1
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Zhang P, Gardini AT, Xu X, Parrinello M. Intramolecular and Water Mediated Tautomerism of Solvated Glycine. J Chem Inf Model 2024; 64:3599-3604. [PMID: 38620066 DOI: 10.1021/acs.jcim.4c00273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Understanding tautomerism and characterizing solvent effects on the dynamic processes pose significant challenges. Using enhanced-sampling molecular dynamics based on state-of-the-art deep learning potentials, we investigated the tautomeric equilibria of glycine in water. We observed that the tautomerism between neutral and zwitterionic glycine can occur through both intramolecular and intermolecular proton transfers. The latter proceeds involving a contact anionic-glycine-hydronium ion pair or separate cationic-glycine-hydroxide ion pair. These pathways with comparable barriers contribute almost equally to the reaction flux.
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Affiliation(s)
- Pengchao Zhang
- Center for Combustion Energy, Department of Energy and Power Engineering, and Key Laboratory for Thermal Science and Power Engineering of Ministry of Education, Tsinghua University, Beijing 100084, China
- Atomistic Simulations, Italian Institute of Technology, Genova 16152, Italy
| | - Axel Tosello Gardini
- Atomistic Simulations, Italian Institute of Technology, Genova 16152, Italy
- Department of Materials Science, Università di Milano-Bicocca, 20126 Milano, Italy
| | - Xuefei Xu
- Center for Combustion Energy, Department of Energy and Power Engineering, and Key Laboratory for Thermal Science and Power Engineering of Ministry of Education, Tsinghua University, Beijing 100084, China
| | - Michele Parrinello
- Atomistic Simulations, Italian Institute of Technology, Genova 16152, Italy
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2
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Saha J, Banerjee S, Malo S, Das AK, Das I. A Torquoselective Thermal 6π-Electrocyclization Approach to 1,4-Cyclohexadienes via Solvent-Aided Proton Transfer: Experimental and Theoretical Studies. Chemistry 2024; 30:e202304009. [PMID: 38179806 DOI: 10.1002/chem.202304009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 12/26/2023] [Accepted: 01/05/2024] [Indexed: 01/06/2024]
Abstract
The thermal 6π-electrocyclization of hexatriene typically delivers 1,3-cyclohexadiene (1,3-CHD). However, there is only limited success in directly synthesizing 1,4-cyclohexadiene (1,4-CHD) using such an approach, probably due to the difficulty in realizing thermally-forbidden 1,3-hydride shift after electrocyclic ring closure. The present study shows that by heating (2E,4E,6E)-hexatrienes bearing ester or ketone substituents at the C1-position in a mixture of toluene/MeOH or EtOH (2 : 1) solvents at 90-100 °C, 1,4-CHDs can be selectively synthesized. This is achieved through a torquoselective disrotatory 6π-electrocyclic ring closure followed by a proton-transfer process. The success of this method depends on the polar protic solvent-assisted intramolecular proton transfer from 1,3-CHD to 1,4-CHD, which has been confirmed by deuterium-labeling experiments. There are no reports to date for such a solvent-assisted isomerization. Density functional theory (DFT) studies have suggested that forming 1,3-CHD and subsequent isomerization is a thermodynamically feasible process, regardless of the functional groups involved. Two possible successive polar solvent-assisted proton-transfer pathways have been identified for isomerization.
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Affiliation(s)
- Jayanta Saha
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical BiologyJadavpur, Kolkata, 700032, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Soumadip Banerjee
- School of Mathematical and Computational Sciences, Indian Association for the Cultivation of Science Jadavpur, Kolkata, 700032, India
| | - Sidhartha Malo
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical BiologyJadavpur, Kolkata, 700032, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Abhijit Kumar Das
- School of Mathematical and Computational Sciences, Indian Association for the Cultivation of Science Jadavpur, Kolkata, 700032, India
| | - Indrajit Das
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical BiologyJadavpur, Kolkata, 700032, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
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3
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Slavova S, Antonov L. Azaindolizine proton cranes attached to 7-hydroxyquinoline and 3-hydroxypyridine: a comparative theoretical study. Phys Chem Chem Phys 2024; 26:7177-7189. [PMID: 38349360 DOI: 10.1039/d3cp04635d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Theoretical design of several proton cranes, based on 7-hydroxyquinoline and 3-hydroxypyridine as proton-transfer frames, has been attempted using ground and excited-state density functional theory (DFT) calculations in various environments. Imidazo[1,2-a]pyridine, pyrazolo[1,5-a]pyridine and benzimidazole were considered as proton crane units. The proton crane action requires the existence of a single enol-like form in the ground state, which under excitation goes to the end keto-like one through a series of consecutive excited-state intramolecular proton transfers (ESIPT) and twisting steps with the participation of a crane unit, resulting in a long-range intramolecular proton transfer. The results suggest that 3-hydroxypyridine is not suitable for a proton-transfer frame and 8-(imidazo[1,2-a]pyridin-2-yl)quinolin-7-ol and 8-(pyrazolo[1,5-a]pyridin-2-yl)quinolin-7-ol behave as non-conjugated proton cranes, instead of tautomeric re-arrangement in the latter, which was thought to be possible.
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Affiliation(s)
- Sofia Slavova
- Institute of Electronics, Bulgarian Academy of Sciences, 1784 Sofia, Bulgaria.
- Institute of General and Inorganic Chemistry, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Liudmil Antonov
- Institute of Electronics, Bulgarian Academy of Sciences, 1784 Sofia, Bulgaria.
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4
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Baranac-Stojanović M, Aleksić J, Stojanović M. Theoretical investigation of tautomerism of 2- and 4-pyridones: origin, substituent and solvent effects. Org Biomol Chem 2023; 22:144-158. [PMID: 38051113 DOI: 10.1039/d3ob01588b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Computational investigation at the BHandHLYP/6-311+G(d,p) level of theory of the gas-phase tautomerism of 2- and 4-pyridones confirmed the slight prevalence of lactim in the case of the former, but its dominance in the case of the latter, as shown previously. Examination of aromaticity by using HOMA, EDDB, NBOdel, NICS and AICD led to the conclusion that tautomerization of 4-pyridone results in greater aromaticity gain. It is also driven by the Pauli repulsion relief, which was revealed by the tautomerization energy decomposition analysis. By contrast, in the case of 2-pyridone, lactim is favoured by orbital and electrostatic interactions and disfavoured by the Pauli repulsion. Aromaticity gain in this case is smaller. The position of the tautomeric equilibrium can be modulated by substituent inductive effects (Cl and F), inductive and resonance effects (NH2 and NO2), hydrogen bonding (NO2), and medium polarity, the increase of which increases lactam population.
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Affiliation(s)
- Marija Baranac-Stojanović
- University of Belgrade - Faculty of Chemistry, Studentski trg 12-16, P. O. Box 158, 11000 Belgrade, Serbia.
| | - Jovana Aleksić
- University of Belgrade - Institute of Chemistry, Technology and Metallurgy - Center for Chemistry, Njegoševa 12, P. O. Box 473, 11000 Belgrade, Serbia
| | - Milovan Stojanović
- University of Belgrade - Institute of Chemistry, Technology and Metallurgy - Center for Chemistry, Njegoševa 12, P. O. Box 473, 11000 Belgrade, Serbia
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5
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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.
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Affiliation(s)
- Ewa Daniela Raczyńska
- Department of Chemistry, Warsaw University of Life Sciences (SGGW), ul. Nowoursynowska 159c, 02-776 Warszawa, Poland
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6
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Mandal S, Erimban S, Banerjee S, Daschakraborty S, Das P. Elucidating the relationship between red fluorescence and structural dynamics of carbon dots dispersed in different solvents. Phys Chem Chem Phys 2023; 25:23645-23657. [PMID: 37609834 DOI: 10.1039/d3cp02498a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
The mechanism of intrinsic fluorescence of carbon dots (CDs), the latest nanomaterial from the carbon family, was supposedly deciphered through multiple theories. However, the much sought-after persistent red emission of CDs as a foreseeable consequence of experiments remains elusive prompting the question of whether tuning of the red emission of CDs is a predictable outcome or a serendipitous coincidence. Herein, we tried to decode the same by exploring Alizarin Red S (ARS)-based red emitting CDs in different solvents with wisely chosen analytical tools. The findings are aptly supported by molecular dynamics studies through an experimental intuition-driven model-building approach. Parallel interception of the CDs with powder X-ray diffraction (pXRD) and photophysical spectroscopic studies revealed an important relationship between the solvent and CDs. Tautomerism, a well-known phenomenon with chemical entities, was found to be operative for CDs that greatly influence the Stokes shift and ultimately the fluorescence outcome. Most importantly, pXRD studies established the turbostratism of the CDs where the well-ordered graphitic structure of CDs gets disrupted with solvent molecules. The extent of such disruption is a function of solvent and CD composition that plays a formidable role in obtaining red fluorescence. Thus, for the first time, we demonstrate that the red emission of CDs is related to its structural integrity and if taken care of could be sustained, a tremendously desirable outcome for relevant applications.
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Affiliation(s)
- Saptarshi Mandal
- Department of Biomedical Engineering, University of Kentucky, Lexington, 40536, USA
- Department of Chemistry, Indian Institute of Technology Patna, Bihta, 801103, India.
| | - Shakkira Erimban
- Department of Chemistry, Indian Institute of Technology Patna, Bihta, 801103, India.
- Department of Chemistry, The University of Utah, Salt Lake City, Utah 84112-0850, USA
| | - Subhrajeet Banerjee
- Department of Chemistry, Indian Institute of Technology Patna, Bihta, 801103, India.
| | | | - Prolay Das
- Department of Chemistry, Indian Institute of Technology Patna, Bihta, 801103, India.
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7
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Barone V. DFT Meets Wave-Function Composite Methods for Characterizing Cytosine Tautomers in the Gas Phase. J Chem Theory Comput 2023; 19:4970-4981. [PMID: 37479680 PMCID: PMC10413851 DOI: 10.1021/acs.jctc.3c00465] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Indexed: 07/23/2023]
Abstract
A general strategy for the accurate computation of structural and spectroscopic properties of biomolecule building blocks in the gas phase has been further improved and validated with a special reference to tautomeric equilibria. The main improvements concern the use of the cc-pVTZ-F12 basis set in both DFT and CCSD(T)-F12 computations, the inclusion of core-valence correlation in geometry optimizations by double hybrid functionals, and the use of the cc-pVQZ-F12 basis set for complete basis set extrapolation at the MP2-F12 level. The resulting model chemistry is applied to the challenging problem of cytosine tautomers in the gas phase. The results are in remarkable agreement with experiment concerning both rotational and vibrational spectroscopic parameters and permit their unbiased interpretation in terms of structural and thermochemical features. Together with the intrinsic interest of the studied molecule, the accuracy of the results obtained at reasonable cost without any empirical parameter suggests that the proposed composite method can be profitably employed for accurate investigations of other molecular bricks of life.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore
di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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8
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Jarończyk M, Ostrowski S, Dobrowolski JC. On Integral INICS Aromaticity of Pyridodiazepine Constitutional Isomers and Tautomers. Molecules 2023; 28:5684. [PMID: 37570653 PMCID: PMC10419959 DOI: 10.3390/molecules28155684] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
The structure, energetics, and aromaticity of c.a. 100 constitutional isomers and tautomers of pyrido[m,n]diazepines (m = 1, 2; n = 2, 3, 4, 5; m ≠ n) were studied at the B3LYP/cc-pVTZ level. The pyrido[1,3]diazepines appear the most, while pyrido[2,4]diazepines are the least stable (ca. 26 kcal/mol). In the pyrido[1,n]diazepine group (n = 2-5), the [1,5] isomers are higher in energy by ca. 4.5 kcal/mol and the [1,4] ones by ca. 7 kcal/mol, and the pyrido[1,2]diazepines are the least stable (ca. 20 kcal/mol). All the most stable pyrido[1,n]diazepines have N-atoms near the ring's junction bond but on opposite sites. The most stable [2,n]-forms are also those with the pyridine ring N6-atom near the junction bond. Surprisingly, for the [1,2]-, [1,3]-, and [1,4]-isomer condensation types of pyridine and diazepine rings, the same N9 > N7 > N6 > N8 stability pattern obeys. The stability remains similar in a water medium simulated with the Polarizable Continuum Model of the solvent and is conserved when calculated using the CAM-B3LYP or BHandHlyp functionals. The ring's aromaticity in the pyridine[m,n]diazepines was established based on the integral INICS index resulting from the NICSzz-scan curves' integration. The integral INICS index is physically justified through its relation to the ringcurrent as demonstrated by Berger, R.J.F., et al. Phys. Chem. Chem. Phys. 2022, 24, 624. The six-membered pyrido rings have negative INICSZZ indices and can be aromatic only if they are not protonated at the N-atom. All protonated pyrido and seven-membered rings exhibit meaningful positive INICSZZ values and can be assigned as antiaromatic. However, some non-protonated pyrido rings also have substantial positive INICSZZ indices and are antiaromatic. A weak linear correlation (R2 = 0.72) between the INICSZZ values of the pyridine I(6) and diazepine I(7) rings exists and is a consequence of the communication between the π-electron systems of the two rings. The juxtaposition of the INICS descriptor of the six- and seven-membered rings and diverse electron density parameters at the Ring Critical Points (RCP) revealed good correlations only with the Electrostatic Potentials from the electrons and nuclei (ESPe and ESPn). The relationships with other RCP parameters like electron density and its Laplacian, total energy, and the Hamiltonian form of kinetic energy density were split into two parts: one nearly constant for the six-membered rings and one linearly correlating for the seven-membered rings. Thus, most of the electron density parameters at the RCP of the six-membered rings of pyridodiazepines practically do not change with the diazepine type and the labile proton position. In contrast, those of the seven-membered rings display aromaticity changes in the antiaromatic diazepine with its ring structural modifications.
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Affiliation(s)
| | - Sławomir Ostrowski
- Institute of Chemistry and Nuclear Technology, 16 Dorodna Street, 03-195 Warsaw, Poland;
| | - Jan Cz. Dobrowolski
- National Medicines Institute, 30/34 Chełmska Street, 00-725 Warsaw, Poland
- Institute of Chemistry and Nuclear Technology, 16 Dorodna Street, 03-195 Warsaw, Poland;
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9
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Szymańska M, Majerz I. Prototropy, Intramolecular Interactions, Electron Delocalization, and Physicochemical Properties of 1,8-dihydroxy-9-anthrone-DFT-D3 Study of Substituent Effects. MOLECULES (BASEL, SWITZERLAND) 2023; 28:molecules28010344. [PMID: 36615539 PMCID: PMC9822037 DOI: 10.3390/molecules28010344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 01/04/2023]
Abstract
1,8-dihydroxy-9-anthrone are tricyclic compounds with a ketone group in the middle ring and two hydroxyl groups substituted in the side-aromatic rings what results in formation of two intramolecular hydrogen bonds in which the oxygen atom from the ketone group is the proton acceptor. 1,8-dihydroxy-9-anthrones in which intramolecular proton transfer between C10 and CO in the middle ring occurs, can exist in a tautomeric keto-enol equilibrium. For anthralin, the most important representative of this group, this equilibrium has been studied previously, but it has not been studied for its derivatives. Substituents in the middle ring change the geometry of 1,8-dihydroxy-9-anthrones so they are also expected to affect the keto-enol equilibrium. It is also important to study the effect of intramolecular hydrogen bonds on the structure of both tautomeric forms. It was found that the nature of the substituent in the middle ring could affect the antioxidant properties of the investigated compound.
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10
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Deneva V, Slavova S, Kumanova A, Vassilev N, Nedeltcheva-Antonova D, Antonov L. Favipiravir-Tautomeric and Complexation Properties in Solution. Pharmaceuticals (Basel) 2022; 16:ph16010045. [PMID: 36678542 PMCID: PMC9864296 DOI: 10.3390/ph16010045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/16/2022] [Accepted: 12/23/2022] [Indexed: 12/31/2022] Open
Abstract
The tautomeric properties of favipiravir were investigated experimentally for the first time by using molecular spectroscopy (UV-Vis absorption, fluorescence and NMR), as well as DFT quantum-chemical calculations. According to the obtained results, the enol tautomer is substantially more stable in most of the organic solvents. In the presence of water, a keto form appears to be favored due to the specific solute-solvent interactions. Upon the addition of alkaline-earth-metal ions, deprotonation and complexation occurred simultaneously, giving the formation of 2 : 1 ligand : metal complexes. According to the theoretical simulations, the metal ion is captured between the carbonyl groups as a result of the size-fit effect.
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Affiliation(s)
- Vera Deneva
- Institute of Electronics, Bulgarian Academy of Sciences, 1784 Sofia, Bulgaria
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
- Correspondence: (V.D.); (L.A.)
| | - Sofia Slavova
- Institute of Electronics, Bulgarian Academy of Sciences, 1784 Sofia, Bulgaria
- Institute of General and Inorganic Chemistry, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Alina Kumanova
- Institute of Electronics, Bulgarian Academy of Sciences, 1784 Sofia, Bulgaria
| | - Nikolay Vassilev
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Daniela Nedeltcheva-Antonova
- Institute of Electronics, Bulgarian Academy of Sciences, 1784 Sofia, Bulgaria
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Luidmil Antonov
- Institute of Electronics, Bulgarian Academy of Sciences, 1784 Sofia, Bulgaria
- Correspondence: (V.D.); (L.A.)
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11
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Oznobikhina LP, Lazarev IM, Lazareva NF. Experimental and Theoretical Investigation of the Structure of Acetoacetanilide. RUSS J GEN CHEM+ 2022. [DOI: 10.1134/s1070363222110020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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12
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Parihar H, Thirupathi N. Cobalt(II)-Catalyzed Directed C–H Functionalization/[3+2] Annulation of N-Arylguanidines with Alkynes. Org Lett 2022; 24:8098-8103. [DOI: 10.1021/acs.orglett.2c02503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Harish Parihar
- Department of Chemistry, University of Delhi, Delhi 110 007, India
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13
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Sinha NK, Thirupathi N. Palladium(II) Pincer Complexes Derived From
N
,
N
’,
N
’’‐Tris(2‐thioanisyl)guanidine. Syntheses, Structural Aspects, Solution Behaviour and Suzuki‐Miyaura Coupling Reactions. ChemistrySelect 2022. [DOI: 10.1002/slct.202202778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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14
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Garrido-Zoido JM, Cajina F, Matamoros E, Gil MV, Cintas P, Palacios JC. A synthetically benign one-pot construction of enamino-xanthene dyes. Org Biomol Chem 2022; 20:8108-8119. [PMID: 36214790 DOI: 10.1039/d2ob01358d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Polyhydroxylated phenols are components of biomass and precursors of pigments in plants. This paper reports a novel entry to xanthene dyes, involving the reaction of 2,4,6-trihydroxybenzaldehyde with primary aliphatic amines. This catalyst-free synthesis exhibits a high atom economy and can be conducted under eco-friendly conditions and operational simplicity.
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Affiliation(s)
- Juan Manuel Garrido-Zoido
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencias and IACYS-Unidad de Química Verde y Desarrollo Sostenible, Universidad de Extremadura, E-06006 Badajoz, Spain.
| | - Franklin Cajina
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencias and IACYS-Unidad de Química Verde y Desarrollo Sostenible, Universidad de Extremadura, E-06006 Badajoz, Spain.
| | - Esther Matamoros
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencias and IACYS-Unidad de Química Verde y Desarrollo Sostenible, Universidad de Extremadura, E-06006 Badajoz, Spain.
| | - M Victoria Gil
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencias and IACYS-Unidad de Química Verde y Desarrollo Sostenible, Universidad de Extremadura, E-06006 Badajoz, Spain.
| | - Pedro Cintas
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencias and IACYS-Unidad de Química Verde y Desarrollo Sostenible, Universidad de Extremadura, E-06006 Badajoz, Spain.
| | - Juan C Palacios
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencias and IACYS-Unidad de Química Verde y Desarrollo Sostenible, Universidad de Extremadura, E-06006 Badajoz, Spain.
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15
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Extraordinary behavior of 5-(3,4-dihydroxyphenyl)-10,15,20-tris(N-methylpyridinium-3-yl)porphyrin triiodide in titration with bases and in albumin oxidation. MENDELEEV COMMUNICATIONS 2022. [DOI: 10.1016/j.mencom.2022.07.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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16
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Bhatt A, Mukhopadhyaya A, Ali ME. α-Helix in Cystathionine β-Synthase Enzyme Acts as an Electron Reservoir. J Phys Chem B 2022; 126:4754-4760. [PMID: 35687358 DOI: 10.1021/acs.jpcb.2c01657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The modulation of electron density at the Pyridoxal 5'-phosphate (PLP) catalytic center, because of charge transfer across the α-helix/PLP interface, is the determining factor for the enzymatic activities in the human Cystathionine β-Synthase (hCBS) enzyme. Applying density functional theory calculations, in conjunction with the real space density analysis, we investigated the charge density delocalization across the entire heme-α-helix-PLP electron communication channels. The electron delocalization due to hydrogen bonds at the heme/α-helix and α-helix/PLP interfaces are found to be extended over a very long range, as a result of redistribution of electron densities of the cofactors. Moreover, the internal hydrogen bonds of α-helix that are crucial for its secondary structure also participate in the electron redistribution through the structured hydrogen-bond network. α-Helix is found to accumulate the electron density at the ground state from both of the cofactors and behaves as an electron reservoir for catalytic reaction at the electrophilic center of PLP.
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Affiliation(s)
- Aashish Bhatt
- Institute of Nano Science and Technology, Sector-81, Mohali, Punjab-140306, India
| | - Aritra Mukhopadhyaya
- Institute of Nano Science and Technology, Sector-81, Mohali, Punjab-140306, India
| | - Md Ehesan Ali
- Institute of Nano Science and Technology, Sector-81, Mohali, Punjab-140306, India
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17
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Duan Y, Zhao H, Xue G, Sun F, Stricker F, Wang Z, Mao L, He C, de Alaniz JR, Zheng Y, Wang D. Controlling the Isomerization of Photoresponsive Molecules through a Limiting Tautomerization Strategy. J Phys Chem B 2022; 126:3347-3354. [PMID: 35471969 DOI: 10.1021/acs.jpcb.2c02005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Controlling the multistage photoresponsivity remains a challenge, in part, due to the spontaneous tautomerization between isomers. Herein, we present a strategy to access three independent states (linear, cyclic keto, and cyclic enolate) of crown ether (CE)-substituted donor-acceptor Stenhouse adducts (DASAs) by limiting the tautomerization of the closed isomers. The linear-cyclic keto isomerization is reversibly triggered by treatment with metal ions (Na+ or K+) and CE, while the linear-cyclic enolate isomerization is induced by green light and heat. Density functional theory and molecular dynamics calculation results suggest that the steric effect and supramolecular interaction between the electron-donating and electron-withdrawing moieties play an important role in hindering the tautomerization between cyclic keto and cyclic enolate DASA-CE. The strategy to influence key steps in the photoswitching process inspires well-controlled multistage isomerization of photoresponsive molecules.
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Affiliation(s)
- Yongli Duan
- School of Optoelectronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Haiquan Zhao
- School of Optoelectronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Guodong Xue
- School of Optoelectronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Fanxi Sun
- School of Optoelectronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Friedrich Stricker
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, California 93106-5050, United States
| | - Zhen Wang
- School of Optoelectronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Lijun Mao
- School of Optoelectronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Chao He
- College of Polymer Science and Engineering, Sichuan University, Chengdu 610054, China
| | - Javier Read de Alaniz
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, California 93106-5050, United States
| | - Yonghao Zheng
- School of Optoelectronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Dongsheng Wang
- School of Optoelectronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu 610054, China.,Institute of Electronic and Information Engineering of UESTC in Guangdong, Dongguang 523808, China
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18
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Vaz da Cruz V, Büchner R, Fondell M, Pietzsch A, Eckert S, Föhlisch A. Targeting Individual Tautomers in Equilibrium by Resonant Inelastic X-ray Scattering. J Phys Chem Lett 2022; 13:2459-2466. [PMID: 35266716 PMCID: PMC8935368 DOI: 10.1021/acs.jpclett.1c03453] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 02/01/2022] [Indexed: 06/14/2023]
Abstract
Tautomerism is one of the most important forms of isomerism, owing to the facile interconversion between species and the large differences in chemical properties introduced by the proton transfer connecting the tautomers. Spectroscopic techniques are often used for the characterization of tautomers. In this context, separating the overlapping spectral response of coexisting tautomers is a long-standing challenge in chemistry. Here, we demonstrate that by using resonant inelastic X-ray scattering tuned to the core excited states at the site of proton exchange between tautomers one is able to experimentally disentangle the manifold of valence excited states of each tautomer in a mixture. The technique is applied to the prototypical keto-enol equilibrium of 3-hydroxypyridine in aqueous solution. We detect transitions from the occupied orbitals into the LUMO for each tautomer in solution, which report on intrinsic and hydrogen-bond-induced orbital polarization within the π and σ manifolds at the proton-transfer site.
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Affiliation(s)
- Vinícius Vaz da Cruz
- Helmholtz-Zentrum
Berlin für Materialien und Energie GmbH, Institute for Methods
and Instrumentation for Synchrotron Radiation Research, 12489 Berlin, Germany
| | - Robby Büchner
- Universität
Potsdam, Institut für Physik und Astronomie, 14476 Potsdam, Germany
| | - Mattis Fondell
- Helmholtz-Zentrum
Berlin für Materialien und Energie GmbH, Institute for Methods
and Instrumentation for Synchrotron Radiation Research, 12489 Berlin, Germany
| | - Annette Pietzsch
- Helmholtz-Zentrum
Berlin für Materialien und Energie GmbH, Institute for Methods
and Instrumentation for Synchrotron Radiation Research, 12489 Berlin, Germany
| | - Sebastian Eckert
- Helmholtz-Zentrum
Berlin für Materialien und Energie GmbH, Institute for Methods
and Instrumentation for Synchrotron Radiation Research, 12489 Berlin, Germany
| | - Alexander Föhlisch
- Helmholtz-Zentrum
Berlin für Materialien und Energie GmbH, Institute for Methods
and Instrumentation for Synchrotron Radiation Research, 12489 Berlin, Germany
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19
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Li Z, Zhang L, Zhou Y, Zha D, Hai Y, You L. Dynamic Covalent Reactions Controlled by Ring‐Chain Tautomerism of 2‐Formylbenzoic Acid. European J Org Chem 2022. [DOI: 10.1002/ejoc.202101461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Ziyi Li
- College of Chemistry and Material Science Fujian Normal University Fuzhou Fujian 350007 China
- State Key Laboratory of Structural Chemistry Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences Fuzhou Fujian 350002 China
| | - Ling Zhang
- State Key Laboratory of Structural Chemistry Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences Fuzhou Fujian 350002 China
| | - Yuntao Zhou
- State Key Laboratory of Structural Chemistry Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences Fuzhou Fujian 350002 China
| | - Daijun Zha
- State Key Laboratory of Structural Chemistry Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences Fuzhou Fujian 350002 China
| | - Yu Hai
- State Key Laboratory of Structural Chemistry Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences Fuzhou Fujian 350002 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Lei You
- State Key Laboratory of Structural Chemistry Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences Fuzhou Fujian 350002 China
- University of Chinese Academy of Sciences Beijing 100049 China
- Fujian Science & Technology Innovation Laboratory for Optoelectronic Information of China Fuzhou Fujian 350108 China
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20
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Chen K, Kang QK, Li Y, Wu WQ, Zhu H, Shi H. Catalytic Amination of Phenols with Amines. J Am Chem Soc 2022; 144:1144-1151. [PMID: 35015956 DOI: 10.1021/jacs.1c12622] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Given the wide prevalence and ready availability of both phenols and amines, aniline synthesis through direct coupling between these starting materials would be extremely attractive. Herein, we describe a rhodium-catalyzed amination of phenols, which provides concise access to diverse anilines, with water as the sole byproduct. The arenophilic rhodium catalyst facilitates the inherently difficult keto-enol tautomerization of phenols by means of π-coordination, allowing for the subsequent dehydrative condensation with amines. We demonstrate the generality of this redox-neutral catalysis by carrying out reactions of a large array of phenols with various electronic properties and a wide variety of primary and secondary amines. Several examples of late-stage functionalization of structurally complex bioactive molecules, including pharmaceuticals, further illustrate the potential broad utility of the method.
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Affiliation(s)
- Kai Chen
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province. China
| | - Qi-Kai Kang
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province. China
| | - Yuntong Li
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province. China
| | - Wen-Qiang Wu
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province. China
| | - Hui Zhu
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province. China
| | - Hang Shi
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province. China.,Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
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21
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Theoretical Study of the Geometry of Dibenzoazepine Analogues. Molecules 2022; 27:molecules27030790. [PMID: 35164062 PMCID: PMC8839008 DOI: 10.3390/molecules27030790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/14/2022] [Accepted: 01/19/2022] [Indexed: 11/17/2022] Open
Abstract
The geometry of dibenzoazepine analogues—typical multifunctional drugs—was investigated to find the geometrical parameters sensitive to the substitution of the central seven-membered ring. Exploration of the crystal structure database (CSD) shows that the geometrical parameter sensitive to the substitution of the carbon atom distance of the central ring not included in the aromatic rings to the plane through the carbon atoms common for the central ring and the aromatic side rings. Presence of the double bond in the central ring was reflected in its partial aromaticity expressed by the HOMED parameter. Some derivatives of 5H-dibenzo[b,f]azepine with flat conformation of the central ring are characterized by mobility of the electron density comparable to the mobility in the aromatic side rings. Influence of the surrounding on the investigated compounds was confirmed by comparison of the optimized molecules and the molecules in the crystal state where the packing forces can influence the molecular geometry.
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22
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Sıdır İ, Sarı T, Gülseven Sıdır Y, Berber H. Synthesis, solvatochromism and dipole moment in the ground and excited states of substitute phenol derivative fluorescent Schiff base compounds. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.117075] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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23
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Push–Pull Effect on the Gas-Phase Basicity of Nitriles: Transmission of the Resonance Effects by Methylenecyclopropene and Cyclopropenimine π-Systems Substituted by Two Identical Strong Electron Donors. Symmetry (Basel) 2021. [DOI: 10.3390/sym13091554] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The gas-phase basicity of nitriles can be enhanced by a push–pull effect. The role of the intercalated scaffold between the pushing group (electron-donor) and the pulling (electron-acceptor) nitrile group is crucial in the basicity enhancement, simultaneously having a transmission function and an intrinsic contribution to the basicity. In this study, we examine the methylenecyclopropene and the N-analog, cyclopropenimine, as the smallest cyclic π systems that can be considered for resonance propagation in a push–pull system, as well as their derivatives possessing two strong pushing groups (X) attached symmetrically to the cyclopropene scaffold. For basicity and push–pull effect investigations, we apply theoretical methods (DFT and G2). The effects of geometrical and rotational isomerism on the basicity are explored. We establish that the protonation of the cyano group is always favored. The push–pull effect of strong electron donor X substituents is very similar and the two π-systems appear to be good relays for this effect. The effects of groups in the two cyclopropene series are found to be proportional to the effects in the directly substituted nitrile series X–C≡N. In parallel to the basicity, changes in electron delocalization caused by protonation are also assessed on the basis of aromaticity indices. The calculated proton affinities of the nitrile series reported in this study enrich the gas-phase basicity scale of nitriles to around 1000 kJ mol−1.
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24
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Tang M, Gu H, He S, Rajkumar S, Yang X. Asymmetric Enamide–Imine Tautomerism in the Kinetic Resolution of Tertiary Alcohols. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106151] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Mengyao Tang
- School of Physical Science and Technology ShanghaiTech University Shanghai 201210 China
- University of Chinese Academy of Sciences Beijing 100049 China
- Shanghai Institute of Organic Chemistry Shanghai 200032 China
| | - Huanchao Gu
- School of Physical Science and Technology ShanghaiTech University Shanghai 201210 China
| | - Shunlong He
- School of Physical Science and Technology ShanghaiTech University Shanghai 201210 China
| | - Subramani Rajkumar
- School of Physical Science and Technology ShanghaiTech University Shanghai 201210 China
| | - Xiaoyu Yang
- School of Physical Science and Technology ShanghaiTech University Shanghai 201210 China
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25
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Kaczorowska MA, Kaczmarek-Kędziera A, Ośmiałowski B. Tautomeric equilibrium, proton affinity and mass spectrometry fragmentation of flexible hydrogen-bonded precursors and rigid [Formula: see text] fluorescent dyes. Sci Rep 2021; 11:15995. [PMID: 34362952 PMCID: PMC8346630 DOI: 10.1038/s41598-021-94978-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/12/2021] [Indexed: 11/09/2022] Open
Abstract
The stability of two groups of conformationally locked molecules, similar in topology, but differing only by the type of the bridge rigidifying their structure, is studied. The series of the less-rigid 2-phenacylheterocyclic compounds and their stiff difluoroboranyl derivatives are investigated for the determination of the effect of [Formula: see text]/S/O replacement in a five-membered heterocyclic ring and the presence of a strong electron-donating group on the tautomeric equilibrium, protonation affinity, and fragmentation pattern observed in the structural elucidation by means of mass spectrometry technique. The results of the [Formula: see text]B97X-D/6-311++G(d,p) calculations, the topological analysis of electron density as well as the experimental MS measurements show the importance of the number of heteroatoms, their properties, and location in the molecule for the rational design of the systems of desired stable tautomers or the favorable protonation sites. The obtained data allow for the understanding of the fundamentals of the novel highly fluorescent difluoroborates fragmentation behavior, vital for their structural elucidation with the application of high-resolution tandem mass spectrometry methods.
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Affiliation(s)
- Małgorzata A. Kaczorowska
- Faculty of Chemical Technology and Engineering, UTP University of Science and Technology, Seminaryjna 3, 85-326 Bydgoszcz, Poland
| | - Anna Kaczmarek-Kędziera
- Faculty of Chemistry, Nicolaus Copernicus University in Torun, Gagarina 7, 87–100 Toruń, Poland
| | - Borys Ośmiałowski
- Faculty of Chemistry, Nicolaus Copernicus University in Torun, Gagarina 7, 87–100 Toruń, Poland
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26
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Pereira NAM, Nunes CM, Reva I, Fausto R. Evidence of IR-Induced Chemistry in a Neat Solid: Tautomerization of Thiotropolone by Thermal, Electronic, and Vibrational Excitations. J Phys Chem A 2021; 125:6394-6403. [PMID: 34275275 DOI: 10.1021/acs.jpca.1c04081] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Thiotropolone isolated in argon and xenon matrices (as monomers) or in a neat solid (as the crystalline or amorphous state) at low temperature was found to exist only in the thione-enol form. Visible light irradiation (λ ≥ 400 nm) leads to thione-enol → thiol-keto tautomerization in matrices and under neat solid conditions at 15 K. The assignment of the IR spectra of the two thiotropolone tautomers (thione-enol and thiol-keto) was carried out with the support of B3LYP/6-311+G(2d,p) computations. The thiol-keto form generated in situ in a neat solid was found to tautomerize back to the thione-enol upon annealing up to 100 K. Gaussian-4 (G4) computations estimate that such a tautomerization process has an energy barrier of ∼25 kJ mol-1, which is consistent with the observations. Moreover, it was found that narrowband IR irradiation of the thiol-keto form in a neat solid, at the frequency of its CH stretching overtones/combination modes, also induces tautomerization to the thione-enol form. Such a result constitutes an important demonstration of vibrationally induced chemistry under neat solid conditions.
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Affiliation(s)
- Nelson A M Pereira
- CQC, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Cláudio M Nunes
- CQC, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Igor Reva
- CQC, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal.,CIEPQPF, Department of Chemical Engineering, University of Coimbra, 3030-790 Coimbra, Portugal
| | - Rui Fausto
- CQC, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
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27
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Tang M, Gu H, He S, Rajkumar S, Yang X. Asymmetric Enamide-Imine Tautomerism in the Kinetic Resolution of Tertiary Alcohols. Angew Chem Int Ed Engl 2021; 60:21334-21339. [PMID: 34312956 DOI: 10.1002/anie.202106151] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Indexed: 12/23/2022]
Abstract
An efficient protocol for kinetic resolution of tertiary alcohols has been developed through an unprecedented asymmetric enamide-imine tautomerism process enabled by chiral phosphoric acid catalysis. A broad range of racemic 2-arylsulfonamido tertiary allyl alcohols could be kinetically resolved with excellent kinetic resolution performances (with s-factor up to >200). This method is particularly effective for a series of 1,1-dialkyl substituted allyl alcohols, which produced chiral tertiary alcohols that would be difficult to access via other asymmetric methods. Facile and versatile transformations of the chiral α-hydroxy imine and enamide products, especially the efficient stereodivergent synthesis of all four stereoisomers of β-amino tertiary alcohols using one enantiomer of the catalyst, demonstrated the value of this kinetic resolution method.
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Affiliation(s)
- Mengyao Tang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Shanghai Institute of Organic Chemistry, Shanghai, 200032, China
| | - Huanchao Gu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Shunlong He
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Subramani Rajkumar
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Xiaoyu Yang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
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28
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Vazquez-Salazar LI, Boittier ED, Unke OT, Meuwly M. Impact of the Characteristics of Quantum Chemical Databases on Machine Learning Prediction of Tautomerization Energies. J Chem Theory Comput 2021; 17:4769-4785. [PMID: 34288675 DOI: 10.1021/acs.jctc.1c00363] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
An essential aspect for adequate predictions of chemical properties by machine learning models is the database used for training them. However, studies that analyze how the content and structure of the databases used for training impact the prediction quality are scarce. In this work, we analyze and quantify the relationships learned by a machine learning model (Neural Network) trained on five different reference databases (QM9, PC9, ANI-1E, ANI-1, and ANI-1x) to predict tautomerization energies from molecules in Tautobase. For this, characteristics such as the number of heavy atoms in a molecule, number of atoms of a given element, bond composition, or initial geometry on the quality of the predictions are considered. The results indicate that training on a chemically diverse database is crucial for obtaining good results and also that conformational sampling can partly compensate for limited coverage of chemical diversity. The overall best-performing reference database (ANI-1x) performs on average by 1 kcal/mol better than PC9, which, however, contains about 2 orders of magnitude fewer reference structures. On the other hand, PC9 is chemically more diverse by a factor of ∼5 as quantified by the number of atom-in-molecule-based fragments (amons) it contains compared with the ANI family of databases. A quantitative measure for deficiencies is the Kullback-Leibler divergence between reference and target distributions. It is explicitly demonstrated that when certain types of bonds need to be covered in the target database (Tautobase) but are undersampled in the reference databases, the resulting predictions are poor. Examples of this include the poor performance of all databases analyzed to predict C(sp2)-C(sp2) double bonds close to heteroatoms and azoles containing N-N and N-O bonds. Analysis of the results with a Tree MAP algorithm provides deeper understanding of specific deficiencies in predicting tautomerization energies by the reference datasets due to inadequate coverage of chemical space. Capitalizing on this information can be used to either improve existing databases or generate new databases of sufficient diversity for a range of machine learning (ML) applications in chemistry.
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Affiliation(s)
| | - Eric D Boittier
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Oliver T Unke
- Machine Learning Group, Technische Universität Berlin, 10587 Berlin, Germany.,DFG Cluster of Excellence "Unifying Systems in Catalysis" (UniSysCat), Technische Universität Berlin, 10623 Berlin, Germany
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.,Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
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29
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Sugiura S, Maeda H. Pyrrole-bridged quinones: π-electronic systems that modulate electronic structures by tautomerism and deprotonation. Chem Commun (Camb) 2021; 57:6983-6986. [PMID: 34160483 DOI: 10.1039/d1cc02691g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
A new series of π-extended quinone derivatives containing a pyrrole bridge exhibited NH/OH-type tautomerization and anion binding along with deprotonation that induced near-infrared absorption and ion-pairing assemblies.
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Affiliation(s)
- Shinya Sugiura
- Department of Applied Chemistry, College of Life Sciences, Ritsumeikan University, Kusatsu 525-8577, Japan.
| | - Hiromitsu Maeda
- Department of Applied Chemistry, College of Life Sciences, Ritsumeikan University, Kusatsu 525-8577, Japan.
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30
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Szatylowicz H, Stasyuk OA, Solà M, Krygowski TM. Aromaticity of nucleic acid bases. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1509] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Halina Szatylowicz
- Faculty of Chemistry Warsaw University of Technology, Noakowskiego 3, 00‐664 Warsaw Poland
| | - Olga A. Stasyuk
- Institute of Computational Chemistry and Catalysis and Department of Chemistry, University of Girona, C/ Maria Aurélia Capmany 69, 17003 Girona Spain
| | - Miquel Solà
- Institute of Computational Chemistry and Catalysis and Department of Chemistry, University of Girona, C/ Maria Aurélia Capmany 69, 17003 Girona Spain
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31
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Ghassami A, Oleiki E, Kim DY, Shin HJ, Lee G, Kim KS. Facile room-temperature self-assembly of extended cation-free guanine-quartet network on Mo-doped Au(111) surface. NANOSCALE ADVANCES 2021; 3:3867-3874. [PMID: 36133009 PMCID: PMC9418868 DOI: 10.1039/d1na00235j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/05/2021] [Indexed: 06/16/2023]
Abstract
Guanine-quadruplex, consisting of several stacked guanine-quartets (GQs), has emerged as an important category of novel molecular targets with applications from nanoelectronic devices to anticancer drugs. Incorporation of metal cations into a GQ structure is utilized to form stable G-quadruplexes, while formation of a cation-free GQ network has been challenging. Here we report the room temperature (RT) molecular self-assembly of extended pristine GQ networks on an Au(111) surface. An implanted molybdenum atom within the Au(111) surface is used to nucleate and stabilize the cation-free GQ network. Additionally, decoration of the Au(111) surface with 7-armchair graphene nanoribbons (7-AGNRs) enhances the GQ domain size by suppressing the influence of the disordered phase nucleated from Au step edges. Scanning tunneling microscopy/spectroscopy (STM/STS) and density functional theory (DFT) calculations confirm the formation of GQ networks and unravel the nucleation and growth mechanism. Our work, utilizing a hetero-atom doped substrate, provides a facile approach to enhance the stability and domain size of the GQ self-assembly, which would be applicable for other molecular structures.
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Affiliation(s)
- Amirreza Ghassami
- Center for Superfunctional Materials, Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST) 50 UNIST-gil Ulsan 44919 Republic of Korea
| | - Elham Oleiki
- Center for Superfunctional Materials, Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST) 50 UNIST-gil Ulsan 44919 Republic of Korea
| | - Dong Yeon Kim
- Center for Superfunctional Materials, Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST) 50 UNIST-gil Ulsan 44919 Republic of Korea
| | - Hyung-Joon Shin
- Department of Materials Science and Engineering, Ulsan National Institute of Science and Technology (UNIST) 50 UNIST-gil Ulsan 44919 Republic of Korea
| | - Geunsik Lee
- Center for Superfunctional Materials, Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST) 50 UNIST-gil Ulsan 44919 Republic of Korea
| | - Kwang S Kim
- Center for Superfunctional Materials, Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST) 50 UNIST-gil Ulsan 44919 Republic of Korea
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32
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Parshotam S, Joy M, Rossano-Tapia M, Mora-Gomez VA, Brown A. The thermochemical, structural, and spectroscopic analyses of the tautomers of sulfur and selenium modified emissive nucleobases. CAN J CHEM 2021. [DOI: 10.1139/cjc-2020-0294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this study, density functional theory (DFT) and time dependent density functional theory (TD-DFT) are used to investigate the stabilities and spectral properties [IR, UV–vis, and two-photon absorption (2PA)] of two sets of modified RNA nucleobase tautomers. The modifications introduce either a sulfur or selenium atom to form an isothiazolo[4,3-d]pyrimidine or isoselenazolo[4,3-d]pyrimidine heterocyclic core, respectively. The relative stabilities of both sets of modified tautomers determined with B3LYP/6-31++G(d,p) reveal that in water (with a polarizable continuum model), the 6-keto-2-amino tautomer of guanine and the rare 4-imino-2-keto tautomer of cytosine may be present at significant populations, whereas the 6-enol-2-amino tautomer of guanine is more common in the gas phase. The identification of these modified tautomers is possible due to the natural differences in their vibrational modes and hence IR spectra. Furthermore, the photophysical properties of both these sets of modified tautomers indicate that excitation and emission energies are shifted relative to their more abundant form in both one photon absorption and emission and 2PA spectra, as determined at the B3LYP/6-31++G(d,p) and CAM-B3LYP/aug-cc-pVDZ levels of theory, respectively. Even though the 2PA cross sections in water for all of the species are small (0.3–2.3 GM), the modified cytosine tautomer shows promise, as its cross section is larger than the more dominant form. The spectral separation between the dominant form and the tautomers of isoselenazole and isothiazole modified cytosine and guanine are relatively similar, suggesting both modifications could be useful in elucidating the tautomers from their more abundant counterparts.
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Affiliation(s)
- Shyam Parshotam
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
| | - Megan Joy
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
| | - Maria Rossano-Tapia
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
| | - V. A. Mora-Gomez
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
| | - Alex Brown
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
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Mono- and Diamination of 4,6-Dichloropyrimidine, 2,6-Dichloropyrazine and 1,3-Dichloroisoquinoline with Adamantane-Containing Amines. Molecules 2021; 26:molecules26071910. [PMID: 33805408 PMCID: PMC8037717 DOI: 10.3390/molecules26071910] [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: 02/23/2021] [Revised: 03/19/2021] [Accepted: 03/24/2021] [Indexed: 11/16/2022] Open
Abstract
N-heteroaryl substituted adamantane-containing amines are of substantial interest for their perspective antiviral and psychotherapeutic activities. Chlorine atom at alpha-position of N-heterocycles has been substituted by the amino group using convenient nucleophilic substitution reactions with a series of adamantylalkylamines. The prototropic equilibrium in these compounds was studied using NMR spectroscopy. The introduction of the second amino substituent in 4-amino-6-chloropyrimidine, 2-amino-chloropyrazine, and 1-amino-3-chloroisoquinoline was achieved using Pd(0) catalysis.
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Lozynski M, Rusinska-Roszak D. Finding the direct energy-structure correlations in intramolecular aromaticity assisted hydrogen bonding (AAHB). J Mol Graph Model 2021; 105:107884. [PMID: 33725643 DOI: 10.1016/j.jmgm.2021.107884] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 02/25/2021] [Accepted: 02/25/2021] [Indexed: 11/25/2022]
Abstract
A predictive model for intramolecular hydrogen bond energy (EHB) calculation of polyaromatic ortho-hydroxyaldehydes based on a set of small, functionalized hydrocarbons is developed. The complete data set of 18 compounds was used for this study. The model is based on one of four optional categories of molecular descriptors: geometric, spectroscopic, bond order and topological indices. The model of Wiberg bond indices (WBIs) as descriptors of the CC involved bond based on stepwise regression has acceptable prediction abilities for 14 structures of ortho-hydroxyformylobenzo[a]pyrene derivatives already at the semiempirical level. The presented correlation enables a significantly more rapid and quantitative description of the hydrogen bonding strength than the much more time-consuming MTA method. Thus, WBIs are shown to provide a reliable means for fast prescreening of the energy of chelate hydrogen bonds potentially for any polyaromatic derivatives.
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Affiliation(s)
- Marek Lozynski
- Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, 60-965, Poznan, Poland
| | - Danuta Rusinska-Roszak
- Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, 60-965, Poznan, Poland.
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Kostritskiy AY, Dmitriev MV, Grinev VS, Fedotova OV. CRYSTAL STRUCTURE AND PACKING FEATURES
OF 3-(5-METHYL-1H-PYRAZOL-3-YL)-2H-CHROMEN-2-ONE
AND 3-(3-METHYL-1H-PYRAZOL-3-YL)-2H-CHROMEN-2-ONE. J STRUCT CHEM+ 2021. [DOI: 10.1134/s0022476621030112] [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]
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36
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Padash R, Ramazani S. Investigation of stability of adenine and its tautomers in RNA and DNA, and their interaction with Na+, K+, Mg2+, Ca2+ and Zn2+. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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37
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Park H, Lee D. Biomimetic hydrogen-bonding cascade for chemical activation: telling a nucleophile from a base. Chem Sci 2020; 12:590-598. [PMID: 34163789 PMCID: PMC8178988 DOI: 10.1039/d0sc05067a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Hydrogen bonding-assisted polarization is an effective strategy to promote bond-making and bond-breaking chemical reactions. Taking inspiration from the catalytic triad of serine protease active sites, we have devised a conformationally well-defined benzimidazole platform that can be systematically functionalized to install multiple hydrogen bonding donor (HBD) and acceptor (HBA) pairs in a serial fashion. We found that an increasing number of interdependent and mutually reinforcing HBD–HBA contacts facilitate the bond-forming reaction of a fluorescence-quenching aldehyde group with the cyanide ion, while suppressing the undesired Brønsted acid–base reaction. The most advanced system, evolved through iterative rule-finding studies, reacts rapidly and selectively with CN− to produce a large (>180-fold) enhancement in the fluorescence intensity at λmax = 450 nm. Biomimetic cascade hydrogen bonds promote covalent capture of a nucleophile by polarizing the electrophilic reaction site, while suppressing non-productive acid–base chemistry as the competing reaction pathway.![]()
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Affiliation(s)
- Hyunchang Park
- Department of Chemistry, Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Korea
| | - Dongwhan Lee
- Department of Chemistry, Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Korea
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38
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Yamashita KI, Hirano D, Fujimaki K, Sugiura KI. Synthesis of Porphyrinquinone and Doubly-Fused Diporphyrin Quinone Through Oxidation of Diarylporphyrins Using a Hypervalent Iodine Compound. Chem Asian J 2020; 15:3037-3043. [PMID: 32749058 DOI: 10.1002/asia.202000781] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 07/28/2020] [Indexed: 11/06/2022]
Abstract
Treatment of a meso-diarylporphyrin with PhI(OAc)2 in the presence of BF3 ⋅ OEt2 and propionic acid affords the corresponding porphyrinquinone in a high yield (91%). A novel quinone derived from meso-meso β-β doubly-fused diporphyrin was obtained as the sole byproduct (16% yield), which exhibits strong panchromatic absorption between 300 and 1000 nm. It has a low HOMO-LUMO gap owing to expanded and low-symmetry π-planes.
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Affiliation(s)
- Ken-Ichi Yamashita
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo, 192-0397, Japan.,Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Daisuke Hirano
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo, 192-0397, Japan
| | - Keisuke Fujimaki
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo, 192-0397, Japan
| | - Ken-Ichi Sugiura
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo, 192-0397, Japan
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39
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Zhang J, Qi S, Zhang C, Fan Z, Ding Q, Mao S, Dong Z. Controlling Keto–Enol Tautomerism of Ureidopyrimidinone to Generate a Single-Quadruple AADD-DDAA Dimeric Array. Org Lett 2020; 22:7305-7309. [DOI: 10.1021/acs.orglett.0c02644] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jing Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Shuaiwei Qi
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Chenyang Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Zengming Fan
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Qinwen Ding
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Shizhong Mao
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Zeyuan Dong
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
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40
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Raczyńska ED, Kurpiewski J, Igielska M, Kamińska B. Quantitative description of bond lengths alternation for caffeine−effects of ionization, proton-transfer, and noncovalent interaction. COMPUT THEOR CHEM 2020. [DOI: 10.1016/j.comptc.2020.112811] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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41
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Martínez RF, Matamoros E, Cintas P, Palacios JC. Imine or Enamine? Insights and Predictive Guidelines from the Electronic Effect of Substituents in H-Bonded Salicylimines. J Org Chem 2020; 85:5838-5862. [PMID: 32259438 DOI: 10.1021/acs.joc.0c00130] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Imine and enamine bonds decorate the skeleton of numerous reagents, catalysts, and organic materials. However, it is difficult to isolate at will a single tautomer, as dynamic equilibria occur easily, even in the solid state, and are sensitive to electronic and steric effect, including π-conjugation and H-bonding. Here, using as model Schiff bases generated from salicylaldehydes and TRIS in a set of linear free energy relationships (LFER), we disclose how the formation of either imines or enamines can be controlled and provide a comprehensive framework that captures the structural underpinning of this prediction. This work highlights the potentiality of tailor-made designs en route to compounds with desirable functionality.
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Affiliation(s)
- R Fernando Martínez
- Departamento de Quı́mica Orgánica e Inorgánica, Facultad de Ciencias and IACYS-Unidad de Quı́mica Verde y Desarrollo Sostenible, Universidad de Extremadura, E-06006 Badajoz, Spain
| | - Esther Matamoros
- Departamento de Quı́mica Orgánica e Inorgánica, Facultad de Ciencias and IACYS-Unidad de Quı́mica Verde y Desarrollo Sostenible, Universidad de Extremadura, E-06006 Badajoz, Spain
| | - Pedro Cintas
- Departamento de Quı́mica Orgánica e Inorgánica, Facultad de Ciencias and IACYS-Unidad de Quı́mica Verde y Desarrollo Sostenible, Universidad de Extremadura, E-06006 Badajoz, Spain
| | - Juan C Palacios
- Departamento de Quı́mica Orgánica e Inorgánica, Facultad de Ciencias and IACYS-Unidad de Quı́mica Verde y Desarrollo Sostenible, Universidad de Extremadura, E-06006 Badajoz, Spain
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42
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Raczyńska ED, Gal JF, Maria PC, Kamińska B, Igielska M, Kurpiewski J, Juras W. Purine tautomeric preferences and bond-length alternation in relation with protonation-deprotonation and alkali metal cationization. J Mol Model 2020; 26:93. [PMID: 32248379 PMCID: PMC7256107 DOI: 10.1007/s00894-020-4343-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 03/05/2020] [Indexed: 11/03/2022]
Abstract
Quantum chemical calculations were carried out for deprotonated (P-) and protonated purine (PH+) and for adducts with one alkali metal cation (P-M+ and PM+, where M+ is Li+ or Na+) in the gas phase {B3LYP/6-311+G(d,p)}, a model of perfectly apolar environment, and for selected structures in aqueous solution {PCM(water)//B3LYP/6-311+G(d,p)}, a reference polar medium for biological studies. All potential isomers of purine derivatives were considered, the favored structures indicated, and the preferred sites for protonation/deprotonation and cationization reactions determined. Proton and metal cation basicities of purine in the gas phase were discussed and compared with those of imidazole and pyrimidine. Bond-length alternations in the P, PH+, P-M+, and PM+ forms were quantitatively measured using the harmonic oscillator model of electron delocalization (HOMED) indices and compared with those for P. Variations of the HOMED values when proceeding from the purine structural building blocks, pyrimidine and imidazole, to the bicyclic purine system were also examined. Generally, the isolated NH isomers exhibit a strongly delocalized π-system (HOMED > 0.8). Deprotonation slightly increases the HOMED values, whereas protonation and cationization change the HOMED indices in different way. For bidentate M+-adducts, the HOMED values are larger than 0.9 like for the largely delocalized P-. The HOMED values correlate well in a comprehensive relationship with the relative Gibbs energies (ΔG) calculated for individual isomers whatever the purine form is, neutral, protonated, or cationized. When PCM-DFT model was utilized for P-, PH+, PM+, and P-M+ (M+ = Li+) both electron delocalization and relative stability are different from those for the molecules in vacuo. The solvation effects cause a slight increase in HOMEDs, whereas the ΔEs decrease, but in different ways. Hence, contribution of particular isomers in the isomeric mixtures of PH+, PM+, and P-M+ also varies. HOMED variations for the favored neutral, deprotonated, protonated, and lithiated forms of purine in the gas phase and aqueous solution.
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Affiliation(s)
- Ewa D Raczyńska
- Department of Chemistry, Warsaw University of Life Sciences (SGGW), 02-776, Warszawa, Poland.
| | - Jean-François Gal
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272, 06108, Nice, France
| | - Pierre-Charles Maria
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272, 06108, Nice, France
| | - Beata Kamińska
- Department of Chemistry, Warsaw University of Life Sciences (SGGW), 02-776, Warszawa, Poland
| | - Małgorzata Igielska
- Department of Biotechnology, Warsaw University of Life Sciences (SGGW), 02-776, Warszawa, Poland
| | - Julian Kurpiewski
- Department of Biotechnology, Warsaw University of Life Sciences (SGGW), 02-776, Warszawa, Poland
| | - Weronika Juras
- Department of Biotechnology, Warsaw University of Life Sciences (SGGW), 02-776, Warszawa, Poland
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43
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Eberlein L, Beierlein FR, van Eikema Hommes NJR, Radadiya A, Heil J, Benner SA, Clark T, Kast SM, Richards NGJ. Tautomeric Equilibria of Nucleobases in the Hachimoji Expanded Genetic Alphabet. J Chem Theory Comput 2020; 16:2766-2777. [PMID: 32125859 DOI: 10.1021/acs.jctc.9b01079] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Evolution has yielded biopolymers that are constructed from exactly four building blocks and are able to support Darwinian evolution. Synthetic biology aims to extend this alphabet, and we recently showed that 8-letter (hachimoji) DNA can support rule-based information encoding. One source of replicative error in non-natural DNA-like systems, however, is the occurrence of alternative tautomeric forms, which pair differently. Unfortunately, little is known about how structural modifications impact free-energy differences between tautomers of the non-natural nucleobases used in the hachimoji expanded genetic alphabet. Determining experimental tautomer ratios is technically difficult, and so, strategies for improving hachimoji DNA replication efficiency will benefit from accurate computational predictions of equilibrium tautomeric ratios. We now report that high-level quantum-chemical calculations in aqueous solution by the embedded cluster reference interaction site model, benchmarked against free-energy molecular simulations for solvation thermodynamics, provide useful quantitative information on the tautomer ratios of both Watson-Crick and hachimoji nucleobases. In agreement with previous computational studies, all four Watson-Crick nucleobases adopt essentially only one tautomer in water. This is not the case, however, for non-natural nucleobases and their analogues. For example, although the enols of isoguanine and a series of related purines are not populated in water, these heterocycles possess N1-H and N3-H keto tautomers that are similar in energy, thereby adversely impacting accurate nucleobase pairing. These robust computational strategies offer a firm basis for improving experimental measurements of tautomeric ratios, which are currently limited to studying molecules that exist only as two tautomers in solution.
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Affiliation(s)
- Lukas Eberlein
- Physikalische Chemie III, Technische Universität Dortmund, Dortmund 44227, Germany
| | - Frank R Beierlein
- Computer-Chemistry-Centre and Interdisciplinary Centre for Molecular Materials, Department of Chemistry & Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen 91054, Germany
| | - Nico J R van Eikema Hommes
- Computer-Chemistry-Centre and Interdisciplinary Centre for Molecular Materials, Department of Chemistry & Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen 91054, Germany
| | - Ashish Radadiya
- School of Chemistry, Cardiff University, Cardiff CF10 3AT, U.K
| | - Jochen Heil
- Physikalische Chemie III, Technische Universität Dortmund, Dortmund 44227, Germany
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615, United States
| | - Timothy Clark
- Computer-Chemistry-Centre and Interdisciplinary Centre for Molecular Materials, Department of Chemistry & Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen 91054, Germany
| | - Stefan M Kast
- Physikalische Chemie III, Technische Universität Dortmund, Dortmund 44227, Germany
| | - Nigel G J Richards
- School of Chemistry, Cardiff University, Cardiff CF10 3AT, U.K.,Foundation for Applied Molecular Evolution, Alachua, Florida 32615, United States
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A Hidden Side of the Conformational Mobility of the Quercetin Molecule Caused by the Rotations of the O3H, O5H and O7H Hydroxyl Groups: In Silico Scrupulous Study. Symmetry (Basel) 2020. [DOI: 10.3390/sym12020230] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
In this study at the MP2/6-311++G(2df,pd)//B3LYP/6-311++G(d,p) level of quantum-mechanical theory it was explored conformational variety of the isolated quercetin molecule due to the mirror-symmetrical hindered turnings of the O3H, O5H and O7H hydroxyl groups, belonging to the A and C rings, around the exocyclic C–O bonds. These dipole active conformational transformations proceed through the 72 transition states (TSs; C1 point symmetry) with non-orthogonal orientation of the hydroxyl groups relatively the plane of the A or C rings of the molecule (HO7C7C8/HO7C7C6 = ±(89.9–93.3), HO5C5C10 = ±(108.9–114.4) and HO3C3C4 = ±(113.6–118.8 degrees) (here and below signs ‘±’ corresponds to the enantiomers)) with Gibbs free energy barrier of activation ΔΔGTS in the range 3.51–16.17 kcal·mol−1 under the standard conditions (T = 298.1 K and pressure 1 atm): ΔΔGTSO7H (3.51–4.27) < ΔΔGTSO3H (9.04–11.26) < ΔΔGTSO5H (12.34–16.17 kcal mol−1). Conformational dynamics of the O3H and O5H groups is partially controlled by the intramolecular specific interactions O3H…O4, C2′/C6′H…O3, O3H…C2′/C6′, O5H…O4 and O4…O5, which are flexible and cooperative. Dipole-active interconversions of the enantiomers of the non-planar conformers of the quercetin molecule (C1 point symmetry) is realized via the 24 TSs with C1 point symmetry (HO3C3C2C1 = ±(11.0–19.1), HC2′/C6′C1′C2 = ±(0.6–2.9) and C3C2C1′C2′/C3C2C1′C6′ = ±(1.7–9.1) degree; ΔΔGTS = 1.65–5.59 kcal·mol−1), which are stabilized by the participation of the intramolecular C2′/C6′H…O1 and O3H…HC2′/C6′ H-bonds. Investigated conformational rearrangements are rather quick processes, since the time, which is necessary to acquire thermal equilibrium does not exceed 6.5 ns.
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Bomzon B, Khunger Y, Subramanian R. A dielectric and spectrophotometric study of the tautomerization of 2-hydroxypyridine and 2-mercaptopyridine in water. RSC Adv 2020; 10:2389-2395. [PMID: 35494609 PMCID: PMC9048638 DOI: 10.1039/c9ra08392h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 12/17/2019] [Indexed: 11/21/2022] Open
Abstract
The basic ionization (pk1) and acidic ionization (pk2) constants and equilibrium constant (KT) of 2HPy and 2MPy were determined. The pk1(s) of their N- and X-methyl derivatives (X = O, S) were also determined. The equilibrium constant of 2MPy is approximately 60 times greater than its oxygen analog, 2HPy. The micro-ionization constants of the functional groups, –NH (pkA and pkC) and –XH (pkB and pkD), were determined to provide further insights into the ionization equilibria of these N-heteroaromatic XH compounds (2HPy and 2MPy). The relaxation time of water (τ) in aqueous solutions of 2HPy and 2MPy are collectively used with the KT values to determine the forward (kf) and backward (kb) rate constants of tautomerization. Subsequently, the kf and kb are used to provide the rationale for the KT and τ values. The basic ionization (pk1) and acidic ionization (pk2) constants and equilibrium constant (KT) of 2HPy and 2MPy were determined.![]()
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Affiliation(s)
- Biswadeep Bomzon
- Department of Chemistry, Indian Institute of Technology Patna 801106 India
| | - Yashita Khunger
- Department of Chemistry, Indian Institute of Technology Patna 801106 India
| | - Ranga Subramanian
- Department of Chemistry, Indian Institute of Technology Patna 801106 India
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Makhaeva GF, Kovaleva NV, Boltneva NP, Lushchekina SV, Rudakova EV, Stupina TS, Terentiev AA, Serkov IV, Proshin AN, Radchenko EV, Palyulin VA, Bachurin SO, Richardson RJ. Conjugates of tacrine and 1,2,4-thiadiazole derivatives as new potential multifunctional agents for Alzheimer’s disease treatment: Synthesis, quantum-chemical characterization, molecular docking, and biological evaluation. Bioorg Chem 2020; 94:103387. [DOI: 10.1016/j.bioorg.2019.103387] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 10/12/2019] [Accepted: 10/21/2019] [Indexed: 12/13/2022]
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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.
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Matamoros E, Cintas P, Light ME, Palacios JC. Electronic effects in tautomeric equilibria: the case of chiral imines from d-glucamine and 2-hydroxyacetophenones. Org Biomol Chem 2019; 17:10209-10222. [PMID: 31774417 DOI: 10.1039/c9ob02147g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A one-pot procedure for preparing a series of chiral imines by direct condensation of d-glucamine with 2-hydroxyacetophenones is described. Under conventional acetylation an unexpected mixture of two different peracetylated molecules is obtained, one with an open enamine structure, and the other incorporating an N-acetyl-1,3-oxazolidine into the acyclic skeleton. Surprisingly, both molecules coexist within the crystal's unit cell, as inferred from single-crystal X-ray analysis of a 5-bromo-substituted aryl derivative. Moreover, the 1,3-oxazolidine ring exists as rotational conformers (E,Z) owing to the restricted rotation around the N-acetyl bond. The equilibrium involving imine and enamine structures has been assessed in detail, providing in addition linear free-energy relationships between the tautomerization constants (KT) and the electronic effect of the substituents.
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Affiliation(s)
- Esther Matamoros
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencias, and IACYS-Unidad de Química Verde y Desarrollo Sostenible, Universidad de Extremadura, E-06006 Badajoz, Spain.
| | - Pedro Cintas
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencias, and IACYS-Unidad de Química Verde y Desarrollo Sostenible, Universidad de Extremadura, E-06006 Badajoz, Spain.
| | - Mark E Light
- Department of Chemistry, Faculty of Natural and Environmental Sciences, The University of Southampton, Southampton SO17 1BJ, UK
| | - Juan C Palacios
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencias, and IACYS-Unidad de Química Verde y Desarrollo Sostenible, Universidad de Extremadura, E-06006 Badajoz, Spain.
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Secrieru A, O’Neill PM, Cristiano MLS. Revisiting the Structure and Chemistry of 3(5)-Substituted Pyrazoles. Molecules 2019; 25:molecules25010042. [PMID: 31877672 PMCID: PMC6982847 DOI: 10.3390/molecules25010042] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/13/2019] [Accepted: 12/19/2019] [Indexed: 11/16/2022] Open
Abstract
Pyrazoles are known as versatile scaffolds in organic synthesis and medicinal chemistry, often used as starting materials for the preparation of more complex heterocyclic systems with relevance in the pharmaceutical field. Pyrazoles are also interesting compounds from a structural viewpoint, mainly because they exhibit tautomerism. This phenomenon may influence their reactivity, with possible impact on the synthetic strategies where pyrazoles take part, as well as on the biological activities of targets bearing a pyrazole moiety, since a change in structure translates into changes in properties. Investigations of the structure of pyrazoles that unravel the tautomeric and conformational preferences are therefore of upmost relevance. 3(5)-Aminopyrazoles are largely explored as precursors in the synthesis of condensed heterocyclic systems, namely pyrazolo[1,5-a]pyrimidines. However, the information available in the literature concerning the structure and chemistry of 3(5)-aminopyrazoles is scarce and disperse. We provide a revision of data on the present subject, based on investigations using theoretical and experimental methods, together with the applications of the compounds in synthesis. It is expected that the combined information will contribute to a deeper understanding of structure/reactivity relationships in this class of heterocycles, with a positive impact in the design of synthetic methods, where they take part.
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Affiliation(s)
- Alina Secrieru
- Center of Marine Sciences, CCMAR, Gambelas Campus, University of Algarve, UAlg, 8005-139 Faro, Portugal;
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, UK;
- Department of Chemistry and Pharmacy, Faculty of Sciences and Technology, FCT, Gambelas Campus, University of Algarve, UAlg, 8005-139 Faro, Portugal
| | | | - Maria Lurdes Santos Cristiano
- Center of Marine Sciences, CCMAR, Gambelas Campus, University of Algarve, UAlg, 8005-139 Faro, Portugal;
- Department of Chemistry and Pharmacy, Faculty of Sciences and Technology, FCT, Gambelas Campus, University of Algarve, UAlg, 8005-139 Faro, Portugal
- Correspondence: ; Tel.: +351-289-800-953
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Tanii S, Arisawa M, Yamaguchi M. Acid-catalyzed synthesis of condensed polycyclic diaryl ethers from arenols. Chem Commun (Camb) 2019; 55:14078-14080. [PMID: 31696874 DOI: 10.1039/c9cc07172e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Diaryl ethers containing condensed polycyclic aryl groups were synthesized from arenols in the presence of a catalytic amount of p-chlorobenzenesulfonic acid. Symmetrical binaphthyl, biphenanthryl, and bipyrenyl ethers were obtained in high yields. Unsymmetrical derivatives were also synthesized from 9-phenanthrol and arenols, using combinations of reactive and unreactive substrates.
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Affiliation(s)
- Saori Tanii
- Department of Organic Chemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, Aoba, Sendai, 980-8578, Japan.
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