Do traditional, chlorine-shared, and ion-pair halogen bonds exist? An ab initio investigation of FCl:CNX complexes

Ab initio MP2/aug'-cc-pVTZ calculations have been carried out to determine the structures, binding energies, and bonding of complexes FCl:CNX, with X = CN, NC, NO(2), F, CF(3), Cl, Br, H, CCF, CCH, CH(3), SiH(3), Li, and Na. Equation-of-motion coupled cluster calculations have also been carried out to determine the coupling constants (1)J(F-Cl), (1X)J(Cl-C), and (2X)J(F-C) across these halogen bonds. As the strength of the base is systematically increased, the nature of the halogen bond changes from traditional, to chlorine-shared, to ion-pair. The type of halogen bond present in a complex can be readily determined from its structure, binding energy, AIM bonding analyses, and spin-spin coupling constants. Coupling constants across halogen bonds are compared with corresponding coupling constants across traditional, proton-shared, and ion-pair hydrogen bonds.     

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.     

The interaction strength of intermolecular systems formed by NaH⋯2(HF) and NaH⋯4(HF): Hydrogen bonds,dihydrogen bonds and halogen–hydride bonds

In this paper, a theoretical study of the molecular properties of NaH⋯2(HF) and NaH⋯4(HF) complexes is reported. Based on MP2/6-311++G(d,p) calculations, the dihydrogen bonds (H⋯H), hydrogen bonds (F⋯H) and halogen-hydride bonds (F⋯Na) of these intermolecular systems were fully characterized. The characterization involved the following procedures: the examination of structural parameters, analysis of vibration modes such as frequencies shifted to red or blue in the infrared spectrum, modeling of the electronic topology, quantification of the cooperative energy followed by charge transfer and, finally, natural bond orbital analysis. The results show short intermolecular distances with high electronic density, while the stretch frequencies of the proton donors and acceptors are unusually shifted, and some values reach 1000 cm⁻¹. When all subunits of the complexes are taken into account, in this case the NaH and HF molecules, the high value for the strength of the H⋯H dihydrogen bond in NaH⋯2(HF) suggests the formation of an additional subpart, i.e., the H₂ molecule.     

C-H⋯O, O-H⋯C, and C-H⋯C interactions in complexes of carbocations and carboanions

Molecular complexes formed by different forms of carbocations (carbenium ions) and carboanions with water, acetylene, and methane molecules have been calculated by the MP2/6-311++G(2df,2pd) method. In complexes with water where the carbon atom of the carbocation (carboanion) acts as the proton donor (acceptor), the energies of the C-H?O and O-H?C hydrogen bonds turn out to be approximately the same being 13–20 kcal/mol for carbocation (carboanion) species differing in the valence state of the carbon atom. Two types of C-H?C interactions have been revealed depending on the charge at the bridging hydrogen atom, which is determined by the hybridization of the donor carbon atom. The C-H?C interaction energy in molecular complexes with the positively charged hydrogen atom (carboanion complexes with acetylene) is an order of magnitude higher than in the complexes where the bridging hydrogen atom has an excess of electron density (carbocation complexes with methane). In all the complexes under consideration, the covalent C-H bond involved in interaction is elongated, and the negative charge is transferred from the acceptor to the donor.     

A smorgasbord of halogen bonds?

There is an urgent need to improve our charge–density modelling capabilities for heavy atoms. A recent article opens up new opportunities in the charge–density and crystal engineering fields and in the overlap region between these fields.     

The synergistic cooperation of NH⋯O and CH⋯O hydrogen bonds in the structures of three new phosphoric triamides

The supramolecular assemblies of three new phosphoric triamides, {(C₆H₅CH₂)(CH₃)N}₂(4-CH₃-C₆H₄C(O)NH)P(O) (1), {(C₆H₁₁)(CH₃)N}₂(4-CH₃-C₆H₄C(O)NH)P(O) (2) and {(C₂H₅)₂N}₂(4-CH₃-C₆H₄C(O)NH)P(O) (3) were studied by single crystal X-ray diffraction as well as by Hirshfeld surface analysis. It was found that a synergistic cooperation of NH?O and CH?O hydrogen bonds occurs in all three structures, but forming unique supramolecular architectures individually. Along with the presence of centrosymmetric dimers in 1, 2 and 3, based on a classical NH?O hydrogen bond, the presence of weak CH?O interactions play an additional and vital role in crystal architecture and construction of the final assemblies, collectively identified as a centrosymmetric dimer (0D), a 1-D array and a 3-D network, respectively. These differences in superstructures are related to the effect of aromatic, bulk and flexible groups used in the molecules designed, with a similar C(O)NHP(O) backbone. The NH?O contacts in 1, 2 and 3 are of the “resonance-assisted hydrogen bond” types and also the anti-cooperativity effect can be considered in the multi-acceptor sites P═O in 1 and 2 and C═O in 3. All three compounds were further studied by 1D NMR experiments, 2D NMR techniques (HMQC and HMBC (H–C correlation)), high resolution ESI–MS, EI–MS spectrometry and IR spectroscopy methods.     

Energies of OH⋯X− hydrogen bonds in the gas phase and proton affinities

The energies of hydrogen-bond formation (−ΔH⁰_HX) between hydroxy derivatives and halide ions in the gas phase obey the following relationship: −ΔH⁰_HX = 0 (ΔPA > 0)+32 e^{−0.0156&mid;ΔPA&mid;}, or −ΔH⁰_HX = −ΔPA (ΔPA < 0) + 32 e^{−0.0156∣ΔPA∣}, where ΔPA is the difference between the heterolytic dissociation energy of the -OH and HX bonds. This relation is discussed as a function of the different factors (electrostatic, repulsion, polarization and charge transfer) contributing to the protonation reaction or hydrogen-bond formation.     

Study of correlation effects on stretching force constants of the H3N⋯LiF lithium-bonded and H3N⋯HF hydrogen-bonded complexes

All quadratic, cubic and quartic force constants associated with high and low vibrational modes of the H₃N⋯HF hydrogen-bonded and H₃N⋯LiF lithium-bonded complexes have been calculated employing the Møller—Plesset perturbation theory to the second order (MP2) with the 4-31G** basis set.     

Hydrocarbons as proton donors in C–H⋯N and C–H⋯S hydrogen bonds

C–H?N and C–H?S hydrogen bonds were analyzed in complexes where acetylene, ethylene, methane and their derivatives are proton donors while ammonia and hydrogen sulfide are proton acceptors. Ab initio calculations were performed to analyze those interactions; MP2 method was applied and the following basis sets were used: 6-311++G(d,p), aug-cc-pVDZ and aug-cc-pVTZ. The results showed that hydrogen bonds for complexes with ammonia are systematically stronger than such interactions in complexes with hydrogen sulfide. If the fluorine substituted hydrocarbons are considered then F-substituents enhance the strength of hydrogen bonding. For a few complexes, mainly those where carbon atom in proton donating C–H bond possesses sp³ hybridization, the blue-shifting hydrogen bonds were detected. Additionally, Quantum Theory of ‘Atoms in Molecules’ and Natural Bond Orbitals method were applied to analyze H-bond interactions.     

Influence of OH⋯N and NH⋯O inter- and intramolecular hydrogen bonds in the conformational equilibrium of some 1,3-disubstituted cyclohexanes through NMR spectroscopy and theoretical calculations

The analysis of concentration effects in the (1)H NMR data of cis-3-aminocyclohexanol (ACOL) showed that its diequatorial conformer changes from 60% at 0.01 mol L(-1) to 70% at 0.40 mol L(-1) in acetone-d(6). A similar increase was also observed for the diequatorial conformer of cis-3-N-methylaminocyclohexanol (MCOL), from 32% (CDCl(3) 0.01 mol L(-1)) to 55% (CDCl(3) 0.40 mol L(-1)). The increase in solvent basicity leads to a large stabilization effect for the diequatorial conformer of both compounds too. For ACOL, it changes from 47% (ΔG(eqeq-axax)=0.06 kcal mol(-1)) in CCl(4) to 93% (ΔG(eqeq-axax)=-1.53 kcal mol(-1)) in DMSO, while for MCOL it goes from 7% (ΔG(eqeq-axax)=1.54 kcal mol(-1)) in CCl(4) to 82% (ΔG(eqeq-axax)=-0.88 kcal mol(-1)) in pyridine-d(6). These results indicate that the intramolecular hydrogen bonds (IAHB) OH?N and NH?O stabilize the diaxial conformers of these compounds in a non-polar solvent. For cis-3-amino-1-methoxycyclohexane (ACNE) and cis-3-N-methylamino-1-methoxy-cyclohexane (MCNE) no changes were observed in equilibrium with the variation of solvent polarity. These results indicate for the first time that the IAHB NH?O is not strong enough to stabilize the diaxial conformer of these compounds and that the conformation equilibria of the cis isomers of compounds ACOL and MCOL are influenced only by the IAHB OH?N. Moreover, the presence of a secondary amino group (93% of diaxial conformer in CCl(4)) leads to an IAHB OH?N stronger than in primary and tertiary amino-derivatives (53 and 54% of diaxial conformer, respectively) for 1,3-disubstituted cyclohexanes. Values obtained from the theoretical data through the B3LYP functional are in agreement with the experimental results and indicate that the IAHB strength that influences the conformational equilibrium of these compounds is the IAHB OH?N. Thus, the IAHB NH?O do not stabilize the diaxial conformer of the cis isomer of compounds ACNE and MCNE showing that the diequatorial conformer will always be more stable than the diaxial conformer, independent of concentration or solvent.     

Thermodynamic and aromaticity studies for the assessment of the halogen⋯cyano interactions on Iodobenzonitrile

The standard (p° = 0.1 MPa) molar enthalpies of formation, in the gaseous phase, of the 2-, 3- and 4-iodobenzonitrile isomers were derived from the combination of the corresponding standard molar enthalpies of formation, in the condensed phase, at T = 298.15 K, and the standard molar enthalpies of sublimation, at the same temperature, calculated respectively from the standard molar energies of combustion in oxygen, measured by rotating-bomb calorimetry, and from the vapour-pressure study of the referred compounds, measured by mass-loss Knudsen effusion technique. The strength of the halogen-halogen and the halogen-cyano intermolecular interactions, in the crystal, are evaluated by the enthalpies and entropies of phase transition of the iodobenzonitrile derived from mass-loss Knudsen technique and differential scanning calorimetry measurements and compared with those reported to fluorobenzonitrile and bromobenzonitrile isomers. The computational calculations complement the experimental work, using different aromaticity criteria (HOMA, NICS, Shannom Aromaticity, PDI and ATI) for the analysis of the electronic behaviour of each iodobenzonitrile isomer.     

Energetic effects between halogen bonds and anion-π or lone pair-π interactions: a theoretical study

Energetic effects between halogen bonds and anion-π or lone pair-π interactions have been investigated by means of ab initio MP2 calculations. 1,4-diiodo-perfluorobenzene, a very effective building block for crystal engineering based on halogen bonding, is selected in this work both as electron-deficient π aromatic ring and as halogen bond donor. Additive and diminutive effects are observed when halogen bonds and anion-π/lone pair-π interactions coexist in the same complex, which can be ascribed to the same direction of charge transfer for the two interactions. These effects have been analyzed in detail by the structural, energetic, and AIM properties of the complexes. Finally, experimental evidence of the combination of the interactions has been obtained from the Cambridge Structural Database.     

Construction of M–M bonds in late transition metal complexes

The 16-electron Co, Rh and Ir half-sandwich complexes of Cp^#M[E₂C₂(B₁₀H₁₀)] and Cp^#M(E₂S₂C₆H₄) (M = Co, Rh, Ir, Ru; E = S, Se) containing chelating 1,2-dicarba-closo-dodecaborane-1,2-dichalcogenolato ligands and benzenedithiolato ligands are promising precursors to build multimetallic clusters by reactions with low oxidation state late transition metal reagents. Such reactions lead to successful constructions of M–M bonds between iridium, rhodium, cobalt, ruthenium, and other late transition metals. Most of these complexes have been characterized by X-ray single crystal determinations and some have been studied by computational methods. Such theoretical studies reveal the covalent bonding nature of those multinuclear complexes. Some of these clusters have been found to have interesting nonlinear optical properties.     

Crystal and molecular structure analysis of flutamide. Bifurcated helicoidal C-H ⋯ O hydrogen bonds

Crystal structure determination and semiempirical AM1 and PM3 calculations were performed on flutamide {2-methyl-N[4 nitro-3-(trifluoromethyl) phenyl] propamide}, a powerful nonsteroidal androgen antagonist. The molecule is almost planar apart from CF₃, NO₂, and CH₃ groups. The NO₂ plane makes an angle of 36.3(4) with the least-square plane of the phenyl ring. The molecules are intermolecularly linked by one N-H O and one C-H O hydrogen bonds. A bifurcated helicoidal hydrogen bond network is formed by the intermolecular C-H O hydrogen bond together with another intramolecular C-H O hydrogen bond. The calculated structures are in good agreement with the crystallographic conformations. AM1 is more accurate for predicting the intramolecular C-H O hydrogen bond while PM3 gives a better geometry for the crowded nitro group. AM1 and PM3 charges of benzenic hydrogens are used to predict the propensity of these atoms to form hydrogen bonds. The noncentrosymmetric space group of the crystal (Pna2₁), the calculated dipole moment (8.88 D), and the calculated angle between molecular dipoles and the twofold axis (–49) close to the optimal value (54.7) indicate that flutamide might be a possible candidate for nonlinear optical material.     

Effect of molecular association and reactivity on substitution in chromium(III)–salprn complexes

A new chromium(III)–Schiff base complex, [Cr(5-chlorosalprn)(H₂O)₂]ClO₄, where salprn = N,N-propylenebis(salicylideneimine) has been prepared and characterized by electrospray ionization mass spectrometric (ESIMS) analysis and other spectroscopic techniques. Single crystal X-ray data reveal that the complex assumes a trans-diaquo structure, [Cr(C₁₇H₁₈Cl₂N₂O₄)]ClO₄ · H₂O. The effect of phenyl ring substituents on the rate of formation of [O=Cr^V Schiff base]⁺ has been investigated. The bimolecular rate constant for the formation of O=Cr^V species by the [Cr(Schiff base)(H₂O)₂]ClO₄, where the Schiff base = salprn, (1) and 5-chlorosalprn, (2) with PhOI was compared. In the case of (2) the rate was found to be faster by an order of magnitude at pH = 4 compared to (1). The introduction of a chloro-substituent on the phenyl ring not only influences the rate of redox reactivity but also the pKa values of aquo ligands of the complexes, indicating the difference in the electronic environment around the metal ion in both (1) and (2).     

Cocrystals assembled from iodoperfluorobenzene and flexible NTPO via halogen and π-hole bonds

Two binary cocrystals of 1,4-diiodotetrafluorobenzene (1,4-DITFB, C₆F₄I₂) and 1,3,5-trifluoro-2,4,6-triiodobenzene (1,3,5-TITFB, C₆F₃I₃) with the flexible 2-{[(naphthalen-2-yl)methyl]sulfanyl}pyridine 1-oxide (NTPO, C₁₆H₁₃NOS) molecule were successfully prepared and characterized by X-ray diffraction and quantum chemistry calculation methods. X-ray diffraction analysis reveals that the conformation of the flexible NTPO molecule has been changed significantly after introducing the 1,4-DITFB or 1,3,5-TITFB molecule into the NTPO lattice. Also the formation of the binary cocrystals is driven mainly by robust C—I…⁻O—N⁺ halogen bonds and π-hole…π-bond interactions, and they possess `sandwich' structural frameworks. Moreover, interaction energy analysis and AIM analysis were used to explore the contribution of different fragments to the structural stability and the corresponding electronic properties, which reveals that the robust halogen bonds with shorter bonding lengths [2.768 (4) and 2.789 (3) Å] are suggested to be covalent to a certain degree.     

Computationally rational design of metal-involving halogen bonds with π-covalency: Structures and bonding analysis

Traditional π-covalent interactions have been proved in the non-metal halogen bond adducts formed by chloride and halogenated triphenylamine-based radical cations. In this study, we have rationally designed two metal-involving halogen bond adducts with π-covalency property, such as [L1-Pd···I-PTZ]⁺ (i.e., 1) and [L2-Pd···I-PTZ]⁺ (i.e., 2), in which the square-planar palladium complexes serve as halogen bond acceptor and 3,7-diiodo-10H-phenothiazine radical cation (i.e., [I-PTZ]^•+) acts as halogen bond donor. Noncovalent interaction analysis and quantum theory of atoms in molecules analysis revealed that there are notable halogen bond interactions along the Pd···I direction without genuine chemical bond formed in both designed adducts. Energy decomposition analysis together with natural orbital for chemical valence calculations were performed to gain insight into their bonding nature, which demonstrated the presence of remarkable π-covalent interactions and σ-covalent interactions in both 1 and 2. We therefore proposed a new strategy for building the metal-involving halogen bonds with π-covalency property, which will help the further development of new types of halogen bonds.     

Strength of Si–H ⋯ B charge-inverted hydrogen bonds in 1-silacyclopent-2-enes and 1-silacyclohex-2-enes

It is shown that the H ? B contacts in 1-silacyclohex-2-enes are clearly stabilizing and strong, whereas those in 1-silacyclopent-2-enes are much weaker. This result is supported by analysis of QTAIM-based parameters and appropriate structural changes taking place upon the open form → closed form transformation and is in full agreement with previous NMR spectroscopic data [Wrackmeyer et al. (2006) Appl Organometal Chem 20:99–105]. Also, the influence of electronic and steric effects originating from the presence of specific substituents on the strength of the H ? B contacts is discussed in detail. Some problems and ideas associated with the use of the so-called open-closed method utilized in assessing values of interaction energies are discussed in detail. Particular attention is paid to the correct choice of reference open systems. It is shown that their partial geometry optimization leads to reliable values of interaction energies.     

Chemistry of Fischer-type rhenacyclobutadiene complexes. I. Deprotonation, addition/substitution of nucleophilic reagents at α-carbon, and insertion of heteroatoms into rhenium-carbon bonds

The rhenacyclobutadienes (CO)₄Re(η²- C(R)C(CO₂Me)C(OR^′)) (2) undergo a number of reactions that mirror those of Fischer alkoxycarbene complexes. Thus, (CO)₄Re(η²-C(Me)C(CO₂Me)C(OEt)) (2a) can be deprotonated by LDA, Na[OBu-t], or Na[CH(CO₂Me)₂] to give the ylide-like conjugate base [(CO)₄Re(η²-C(CH₂)C(CO₂Me)C(OEt)]⁻ (3), which was isolated as PPN(3). Li(3) undergoes deuteriation with DCl/D₂O and alkylation with Et₃OPF₆ at ReCCH₂, with the latter reaction affording (CO)₄Re(η²-C(CH₂Et)C(CO₂Me)C(OEt)) (4). Repetition of the sequence deprotonation-ethylation on 4 generates (CO)₄Re(η²-C(CHEt₂)C(CO₂Me)C(OEt)) (5). The nature of the alkoxy substituent in 2 can be varied by use of the rhenacyclobutenones Na[(CO)₄Re(η²-C(R)C(CO₂Me)C(O))] (Na(1)) in conjunction with AcCl and R^′OH to produce a series of new complexes (R=Ph, R^′=Et (2b); R=Me, R^′=CH₂CHCH₂ (2c), (CH₂)₃CCH (2d), Me (2e)). Aminolysis of 2a with the primary and secondary amines PhNH₂, HO(CH₂)₂NH, p-TolNH₂, and Et₂NH yields the aminorhenacyclobutadiene complexes (CO)₄Re(η²-C(Me)C(CO₂Me)C(NHR^′ or NR^′₂)) (R₂^′=Et₂ (6a); R^′=Ph (6b), (CH₂)₂OH (6c), p-Tol (6d)). These complexes display lesser carbene-like character than their alkoxy counterparts 2, as evidenced by ¹H and ¹³C NMR spectroscopic properties and lack of reactivity toward LDA by 6a. Reactions of each 2a and 6a with PPhMe₂ at low temperature afford (CO)₄Re(η²-C(Me)(PPhMe₂)C(CO₂Me)C(OEt)) (7) and (CO)₃(PPhMe₂)Re(η²-C(Me)C(CO₂Me)C(NEt₂)) (9), respectively, further in agreement with the more carbenoid nature of 2a than 6a. 7 undergoes conversion to (CO)₃(PPhMe₂)Re(η²-C(Me)C(CO₂Me)C(OEt)) (8) upon heating. 2a reacts with each of (NH₄)₂[Ce(NO₃)₆], DMSO, EtNO₂/Et₃N, and Me₃NO under various conditions to afford one or both of the oxygen atom insertion products into the ReC bonds, (CO)₄Re(κ²-OC(Me)C(CO₂Me)C(OEt)) (10) and (CO)₄Re(κ²-C(Me)C(CO₂Me)C(OEt)O) (11). In contrast, no reaction occurred between 2a and S₈ on heating. However, 6a was converted to the NH insertion product (CO)₄Re(κ²-NHC(Me)C(CO₂Me)C(NEt₂)) (12) by the action of H₂NNH₂ · H₂O at 0 °C. All new compounds were characterized by a combination of elemental analysis, mass spectrometry, and IR and NMR spectroscopy.