Tunable Regioselectivity in C-H-Activated Direct Arylation Reactions of Dithieno[3,2-b:2',3'-d]pyrroles.

In this study, regioselectively controlled direct arylation of dithieno[3,2-b:2,3'-d]pyrroles (DTPs) is reported. By carefully selecting the catalytic system, Pd source, ligand, and additives, we achieved either selective N-arylation or unprecedented ß-arylation and ß,ß'-diarylation of the DTP core through C-H activation when reacting unsubstituted H-DTP with 9-anthracenyl halides. For N-substituted DTPs, we obtained regioselective carboxylate-assisted arylation of the α-position(s). Consequently, depending on the catalytic system and substitution at the DTP nitrogen, we successfully synthesized novel regioselectively substituted DTPs, including N-aryl, rarely reported ß-aryl, ß,ß'-diaryl, α-aryl, and α,α'-diaryl scaffolds. These compounds can be straightforwardly prepared and further functionalized for applications as organic electronic materials.

Exploring Epigenetic Marks by Analysis of Noncovalent Interactions.

Epigenetic marks are modest chemical modifications on DNA and histone proteins that regulate the activation or silencing of genes through modulation of the intermolecular interactions between the DNA strands and the protein machinery. The process is complex and not always well understood. One of the systems studied in greater detail is the epigenetic mark on H3K9: lysine 9 of histone 3. The degree of methylation or acetylation of this histone is linked to silencing or activation of the corresponding gene, but it is not clear which effect each mark has in gene expression. We shed light on this particular methylation process by using density functional theory (DFT) calculations. First, we built a model consisting of a DNA double strand containing three base pairs and a sequence of three amino acids of the histone's tail. Then, we computed the modulation introduced into the intermolecular interactions by each epigenetic modification: from mono- to trimethylation and acetylation. The calculations show that whereas acetylation and trimethylation result in a reduction of the DNA-peptide interaction; non-, mono-, and dimethylation increase the intermolecular interactions. Such observations compare well with the findings reported in the literature, and highlight the correlation between the balance of intermolecular forces and biological properties, simultaneously advancing quantum-mechanical studies of large biochemical systems at molecular level through the use of DFT methods.

Isomerism of the Aniline Trimer.

Weaker intermolecular forces expand the isomerization alternatives for molecular aggregation, as observed for the prototype models of the aniline trimer (An3 ) and the monohydrated aniline dimer (An2 -W) when compared to the phenol trimer. In this experiment the aniline clusters were generated in a jet-cooled expansion and probed using broadband (chirped-pulsed) microwave spectroscopy. Three isomers of the aniline trimer and two isomers of the hydrated dimer were detected and characterized in the rotational spectrum. In the homotrimer the weak N-H⋅⋅⋅N hydrogen bonds are assisted by subtle combinations of N-H⋅⋅⋅π and C-H⋅⋅⋅π interactions, producing several competing low-lying ring species in the gas phase. One of the aniline trimers is a symmetric top, topologically equivalent to the only observed phenol trimer. Conversely, addition of a water molecule to the aniline dimer introduces a leading O-H⋅⋅⋅N interaction, making water to behave as dominant hydrogen-bond pivot between the two aniline molecules. This combination of weak intermolecular interactions critically tests the performance of dispersion-corrected or parametrized density-functional methods. Evaluation of the B3LYP-D3(BJ) and M06-2X methods revealed deficiencies of the Truhlar functional to reproduce the experimental rotational data.

Competition between stacked and hydrogen bonded structures of cytosine aggregates.

The four bases of DNA constitute what is known as the "alphabet of life". Their combination of proton-donor and acceptor groups and aromatic rings allows them to form stacking structures and at the same time establish hydrogen bonds with their counterparts, resulting in the formation of the well-known double-helix structure of DNA. Here we explore the aggregation preferences of cytosine in supersonic expansions, using a combination of laser spectroscopic techniques and computations. The data obtained from the experiments carried out in the cold and isolated environment of the expansion allowed us to establish which are the leading interactions behind aggregation of cytosine molecules. The results obtained demonstrated that ribbon-like structures held together by hydrogen bonds are the preferred conformations in the small clusters, but once the tetramer was reached, the stacking structures became enthalpically more stable. Stacking is further favoured when cytosine is replaced by its 1'-methylated version, as demonstrated by quantum-mechanical calculations performed using the same level that reproduced the experimental results obtained for cytosine aggregates. A discussion on the biological implications that such observations may have is also offered.

Structural distortion of the epoxy groups in norbornanes: a rotational study of exo-2,3-epoxynorbornane.

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.

Molecular hydration of propofol dimers in supersonic expansions: formation of active centre-like structures.

Spectroscopic studies of molecular aggregates are a powerful tool to understand the weak interactions between molecules. Here, propofol2(H2O)6,7 clusters were formed in supersonic expansions and their electronic and infrared spectroscopy was explored using several mass-resolved laser-based spectroscopic techniques. Using REMPI, their S1 ← S0 electronic spectrum was obtained with vibrational resolution, while the UV/UV hole burning revealed the presence of a single isomer of propofol2(H2O)6 and of two isomers of propofol2(H2O)7. Employment of IR/UV double resonance yielded the IR spectrum in the OH stretch region. Comparison with the spectra predicted for the structures calculated at the M06-2X/6-31+G(d) level demonstrated that the two propofol molecules interact mainly through C-Hπ contacts between the lipophilic sides of the molecules, while the hydroxyl moieties are in close contact, forming a kind of "active centre" with which the water molecules interact, forming polyhedral structures.

Water encapsulation by nanomicelles.

Reported is the hydration of nanomicelles in the gas-phase using spectroscopic methods and quantum chemical calculations. A fine-tuning of the experimental conditions allowed formation of a propofol trimer and tetramer with a water molecule and to determine the structure of the aggregates. Their electronic and IR spectra were obtained using mass-resolved laser spectroscopy, together with the number of conformational isomers for each stoichiometry. Interpretation of the spectra in the light of high-level calculations allowed determination of the cluster's structure and demonstration that the trimer of propofol with a water molecule forms cyclic hydrogen-bond networks but, on the other hand, the tetramer is big enough to encapsulate the water molecule inside its hydrophilic core. Furthermore, these hydrated nanomicelles present an unusually high binding energy, thus reflecting their high stability and their capability to trap water inside.

Mimicking anesthetic-receptor interactions in jets: the propofol-isopropanol cluster.

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.

Behind the reactivity of lactones: a computational and spectroscopic study of phenol·Î³-butyrolactone.

In this work, the intermolecular interaction between phenol and γ-butyrolactone (GBL) has been studied by a combination of spectroscopic and computational techniques. The electronic and vibrational transitions of phenol · GBL were measured in a supersonic jet expansion by resonant two-photon ionization (R2PI) and ion dip IR (IDIR) spectroscopy. The results obtained were compared with calculations carried out with both M06-2X and MP2 molecular orbital methods in order to characterize the intermolecular interactions. The singly detected conformer is stabilized by a relatively strong hydrogen bond in which phenol acts as a proton donor to the carbonyl group of GBL. The phenol · GBL2 cluster has also been studied, finding up to three populated conformers. Nevertheless, in the three species, the main interaction between the phenolic hydroxyl group and the GBL's carbonyl group remains similar to that of phenol · GBL. Furthermore, the C ═ O · · · H interaction is reinforced.

Unraveling the benzocaine-receptor interaction at molecular level using mass-resolved spectroscopy.

The benzocaine-toluene cluster has been used as a model system to mimic the interaction between the local anesthetic benzocaine and the phenylalanine residue in Na(+) channels. The cluster was generated in a supersonic expansion of benzocaine and toluene in helium. Using a combination of mass-resolved laser-based experimental techniques and computational methods, the complex was fully characterized, finding four conformational isomers in which the molecules are bound through N-H···π and π···π weak hydrogen bonds. The structures of the detected isomers closely resemble those predicted for benzocaine in the inner pore of the ion channels, giving experimental support to previously reported molecular chemistry models.

Shaping micelles: the interplay between hydrogen bonds and dispersive interactions.

A subtle interplay: In the formation of a 1.6 nm micelle containing up to six molecules of propofol, a hydrogen-bond network is shown to influence the structure of the micelle, whereas the nonpolar groups arrange in such a way that the remaining noncovalent interactions are maximized. Such globular structures present a characteristic signature in the IR spectrum that will allow their identification in more complex media.

Transition from planar to nonplanar hydrogen bond networks in the solvation of aromatic dimers: propofol2-(H2O)(2-4).

Propofol (2,6-diisopropylphenol) is probably the most widely used intravenous general anesthetic. In this work, the interaction of propofol dimer with 2-4 water molecules was analyzed. The molecular aggregates were formed by using supersonic expansions, which maintain the molecules confined in a cold, collision-free environment. The clusters were then examined by using a number of mass-resolved laser-based spectroscopic techniques, including 2-color REMPI (resonance enhanced multiphoton ionization), UV/UV hole burning, and IR/UV double resonance. Two isomers were found for each stoichiometry, whose final structures were determined by comparison between the experimental data and those from density-functional-theory calculations (M06-2X/6-31+G(d)). The analysis of the observed structures allows the conclusion that the water molecules always form hydrogen bond networks, whose contribution to the cluster's total binding energy increases with the number of water molecules. In the cluster with four water molecules, the two propofol molecules lose most of their contact points. In addition, the steric hindrance produces a change from cyclic to noncyclic hydrogen bond networks earlier than in similar systems.

Formation of water polyhedrons in propofol-water clusters.

Following previous structural investigations on the hydrated clusters of the anesthetic propofol we analyze here the spectroscopy of propofol·(H(2)O)(7-9) in supersonic expansions, to approach to the solution limit. Using 2-color REMPI the mass-resolved electronic spectrum of each solvated species was obtained. The UV/UV hole burning demonstrated the presence of at least two conformers for propofol·(H(2)O)(7) and propofol·(H(2)O)(8), while a single conformer was observed for propofol·(H(2)O)(9). Structural information from each isomer was obtained using IR/UV hole burning, both in the mid-IR and in the OH region. Comparison of vibrational data with those from calculations at M06-2X/6-311++G(d,p) demonstrates that the water molecules form polyhedral structures that resemble those found in pure water clusters. Comparison with the results obtained for the hydrated clusters of phenol and benzene shows that similar structures are formed, although some relevant differences are found, mainly in the number of isomers present for each stoichiometry.

A spectroscopic and computational study of propofol dimers and their hydrated clusters.

Propofol (2,6-diisopropylphenol, PPF) homodimers and their complexes with one water molecule are analyzed by means of mass-resolved excitation spectroscopy. Using two-color resonance-enhanced multiphoton ionization (REMPI) the S(1) electronic spectra of these systems are obtained, avoiding fragmentation. Due to the large size of these species, the spectra present a large abundance of lines. Using UV/UV hole-burning spectroscopy, two isomers of PPF(2) are found and the existence of at least three isomers for propofol(2)(H(2)O)(1) (PPF(2)W(1)) is demonstrated. Comparison with the structures calculated at the M06-2X/6-311++G(d,p) and M06-2X/6-31+G(d) levels of theory shows that the main driving forces in PPF(2) are several C-H···π interactions accompanied by dipole-dipole interaction between the OH moieties. On the other hand, there is evidence for the formation of cyclic hydrogen-bond structures in the heterotrimers. A comparison of the results obtained herein with those of similar systems from previously published studies follows.

Single hydration of the peptide bond: the case of the Vince lactam.

2-Azabicyclo[2.2.1]hept-5-en-3-one (ABH or Vince lactam) and its monohydrated complex (ABH···H(2)O) have been observed in a supersonic jet by Fourier transform microwave spectroscopy. ABH is broadly used in the synthesis of therapeutic drugs, whereas the ABH···H(2)O system offers a simple model to explain the conformational preferences of water linked to a constrained peptidic bond. A single predominant form of the Vince lactam and its singly hydrated complex have been detected, determining the rotational constants, centrifugal distortion constants, and nuclear quadrupole coupling tensor. The monohydrated complex is stabilized by two hydrogen bonds (C═O···H-O and N-H···O) closing a six-membered ring. The complexation energy has been estimated to be ∼10 kJ mol(-1) from experimental results. In addition, the observed structure in the gas phase has been compared with solid-phase diffraction data. The structural parameters and binding energies of ABH···H(2)O have also been compared with similar molecules containing peptide bonds. Ab initio (MP2) and density functional (M06-2X and B3LYP) methods have supported the experimental work, describing the rotational parameters and conformational landscape of the title compound and its singly hydrated complex.

A combined spectroscopic and theoretical study of propofol·(H2O)3.

Propofol (2,6-di-isopropylphenol) is probably the most widely used general anesthetic. Previous studies focused on its complexes containing 1 and 2 water molecules. In this work, propofol clusters containing three water molecules were formed using supersonic expansions and probed by means of a number of mass-resolved laser spectroscopic techniques. The 2-color REMPI spectrum of propofol[middle dot](H(2)O)(3) contains contributions from at least two conformational isomers, as demonstrated by UV/UV hole burning. Using the infrared IR/UV double resonance technique, the IR spectrum of each isomer was obtained both in ground and first excited electronic states and interpreted in the light of density functional theory (DFT) calculations at M06-2X/6-311++G(d,p) and B3LYP/6-311++G(d,p) levels. The spectral analysis reveals that in both isomers the water molecules are forming cyclic hydrogen bond networks around propofol's OH moiety. Furthermore, some evidences point to the existence of isomerization processes, due to a complicated conformational landscape and the existence of multiple paths with low energy barriers connecting the different conformers. Such processes are discussed with the aid of DFT calculations.

Mimicking anaesthetic-receptor interaction: a combined spectroscopic and computational study of propofol···phenol.

Propofol is a general anaesthetic that exerts its action by interaction with the GABA(A) receptor. Crystallographic studies suggest that there is a direct interaction between propofol and the phenolic residue of a tyrosine in the channel. In this study we create propofol···phenol clusters by their co-expansion in jets. The complex is probed using a set of mass-resolved spectroscopic strategies: 2-color REMPI, UV/UV hole-burning, IR/UV double resonance and the novel technique IR/IR/UV triple resonance. The existence of at least six different isomers in the expansion is demonstrated. All the isomers are stabilized by interactions between their aromatic rings. Additionally, in some conformers the OH moieties form hydrogen bonds in some of the isomers, with propofol and phenol alternating their donor-acceptor roles, while in others the -OH···OH angle points to a dipole-dipole interaction. Interpretation of the data in the light of dispersion-corrected DFT calculations shows that shallow barriers separate all the isomers, both in the ground and excited electronic states. Comparison of the structures of the complex with the X-ray diffraction data is also offered.

Exploring microsolvation of the anesthetic propofol.

Propofol (2,6-diisopropylphenol) is a broadly used general anesthetic. By combining spectroscopic techniques such as 1- and 2-color REMPI, UV/UV hole burning, infrared ion-dip spectroscopy (IRIDS) obtained under cooled and isolated conditions with high-level ab initio calculations, detailed information on the molecular structure of propofol and on its interactions with water can be obtained. Four isomers are found for the bare propofol, while only three are detected for the monohydrated species and two for propofol·(H(2)O)(2). The isopropyl groups do not completely block the OH solvation site, but reduce considerably the strength of the hydrogen bonds between propofol and water. Such results may explain the high mobility of propofol in the GABA(A) active site, where it cannot form a strong hydrogen bond with the tyrosine residue.

Discriminating the structure of exo-2-aminonorbornane using nuclear quadrupole coupling interactions.

The intrinsic conformational and structural properties of the bicycle exo-2-aminonorbornane have been probed in a supersonic jet expansion using Fourier-transform microwave (FT-MW) spectroscopy and quantum chemical calculations. The rotational spectrum revealed two different conformers arising from the internal rotation of the amino group, exhibiting small (MHz) hyperfine patterns originated by the (14)N nuclear quadrupole coupling interaction. Complementary ab initio (MP2) and DFT (B3LYP and M05-2X) calculations provided comparative predictions for the structural properties, rotational and centrifugal distortion data, hyperfine parameters, and isomerization barriers. Due to the similarity of the rotational constants, the structural assignment of the observed rotamers and the calculation of the torsion angles of the amino group were based on the conformational dependence of the (14)N nuclear quadrupole coupling hyperfine tensor. In the most stable conformation (ss), the two amino N-H bonds are staggered with respect to the adjacent C-H bond. In the second conformer (st), only one of the N-H bonds is staggered and the other is trans. A third predicted conformer (ts) was not detected, consistent with a predicted conformational relaxation to conformer ss through a low barrier of 5.2 kJ mol(-1).