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.     

The Bright Future of Unconventional σ/π‐Hole Interactions

Non‐covalent interactions play a crucial role in (supramolecular) chemistry and much of biology. Supramolecular forces can indeed determine the structure and function of a host–guest system. Many sensors, for example, rely on reversible bonding with the analyte. Natural machineries also often have a significant non‐covalent component (e.g. protein folding, recognition) and rational interference in such ‘living’ devices can have pharmacological implications. For the rational design/tweaking of supramolecular systems it is helpful to know what supramolecular synthons are available and to understand the forces that make these synthons stick to one another. In this review we focus on σ‐hole and π‐hole interactions. A σ‐ or π‐hole can be seen as positive electrostatic potential on unpopulated σ* or π⁽*⁾ orbitals, which are thus capable of interacting with some electron dense region. A σ‐hole is typically located along the vector of a covalent bond such as X?H or X?Hlg (X=any atom, Hlg=halogen), which are respectively known as hydrogen and halogen bond donors. Only recently it has become clear that σ‐holes can also be found along a covalent bond with chalcogen (X?Ch), pnictogen (X?Pn) and tetrel (X?Tr) atoms. Interactions with these synthons are named chalcogen, pnigtogen and tetrel interactions. A π‐hole is typically located perpendicular to the molecular framework of diatomic π‐systems such as carbonyls, or conjugated π‐systems such as hexafluorobenzene. Anion–π and lone‐pair–π interactions are examples of named π‐hole interactions between conjugated π‐systems and anions or lone‐pair electrons respectively. While the above nomenclature indicates the distinct chemical identity of the supramolecular synthon acting as Lewis acid, it is worth stressing that the underlying physics is very similar. This implies that interactions that are now not so well‐established might turn out to be equally useful as conventional hydrogen and halogen bonds. In summary, we describe the physical nature of σ‐ and π‐hole interactions, present a selection of inquiries that utilise σ‐ and π‐holes, and give an overview of analyses of structural databases (CSD/PDB) that demonstrate how prevalent these interactions already are in solid‐state structures.     

New Routes to a Series of σ‐Borane/Borate Complexes of Molybdenum and Ruthenium

A series of agostic σ‐borane/borate complexes have been synthesized and structurally characterized from simple borane adducts. A room‐temperature reaction of [Cp*Mo(CO)₃Me], 1 with Li[BH₃(EPh)] (Cp*=pentamethylcyclopentadienyl, E=S, Se, Te) yielded hydroborate complexes [Cp*Mo(CO)₂(μ‐H)BH₂EPh] in good yields. With 2‐mercapto‐benzothiazole, an N,S‐carbene‐anchored σ‐borate complex [Cp*Mo(CO)₂BH₃(1‐benzothiazol‐2‐ylidene)] ( 5 ) was isolated. Further, a transmetalation of the B‐agostic ruthenium complex [Cp*Ru(μ‐H)BHL₂] ( 6 , L=C₇H₄NS₂) with [Mn₂(CO)₁₀] affords a new B‐agostic complex, [Mn(CO)₃(μ‐H)BHL₂] ( 7 ) with the same structural motif in which the central metal is replaced by an isolobal and isoelectronic [Mn(CO)₃] unit. Natural‐bond‐orbital analyses of 5–7 indicate significant delocalization of the electron density from the filled σ_B?H orbital to the vacant metal orbital.     

The Pi‐Nature of Methyl Obtained by the Natural Bond Orbital Method: Orbital‐Based Rationalizations of Site‐Dependent Substitution Effects on Fine Color‐Tuning of Luminescence

Both C‐H bonding and antibonding (σ_CH and σ*_CH) of a methyl group would contribute to the highest occupied or lowest unoccupied molecular orbitals (HOMO or LUMO) in methylated derivatives of Ir(ppz)₂ 3 iq (ppz = 1‐phenylpyrazole and 3iq = isoquinoline‐3‐carboxylate). This is found by analysis of HOMO (or LUMO) formed by linear combination of bond orbitals using the natural bond orbital (NBO) method. The elevated level of HOMO (or LUMO) uniformly found for each methylated derivative, indicating the σ_CH‐destabilization outweighs the σ*_CH‐stabilization. To broaden the HOMO‐LUMO gap, methylation at a carbon having smaller contribution to HOMO and/or larger contribution to LUMO is suggested.     

Theoretical and Structural Analysis of Long CC Bonds in the Adducts of Polycyanoethylene and Anthracene Derivatives and Their Connection to the Reversibility of Diels–Alder Reactions

X‐ray structure determinations on four Diels–Alder adducts derived from the reactions of cyano‐ and ester‐substituted alkenes with anthracene and 9,10‐dimethylanthracene have shown the bonds formed in the adduction to be particularly long. Their lengths range from 1.58 to 1.62 Å, some of the longest known for Diels–Alder adducts. Formation of the four adducts is detectably reversible at ambient temperature and is associated with free energies of reaction ranging from ?2.5 to ?40.6 kJ mol^?1. The solution equilibria have been experimentally characterised by NMR spectroscopy. Density‐functional‐theory calculations at the MPW1K/6‐31+G(d,p) level with PCM solvation agree with experiment with average errors of 6 kJ mol^?1 in free energies of reaction and structural agreement in adduct bond lengths of 0.013 Å. To understand more fully the cause of the reversibility and its relationship to the long adduct bond lengths, natural‐bond‐orbital (NBO) analysis was applied to quantify donor–acceptor interactions within the molecules. Both electron donation into the σ*‐anti‐bonding orbital of the adduct bond and electron withdrawal from the σ‐bonding orbital are found to be responsible for this bond elongation.     

Comparative analysis of blue‐shifted hydrogen bond versus conventional hydrogen bond in methyl radical complexes

Methyl radical complexes H₃C…HCN and H₃C…HNC have been investigated at the UMP2(full)/aug‐cc‐pVTZ level to elucidate the nature of hydrogen bonds. To better understand the intermolecular H‐bond interactions, topological analysis of electron density at bond critical points (BCP) is executed using Bader's atoms‐in‐molecules (AIM) theory. Natural bond orbital (NBO) analysis has also been performed to study the orbital interactions and change of hybridization. Theoretical calculations show that there is no essential difference between the blue‐shift H‐bond and the conventional one. In H₃C…HNC complex, rehybridization is responsible for shortening of the N? H bond. The hyperconjugative interaction between the single electron of the methyl radical and N? H antibonding orbital is up to 7.0 kcal/mol, exceeding 3.0 kcal/mol, the upper limit of hyperconjugative n(Y)→σ*(X–H) interaction to form the blue‐shifted H‐bond according to Alabugin's theory. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Theoretical study of the red‐ and blue‐shifted hydrogen bonds of nitroxyl and acetylene dimers

Ab initio molecular orbital and density functional theory (DFT) in conjunction with different basis sets calculations were performed to study the C? H…O red‐shifted and N? H…π blue‐shifted hydrogen bonds in HNO? C₂H₂ dimers. The geometric structures, vibrational frequencies and interaction energies were calculated by both standard and counterpoise (CP)‐corrected methods. In addition, the G3B3 method was employed to calculate the interaction energies. The topological and natural bond orbital (NBO) analysis were investigated the origin of N? H…π blue‐shifted hydrogen bond. From the NBO analysis, the electron density decrease in the σ* (N? H) is due to the significant electron density redistribution effect. The blue shifts of the N? H stretching frequency are attributed to a cooperative effect between the rehybridization and electron density redistribution. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Observation of CH⋅⋅⋅π Interactions between Methyl and Carbonyl Groups in Proteins

Protein structure and function is dependent on myriad noncovalent interactions. Direct detection and characterization of these weak interactions in large biomolecules, such as proteins, is experimentally challenging. Herein, we report the first observation and measurement of long‐range “through‐space” scalar couplings between methyl and backbone carbonyl groups in proteins. These J couplings are indicative of the presence of noncovalent C−H⋅⋅⋅π hydrogen‐bond‐like interactions involving the amide π network. Experimentally detected scalar couplings were corroborated by a natural bond orbital analysis, which revealed the orbital nature of the interaction and the origins of the through‐space J couplings. The experimental observation of this type of CH⋅⋅⋅π interaction adds a new dimension to the study of protein structure, function, and dynamics by NMR spectroscopy.     

The MoMo Quintuple Bond as a Ligand to Stabilize Transition‐Metal Complexes

Herein, we report the employment of the Mo? Mo quintuple bonded amidinate complex to stabilize Group 10 metal fragments {(Et₃P)₂M} (M=Pd, Pt) and give rise to the isolation of the unprecedented δ complexes. X‐ray analysis unambiguously revealed short contacts between Pd or Pt and two Mo atoms and a slight elongation of the Mo? Mo quintuple bond in these two compounds. Computational studies show donation of the Mo? Mo quintuple‐bond δ electrons to an empty σ orbital on Pd or Pt, and back‐donation from a filled Pd or Pt d_π orbital into the Mo? Mo δ* level (LUMO), consistent with the Dewar–Chatt–Duncanson model.     

The ability of Ex2Box4+ to interact with guests containing π‐electron‐rich and π‐electron‐poor moieties

The ability of Ex 2 Box⁴⁺ as a host, able to trap guests containing both π‐electron rich (polycyclic aromatic hydrocarbons‐PAHs) and π‐electron poor (quinoid‐ and nitro‐PAHs) moieties was investigated to shed light on the main factors that control the host–guest (HG) interaction. The nature of the HG interactions was elucidated by energy decomposition (EDA‐NOCV), noncovalent interaction (NCI), and magnetic response analyses. EDA‐NOCV reveals that dispersion contributions are the most significant to sustain the HG interaction, while electrostatic and orbital contributions are very tiny. In fact, no significant covalent character in the HG interactions was observed. The obtained results point strictly to NCIs, modulated by dispersion contributions. Regardless of whether the guests contain π‐electron‐rich or π‐electron‐poor moieties, and no significant charge‐transfer was observed. All in all, HG interactions between guests 3‐14 and host 2 are predominantly modulated by π‐π stacking.     

NBO‐based CI/MP through‐space/bond interaction analysis and its application to stereoelectronic effects in SN2 reactions

NBO‐based CI/MP through‐space/bond interaction analysis was developed to analyze specific orbital interactions under consideration of the effects of electron correlation. This treatment was applied to the analysis of stereoelectronic effects in S_N2 reactions of allyl bromide in which the effects of electron correlation play an important role (ammonia was used as the nucleophilic reagent). The S_N2 activation energy in allyl bromide is lower than that in propyl bromide, because both the σ–π* and π–σ* interactions in allyl bromide contribute equally to the stabilization of the transition state. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Ladder‐Type π‐Conjugated 4‐Hetero‐1,4‐dihydrophosphinines: A Structure–Property Study

π‐Conjugated six‐membered 1,4‐dihydrophosphinines containing a heteroatom (Si, P, S) at the 4 position were synthesized and systematically studied. X‐ray crystallographic analyses showed that the central six‐membered heterocyclic rings are almost planar. The sum of the angles around the phosphorus atom increases by 23° from the trivalent phosphorus to the phosphonium atom in the thiaphosphinine system, which is consistent with the NMR spectroscopic studies. UV/Vis spectroscopy and theoretical calculations revealed that the communication between the phosphorus center and the benzothiophene moiety is enhanced by the incorporation of a sulfur atom into the molecular scaffold. The increased conjugation endows the thiaphosphinines with interesting emission properties. Theoretical calculations supported the postulation that the orbital coupling between the π system and a σ* orbital could be enhanced in the thiaphosphinine system, especially through a phosphonium center. Cyclic voltammetry studies revealed that the thiaphosphinine oxide, thiaphosphonium, and cis‐diphosphinine oxide exhibit quasi‐reversible reduction processes, which demonstrate that simple changes in the bridge heteroatoms help to efficiently tune the redox properties of the ladder‐type 4‐hetero‐1,4‐dihydrophosphinines.     

Pentafluorobenzoato‐dimolybdenum(II) Solvate and Co‐crystal Complexes with Benzene and Naphthalin

The quadruply bonded Mo₂⁴⁺ complex Mo₂(DAniF)₃(OOCC₆F₅) ( 1 ) [DAniF = N,N′‐bis(4‐methoxyphenyl)formamidinate] was synthesized. The solvate Mo₂(DAniF)₃(OOCC₆F₅) · (C₆H₆) ( 2 ) and co‐crystal Mo₂(DAniF)₃(OOCC₆F₅) · (C₁₀H₈) ( 3 ) complexes were obtained by self‐assembly of crystals of 1 with benzene and naphthalin, respectively. Compounds 1 , 2 , and 3 were structurally characterized by single‐crystal X‐ray diffraction. In monomer 1 , the Mo–Mo bond length of 2.0874(6) Å is typical for dimolybdenum quadruple bonds. The solvate complex 2 was stabilized by weak π–π stacking interactions between the benzene molecule and the pentafluorophenyl ring (as indicated by a center‐to‐center distance of 3.838(10) Å and a center‐to‐plane distance of 3.712(4) Å between phenyl and pentafluorophenyl ring) and intermolecular C–H ··· F–C interactions (the shortest F ··· H distance is 2.560(2) Å). In complex 3 , a one‐dimensional chain was formed by C–H ··· F–C interactions between the hydrogen atoms in naphthalin and the fluorine atoms in the monomer (H ··· F distances of 2.582(2) Å). Information on the structures in solution of the three crystals was obtained by ¹H NMR spectroscopy.     

The Bond Order of C2 from a Strictly N‐Representable Natural Orbital Energy Functional Perspective

The bond order of the ground electronic state of the carbon dimer has been analyzed in the light of natural orbital functional theory calculations carried out with an approximate, albeit strictly N‐representable, energy functional. Three distinct solutions have been found from the Euler equations of the minimization of the energy functional with respect to the natural orbitals and their occupation numbers, which expand upon increasing values of the internuclear coordinate. In the close vicinity of the minimum energy region, two of the solutions compete around a discontinuity point. The former, corresponding to the absolute minimum energy, features two valence natural orbitals of each of the following symmetries, σ, σ*, π and π*, and has three bonding interactions and one antibonding interaction, which is very suggestive of a bond order large than two but smaller than three. The latter, features one σ–σ* linked pair of natural orbitals and three degenerate pseudo‐bonding like orbitals, paired each with one triply degenerate pseudo‐antibonding orbital, which points to a bond order larger than three. When correlation effects, other than Hartree–Fock for example, between the paired natural orbitals are accounted for, this second solution vanishes yielding a smooth continuous dissociation curve. Comparison of the vibrational energies and electron ionization energies, calculated on this curve, with their corresponding experimental marks, lend further support to a bond order for C ₂ intermediate between acetylene and ethylene.     

How the oxazole fragment influences the conformation of the tetraoxazocane ring in a cyclohexanespiro‐3′‐(1,2,4,5,7‐tetraoxazocane): single‐crystal X‐ray and theoretical study

Single crystals of (2S,5R)‐2‐isopropyl‐5‐methyl‐7‐(5‐methylisoxazol‐3‐yl)cyclohexanespiro‐3′‐(1,2,4,5,7‐tetraoxazocane), C₁₆H₂₆N₂O₅, have been studied via X‐ray diffraction. The tetraoxazocane ring adopts a boat–chair conformation in the crystalline state, which is due to intramolecular interactions. Conformational analysis of the tetraoxazocane fragment performed at the B3LYP/6‐31G(d,2p) level of theory showed that there are three minima on the potential energy surface, one of which corresponds to the conformation realized in the solid state, but not to a global minimum. Analysis of the geometry and the topological parameters of the electron density at the (3,?1) bond critical points (BCPs), and the charge transfer in the tetraoxazocane ring indicated that there are stereoelectronic effects in the O—C—O and N—C—O fragments. There is a two‐cross hyperconjugation in the N—C—O fragment between the lone electron pair of the N atom (lpN) and the antibonding orbital of a C—O bond (σ*_C—O) and vice versa between lpO and σ*_C—N. The oxazole substituent has a considerable effect on the geometry and the topological parameters of the electron density at the (3,?1) BCPs of the tetraoxazocane ring. The crystal structure is stabilized via intermolecular C—H…N and C—H…O hydrogen bonds, which is unambiguously confirmed with PIXEL calculations, a quantum theory of atoms in molecules (QTAIM) topological analysis of the electron density at the (3,?1) BCPs and a Hirshfeld analysis of the electrostatic potential. The molecules form zigzag chains in the crystal due to intermolecular C—H…N interactions being electrostatic in origin. The molecules are further stacked due to C—H…O hydrogen bonds. The dispersion component in the total stabilization energy of the crystal lattice is 68.09%.     

Ab initio and AIM studies on typical π‐type and pseudo‐π‐type halogen bonds: Comparison with hydrogen bonds

Series of typical π‐type and pseudo‐π‐type halogen‐bonded complexes B ··· ClY and B ··· BrY and hydrogen‐bonded complex B ··· HY (B = C₂H₄, C₂H₂, and C₃H₆; Y = F, Cl, and Br) have been investigated using the MP2/aug‐cc‐pVDZ method. A striking parallelism was found in the geometries, vibrational frequencies, binding energies, and topological properties between B ··· XY and B ··· HY (X = Cl and Br). It has been found that the lengths of the weak bond d(X ··· π)/d(H ··· π), the frequencies of the weak bond ν(X ··· π)/ν(H ··· π), the frequency shifts Δν(X? Y)/Δν(H? Y), the electron densities at the bond critical point of the weak bonds ρ_c(X ··· π)/ρ_c(H ··· π), and the electron density changes Δρ_c(X? Y)/Δρ_c(H? Y) could be used as measures of the strengths of typical π‐type and pseudo‐π‐type halogen/hydrogen bonds. The typical π‐type and pseudo‐π‐type halogen bond and hydrogen bond are noncovalent interactions. For the same Y, the halogen bond strengths are in the order B ··· ClY < B ··· BrY. For the same X, the halogen bond strength decreases according to the sequence F > Cl > Br that is in agreement with the hydrogen bond strengths B ··· HF > B ··· HCl > B ··· HBr. All of these typical π‐type and pseudo‐π‐type hydrogen‐bonded and halogen‐bonded complexes have the “conflict‐type” structure. Contour maps of the Laplacian of π electron density indicate that the formation of B ··· XY halogen‐bonded complex and B ··· HY hydrogen‐bonded complex is very similar. Charge transfer is observed from B to XY/HY and both the dipolar polarization and the volume of the halogen atom or hydrogen atom decrease on B ··· XY/B ··· HY complex formation. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Homonuclear chalcogen–chalcogen bond interactions in complexes pairing YO3 and YHX molecules (Y = S,Se; X = H,Cl, Br,CCH, NC,OH, OCH3): Influence of substitution and cooperativity

MP2/aug‐cc‐pVTZ calculations are performed on complexes of YO₃ (Y = S, Se) with a series of electron‐donating chalcogen bases YHX (X = H, Cl, Br, CCH, NC, OH, OCH₃). These complexes are formed through the interaction of a positive electrostatic potential region (π‐hole) on the YO₃ molecule with the negative region in YHX. Interaction energies of the binary O₃Y???YHX complexes are in the range of ?4.37 to ?12.09 kcal/mol. The quantum theory of atoms in molecules and the natural bond orbital analysis were applied to characterize the nature of interactions. It was found that the formation and stability of these binary complexes are ruled mainly by electrostatic effects, although the electron charge transfer from YHX to YO₃ unit also seems to play an important role. In addition, mutual influence between the Y???N and Y???Y interactions is studied in the ternary HCN???O₃Y???YHX complexes. The results indicate that the formation of a Y???N interaction tends to weaken Y???Y bond in the ternary systems. Although the Y???Y interaction is weaker than the Y???N one, however, both types of interactions seem to compete with each other in the HCN???O₃Y???YHX complexes. © 2016 Wiley Periodicals, Inc.     

Cooperative enhancement of water binding to antiparallel β‐sheet models: Analysis by ab initio calculations

The cooperative enhancement of water binding to the antiparallel β‐sheet models has been studied by quantum chemical calculations at the MP2/6‐311++G**//MP2/6‐31G* level. The binding energies of the two antiparallel β‐sheet models consisting of two strands of diglypeptide are calculated by supermolecular approach. Then water molecules are gradually bonded to the diglypeptide by N? H···OH₂ and C?O···HOH hydrogen bonds. Our calculation results indicated that the hydrogen bond length and the atom charge distribution are affected by the addition of H₂O molecules. The binding energy of antiparallel diglypeptide β‐sheet models has a great improvement by the increasing of the hydrogen bond cooperativity and the more H₂O molecules added the more cooperativity enhancement can be found. The orbital interactions are calculated by natural bond orbital analysis, and the results indicate that the cooperative enhancement is closely related to the orbital interaction. © 2012 Wiley Periodicals, Inc.