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Li X, Jin Y, Gou Q, Xia Z, Feng G. Microwave spectrum and non-covalent interactions of the 1, 2, 3, 4-tetrafluorobenzene-water complex. J Chem Phys 2018; 149:164306. [PMID: 30384754 DOI: 10.1063/1.5048101] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The 1, 2, 3, 4-tetrafluorobenzene-water complex was investigated by pulsed-jet Fourier transform microwave spectroscopy. One isomer was detected in the jet expansion. Ab initio calculations and non-covalent interaction (NCI) analysis were performed to characterize the intermolecular NCIs. In the observed isomer, the water molecule lies almost in the plane of the benzene ring acting as a proton donor to one of the fluorine atoms and as an acceptor to one of the hydrogen atoms forming a six-membered ring structure. The CH⋯O and H⋯FC bonding distances are determined to be 2.385(1) Å and 2.429(1) Å, respectively. The interaction energy is calculated to be -18.0 kJ mol-1 at the SAPT2+(3)/aug-cc-pVDZ level of theory. The observed transitions exhibit splitting in the order of tens to hundreds of kHz due to the internal rotation of water moiety. The possible tunneling paths of water were investigated by ab initio calculations resulting in a barrier for an internal rotation of about 201 cm-1.
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Affiliation(s)
- Xiaolong Li
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331 Chongqing, China
| | - Yan Jin
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331 Chongqing, China
| | - Qian Gou
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331 Chongqing, China
| | - Zhining Xia
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331 Chongqing, China
| | - Gang Feng
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331 Chongqing, China
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2
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Bhattacherjee A, Wategaonkar S. Water bridges anchored by a C–H⋯O hydrogen bond: the role of weak interactions in molecular solvation. Phys Chem Chem Phys 2016; 18:27745-27749. [DOI: 10.1039/c6cp05469b] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydrogen-bonded water bridges are re-directed from a polar NH bond to a weakly activated C(2)–H bond upon N-methylation. Infrared spectra, supported by ab initio calculations, provide direct evidence of the role of the C(2)–H donor in the solvation of the imidazole ring.
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Affiliation(s)
- Aditi Bhattacherjee
- Department of Chemical Sciences
- Tata Institute of Fundamental Research
- Mumbai 400 005
- India
| | - Sanjay Wategaonkar
- Department of Chemical Sciences
- Tata Institute of Fundamental Research
- Mumbai 400 005
- India
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3
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Yurenko YP, Novotný J, Sklenář V, Marek R. Substituting CF2 for O4' in Components of Nucleic Acids: Towards Systems with Reduced Propensity to Form Abasic Lesions. Chemistry 2015; 21:17933-43. [PMID: 26493955 DOI: 10.1002/chem.201502977] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Indexed: 01/22/2023]
Abstract
Intrinsic structural features and energetics of nucleotides containing variously fluorinated sugars as potential building blocks of DNA duplexes and quadruplexes are explored systematically using the modern methods of density functional theory (DFT) and quantum chemical topology (QCT). Our results suggest that fluorination at the 2'-β or 2'-α,β positions somewhat stabilizes in vacuo the AI relative to the BI conformations. In contrast, substitution of the CF2 group for the O4' atom (O4'-CF2 modification) leads to a preference of the BI relative to AI DNA-like conformers. All the studied modifications result in a noticeable increase in the stability of the glycosidic bond [estimated by the relaxed force constants (RFC) approach], with particularly encouraging results for the O4'-CF2 derivative. Consequently, the O4'-CF2 modified systems are suggested and explored as promising scaffolds for the development of duplex and quadruplex structures with reduced propensity to form abasic lesions and to undergo DNA damage.
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Affiliation(s)
- Yevgen P Yurenko
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno (Czech Republic).
| | - Jan Novotný
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno (Czech Republic)
| | - Vladimir Sklenář
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno (Czech Republic).,National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno (Czech Republic).,Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno (Czech Republic)
| | - Radek Marek
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno (Czech Republic). .,National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno (Czech Republic). .,Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno (Czech Republic).
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4
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Frey JA, Ottiger P, Leutwyler S. Watson–Crick and Sugar-Edge Base Pairing of Cytosine in the Gas Phase: UV and Infrared Spectra of Cytosine·2-Pyridone. J Phys Chem B 2014; 118:682-91. [DOI: 10.1021/jp409660b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jann A. Frey
- Department
of Chemistry and
Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Philipp Ottiger
- 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
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5
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Kumar S, Das A. Observation of exclusively π-stacked heterodimer of indole and hexafluorobenzene in the gas phase. J Chem Phys 2013; 139:104311. [DOI: 10.1063/1.4820532] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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6
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Reid SA, Nyambo S, Muzangwa L, Uhler B. π-Stacking, C–H/π, and Halogen Bonding Interactions in Bromobenzene and Mixed Bromobenzene–Benzene Clusters. J Phys Chem A 2013; 117:13556-63. [DOI: 10.1021/jp407544c] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Scott A. Reid
- Department of Chemistry, Marquette University,
P.O. Box 1881, Milwaukee, Wisconsin 53201-1881, United States
| | - Silver Nyambo
- Department of Chemistry, Marquette University,
P.O. Box 1881, Milwaukee, Wisconsin 53201-1881, United States
| | - Lloyd Muzangwa
- Department of Chemistry, Marquette University,
P.O. Box 1881, Milwaukee, Wisconsin 53201-1881, United States
| | - Brandon Uhler
- Department of Chemistry, Marquette University,
P.O. Box 1881, Milwaukee, Wisconsin 53201-1881, United States
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7
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Muzangwa L, Nyambo S, Uhler B, Reid SA. On π-stacking, C-H/π, and halogen bonding interactions in halobenzene clusters: Resonant two-photon ionization studies of chlorobenzene. J Chem Phys 2012; 137:184307. [DOI: 10.1063/1.4765102] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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8
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So LC, Liu CC, Chan MCW, Lo JCY, Sze KH, Zhu N. Scalar coupling across [C-H···F-C] interactions in (σ-aryl)-chelating post-metallocenes. Chemistry 2011; 18:565-73. [PMID: 22161818 DOI: 10.1002/chem.201102439] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Indexed: 11/07/2022]
Abstract
The nature and importance of C-H···F-C interactions is a topical yet controversial issue, and the development of spectroscopic methods to probe such contacts is therefore warranted. A series of Group 4 bis(benzyl) complexes supported by (σ-aryl)-2-phenolate-6-pyridyl [O,C,N-R(1)] ligands bearing a fluorinated R(1) group (CF(3) or F) in the vicinity of the metal has been prepared. The X-ray crystal structure of the CF(3)-substituted Hf derivative features intramolecular C-H···F-C and Hf···F-C contacts. All complexes have been characterized by multinuclear NMR spectroscopy. The (1)H and (13)C NMR spectra of [M(O,C,N-CF(3))(CH(2)Ph)(2)] derivatives display coupling (assigned to (1h)J(HF) and (2h)J(CF) for Ti; (3)J(HF) and (2)J(CF) (through M···F) for Hf and Zr) between the benzyl CH(2) and CF(3) moieties. [(1)H,(19)F]-HMBC NMR experiments have been performed for the M-[O,C,N-R(1)] complexes and their [O,N,C] counterparts, revealing significant scalar coupling across the C-H···F-C interactions for Ti-[O,C,N] and [O,N,C] species.
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Affiliation(s)
- Loi-Chi So
- Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, PR China
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9
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Kumar S, Kaul I, Biswas P, Das A. Structure of 7-Azaindole···2-Fluoropyridine Dimer in a Supersonic Jet: Competition between N–H···N and N–H···F Interactions. J Phys Chem A 2011; 115:10299-308. [DOI: 10.1021/jp205894q] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Sumit Kumar
- Department of Chemistry, Indian Institute of Science Education & Research (IISER), 900 NCL Innovation Park, Dr. Homi Bhabha Road, Pune-411008 Maharashtra, India
| | - Indu Kaul
- Department of Chemistry, Indian Institute of Science Education & Research (IISER), 900 NCL Innovation Park, Dr. Homi Bhabha Road, Pune-411008 Maharashtra, India
| | - Partha Biswas
- Department of Chemistry, Indian Institute of Science Education & Research (IISER), 900 NCL Innovation Park, Dr. Homi Bhabha Road, Pune-411008 Maharashtra, India
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education & Research (IISER), 900 NCL Innovation Park, Dr. Homi Bhabha Road, Pune-411008 Maharashtra, India
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10
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Anzahaee MY, Watts JK, Alla NR, Nicholson AW, Damha MJ. Energetically important C-H···F-C pseudohydrogen bonding in water: evidence and application to rational design of oligonucleotides with high binding affinity. J Am Chem Soc 2010; 133:728-31. [PMID: 21171597 DOI: 10.1021/ja109817p] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
It is controversial whether organic fluorine can form energetically important hydrogen bonds in aqueous environments. We previously showed by NMR and molecular modeling that the unexpectedly high binding affinity of 2'F-ANA is largely due to a C-H···F-C pseudohydrogen bond at pyrimidine-purine steps. Comparisons of the melting of duplexes with identical sequence composition but a rearranged sequence confirm that energetically important fluorine-mediated pseudohydrogen bonding is in operation in these sequences. The effect is of particular importance when the H-bond donor (purine H8) is activated by the presence of fluorine at its own 2'-position. These results provide a rational method to increase the binding affinity of antisense oligonucleotides by placement of 2'F-ANA modifications at pyrimidine-purine steps.
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Affiliation(s)
- Maryam Yahyaee Anzahaee
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC, Canada H3A 2K6
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11
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Pfaffen C, Frey HM, Ottiger P, Leutwyler S, Bachorz RA, Klopper W. Large-amplitude vibrations of an N–H⋯π hydrogen bonded cis-amide–benzene complex. Phys Chem Chem Phys 2010; 12:8208-18. [DOI: 10.1039/c002056g] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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12
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Ottiger P, Pfaffen C, Leist R, Leutwyler S, Bachorz RA, Klopper W. Strong N−H···π Hydrogen Bonding in Amide−Benzene Interactions. J Phys Chem B 2009; 113:2937-43. [DOI: 10.1021/jp8110474] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Philipp Ottiger
- Departement für Chemie and Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Chantal Pfaffen
- Departement für Chemie and Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Roman Leist
- Departement für Chemie and Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Samuel Leutwyler
- Departement für Chemie and Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Rafał A. Bachorz
- Center for Functional Nanostructures (CFN) and Institut für Physikalische Chemie, UniversitätKarlsruhe (TH), D-76128 Karlsruhe, Germany
| | - Wim Klopper
- Center for Functional Nanostructures (CFN) and Institut für Physikalische Chemie, UniversitätKarlsruhe (TH), D-76128 Karlsruhe, Germany
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13
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Niebel C, Lokshin V, Sigalov M, Krief P, Khodorkovsky V. Intra- and Intermolecular C(sp2)-H···O Hydrogen Bonds in a Series of Isobenzofuranone Derivatives: Manifestation and Energetics. European J Org Chem 2008. [DOI: 10.1002/ejoc.200800357] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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14
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Gu Q, Knee JL. Binding energies and dissociation pathways in the aniline-Ar2 cation complex. J Chem Phys 2008; 128:064311. [DOI: 10.1063/1.2827458] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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15
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Bachorz RA, Bischoff FA, Höfener S, Klopper W, Ottiger P, Leist R, Frey JA, Leutwyler S. Scope and limitations of the SCS-MP2 method for stacking and hydrogen bonding interactions. Phys Chem Chem Phys 2008; 10:2758-66. [DOI: 10.1039/b718494h] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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16
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Leist R, Frey J, Ottiger P, Frey HM, Leutwyler S, Bachorz R, Klopper W. Nucleobase–Fluorobenzene Interactions: Hydrogen Bonding Wins over π Stacking. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200701171] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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17
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Leist R, Frey JA, Ottiger P, Frey HM, Leutwyler S, Bachorz RA, Klopper W. Nucleobase–Fluorobenzene Interactions: Hydrogen Bonding Wins over π Stacking. Angew Chem Int Ed Engl 2007; 46:7449-52. [PMID: 17722215 DOI: 10.1002/anie.200701171] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Roman Leist
- Department of Chemistry and Biochemistry, Universität Bern, Freiestrasse 3, 3012 Bern, Switzerland
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Frey JA, Leist R, Tanner C, Frey HM, Leutwyler S. 2-pyridone: The role of out-of-plane vibrations on the S1↔S0 spectra and S1 state reactivity. J Chem Phys 2006; 125:114308. [PMID: 16999475 DOI: 10.1063/1.2338042] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The S(1)<-->S(0) vibronic spectra of supersonic jet-cooled 2-pyridone [pyridin-2-one (2PY)] and its N-H deuterated isotopomer (d-2PY) have been recorded by two-color resonant two-photon ionization, laser-induced fluorescence and emission, and fluorescence depletion spectroscopies. By combining these methods, the B origin of 2PY at 0(0) (0)+98 cm(-1) and the bands at +218 and +252 cm(-1) are identified as overtones of the S(1) state out-of-plane vibrations nu(1) (') and nu(2) ('), as are the analogous bands of d-2PY. Anharmonic double-minimum potentials are derived for the respective out-of-plane coordinates that predict further nu(1) (') and nu(2) (') overtones and combinations, reproducing approximately 80% of the vibronic bands up to 600 cm(-1) above the 0(0) (0) band. The fluorescence spectra excited at the electronic origins and the nu(1) (') and nu(2) (') out-of-plane overtone levels confirm these assignments. The S(1) nonplanar minima and S(1)<--S(0) out-of-plane progressions are in agreement with the determination of nonplanar vibrationally averaged geometries for the 0(0) (0) and 0(0) (0)+98 cm(-1) upper states by Held et al. [J. Chem. Phys. 95, 8732 (1991)]. The fluorescence lifetimes of the S(1) state vibrations show strong mode dependence: Those of the out-of-plane levels decrease rapidly above 200 cm(-1) excess vibrational energy, while the in-plane vibrations nu(5) ('), nu(8) ('), and nu(9) (') have longer lifetimes, although they are above or interspersed with the "dark" out-of-plane states. This is interpreted in terms of an S(1) (') state reaction with a low barrier towards a conical intersection with a prefulvenic geometry. Out-of-plane vibrational states can directly surmount this barrier, whereas in-plane vibrations are much less efficient in this respect. Analysis of the fluorescence spectra allows to identify nine in-plane S(0) (') state fundamentals, overtones of the S(0) state nu(1) (") and nu(2) (") out-of-plane vibrations, and >30 other overtones and combination bands. The B3LYP6-311++G(d,p) calculated anharmonic wave numbers are in very good agreement with the observed fundamentals, overtones, and combinations, with a deviation Delta(rms)=1.3%.
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Affiliation(s)
- Jann A Frey
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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Abstract
2,4-Difluorotoluene is unusual among hydrofluorocarbons because it is shaped like the DNA base thymine. It was first synthesised as a nucleotide analogue and incorporated into DNA a decade ago. Although it is a nonpolar molecule, it was found to be replicated by DNA polymerase enzymes as if it were thymine. We concluded that replication of DNA base pairs can occur without Watson-Crick hydrogen bonds, and hypothesised that steric effects, rather than these hydrogen bonds, were the main arbiters of DNA replication fidelity. A debate was initiated then, with claims by some that the molecule is polar and forms hydrogen bonds with adenine, thus supporting the hydrogen bonding theory of DNA replication. Here we discuss the evolution of this debate, and reflect on the relevant data that have since come from hundreds of papers and dozens of laboratories. Although discussion on this topic continues, the steric hypothesis for DNA replication is now widely accepted among biochemists, and the changing paradigm has been reflected in textbooks.
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Affiliation(s)
- Eric T Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
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Frey JA, Leist R, Leutwyler S. Hydrogen Bonding of the Nucleobase Mimic 2-Pyridone to Fluorobenzenes: An ab Initio Investigation. J Phys Chem A 2006; 110:4188-95. [PMID: 16553369 DOI: 10.1021/jp057101+] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The hydrogen-bonded complexes of the nucleobase mimic 2-pyridone (2PY) with seven different fluorinated benzenes (1-, 1,2-, 1,4-, 1,2,3-, 1,3,5-, 1,2,3,4-, and 1,2,4,5-fluorobenzene) are important model systems for investigating the relative importance of hydrogen bonding versus pi-stacking interactions in DNA. We have shown by supersonic-jet spectroscopy that these dimers are hydrogen bonded and not pi-stacked at low temperature (Leist, R.; Frey, J. A.; Leutwyler, S. J. Phys. Chem. A 2006, 110, 4180). Their geometries and binding energies D(e) were calculated using the resolution of identity (RI) Møller-Plesset second-order perturbation theory method (RIMP2). The most stable dimers are bound by antiparallel N-H...F-C and C-H...O=C hydrogen bonds. The binding energies are extrapolated to the complete basis set (CBS) limit, , using the aug-cc-pVXZ basis set series. The CBS binding energies range from -D(e,CBS) = 6.4-6.9 kcal/mol and the respective dissociation energies from -D(0,CBS) = 5.9-6.3 kcal/mol. In combination with experiment, the latter represent upper limits to the dissociation energies of the pi-stacked isomers (which are not observed experimentally). The individual C-H...O=C and N-H...F-C contributions to D(e) can be approximately separated. They are nearly equal for 2PY.fluorobenzene; each additional F atom strengthens the C-H...O=C hydrogen bond by approximately 0.5 kcal/mol and weakens the C-F...H-N hydrogen bond by approximately 0.3 kcal/mol. The single H-bond strengths and lengths correlate with the gas-phase acid-base properties of the C-H and C-F groups of the fluorobenzenes.
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Affiliation(s)
- Jann A Frey
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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