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Uriarte I, Pérez C, Caballero-Mancebo E, Basterretxea FJ, Lesarri A, Fernández JA, Cocinero EJ. Structural Studies of Nicotinoids: Cotinine versus Nicotine. Chemistry 2017; 23:7238-7244. [PMID: 28212459 DOI: 10.1002/chem.201700023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Indexed: 01/28/2023]
Abstract
Nicotinoids are agonists of the acetylcholine receptor (nAChR) and play important biochemical and pharmacological roles. Herein, we report on the structure and conformation of cotinine, and compare its molecular properties with the nicotine prototype, from which it only differs in the addition of a carbonyl group. This investigation included a theoretical survey of the effects of rotamerization of the pyridine moiety, the puckering of the pyrrolidinone ring and the internal rotation of the methyl group. The experimental work examined the rotational spectrum of the molecule in a supersonic expansion, using both broadband chirped-pulse excitation techniques and cavity microwave spectrometers. Two conformers were observed for cotinine, and the fine and hyperfine structures arising from the two quadrupolar 14 N nuclei and the methyl internal rotor were fully analyzed. The two observed conformers share the same twisted conformation of the five-membered ring, but differ in a roughly 180° rotamerization around the C-C bond connecting the two rings. The energy barriers for the internal rotation of the methyl group in cotinine (4.55(4) and 4.64(3) kJ mol-1 , respectively) are much lower than in nicotine (estimated in 16.5 kJ mol-1 ). The combination of different intramolecular electronic effects, hydrogen bonding and possible binding differences to receptor molecules arising from the carbonyl group could explain the lower affinity of cotinine for nAChRs.
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Jaraíz M, Enríquez L, Pinacho R, Rubio JE, Lesarri A, López-Pérez JL. A DFT-Based Computational-Experimental Methodology for Synthetic Chemistry: Example of Application to the Catalytic Opening of Epoxides by Titanocene. J Org Chem 2017; 82:3760-3766. [PMID: 28288276 DOI: 10.1021/acs.joc.7b00220] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A novel DFT-based Reaction Kinetics (DFT-RK) simulation approach, employed in combination with real-time data from reaction monitoring instrumentation (like UV-vis, FTIR, Raman, and 2D NMR benchtop spectrometers), is shown to provide a detailed methodology for the analysis and design of complex synthetic chemistry schemes. As an example, it is applied to the opening of epoxides by titanocene in THF, a catalytic system with abundant experimental data available. Through a DFT-RK analysis of real-time IR data, we have developed a comprehensive mechanistic model that opens new perspectives to understand previous experiments. Although derived specifically from the opening of epoxides, the prediction capabilities of the model, built on elementary reactions, together with its practical side (reaction kinetics simulations of real experimental conditions) make it a useful simulation tool for the design of new experiments, as well as for the conception and development of improved versions of the reagents. From the perspective of the methodology employed, because both the computational (DFT-RK) and the experimental (spectroscopic data) components can follow the time evolution of several species simultaneously, it is expected to provide a helpful tool for the study of complex systems in synthetic chemistry.
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Uriarte I, Pérez C, Caballero-Mancebo E, Basterretxea FJ, Lesarri A, Fernández JA, Cocinero EJ. Structural Studies of Nicotinoids: Cotinine versus Nicotine. Chemistry 2017. [DOI: 10.1002/chem.201701076] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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54
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Evangelisti L, Spada L, Li W, Blanco S, López JC, Lesarri A, Grabow JU, Caminati W. A butterfly motion of formic acid and cyclobutanone in the 1 : 1 hydrogen bonded molecular cluster. Phys Chem Chem Phys 2017; 19:204-209. [DOI: 10.1039/c6cp06941j] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Large tunnelling splittings reveal the relative motions and the inversion pathway in the formic acid–cyclobutanone cluster.
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Juanes M, Vogt N, Demaison J, León I, Lesarri A, Rudolph HD. Axial–equatorial isomerism and semiexperimental equilibrium structures of fluorocyclohexane. Phys Chem Chem Phys 2017; 19:29162-29169. [DOI: 10.1039/c7cp06135h] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Accuracy vs. computational effort: the mixed estimation method provides very accurate semiexperimental equilibrium structures, as illustrated by the subtle differences between axial/equatorial fluorocyclohexane.
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Écija P, Vallejo-López M, Uriarte I, Basterretxea FJ, Lesarri A, Fernández JA, Cocinero EJ. Scopine Isolated in the Gas Phase. Chemphyschem 2016; 17:3030-3034. [DOI: 10.1002/cphc.201600368] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 06/16/2016] [Indexed: 11/06/2022]
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Pérez C, Caballero-Mancebo E, Lesarri A, Cocinero EJ, Alkorta I, Suenram RD, Grabow JU, Pate BH. The Conformational Map of Volatile Anesthetics: Enflurane Revisited. Chemistry 2016; 22:9804-11. [PMID: 27258776 DOI: 10.1002/chem.201601201] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Indexed: 11/10/2022]
Abstract
Previous ambiguities in the conformational and structural landscape of the volatile anesthetic enflurane have been solved combining microwave spectroscopy in a jet expansion and ab initio calculations. The broadband (2-18 GHz) rotational spectra identified three different rotamers, sharing a common trans ether skeleton but differing in the ±gauche/trans position of the terminal chlorine atom. For each chlorine conformation two different gauche orientations were predicted for the opposite difluoromethyl group, but only one is experimentally observable due to collisional relaxation in the jet. The experimental dataset comprised nine different isotopologues ((35) Cl, (37) Cl, (13) C) and a large number (>6500) of rotational transitions. The inertial data provided structural information using the substitution and effective procedures. The structural preferences were rationalized with additional ab initio, natural-bond-orbital and non-covalent-interaction analysis, which suggest that plausible anomeric effects at the difluoromethyl group could be overridden by other intramolecular effects. The difluoromethyl orientation thus reflects a minimization of inter-fluorine repulsions while maximizing F⋅⋅⋅H attractive interactions. A comparison with previous electron diffraction and spectroscopic data in the gas and condensed phases finally resulted in a comprehensive description of this ether, completing a rotational description of the most common multi-halogenated anesthetics.
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Gou Q, Spada L, Vallejo-Lopez M, Melandri S, Lesarri A, Cocinero EJ, Caminati W. Intermolecular Hydrogen Bonding in 2-Fluoropyridine-Water. ChemistrySelect 2016. [DOI: 10.1002/slct.201600370] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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59
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González J, Baños I, León I, Contreras-García J, Cocinero EJ, Lesarri A, Fernández JA, Millán J. Unravelling Protein–DNA Interactions at Molecular Level: A DFT and NCI Study. J Chem Theory Comput 2016; 12:523-34. [DOI: 10.1021/acs.jctc.5b00330] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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60
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Uriarte I, Écija P, Spada L, Zabalza E, Lesarri A, Basterretxea FJ, Fernández JA, Caminati W, Cocinero EJ. Potential energy surface of fluoroxene: experiment and theory. Phys Chem Chem Phys 2016; 18:3966-74. [DOI: 10.1039/c5cp06522d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The potential energy surface (PES) of the general anesthetic fluoroxene was probed in a supersonic jet expansion using broadband CP-FTMW spectroscopy and theoretical calculations.
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Vogt N, Demaison J, Cocinero EJ, Écija P, Lesarri A, Rudolph HD, Vogt J. The equilibrium molecular structures of 2-deoxyribose and fructose by the semiexperimental mixed estimation method and coupled-cluster computations. Phys Chem Chem Phys 2016; 18:15555-63. [PMID: 27212641 DOI: 10.1039/c6cp01842d] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The mixed estimation method yields very accurate equilibrium structures, as observed in deoxyribose and fructose.
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Écija P, Uriarte I, Spada L, Davis BG, Caminati W, Basterretxea FJ, Lesarri A, Cocinero EJ. Furanosic forms of sugars: conformational equilibrium of methyl β-d-ribofuranoside. Chem Commun (Camb) 2016; 52:6241-4. [DOI: 10.1039/c6cc01180b] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The rotational spectrum of the isolated ribofuranoside unit, the biologically active sugar form, revealed two structures with a similar puckering to the RNA units in crystals.
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Écija P, Uriarte I, Basterretxea FJ, Millán J, Lesarri A, Fernández JA, Cocinero EJ. Structural distortion of the epoxy groups in norbornanes: a rotational study of exo-2,3-epoxynorbornane. Chemphyschem 2015; 16:2609-14. [PMID: 26182910 DOI: 10.1002/cphc.201500334] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Indexed: 11/07/2022]
Abstract
Exo-2,3-epoxynorbornane is studied in the gas phase by pulsed jet Fourier transform microwave spectroscopy in the 4-18 GHz region. Six isotopologues were observed and characterized in their natural abundance. The experimental substitution and effective structures were obtained. Comparison with the structure of norbornane shows significant differences in several bond lengths and valence angles upon introduction of the epoxy group. All the work is supported by quantum chemical calculations.
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Gou Q, Spada L, Vallejo-López M, Lesarri A, Cocinero EJ, Caminati W. Interactions between alkanes and aromatic molecules: a rotational study of pyridine-methane. Phys Chem Chem Phys 2015; 16:13041-6. [PMID: 24668141 DOI: 10.1039/c4cp00204k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The rotational spectrum of the adduct pyridine-methane shows that methane links to an aromatic molecule apparently through a C-H···π weak hydrogen bond. The shape and the internal dynamics behaviour of this complex are very similar to that of the van der Waals complexes involving aromatic molecules with rare gases.
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Gou Q, Feng G, Evangelisti L, Vallejo-López M, Spada L, Lesarri A, Cocinero EJ, Caminati W. Internal Dynamics in Halogen-Bonded Adducts: A Rotational Study of Chlorotrifluoromethane-Formaldehyde. Chemistry 2015; 21:4148-52. [DOI: 10.1002/chem.201406122] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Indexed: 11/07/2022]
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66
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Rajappan Nair KP, Jahn MK, Lesarri A, Ilyushin VV, Grabow JU. Six-fold-symmetry internal rotation in toluenes: the low barrier challenge of 2,6- and 3,5-difluorotoluene. Phys Chem Chem Phys 2015; 17:26463-70. [DOI: 10.1039/c5cp03751d] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Pure six-fold symmetry (V6) internal rotation poses significant challenges to experimental and theoretical determination, as the very low torsional barriers result in huge tunneling splittings difficult to identify and to model.
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67
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Seifert NA, Pérez C, Neill JL, Pate BH, Vallejo-López M, Lesarri A, Cocinero EJ, Castaño F. Chiral recognition and atropisomerism in the sevoflurane dimer. Phys Chem Chem Phys 2015; 17:18282-7. [DOI: 10.1039/c5cp01025j] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Transient chirality in the anesthetic sevoflurane results in two different homo- and heterochiral clusters on formation of the dimer, as observed by rotational spectroscopy.
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Alkorta I, Cancedda C, Cocinero EJ, Dávalos JZ, Ecija P, Elguero J, González J, Lesarri A, Ramos R, Reviriego F, Roussel C, Uriarte I, Vanthuyne N. Static and dynamic properties of 1,1'-bi-2-naphthol and its conjugated acids and bases. Chemistry 2014; 20:14816-25. [PMID: 25234135 DOI: 10.1002/chem.201402686] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 07/10/2014] [Indexed: 11/10/2022]
Abstract
Several convergent techniques were used to characterize 1,1'-bi-2-naphthol (BINOL) and some of its properties. Its acidity in the gas-phase, from neutral species to monoanion, was measured by mass spectrometry. The conformation and structure of BINOL in the gas phase was determined by microwave rotational spectroscopy. NMR experiments in fluorosulfonic acid established that BINOL was monoprotonated on one of the hydroxyl oxygen atoms. The enantiomerization barriers reported in the literature for BINOL under neutral, basic, and acid conditions were analyzed with regard to the species involved. Finally, DFT calculations allowed all of these results to be gathered in a coherent picture of the BINOL structure.
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Jahn MK, Dewald DA, Vallejo‐López M, Cocinero EJ, Lesarri A, Zou W, Cremer D, Grabow J. Pseudorotational Landscape of Seven‐Membered Rings: The Most Stable Chair and Twist‐Boat Conformers of ε‐Caprolactone. Chemistry 2014; 20:14084-9. [DOI: 10.1002/chem.201403379] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Indexed: 11/07/2022]
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70
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León I, Usabiaga I, Millán J, Cocinero EJ, Lesarri A, Fernández JA. Mimicking anesthetic-receptor interactions in jets: the propofol-isopropanol cluster. Phys Chem Chem Phys 2014; 16:16968-75. [PMID: 25005780 DOI: 10.1039/c4cp01702a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The interaction of the general anesthetic propofol with an individual residue of threonine in the membrane receptors has been modeled in the gas phase by examining the adduct of propofol with the isopropanol side-chain. We determined the structural preferences of the cluster using a combination of mass-resolved laser spectroscopy and quantum mechanical calculations. The first electronic transition of propofol-isopropanol was recorded with vibrational resolution using resonant two-photon ionization (R2PI) and ion dip IR spectroscopy. The spectra obtained were compared with density-functional calculations (DFT) using the M06-2X functional in order to obtain the cluster's structure. Three isomers have been detected. The results suggest that propofol acts as a Brønsted acid, donating a proton to the isopropanol molecule in a conformation that resembles that of propofol-water, but displaced towards the aromatic ring, due to the interaction with the aliphatic side of isopropanol. The higher affinity of propofol for isopropanol compared to water may correlate with the biological role of propofol at the protein binding site. On the other hand, propofol shows a similar affinity for isopropanol and phenol, which could explain the mobility that propofol experiences inside the GABAA cavity.
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León I, Millán J, Cocinero EJ, Lesarri A, Fernández JA. Water Encapsulation by Nanomicelles. Angew Chem Int Ed Engl 2014; 53:12480-3. [DOI: 10.1002/anie.201405652] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Indexed: 11/07/2022]
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León I, Millán J, Cocinero EJ, Lesarri A, Fernández JA. Water Encapsulation by Nanomicelles. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201405652] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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73
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Demaison J, Craig NC, Groner P, Écija P, Cocinero EJ, Lesarri A, Rudolph HD. Accurate Equilibrium Structures for Piperidine and Cyclohexane. J Phys Chem A 2014; 119:1486-93. [DOI: 10.1021/jp505765t] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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74
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Blanco S, Lesarri A, López JC, Alonso JL, Guarnieri A. The Rotational Spectrum and Nuclear Quadrupole Coupling of CH35C1F2. ACTA ACUST UNITED AC 2014. [DOI: 10.1515/zna-1996-1-219] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The rotational spectrum of CH35CIF2 in the ground vibrational state has been measured in the frequency range 8-18 GHz using a waveguide Fourier transform microwave (FTMW) spectrometer in order to determine accurate nuclear quadrupole coupling constants. The spectra of the excited vibrational states ν5 = 1, ν6 = 1 and ν9 = 1 have been also observed and analyzed in the frequency region 8-250 GHz using FTMW, Stark, and source modulation spectrometers. Quadrupole coupling constants are also reported for these states.
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75
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Écija P, Evangelisti L, Vallejo M, Basterretxea FJ, Lesarri A, Castaño F, Caminati W, Cocinero EJ. Conformational flexibility of mephenesin. J Phys Chem B 2014; 118:5357-64. [PMID: 24754523 DOI: 10.1021/jp5014785] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mephenesin molecule (3-(2-methylphenoxy)propane-1,2-diol) serves as a test bank to explore several structural and dynamical issues, such as conformational flexibility, the orientation of the carbon linear chain relative to the benzene plane, or the effect of substituent position on the rotational barrier of a methyl group. The molecule has been studied by rotational spectroscopy in the 4-18 GHz frequency range by Fourier-transform methods in a supersonic expansion. The experiment has been backed by a previous conformational search plus optimization of the lowest energy structures by ab initio and density functional quantum calculations. The three lowest-lying conformers that can interconvert to each other by simple bond rotations have been detected in the jet. Rotational parameters for all structures have been obtained, and methyl torsional barriers have been determined for the two lowest-lying rotamers. The lowest-lying structure of mephenesin is highly planar, with all carbon atoms lying nearly in the benzene ring plane, and is stabilized by the formation of cooperative intramolecular hydrogen bonding. An estimation of the relative abundance of the detected conformers indicates that the energetically most stable conformer will have an abundance near 80% at temperatures relevant for biological activity.
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