Hydrogen bonding is an important interaction playing a key role in chemical, physical, and biochemical processes. One can mention numerous examples such as the role of hydrogen bonding in enzymatic catalysis, arrangement of molecules in crystals, crystal engineering, proton transfer reactions, and also its important role in life processes. Hence, its nature is often the subject of investigations and polemics. One of the first definitions of hydrogen bonding was formulated by Pauling who stated that “under certain conditions an atom of hydrogen is attracted by rather strong forces to two atoms, instead of only one, so that it may be considered to be acting as a bond between them. This is called the hydrogen bond”. Pauling also pointed out that the hydrogen atom is situated only between the most electronegative atoms and it usually interacts much stronger with one of them. The latter interaction is a typical covalent bond (A-H). The interaction between hydrogen and another electronegative atom is much weaker and mostly electrostatic in nature; it is a nonbonding interaction (H 3 3 3B). This system is often designated as AH 3 3 3B where the B-center (acceptor of proton) should possess at least one lone electron pair; A-H is called the protondonating bond. Pauling stated that sometimes the H 3 3 3B interaction possesses characteristics of the covalent bond. The [FHF] ion is an example where the proton is inserted between two negative fluorine ions, accurately in the middle of the F 3 3 3 F distance. Hence, both H 3 3 3 F interactions are equivalent. This is in line with an early conclusion of Lewis that “an atom of hydrogen may at times be attached to two electron pairs of two different atoms” and with the statement of Latimer and Rodebush that “the hydrogen nucleus held by two octets constitutes a weak bond”. The latter statements correspond to recent studies on proton bound homodimers, that is, systems where the proton is inserted between two closed-shell moieties and where it often interacts equivalently with both of them. Chan and co-workers analyzed recently what factors determine whether the protonbound homodimer has a symmetric or an asymmetric hydrogen bond. In the other study, it is discussed what conditions should be fulfilled for the proton situated accurately in the midpoint of the donor-acceptor distance. The high level calculations up to CCSD(T)/6-311þþ(3df,3pd)//CCSD/6-311þþ(3df,3pd) were performed on the [FHF] ion and systems with O-H 3 3 3O or N-H 3 3 3N hydrogen bonds. The latter study is supported by the experimental X-ray and neutron diffraction data because there are numerous crystal structures with short O-H 3 3 3O hydrogen bonds and the proton situated in the central position or nearly so. Also recently, homogeneous and heterogeneous short and strong hydrogen bonds (SSHBs) as well as the proton bound homodimers were analyzed theoretically at MP2/aug-ccpVDZ þ diffuse(2s,2p) level. Among various topics, the matter was raised if hydrogen bonding is an electrostatic or covalent interaction. The following question arises: what does the covalency of hydrogen bonding mean? The decomposition of the interaction energy is useful to analyze hydrogen bonding and particularly to answer the latter question. One of the first decomposition schemes introduced is one of Morokuma and Kitaura, where the interaction energy is calculated within the Hartree-Fock one-electron approximation and it is decomposed into the following components: the exchange energy, EEX (arising from repulsive forces), and the other components, which might be a result of attractive forces: the polarization energy, EPL, the charge transfer energy, ECT, and the electrostatic energy, EES. If a method is applied where the correlation of electrons is taken into account, then the correlation energy may be included. One of the most important attractive components of the correlation energy is the dispersive energy. Different H-bonded systems were analyzed early by Umeyama and Morokuma who stated that: “The energy components are strongly distance dependent. At a relatively small separation, ES, CT, and PL can all be important attractive components, competing against a large EX repulsion. At larger distances for the same complex the short-range attractions CT and PL are usually unimportant and ES is the only important attraction.” One can see that the “covalency of interaction”may be connected with short H 3 3 3B distances where terms other than the electrostatic attractive one are important.

What is the covalency of hydrogen bonding

This tutorial review covers imidazolium receptors for anion recognition according to their topological and structural classification, and includes benzene tripodal, cyclophane and calix-imidazolium, fluorescent imidazolium, ferrocenyl imidazolium, cavitand and calixarene, and polymeric imidazolium systems.

Imidazolium receptors for the recognition of anions.

More than 20 years ago, we published in Chemical Reviews a paper entitled “Intermolecular Interactions between Medium-Sized Systems. Nonempirical and Empirical Calculations of Interaction Energy: Successes and Failures”. The situation in calculations of noncovalent interactions at that time can be best characterized by the question we posed at the very beginning of the review: “Can quantum chemistry describe vdW (van der Waals; today we call it noncovalent) interactions as successfully as covalent interactions?” Our answer then was “unambiguously yes”. We had good reason for an optimistic “yes” since we presented the first coupledcluster calculations including triple excitations for a (at that time) large complexsthe water dimer. We stressed the importance of the triple excitations for noncovalent interactions, and in the section called Prospects, we wrote that “significant progress is highly desirable with beyond-SCF methods, where new, more accurate and efficient procedures are developed”. In this respect we were right, and in the past 20 years, we have witnessed an enormous growth of interest in the fast and accurate calculation of intermolecular interactions. What is the reason for such an interest, or more generally, why are noncovalent interactions so relevant in modern research? Is it the mere existence of noncovalent complexesmore » in the gas and liquid phases? Certainly not. The answer should be sought in the role that noncovalent interactions are playing in both bio- and nanostructures.« less

Stabilization and structure calculations for noncovalent interactions in extended molecular systems based on wave function and density functional theories.

Through molecular engineering, single diarylethenes were covalently sandwiched between graphene electrodes to form stable molecular conduction junctions. Our experimental and theoretical studies of these junctions consistently show and interpret reversible conductance photoswitching at room temperature and stochastic switching between different conductive states at low temperature at a single-molecule level. We demonstrate a fully reversible, two-mode, single-molecule electrical switch with unprecedented levels of accuracy (on/off ratio of ~100), stability (over a year), and reproducibility (46 devices with more than 100 cycles for photoswitching and ~10 5 to 10 6 cycles for stochastic switching).

Covalently bonded single-molecule junctions with stable and reversible photoswitched conductivity.

Interactions involving aromatic rings are important in molecular/biomolecular assembly and engineering. As a consequence, there have been a number of investigations on dimers involving benzene or other substituted π systems. In this Feature Article, we examine the relevance of the magnitudes of their attractive and repulsive interaction energy components in governing the geometries of several π−π systems. The geometries and the associated binding energies were evaluated at the complete basis set (CBS) limit of coupled cluster theory with singles, doubles, and perturbative triples excitations [CCSD(T)] using a least biased scheme for the given data set. The results for the benzene dimer indicate that the floppy T-shaped structure (center-to-center distance:  4.96 A, with an axial benzene off-centered above the facial benzene) is isoenergetic in zero-point-energy (ZPE) corrected binding energy (D0) to the displaced-stacked structure (vertical interplanar distance:  3.54 A). However, the T-shaped structure i...

Understanding of assembly phenomena by aromatic-aromatic interactions: benzene dimer and the substituted systems.

The spectral properties of protonated water clusters, especially the difference between Eigen (H3O+) and Zundel (H5O2+) conformers and the difference between their unhydrated and dominant hydrated forms are investigated with the first principles molecular dynamics simulations as well as with the high level ab initio calculations. The vibrational modes of the excess proton in H3O+ are sensitive to the hydration, while those in H5O2+ are sensitive to the messenger atom such as Ar (which was assumed to be weakly bound to the water cluster during acquisitions of experimental spectra). The spectral feature around ∼2700 cm-1 (experimental value:  2665 cm-1) for the Eigen moiety appears when H3O+ is hydrated. This feature corresponds to the hydrating water interacting with H3O+, so it cannot appear in the Eigen core. Thus, H3O+ alone would be somewhat different from the Eigen forms in water. For the Zundel form (in particular, H5O2+), there have been some differences in spectral features among different experime...

Eigen and Zundel forms of small protonated water clusters: structures and infrared spectra.

Magic and antimagic protonated water clusters: exotic structures with unusual dynamic effects.

The acceleration of electron transfer (ET) rates in redox proteins relative to aqueous solutes can be attributed to the protein’s ability to reduce the nuclear response or reorganization upon ET, while maintaining sufficiently high electronic coupling. Quantitative predictions of reorganization free energy remain a challenge, both experimentally and computationally. Using density functional calculations and molecular dynamics simulation with an electronically polarizable force field, we report reorganization free energies for intraprotein ET in four heme-containing ET proteins that differ in their protein fold, hydrophilicity, and solvent accessibility of the electron-accepting group. The reorganization free energies for ET from the heme cofactors of cytochrome c and b5 to solvent exposed Ru-complexes docked to histidine residues at the surface of these proteins fall within a narrow range of 1.2−1.3 eV. Reorganization free energy is significantly lowered in a designed 4-helix bundle protein where both red...

Prediction of reorganization free energies for biological electron transfer: a comparative study of Ru-modified cytochromes and a 4-helix bundle protein.

The two dimensional (2D) to three dimensional (3D) transition for the protonated water cluster has been controversial, in particular, for H+(H2O)7. For H+(H2O)7 the 3D structure is predicted to be lower in energy than the 2D structure at most levels of theory without zero-point energy (ZPE) correction. On the other hand, with ZPE correction it is predicted to be either 2D or 3D depending on the calculational levels. Although the ZPE correction favors the 3D structure at the level of coupled cluster theory with singles, doubles, and perturbative triples excitations [CCSD(T)] using the aug-cc-pVDZ basis set, the result based on the anharmonic zero-point vibrational energy correction favors the 2D structure. Therefore, the authors investigated the energies based on the complete basis set limit scheme (which we devised in an unbiased way) at the resolution of the identity approximation Moller-Plesset second order perturbation theory and CCSD(T) levels, and found that the 2D structure has the lowest energy for...

Structure and spectral features of H+(H2O)7: Eigen versus Zundel forms.

In earlier studies, the interactions of isolated ionic species with various solvents were investigated using ab initio calculations. The ionic species investigated included cations (proton, hydronium, ammonium, and metal cations) and anions (single electron, hydroxide, and halide anions). However in the present study, we investigate the interactions of these ionic species with the solvent in the presence of other competing ionic species. We also elaborate on how the information obtained from these extensive studies have been employed in designing and synthesizing various kinds of novel ionophores and receptors.

Mina Park

Papers

Eigen and Zundel forms of small protonated water clusters: structures and infrared spectra.

Magic and antimagic protonated water clusters: exotic structures with unusual dynamic effects.

Prediction of reorganization free energies for biological electron transfer: a comparative study of Ru-modified cytochromes and a 4-helix bundle protein.

Structure and spectral features of H+(H2O)7: Eigen versus Zundel forms.

Study of interactions of various ionic species with solvents toward the design of receptors