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Camiruaga A, Usabiaga I, Pinillos P, Basterretxea FJ, Fernández JA, Martínez R. Aggregation of nucleobases and metabolites: Adenine-theobromine trimers. J Chem Phys 2023; 158:064304. [PMID: 36792500 DOI: 10.1063/5.0137717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The selection of cytosine, guanine, thymine, and adenine as components of the information biopolymers was a complex process influenced by several factors. Among them, the intermolecular interactions may have played a determinant role. Thus, a deep understanding of the intermolecular interactions between nucleobases and other prebiotic molecules may help understand the first instants of chemical evolution. Following this hypothesis, we present here a combined spectroscopic and computational study of theobromine2-adenine and thebromine-adenine2 trimers. While adenine is a nucleobase, theobromine was probably part of the prebiotic chemistry. The trimers were formed in jets and probed by a combination of UV and IR spectroscopic techniques. The spectra were interpreted in light of the predictions obtained using density-functional methods. The results suggest the existence of a subtle balance between formation of hydrogen bonds and π-π interactions. Thus, while theobromine2-adenine tends to form complex in stacked structures, theobromine-adenine2 prefers formation of planar structures, maximizing the interaction by hydrogen bonds. The small energy difference between planar and stacked structures highlights the importance of accurately modeling the dispersion forces in the functionals to produce reliable predictions.
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Affiliation(s)
- Ander Camiruaga
- Faculty of Science and Technology, Department of Physical Chemistry, University of the Basque Country (UPV/EHU), B Sarriena S/N, Leioa 48940, Spain
| | - Imanol Usabiaga
- Faculty of Science and Technology, Department of Physical Chemistry, University of the Basque Country (UPV/EHU), B Sarriena S/N, Leioa 48940, Spain
| | - Paul Pinillos
- Faculty of Science and Technology, Department of Physical Chemistry, University of the Basque Country (UPV/EHU), B Sarriena S/N, Leioa 48940, Spain
| | - Francisco J Basterretxea
- Faculty of Science and Technology, Department of Physical Chemistry, University of the Basque Country (UPV/EHU), B Sarriena S/N, Leioa 48940, Spain
| | - José A Fernández
- Faculty of Science and Technology, Department of Physical Chemistry, University of the Basque Country (UPV/EHU), B Sarriena S/N, Leioa 48940, Spain
| | - Rodrigo Martínez
- Faculty of Science and Technology, Department of Chemistry, Univ. of La Rioja, Madre de Dios 53, 26006 Logroño, Spain
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Khalili F, Vafaee M, Shokri B. Attosecond charge migration following oxygen K-shell ionization in DNA bases and base pairs. Phys Chem Chem Phys 2021; 23:23005-23013. [PMID: 34611693 DOI: 10.1039/d1cp02920g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Core ionization of DNA begins a cascade of events which could lead to cellular inactivation or death. The created core-hole following an impulse inner-shell ionization of molecules naturally decays in the auger timescale. We simulated charge migration (CM) phenomena following an impulsive core ionization of individual DNA bases at the oxygen K-edge which occurs before Auger decay of the oxygen. Our approach is based on real-time time dependent density functional theory (RT-TDDFT). It is shown that the pronounced hole fluctuation observed around bonds of the initial core-hole results in various valence orbital migrations. Also, the same photo-core-ionized dynamics is studied for the related base pairs. We investigate the role of base pairing and H-bonding interactions in the attosecond CM dynamics. In particular, the creation of a core-hole in the oxygen involved in H-bonding leads to an enhancement of charge migration relative to the respective single bases. Importantly, the hole oscillation of the adenine-thymine base pair upon creation of a core-hole at the oxygen, which does not contribute to the donor-acceptor interactions (not H-bonded), decreases compared to the single thymine base. Understanding the detailed dynamics of the localized core-hole initiating CM process would open the way for chemically controlling DNA damage/repair in the future.
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Affiliation(s)
- Fatemeh Khalili
- Department of Physics, Shahid Beheshti University, Velenjak, Tehran 19839, Iran.
| | - Mohsen Vafaee
- Department of Chemistry, Tarbiat Modares University, P. O. Box 14115-175, Tehran, Iran.
| | - Babak Shokri
- Department of Physics, Shahid Beheshti University, Velenjak, Tehran 19839, Iran. .,Laser-Plasma Research Institute, Shahid Beheshti University, Velenjak, Tehran 19839, Iran
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González J, Usabiaga I, Arnaiz PF, León I, Martínez R, Millán J, Fernández JA. Competition between stacked and hydrogen bonded structures of cytosine aggregates. Phys Chem Chem Phys 2017; 19:8826-8834. [DOI: 10.1039/c6cp08476a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The four bases of DNA constitute what is known as the “alphabet of life”.
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Affiliation(s)
- Jorge González
- Department of Physical Chemistry
- Faculty of Science and Technology
- University of the Basque Country (UPV/EHU)
- Leioa
- Spain
| | - Imanol Usabiaga
- Department of Physical Chemistry
- Faculty of Science and Technology
- University of the Basque Country (UPV/EHU)
- Leioa
- Spain
| | - Pedro F. Arnaiz
- Department of Physical Chemistry
- Faculty of Science and Technology
- University of the Basque Country (UPV/EHU)
- Leioa
- Spain
| | - Iker León
- Department of Physical Chemistry
- Faculty of Science and Technology
- University of the Basque Country (UPV/EHU)
- Leioa
- Spain
| | - Rodrigo Martínez
- Department of Chemistry
- Faculty of Science and Technology
- University of La Rioja
- Logroño
- Spain
| | - Judith Millán
- Department of Chemistry
- Faculty of Science and Technology
- University of La Rioja
- Logroño
- Spain
| | - José A. Fernández
- Department of Physical Chemistry
- Faculty of Science and Technology
- University of the Basque Country (UPV/EHU)
- Leioa
- Spain
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Yuan Y, Chen P, Yang L, Ju Y, Wang H. Quantum chemical insight into the reactivity of 1,3-dipoles on coronene as model for nanographenes. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2015. [DOI: 10.1134/s0036024416010337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Mantela M, Morphis A, Tassi M, Simserides C. Lowest ionisation and excitation energies of biologically important heterocyclic planar molecules. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1113313] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Bou Zerdan R, Cohn P, Puodziukynaite E, Baker MB, Voisin M, Sarun C, Castellano RK. Synthesis, optical properties, and electronic structures of nucleobase-containing π-conjugated oligomers. J Org Chem 2015; 80:1828-40. [PMID: 25581330 DOI: 10.1021/jo502773g] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The molecular recognition properties of the nucleobases instruct the formation of complex three-dimensional architectures in natural and synthetic systems; relatively unexplored is their use as building blocks for π-conjugated materials where they might mutually tune electronic and supramolecular structures. Toward this goal, an introductory set (1a-d and 2a-d) of six purine-terminated and two pyrimidine-terminated π-conjugated oligomers has been synthesized and used to develop experimental electronic and photophysical structure-property trends. Unlike 2,2':5',2″-terthiophene (TTT) derivatives 2a-d, intramolecular charge transfer dominates oligomers 1a-d bearing a 4,7-bisthienylbenzothiadiazole (TBT) spacer due to the strong electron-accepting ability of its benzothiadiazole (BTD) ring. The resulting donor-acceptor-donor systems feature lower HOMO-LUMO gaps than the terthiophene-linked nucleobases (ΔE(g) ∼ 1.8 eV vs 2.4 eV based on electrochemical measurements), and the lowest so far for π-conjugated molecules that include nucleobases within the π-framework. Experiments reveal a dependence of photophysical and electronic structure on the nature of the nucleobase and are in good agreement with theoretical calculations performed at the B3LYP/6-31+G** level. Overall, the results show how nucleobase heterocycles can be installed within π-systems to tune optical and electronic properties. Future work will evaluate the consequences of these information-rich components on supramolecular π-conjugated structure.
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Affiliation(s)
- Raghida Bou Zerdan
- Department of Chemistry, University of Florida , P.O. Box 117200, Gainesville, Florida 32611, United States
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Ramos P, Pavanello M. Quantifying Environmental Effects on the Decay of Hole Transfer Couplings in Biosystems. J Chem Theory Comput 2014; 10:2546-56. [DOI: 10.1021/ct400921r] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Pablo Ramos
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
| | - Michele Pavanello
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
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Impact of a single base pair substitution on the charge transfer rate along short DNA hairpins. Proc Natl Acad Sci U S A 2013; 110:14867-71. [PMID: 23980166 DOI: 10.1073/pnas.1309139110] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Numerical studies of hole migration along short DNA hairpins were performed with a particular emphasis on the variations of the rate and quantum yield of the charge separation process with the location of a single guanine:cytosine (G:C) base pair. Our calculations show that the hole arrival rate increases as the position of the guanine:cytosine base pair shifts from the beginning to the end of the sequence. Although these results are in agreement with recent experimental findings, the mechanism governing the charge migration along these sequences is revisited here. Instead of the phenomenological two-step hopping mechanism via the guanine base, the charge propagation occurs through a delocalization of the hole density along the base pair stack. Furthermore, the variations of the charge transfer with the position of the guanine base are explained by the impact of the base pair substitutions on the delocalized conduction channels.
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Renaud N, Berlin YA, Lewis FD, Ratner MA. Between superexchange and hopping: an intermediate charge-transfer mechanism in poly(A)-poly(T) DNA hairpins. J Am Chem Soc 2013; 135:3953-63. [PMID: 23402652 DOI: 10.1021/ja3113998] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We developed a model for hole migration along relatively short DNA hairpins with fewer that seven adenine (A):thymine (T) base pairs. The model was used to simulate hole migration along poly(A)-poly(T) sequences with a particular emphasis on the impact of partial hole localization on the different rate processes. The simulations, performed within the framework of the stochastic surrogate Hamiltonian approach, give values for the arrival rate in good agreement with experimental data. Theoretical results obtained for hairpins with fewer than three A:T base pairs suggest that hole transfer along short hairpins occurs via superexchange. This mechanism is characterized by the exponential distance dependence of the arrival rate on the donor/acceptor distance, k(a) ≃ e(-βR), with β = 0.9 Å(-1). For longer systems, up to six A:T pairs, the distance dependence follows a power law k(a) ≃ R(-η) with η = 2. Despite this seemingly clear signature of unbiased hopping, our simulations show the complete delocalization of the hole density along the entire hairpin. According to our analysis, the hole transfer along relatively long sequences may proceed through a mechanism which is distinct from both coherent single-step superexchange and incoherent multistep hopping. The criterion for the validity of this mechanism intermediate between superexchange and hopping is proposed. The impact of partial localization on the rate of hole transfer between neighboring A bases was also investigated.
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Affiliation(s)
- Nicolas Renaud
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, USA.
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Boeckx B, Maes G. Simulating the Interaction between Amino Acids and DNA: A Combined Matrix-Isolation FT-IR and Theoretical Study of the 1-Methyluracil·Glycine H-Bond Complexes Using a Dual Sublimation Furnace. J Phys Chem B 2012; 116:11890-8. [DOI: 10.1021/jp307388e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bram Boeckx
- Department of Chemistry, University of Leuven, Celestijnenlaan 200F, Leuven, Belgium
| | - Guido Maes
- Department of Chemistry, University of Leuven, Celestijnenlaan 200F, Leuven, Belgium
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Song SM, Park MB, Kim IH. Three-zone simulated moving-bed (SMB) for separation of cytosine and guanine. KOREAN J CHEM ENG 2012. [DOI: 10.1007/s11814-011-0247-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Ebrahimi A, Habibi-khorassani M, Haghani A. Effect of protonation on individual hydrogen bonds in the 8-oxoguanine-cytosine base pair: NMR, NBO and AIM analyses. Mol Phys 2011. [DOI: 10.1080/00268976.2010.521781] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Tachikawa H, Fukuzumi T. Ionization dynamics of aminopyridine dimer: a direct ab initio molecular dynamics (MD) study. Phys Chem Chem Phys 2011; 13:5881-7. [DOI: 10.1039/c0cp01542c] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Mineva T, Russo N. Atomic Fukui indices and orbital hardnesses of adenine, thymine, uracil, guanine and cytosine from density functional computations. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2009.10.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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