Unusual Hydrogen Bonds: H···π Interactions

How the addition of atomic hydrogen to a multiple bond can be catalyzed by water molecules

Observational data show complex organic molecules in the interstellar medium (ISM). Hydrogenation of small unsaturated carbon double bond could be one way for molecular complexification. It is important to understand how such reactivity occurs in the very cold and low-pressure ISM. Yet, there is water ice in the ISM, either as grain or as mantle around grains. Therefore, the addition of atomic hydrogen on double-bonded carbon in a series of seven molecules have been studied and it was found that water catalyzes this reaction. The origin of the catalysis is a weak charge transfer between the π MO of the unsaturated molecule and H atom, allowing a stabilizing interaction with H2O. This mechanism is rationalized using the non-covalent interaction and the quantum theory of atoms in molecules approaches.

Hydrogen bond types which do not fit accepted definitions

There are various interactions that either partially fit or do not fit the currently accepted definitions of the hydrogen bond. However, they possess characteristics of this interaction. It seems that it is partly connected to the fact that these definitions are not precise. The typical 3c-4e (three centres - four electrons) A-H⋯B hydrogen bond is characterized by the single-atom A and B centres that are highly electronegative. On the other hand, non-typical interactions that do not fit the hydrogen bond definitions well are characterised by uncommon proton donors and/or proton acceptors. The cases of multi-centre proton acceptors, π-electron or σ-electron systems are well known - such interactions are designated as A-H⋯π and A-H⋯σ hydrogen bonds, respectively. However, the cases of interactions with the multi-centre proton donors and proton acceptors do not fit the majority of definitions of hydrogen bond. The π⋯H+⋯π system in the proton-bound homodimer of acetylene is an example. This system can be classified as a hydrogen bond according to the two-sites hydrogen bond, 2sHB, definition. There are various types of interactions discussed in this review; among them, those that are undoubtedly unclassified as hydrogen bonds, i.e., hydride bonds, and charge inverted hydrogen bonds, CIHBs. Special emphasis is also put here on the proton sponges and other systems such as the [FHF]- anion or [NgHNg]+ cation (Ng is the noble gas centre).

Cooperativity between Intermolecular Hydrogen and Carbon Bonds in ZY···CH3CN/CH3NC···HX Trimers (ZY = H2O, H2S, HF, HCl, HBr, NH3, and H2CO; HX = HF, HCl, and HBr)

Hydrogen-bonding and carbon-bonding interactions are widespread in nature. We studied the cooperativity between these interactions in 42 trimeric complexes ZY···CH3CN/CH3NC···HX, where ZY molecules are H2O, H2S, HF, HCl, HBr, NH3, and H2CO, and HX molecules are HF, HCl, and HBr. Acetonitrile (CH3CN) and isoacetonitrile (CH3NC) act as hydrogen bond acceptors as well as carbon bond donors in these trimers. Various theoretical methods, such as electronic structure calculations, quantum theory of atoms in molecule (QTAIM), natural bond orbital (NBO), and reduced density gradient analysis, are employed to study these trimers, and the results are compared with the corresponding ZY···CH3CN/CH3NC and CH3CN/CH3NC···HX dimers. Electronic structure calculations are performed at the second-order Mo̷ller-Plesset perturbation theory using the 6-311++G(2d,2p) basis set. We show that both the interactions act synergistically in these trimers leading to an increase in their bond strength as compared to the strength in the individual dimers. The cooperative energies for these trimers are in the range of 0.69 to 3.22 kJ/mol. It is seen that the carbon bonds benefit more from the cooperativity than the hydrogen bonds. The trends of cooperativity and correlations of interaction energies and cooperative energies with relevant QTAIM and NBO parameters are reported.

Development of Novel Nano-Sized Imine Complexes Using Coriandrum sativum Extract: Structural Elucidation, Non-Isothermal Kinetic Study, Theoretical Investigation and Pharmaceutical Applications

A new Schiff base (H2L) generated from sulfamethazine (SMT), as well as its novel micro- and nanocomplexes with Ni(II) and Cd(II) metal ions, have been synthesized. The proposed structures of all isolated solid compounds were identified with physicochemical, spectral, and thermal techniques. Molar conductance studies confirmed that the metal complexes are not electrolytic. The molecular geometry located at the central metal ion was found to be square planar for the NiL2 and tetrahedral for the CdL2 complexes. The kinetic and thermal parameters were obtained using the Coats and Redfern approach. Coriandrum sativum (CS) in ethanol was used to create the eco-friendly Ni and Cd nanocomplexes. The size of the obtained nanoparticles was examined using PXRD and TEM, and found to be in the sub-nano range (3.07-4.61 nm). Furthermore, the TEM micrograph demonstrated a uniform and homogeneous surface morphology. The chemistry of the prepared nanocomplexes was studied using TGA and TEM techniques. The effect of temperature on the prepared nanocomplexes' size revealed a decrease in size by heating. Furthermore, the nanocomplexes' antimicrobial and anticancer properties were evaluated. The outcomes demonstrated that the nanocomplexes exhibited better antimicrobial properties. Moreover, the antitumor results showed that after heating, the Ni nanocomplex exhibited a substantial antitumor activity (IC50 = 1.280 g/mL), which was higher than the activity of cis-platin (IC50 = 1.714 g/mL). Finally, molecular-docking studies were performed to understand the evaluated compounds' ability to bind to methionine adenosyl-transferases (PDB ID: 5A19) in liver cancer and COVID-19 main protease (PDB ID: 6lu7) cell-proteins. The findings reveal that [NiL2]·1.5H2O2 has a higher binding energy of -37.5 kcal/mol with (PDB ID: 5A19) cell protein.

A-X⋯σ Interactions-Halogen Bonds with σ-Electrons as the Lewis Base Centre

CCSD(T)/aug-cc-pVTZ//ωB97XD/aug-cc-pVTZ calculations were performed for halogen-bonded complexes. Here, the molecular hydrogen, cyclopropane, cyclobutane and cyclopentane act as Lewis base units that interact through the electrons of the H–H or C–C σ-bond. The FCCH, ClCCH, BrCCH and ICCH species, as well as the F₂, Cl₂, Br₂ and I₂ molecular halogens, act as Lewis acid units in these complexes, interacting through the σ-hole localised at the halogen centre. The Quantum Theory of Atoms in Molecules (QTAIM), the Natural Bond Orbital (NBO) and the Energy Decomposition Analysis (EDA) approaches were applied to analyse these aforementioned complexes. These complexes may be classified as linked by A–X···σ halogen bonds, where A = C, X (halogen). However, distinct properties of these halogen bonds are observed that depend partly on the kind of electron donor: dihydrogen, cyclopropane, or another cycloalkane. Examples of similar interactions that occur in crystals are presented; Cambridge Structural Database (CSD) searches were carried out to find species linked by the A–X···σ halogen bonds.

Rivalry between Regium and Hydrogen Bonds Established within Diatomic Coinage Molecules and Lewis Acids/Bases

A theoretical study of the complexes formed by Ag₂ and Cu₂ with different molecules, XH (FH, ClH, OH₂ , SH₂ , HCN, HNC, HCCH, NH₃ and PH₃ ) that can act as hydrogen-bond donors (Lewis acids) or regium-bond acceptors (Lewis bases) was carried out at the CCSD(T)/CBS computational level. The heteronuclear diatomic coinage molecules (AuAg, AuCu, and AgCu) have also been considered. With the exception of some of the hydrogen-bonded complexes with FH, the regium-bonded binary complexes are more stable. The AuAg and AuCu molecules show large dipole moments that weaken the regium bond (RB) with Au and favour those through the Ag and Cu atoms, respectively.

Molecular Hydrogen as a Lewis Base in Hydrogen Bonds and Other Interactions

The second-order Møller–Plesset perturbation theory calculations with the aug-cc-pVTZ basis set were performed for complexes of molecular hydrogen. These complexes are connected by various types of interactions, the hydrogen bonds and halogen bonds are most often represented in the sample of species analysed; most interactions can be classified as σ-hole and π-hole bonds. Different theoretical approaches were applied to describe these interactions: Quantum Theory of ‘Atoms in Molecules’, Natural Bond Orbital method, or the decomposition of the energy of interaction. The energetic, geometrical, and topological parameters are analysed and spectroscopic properties are discussed. The stretching frequency of the H-H bond of molecular hydrogen involved in intermolecular interactions is considered as a parameter expressing the strength of interaction.

Understanding Regium Bonds and their Competition with Hydrogen Bonds in Au2 :HX Complexes

A theoretical study of the regium and hydrogen bonds (RB and HB, respectively) in Au₂ :HX complexes has been carried out by means of CCSD(T) calculations. The theoretical study shows as overall outcome that in all cases the complexes exhibiting RB are more stable that those with HB. The binding energies for RB complexes range between -24 and -180 kJ ⋅ mol^-1, whereas those of the HB complexes are between -6 and -19 kJ ⋅ mol^-1 . DFT-SAPT also indicated that HB complexes are governed by electrostatics, but RB complexes present larger contribution of the induction term to the total attractive forces. ¹⁹⁷ Au chemical shifts have been calculated using the relativistic ZORA Hamiltonian.

A-H…σ Hydrogen Bonds: Dihydrogen and Cycloalkanes as Proton Acceptors

ωB97XD/aug-cc-pVTZ calculations were performed for complexes of dihydrogen, cyclopropane, cyclobutane and cyclopentane, with simple proton donating species such as hydrogen fluoride, hydrogen chloride, water, hydrogen cyanide and acetylene. Numerous dependencies between geometrical, energetic and topological parameters of complexes considered were found, since various theoretical approaches were applied: Quantum Theory of 'Atoms in Molecules' (QTAIM), Natural Bond Orbital (NBO) method and energy decomposition analysis (EDA). It was confirmed that complexes of dihydrogen and cyclopropane are linked through the A-H…σ interactions that may be classified as hydrogen bonds. In the case of complexes of cyclobutane such hydrogen bonds are rather weak. Other type and also weak A-H…C hydrogen bonds are formed for complexes with cyclopentane.

π-Hydrogen bonding and aromaticity: a systematic interplay study

Quantum DFT calculations, corrected for long-range interactions, have been carried out on complex models formed between HF as a proton donor and 2-methylene-2H-indene derivatives as proton acceptors. Using various exocyclic X substitutions, mutual effects of the aromaticity and the strength of the resulting π-hydrogen bond (after its evaluation by AIM methodology) have been investigated. The results show that the aromaticity of 6-membered rings and the hydrogen bond strength increase upon increasing the electron-donating character of the X-substituents. Based on some aromaticity indices (HOMA, FLU, SA and NICS(1)zz), it has been shown that the formation of a π-hydrogen bond causes an increase of aromaticity of the 6-membered ring. Also, the strength of the resulting π-hydrogen bond (with an energy of about 4.0 to 7.0 kcal mol-1) depends on the aromaticity of the 6-membered ring and increases with an increase in the aromaticity. In addition, a linear relationship was found between the most negative value of the molecular electrostatic potential (Vmin) and the HOMA, which confirms that the Vmin in the region of the studied ring could be used as a new index to estimate the amount of aromaticity. The electronic properties of the complexes have also been evaluated by means of the molecular electrostatic potential (MEP), the atoms in molecules (AIM) and the natural bond orbital (NBO) analyses.

Hydrogen-Bonding Acceptor Character of Be3, the Beryllium Three-Membered Ring

The ability of Be₃ as a hydrogen bond acceptor has been explored by studying the potential complexes between this molecule and a set of hydrogen bond donors (HF, HCl, HNC, HCN, H₂O, and HCCH). The electronic structure calculations for these complexes were carried out at the MP2 and CCSD(T) computational levels together with an extensive NBO, ELF, AIM, and electrostatic potential characterization of the isolated Be₃ system. In all the complexes, the Be-Be σ bond acts as electron donor, with binding energies between 19 and 6 kJ mol^-1. A comparison with the analogous cyclopropane:HX complexes shows similar binding energies and contributions of the DFT-SAPT energetic terms. A blue-shift of the harmonic frequencies of Be₃ is observed upon complexation.

Screening of different interactions in oxo-manganese porphyrin dimers containing axial N-donor ligands: a theoretical study

A DFT analysis for describing the dimeric assemblies of high-valent manganese(v)-oxo meso-tetraphenylporphyrin ([(TPP)Mn^VO]₂²⁺) and meso-tetrakis(pentafluorophenyl)porphyrin ([(TPFPP)Mn^VO]₂²⁺) in the presence of axial N-donor ligands is presented.

Complexes between neutral oxyacid beryllium salts and dihydrogen: a possible way for hydrogen storage?

Very stable 1 : 1 and 1 : 2 complexes between oxyacid beryllium salts and H₂ are found.

Identification of Breast Cancer Inhibitors Specific for G Protein-Coupled Estrogen Receptor (GPER)-Expressing Cells

Together with estrogen receptors ERα and ERβ, the G protein-coupled estrogen receptor (GPER) mediates important pathophysiological signaling pathways induced by estrogens and is currently regarded as a promising target for ER-negative (ER-) and triple-negative (TN) breast cancer. Only a few selective GPER modulators have been reported to date, and their use in cancer cell lines has often led to contradictory results. Herein we report the application of virtual screening and cell-based studies for the identification of new chemical scaffolds with a specific antiproliferative effect against GPER-expressing breast cancer cell lines. Out of the four different scaffolds identified, 8-chloro-4-(4-chlorophenyl)pyrrolo[1,2-a]quinoxaline 14 c was found to be the most promising compound able to induce: 1) antiproliferative activity in GPER-expressing cell lines (MCF7 and SKBR3), similarly to G15; 2) no effect on cells that do not express GPER (HEK293); 3) a decrease in cyclin D1 expression; and 4) a sustained induction of cell-cycle negative regulators p53 and p21.

DFT and TD-DFT study of the enol and thiol tautomers of 3-thioxopropanal in the ground and first singlet excited states

In the first part of this paper, a comprehensive theoretical study of molecular structure, stability, intramolecular hydrogen bond (IMHB) and [Formula: see text]-electron delocalization ([Formula: see text]-ED) of the enol and thiol tautomers of 3-thioxopropanal (TPA) in the ground state is performed. In this regard, all of the plausible conformations of TPA at M06-2X/6-311[Formula: see text]G(d,p) are optimized and a variety of theoretical levels are employed to identify the global minimum. Our calculations show that E1 is the most stable form that is in contrast to the results of Gonzalez et al. [J Phys Chem 101: 9710, 1997]. In order to elucidate this duality, the IMHB and [Formula: see text]-ED of chelated forms (E1 and T1) have been extensively investigated. So, it is found that both of the IMHB analysis and [Formula: see text]-ED concepts emphasize on the E1, as the global minimum. In the second part of this study, a set of simple electron-withdrawing and electron-donating substituents such as CN, F, Cl, CH3 and NH2 have been considered to evaluate their effects on the IMHB of the first singlet excited state of E1 and T1 at TD-DFT/6–311[Formula: see text]G(d,p) level of theory. According to our analysis, it was found that the IMHB strength of the excited states are much weaker than the ground states. Surprisingly, the IMHB of thiol derivatives is stronger than the enol ones in contrast to the ground state. Furthermore, the substitution effects in the ground and excited states are significantly different. Finally, various linear correlations between the IMHB energies with geometrical, topological and molecular orbital parameters are obtained.

About the nature of halogen bond interaction under the spatial confinement

Nowadays, much attention is put toward the description of noncovalent complexes exposed to the high pressure or embedded in confining environments. Such conditions may strongly modify the physical and chemical properties of molecular systems. This study focuses on the theoretical description of the confinement induced changes in geometry and energetic parameters of the halogen bonded FCl⋯CNF complex. A model analytical potential is applied to render the effect of orbital compression. In order to analyze the nature of halogen bond interaction, in the presence of spatial confinement, the supermolecular approach together with the symmetry-adapted perturbation theory is used. Furthermore, a thorough analysis of topological parameters, characterizing the halogen bond upon orbital compression, is performed within the quantum theory of atoms in molecules. The calculations are carried out using the ωB97x and CCSD(T) methods in connection with the aug-cc-pVTZ basis set. Among others, the obtained results indicate that the spatial confinement not only modifies the nature of halogen bond interaction but also induces the appearance of a completely new form of the studied FCl⋯CNF system.

H-Bond: Τhe Chemistry-Biology H-Bridge

H-bonding, as a non covalent stabilizing interaction of diverse nature, has a central role in the structure, function and dynamics of chemical and biological processes, pivotal to molecular recognition and eventually to drug design. Types of conventional and non conventional (H-H, dihydrogen, H- π, CH- π, anti- , proton coordination and H-S) H-bonding interactions are discussed as well as features emerging from their interplay, such as cooperativity (σ- and π-) effects and allostery. Its utility in many applications is described. Catalysis, proton and electron transfer processes in various materials or supramolecular architectures of preorganized hosts for guest binding, are front-line technology. The H-bond-related concept of proton transfer (PT) addresses energy issues or deciphering the mechanism of many natural and synthetic processes. PT is also of paramount importance in the functions of cells and is assisted by large complex proteins embedded in membranes. Both intermolecular and intramolecular PT in H-bonded systems has received attention, theoretically and experimentally, using prototype molecules. It is found in rearrangement reactions, protein functions, and enzyme reactions or across proton channels and pumps. Investigations on the competition between intra- and intermolecular H bonding are discussed. Of particular interest is the H-bond furcation, a common phenomenon in protein-ligand binding. Multiple H-bonding (H-bond furcation) is observed in supramolecular structures.

Significant hydrogen-bonding effect on the reactivity of high-valent manganese(V)–oxo porphyrins in C–H bond activation: A DFT study

The stereo electronic effects as well as hydrogen bonding effects of imidazole, pyridine and 2,6-dimethylpyridine as N-donor axial ligands on the C–H oxidation activity of high-valent manganese(V)–oxo meso-tetraphenylporphyrin (TPP) and meso-tetrakis(pentaflourophenyl)porphyrin (TPFPP), are investigated by DFT calculations. The electronic and steric properties of axial donors and porphyrin ligands affected on the activation energy of cyclohexane hydroxylation as well as the Mn–O bond strength of the oxo species in transition state. Imidazole with the strong [Formula: see text]-donating ability and the least steric hindrance showed greater co-catalytic activity than those of pyridine and in particularly hindered 2,6-Me2 pyridine in the presence of simple [(TPP)MnO][Formula: see text]. Nevertheless, the C–H bond activation by hindered and electron-deficient perfluorinated catalyst [(TPFPP)MnO][Formula: see text] is in the order of pyridine >2, 6-Me2 pyridine >imidazole. AIM analysis showed hydrogen bonding (HB) between the C–H [Formula: see text] bonds of pyridine (C[Formula: see text]-H of ring) and 2,6-Me2Py (C[Formula: see text]-H of methyl groups) with ortho-C–F bond of phenyl rings of TPFPP in Mn[Formula: see text]O species (C–H…..F–C hydrogen bond) which might be responsible for this unusual behavior. These results are supported by natural bond orbital (NBO) analysis.

Stereoelectronic effects of porphyrin ligand on the oxygen transfer efficiency of high valent manganese-oxo porphyrin species: A DFT study

The structure and properties of the N[Formula: see text]–Mn–O bonds of high valent manganese-oxo of the second and third generation porphyrins in the presence of imidazole have been studied by means of density functional (DFT) method with 6-31G* basis set in the gas phase as well as water solution. The geometric structures, frontier molecular orbitals, thermodynamic parameters, aromaticity indices and physical properties such as chemical potential and chemical hardness of [(TPP)(ImH)MnO][Formula: see text] and its derivatives were calculated. The obtained results showed that [(TPP)(ImH)MnO][Formula: see text] bearing halogen atoms at the [Formula: see text]-pyrrole positions had a saddle conformation with low Mn–O strength. The electron density ([Formula: see text] and Laplacian ([Formula: see text] properties at critical points of the N[Formula: see text]–Mn–O bonds, estimated by AIM calculations, indicate that Mn–O bonds in third generation porphyrins have lower [Formula: see text] and Mn–N[Formula: see text] distances have higher [Formula: see text] than the second generation ones. The calculations of aromaticity indices for chelated rings at the porphyrin center show that HOMA and NICS in third generation porphyrins are generally lower than that of second ones which is in agreement with their saddle conformation. These results are supported by natural bond orbital (NBO) analysis.

Fullerene and corannulene derivatives acting as insulators of Cl−and BeH2

Corannulene and its benzo-derivatives C_xH₁₀(x= 20–60) as prototypes of non-planar π-aromatic systems have been studied as insulators of BeH₂and Cl⁻.

A DFT investigation of axial N-donor ligands effects on the high valent manganese-oxo meso-tetraphenyl porphyrin

The effect of different electronic and structural nitrogen donors (L) on the N ( ax )- Mn - O properties in the high valent manganese-oxo meso-tetraphenylporphyrin intermediate is investigated by the density functional B3LYP method with 6-31g* basis set. The geometric structures, frontier molecular orbitals, thermodynamic parameters and physical properties such as chemical potential and chemical hardness of [( TPP )( L ) MnO ]+ complexes in the gas phase as well as water solution are calculated. Our theoretical results confirm that the Mn - O distances in [( TPP )( L ) MnO ]+ species decrease by replacing imidazoles with pyridines, amins as well as electron-poor and hindered nitrogen donors resulting from extending the Mn – N ( ax ) bonds. These results are supported by vibrational frequencies, atoms in molecules (AIM) and natural bond orbital (NBO) analysis. It is worth mentioning that the co-catalytic activity trend of different nitrogen donors observed experimentally in the presence of title Mn porphyrin is consistent with the calculated Mn – N ( ax ) and Mn – O bond lengths in this work.

A computational study on 3-azonia-, 3-phosphonia-, and 3-arsoniaspiro[2.2]pentanes and related three-membered heterocycles

A theoretical study at the ab initio MP2/6-311++G(d,p) level of theory is carried out to characterize several heterocyclic spiro[2.2]pentane cations with N, P, and As as spiro atoms. The strain and relative stability of the spiropentanes are obtained through isodesmic reactions. Nucleus-independent chemical shifts (NICS) and 3D NICS isosurfaces show σ-aromatic characteristics, similar to those found in cyclopropane. The interaction with the Cl(-) anion, which results in four different stationary structures, is studied and characterized by means of the atoms in molecules methodology, and Cl⋅⋅⋅pnicogen, Cl⋅⋅⋅H, and Cl⋅⋅⋅C interactions are found. The most stable structure in all cases corresponds to opening of one of the three-membered rings, due to the attack of the Cl atom, and C-Cl bond formation. Furthermore, the reaction with the 3-boranuidaspiro[2.2]pentane anion results in the formation of a new compound through cleavage of one ring of both reactants.

Why does substitution of thymine by 6-ethynylpyridone increase the thermostability of DNA double helices?

Efficiency of 6-ethynylpyridone (E), a potential thymine (T) analogue, which forms high-fidelity base pairs with adenine (A) and gives rise to stabler DNA duplexes, with stability comparable to those containing canonical cytosine(C):guanine(G) base pairs, has been reported recently. Estimates of the interaction energies, involving geometry optimization at the DFT level (including middle range dispersion interactions) followed by single point energy calculation at MP2 level, in excellent correlation with the experimentally observed trends, show that E binds more strongly and more discriminately with A than T does. Detailed analysis reveals that the increase in base-base interaction arises out of conjugation of acetylenic π electrons with the ring π system of E, which results in not only an extra stabilizing C-H···π interaction in the EA pair, but also a strengthening of the conventional hydrogen bonds. However, the computed base-base interaction energy for the EA pair was found to be much less than that of the canonical CG pair, implying that the difference in the TA versus EA base pairing interaction alone cannot explain the large experimentally observed increase in the thermostability of DNA duplexes, where a TA pair is replaced with an EA pair. Our computations show that the conjugation of acetylenic π electrons with the ring π system also possibly plays a role in increasing the stacking potential of the EA pair, which in turn can explain its marked influence in the enhancement of duplex stability.