1
|
Buczek A, Rzepiela K, Kupka T, Broda MA, Kar T. Uracil-water interaction revisited - in search of single H-bonded secondary minima. Phys Chem Chem Phys 2024; 26:5169-5182. [PMID: 38261334 DOI: 10.1039/d3cp04057g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Monohydrated uracil (UW) complexes are stabilized by both O⋯HO and NH⋯O hydrogen bonds (H-bonds), simultaneously participating in forming three stable cyclic structures. The role and contribution of these individual H-bonds (O⋯HO and NH⋯O) to the stability of the three UW complexes are still not understood, because of the technical problems in obtaining their optimized structures by standard geometry optimization. The present study explores a non-standard approach to identify three single H-bonded local minima structures without imaginary frequency using DFT (M06-2X, B3LYP and B3LYP-D3), MP2 and CCSD(T) theories and Dunning's correlation-consistent aug-cc-pVTZ basis set, in both vacuum and aqueous media (CPCM method). The results reveal that these new structures are very shallow secondary minima between two deep wells or next to a deep well of primary minima (double H-bonded structures) in the potential energy surface. The H-bond energy of these single H-bonded complexes is found to be less sensitive to a wide range (about 15-20 degrees) of O⋯HO and NH⋯O angles, and the linearity is preferred in the stable three single H-bonded structures. The technical method used to locate such a shallow minimum is described in detail and may be useful for identifying local minima in other cases where consecutive multiple H-bonded structures are global minima. Energy decomposition (using symmetry adapted perturbation theory (SAPT)) of interaction energy, electron redistribution, and relevant vibrational modes are discussed.
Collapse
Affiliation(s)
- Aneta Buczek
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052 Opole, Poland.
| | - Kacper Rzepiela
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052 Opole, Poland.
| | - Teobald Kupka
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052 Opole, Poland.
| | - Małgorzata A Broda
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052 Opole, Poland.
| | - Tapas Kar
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322, USA.
| |
Collapse
|
2
|
Density Functional Method Study on the Cooperativity of Intermolecular H-bonding and π-π + Stacking Interactions in Thymine-[C nmim]Br ( n = 2, 4, 6, 8, 10) Microhydrates. Molecules 2022; 27:molecules27196242. [PMID: 36234781 PMCID: PMC9572290 DOI: 10.3390/molecules27196242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/12/2022] [Accepted: 09/16/2022] [Indexed: 11/17/2022] Open
Abstract
The exploration of the ionic liquids’ mechanism of action on nucleobase’s structure and properties is still limited. In this work, the binding model of the 1-alkyl-3-methylimidazolium bromide ([Cnmim]Br, n = 2, 4, 6, 8, 10) ionic liquids to the thymine (T) was studied in a water environment (PCM) and a microhydrated surroundings (PCM + wH2O). Geometries of the mono-, di-, tri-, and tetra-ionic thymine (T-wH2O-y[Cnmim]+-xBr−, w = 5~1 and x + y = 0~4) complexes were optimized at the M06-2X/6-311++G(2d, p) level. The IR and UV-Vis spectra, QTAIM, and NBO analysis for the most stable T-4H2O-Br−-1, T-3H2O-[Cnmim]+-Br−-1, T-2H2O-[Cnmim]+-2Br−-1, and T-1H2O-2[Cnmim]+-2Br−-1 hydrates were presented in great detail. The results show that the order of the arrangement stability of thymine with the cations (T-[Cnmim]+) by PCM is stacking > perpendicular > coplanar, and with the anion (T-Br−) is front > top. The stability order for the different microhydrates is following T-5H2O-1 < T-4H2O-Br−-1 < T-3H2O-[Cnmim]+-Br−-1 < T-2H2O-[Cnmim]+-2Br−-1 < T-1H2O-2[Cnmim]+-2Br−-1. A good linear relationship between binding EB values and the increasing number (x + y) of ions has been found, which indicates that the cooperativity of interactions for the H-bonding and π-π+ stacking is varying incrementally in the growing ionic clusters. The stacking model between thymine and [Cnmim]+ cations is accompanied by weaker hydrogen bonds which are always much less favorable than those in T-xBr− complexes; the same trend holds when the clusters in size grow and the length of alkyl chains in the imidazolium cations increase. QTAIM and NBO analytical methods support the existence of mutually reinforcing hydrogen bonds and π-π cooperativity in the systems.
Collapse
|
3
|
Thakare P, Vasile F, Vallaro M, Visentin S, Caron G, Licandro E, Cauteruccio S. Acid-base and lipophilic properties of peptide nucleic acid derivatives. J Pharm Anal 2021; 11:638-645. [PMID: 34765277 PMCID: PMC8572665 DOI: 10.1016/j.jpha.2020.07.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 11/26/2022] Open
Abstract
The first combined experimental and theoretical study on the ionization and lipophilic properties of peptide nucleic acid (PNA) derivatives, including eleven PNA monomers and two PNA decamers, is described. The acidity constants (pKa) of individual acidic and basic centers of PNA monomers were measured by automated potentiometric pH titrations in water/methanol solution, and these values were found to be in agreement with those obtained by MoKa software. These results indicate that single nucleobases do not change their pKa values when included in PNA monomers and oligomers. In addition, immobilized artificial membrane chromatography was employed to evaluate the lipophilic properties of PNA monomers and oligomers, which showed the PNA derivatives had poor affinity towards membrane phospholipids, and confirmed their scarce cell penetrating ability. Overall, our study not only is of potential relevance to evaluate the pharmacokinetic properties of PNA, but also constitutes a reliable basis to properly modify PNA to obtain mimics with enhanced cell penetration properties. The first study on acid-base and lipophilic properties of peptide nucleic acids (PNA). pKa of acid-base centers of PNA evaluated by potentiometric method and MoKa prediction. NMR experiments provide additional information on the protonation of PNA monomers. Lipophilicity of PNA monomers and oligomers is investigated by IAM chromatography. This study can lay the basis of evaluating the pharmacokinetic properties of PNA.
Collapse
Affiliation(s)
- Pramod Thakare
- Department of Chemistry, University of Milan, 20133, Milan, Italy
| | - Francesca Vasile
- Department of Chemistry, University of Milan, 20133, Milan, Italy
| | - Maura Vallaro
- Molecular Biotechnology & Health Sciences Department, University of Turin, 10135, Turin, Italy
| | - Sonja Visentin
- Molecular Biotechnology & Health Sciences Department, University of Turin, 10135, Turin, Italy
| | - Giulia Caron
- Molecular Biotechnology & Health Sciences Department, University of Turin, 10135, Turin, Italy
| | | | | |
Collapse
|
4
|
Świderski G, Kalinowska M, Jabłońska-Trypuć A, Wołejko E, Wydro U, Łyszczek R, Rusinek I, Lewandowski W. Studies on the relationship between the structure of pyrimidinecarboxylic, pyridazinecarboxylic and pyrazinecarboxylic acids and their antimicrobial and cytotoxic activity. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.129903] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
5
|
|
6
|
Boga C, Bonamartini AC, Forlani L, Modarelli V, Righi L, Sgarabotto P. Reactions of Cytosine, Thymine and Uracil toward 2,4,6-trinitro-chlorobenzene. JOURNAL OF CHEMICAL RESEARCH 2019. [DOI: 10.3184/030823401103168848] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The title reactions are an example of direct introduction of an aryl group into DNA bases.
Collapse
Affiliation(s)
- Carla Boga
- Dipartimento di Chimica Organica “A. Mangini”, Università di Bologna, viale Risorgimento 4. 40136, Bologna, Italia
| | - Anna C. Bonamartini
- Dipartimento di Chimica, Facoltà d'Ingegneria, Università di Modena, via Campi 183, 41100 Modena, Italia
| | - Luciano Forlani
- Dipartimento di Chimica Organica “A. Mangini”, Università di Bologna, viale Risorgimento 4. 40136, Bologna, Italia
| | - Vincenzo Modarelli
- Dipartimento di Chimica Organica “A. Mangini”, Università di Bologna, viale Risorgimento 4. 40136, Bologna, Italia
| | - Lara Righi
- Dipartimento di Chimica Generale ed Inorganica, Chimica Analitica, Chimica Fisica. Università di Parma, viale delle Scienze 43100 Parma, Italia. Centro di Studio per la Strutturistica Diffrattometrica del CNR
| | - Paolo Sgarabotto
- Dipartimento di Chimica Generale ed Inorganica, Chimica Analitica, Chimica Fisica. Università di Parma, viale delle Scienze 43100 Parma, Italia. Centro di Studio per la Strutturistica Diffrattometrica del CNR
| |
Collapse
|
7
|
Grinvald II, Kalagaev IY, Petuchov AN, Vorotyntsev IV, Vorotyntsev VM, Spirin IA, Grushevskaya AI, Kapustin RV. Formation of Water Complexes with Organic Compounds in Solid Matter. IR Manifestation and DFT Study. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2018. [DOI: 10.1134/s0036024417130106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
8
|
Computational chemistry applied to vibrational spectroscopy: A tool for characterization of nucleic acid bases and some of their 5-substituted derivatives. PHYSICAL SCIENCES REVIEWS 2017. [DOI: 10.1515/psr-2016-0132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Computational chemistry can be applied to vibrational spectroscopy in different ways, such as for a better characterization and assignment of all the bands of the experimental spectra, as a tool in the identification of the tautomers present in the gas phase and in the solid state through their spectra and for the simulation of the solid and liquid phase of a compound and the consequent simulation and interpretation of their spectra. In the present study, as an example of the applicability of computational chemistry, the structure and spectra of cytosine and uracil nucleic acid bases and two cytosine derivatives are shown. The FTIR and Raman spectra were analysed with the support of ab initio (Hartree-Fock (HF), MP2) and density functional theory (DFT) (B3LYP, PBE, B-P, etc.) calculations using several basis sets and several scaling equations. The calculations predict an easier tautomerization of cytosine than uracil molecule, but the tautomerization is hindered in the 5-bromocytosine molecule. Thus, in the solid state, this molecule only exists in the amino-oxo tautomeric form.
Collapse
|
9
|
Ten GN, Glukhova OE, Slepchenkov MM, Shcherbakova NE, Baranov VI. A theoretical and optical spectroscopic study of the mechanism of a tautomeric transformation in the 7-azaindole dimer and the 7-azaindole complex with a water molecule. J STRUCT CHEM+ 2017. [DOI: 10.1134/s0022476617020020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
10
|
Effects of hydrogen bonding with H2O on the resonance Raman spectra of uracil and thymine. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2016.12.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
11
|
Simoncelli S, Roller EM, Urban P, Schreiber R, Turberfield AJ, Liedl T, Lohmüller T. Quantitative Single-Molecule Surface-Enhanced Raman Scattering by Optothermal Tuning of DNA Origami-Assembled Plasmonic Nanoantennas. ACS NANO 2016; 10:9809-9815. [PMID: 27649370 DOI: 10.1021/acsnano.6b05276] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
DNA origami is a powerful approach for assembling plasmonic nanoparticle dimers and Raman dyes with high yields and excellent positioning control. Here we show how optothermal-induced shrinking of a DNA origami template can be employed to control the gap sizes between two 40 nm gold nanoparticles in a range from 1 to 2 nm. The high field confinement achieved with this optothermal approach was demonstrated by detection of surface-enhanced Raman spectroscopy (SERS) signals from single molecules that are precisely placed within the DNA origami template that spans the nanoparticle gap. By comparing the SERS intensity with respect to the field enhancement in the plasmonic hot-spot region, we found good agreement between measurement and theory. Our straightforward approach for the fabrication of addressable plasmonic nanosensors by DNA origami demonstrates a path toward future sensing applications with single-molecule resolution.
Collapse
Affiliation(s)
- Sabrina Simoncelli
- Photonics and Optoelectronics Group, Department of Physics and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität München , Amalienstraße 54, Munich 80799, Germany
| | - Eva-Maria Roller
- Department of Physics and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität München , Geschwister-Scholl-Platz 1, Munich 80539, Germany
| | - Patrick Urban
- Photonics and Optoelectronics Group, Department of Physics and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität München , Amalienstraße 54, Munich 80799, Germany
| | - Robert Schreiber
- Clarendon Laboratory, Department of Physics, University of Oxford , Parks Road, Oxford OX1 3PU, United Kingdom
| | - Andrew J Turberfield
- Clarendon Laboratory, Department of Physics, University of Oxford , Parks Road, Oxford OX1 3PU, United Kingdom
| | - Tim Liedl
- Department of Physics and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität München , Geschwister-Scholl-Platz 1, Munich 80539, Germany
- Nanosystems Initiative Munich (NIM) , Schellingstraße 4, Munich 80539, Germany
| | - Theobald Lohmüller
- Photonics and Optoelectronics Group, Department of Physics and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität München , Amalienstraße 54, Munich 80799, Germany
- Nanosystems Initiative Munich (NIM) , Schellingstraße 4, Munich 80539, Germany
| |
Collapse
|
12
|
Wincel H. Microhydration of Deprotonated Nucleobases. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1383-92. [PMID: 27178262 PMCID: PMC4942500 DOI: 10.1007/s13361-016-1411-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 04/17/2016] [Accepted: 04/19/2016] [Indexed: 06/05/2023]
Abstract
Hydration reactions of deprotonated nucleobases (uracil, thymine, 5-fluorouracil,2-thiouracil, cytosine, adenine, and hypoxanthine) produced by electrospray have been experimentally studied in the gas phase at 10 mbar using a pulsed ion-beam high-pressure mass spectrometer. The thermochemical data, ΔH (o) , ΔS (o) , and ΔG (o) , for the monohydrated systems were determined. The hydration enthalpies were found to be similar for all studied systems and varied between 39.4 and 44.8 kJ/mol. A linear correlation was found between water binding energies in the hydrated complexes and the corresponding acidities of the most acidic site of nucleobases. The structural and energetic aspects of the precursors for the hydrated complexes are discussed in conjunction with available literature data. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Henryk Wincel
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224, Warsaw, Poland.
| |
Collapse
|
13
|
Freeman LM, Smolyaninov A, Pang L, Fainman Y. Simulated Raman correlation spectroscopy for quantifying nucleic acid-silver composites. Sci Rep 2016; 6:23535. [PMID: 27010074 PMCID: PMC4806353 DOI: 10.1038/srep23535] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 03/08/2016] [Indexed: 01/20/2023] Open
Abstract
Plasmonic devices are of great interest due to their ability to confine light to the nanoscale level and dramatically increase the intensity of the electromagnetic field, functioning as high performance platforms for Raman signal enhancement. While Raman spectroscopy has been proposed as a tool to identify the preferential binding sites and adsorption configurations of molecules to nanoparticles, the results have been limited by the assumption that a single binding site is responsible for molecular adsorption. Here, we develop the simulated Raman correlation spectroscopy (SRCS) process to determine which binding sites of a molecule preferentially bind to a plasmonic material and in what capacity. We apply the method to the case of nucleic acids binding to silver, discovering that multiple atoms are responsible for adsorption kinetics. This method can be applied to future systems, such as to study the molecular orientation of adsorbates to films or protein conformation upon adsorption.
Collapse
Affiliation(s)
- Lindsay M Freeman
- Department of Electrical and Computer Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093-0407, USA
| | - Alexei Smolyaninov
- Department of Electrical and Computer Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093-0407, USA
| | - Lin Pang
- Department of Electrical and Computer Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093-0407, USA
| | - Yeshaiahu Fainman
- Department of Electrical and Computer Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093-0407, USA
| |
Collapse
|
14
|
Shao P, Ding LP, Cai JT, Lu C, Liu B, Sun CB. Microhydration effects on the structures and electrophilic properties of cytidine. RSC Adv 2016. [DOI: 10.1039/c6ra11720a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Adiabatic electron affinities (AEAs) for cytidine hydrates with up to four water molecules.
Collapse
Affiliation(s)
- Peng Shao
- Department of Physics
- Shaanxi University of Science & Technology
- Xi'an 710021
- China
| | - Li-Ping Ding
- Department of Optoelectronic Science & Technology
- College of Electrical & Information Engineering
- Shaanxi University of Science & Technology
- Xi'an 710021
- China
| | - Jiang-Tao Cai
- Department of Physics
- Shaanxi University of Science & Technology
- Xi'an 710021
- China
| | - Cheng Lu
- Beijing Computational Science Research Center
- Beijing 100084
- China
| | - Bo Liu
- Department of Physics
- Shaanxi University of Science & Technology
- Xi'an 710021
- China
| | - Chang-Bo Sun
- Department of Physics
- Shaanxi University of Science & Technology
- Xi'an 710021
- China
| |
Collapse
|
15
|
Sukker GM, Elroby SA, Hilal R. Gas-phase acidity and dynamics of the protonation processes of carbidopa and levodopa. A QM/QD study. J Biomol Struct Dyn 2015; 34:2268-80. [PMID: 26511889 DOI: 10.1080/07391102.2015.1113385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The present work details, our efforts to investigate and compare the acid-base properties of levodopa (LD) and carbidopa (CD), a drug combination being used in the treatment of Parkinson's disease. Protonation and deprotonation were examined for all possible sites in the two drugs. Proton affinity and proton detachment enthalpies were computed at the B3LYP/6-311++G** level of theory. Results of the present work reveal that CD is more basic and can abstract protons in solution much more efficiently than LD. Furthermore, at all deportation sites considered, CD is more acidic than LD. DFT-based ADMP, dynamic simulations have been performed to explore the dynamics of the protonation processes in LD and CD. Thus, while the dynamics of the protonation process of LD is very straightforward leading to the formation of the corresponding cation, the protonation process in CD is very complex involving a major geometry change and rearrangement. Results of the present work reveal that the active species in acid medium is not CD in its normal geometry but a carbonyl hydrazine form instead. The presence of the carbonyl group β to the hydrazine group may very well underlie its enhanced activity which allows it to bind to the active site of the DDC enzyme. The relative stabilities of various water-water-CD complexes have been computed and compared.
Collapse
Affiliation(s)
- Ghader M Sukker
- a Faculty of Science, Chemistry Department , King Abdulaziz University , Jeddah , Saudi Arabia
| | - Shaaban A Elroby
- a Faculty of Science, Chemistry Department , King Abdulaziz University , Jeddah , Saudi Arabia.,c Faculty of Science, Chemistry Department , Beni-Suef University , Beni-Suef , Egypt
| | - Rifaat Hilal
- a Faculty of Science, Chemistry Department , King Abdulaziz University , Jeddah , Saudi Arabia.,b Faculty of Science, Chemistry Department , Cairo University , Giza 12613 , Egypt
| |
Collapse
|
16
|
Salpin JY, Scuderi D. Structure of protonated thymidine characterized by infrared multiple photon dissociation and quantum calculations. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:1898-1904. [PMID: 26411511 DOI: 10.1002/rcm.7296] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/23/2015] [Accepted: 07/29/2015] [Indexed: 06/05/2023]
Abstract
RATIONALE Many fundamental studies are motivated by the probable relationship between the presence of rare enol tautomers of nucleobases and point mutation developing during nucleic acid replication. The evaluation of the tautomeric behaviour of nucleobases is therefore of fundamental importance. This can be probed in the gas phase by combining action spectroscopy and mass spectrometry. METHODS Experimental Infrared Multiple Photon Dissociation spectra in the fingerprint region of electrospray-generated and subsequently selected ions were recorded at the CLIO free electron laser (FEL) facility, by coupling the FEL to a quadrupole ion trap, and compared to calculated harmonic vibrational infrared spectra of the different low-lying isomers computed at the B3LYP/6-31++G(d,p) level. Relative energies were refined using the extended basis set 6-311++G(3df,2p). RESULTS The Density Functional Theory (DFT) study shows that, as for protonated thymine, the global energy minimum of protonated thymidine corresponds to an enol tautomer, whose infrared absorption spectrum is found to be in very good agreement with the experimental IRMPD spectrum. A very weak IRMPD signal observed at ~1780 cm(-1) is very likely the signature of an oxo tautomer. Consequently, as for thymine, protonated thymidine generated by electrospray corresponds to a mixture of at least two tautomeric forms. CONCLUSIONS Tautomerization can be characterized by IRMPD spectroscopy. Interestingly, the dominant enolic tautomeric form(s) presently observed cannot be directly generated from the most stable neutral tautomer of the thymine residue.
Collapse
Affiliation(s)
- Jean-Yves Salpin
- Université d'Evry Val d'Essonne, Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Boulevard François Mitterrand, 91025, Evry, France
- CNRS-UMR 8587
| | - Debora Scuderi
- Université Paris Sud Orsay, Laboratoire de Chimie Physique, Bâtiment 350, 91405, Orsay, France
- CNRS - UMR 8000
| |
Collapse
|
17
|
Ho JJ, Skoff DR, Ghosh A, Zanni MT. Structural Characterization of Single-Stranded DNA Monolayers Using Two-Dimensional Sum Frequency Generation Spectroscopy. J Phys Chem B 2015. [PMID: 26222775 DOI: 10.1021/acs.jpcb.5b07078] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
DNA-covered materials are important in technological applications such as biosensors and microarrays, but obtaining structural information on surface-bound biomolecules is experimentally challenging. In this paper, we structurally characterize single-stranded DNA monolayers of poly(thymine) from 10 to 25 bases in length with an emerging surface technique called two-dimensional sum frequency generation (2D SFG) spectroscopy. These experiments are carried out by adding a mid-IR pulse shaper to a femtosecond broad-band SFG spectrometer. Cross peaks and 2D line shapes in the 2D SFG spectra provide information about structure and dynamics. Because the 2D SFG spectra are heterodyne detected, the monolayer spectra can be directly compared to 2D infrared (2D IR) spectra of poly(thymine) in solution, which aids interpretation. We simulate the 2D SFG spectra using DFT calculations and an excitonic Hamiltonian that relates the molecular geometry to the vibrational coupling. Intrabase cross peaks help define the orientation of the bases and interbase cross peaks, created by coupling between bases, and resolves features not observed in 1D SFG spectra that constrain the relative geometries of stacked bases. We present a structure for the poly(T) oligomer that is consistent with the 2D SFG data. These experiments provide insight into the DNA monolayer structure and set precedent for studying complex biomolecules on surfaces with 2D SFG spectroscopy.
Collapse
Affiliation(s)
- Jia-Jung Ho
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - David R Skoff
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Ayanjeet Ghosh
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Martin T Zanni
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| |
Collapse
|
18
|
Allehyani BH, Elroby SA, Aziz SG, Hilal RH. Protonation and deprotonation enthalpies of alloxan and implications for the structure and energy of its complexes with water: a computational study. J Biomol Struct Dyn 2014; 33:897-910. [DOI: 10.1080/07391102.2014.919238] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Basmah H. Allehyani
- Faculty of Science, Chemistry Department, King Abdullaziz University, Jeddah, Saudi Arabia
| | - Shaaban A. Elroby
- Faculty of Science, Chemistry Department, King Abdullaziz University, Jeddah, Saudi Arabia
- Faculty of Science, Chemistry Department, Benisuief University, Benisuief, Egypt
| | - Saadullah G. Aziz
- Faculty of Science, Chemistry Department, King Abdullaziz University, Jeddah, Saudi Arabia
| | - Rifaat H. Hilal
- Faculty of Science, Chemistry Department, King Abdullaziz University, Jeddah, Saudi Arabia
- Faculty of Science, Chemistry Department, Cairo University, Cairo, Egypt
| |
Collapse
|
19
|
Anizelli PR, Baú JPT, Nabeshima HS, da Costa MF, de Santana H, Zaia DAM. An experimental and theoretical vibrational study of interaction of adenine and thymine with artificial seawaters: A prebiotic chemistry experiment. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 126:184-196. [PMID: 24607468 DOI: 10.1016/j.saa.2014.02.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 01/29/2014] [Accepted: 02/07/2014] [Indexed: 06/03/2023]
Abstract
Nucleic acid bases play important roles in living beings. Thus, their interaction with salts the prebiotic Earth could be an important issue for the understanding of origin of life. In this study, the effect of pH and artificial seawaters on the structure of adenine and thymine was studied via parallel determinations using FT-IR, Raman spectroscopy and theoretical calculations. Thymine and adenine lyophilized in solutions at basic and acidic conditions showed characteristic bands of the enol-imino tautomer due to the deprotonation and the hydrochloride form due to protonation, respectively. The interaction of thymine and adenine with different seawaters representative of different geological periods on Earth was also studied. In the case of thymine a strong interaction with Sr(2+) promoted changes in the Raman and infrared spectra. For adenine changes in infrared and Raman spectra were observed in the presence of salts from all seawaters tested. The experimental results were compared to theoretical calculations, which showed structural changes due to the presence of ions Na(+), Mg(2+), Ca(2+) and Sr(2+) of artificial seawaters. For thymine the bands arising from C4=C5 and C6=O stretching were shifted to lower values, and for adenine, a new band at 1310cm(-1) was observed. The reactivity of adenine and thymine was studied by comparing changes in nucleophilicity and energy of the HOMO orbital.
Collapse
Affiliation(s)
- Pedro R Anizelli
- Laboratório de Química Prebiótica, Departamento de Química-CCE, Universidade Estadual de Londrina, 86051-990 Londrina, PR, Brazil
| | - João P T Baú
- Laboratório de Química Prebiótica, Departamento de Química-CCE, Universidade Estadual de Londrina, 86051-990 Londrina, PR, Brazil
| | - Henrique S Nabeshima
- Departamento de Física-CCE, Universidade Estadual de Londrina, 86051-990 Londrina, PR, Brazil
| | - Marcello F da Costa
- Departamento de Física-CCE, Universidade Estadual de Londrina, 86051-990 Londrina, PR, Brazil
| | - Henrique de Santana
- Laboratório de Química Prebiótica, Departamento de Química-CCE, Universidade Estadual de Londrina, 86051-990 Londrina, PR, Brazil
| | - Dimas A M Zaia
- Laboratório de Química Prebiótica, Departamento de Química-CCE, Universidade Estadual de Londrina, 86051-990 Londrina, PR, Brazil.
| |
Collapse
|
20
|
Shao P, Kuang XY, Ding LP, Zhao YR. Structures, electrophilic properties, and hydrogen bonds of cytidine, uridine, and their radical anions: Microhydration effects. J Chem Phys 2013; 139:024305. [PMID: 23862941 DOI: 10.1063/1.4812500] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Structures, electrophilic properties, and hydrogen bonds of the neutral and anionic monohydrated nucleoside, (cytidine)H2O, and (uridine)H2O have been systematically investigated using density functional theory. Various water-binding sites were predicted by explicitly considering the optimized monohydrated structures. Meanwhile, predictions of electron affinities and vertical detachment energies were also carried out to investigate their electrophilic properties. By examining the singly occupied molecular orbital and natural population analysis, we found the excess negative charge is localized on the cytidine and uridine moiety in anionic monohydrates. This may be the reason why the strength of hydrogen bonding undergoes an obvious change upon the extra electron attachment. Based on the electron density (ρ) and reduced density gradient (RDG), we present an approach to map and analyze the weak interaction (especially hydrogen bond) in monohydrated cytidine and uridine. The scatter plots of RDG versus ρ allow us to identify the different type interactions. Meanwhile, the maps of the gradient isosurfaces show a rich visualization of hydrogen bond, van der Waals interaction, and steric effect.
Collapse
Affiliation(s)
- Peng Shao
- Institute of Atomic and Molecular Physics, Sichuan University, Chengdu 610065, China
| | | | | | | |
Collapse
|
21
|
Araújo JMM, Pereiro AB, Canongia Lopes JN, Rebelo LPN, Marrucho IM. Hydrogen-Bonding and the Dissolution Mechanism of Uracil in an Acetate Ionic Liquid: New Insights from NMR Spectroscopy and Quantum Chemical Calculations. J Phys Chem B 2013; 117:4109-20. [DOI: 10.1021/jp400749j] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- João M. M. Araújo
- Instituto de Tecnologia
Química
e Biológica, Universidade Nova de Lisboa, Apartado 127, 2780-157 Oeiras, Portugal
| | - Ana B. Pereiro
- Instituto de Tecnologia
Química
e Biológica, Universidade Nova de Lisboa, Apartado 127, 2780-157 Oeiras, Portugal
| | - José N. Canongia Lopes
- Instituto de Tecnologia
Química
e Biológica, Universidade Nova de Lisboa, Apartado 127, 2780-157 Oeiras, Portugal
- Centro de Química Estrutural, Instituto Superior Técnico, 1049-001 Lisboa,
Portugal
| | - Luís P. N. Rebelo
- Instituto de Tecnologia
Química
e Biológica, Universidade Nova de Lisboa, Apartado 127, 2780-157 Oeiras, Portugal
| | - Isabel M. Marrucho
- Instituto de Tecnologia
Química
e Biológica, Universidade Nova de Lisboa, Apartado 127, 2780-157 Oeiras, Portugal
- Departamento de
Química,
CICECO, Universidade de Aveiro, 3810-193
Aveiro, Portugal
| |
Collapse
|
22
|
Lanucara F, Crestoni ME, Chiavarino B, Fornarini S, Hernandez O, Scuderi D, Maitre P. Infrared spectroscopy of nucleotides in the gas phase 2. The protonated cyclic 3′,5′-adenosine monophosphate. RSC Adv 2013. [DOI: 10.1039/c3ra41117f] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
23
|
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]
|
24
|
Shabaan AKE, Hassan AE, Saadullah GA. Effects of protonation and deprotonation on the reactivity of quinolone: A theoretical study. CHINESE SCIENCE BULLETIN-CHINESE 2012. [DOI: 10.1007/s11434-011-4922-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
25
|
Chandra AK, Zeegers-Huyskens T. A theoretical investigation of the interaction between substituted carbonyl derivatives and water: Open or cyclic complexes? J Comput Chem 2012; 33:1131-41. [PMID: 22344933 DOI: 10.1002/jcc.22943] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Revised: 12/17/2011] [Accepted: 01/08/2012] [Indexed: 02/06/2023]
Affiliation(s)
- Asit K Chandra
- Department of Chemistry, North Eastern Hill University, Shillong 793022, India.
| | | |
Collapse
|
26
|
Huang S, Gronert S, Wu W. Polarization in the structures of uracil and thiouracils: Implication for binding with orotidine 5'-monophosphate decarboxylase. Bioorg Med Chem Lett 2011; 21:6341-2. [PMID: 21937230 DOI: 10.1016/j.bmcl.2011.08.109] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Revised: 08/20/2011] [Accepted: 08/25/2011] [Indexed: 11/18/2022]
Abstract
The structures of the uracil and thiouracils were examined using NMR spectroscopy and crystal structure data when available. The relationships between the extent of polarization and the C5-C6 bond length as well as the H5-H6 coupling constants were probed. It was found that the bond length and coupling constants correlate well with the proton affinities at the carbonyl or thiocarbonyl groups at C4 but not C2. The possible implication in the tighter binding of thiouracil based nucleotides to orotidine-5'-monophosphate decarboxylase was discussed.
Collapse
Affiliation(s)
- Sha Huang
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA
| | | | | |
Collapse
|
27
|
Nosenko Y, Kunitski M, Brutschy B. Specific photodynamics in thymine clusters: the role of hydrogen bonding. J Phys Chem A 2011; 115:9429-39. [PMID: 21648386 DOI: 10.1021/jp111373t] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A photoionization detected IR study of thymine and 1-methylthymine monohydrates and of their homodimers was carried out to shed some light on the structure of the thymine clusters whose complex photodynamics has recently been the subject of great interest. Under supersonic jet conditions, thymine forms doubly H-bonded cyclic clusters with water or another base preferentially via its N1-H group and the adjacent carbonyl group. This hydrate is of no biological relevance since the N1-H group is the sugar binding site in thymidine. On the other hand, 1-methylthymine forms the donor H-bonds only via the N3-H group. Hence, properties of the N1-H and the N3-H bound clusters of thymine can be studied using thymine and 1-methylthymine molecules, respectively. No biologically relevant conformations of the dimers and hydrates of thymine, contrary to those of 1-methylthymine, are observed under supersonic jet conditions. Thymine homodimer, which extensively fragments upon UV ionization by formation of a protonated monomer, exhibits two N1-H···O═C2 hydrogen bonds. The photodynamics of hydrated thymines is found to be extremely sensitive to the hydration site: ranging from an ultrafast relaxation in less than 100 fs up to formation of a dark state with the lifetime on the microsecond time scale.
Collapse
Affiliation(s)
- Yevgeniy Nosenko
- Institut für Physikalische und Theoretische Chemie, Goethe-Universität, Max-von-Laue-str. 7, 60438 Frankfurt/Main, Germany
| | | | | |
Collapse
|
28
|
Michalkova A, Robinson TL, Leszczynski J. Adsorption of thymine and uracil on 1:1 clay mineral surfaces: comprehensive ab initio study on influence of sodium cation and water. Phys Chem Chem Phys 2011; 13:7862-81. [PMID: 21437301 DOI: 10.1039/c1cp00008j] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This computational study performed using the density functional theory shows that hydrated and non-hydrated tetrahedral and octahedral kaolinite mineral surfaces in the presence of a cation adsorb the nucleic acid bases thymine and uracil well. Differences in the structure and chemistry of specific clay mineral surfaces led to a variety of DNA bases adsorption mechanisms. The energetically most predisposed positions for an adsorbate molecule on the mineral surface were revealed. The target molecule binding with the surface can be characterized as physisorption, which occurs mainly due to a cation-molecular oxygen interaction, with hydrogen bonds providing an additional stabilization. The adsorption strength is proportional to the number of intermolecular interactions formed between the target molecule and the surface. From the Atoms in Molecules analysis and comparison of binding energy values of studied systems it is concluded that the sorption activity of kaolinite minerals for thymine and uracil depends on various factors, among which are the structure and accessibility of the organic compounds. The adsorption is governed mostly by the surface type, its properties and presence of cation, which cause a selective binding of the nucleobase. Adsorbate stabilization on the mineral surface increases only slightly with explicit addition of water. Comparison of activity of different studied kaolinite mineral models reveals the following order for stabilization: octahedral-Na-water > octahedral-Na > tetrahedral-Na > tetrahedral-Na-water. Further investigation of the electrostatic potentials helps understanding of the adsorption process and confirmation of the active sites on the kaolinite mineral surfaces. Based on the conclusions that clay mineral affinity for DNA and RNA bases can vary due to different structural and chemical properties of the surface, a hypothesis on possible role of clays in the origin of life was made.
Collapse
Affiliation(s)
- A Michalkova
- Interdisciplinary Nanotoxicity Center, Department of Chemistry, Jackson State University, Jackson, MS 39217, USA
| | | | | |
Collapse
|
29
|
Sinha RK, Lobsiger S, Trachsel M, Leutwyler S. Vibronic Spectra of Jet-Cooled 2-Aminopurine·H2O Clusters Studied by UV Resonant Two-Photon Ionization Spectroscopy and Quantum Chemical Calculations. J Phys Chem A 2011; 115:6208-17. [DOI: 10.1021/jp111469n] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rajeev K. Sinha
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Simon Lobsiger
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Maria Trachsel
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Samuel Leutwyler
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| |
Collapse
|
30
|
Glancy P, Beyermann WP. Dielectric properties of fully hydrated nucleotides in the terahertz frequency range. J Chem Phys 2010; 132:245102. [PMID: 20590216 DOI: 10.1063/1.3457941] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We use terahertz time domain spectroscopy (THz-TDS) to determine the complex frequency-dependent dielectric response of all four nucleotides at different dilute concentrations. In addition, the suspension model's ability to extract the dielectric response of just the nucleotide with the hydration shell epsilon(b) excluding the dielectric information relating to the bulk will be verified. The suspension model enables us to make the determination that the nucleotides have influences on the water molecules out to the fourth hydration shell. We use a two Debye relaxation fit model for water, all concentrations and all epsilon(b) values. We observed how the nucleotides affect the relaxation parameters in relation to that of pure bulk water. With this information, we notice a transition between purines and pyrimidines, where one is a hydrogen-bond network structure building type material with a low concentration increment and the other is a structure breaking type material with a low concentration decrement. Due to conductivity measurements, we determine that kinetic depolarization is a negligible affect compared to that of dielectric saturation, which we find to dominate where a decrement is found.
Collapse
Affiliation(s)
- P Glancy
- Department of Physics and Astronomy, University of California, Riverside, Riverside, California 92521, USA.
| | | |
Collapse
|
31
|
Yuan XX, Wang YF, Wang X, Chen W, Fossey JS, Wong NB. An ab initio and AIM investigation into the hydration of 2-thioxanthine. Chem Cent J 2010; 4:6. [PMID: 20331849 PMCID: PMC2853538 DOI: 10.1186/1752-153x-4-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Accepted: 03/23/2010] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Hydration is a universal phenomenon in nature. The interactions between biomolecules and water of hydration play a pivotal role in molecular biology. 2-Thioxanthine (2TX), a thio-modified nucleic acid base, is of significant interest as a DNA inhibitor yet its interactions with hydration water have not been investigated either computationally or experimentally. Here in, we reported an ab initio study of the hydration of 2TX, revealing water can form seven hydrated complexes. RESULTS Hydrogen-bond (H-bond) interactions in 1:1 complexes of 2TX with water are studied at the MP2/6-311G(d, p) and B3LYP/6-311G(d, p) levels. Seven 2TX...H2O hydrogen bonded complexes have been theoretically identified and reported for the first time. The proton affinities (PAs) of the O, S, and N atoms and deprotonantion enthalpies (DPEs) of different N-H bonds in 2TX are calculated, factors surrounding why the seven complexes have different hydrogen bond energies are discussed. The theoretical infrared and NMR spectra of hydrated 2TX complexes are reported to probe the characteristics of the proposed H-bonds. An improper blue-shifting H-bond with a shortened C-H bond was found in one case. NBO and AIM analysis were carried out to explain the formation of improper blue-shifting H-bonds, and the H-bonding characteristics are discussed. CONCLUSION 2TX can interact with water by five different H-bonding regimes, N-H...O, O-H...N, O-H...O, O-H...S and C-H...O, all of which are medium strength hydrogen bonds. The most stable H-bond complex has a closed structure with two hydrogen bonds (N(7)-H...O and O-H...O), whereas the least stable one has an open structure with one H-bond. The interaction energies of the studied complexes are correlated to the PA and DPE involved in H-bond formation. After formation of H-bonds, the calculated IR and NMR spectra of the 2TX-water complexes change greatly, which serves to identify the hydration of 2TX.
Collapse
Affiliation(s)
- Xiu-Xiang Yuan
- Faculty of Chemistry, Sichuan University, Chengdu, PR China
| | | | | | | | | | | |
Collapse
|
32
|
Rasmussen AM, Lind MC, Kim S, Schaefer HF. Hydration of the Lowest Triplet States of the DNA/RNA Pyrimidines. J Chem Theory Comput 2010; 6:930-9. [DOI: 10.1021/ct900478c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Andrew M. Rasmussen
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602
| | - Maria C. Lind
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602
| | - Sunghwan Kim
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602
| | - Henry F. Schaefer
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602
| |
Collapse
|
33
|
Wincel H. Microhydration of protonated nucleic acid bases and protonated nucleosides in the gas phase. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:1900-1905. [PMID: 19665394 DOI: 10.1016/j.jasms.2009.06.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2009] [Revised: 06/28/2009] [Accepted: 06/29/2009] [Indexed: 05/28/2023]
Abstract
Thermochemical data, DeltaH(o)(n), DeltaS(o)(n), and DeltaG(o)(n), for the hydration of protonated nucleic acid bases and protonated nucleosides have been experimentally studied by equilibrium measurements using an electrospray high-pressure mass spectrometer equipped with a pulsed ion-beam reaction chamber. For protonated nucleobases the hydration enthalpies were found to be similar for all studied systems and varied between 12.4-13.1 kcal/mol for the first and 11.2-11.5 kcal/mol for the second water molecule. While for protonated nucleosides the water binding enthalpies (11.7-13.3 kcal/mol) are very close to those for protonated nucleobases, the entropy values are "more negative." The structural and energetic aspects of hydrated ions are discussed in conjunction with the available theoretical data.
Collapse
Affiliation(s)
- Henryk Wincel
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland.
| |
Collapse
|
34
|
Hammerum S. Alkyl Radicals as Hydrogen Bond Acceptors: Computational Evidence. J Am Chem Soc 2009; 131:8627-35. [DOI: 10.1021/ja901854t] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Steen Hammerum
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| |
Collapse
|
35
|
Abstract
The structures and the relative energies of six possible tautomers of the thymine base have been studied by density functional theory (DFT) using the B3LYP and BP86 functionals. The keto-thymine (T1) is predicted to be the most stable thymine tautomer, which is consistent with the other theoretical results and experimental data. The corresponding thymine cations and anions are studied using the same level of theory with double-ζ plus polarization and diffuse functions (DZP++) basis sets. The ionization potentials (IPs), the electron affinities (EAs), and proton affinities (PAs) for different protonation sites in thymine base are obtained. T1 has the largest ionization potential and the lowest proton affinity among all the considered thymine tautomers.
Collapse
Affiliation(s)
- Dongsheng Jiao
- Institute of Atomic and Molecular Physics, Sichuan University, Chengdu 610065, P.R. China
- College of Sciences, Southwest Jiaotong University, Chengdu 610031, P.R. China
| | - Hongyan Wang
- Institute of Atomic and Molecular Physics, Sichuan University, Chengdu 610065, P.R. China
- College of Sciences, Southwest Jiaotong University, Chengdu 610031, P.R. China
| | - Yanlan Zhang
- Institute of Atomic and Molecular Physics, Sichuan University, Chengdu 610065, P.R. China
- College of Sciences, Southwest Jiaotong University, Chengdu 610031, P.R. China
| | - Yu Tang
- Institute of Atomic and Molecular Physics, Sichuan University, Chengdu 610065, P.R. China
- College of Sciences, Southwest Jiaotong University, Chengdu 610031, P.R. China
| |
Collapse
|
36
|
Verdolino V, Cammi R, Munk BH, Schlegel HB. Calculation of pKa Values of Nucleobases and the Guanine Oxidation Products Guanidinohydantoin and Spiroiminodihydantoin using Density Functional Theory and a Polarizable Continuum Model. J Phys Chem B 2008; 112:16860-73. [DOI: 10.1021/jp8068877] [Citation(s) in RCA: 162] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Vincenzo Verdolino
- Department o di Chimica Generale ed Inorganica, Università di Parma, Parco Area della Scienze 1, 43100 Parma, Italy and Department of Chemistry, Wayne State University, Detroit, Michigan, 48202
| | - Roberto Cammi
- Department o di Chimica Generale ed Inorganica, Università di Parma, Parco Area della Scienze 1, 43100 Parma, Italy and Department of Chemistry, Wayne State University, Detroit, Michigan, 48202
| | - Barbara H. Munk
- Department o di Chimica Generale ed Inorganica, Università di Parma, Parco Area della Scienze 1, 43100 Parma, Italy and Department of Chemistry, Wayne State University, Detroit, Michigan, 48202
| | - H. Bernhard Schlegel
- Department o di Chimica Generale ed Inorganica, Università di Parma, Parco Area della Scienze 1, 43100 Parma, Italy and Department of Chemistry, Wayne State University, Detroit, Michigan, 48202
| |
Collapse
|
37
|
Bakker JM, Sinha RK, Besson T, Brugnara M, Tosi P, Salpin JY, Maître P. Tautomerism of Uracil Probed via Infrared Spectroscopy of Singly Hydrated Protonated Uracil. J Phys Chem A 2008; 112:12393-400. [DOI: 10.1021/jp806396t] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joost M. Bakker
- Laboratoire de Chimie Physique, UMR 8000 CNRS, Faculté des sciences, Université Paris-Sud 11, Bâtiment 350, 91405 Orsay, France, FOM Institute for Plasma Physics Rijnhuizen, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands, Dipartimento di Fisica, Università di Trento, 38100 Povo Trento, Italy, and Laboratoire d’Analyse et de Modélisation pour la Biologie et l’Environnement, Université d’Evry Val d’Essonne, CNRS, Bâtiment Maupertuis, Boulevard François Mitterrand 91025 Evry, France
| | - Rajeev K. Sinha
- Laboratoire de Chimie Physique, UMR 8000 CNRS, Faculté des sciences, Université Paris-Sud 11, Bâtiment 350, 91405 Orsay, France, FOM Institute for Plasma Physics Rijnhuizen, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands, Dipartimento di Fisica, Università di Trento, 38100 Povo Trento, Italy, and Laboratoire d’Analyse et de Modélisation pour la Biologie et l’Environnement, Université d’Evry Val d’Essonne, CNRS, Bâtiment Maupertuis, Boulevard François Mitterrand 91025 Evry, France
| | - Thierry Besson
- Laboratoire de Chimie Physique, UMR 8000 CNRS, Faculté des sciences, Université Paris-Sud 11, Bâtiment 350, 91405 Orsay, France, FOM Institute for Plasma Physics Rijnhuizen, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands, Dipartimento di Fisica, Università di Trento, 38100 Povo Trento, Italy, and Laboratoire d’Analyse et de Modélisation pour la Biologie et l’Environnement, Université d’Evry Val d’Essonne, CNRS, Bâtiment Maupertuis, Boulevard François Mitterrand 91025 Evry, France
| | - Maurizio Brugnara
- Laboratoire de Chimie Physique, UMR 8000 CNRS, Faculté des sciences, Université Paris-Sud 11, Bâtiment 350, 91405 Orsay, France, FOM Institute for Plasma Physics Rijnhuizen, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands, Dipartimento di Fisica, Università di Trento, 38100 Povo Trento, Italy, and Laboratoire d’Analyse et de Modélisation pour la Biologie et l’Environnement, Université d’Evry Val d’Essonne, CNRS, Bâtiment Maupertuis, Boulevard François Mitterrand 91025 Evry, France
| | - Paolo Tosi
- Laboratoire de Chimie Physique, UMR 8000 CNRS, Faculté des sciences, Université Paris-Sud 11, Bâtiment 350, 91405 Orsay, France, FOM Institute for Plasma Physics Rijnhuizen, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands, Dipartimento di Fisica, Università di Trento, 38100 Povo Trento, Italy, and Laboratoire d’Analyse et de Modélisation pour la Biologie et l’Environnement, Université d’Evry Val d’Essonne, CNRS, Bâtiment Maupertuis, Boulevard François Mitterrand 91025 Evry, France
| | - Jean-Yves Salpin
- Laboratoire de Chimie Physique, UMR 8000 CNRS, Faculté des sciences, Université Paris-Sud 11, Bâtiment 350, 91405 Orsay, France, FOM Institute for Plasma Physics Rijnhuizen, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands, Dipartimento di Fisica, Università di Trento, 38100 Povo Trento, Italy, and Laboratoire d’Analyse et de Modélisation pour la Biologie et l’Environnement, Université d’Evry Val d’Essonne, CNRS, Bâtiment Maupertuis, Boulevard François Mitterrand 91025 Evry, France
| | - Philippe Maître
- Laboratoire de Chimie Physique, UMR 8000 CNRS, Faculté des sciences, Université Paris-Sud 11, Bâtiment 350, 91405 Orsay, France, FOM Institute for Plasma Physics Rijnhuizen, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands, Dipartimento di Fisica, Università di Trento, 38100 Povo Trento, Italy, and Laboratoire d’Analyse et de Modélisation pour la Biologie et l’Environnement, Université d’Evry Val d’Essonne, CNRS, Bâtiment Maupertuis, Boulevard François Mitterrand 91025 Evry, France
| |
Collapse
|
38
|
Liu M, Li T, Amegayibor FS, Cardoso DS, Fu Y, Lee JK. Gas-Phase Thermochemical Properties of Pyrimidine Nucleobases. J Org Chem 2008; 73:9283-91. [DOI: 10.1021/jo801822s] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Min Liu
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
| | - Tingting Li
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
| | - F. Sedinam Amegayibor
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
| | - Daisy S. Cardoso
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
| | - Yunlin Fu
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
| | - Jeehiun K. Lee
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
| |
Collapse
|
39
|
Li QZ, Hu T, An XL, Gong BA, Cheng JB. Cooperativity between the Dihydrogen Bond and the N⋅⋅⋅HC Hydrogen Bond in LiH-(HCN)nComplexes. Chemphyschem 2008; 9:1942-6. [DOI: 10.1002/cphc.200800320] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
40
|
Touboul D, Bouchoux G, Zenobi R. Gas-Phase Protonation Thermochemistry of Adenosine. J Phys Chem B 2008; 112:11716-25. [DOI: 10.1021/jp804786e] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- David Touboul
- Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland, and Laboratoire des Mécanismes Réactionnels, Ecole Polytechnique, 91128 Palaiseau, France
| | - Guy Bouchoux
- Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland, and Laboratoire des Mécanismes Réactionnels, Ecole Polytechnique, 91128 Palaiseau, France
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland, and Laboratoire des Mécanismes Réactionnels, Ecole Polytechnique, 91128 Palaiseau, France
| |
Collapse
|
41
|
Dkhissi A, Blossey R. Metahybrid Density Functional Theory and Correlated ab Initio Studies on Microhydrated Adenine−Thymine Base Pairs. J Phys Chem B 2008; 112:9182-6. [DOI: 10.1021/jp803110n] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ahmed Dkhissi
- Interdisciplinary Research Institute, USTL, USR 3078 CNRS, c/o IEMN UMR 8520 CNRS, Avenue Poincaré BP 60069, Cite Scientifique, Villeneuve d‘Ascq F-59652 France, and Laboratoire d’Analyse et d’Architecture des Systèmes - CNRS, 7 Av du Colonel Roche 31077 Toulouse Cedex 04, France
| | - Ralf Blossey
- Interdisciplinary Research Institute, USTL, USR 3078 CNRS, c/o IEMN UMR 8520 CNRS, Avenue Poincaré BP 60069, Cite Scientifique, Villeneuve d‘Ascq F-59652 France, and Laboratoire d’Analyse et d’Architecture des Systèmes - CNRS, 7 Av du Colonel Roche 31077 Toulouse Cedex 04, France
| |
Collapse
|
42
|
Radiation Effects On DNA: Theoretical Investigations Of Electron, Hole And Excitation Pathways To DNA Damage. ACTA ACUST UNITED AC 2008. [DOI: 10.1007/978-1-4020-8184-2_20] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
|
43
|
Salpin JY, Guillaumont S, Tortajada J, MacAleese L, Lemaire J, Maitre P. Infrared spectra of protonated uracil, thymine and cytosine. Chemphyschem 2007; 8:2235-44. [PMID: 17910021 DOI: 10.1002/cphc.200700284] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The gas-phase structures of protonated uracil, thymine, and cytosine are probed by using mid-infrared multiple-photon dissociation (IRMPD) spectroscopy performed at the Free Electron Laser facility of the Centre Laser Infrarouge d'Orsay (CLIO), France. Experimental infrared (IR) spectra are recorded for ions that were generated by electrospray ionization, isolated, and then irradiated in a quadrupole ion trap; the results are compared to the calculated infrared absorption spectra of the different low-lying isomers (computed at the B3LYP/6-31++G(d,p) level). For each protonated base, the global energy minimum corresponds to an enolic tautomer, whose infrared absorption spectrum matched very well with the experimental IRMPD spectrum, with the exception of a very weak IRMPD signal observed at about 1800 cm(-1) in the case of the three protonated bases. This signal is likely to be the signature of the second-energy-lying oxo tautomer. We thus conclude that within our experimental conditions, two tautomeric ions are formed which coexist in the quadrupole ion trap.
Collapse
Affiliation(s)
- Jean-Yves Salpin
- Laboratoire d'Analyse et de Modélisation pour la Biologie et l'Environnement (LAMBE), Université d'Evry Val d'Esonne-CNRS, Bâtiment Maupertuis, Boulevard François Mitterrand, 91025 Evry, France.
| | | | | | | | | | | |
Collapse
|
44
|
Greisch JF, Weinkauf R, DePauw E, Kryachko ES, Remacle F. Charge Distribution in 3′-Deoxythymidine-Fullerene: Mass Spectrometry, Laser Excitation, and Computational Studies. Isr J Chem 2007. [DOI: 10.1560/ijc.47.1.25] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
45
|
|
46
|
|
47
|
Ten GN, Baranov VI. Investigation of the tautomeric equilibrium of nucleic acid bases in aqueous solution. J STRUCT CHEM+ 2007. [DOI: 10.1007/s10947-007-0131-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
48
|
Lee C, Park KH, Cho M. Vibrational dynamics of DNA. I. Vibrational basis modes and couplings. J Chem Phys 2007; 125:114508. [PMID: 16999491 DOI: 10.1063/1.2213257] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Carrying out density functional theory calculations of four DNA bases, base derivatives, Watson-Crick (WC) base pairs, and multiple-layer base pair stacks, we studied vibrational dynamics of delocalized modes with frequency ranging from 1400 to 1800 cm(-1). These modes have been found to be highly sensitive to structure fluctuation and base pair conformation of DNA. By identifying eight fundamental basis modes, it is shown that the normal modes of base pairs and multilayer base pair stacks can be described by linear combinations of these vibrational basis modes. By using the Hessian matrix reconstruction method, vibrational coupling constants between the basis modes are determined for WC base pairs and multilayer systems and are found to be most strongly affected by the hydrogen bonding interaction between bases. It is also found that the propeller twist and buckle motions do not strongly affect vibrational couplings and basis mode frequencies. Numerically simulated IR spectra of guanine-cytosine and adenine-thymine bases pairs as well as of multilayer base pair stacks are presented and described in terms of coupled basis modes. It turns out that, due to the small interlayer base-base vibrational interactions, the IR absorption spectrum of multilayer base pair system does not strongly depend on the number of base pairs.
Collapse
Affiliation(s)
- Chewook Lee
- Department of Chemistry and Center for Multidimensional Spectroscopy, Division of Chemistry and Molecular Engineering, Korea University, Seoul 136-701, Korea
| | | | | |
Collapse
|
49
|
Theoretical study of the acidity and basicity of uric acid and its interaction with water. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.theochem.2007.02.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
50
|
Zhang RB, Eriksson LA. Effects of OH Radical Addition on Proton Transfer in the Guanine−Cytosine Base Pair. J Phys Chem B 2007; 111:6571-6. [PMID: 17506547 DOI: 10.1021/jp071772l] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Double proton transfer (PT) reactions in guanine-cytosine OH radical adducts are studied by the hybrid density functional B3LYP approach. Concerted and stepwise proton-transfer processes are explored between N1(H) on guanine (G) and N3 on cytosine (C), and between N4(H) on C and O6 on G. All systems except GC6OH display a concerted mechanism. 8OHGC has the highest dissociation energy and is 1.2 kcal/mol more stable than the nonradical GC base pair. The origin of the interactions are investigated through the estimation of intrinsic acid-basic properties of the *OH-X monomer (X = G or C). Solvent effects play a significant role in reducing the dissociation energy. The reactions including *OH-C adducts have significantly lower PT barriers than both the nonradical GC pair and the *OH-G adducts. All reactions are endothermic, with the GC6OH --> GC6OHPT reaction has the lowest reaction energy (4.6 kcal/mol). In accordance with earlier results, the estimated NBO charges show that the G moiety carries a slight negative charge (and C a corresponding positive one) in each adduct. The formation of a partial ion pair may be a potential factor leading to the PT reactions being thermodynamically unfavored.
Collapse
Affiliation(s)
- Ru bo Zhang
- The Institute for Chemical Physics and School of Science, Beijing Institute of Technology, Beijing 100081, China
| | | |
Collapse
|