1
|
Raczyńska ED. On Prototropy and Bond Length Alternation in Neutral and Ionized Pyrimidine Bases and Their Model Azines in Vacuo. Molecules 2023; 28:7282. [PMID: 37959699 PMCID: PMC10648772 DOI: 10.3390/molecules28217282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/21/2023] [Accepted: 10/22/2023] [Indexed: 11/15/2023] Open
Abstract
In this review, the complete tautomeric equilibria are derived for disubstituted pyrimidine nucleic acid bases starting from phenol, aniline, and their model compounds-monosubstituted aromatic azines. The differences in tautomeric preferences for isolated (gaseous) neutral pyrimidine bases and their model compounds are discussed in light of different functional groups, their positions within the six-membered ring, electronic effects, and intramolecular interactions. For the discussion of tautomeric preferences and for the analysis of internal effects, recent quantum-chemical results are taken into account and compared to some experimental ones. For each possible tautomer-rotamer of the title compounds, the bond length alternation, measured by means of the harmonic oscillator model of electron delocalization (HOMED) index, is examined. Significant HOMED similarities exist for mono- and disubstituted derivatives. The lack of parallelism between the geometric (HOMED) and energetic (ΔG) parameters for all possible isomers clearly shows that aromaticity is not the main factor that dictates tautomeric preferences for pyrimidine bases, particularly for uracil and thymine. The effects of one-electron loss (positive ionization) and one-electron gain (negative ionization) on prototropy and bond length alternation are also reviewed for pyrimidine bases and their models.
Collapse
Affiliation(s)
- Ewa Daniela Raczyńska
- Department of Chemistry, Warsaw University of Life Sciences (SGGW), ul. Nowoursynowska 159c, 02-776 Warszawa, Poland
| |
Collapse
|
2
|
Zhu H, Gong F, Ma P, Qian Y, He L, Chen L, Qin X, Xu L. Protein-activated and FRET enhanced excited-state intermolecular proton transfer fluorescent probes for high-resolution imaging of cilia and tunneling nanotubes in live cells. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 288:122142. [PMID: 36446173 DOI: 10.1016/j.saa.2022.122142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/13/2022] [Accepted: 11/20/2022] [Indexed: 06/16/2023]
Abstract
Excited-state intermolecular proton transfer (inter-ESPT) fluorescent probes responsive to specific bioactive molecules should be greatly promising for protein sensing, DNA mutation simulating and cellular process regulating. However, the inter-ESPT molecules are recessive ESPT fluorophores, which need the assistance of other molecules with both hydrogen-bond accepting and donating abilities to turn on the tautomeric fluorescence. Valid design strategies to create powerful inter-ESPT fluorescent probes are poorly developed, particularly for proteins as targets. We recently reported a unique supramolecular strategy to trigger the inter-ESPT process based on the probe-protein recognition by H-bonding and to image protein-based subcellular structures in live cells. Herein, we found that our inter-ESPT probes (inter-ESPT-01) bearing a 2-amino-3-cyanopyridine scaffold can anchor proteins and light up the "invisible" ESPT state, so as to image the proteins or the protein-based subcellular organelles. More importantly, the inter-ESPT emission of inter-ESPT-01 can be significantly enhanced by the FRET process between amino and imino tautomers, endowing the inter-ESPT-01 probes with super-bright tautomeric fluorescence. The expressed proteins Ecallantide and MarTX were selected as the models to light up the inter-ESPT fluorescence of the probes and revealed that the inter-ESPT process can be triggered by the specific probe-protein recognition events. In the use of the super-bright inter-ESPT fluorescence, not only the proteins, but also the protein-based cilia and tunneling nanotubes (TNTs) can be specifically visualized in living cancer cells. Furthermore, such recognition-driven strategy allows us to construct a unique inter-ESPT probe to track and image specific endogenous proteins in live cells, highlighting the potential of inter-ESPT fluorogens as novel intelligent biomaterials.
Collapse
Affiliation(s)
- Hanming Zhu
- College of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha 410114, PR China
| | - Fuchun Gong
- College of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha 410114, PR China.
| | - Pan Ma
- College of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha 410114, PR China
| | - You Qian
- College of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha 410114, PR China
| | - Lingzhi He
- College of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha 410114, PR China
| | - Lusen Chen
- College of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha 410114, PR China
| | - Xiaoling Qin
- College of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha 410114, PR China
| | - Lujie Xu
- College of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha 410114, PR China
| |
Collapse
|
3
|
Using Chou’s 5-Step Rule to Evaluate the Stability of Tautomers: Susceptibility of 2-[(Phenylimino)-methyl]-cyclohexane-1,3-diones to Tautomerization Based on the Calculated Gibbs Free Energies. ENERGIES 2020. [DOI: 10.3390/en13010183] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Gibbs free energies, based on DFT (Density Functional Theory) calculations, prove that enaminone (2-(anilinemethylidene)cyclohexane-1,3-dione) and ketamine (2-[(phenylimino)-methyl]cyclohexane-1,3-dione) are the most and least stable tautomeric forms of the studied systems, respectively. 1H and 13C NMR spectra prove that 2-(anilinemethylidene)cyclohexane-1,3-diones are the only tautomeric species present in dimethylsulfoxide solution (a very weak signal can be seen only for the p-methoxy derivatives). The zwitterionic character of these enaminones is strengthened by naphthoannulation and by the insertion of the electron-withdrawing substituent into the benzene ring (the latter weakens the intramolecular hydrogen bond in the compound). Substituent and naphtoannulation have no effect on the stability of the studied tautomers. Slight twisting of the benzene ring, with respect to the CArNC plane (seen in the crystalline state), was proven to also take place in vacuum and in solution.
Collapse
|
4
|
Wu JI, Jackson JE, Schleyer PVR. Reciprocal Hydrogen Bonding–Aromaticity Relationships. J Am Chem Soc 2014; 136:13526-9. [DOI: 10.1021/ja507202f] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Judy I. Wu
- Center
for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - James E. Jackson
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Paul von Ragué Schleyer
- Center
for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, United States
| |
Collapse
|
5
|
Krygowski TM, Szatylowicz H, Stasyuk OA, Dominikowska J, Palusiak M. Aromaticity from the viewpoint of molecular geometry: application to planar systems. Chem Rev 2014; 114:6383-422. [PMID: 24779633 DOI: 10.1021/cr400252h] [Citation(s) in RCA: 366] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Tadeusz M Krygowski
- Department of Chemistry, Warsaw University , Pasteura 1, 02-093 Warsaw, Poland
| | | | | | | | | |
Collapse
|
6
|
JIMÉNEZ-PULIDO SONIAB, ILLÁN-CABEZA NURIAA, HUESO-UREÑA FRANCISCO, MORENO-CARRETERO MIGUELN. TAUTOMERISM IN NEUTRAL AND DEPROTONATED 6-AMINO-5-FORMYLURACILS: A PM3-COSMO APPROACH. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2013. [DOI: 10.1142/s0219633613500326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In order to identify the structure of the most stable tautomers of 6-amino-5-formyluracil and its N-methylated derivatives in different pH conditions, relative stabilities of potential tautomers in aqueous phase have been calculated taking into account the entropy effects over the tautomeric equilibria. In each medium, the tautomer with lower energy must be the most representative form at the corresponding pH and the knowledge of the effect of the medium in the tautomerization energies allows evaluating the possible effect of the medium over the molecular stability. The results show that, in aqueous phase, the order of basicity of protonation sites in the 6-amino-5-formyluracil derivatives is N 9 > ( N 3 > N 1) > ( O 8 > O 4 > O 2). The 6-amino-5-formyluracil derivatives act as an amino-formyl-keto tautomer with a strong imino character, although, upon successive deprotonations, a growing contribution of enolyzed forms which explain the increasing labilization of carbonyl bonds must be pointed out.
Collapse
Affiliation(s)
| | - NURIA A. ILLÁN-CABEZA
- Department of Inorganic and Organic Chemistry, University of Jaén, 23071-Jaén, Spain
| | - FRANCISCO HUESO-UREÑA
- Department of Inorganic and Organic Chemistry, University of Jaén, 23071-Jaén, Spain
| | | |
Collapse
|
7
|
Ośmiałowski B, Kolehmainen E, Ikonen S, Valkonen A, Kwiatkowski A, Grela I, Haapaniemi E. 2-Acylamino- and 2,4-Bis(acylamino)pyrimidines as Supramolecular Synthons Analyzed by Multiple Noncovalent Interactions. DFT, X-ray Diffraction, and NMR Spectral Studies. J Org Chem 2012; 77:9609-19. [PMID: 23020688 DOI: 10.1021/jo301643z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Borys Ośmiałowski
- Faculty of Chemical Technology and Engineering, University of Technology and Life Sciences, Seminaryjna
3, PL-85-326 Bydgoszcz, Poland
| | - Erkki Kolehmainen
- Department of Chemistry, University of Jyväskylä, P.O. Box 35, FI-40014 Finland
| | - Satu Ikonen
- Department of Chemistry, University of Jyväskylä, P.O. Box 35, FI-40014 Finland
| | - Arto Valkonen
- Department of Chemistry, University of Jyväskylä, P.O. Box 35, FI-40014 Finland
| | - Adam Kwiatkowski
- Faculty of Chemical Technology and Engineering, University of Technology and Life Sciences, Seminaryjna
3, PL-85-326 Bydgoszcz, Poland
| | - Izabela Grela
- Faculty of Chemical Technology and Engineering, University of Technology and Life Sciences, Seminaryjna
3, PL-85-326 Bydgoszcz, Poland
| | - Esa Haapaniemi
- Department of Chemistry, University of Jyväskylä, P.O. Box 35, FI-40014 Finland
| |
Collapse
|
8
|
Ośmiałowski B. Noncovalent interactions between classical supramolecular synthons in solution: Hydrogen bonding in hindered 2-acylaminopyridine/2-pyridone associates. J Mol Struct 2012. [DOI: 10.1016/j.molstruc.2011.11.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
9
|
Ośmiałowski B, Kolehmainen E, Kowalska M. 2-Acylamino-6-pyridones: Breaking of an Intramolecular Hydrogen Bond by Self-association and Complexation with Double and Triple Hydrogen Bonding Counterparts. Uncommon Steric Effect on Intermolecular Interactions. J Org Chem 2012; 77:1653-62. [DOI: 10.1021/jo201800u] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Borys Ośmiałowski
- Faculty of Chemical Technology
and Engineering, University of Technology and Life Sciences, Seminaryjna 3, PL-85-326 Bydgoszcz, Poland
| | - Erkki Kolehmainen
- Department of Chemistry, University of Jyväskylä, P.O. Box 35,
FI-40014 Finland
| | - Magdalena Kowalska
- Faculty of Chemical Technology
and Engineering, University of Technology and Life Sciences, Seminaryjna 3, PL-85-326 Bydgoszcz, Poland
| |
Collapse
|
10
|
Ośmiałowski B. Proton transfer reaction and intermolecular interactions in associates of 2,5-dihydroxy-1,8-naphthyridine. J Mol Model 2011; 18:1633-44. [PMID: 21805130 DOI: 10.1007/s00894-011-1178-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Accepted: 07/04/2011] [Indexed: 10/17/2022]
|