1
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Moscato D, Mandelli G, Bondanza M, Lipparini F, Conte R, Mennucci B, Ceotto M. Unraveling Water Solvation Effects with Quantum Mechanics/Molecular Mechanics Semiclassical Vibrational Spectroscopy: The Case of Thymidine. J Am Chem Soc 2024; 146:8179-8188. [PMID: 38470354 DOI: 10.1021/jacs.3c12700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
We introduce a quantum mechanics/molecular mechanics semiclassical method for studying the solvation process of molecules in water at the nuclear quantum mechanical level with atomistic detail. We employ it in vibrational spectroscopy calculations because this is a tool that is very sensitive to the molecular environment. Specifically, we look at the vibrational spectroscopy of thymidine in liquid water. We find that the C═O frequency red shift and the C═C frequency blue shift, experienced by thymidyne upon solvation, are mainly due to reciprocal polarization effects, that the molecule and the water solvent exert on each other, and nuclear zero-point energy effects. In general, this work provides an accurate and practical tool to study quantum vibrational spectroscopy in solution and condensed phase, incorporating high-level and computationally affordable descriptions of both electronic and nuclear problems.
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Affiliation(s)
- Davide Moscato
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi, 19, 20133 Milano, Italy
| | - Giacomo Mandelli
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi, 19, 20133 Milano, Italy
| | - Mattia Bondanza
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe Moruzzi, 13, 56124 Pisa, Italy
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe Moruzzi, 13, 56124 Pisa, Italy
| | - Riccardo Conte
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi, 19, 20133 Milano, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe Moruzzi, 13, 56124 Pisa, Italy
| | - Michele Ceotto
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi, 19, 20133 Milano, Italy
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2
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Gustin I, Kim CW, McCamant DW, Franco I. Mapping electronic decoherence pathways in molecules. Proc Natl Acad Sci U S A 2023; 120:e2309987120. [PMID: 38015846 PMCID: PMC10710033 DOI: 10.1073/pnas.2309987120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/25/2023] [Indexed: 11/30/2023] Open
Abstract
Establishing the fundamental chemical principles that govern molecular electronic quantum decoherence has remained an outstanding challenge. Fundamental questions such as how solvent and intramolecular vibrations or chemical functionalization contribute to the decoherence remain unanswered and are beyond the reach of state-of-the-art theoretical and experimental approaches. Here we address this challenge by developing a strategy to isolate electronic decoherence pathways for molecular chromophores immersed in condensed phase environments that enables elucidating how electronic quantum coherence is lost. For this, we first identify resonance Raman spectroscopy as a general experimental method to reconstruct molecular spectral densities with full chemical complexity at room temperature, in solvent, and for fluorescent and non-fluorescent molecules. We then show how to quantitatively capture the decoherence dynamics from the spectral density and identify decoherence pathways by decomposing the overall coherence loss into contributions due to individual molecular vibrations and solvent modes. We illustrate the utility of the strategy by analyzing the electronic decoherence pathways of the DNA base thymine in water. Its electronic coherences decay in [Formula: see text]30 fs. The early-time decoherence is determined by intramolecular vibrations while the overall decay by solvent. Chemical substitution of thymine modulates the decoherence with hydrogen-bond interactions of the thymine ring with water leading to the fastest decoherence. Increasing temperature leads to faster decoherence as it enhances the importance of solvent contributions but leaves the early-time decoherence dynamics intact. The developed strategy opens key opportunities to establish the connection between molecular structure and quantum decoherence as needed to develop chemical strategies to rationally modulate it.
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Affiliation(s)
- Ignacio Gustin
- Department of Chemistry, University of Rochester, Rochester, NY14627
| | - Chang Woo Kim
- Department of Chemistry, Chonnam National University, Gwangju61186, South Korea
| | - David W. McCamant
- Department of Chemistry, University of Rochester, Rochester, NY14627
| | - Ignacio Franco
- Department of Chemistry, University of Rochester, Rochester, NY14627
- Department of Physics, University of Rochester, Rochester, NY14627
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3
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Gabas F, Conte R, Ceotto M. Quantum Vibrational Spectroscopy of Explicitly Solvated Thymidine in Semiclassical Approximation. J Phys Chem Lett 2022; 13:1350-1355. [PMID: 35109652 PMCID: PMC8842300 DOI: 10.1021/acs.jpclett.1c04087] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
In this paper, we demonstrate the possibility to perform spectroscopy simulations of solvated biological species taking into consideration quantum effects and explicit solvation. We achieve this goal by interfacing our recently developed divide-and-conquer approach for semiclassical initial value representation molecular dynamics with the polarizable AMOEBABIO18 force field. The method is applied to the study of solvation of the thymidine nucleoside in two different polar solvents, water and N,N-dimethylformamide. Such systems are made of up to 2476 atoms. Experimental evidence concerning the different behavior of thymidine in the two solvents is well reproduced by our study, even though quantitative estimates are hampered by the limited accuracy of the classical force field employed. Overall, this study shows that semiclassically approximate quantum dynamical studies of explicitly solvated biological systems are both computationally affordable and insightful.
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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.
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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
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5
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Wang J, Liu B, Ru G, Bai J, Feng J. Effect of Urea on Phase Transition of Poly(N-isopropylacrylamide) and Poly(N,N-diethylacrylamide) Hydrogels: A Clue for Urea-Induced Denaturation. Macromolecules 2015. [DOI: 10.1021/acs.macromol.5b01949] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Jian Wang
- State
Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
- University of
Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Biaolan Liu
- State
Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
- University of
Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Geying Ru
- State
Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Jia Bai
- State
Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
- University of
Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jiwen Feng
- State
Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
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6
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Thicoipe S, Carbonnière P, Pouchan C. Structural investigation of microhydrated thymine clusters and vibrational study of isolated and aqueous forms of thymine using DFT level of theory. Phys Chem Chem Phys 2013; 15:11646-52. [DOI: 10.1039/c3cp50424g] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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7
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Billinghurst BE, Oladepo SA, Loppnow GR. Initial excited-state structural dynamics of thymine derivatives. J Phys Chem B 2012; 116:10496-503. [PMID: 22697627 DOI: 10.1021/jp301952v] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Thymine is one of the pyrimidine nucleobases found in DNA. Upon absorption of UV light, thymine forms a number of photoproducts, including the cyclobutyl photodimer, the pyrimidine pyrimidinone [6-4] photoproduct and the photohydrate. Here, we use UV resonance Raman spectroscopy to measure the initial excited-state structural dynamics of the N(1)-substituted thymine derivatives N(1)-methylthymine, thymidine, and thymidine 5'-monophosphate in an effort to understand the role of the N1 substituent in determining the excited-state structural dynamics and the subsequent photochemistry. The UV resonance Raman spectrum of thymidine and thymidine 5'-monophosphate are similar to that of thymine, suggesting that large masses at N(1) effectively isolate the vibrations of the nucleobase. However, the UV resonance Raman spectrum of N(1)-methylthymine is significantly different, suggesting that the methyl group couples into the thymine ring vibrations. The resulting resonance Raman intensities and absorption spectra are self-consistently simulated with a time-dependent expression to quantitatively extract the initial excited-state slopes, homogeneous and inhomogeneous linewidths, and electronic parameters. These results are discussed in the context of the known photochemistry of thymine and its derivatives.
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Affiliation(s)
- Brant E Billinghurst
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
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8
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Grosmaire L, Delarbre JL. Vibrational spectra of 6-methyluracil, 6-methyl-2-thiouracil and their deuterated analogues. J Mol Struct 2012. [DOI: 10.1016/j.molstruc.2011.12.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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9
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Yarasi S, Ng S, Loppnow GR. Initial Excited-State Structural Dynamics of Uracil from Resonance Raman Spectroscopy Are Different from Those of Thymine (5-Methyluracil). J Phys Chem B 2009; 113:14336-42. [DOI: 10.1021/jp9053378] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Soujanya Yarasi
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Susan Ng
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Glen R. Loppnow
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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Billinghurst BE, Oladepo SA, Loppnow GR. pH-Dependent UV Resonance Raman Spectra of Cytosine and Uracil. J Phys Chem B 2009; 113:7392-7. [DOI: 10.1021/jp811327w] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Sulayman A. Oladepo
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Glen R. Loppnow
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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11
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Ground state intermolecular proton transfer in the supersystems thymine–(H2O)n and thymine–(CH3OH)n, n = 1,2: a theoretical study. J Mol Model 2008; 15:411-9. [DOI: 10.1007/s00894-008-0407-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2008] [Accepted: 07/08/2008] [Indexed: 10/21/2022]
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Ng S, Yarasi S, Brost P, Loppnow GR. Initial Excited-State Structural Dynamics of Thymine Are Coincident with the Expected Photochemical Dynamics. J Phys Chem A 2007; 111:5130-5. [PMID: 17530833 DOI: 10.1021/jp071443t] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To explore the excited-state structural dynamics of thymine, a DNA nucleobase, we measured the resonance Raman spectra of thymine in aqueous solution at wavelengths throughout the lowest-energy absorption band. Self-consistent analysis of the resulting resonance Raman excitation profiles and absorption spectrum using a time-dependent wave packet formalism yielded the excited-state structural dynamics. The photochemically relevant C=C stretching and C-H deformation vibrational modes were found to exhibit maximum resonance Raman intensity and structural change upon photoexcitation for thymine, suggesting that the initial dynamics of thymine lie along the photochemical reaction coordinate.
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Affiliation(s)
- Susan Ng
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
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13
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Seba HB, Thureau P, Ancian B, Thévand A. Combined use of Overhauser spectroscopy and NMR diffusion experiments for mapping the hydration structure of nucleosides: structure and dynamics of uridine in water. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2006; 44:1109-17. [PMID: 17016868 DOI: 10.1002/mrc.1909] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Complementary results from 13C intermolecular nuclear Overhauser effects (NOE), 1H-13C heteronuclear Overhauser spectroscopy (HOSEY) and 1H-NMR diffusion measurements were used for probing the structure of the first solvation shell of uridine in water. It is demonstrated that a cyclic dihydrate is formed. The two water molecules produce two hydrogen bonds with the two oxygen atoms from the pyrimidine ring and accept only one hydrogen bond from the amide proton. The dihydrate has only a short lifetime as compared with the rotational correlation time of the free nucleoside. The chemical exchange constant of the amide proton with water is then estimated by diffusion experiments. The results are consistent with previous data obtained for uracil in water and provide interesting information about water accessibility in nucleic acid bases.
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Affiliation(s)
- Hadj B Seba
- Jeune Equipe 2421 TRACES, Université de Provence, case 512, Centre St Jérôme, 13397 Marseille Cedex 20, France
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