Hydrogen Bonding in the Dimer and Monohydrate of 2-Adamantanol: A Test Case for Dispersion-Corrected Density Functional Methods.

Weakly-bound intermolecular clusters constitute reductionist physical models for non-covalent interactions. Here we report the observation of the monomer, the dimer and the monohydrate of 2-adamantanol, a secondary alcohol with a bulky ten-carbon aliphatic skeleton. The molecular species were generated in a supersonic jet expansion and characterized using broadband chirped-pulse microwave spectroscopy in the 2-8 GHz frequency region. Two different gauche-gauche O-H···O hydrogen-bonded isomers were observed for the dimer of 2-adamantanol, while a single isomer was observed for the monomer and the monohydrate. The experimental rotational parameters were compared with molecular orbital calculations using density functional theory (B3LYP-D3(BJ), B2PLYP-D3(BJ), CAM-B3LYP-D3(BJ), ωB97XD), additionally providing energetic and electron density characterization. The shallow potential energy surface makes the dimer an interesting case study to benchmark dispersion-corrected computational methods and conformational search procedures.

Torsional chirality and molecular recognition: the homo and heterochiral dimers of thenyl and furfuryl alcohol.

Furfuryl alcohol and thenyl alcohol contain a labile torsional chiral center, producing transiently chiral enantiomers interconverting in the nanosecond time-scale. We explored chiral molecular recognition using the weakly-bound intermolecular dimers of both alcohols, freezing stereomutation. Supersonic jet broadband microwave spectroscopy revealed homo and heterochiral diastereoisomers for each alcohol dimer and the structural characteristics of the clusters. All dimers are primarily stabilized by a moderately intense O-H⋯O hydrogen bond, but differ in the secondary interactions, which introduce additional hydrogen bonds either to the ring oxygen in furfuryl alcohol or to the π ring system in thenyl alcohol. Density-functional calculations (B2PLYP-D3(BJ)/def2-TZVP) show no clear preferences for a particular stereochemistry in the dimers, with relative energies of the order 1-2 kJ mol-1. The study suggests opportunities for the investigation of chiral recognition in molecules with torsional barriers in between transient and permanent interconversion regimes.

Molecular Rotation Spectrum of Tetracyclic Quinolizidines: Observation of trans-Matrine and the Elusive cis-Matrine.

We characterized the bis-quinolizidine tetracyclic alkaloid (5S, 6S, 7R, 11R)-matrine in a supersonic jet expansion, using chirped-pulsed broadband microwave spectroscopy. Previous crystal diffraction analyses suggested 16 diastereoisomers associated with matrine's four carbon stereocenters but were inconclusive whether the lactamic nitrogen atom would additionally produce separated trans-/cis- diastereoisomers or if both species may interconvert through low potential barriers. Our experiment simultaneously detected trans- and cis-matrine through their rotational spectrum, confirming the possibility of conformational rearrangement in matrine alkaloids. The two matrine conformers mainly differ in the envelope or half-chair lactamic ring, as evidenced by the experimental rotational and nuclear quadrupole coupling parameters. Molecular orbital calculations with ab initio (MP2) and density functional methods (B3LYP-D3(BJ) and MN15) were tested against the experiment, additionally offering an estimation of the cis-/trans- barrier of 24.9-26.9 kJ mol-1. The experiment illustrates the structural potential of chirped-pulsed broadband microwave spectroscopy for high-resolution rotational studies of biomolecules in the range of 20-40 atoms.

A Concise Route for the Synthesis of Tetracyclic Meroterpenoids: (±)-Aureol Preparation and Mechanistic Interpretation.

A new concise general methodology for the synthesis of different tetracyclic meroterpenoids is reported: (±)-aureol (1), the key intermediate of this general route. The synthesis of (±)-aureol (1) was achieved in seven steps (28% overall yield) from (±)-albicanol. The key steps of this route include a C-C bond-forming reaction between (±)-albicanal and a lithiated arene unit and a rearrangement involving 1,2-hydride and 1,2-methyl shifts promoted by BF3•Et2O as activator and water as initiator.

Rational selection of co-catalysts for the deaminative hydrogenation of amides.

The catalytic hydrogenation of amides is an atom economical method to synthesize amines. Previously, it was serendipitously discovered that the combination of a secondary amide co-catalyst with (iPrPNP)Fe(H)(CO) (iPrPNP = N[CH2CH2(PiPr2)]2 -), results in a highly active base metal system for deaminative amide hydrogenation. Here, we use DFT to develop an improved co-catalyst for amide hydrogenation. Initially, we computationally evaluated the ability of a series of co-catalysts to accelerate the turnover-limiting proton transfer during C-N bond cleavage and poison the (iPrPNP)Fe(H)(CO) catalyst through a side reaction. TBD (triazabicyclodecene) was identified as the leading co-catalyst. It was experimentally confirmed that when TBD is combined with (iPrPNP)Fe(H)(CO) a remarkably active system for amide hydrogenation is generated. TBD also enhances the activity of other catalysts for amide hydrogenation and our results provide guidelines for the rational design of future co-catalysts.

Rotational Spectrum, Tunneling Motions, and Intramolecular Potential Barriers in Benzyl Mercaptan.

The rotational spectrum of benzyl mercaptan (parent and four isotopologues) has been assigned in a supersonic jet expansion using chirped-pulse Fourier transform microwave spectroscopy. The spectrum is characterized by torsional tunneling doublings, strongly perturbed by Coriolis interactions. The experimental rotational constants reveal that the sulfur atom is located above the ring plane in a gauche conformation. The torsion dihedral θ0 = φ (SCα-C1C2) is approximately 74°, according to a flexible molecular model calculation reproducing the energy separation (ΔE01 ∼ 2180.4 MHz) between the first two torsional substates. The global minimum configuration is 4-fold degenerate, corresponding to potential minima with θ0 ≈ ±74° and ±(180-74)°. The four equivalent minima are separated by potential barriers at θ = ±90°, 0°, or 180°. The tunneling splittings are caused by the potential barrier at θ = ± 90°, while the barriers at torsions of 0° or 180° are too large to generate detectable splittings. The tunnelling barrier has been determined as 248 cm-1, similar to the value obtained with high-level MP2 ab initio calculations (259 cm-1), but smaller than in benzyl alcohol (280 cm-1).

Mimicking Halimane Synthases: Monitoring a Cascade of Cyclizations and Rearrangements from Epoxypolyprenes.

We have developed and rationalized a biomimetic transformation mimicking halimane synthases based on a Lewis acid-catalyzed cascade of cyclizations and rearrangements of epoxypolyprenes. Two rings, three stereogenic centers, and a new double bond were generated in a single chemical operation. Based on this cascade transformation, we achieved a unified strategy toward the stereoselective total syntheses of halimene-type terpenoids and analogues as a proof-of-concept study. This method has been applied to the rapid synthesis of diterpene isotuberculosinol, a virulence factor of Mycobacterium tuberculosis as a representative example.

15-Hydroxygermacranolides as Sources of Structural Diversity: Synthesis of Sesquiterpene Lactones by Cyclization and Rearrangement Reactions. Experimental and DFT Study.

A study on the electrophile-induced rearrangement of two 15-hydroxygermacranolides, salonitenolide and artemisiifolin, was carried out. These compounds underwent electrophilic intramolecular cyclizations or acid-mediated rearrangements to give sesquiterpene lactones with different skeletons such as eudesmanolides, guaianolides, amorphanolides, or other germacranolides. The cyclization that gives guaianolides can be considered a biomimetic route to this type of sesquiterpene lactones. The use of acetone as a solvent changes the reactivity of the two starting germacranolides to the acid catalysts, with a 4,15-diol acetonide being the main product obtained. The δ-amorphenolide obtained by intramolecular cyclization of this acetonide is a valuable intermediate for accessing the antimalarials artemisinin and its derivatives. Mechanistic proposals for the transformations are raised, and to provide support them, quantum chemical calculations [DFT B3LYP/6-31+G(d,p) level] were undertaken.

Sulfur Hydrogen Bonding in Isolated Monohydrates: Furfuryl Mercaptan versus Furfuryl Alcohol.

The hydrogen bonds involving sulfur in the furfuryl mercaptan monohydrate are compared with the interactions originating from the hydroxyl group in furfuryl alcohol. The dimers with water were created in a supersonic jet expansion and characterized using microwave spectroscopy and supporting molecular orbital calculations. In furfuryl alcohol-water, a single isomer is observed, in which the water molecule forms an insertion complex with two simultaneous hydrogen bonds to the alcohol (O-H⋅⋅⋅Ow ) and the ring oxygen (Ow -H⋅⋅⋅Or ). When the alcohol is replaced by a thiol group in furfuryl mercaptan-water, two isomers are observed, with the thiol group preferentially behaving as proton donor to water. The first isomer is topologically equivalent to the alcohol analog but the stronger hydrogen bond is now established by water and the ring oxygen, assisted by a thiol S-H⋅⋅⋅Ow hydrogen bond. In the second isomer the sulfur group accepts a proton from water, forming a Ow -H⋅⋅⋅S hydrogen bond. Binding energies for the mercaptan-water dimer are predicted around 12 kJ mol-1 weaker than in the alcohol hydrate (B3LYP-D3(BJ)). The non-covalent interactions in the furfuryl dimers are dominantly electrostatic according to a SAPT(0) energy decomposition, but with increasing dispersion components in the mercaptan dimers, which are larger for the isomer with the weaker Ow -H⋅⋅⋅S interaction.

Rotational spectra of tetracyclic quinolizidine alkaloids: does a water molecule flip sparteine?

Sparteine is a quinolizidine alkaloid used as a chiral auxiliary in asymmetric synthesis. We examine whether hydration by a single molecule can flip sparteine from the most stable trans conformation to the bidentate cis arrangement observed in catalytic complexation to a metal center. Sparteine and the sparteine-water dimer were generated in a supersonic jet expansion with H216O and H218O, and characterized by broadband chirped-pulse microwave spectroscopy. Even though the bidentate water dimer was predicted with larger binding energy, a single isomer was observed for the monohydrated cluster, with sparteine retaining the trans conformation observed for the free molecule. The absence of the bidentate dimer is attributed to the kinetic control of cluster formation, favoring the pre-expansion most abundant monomer. The structural properties of the O-HN hydrogen bond in the dimer are compared with those of complexes of other secondary and tertiary amines.

A DFT-Based Computational-Experimental Methodology for Synthetic Chemistry: Example of Application to the Catalytic Opening of Epoxides by Titanocene.

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.

Homocoupling versus reduction of radicals: an experimental and theoretical study of Ti(III)-mediated deoxygenation of activated alcohols.

A detailed experimental and theoretical study corroborates that the reductive deoxygenation of activated (allylic or benzylic) alcohols with excess Ti(III) proceeds via an allyl(benzyl)-radical and allyl(benzyl)-Ti, which is protonated, regioselectively in the case of allylic derivatives. The H atom of the newly formed C-H bond in the product originates from the -OH group of the starting material. The deoxygenation of lithium alkoxides or alcohols by using 1.0 mol of Ti(III) leads to the corresponding dimerization products in good yields. An excellent agreement with the experimental data was obtained by using a reaction kinetics simulator to discriminate between competing reactions.

Structural diversity from the transannular cyclizations of natural germacrone and epoxy derivatives: a theoretical-experimental study.

Treatment of germacrone (1) with different electrophiles, and of its epoxy derivatives germacrone-4,5-epoxide (2), germacrone-1,10-epoxide (3) and isogermacrone-4,5-epoxide (4) with Brönsted/Lewis acids and Ti(III), gives rise to a great structural diversity. Thus, by using a maximum of two steps, the production of more than 40 compounds corresponding to 14 skeletons is described. Computational calculations rationalizing the structural divergence produced are also described. Finally, since some of the compounds generated are bioactive natural sesquiterpenes, the mechanisms of formation of these substances will provide new insights in their biosynthesis.