Intermolecular interactions in group 14 hydrides: Beyond C?H···H?C contacts

In line with previous work in which we established the factors that enhance attractive C? H···H? C dihydrogen interactions in alkanes, an extended theoretical analysis of noncovalent intermolecular interactions in group 14 hydrides is presented here. Remarkably, these weak interactions may play a major role in determining the crystal structures adopted by several families of molecules. A combined structural and computational analysis at the MP2 level allowed us to identify and characterize different interactions of the type E? H···H? E and E···H? E (E = Si, Ge, Sn, and Pb), and to find also the most suitable scenario for the establishment of each particular type. The nature of the interactions has been analyzed in terms of natural charges of the atoms involved and a topological analysis of the electron density of several dimers confirms the existence of H···H and H···E attractive contacts. We have observed that the interaction strength increases when descending down the periodic group and that silicon has a marked tendency to establish Si···H? Si interactions. A size‐dependent backbone effect that reinforces H···H dihydrogen interactions in polyhedral systems has also been found.     

Intermolecular interactions in group 14 hydrides: Beyond CH···HC contacts

In line with previous work in which we established the factors that enhance attractive C?H···H?C dihydrogen interactions in alkanes, an extended theoretical analysis of noncovalent intermolecular interactions in group 14 hydrides is presented here. Remarkably, these weak interactions may play a major role in determining the crystal structures adopted by several families of molecules. A combined structural and computational analysis at the MP2 level allowed us to identify and characterize different interactions of the type E?H···H?E and E···H?E (E = Si, Ge, Sn, and Pb), and to find also the most suitable scenario for the establishment of each particular type. The nature of the interactions has been analyzed in terms of natural charges of the atoms involved and a topological analysis of the electron density of several dimers confirms the existence of H···H and H···E attractive contacts. We have observed that the interaction strength increases when descending down the periodic group and that silicon has a marked tendency to establish Si···H?Si interactions. A size‐dependent backbone effect that reinforces H···H dihydrogen interactions in polyhedral systems has also been found.     

Theoretical study of molecular interactions of sulfur ylide with HSX (X = F, Cl, and Br) molecules

The molecular interactions between sulfur ylide (SY) and HSX molecules (X = F, Cl and Br) were investigated using the MP2 method with the 6-311++G (2d, 2p) basis set. The SY (CH₂=SH₂) have two reactive sites: CH₂ (denoted as C-interaction) and SH₂ (S-interaction) that both could interact with three atoms of HSX molecules. The results show that S···C, X···C, and H···C interactions (C-interactions) is preference over the X···S, H···S, and H···X interactions. Quantum theories of atoms in molecules and natural bond orbitals methods have been applied to analyze the intermolecular interactions. Good correlations have been found between the interaction energies, the second-order perturbation energies E⁽²⁾, and the charge transfer qCT in the studied systems.     

Theoretical study of molecular interactions of phosphorus ylide with HF, HCN, and HN3

The molecular interactions between phosphorous ylide (PY) and HX molecules (X?=?F, CN, and N₃) were investigated using the MP2 method at 6-311++G(2d,2p) basis set. Three different patterns including non-classical hydrogen bond H···C, X···P interaction and classical hydrogen bond H···X were found for complex formation between PY and HX molecules. From the predicted models, stability of the H···C type complexes are greater than other types. Quantum theories of atoms in molecules and natural bond orbitals methods have been applied to analyze the intermolecular interactions. Good correlations have been found between the interaction energies (SE), the second-order perturbation energy E ⁽²⁾, and the charge transfer qCT in the studied systems.     

Theoretical study of molecular interactions of sulfur ylide with HF, HCN, and HN3

The molecular interactions between sulfur ylide (SY) and HX molecules (X = F, CN, and N₃) were investigated using the MP2 method at 6-311++G(2d,2p) basis set. Three different patterns including non-classical hydrogen bond (HB) H···C and classical HB H···X were found for complex formation between SY and HX molecules. Stability of the H···C type complexes are greater than H···X complexes. Quantum theories of atoms in molecules, natural bond orbitals, and energy decomposition analysis methods have been applied to analyze the intermolecular interactions. Good correlations have been found between the interaction energies (SE), the second-order perturbation energy E ⁽²⁾ and the charge transfer qCT in the studied systems.     

Interaction between NH2NO and H2O2: A quantum chemistry study

The H‐bonded complexes formed from interaction between NH₂NO (NA) and H₂O₂ (HP) have been investigated by using B3LYP and MP2 methods with a wide range of basis sets. We found six H‐bonded complexes in which three of them have cyclic structure. Calculations carried out at various levels show that the seven‐membered cyclic structure with O···HO and O···HN hydrogen bonding interactions is the most stable complex. The large binding energy obtained for A1 complex probably results from a more linear arrangement of the O···H N and O H···OH‐bonds in the seven‐membered structure A1. The natural bond orbital (NBO) analysis and the Bader's quantum theory of atoms in molecules have been used to elucidate the interaction characteristics of the NA‐HP complexes. The NBO results reveal that the charge transfer energy corresponds to the H‐bond interactions for A1 complex is grater than other complexes. The electrostatic nature of H‐bond interactions is predicted from QTAIM analysis. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Time-Dependent Density Functional Theory Study on Hydrogen and Dihydrogen Bonding in Electronically Excited State of 2-Pyridone–Borane–Trimethylamine Cluster

In this work, the intermolecular dihydrogen and hydrogen bonding interactions in electronically excited states of a 2-pyridone (2PY)–borane–trimethylamine (BTMA) cluster have been theoretically studied using time-dependent density functional theory method. Our computational results show that the S₁ state of 2PY–BTMA cluster is a locally excited state, in which only 2PY moiety is electronically excited. The theoretical infrared (IR) spectra of the 2PY–BTMA cluster demonstrate that the N–H stretching vibrational mode is slightly blue-shifted upon the electronic excitation. Moreover, the computed IR spectrum of the 2PY–BTMA cluster exhibits no carbonyl character due to the extension of the C=O bond length in the S₁ state. However, the N–H bond is shortened slightly upon photoexcitation. At the same time, the H···H and H···O distances are obviously lengthened in the S₁ sate by comparison with those in ground state. In addition, the electron density of the carbonyl oxygen is diminished due to the electronic excitation. Consequently, the proton acceptor ability of carbonyl oxygen is decreased in the electronic excited state. As a result, it is demonstrated that the intermolecular dihydrogen and hydrogen bonds are significantly weakened in the electronically excited state.     

Physical- and Bio-Organic Chemstry of Nonbonded Selenium· · ·Oxygen Interactions

Weak nonbonded interaction between a divalent selenium and an oxygen atom (i.e., Se···O interaction) frequently plays important roles in chemical and biological functions of selenium compounds. To establish that ⁷⁷ Se NMR is an easy experimental probe to diagnose the strength of an Se···O interaction, 3 series of 2-substituted benzeneselenenyl derivatives, which have an intramolecular Se···O interaction in solution, were employed. By comparing the ⁷⁷ Se NMR chemical shifts (δ _Se ) with those observed for other series of selenium compounds, which have an intramolecular Se···Y (Y = N, O, F, Cl, or Br) interaction, approximate linear correlation was found between the δ _Se values and the strengths of the nonbonded Se···Y interactions evaluated by natural bond orbital analysis at the B3LYP level. The correlation will be useful for estimating the strength of an Se···O interaction simply from the ⁷⁷ Se NMR chemical shift. By extending the chemistry of nonbonded Se···O interactions to structural biology, analogous S···O interactions have been discovered in protein architecture. The directional features were, however, different from those of Se···O and S···O interactions of small organic compounds.     

Weak noncovalent Si···F?C interactions stabilized fluoroalkylated rod-like polysilanes as ultrasensitive chemosensors

Noncovalent interactions, such as hydrogen bonding, metal coordination, and π-π stacking, are increasingly being utilized to develop well-ordered and self-organized supramolecular materials. Recently, new types of nonclassical weak interactions, such as C H···π, C H···F C, and C H···O, have been exploited in stabilizing the specific conformations of molecules and molecular assemblies in the solid state. These noncovalent interactions play an important role in materials comprised of polymer chains, because cooperative effects from a large number of weak interactions can lead to drastic changes in its conformation, several properties, and functionalities. The programmed design of synthetic helical polymer with well-defined molecular conformation has been the main subject in modern polymer science and engineering. Silicon-catenated polysilane is an ideal helical silicon quantum wire and polymers with unique photophysical properties. The present review highlights the spectroscopic evidences for through-space weak Si···F C interaction in poly(methyl-3,3,3-trifluoropropylsilane) ( 1 ) in noncoordinating and coordinating solvents by means of NMR (²⁹Si and ¹⁹F) and IR spectroscopies, and viscometric measurement. It was found that 1 is applicable for chemosensors with an extremely high sensitivity and selectivity toward fluoride ions in tetrahydrofuran (THF) and with high sensitivity for nitroaromatic compounds, detected by a decrease in the photoluminescence intensity in THF and in thin solid film. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 5060–5075, 2006     

Mutual enhancing effects of the σ-hole interactions and halogen/hydrogen-bonded interactions in the iodine-ylide containing complexes

The region of positive electrostatic potentials (σ-hole) has been found along the extension of the C–I bond in the iodine-ylide CH₂IH, which suggests that the iodine-ylide could interact with nucleophiles to form weak, directional noncovalent interactions. MP2 calculations confirmed that the I···N σ-hole interaction exists in the CH₂IH···NCX (X = H, F, Cl, Br, I) bimolecular complexes. The NCCl···CH₂IH···NCX (X = H, F, Cl, Br, I) termolecular complexes were constructed to investigate the weakly bonded σ-hole interactions to be strengthened by Cl···C halogen bond. And then, the NCY···CH₂IH···NCCl (Y = H, F, Cl, Br, I) termolecular complexes were designed to investigate the enhancing effects of the I···N σ-hole interaction on the Y···C halogen/hydrogen-bonded interactions. Accompany with the mutual enhancing processes of the σ-hole interactions and halogen/hydrogen-bonded interactions in the iodine-ylide containing termolecular complexes, both the I···N σ-hole interactions and Y···C halogen/hydrogen-bonded interactions become more polarizable.     

Mixed Ligand Palladium(Ⅱ) Complex with NS-Bidentate S-Allyldithiocarbazate Schiff Base: Synthesis, Spectral Char-acterization, Crystal Structure and Decoding Intermolecular Interactions with Hirshfeld Surface Analysis

A new mixed ligand palladium(II) complex with bidentate NS‐donor chelate, [PdCl(PPh₃)L] (L: S‐allyl β‐N‐(benzylidene)dithiocarbazate), has been prepared and characterized using single crystal X‐ray diffraction and spectroscopic (electronic, IR, ¹H NMR and ¹³C NMR) techniques. The shorter Pd? P bond distance, 2.255(7) Å, than the sum of the single bond radii for palladium and phosphorus (2.41 Å), showed partial double bond character. Visualizing and exploring the crystal structure using Hirshfeld surface analysis showed the presence of π··· π, N··· π, C? H··· π, Cl···H and weak C? H···S interactions as most important intermolecular interactions in the crystal lattice, which are responsible to extension of the supramolecular network of the compound and stabilization of the crystal structure.     

Hirshfeld surface analysis and spectroscopic and DFT studies of p-acetotoluidide and p-thioacetotoluidide

The Hirshfeld surface analysis, theoretical calculation, and IR and Raman spectra of p-acetotoluidide and p-thioacetotoluidide were reported. Hirshfeld surfaces and fingerprint plot have been used for visualizing, exploring, and quantifying intermolecular interactions in the crystal lattice of the title compounds. The packing of the molecules in the crystal structure of p-acetotoluidide and p-thioacetotoluidide forms the chains of N–H···O and N–H···S hydrogen bonds, respectively. The close contacts are also dominated by H···H and H···C/C···H interactions. The analysis of Hirshfeld surface has been well correlated with the spectroscopic studies. Theoretical calculations of the title compounds’ isolated molecule have been carried out using DFT at the B3LYP level.     

Unraveling weak interactions in aniline-pyrrole dimer clusters

Weak intermolecular interactions in aniline-pyrrole dimer clusters have been studied by the dispersion-corrected density functional theory(DFT) calculations. Two distinct types of hydrogen bonds are demonstrated with optimized geometric structures and largest interaction energy moduli. Comprehensive spectroscopic analysis is also addressed revealing the orientation-dependent interactions by noting the altered red-shifts of the infrared and Raman activities. Then we employ natural bond orbital(NBO)analysis and atom in molecules(AIM) theory to have determined the origin and relative energetic contributions of the weak interactions in these systems. NBO and AIM calculations confirm the V-shaped dimer cluster is dominated by N.H···N and C.H···π hydrogen bonds, while the J-aggregated isomer is stabilized by N.H···π, n→π* and weak π···π* stacking interactions.The noncovalent interactions are also demonstrated via energy decomposition analysis associated with electrostatic and dispersion contributions.     

Buckybowls as adsorbents for CO2, CH4, and C2H2: Binding and structural insights from computational study

Noncovalent functionalization of buckybowls sumanene (S), corannulene (R), and coronene (C) with greenhouse gases (GGs) such as CO₂, CH₄ (M), and C₂H₂ (A) has been studied using hybrid density functional theory. The propensity and preferences of these small molecules to interact with the concave and convex surfaces of the buckybowls has been quantitatively estimated. The results indicate that curvature plays a significant role in the adsorption of these small molecules on the π surface and it is observed that buckybowls have higher binding energies (BEs) compared with their planar counterpart coronene. The concave surface of the buckybowl is found to be more feasible for adsorption of small molecules. BEs of small molecules towards π systems is CO₂ > A > M and the BEs of π systems toward small molecules is S > R > C. Obviously, the binding preference is dictated by the way in which various noncovalent interactions, such as π···π, lone pair···π, and CH···π manifest themselves on carbaneous surfaces. To delineate the intricate details of the interactions, we have employed Bader's quantum theory of atoms in molecule and localized molecular orbital energy decomposition analysis (LMO‐EDA). LMO‐EDA, which measures the contribution of various components and traces the physical origin of the interactions, indicates that the complexes are stabilized largely by dispersion interactions. © 2015 Wiley Periodicals, Inc.     

Copper(II) Supramolecular Complex: Synthesis,Crystal Structure,and Electrochemical Property

A novel complex {Cu(Bobb)₂](pic)₂}₂ [pic = picrate anion, Bobb = 1,3‐bis(1‐benzylbenzimidazol‐2‐yl)‐2‐oxopropane] was synthesized and characterized by means of elemental analyses and electrical conductivity. The crystal structure of the copper complex has been determined by single‐crystal X‐ray diffraction. A study of the electrochemistry of the title compound was carried out by using cyclic voltammetry. It revealed that the copper complex exhibits a quasi‐reversible redox process. The X‐ray structure of the above complex shows that the unit cell consists of two centrosymmetric, crystallographically independent molecules, in which the copper(II) ions have the same coordination environment and should be described as distorted octahedron. The complex is formed of { ··· Cu(2) ··· Cu(1) ··· Cu(1) ··· }_∞ supramolecular configuration by π ··· π stacking interactions between the benzimidazole rings. The complex was also identified by IR and electronic spectroscopy.     

F···HO intramolecular hydrogen bond as the main transmission mechanism for 1hJF,H(O) coupling constant in 2′‐fluoroflavonol

Flavonoids are useful compounds in medicinal chemistry and exhibit conformational isomerism, which is ruled by intramolecular interactions. One of the main intramolecular forces governing the stability of conformations is the hydrogen bond. Hydrogen bond involving fluorine covalently bonded to carbon has been found to be rare, but it appears in 2′‐fluoroflavonol, although the F···HO hydrogen bond cannot be considered the main effect governing the conformational stability of this compound. Because ¹⁹F is magnetically active and suitable for NMR studies, the ^1hJ_F,H(O) coupling constant can be used as a probe for such an interaction in 2′‐fluoroflavonol. In fact, the ^1hJ_F,H(O) coupling was computationally analyzed in this work, and the F···HO hydrogen bond was found to be its main transmission mechanism, which modulates this coupling in 2′‐fluoroflavonol, rather than overlap of proximate electronic clouds, such as in 2‐fluorophenol. Copyright © 2012 John Wiley & Sons, Ltd.     

Understanding hydrogen bonding of hydroxamic acids with some amino acid side chain model molecules

The hydrogen-bonding abilities of a few amino acid side chains have been studied through aggregation of methylamine, methanol, and acetic acid (as model molecules) with formo- and thioformo- hydroxamic acids using ab initio calculations. Forty six aggregates representing all possible H-bond interactions between these amino acid side chain groups and two most stable keto and enol tautomeric forms of both hydroxamic acids have been optimized. Although participation of conventional H-bond donors and acceptors leads to significant stabilization energies, yet C–H···O, C–H···N, S–H···O, and S–H···N etc. unconventional H-bonds also contribute to stabilize interactions in many aggregates. Strength of H-bonds of the molecules with formo- and thioformo- hydroxamic acid studied follows the order acetic acid > methylamine > methanol. A comparative study of atomic charges and orbital interactions employing NBO analysis has been carried out to explore the role of bond polarizations, charge transfer, and electron delocalizations as contributors to stabilization energy.     

Assessment of intermolecular interactions at three sites of the arylalkyne in phenylacetylene‐containing lithium‐bonded complexes: Ab initio and QTAIM studies

The intermolecular interactions existing at three different sites between phenylacetylene and LiX (X = OH, NH₂, F, Cl, Br, CN, NC) have been investigated by means of second‐order Møller?Plesset perturbation theory (MP2) calculations and quantum theory of “atoms in molecules” (QTAIM) studies. At each site, the lithium‐bonding interactions with electron‐withdrawing groups (? F, ? Cl, ? Br, ? CN, ? NC) were found to be stronger than those with electron‐donating groups (? OH and ? NH₂). Molecular graphs of C₆H₅C?CH···LiF and πC₆H₅C?CH···LiF show the same connectional positions, and the electron densities at the lithium bond critical points (BCPs) of the πC₆H₅C?CH···LiF complexes are distinctly higher than those of the σC₆H₅C?CH···LiF complexes, indicating that the intermolecular interactions in the C₆H₅C?CH···LiX complexes can be mainly attributed to the π‐type interaction. QTAIM studies have shown that these lithium‐bond interactions display the characteristics of “closed‐shell” noncovalent interactions, and the molecular formation density difference indicates that electron transfer plays an important role in the formation of the lithium bond. For each site, linear relationships have been found between the topological properties at the BCP (the electron density ρ_b, its Laplacian ?²ρ_b, and the eigenvalue λ₃ of the Hessian matrix) and the lithium bond length d(Li‐bond). The shorter the lithium bond length d(Li‐bond), the larger ρ_b, and the stronger the π···Li bond. The shorter d(Li‐bond), the larger ?²ρ_b, and the greater the electrostatic character of the π···Li bond. © 2012 Wiley Periodicals, Inc.     

Origins of catalyst-controlled enantiodivergent hydroamination of enones with pyridazinones: A computational study

Density functional theory calculations have been performed to investigate the dipeptide phosphine-catalyzed hydroamination of enones with pyridazinones. The computations reveal that a number of the NH···O hydrogen-bonding interactions with the pyridazinone moiety and the C–H···O hydrogen-bonding interactions with the enone moiety are present in the enantioselectivity-determining Michael addition transition states. The experimentally-observed catalyst-controlled enantiodivergence is mainly attributed to the significant impact of the substituent of the amide moiety of the dipeptide phosphine on the relative strength of the NH···O hydrogen-bonding interactions, which was found to affect the Si face attack transition state, enabling the enantioselectivity switch upon change of chiral dipeptide phosphine catalyst.     

A computational study on [(PH<Subscript>2</Subscript>X)<Subscript>2</Subscript>]<Superscript>·+</Superscript> homodimers involving intermolecular two-center three-electron bonds

A computational study at CCSD(T) theoretical level has been carried out on radical cation [(PH₂X)₂]^·+ homodimers. Four stable minima configurations have been found for seven substituted phosphine derivatives, X = H, CH₃, CCH, NC, OH, F and Cl. The most stable minimum presents an intermolecular two-center three-electron P···P bond except for X = CCH. The other three minima correspond to an alternative P···P pnicogen bonded complex, to a P···X contact and the last one to the complex resulting from a proton transfer, PH₃X⁺:PHX^·. The complexes obtained have been compared with those of the corresponding neutral ones, (PH₂X)₂, and the analogous protonated ones, PH₃X⁺:PH₂X, recently described in the literature. The spin and charge densities of the complexes have been examined. The electronic characteristics of the complexes have been analyzed with the NBO and AIM methods. The results obtained for the spin density, charge and NBO are coherent for all the complexes.