Experimental and Theoretical Charge Density Study on Di‐2‐pyrazylamine (Hdpza) Molecule in Crystal

Electron density distribution of Di‐2‐pyrazylamine ( Hdpza ) is studied both by single‐crystal X‐ray diffraction method at 100K and theoretical calculation. Structural determination reveals that Hdpza molecules crystalize in a syn‐anti conformation with an intramolecular C? H?N hydrogen bond between two pyrazine rings and then gather together via two intermolecular N? H?N and C? H?N hydrogen interaction and π? π stacking interaction between pyrazine rings. Charge density analysis is made in terms of deformation density (Δπ), Laplacian distribution and topological analysis of total electron density based on multipole model and theoretical calculation. The agreement between experiment and theory is good. The topological properties at bond critical points of C? C and C? N bonds reveal a covalent bond character, and those of intermolecular interactions, such as hydrogen bonds and π? π stacking interactions, reveal a closed‐shell interaction. The potential energy curve of Hdpza molecule shows that the syn‐anti conformation is the most stable one (global minima) than the other two of syn‐syn and anti‐anti conformations.     

Rhodium(II)‐ or Copper(I)‐Catalyzed Formal Intramolecular Carbene Insertion into Vinylic C(sp2)−H Bonds: Access to Substituted 1H‐Indenes

A rhodium(II)‐ or copper(I)‐catalyzed formal intramolecular carbene insertion into vinylic C(sp²)−H bonds is reported herein. This method provides straightforward access to 1H ‐indenes with high efficiency and excellent functional‐group compatibility. Mechanistically, the reaction is proposed to involve the following sequence: metal carbene formation, intramolecular nucleophilic addition of the double bond to the electron‐deficient carbene carbon atom, dearomatization, and finally a 1,5‐H shift.     

The nature of the N?O bond in amine oxides

Despite the ubiquitous presence of amine oxides in chemistry, there is no consensus about the nature of the N O bond in these compounds. In this work, we have used electron density analysis to investigate the nature of this bond in substituted amine oxides, R₃NO, and have compared it with the nature of the N O bond in hydroxylamines, R₂NOR, and model molecules that have well-established chemical bond character. The results showed that the N O bond length and relative stability are proportional to the inductive effect of the substituents. Quantum chemical topology, natural bond orbitals (NBO), and natural resonance theory (NRT) analyses indicated that the N O bond is polar covalent in all the studied amine oxides, but the ionic contribution is different. NBO and NRT analyses revealed that molecules with more electronegative substituents have strongly delocalized N O and N R bonds, whereas molecules with electropositive substituents have localized bonds.     

Toward deformation densities for intramolecular interactions without radical reference states using the fragment,atom, localized,delocalized, and interatomic (FALDI) charge density decomposition scheme

A novel approach for calculating deformation densities is presented, which enables to calculate the deformation density resulting from a change between two chemical states, typically conformers, without the need for radical fragments. The Fragment, Atom, Localized, Delocalized, and Interatomic (FALDI) charge density decomposition scheme is introduced, which is applicable to static electron densities (FALDI‐ED), conformational deformation densities (FALDI‐DD) as well as orthodox fragment‐based deformation densities. The formation of an intramolecular NH⋅⋅⋅N interaction in protonated ethylene diamine is used as a case study where the FALDI‐based conformational deformation densities (with atomic or fragment resolution) are compared with an orthodox EDA‐based approach. Atomic and fragment deformation densities revealed in real‐space details that (i) pointed at the origin of density changes associated with the intramolecular H‐bond formation and (ii) fully support the IUPAC H‐bond representation. The FALDI scheme is equally applicable to intra‐ and intermolecular interactions. © 2017 Wiley Periodicals, Inc.     

Intramolecular Natural Energy Decomposition Analysis: Applications to the Rational Design of Foldamers

We describe an intramolecular version of the natural energy decomposition analysis (NEDA), with the aim of evaluating interactions between molecular fragments across covalent bonds. The electronic energy in intramolecular natural energy decomposition analysis (INEDA) is divided into electrical, core, and charge transfer components. The INEDA method describes the fragments using the nonfragmented electronic density, and, therefore, there are no limitations in how to choose the boundary orbital. We used INEDA to evaluate the interaction energies that give origin to barriers of rotation around C_amide C_aromatic (C_am C_ar) and N_amide C_aromtaic (N_am C_ar) bonds in arylamide‐foldamer building blocks. We found that differences of barrier height between models with different ortho‐aryl substituents stem from charge transfer and core interactions. In three‐center hydrogen‐bond (H‐bond) models with an NH proton donor H‐bound to two electronegative ortho‐aryl substituents, the interaction energy of the three‐center system is larger than in either of the two‐center H‐bond subsystem alone, indicating an increase of overall rigidity. The combination of INEDA and NEDA allows the evaluation of intermolecular and intramolecular interactions using a consistent theoretical framework. © 2018 Wiley Periodicals, Inc.     

Structures,vibrational frequencies,topologies, and energies of hydrogen bonds in cysteine‐formaldehyde complexes

The hydrogen bonding interactions between cysteine (Cys) and formaldehyde (FA) were studied with density functional theory regarding their geometries, energies, vibrational frequencies, and topological features of the electron density. The quantum theory of atoms in molecules and natural bond orbital analyses were employed to elucidate the interaction characteristics in the Cys‐FA complexes. The intramolecular hydrogen bonds (H‐bonds) formed between the hydroxyl and the N atom of cysteine moiety in some Cys‐FA complexes were strengthened because of the cooperativity. Most of intermolecular H‐bonds involve the O atom of cysteine/FA moiety as proton acceptors, while the strongest H‐bond involves the O atom of FA moiety as proton acceptor, which indicates that FA would rather accept proton than providing one. The H‐bonds formed between the CH group of FA and the S atom of cysteine in some complexes are so weak that no hydrogen bonding interactions exist among them. In most of complexes, the orbital interaction of H‐bond is predominant during the formation of complex. The electron density (ρ_b) and its Laplace (?²ρ_b) at the bond critical point significantly correlate with the H‐bond parameter δR, while a linearly relationship between the second‐perturbation energy E(2) and ρ_b has been found as well. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

A density functional theory-time-dependent density functional theory investigation of photo-induced hydrogen bond and proton transfer for 2-(3,5-dichloro-2,6-dihydroxy-phenyl)-benzoxazole-6-carboxylicacid

Given the paramount importance of excited-state relaxation in the photochemical process, excited-state hydrogen bonding interactions and excited-state intramolecular proton transfer (ESIPT) are always hot topics. In this work, we theoretically explore the excited-state dynamical behaviors for a novel 2-(3,5-dichloro-2,6-dihydroxy-phenyl)-benzoxazole-6-carboxylicacid (DDPBC) system. As two intramolecular hydrogen bonds (O1 H2⋯N3 and O4 H5⋯O6) exist in the DDPBC structure, we first check if the double proton transfer form cannot be formed in the S1 state. Then, we explore the changes of geometrical parameters involved in hydrogen bonds, based on which we confirm that the dual intramolecular hydrogen bonds are strengthened on photo-excitation. The O1 H2⋯N3 hydrogen bond particularly plays a more important role in excited state. When it comes to the photo-induced excitation, we find charge transfer and electronic density redistribution around O1 H2 and N3 atom moieties. We verify the ESIPT tendency arising from the O1 H2⋯N3 hydrogen bond. In the analysis of the potential energy curves, along with O1 H2⋯N3 and O4 H5⋯O6, we demonstrate that the ESIPT reaction should occur along with O1 H2⋯N3 rather than O4 H5⋯O6. This work not only clarifies the specific ESIPT mechanism for DDPBC system but also paves the way for further novel applications based on DDPBC structure in the future.     

Trigger bond analysis of nitroaromatic energetic materials using wiberg bond indices

The identification of trigger bonds, bonds that break to initiate explosive decomposition, using computational methods could help direct the development of novel, “green” and efficient high energy density materials (HEDMs). Comparing bond densities in energetic materials to reference molecules using Wiberg bond indices (WBIs) provides a relative scale for bond activation (%ΔWBIs) to assign trigger bonds in a set of 63 nitroaromatic conventional energetic molecules. Intramolecular hydrogen bonding interactions enhance contributions of resonance structures that strengthen, or deactivate, the C NO₂ trigger bonds and reduce the sensitivity of nitroaniline‐based HEDMs. In contrast, unidirectional hydrogen bonding in nitrophenols strengthens the bond to the hydrogen bond acceptor, but the phenol lone pairs repel and activate an adjacent nitro group. Steric effects, electron withdrawing groups and greater nitro dihedral angles also activate the C NO₂ trigger bonds. %ΔWBIs indicate that nitro groups within an energetic molecule are not all necessarily equally activated to contribute to initiation. %ΔWBIs generally correlate well with impact sensitivity, especially for HEDMs with intramolecular hydrogen bonding, and are a better measure of trigger bond strength than bond dissociation energies (BDEs). However, the method is less effective for HEDMs with significant secondary effects in the solid state. Assignment of trigger bonds using %ΔWBIs could contribute to understanding the effect of intramolecular interactions on energetic properties. © 2018 Wiley Periodicals, Inc.     

Si-O bonded interactions in silicate crystals and molecules: a comparison

Bond critical point, local kinetic energy density, G(rc), and local potential energy density, V(rc), properties of the electron density distributions, rho(r), calculated for silicates such as quartz and gas-phase molecules such as disiloxane are similar, indicating that the forces that govern the Si-O bonded interactions in silica are short-ranged and molecular-like. Using the G(rc)/rho(rc) ratio as a measure of bond character, the ratio increases as the Si-O bond length, the local electronic energy density, H(rc)= G(rc) + V(rc), and the coordination number of the Si atom decrease and as the accumulation of the electron density at the bond critical point, rho(rc), and the Laplacian, inverted Delta2 rho(rc), increase. The G(rc)/rho(rc) and H(rc)/rho(rc) ratios categorize the bonded interaction as observed for other second row atom M-O bonds into discrete categories with the covalent character of each of the M-O bonds increasing with the H(rc)/rho(rc) ratio. The character of the bond is examined in terms of the large net atomic charges conferred on the Si atoms comprising disiloxane, stishovite, quartz, and forsterite and the domains of localized electron density along the Si-O bond vectors and on the reflex side of the Si-O-Si angle together with the close similarity of the Si-O bonded interactions observed for a variety of hydroxyacid silicate molecules and a large number of silicate crystals. The bond critical point and local energy density properties of the electron density distribution indicate that the bond is an intermediate interaction between Al-O and P-O bonded interactions rather than being a closed-shell or a shared interaction.     

Dispersion and Hydrogen Bonding Rule: Why the Vaporization Enthalpies of Aprotic Ionic Liquids Are Significantly Larger than those of Protic Ionic liquids

It is well known that gas‐phase experiments and computational methods point to the dominance of dispersion forces in the molecular association of hydrocarbons. Estimates or even quantification of these weak forces are complicated due to solvent effects in solution. The dissection of interaction energies and quantification of dispersion interactions is particularly challenging for polar systems such as ionic liquids (ILs) which are characterized by a subtle balance between Coulomb interactions, hydrogen bonding, and dispersion forces. Here, we have used vaporization enthalpies, far‐infrared spectroscopy, and dispersion‐corrected calculations to dissect the interaction energies between cations and anions in aprotic (AILs), and protic (PILs) ionic liquids. It was found that the higher total interaction energy in PILs results from the strong and directional hydrogen bonds between cation and anion, whereas the larger vaporization enthalpies of AILs clearly arise from increasing dispersion forces between ion pairs.     

Nature of MoH···I bonds in Cp2Mo(L)H···I‐C≡C‐R Complexes (L=H,CN, PPh2, C(CH3)3; R=NO2, Cl,Br, H,OH, CH3, NH2)

The nature of the MoH···I bond in Cp₂Mo(L)H···I‐C≡C‐R (L= H, CN, PPh₂, C(CH₃)₃; R=NO₂, Cl, Br, H, OH, CH₃, NH₂) was investigated using electrostatic potential analysis, topological analysis of the electron density, energy decomposition analysis and natural bond orbital analysis. The calculated results show that MoH···I interactions in the title complexes belong to halogen‐hydride bond, which is similar to halogen bonds, not hydrogen bonds. Different to the classical halogen bonds, the directionality of MoH···I bond is low; Although electrostatic interaction is dorminant, the orbital interactions also play important roles in this kind of halogen bond, and steric interactions are weak; the strength of H···I bond can tuned by the most positive electrostatic potential of the I atom. As the electron‐withdrawing ability of the R substituent in the alkyne increases, the electrostatic potential maximum of the I atom increases, which enhances the strength of the H···I halogen bond, as well as the electron transfer.     

Correlation between electron delocalization and structural planarization in small water rings

The discovery of the covalent‐like character of the hydrogen bonding (H‐bonding) system [Science 342 , 611(2013)] has promoted a renewal of our understanding of the electronic and geometric structures of water clusters. In this work, based on density functional theory calculations, we show that the preferential formation of a stable quasiplanar structure of (H₂O)_n(n = 3–6) is closely related to three kinds of delocalized molecular orbitals (MOs; denoted as MO‐I, II, and III) of water rings. These originate from the 2p lone pair electrons of oxygen (O), the 2p bond electrons of O and the 1s electrons of H and the 2s electrons of O and 1s electrons of H, respectively. To maximize the orbital overlaps of the three MOs, geometric planarization is needed. The contribution of the orbital interaction is more than 30% in all the water rings according to our energy decomposition analysis, highlighting the considerable covalent‐like characters of H‐bonds. © 2015 Wiley Periodicals, Inc.     

Topological analysis of the electronic charge density in the ethene protonation reaction catalyzed by acidic zeolite

In the present work, the distribution of the electronic charge density in the ethene protonation reaction by a zeolite acid site is studied within the framework of the density functional theory and the atoms in molecules (AIM) theory. The key electronic effects such as topological distribution of the charge density involved in the reaction are presented and discussed. The results are obtained at B3LYP/6-31G(**) level theory. Attention is focused on topological parameters such as electron density, its Laplacian, kinetic energy density, potential energy density, and electronic energy density at the bond critical points (BCP) in all bonds involved in the interaction zone, in the reactants, pi-complex, transition state, and alkoxy product. In addition, the topological atomic properties are determined on the selected atoms in the course of the reaction (average electron population, N(Omega), atomic net charge, q(Omega), atomic energy, E(Omega), atomic volume, v(Omega), and first moment of the atomic charge distribution, M(Omega)) and their changes are analyzed exhaustively. The topological study clearly shows that the ethene interaction with the acid site of the zeolite cluster, T5-OH, in the ethene adsorbed, is dominated by a strong O-H...pi interaction with some degree of covalence. AIM analysis based on DFT calculation for the transition state (TS) shows that the hydrogen atom from the acid site in the zeolitic fragment is connected to the carbon atom by a covalent bond with some contribution of electrostatic interaction and to the oxygen atom by closed shell interaction with some contribution of covalent character. The C-O bond formed in the alkoxy product can be defined as a weaker shared interaction. Our results show that in the transition state, the dominant interactions are partially electrostatic and partially covalent in nature, in which the covalent contribution increases as the concentration and accumulation of the charge density along the bond path between the nuclei linked increases.     

Theoretical investigations on the weak nonbonded CS···CH2 interactions: Chalcogen‐bonded complexes with singlet carbene as an electron donor

In this article, we explored the noncovalent bonding interactions between O?C?S, S?C?S, F₂C?S, Cl₂C?S, and singlet carbene. Six chalcogen‐bonded complexes were obtained. It is found that all the vibrational frequencies of C?S bond presented a red shift character. Interaction energy, topology property of the electron density and its Laplacian, and the donor–acceptor interaction have been investigated. All these results show that there exists a weak nonbonded interaction between the chalcogen bond donor and CH₂. An energy decomposition analysis was performed to disclose that the electrostatic interaction is the main stabilized factor in these nonbonded complexes. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Interplay between hydrogen-bond formation and multicenter pi-electron delocalization: intramolecular hydrogen bonds

The specific case of intramolecular hydrogen bonds assisted by pi-electron delocalization is thoroughly investigated using multicenter delocalization analysis. The effect of the pi-electron delocalization on the intramolecular hydrogen-bond strength is determined by means of the relative molecular energies of "open" and "closed" structures, calculated at the B3LYP/6-311++G(d,p) level of theory. These relative energies are compared to variations in the multicenter electron delocalization indices and covalent hydrogen-bond indices, which are shown to correlate very well with the relative strength of the intramolecular hydrogen bonds studied. The multicenter electron delocalization indices and covalent bond indices have been computed using the quantum theory of atoms in molecules approach. The hydrogen bonds are formed with oxygen, nitrogen, or sulfur as acceptor atom, which are also the atoms considered to be bonded to the donor hydrogen. Malonaldehyde is taken as reference; the substitution of oxygen by other atoms at the acceptor and donor positions and the effect of the aromaticity have been studied. The results shown here match perfectly with the qualitative expectations derived from the resonance models. In addition, they provide a quantitative picture of the role played by the pi-electron delocalization on the relative strength of intramolecular hydrogen bonds.     

Theoretical examination of covalency in berkelium(IV) carbonate complexes

Experimental studies on the speciation of berkelium in carbonate media have shown that complexation of berkelium(III) by carbonate results in spontaneous oxidation to berkelium(IV) and that multiple species can be present in solution. We studied two proposed structures present in solution based on theoretical comparisons with spectroscopic data previously reported for Bk(IV) carbonate solutions. The multiconfigurational character of the ground and low-lying excited states in both complexes is demonstrated to result from the strong spin-orbit coupling. Although bonding in Bk(IV) carbonate and carbonate-hydroxide complexes is dominated by strong Coulombic forces, the presence of non-negligible covalent character is supported by ligand-field theory, natural localized orbitals, topological studies of the electron density, and energy transition state natural orbitals for chemical valence. Bond orders based on natural localized molecular orbitals show that Bk OH bonds possess enhanced orbital overlap, which is reflected in the bond strength. This is also observed in the decomposition of the orbital interaction energy into individual deformation density pairs.     

From weak interactions to covalent bonds: a continuum in the complexes of 1,8-bis(dimethylamino)naphthalene

Experimental charge density distributions in a series of ionic complexes of 1,8-bis(dimethylamino)naphthalene (DMAN) with four different acids: 1,2,4,5-benzenetetracarboxylic acid (pyromellitic acid), 4,5-dichlorophthalic acid, dicyanoimidazole, and o-benzoic sulfimide dihydrate (saccharin) have been analyzed. Variation of charge density properties and derived local energy densities are investigated, over all inter- and intramolecular interactions present in altogether five complexes of DMAN. All the interactions studied [[O...H...O](-), C[bond]H...O, [N[bond]H...N](+), O[bond]H...O, C[bond]H...N, C pi...N pi, C pi...C pi, C[bond]H...Cl, N[bond]H(+)] follow exponential dependences of the electron density, local kinetic and potential energies at the bond critical points on the length of the interaction line. The local potential energy density at the bond critical points has a near-linear relationship to the electron density. There is also a Morse-like dependence of the laplacian of rho on the length of interaction line, which allows a differentiation of ionic and covalent bond characters. The strength of the interactions studied varies systematically with the relative penetration of the critical points into the van der Waals spheres of the donor and acceptor atoms, as well as on the interpenetration of the van der Waals spheres themselves. The strong, charge supported hydrogen bond in the DMANH(+) cation in each complex has a multicenter character involving a [[Me(2)N[bond]H....NMe(2)](+)....X(delta-)] assembly, where X is the nearest electronegative atom in the crystal lattice.     

Conformational aspects of glutathione tripeptide: electron density topological & natural bond orbital analyses

Glutathione tripeptide (γ-glutamyl-cysteinyl-glycine) is a flexible molecule and its conformational energy landscape is strongly influenced by forming intramolecular hydrogen bond, its charge and the environment. This study employs DFT-B3LYP method with the 6-31+G (d,p) basis set to carry out conformational analysis of neutral, zwitterionic, cationic, and anionic forms of glutathione. In analyzing the structural characteristics of these structures, intramolecular hydrogen bonds were identified and characterized in details by topological parameters such as electron density ρ(r) and Laplacian of electron density $ \nabla^{2} $ ρ(r) from Bader’s atom in molecules theory. Charge transfer energies based on natural bond orbital analysis are also considered to interpret these intramolecular hydrogen bonds. Our results show that these hydrogen bonds are partially electrostatic and partially covalent in nature, in which the covalent contribution increases as the stabilization energy of hydrogen bond increases. Furthermore, the back bone and side chain (Ramachandran map) orientations of various ionic forms of glutathione have been studied and conformation of each constitution of glutathione tripeptide (i.e., Glu, Cys, and Gly moieties) was determined. In most species side chain conformation were found to be hindered gauche–gauche orientation by intramolecular hydrogen bonds.