Supramolecular Assembly and Chirality of Synthetic Carbohydrate Materials

Hierarchical carbohydrate architectures serve multiple roles in nature. Hardly any correlations between the carbohydrate chemical structures and the material properties are available due to the lack of standards and suitable analytic techniques. Therefore, designer carbohydrate materials remain highly unexplored, as compared to peptides and nucleic acids. A synthetic D-glucose disaccharide, DD, was chosen as a model to explore carbohydrate materials. Microcrystal electron diffraction (MicroED), optimized for oligosaccharides, revealed that DD assembled into highly crystalline left-handed helical fibers. The supramolecular architecture was correlated to the local crystal organization, allowing for the design of the enantiomeric right-handed fibers, based on the L-glucose disaccharide, LL, or flat lamellae, based on the racemic mixture. Tunable morphologies and mechanical properties suggest the potential of carbohydrate materials for nanotechnology applications.

A Critical Check for the Role of Resonance in Intramolecular Hydrogen Bonding

Although resonance-assisted H-bonds (RAHBs) are well recognized, the role of π resonance in RAHBs is controversial, as the seemingly enhanced H-bonds in unsaturated compounds may result from the constraints imposed by the σ skeleton. Herein the block-localized wave function (BLW) method, which can derive optimal yet resonance-quenched structures with related physiochemical properties, was employed to examine the correlation between π resonance and the strength of intramolecular RAHBs. Examination of a series of paradigmatic molecules with RAHBs and their saturated analogues showed that it is inappropriate to compare a conjugated system with its saturated counterpart, as they may have quite different σ frameworks. Nevertheless, comparison between a conjugated system and its resonance-quenched (i.e., electron-localized) state, which have identical σ skeletons, shows that in all studied cases, π resonance unanimously reduces the bonding distance by 0.111-0.477 Å, strengthens the bonding by 40-56 %, and redshifts the D-H vibrational frequency by 104-628 cm^-1 . Furthermore, there is an excellent correlation between hydrogen-bonding strength and the classical Coulomb attraction between the hydrogen-bond donor and the acceptor, which suggests that the dominant role of the electrostatic interaction in H-bonds and RAHBs originates from the charge flow from H-bond donors to acceptors through π conjugation.

Comment on “Conformational analysis of triphenylphosphine ligands in stereogenic monometallic complexes: tools for predicting the preferred configuration of the triphenylphosphine rotor” by J. F. Costello, S. G. Davies, E. T. F. Gould and J. E. Thomson, Dalton Trans., 2015, 44, 5451

The architecture of triphenylphosphine ligands in compounds [Cp^(*)ML¹L²PPh₃] is determined by CH/π interactions.

Torsional and Electronic Factors Control the C-H⋅⋅⋅O Interaction

The precise role of non‐conventional hydrogen bonds such as the C−H⋅⋅⋅O interaction in influencing the conformation of small molecules remains unresolved. Here we survey a series of β‐turn mimetics using X‐ray crystallography and NMR spectroscopy in conjunction with quantum calculation, and conclude that favourable torsional and electronic effects are important for the population of states with conformationally influential C−H⋅⋅⋅O interactions. Our results also highlight the challenge in attempting to deconvolute a myriad of interdependent noncovalent interactions in order to focus on the contribution of a single one. Within a small molecule that is designed to resemble the complexity of the environment within peptides and proteins, the interplay of different steric burdens, hydrogen‐acceptor/‐donor properties and rotational profiles illustrate why unambiguous conclusions based solely on NMR chemical shift data are extremely challenging to rationalize.

Forced bonding and QTAIM deficiencies: a case study of the nature of interactions in He@adamantane and the origin of the high metastability

Calculations within the framework of the interacting quantum atoms (IQA) approach have shown that the interactions of the helium atom with both tertiary, tC, and secondary, sC, carbon atoms in the metastable He@adamantane (He@adam) endohedral complex are bonding in nature, whereas the earlier study performed within the framework of Bader's quantum theory of atoms in molecules (QTAIM) revealed that only He---tC interactions are bonding. The He---tC and He---sC bonding interactions are shown to be forced by the high pressure that the helium and carbon atoms exert upon each other in He@adam. The occurrence of a bonding interaction between the helium and sC atoms, which are not linked by a bond path, clearly shows that the lack of a bond path between two atoms does not necessarily indicate the lack of a bonding interaction, as is asserted by QTAIM. IQA calculations showed that not only the destabilization of the adamantane cage, but also a huge internal destabilization of the helium atom, contribute to the metastability of He@adam, these contributions being roughly equal. This result disproves previous opinions based on QTAIM analysis that only the destabilization of the adamantane cage accounts for the endothermicity of He@adam. Also, it was found that there is no homeomorphism of the ρ(r) and -v(r) fields of He@adam. Comparison of the IQA and QTAIM results on the interactions in He@adam exposes other deficiencies of the QTAIM approach. The reasons for the deficiencies in the QTAIM approach are analyzed.

A bond path and an attractive Ehrenfest force do not necessarily indicate bonding interactions: case study on M2X2 (M = Li, Na, K; X = H, OH, F, Cl)

Interactions in dimers of model alkali metal derivatives M(2)X(2) (M = Li or Na or K; X = H or F, Cl, OH) are studied in the frame of the quantum theory of atoms in molecules (QTAIM) using the interacting quantum atoms approach (IQA). Contrary to opinion prevalent in QTAIM studies, the interaction between two anions linked by a bond path is demonstrated to be strongly repulsive. One may therefore say that a bond path does not necessarily indicate bonding interactions. The interactions between two anions or two cations that are not linked by a bond path are also strongly repulsive. The repulsive anion-anion and cation-cation interactions are outweighed by much stronger attractive anion-cation interactions, and the model molecules are therefore in a stable state. The attractive Ehrenfest forces (calculated in the frame of the QTAIM) acting across interatomic surfaces shared by anions in the dimers do not reflect the repulsive interactions between anions. Probable reasons of this disagreement are discussed. The force exerted on the nucleus and the electrons of a particular atom by the nucleus and the electrons of any another atom in question is proposed. It is assumed that this force unambiguously exposes whether basins of two atoms are attracted or repelled by each other in a polyatomic molecule.

Scalar coupling across [C-H···F-C] interactions in (σ-aryl)-chelating post-metallocenes

The nature and importance of C-H···F-C interactions is a topical yet controversial issue, and the development of spectroscopic methods to probe such contacts is therefore warranted. A series of Group 4 bis(benzyl) complexes supported by (σ-aryl)-2-phenolate-6-pyridyl [O,C,N-R(1)] ligands bearing a fluorinated R(1) group (CF(3) or F) in the vicinity of the metal has been prepared. The X-ray crystal structure of the CF(3)-substituted Hf derivative features intramolecular C-H···F-C and Hf···F-C contacts. All complexes have been characterized by multinuclear NMR spectroscopy. The (1)H and (13)C NMR spectra of [M(O,C,N-CF(3))(CH(2)Ph)(2)] derivatives display coupling (assigned to (1h)J(HF) and (2h)J(CF) for Ti; (3)J(HF) and (2)J(CF) (through M···F) for Hf and Zr) between the benzyl CH(2) and CF(3) moieties. [(1)H,(19)F]-HMBC NMR experiments have been performed for the M-[O,C,N-R(1)] complexes and their [O,N,C] counterparts, revealing significant scalar coupling across the C-H···F-C interactions for Ti-[O,C,N] and [O,N,C] species.

The coordination chemistry of the proton

It is well known that an acidic hydrogen atom can form hydrogen bonds to a hydrogen bond acceptor, a Lewis base. It is considerably less known that the proton can coordinate two or more atoms conveniently in bonding modes that cannot be described as hydrogen bonding. Agostic interactions, bridging hydrides, 3-centre-2-electron bonds in boranes, bifurcated hydrogen atoms, they are all elements of the coordination chemistry of the proton and, of course, the hydrogen bond comes in more than one facette as well.

Dihydrogen bonding: donor-acceptor bonding (AH...HX) versus the H2 molecule (A-H2-X)

Dihydrogen bonds (DHBs) play a role in, among others, crystal packing, organometallic reaction mechanisms, and potential hydrogen-storage materials. In this work we have analyzed the central H-H bond in linear H(4), LiH...HX, BH(4)(-)...HX, and AlH(4)(-)...HX complexes with various X by using the quantitative molecular orbital model contained in Kohn-Sham density functional theory at the BP86/TZ2P level of theory. First, we address the questions of if and how one can distinguish, in principle, between a H...H donor-acceptor DHB and the formation of an H(2) molecule by using the simple H(4) model system. The results of these analyses have been used to gain an understanding of the bonding in more realistic model systems (some of which have been studied experimentally), and how this differs from the bonding in H(4).

Van der waals and polar intermolecular contact distances: quantifying supramolecular synthons

Crystal structures are viewed as being determined by ranges and constraints on interatomic contact distances between neighboring molecules. These distances are considered to arise from environment-dependent atomic sizes, that is, larger sizes for isotropic, van der Waals type contacts and smaller sizes for more-polar, possibly ionic contacts. Although the idea of different, or anisotropic, radii for atoms is not new, we developed a method of obtaining atomic sizes that is based on a theoretical framework. Using different atomic sizes for the same atom in different environments, we were able to rationalize some structural observations and anomalies. For example, benzene with the Pbca structure may be described in terms of two types of CH interactions: a longer contact largely of the van der Waals type, and a shorter, structure-determining type (C(delta-)H(delta+)), which we term "n-polar". Our approach is illustrated with three examples: 1) the equivalence in crystal packing of fluorobenzene, benzonitrile, pyridine N-oxide, and pyridine/HF 1:1 molecular complex, all of which take the not-so-common tetragonal P4(1)2(1)2 space group and are practically isomorphous; 2) the similarity of the Pa3 acetylene and Pbca benzene crystal structures; and 3) the equivalence between an increase in pressure and an increase in the "n-polar" contacts in Pbca benzene; in other words, the equivalence between hydrostatic pressure and chemical pressure. In the context of crystal engineering, we describe a method whereby the topological information conveyed in a supramolecular synthon is recast in a more quantitative manner. A particular synthon, and in turn the crystal structure to which it leads, is viable within small ranges of distances of its constituent atoms, and these distances are determined by chemical factors.

Bond paths as privileged exchange channels

Evidence that the bond paths of the quantum theory of atoms-in-molecules (QTAIM) signal preferred quantum-mechanical exchange channels is presented. We show how bond paths between an atom A and the atoms B in its environment appear to be determined by competition among the A-B exchange-correlation energies that always contribute to stabilize the A-B interactions. These pairwise additive stabilizations depend neither on the attractive or repulsive nature of the classical electrostatic interaction between the atoms' charge densities, nor on the change in the self energies of the atoms involved. These other terms may well cause an overall molecular-energy increase in spite of a possibly large A-B exchange-correlation stabilization. After our proposal, bond paths, both at and out of equilibrium geometries, are endowed with a specific energetic meaning that should contribute to reconcile the orthodox QTAIM interpretation with other widely accepted views, and to settle recent controversies questioning the meaning of hydrogen-hydrogen bonding and the nature of the so-called "steric interactions", the role of bond paths in endohedral complexes, and the generality of the results provided by the QTAIM. Implications for the nature of more general closed-shell interactions are also briefly discussed.

Crystal engineering: a holistic view

Crystal engineering, the design of molecular solids, is the synthesis of functional solid-state structures from neutral or ionic building blocks, using intermolecular interactions in the design strategy. Hydrogen bonds, coordination bonds, and other less directed interactions define substructural patterns, referred to in the literature as supramolecular synthons and secondary building units. Crystal engineering has considerable overlap with supramolecular chemistry, X-ray crystallography, materials science, and solid-state chemistry and yet it is a distinct discipline in itself. The subject goes beyond the traditional divisions of organic, inorganic, and physical chemistry, and this makes for a very eclectic blend of ideas and techniques. The purpose of this Review is to highlight some current challenges in this rapidly evolving subject. Among the topics discussed are the nature of intermolecular interactions and their role in crystal design, the sometimes diverging perceptions of the geometrical and chemical models for a molecular crystal, the relationship of these models to polymorphism, knowledge-based computational prediction of crystal structures, and efforts at mapping the pathway of the crystallization reaction.

Progress in the understanding of drug-receptor interactions, part 2: experimental and theoretical electrostatic moments and interaction energies of an angiotensin II receptor antagonist (C30H30N6(O)3S)

A combined experimental and theoretical charge density study of an angiotensin II receptor antagonist (1) is presented focusing on electrostatic properties such as atomic charges, molecular electric moments up to the fourth rank and energies of the intermolecular interactions, to gain an insight into the physical nature of the drug-receptor interaction. Electrostatic properties were derived from both the experimental electron density (multipole refinement of X-ray data collected at T=17 K) and the ab initio wavefunction (single molecule and fully periodic calculations at the DFT level). The relevance of SO and SN intramolecular interactions on the activity of 1 is highlighted by using both the crystal and gas-phase geometries and their electrostatic nature is documented by means of QTAIM atomic charges. The derived electrostatic properties are consistent with a nearly spherical electron density distribution, characterised by an intermingling of electropositive and -negative zones rather than by a unique electrophilic region opposed to a nucleophilic area. This makes the first molecular moment scarcely significant and ill-determined, whereas the second moment is large, significant and highly reliable. A comparison between experimental and theoretical components of the third electric moment shows a few discrepancies, whereas the agreement for the fourth electric moment is excellent. The most favourable intermolecular bond is show to be an NHN hydrogen bond with an energy of about 50 kJ mol(-1). Key pharmacophoric features responsible for attractive electrostatic interactions include CHX hydrogen bonds. It is shown that methyl and methylene groups, known to be essential for the biological activity of the drug, provide a significant energetic contribution to the total binding energy. Dispersive interactions are important at the thiophene and at both the phenyl fragments. The experimental estimates of the electrostatic contribution to the intermolecular interaction energies of six molecular pairs, obtained by a new model proposed by Spackman, predict the correct relative electrostatic energies with no exceptions.

Molecular pair analysis: C-H...F interactions in the crystal structure of fluorobenzene? And related matters

The crystal structure of fluorobenzene is compared with isomorphous crystal structures of molecules of roughly similar shape. The lowest-energy fluorobenzene dimers are identified by theoretical calculations. Molecular pair analysis of the crystal structure of fluorobenzene and of an isomorphous virtual low-energy polymorph of benzene suggests that the important intermolecular interactions in the two structures are closely similar. In particular, the intermolecular C-H...F interactions in the fluorobenzene crystal have approximately the same structure-directing ability and influence on the intermolecular energy as the corresponding C-H...H interactions in benzene. Molecular pair analysis of the isomorphous crystal structures of benzonitrile, alloxan, and cyclopentene-1,2,3-trione indicates that essentially the same crystal structure can be adopted with quite different patterns of pair energies and atom-atom interactions. The question as to whether the packing radius of organic fluorine is larger or smaller than that of hydrogen, is addressed, but not answered.