Unique interactions between diborane and pi orbitals: blue- or red-shifted hydrogen bonding?

A new type of hydrogen-bonding interaction in the diborane (B 2H 6)...pi (benzene C 6H 6, 1,3-cyclopentadiene C 5H 6, and cyclobutadiene C 4H 4) system is identified with the natural bond orbital and atoms-in-molecules analyses based on ab initio calculations. In comparison with the symmetric and asymmetric stretching vibrational modes of the bridging hydrogen atoms in free B 2H 6, the frequencies of the symmetric mode are red-shifted for B 2H 6...C 6H 6 and B 2H 6...C 5H 6 but blue-shifted for B 2H 6...C 4H 4. The frequency blue shifts of the asymmetric mode are found for all three complexes; the most significant blue shift is 14.73 cm (-1) for the asymmetric mode in B 2H 6...C 4H 4. In these complexes, the electron-deficient three-center two-electron bond B-H 1-B facing the pi orbital is shortened, while the opposite B-H 2-B bond is elongated.     

C–H...O and C–H...N interactions in RNA structures

Small molecule studies indicate that C–H...X interactions (X: O,N) constitute weak H-bonds. We have performed a comprehensive analysis of their occurrence and geometry in RNA structures. Here, we report on statistical properties of the total set of interactions identified and discuss selected motifs. The distance/angle distribution of all interactions exhibits an excluded region where the allowed C–H...X angle range increases with an increasing H...X distance. The preferred short C–H...X interactions in RNA are backbone-backbone contacts between neighbour nucleotides. Distance/angle distributions generated for various interaction types can be used for error recognition and modelling. The axial C2′(H)...O4′ and C5′(H)...O2′ interactions connect two backbone segments and form a seven-membered ring that is specific for RNA. An AA base pair with one standard H-bond and one C–H...N interaction has been identified in various structures. Despite the occurrence of short C–H...X contacts their free energy contribution to RNA stability remains to be assessed. Received: 17 May 1998 / Accepted: 4 August 1998 / Published online: 2 November 1998     

Butalene and related compounds: aromatic or antiaromatic?

Density functional theory (DFT) has been used to study the first three members of the condensed cyclobutadienoid series, butalene (3), bicyclobutadienylene (12), and dicyclobutenobutalene (20). The first is planar and is judged "aromatic" by comparisons with suitable models using both energetic and magnetic criteria. The second is nonplanar, and not aromatic, but not so antiaromatic as cyclobutadiene (11). The third is slightly more antiaromatic and best viewed as a butalene fused to two cyclobutadiene rings; its properties are the sum of aromatic and antiaromatic components, like benzocyclobutadiene. Ring-opening transition states for both 3 and 12 have been located, and these are conrotatorily twisted. The ring-opening barrier for 12 is more than twice that for 3. Ring-opening of 20 involves ring inversion as the only barrier.     

Does the most stable formic acid tetramer have pi stacking or C-H...O interactions?

Density functional theory (DFT), Moller-Plesset (MP) perturbation theory, and coupled-cluster calculations are used to examine low-energy minima on the potential energy surface of the formic acid tetramer (HCOOH)(4). The potential energy surface is rather flat with respect to rotation of one of the dimers, relative to the other dimer in an aligned stack, about the axis passing through the inversion centers of the dimers. Our best calculations suggest that an aligned pi-pi stack of two dimers is very likely to be the global minimum but there are two other pi-pi stacks within 0.5 kcal /mol. Moreover, a fourth pi-pi stack, a planar association of two dimers held together by C-H...O interactions, and a bowl structure all lie within 1 kcal /mol of the lowest-energy structure.     

Structure selection for protein kinase docking and virtual screening: homology models or crystal structures?

There is currently far more sequence information than structural information available, and the ability to use homology models for virtual screening applications is desirable in many cases where structures have not yet been solved. This review focuses on the application of protein kinase homology models for virtual screening use. In addition to reviewing previous cases in which kinase homology models have been used in inhibitor design, we present new data - useful for template selection in homology modeling applications - indicating that the template structure with the highest sequence or structural similarity with the target structure may not always be the best choice. This new work explored the simple hypothesis that better results might be obtained for docking a ligand to a target receptor using a homology model of the target created from a different kinase template co-crystallized with the ligand, than from a crystal structure of the actual kinase target that is unliganded or bound to an unrelated ligand. This hypothesis was tested in docking studies of staurosporine with eight different kinases: AutoDock was used to dock staurosporine to homology models of each kinase created from staurosporine-bound template structures, and the results were compared with docking staurosporine to crystal structures of the target kinase that were obtained in complex with a non-staurosporine ligand or no ligand. It was found that the homology models performed as well as or better than the crystal structures, suggesting that using a homology model created from a template crystallized with a representative ligand may in some cases be a preferred approach, especially in virtual screening experiments that focus on enriching for members of a particular inhibitor class.     

A theoretical investigation of the interaction between substituted carbonyl derivatives and water: Open or cyclic complexes?

The structures and binding energies of complexes between substituted carbonyl bases and water are the B3LYP/6‐311++G(d,p) computational level. The calculations also include the proton affinity (PA) of the O of the C?O group, the deprotonation enthalpies (DPE) of the CH bonds along a natural bond orbital analysis. The calculations reveal that stable open C?O···H_wO_w as well as cyclic CH···O_wH_w···O?C complexes are formed. The binding energies for the open complexes are linearly related to the PAs, whereas the binding energies for the cyclic complexes depend on both the PA and DPE. Different indicators of hydrogen bonds strength such as electron charge density, intramolecular and intermolecular hyperconjugation energy, occupation of orbitals, and charge transfer show significant differences between open and cyclic complexes. The contraction of the CH bond of the formyl group and the corresponding blue shift of the ν(CH) vibration are explained by the classical trans lone pair effect. In contrast, the elongation or contraction of the CH₃ group involved in the interaction with water results from the variation of the orbital interaction energies from the σ(CH) bonding orbital to the σ* and π* antibonding orbitals of the C?O group. The resulting blue or red shifts of the ν(CH₃) vibrations are calculated in the partially deuterated isotopomers. © 2012 Wiley Periodicals, Inc.     

Self-association in HOF and HNF2. Which atoms are the better proton acceptors,fluorine, oxygen or nitrogen?

The infrared and Raman spectra of solid HOF and HNF₂ are best interpreted in terms of hydrogen bridged aggregates involving the oxygen or nitrogen atoms, respectively, and not fluorine as proton acceptors. This results is contrary to intuition and the conclusions previously reached for solid HOF.     

Molecular structures of metal macrocyclic compounds with nitrogen,oxygen, and sulfur atoms in macrocycles arising in “self-assembly” processes: quantum-chemical modeling

The results of quantum-chemical calculations of the molecular structures of d-metal macrocyclic chelate complexes with compartmental and macrocyclic (N,O)- and (N,S) donor atomic ligands arising as a result of “self-assembly” process have been systematized and generalized. It has been noticed that, generally, for such coordination compounds, molecular structures with noncoplanar chelate nodes and noncoplanar macrocycles are more typical than those with coplanar ones. The review covers the works of the author and other researchers carried out mainly over the past 20 years.     

Steric interactions between physically adsorbed polymer-coated colloidal particles: soft or hard?

The steric interaction potential between colloidal particles imparted by adsorbed polymer layers is directly related to their structure. Due to the complexity of these interfacial structures, the steric potential may behave differently at different interparticle separations. In this study, we proposed a combined model of the equivalent hard-sphere model (EHS) and the Hayter-Penfold/Yukawa model (HPY) to describe the steric potential due to adsorbed homopolymers on colloidal particles. The EHS potential describes the dense train/small-loop region and the HPY potential the more diffuse tail/long-loop region. The steric potential was extracted from the structure factors measured by small-angle neutron scattering (SANS). It was found that this combined model gave better agreement with experimental data than either of its component models alone. This study also shows that the adsorbed polymer layer in a good solvent partially collapses when the layers approach one another, which is also supported by an NMR solvent relaxation study.     

Usefulness of π...π aromatic interactions in the selective separation and analysis of imidazolium and pyridinium ionic liquid cations

Current research indicates that replacing organic solvents with room-temperature ionic liquids may lead to remarkable improvements in well-known processes. Ionic liquids have already been utilized as alternative solvents in organic synthesis and catalysis, and also in electrochemistry and in separation sciences. Their wide applicability will soon result in their production on an industrial scale. Therefore, analytical methods applicable to various matrices for product control and environmental monitoring will be very much in demand. In this study, the usefulness of π...π interactions between alkylimidazolium and pyridinium cations and the aromatic π...π active moiety of the stationary phase was investigated for the selective separation and analysis of some ionic liquids. With phenyl-bonded phases, very good separations of the cations were achieved. Special attention was paid to the short-chain hydrophilic entities, known to be poorly separated on conventional reversed-phase columns. Further, the nature of the interactions occurring in the system under study was investigated by varying the content of methanol/acetonitrile used as organic modifiers in the mobile phases. The analytical method developed here is simple and reproducible, and its quantitative analytical performance was excellent. The paper also discusses the applicability of the method for monitoring degraded cations of 1-butyl-3-methylimidazolium salts obtained in the Fenton process.     

Slow relaxation mode in mixtures of water and organic molecules: supramolecular structures or nanobubbles?

Aqueous solutions of tetrahydrofuran, ethanol, urea, and alpha-cyclodextrin were studied by a combination of static and dynamic laser light scattering (LLS). In textbooks, these small organic molecules are soluble in water so that there should be no observable large structures or density fluctuation in either static or dynamic LLS. However, a slow mode has been consistently observed in these aqueous solutions in dynamic LLS. Such a slow mode was previously attributed to some large complexes or supramolecular structures formed between water and these small organic molecules. Our current study reveals that it is actually due to the existence of small bubbles ( approximately 100 nm in diameter) formed inside these solutions. Our direct evidence comes from the fact that it can be removed by repeated filtration and regenerated by air injection. Our results also indicate that the formation of such nanobubbles in small organic molecule aqueous solutions is a universal phenomenon. Such formed nanobubbles are rather stable. The measurement of isothermal compressibility confirms the existence of a low density microphase, presumably nanobubbles, in these aqueous solutions. Using a proposed structural model, that is, each bubble is stabilized by small organic molecules adsorbed at the gas/water interface, we have, for the first time, estimated the pressure inside these nanobubbles.     

The experimental and calculational thermochemistry of 1,2,4,5-benzenetetracarboxylic dianhydride: is this 10 pi multiring species aromatic?

The standard (p degrees = 0.1 MPa) molar enthalpy of formation of 1,2,4,5-benzenetetracarboxylic dianhydride in the gaseous phase, -826.8 +/- 3.1 kJ mol-1, was derived from the standard molar enthalpy of combustion, in oxygen, at T = 298.15 K, measured by static bomb combustion calorimetry and the standard molar enthalpy of sublimation, at T = 298.15 K, measured by Calvet microcalorimetry. In addition, density functional theory calculations have been performed with the B3LYP, MPW1B95, and B3PW91 density functionals and the cc-pVTZ basis set for 1,2,4,5-benzenetetracarboxylic dianhydride and 1,2,4,5-benzenetetracarboxylic diimide. Nucleus-independent chemical shifts calculations show that the aromaticity is restricted to the benzenic ring in both compounds even though they are formally 10 pi polynuclear species.     

Proton transfers in aromatic and antiaromatic systems. How aromatic or antiaromatic is the transition state? An ab initio study

An ab initio study of six carbon-to-carbon identity proton transfers is reported. They refer to the benzenium ion/benzene (C6H7(+)/C6H6), the 2,4-cyclopentadiene/cyclopentadienyl anion (C5H6/C5H5(-)), and the cyclobutenyl cation/cyclobutadiene (C4H5(+)/C4H4) systems and their respective noncyclic reference systems, that is, [structure: see text], [structure: see text] and [structure: see text]. For the aromatic C6H7(+)/C6H6 and C5H6/C5H5(-) systems, geometric parameters and aromaticity indices indicate that the transition states are highly aromatic. The proton-transfer barriers in these systems are quite low, which is consistent with a disproportionately high degree of transition-state aromaticity. For the antiaromatic C4H5(+)/C4H4 system, the geometric parameters and aromaticity indices indicate a rather small degree of antiaromaticity of the transition state. However, the proton-transfer barrier is higher than expected for a transition state with a low antiaromaticity. This implies that another factor contributes to the barrier; it is suggested that this factor is angle and torsional strain in the transition state. The question whether charge delocalization at the transition state might correlate with the development of aromaticity was also examined. No such correlation was found, that is, charge delocalization lags behind proton transfer as is commonly observed in nonaromatic systems involving pi-acceptor groups.     

C-F...π, F...H, and F...F intermolecular interactions and F-aggregation: Role in crystal engineering of fluoroorganic compounds

Systematization of the available literature data on C-F...π, F...H, and F...F interactions, namely, statistical studies of the geometry of the corresponding contacts were carried out using the Cambridge Structural Database (CSD) and theoretical quantum-chemical estimations of their energies. The most typical supramolecular motifs (finite or infinite) involving the F atom were revealed based on recent X-ray studies of a few dozens of fluoroarenes carried out at the Novosibirsk Institute of Organic Chemistry. Our recent data were summarized. To assess the role of the above interactions, we used topological analysis of electron density distribution in terms of Bader’s QTAIM theory. Our DFT/PBE/3z quantum-chemical calculations of the interaction energies of molecular pairs in diazafluorene crystals formed by C-F...π, C-F...H, and F...F nonvalent short contacts are presented.     

Energetic effects between halogen bonds and anion-π or lone pair-π interactions: a theoretical study

Energetic effects between halogen bonds and anion-π or lone pair-π interactions have been investigated by means of ab initio MP2 calculations. 1,4-diiodo-perfluorobenzene, a very effective building block for crystal engineering based on halogen bonding, is selected in this work both as electron-deficient π aromatic ring and as halogen bond donor. Additive and diminutive effects are observed when halogen bonds and anion-π/lone pair-π interactions coexist in the same complex, which can be ascribed to the same direction of charge transfer for the two interactions. These effects have been analyzed in detail by the structural, energetic, and AIM properties of the complexes. Finally, experimental evidence of the combination of the interactions has been obtained from the Cambridge Structural Database.     

Relationship between mechanochromic behavior and crystal structures in donor-π-acceptor compounds consisted of aromatic rings with ester moiety as an acceptor

We investigated the mechanochromic behavior of donor-π-acceptor compounds which consisted of diphenylaminophenylacetylene as a donor-π moiety and (hetero)aromatic ring bearing ester as an acceptor. The compounds with dicyanobenzoic ester gave the bathochromic shift by grinding, whereas the compounds consisted of the ester with benzene, imidazole, and thiazole rings showed the hypsochromic shift. From single-crystal X-ray analysis, we revealed that the compound with bathochromic shift gave the herringbone alignment with H-aggregate-like π-stacking in the crystal structure. On the contrary, the compounds with hypsochromic shift showed the structure with the alignment of long axis of the molecule in crystal structure.     

C-H?Br, C-Br?Br, and C-Br?π interactions in the crystal structures of mesitylene- and dimesitylmethane-derived compounds bearing bromomethyl units

X-ray structure determinations of mesitylene- and dimesitylmethane-derived compounds bearing bromomethyl units (compounds 1-3) show that the crystal packing of the molecules is characterized by the presence of C-H?Br interactions, such as BrCH₂?Br, CH₃?Br, and C_PhH?Br. In addition, C-Br?Br and C-Br?π interactions determine the crystal packing. The bromomethyl groups play a major role in the packing of 1-3.     

How many metal atoms are needed to dehydrogenate an ethylene molecule on metal clusters?: Correlation between reactivity and electronic structures of Fen+, Con+, and Nin+

The absolute cross section for dehydrogenation of an ethylene molecule on Mn+ [Fen+ (n = 2-28), Con+ (n = 8-29), and Nin+ (n = 3-30)] was measured as a function of the cluster size n in a gas-beam geometry at a collision energy of 0.4 eV in the center-of-mass frame in an apparatus equipped with a tandem-type mass spectrometer. It is found that (1) the dehydrogenation cross section increases rapidly above a cluster size of approximately 18 on Fen+, approximately 13 and approximately 18 on Con+, and approximately 10 on Nin+ and (2) the rapid increase of the cross section for Mn+ occurs at a cluster size where the 3d electrons start to contribute to the highest occupied levels of Mn+. These findings lead us to conclude that the 3d electrons of Mn+ play a central role in the dehydrogenation on Mn+.