] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Acetic acid is capable of forming strong multiple hydrogen bonds and therefore different dimeric H-bonded structures in neat liquid phase and in solutions. The low frequency Raman spectra of acetic acid (neat, in aqueous solution and as a function of temperature) were obtained by ultrafast time and polarization resolved optical Kerr effect (OKE) measurements. Isotropic OKE measurements clearly reveal a specific totally symmetric mode related to the dimeric structure H-bond stretching mode. The effects of isotope substitution, water dilution and temperature on this mode were investigated. These results together with anisotropic OKE measurements and density functional theory calculations for a number of possible dimers provide strong evidence for the cyclic dimer structure being the main structure in liquid phase persisting down to acetic acid concentrations of 10 M. Some information about the dimer structure and concentration dependence was inferred.
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Affiliation(s)
- Ismael A Heisler
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, UK.
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Tayama J, Ishihara A, Banno M, Ohta K, Saito S, Tominaga K. Temperature dependence of vibrational frequency fluctuation of N(3) (-) in D(2)O. J Chem Phys 2010; 133:014505. [PMID: 20614974 DOI: 10.1063/1.3428672] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
We have studied the temperature dependence of the vibrational frequency fluctuation of the antisymmetric stretching mode of N(3) (-) in D(2)O by three-pulse infrared (IR) photon echo experiments. IR pump-probe measurements were also carried out to investigate the population relaxation and the orientational relaxation of the same band. It was found that the time-correlation function (TCF) of the frequency fluctuation of this mode is well described by a biexponential function with a quasistatic term. The faster decay component has a time constant of about 0.1 ps, and the slower component varies from 1.4 to 1.1 ps in the temperature range from 283 to 353 K. This result indicates that liquid dynamics related to the frequency fluctuation are not highly sensitive to temperature. We discuss the relationship between the temperature dependence of the vibrational frequency fluctuation and that of the molecular motion of the system to investigate the molecular origin of the frequency fluctuation of the solute. We compare the temperature dependence of the frequency fluctuation with that of other dynamics such as dielectric relaxation of water. In contrast to the Debye dielectric relaxation time of D(2)O, the two time constants of the TCF of the frequency fluctuation do not exhibit strong temperature dependence. We propose a simple theoretical model for the frequency fluctuation in solutions based on perturbation theory and the dipole-dipole interaction between the vibrational mode of the solute and the solvent molecules. This model suggests that the neighboring solvent molecules in the vicinity of the solute play an important role in the frequency fluctuation. We suggest that the picosecond component of the frequency fluctuation results from structural fluctuation of the hydrogen-bonding network in water.
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Affiliation(s)
- Jumpei Tayama
- Graduate School of Science, Kobe University, Nada, Kobe 657-8501, Japan
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18
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Banno M, Ohta K, Yamaguchi S, Hirai S, Tominaga K. Vibrational dynamics of hydrogen-bonded complexes in solutions studied with ultrafast infrared pump-probe spectroscopy. Acc Chem Res 2009; 42:1259-69. [PMID: 19754112 DOI: 10.1021/ar9000229] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In aqueous solution, the basis of all living processes, hydrogen bonding exerts a powerful effect on chemical reactivity. The vibrational energy relaxation (VER) process in hydrogen-bonded complexes in solution is sensitive to the microscopic environment around the oscillator and to the geometrical configuration of the hydrogen-bonded complexes. In this Account, we describe the use of time-resolved infrared (IR) pump-probe spectroscopy to study the vibrational dynamics of (i) the carbonyl CO stretching modes in protic solvents and (ii) the OH stretching modes of phenol and carboxylic acid. In these cases, the carbonyl group acts as a hydrogen-bond acceptor, whereas the hydroxyl group acts as a hydrogen-bond donor. These vibrational modes have different properties depending on their respective chemical bonds, suggesting that hydrogen bonding may have different mechanisms and effects on the VER of the CO and OH modes than previously understood. The IR pump-probe signals of the CO stretching mode of 9-fluorenone and methyl acetate in alcohol, as well as that of acetic acid in water, include several components with different time constants. Quantum chemical calculations indicate that the dynamical components are the result of various hydrogen-bonded complexes that form between solute and solvent molecules. The acceleration of the VER is due to the increasing vibrational density of states caused by the formation of hydrogen bonds. The vibrational dynamics of the OH stretching mode in hydrogen-bonded complexes were studied in several systems. For phenol-base complexes, the decay time constant of the pump-probe signal decreases as the band peak of the IR absorption spectrum shifts to lower wavenumbers (the result of changing the proton acceptor). For phenol oligomers, the decay time constant of the pump-probe signal decreases as the probe wavenumber decreases. These observations show that the VER time strongly correlates with the strength of hydrogen bonding. This acceleration may be due to increased coupling between the OH stretching mode and the accepting mode of the VER, because the low-frequency shift caused by hydrogen bond formation is very large. Unlike phenol oligomers, however, the pump-probe signals of phenol-base complexes did not exhibit probe frequency dependence. For these complexes, rapid interconversion between different conformations causes rapid fluctuations in the vibrational frequency of the OH stretching modes, and these fluctuations level the VER times of different conformations. For the benzoic acid dimer, a quantum beat at a frequency of around 100 cm(-1) is superimposed on the pump-probe signal. This result indicates the presence of strong anharmonic coupling between the intramolecular OH stretching and the intermolecular stretching modes. From a two-dimensional plot of the OH stretching wavenumber and the low-frequency wavenumber, the wavenumber of the low-frequency mode is found to increase monotonically as the probe wavenumber is shifted toward lower wavenumbers. Our results represent a quantitative determination of the acceleration of VER by the formation of hydrogen bonds. Our studies merit further evaluation and raise fundamental questions about the current theory of vibrational dynamics in the condensed phase.
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Affiliation(s)
- Motohiro Banno
- Molecular Photoscience Research Center, Kobe University, 1-1 Rokkodai-cho, Nada, Kobe 657-8501, Japan
| | - Kaoru Ohta
- Molecular Photoscience Research Center, Kobe University, 1-1 Rokkodai-cho, Nada, Kobe 657-8501, Japan
| | - Sayuri Yamaguchi
- Graduate School of Science, Kobe University, 1-1 Rokkodai-cho, Nada, Kobe 657-8501, Japan
| | - Satori Hirai
- Graduate School of Science, Kobe University, 1-1 Rokkodai-cho, Nada, Kobe 657-8501, Japan
| | - Keisuke Tominaga
- Molecular Photoscience Research Center, Kobe University, 1-1 Rokkodai-cho, Nada, Kobe 657-8501, Japan
- Graduate School of Science, Kobe University, 1-1 Rokkodai-cho, Nada, Kobe 657-8501, Japan
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Maçôas EMS, Myllyperkiö P, Kunttu H, Pettersson M. Vibrational Relaxation of Matrix-Isolated Carboxylic Acid Dimers and Monomers. J Phys Chem A 2009; 113:7227-34. [DOI: 10.1021/jp8099384] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Ermelinda M. S. Maçôas
- Nanoscience Center, Department of Chemistry, P.O. Box 35, University of Jyväskylä, FI-40014 Finland
| | - Pasi Myllyperkiö
- Nanoscience Center, Department of Chemistry, P.O. Box 35, University of Jyväskylä, FI-40014 Finland
| | - Henrik Kunttu
- Nanoscience Center, Department of Chemistry, P.O. Box 35, University of Jyväskylä, FI-40014 Finland
| | - Mika Pettersson
- Nanoscience Center, Department of Chemistry, P.O. Box 35, University of Jyväskylä, FI-40014 Finland
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Yamaguchi S, Banno M, Ohta K, Tominaga K, Hayashi T. Vibrational dynamics of benzoic acid in nonpolar solvents studied by subpicosecond infrared pump–probe spectroscopy. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2008.07.108] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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