Theoretical investigation of the mechanism for the reductive dehalogenation of methyl halides mediated by the Co<Superscript>I</Superscript>-based compounds cobalamin and cobaloxime

Theoretical calculations focusing on the cleavage of the C–X bond in methyl halides (CH₃X; X?=?Cl, Br, I) as mediated by Co^I-based systems have been carried out using the hybrid functional ωB97-XD together with the basis set 6–311++G(2d,2p). A total of seven Co^I-based compounds were evaluated: cob[I]alamin (Co^ICbl) in its base-on form and cobaloxime (Co^ICbx) with either no ligand or different ligands (either pyridine (PYR), tributylphosphine (TBP), dimethyl sulfide (DMS), cyclohexylisocyanide (CI), or 5,6-dimethylbenzimidazole (DMB)) at the lower axial position. For the large Co^ICbl system, an ONIOM scheme was employed, where the high layer was described at the DFT level and the low layer was computed using the semi-empirical method PM6. A full DFT model was employed for the Co^ICbx cases. An S_N2-like mechanism was evaluated in all cases. The intrinsic reaction coordinate profiles suggested early transition states with activation energies of ≈ 12 kcal/mol, ≈ 10 kcal/mol, and ≈ 5 kcal/mol for C–Cl, C–Br, and C–I cleavage, respectively, which is consistent with the leaving group abilities of these halides. The evolutions of the atomic charges in and the bond orders of Co–C and C–X were computed, and the results confirmed the existence of early transition states (δB_av≈ 40%), where the polarization C^δ+–X^δ? (%E_v?≈?43%) is the determining factor in the reaction process. Finally, a comparison of all the determined parameters showed that the reaction in the DMB–Co^ICbx system resembles the process that occurs in the larger Co^ICbl, suggesting that the former system could be a reliable model for the study of reductive dehalogenation mediated by vitamin B₁₂, which is key to the anaerobic microbiological treatment of halocarbon contaminants.     

Theoretical study of the effects of substituents (F,Cl, Br,CH<Subscript>3</Subscript>, and CN) on the aromaticity of borazine

This paper presents a theoretical study of the effects of substituents (F, Cl, Br, CH₃, and CN) on the aromaticity of borazine (B₃N₃H₆), using density functional theory (DFT) and the Hartree-Fock (HF) method. The calculations to optimize the geometries, structural properties, and vibrational frequencies were performed using the same 6–311G(d,p) and 6–311++G(d,p) basis sets, comparing the methods with experimental results. In the analysis of the NICS_ZZ values, it was found that that replacing the hydrogen atoms by halogen atoms (F, Cl, and Br) and CH₃ reduced the aromaticity of the borazine molecule, while use of the CN group resulted in NICS_ZZ values (0.9–2.0 Å) very close to those of borazine, presenting the following order of increasing aromaticity: B₃N₃H₃-(Br)₃?<?B₃N₃H₃-(Cl)₃?<?B₃N₃H₃-(F)₃?<?B₃N₃H₃-(CH₃)₃?<?B₃N₃H₆ ~ B₃N₃H₃-(CN)₃. All the spectra of the compounds showed only the presence of transition peaks distant from the UV region, reflecting the large energy difference between the HOMO and LUMO orbitals. After the substitution of the borazine ring, all the compounds presented an intensification of the spectrum, with a shift of the maximum absorbance toward red, indicative of a bathochromic effect. There was a direct inverse relation between the energy gap and the maximum wavelength of the compounds.     

Exohedral and endohedral adsorption of alkaline earth cations in BN nanocluster

Adsorption of three alkaline earth cations inside and outside of a B₁₂N₁₂ nano-cage in aqueous medium was investigated using density functional theory. The results obtained are discussed in terms of thermodynamic, geometric, and electronic properties. Based on the calculation of enthalpy changes at 298 K and 1 atm, the adsorption of the considered cations was found to be exothermic outside the cluster while it is endothermic inside. It was also found that the exohedral adsorption favorability of the cluster increases in the series: Ca²⁺?<?Mg²⁺?<<?Be²⁺ with Gibbs free energy changes in the range of ?0.08 to ?1.53 eV at B3LYP/6-31G (d) level of theory. Overall, interaction of the cations with the cluster influences the electronic properties of the cluster through stabilizing the HOMO and LUMO as well as reducing the energy gap between them. However, the electronic properties changed much more in the case of endohedral adsorption in comparison with the exohedral adsorption.     

Theoretical study on cooperative effects between X⋯N and X⋯Carbene halogen bonds (X = F,Cl,Br and I)

Quantum chemical calculations are performed to study the interplay between halogen?nitrogen and halogen?carbene interactions in NCX?NCX?CH₂ complexes, where X?=?F, Cl, Br and I. Molecular geometries and interaction energies of dyads and triads are investigated at the MP2/aug-cc-pVTZ level of theory. It is found that the X?N and X?C_carbene interaction energies in the triads are larger than those in the dyads, indicating that both the halogen bonding interactions are enhanced. The estimated values of cooperative energy E _coop are all negative with much larger E _coop in absolute value for the systems including iodine. The nature of halogen bond interactions of the complexes is analyzed using parameters derived from the quantum theory atoms in molecules methodology and energy decomposition analysis.

Electronic, magnetic and optical properties of Cu, Ag, Au-doped Si clusters

The structural, optical and magnetic properties of Cu, Ag, Au-doped Si₇ Clusters have been systematically investigated using density functional theory calculations. The global optimized structures of Cu, Ag, Au-doped Si clusters are predicted to have a lower HOMO–LUMO gap and higher magnetic moment. M-doping (M?=?Cu, Ag, Au) in Si cluster widens a range of adsorption wavelength, especially Au-doping. The characteristics in electronic density of states (DOSs) show that C_5v-Si₆Cu has a big asymmetrical spin-up and spin-down. The average atomic moment is 0.428 mμ_B per atom for the Si₆Cu cluster with C_5v symmetry, while the average paramagnetic moment is 0.143 mμ_B per atom for other M-doped (M?=?Cu, Ag, Au) Si₇ clusters.     

Insights into the strength and nature of carbene···halogen bond interactions: a theoretical perspective

Halogen-bonding, a noncovalent interaction between a halogen atom X in one molecule and a negative site in another, plays critical roles in fields as diverse as molecular biology, drug design and material engineering. In this work, we have examined the strength and origin of halogen bonds between carbene CH₂ and XCCY molecules, where X?=?Cl, Br, I, and Y?=?H, F, COF, COOH, CF₃, NO₂, CN, NH₂, CH₃, OH. These calculations have been carried out using M06-2X, MP2 and CCSD(T) methods, through analyses of surface electrostatic potentials V _S(r) and intermolecular interaction energies. Not surprisingly, the strength of the halogen bonds in the CH₂···XCCY complexes depend on the polarizability of the halogen X and the electron-withdrawing power of the Y group. It is revealed that for a given carbene···X interaction, the electrostatic term is slightly larger (i.e., more negative) than the dispersion term. Comparing the data for the chlorine, bromine and iodine substituted CH₂···XCCY systems, it can be seen that both the polarization and dispersion components of the interaction energy increase with increasing halogen size. One can see that increasing the size and positive nature of a halogen’s σ-hole markedly enhances the electrostatic contribution of the halogen-bonding interaction.

Effect of superalkali substituents on the strengths and properties of hydrogen and halogen bonds

Quantum chemical calculations have been performed for the complexes Li₃OCCX–Y (X?=?Cl, Br, H; Y?=?NH₃, H₂O, H₂S) and Li₃OCN–X′Y′ (X′Y′?=?ClF, BrCl, BrF, HF) to study the role of superalkalis in hydrogen and halogen bonds. The results show that the presence of an Li₃O cluster in a Lewis acid weakens its acidity, while its presence in a Lewis base enhances its basicity. Furthermore, the latter effect is more prominent than the former one, and the presence of an Na₃O cluster causes an even greater effect than Li₃O. The strengths of hydrogen and halogen bonds were analyzed using molecular electrostatic potentials. The contributions of superalkalis to the strength of hydrogen and halogen bonds were elucidated by analyzing differences in electron density.     

A new reaction mode of germanium-silicon bond formation: insertion reactions of H2GeLiF with SiH3X (X = F, Cl, Br)

A combined density functional and ab initio quantum chemical study of the insertion reactions of the germylenoid H₂GeLiF with SiH₃X (X?=?F, Cl, Br) was carried out. The geometries of all the stationary points of the reactions were optimized using the DFT B3LYP method and then the QCISD method was used to calculate the single-point energies. The theoretical calculations indicated that along the potential energy surface, there were one precursor complex (Q), one transition state (TS), and one intermediate (IM) which connected the reactants and the products. The calculated barrier heights relative to the respective precursors are 102.26 (X?=?F), 95.28 (X?=?Cl), and 84.42 (X?=?Br) kJ mol^-1 for the three different insertion reactions, respectively, indicating the insertion reactions should occur easily according to the following order: SiH₃-Br?>?SiH₃-Cl?>?SiH₃-F under the same situation. The solvent effects on the insertion reactions were also calculated and it was found that the larger the dielectric constant, the easier the insertion reactions. The elucidations of the mechanism of these insertion reactions provided a new reaction model of germanium-silicon bond formation.     

Enhancing the hydrogen bond between the bridged hydrogen atom of diborane and ammonia

The character of the bridged hydrogen atom (H_b) of B₂H₆ has become a hot issue in recent years. In this work, the complexes B₂H₆?·?·?·?NH₃, B₂H₂X₄?·?·?·?nNH₃ (n?=?1, 2) and 2HF?·?·?·?B₂H₂X₄?·?·?·?2NH₃ (X?=?Cl, Br, I) were constructed and studied based on the M06-2X calculations to investigate how to enhance the H_b?·?·?·?N hydrogen-bonded interaction. When the terminal hydrogen atoms (H_t) of B₂H₆ were replaced by X (X?=?Cl, Br, I) atoms, the H_b?·?·?·?N hydrogen bond were strengthened. According to the electrostatic potentials in B₂H₂X₄, two HF molecules were added to the interspace of the B-H-B-H four-membered ring of the B₂H₂X₄?·?·?·?2NH₃ complexes, and H?·?·?·?X hydrogen bond formed, resulting in further enhancing effect of H_b?·?·?·?N hydrogen bond. As a result, the positive cooperative effect of H_b?·?·?·?N hydrogen bond and H?·?·?·?X hydrogen bond do enhance the interactions of each other. The two measures not only enhance the strength of H_b?·?·?·?N hydrogen bond, but also achieve the goal to make the H_b?·?·?·?N hydrogen bond perpendicular to B?·?·?·?B direction.

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Graphical Abstract Enhancing the hydrogen bond between the bridged hydrogen atom of diborane and ammonia?

     

The competition of C-X⋯O=P halogen bond and π-hole⋯O=P bond between halopentafluorobenzenes C6F5X (X=F, Cl, Br, I) and triethylphosphine oxide

Calculation predicted the interacting forms of halopentafluorobenzene C₆F₅X (X=F, Cl, Br, I) with triethylphosphine oxide which is biologically interested and easily detected by ³¹P NMR. The interaction energy and geometric parameters of resultant halogen or π-hole bonding complexes were estimated and compared. Moreover, the bonding constants were determined by ³¹P NMR. Both theory and experiments indicated the C₆F₆ and C₆F₅Cl interact with triethylphosphine oxide by π-hole bonding pattern, while C₆F₅I by halogen/σ-hole bonding form. For C₆F₅Br, two interactions are comparative and should coexist competitively. The calculated interaction energies of σ-hole bonding complexes, ?5.07 kcal mol^?1 for C₆F₅Br?O=P and ?8.25 kcal mol^?1 for C₆F₅I?O=P, and π-hole bonding complexes, ?7.29 kcal mol^?1 for C₆F₆?O=P and ?7.24 kcal mol^?1 for C₆F₅Cl?O=P, are consistent with the changing tendency of bonding constants measured by ³¹P NMR, 4.37, 19.7, 2.42 and 2.23 M^?1, respectively.

Carbon nanotube functionalization with carboxylic derivatives: a DFT study

Chemical functionalization of a single-walled carbon nanotube (CNT) with different carboxylic derivatives including –COOX (X?=?H, CH₃, CH₂NH₂, CH₃Ph, CH₂NO₂, and CH₂CN) has been theoretically investigated in terms of geometric, energetic, and electronic properties. Reaction energies have been calculated to be in the range of ?0.23 to ?7.07 eV. The results reveal that the reaction energy is increased by increasing the electron withdrawing character of the functional groups so that the relative magnitude order is ?CH₂NO₂?>?CH₂CN?>?H?>?CH₂Ph?>?CH₃?>?CH₂NH₂. The chemical functionalization leads to an increase in HOMO/LUMO energy gap of CNT by about 0.32 to 0.35 eV (except for ?H). LUMO, HOMO, and Fermi level of the CNT are shifted to lower energies especially in the case of ?CH₂NO₂ and _?CH₂CN functional groups. Therefore, it leads to an increment in work function of the tube, impeding the field electron emission.     

Quantum chemical topological analysis of hydrogen bonding in HX…HX and CH3X…HX dimers (X = Br,Cl, F)

We present a systematic investigation of the nature and strength of the hydrogen bonding in HX···HX and CH₃X…HX (X = Br, Cl and F) dimers using ab initio MP2/aug-cc-pVTZ calculations in the framework of the quantum theory of atoms in molecules (QTAIM) and electron localisation functions (ELFs) methods. The electron density of the complexes has been characterised, and the hydrogen bonding energy, as well as the QTAIM and ELF parameters, is consistent, providing deep insight into the origin of the hydrogen bonding in these complexes. It was found that in both linear and angular HX…HX and CH₃X…HX dimers, F atoms form stronger HB than Br and Cl, but they need short (～2 Å) X…HX contacts.     

Enhancement in anti-tubercular activity of indole based thiosemicarbazones on complexation with copper(I) and silver(I) halides: Structure elucidation,evaluation and molecular modelling

A series of monomeric tetrahedral complexes of stoichiometry, [MX(HL)(Ph₃P)₂] (In case of M = Cu, H¹L, X = I, 1; Br, 2; Cl, 3; H³L, X = I, 4; Br, 5; Cl, 6; H⁴L, X = I, 7; Br, 8; Cl, 9 and in case of M = Ag, H¹L, X = Cl, 13; Br, 14; H²L, X = Cl, 15, Br 16; H³L, X = Cl, 17, Br, 18) were synthesized by the reaction of copper (I) or silver (I) halides with indole-3-thiosemicarbazone (H¹L) or 5-methoxy indole-3-thiosemicarbazone (H²L) or 5-methoxy indole-N¹-methyl-3-thiosemicarbazone (H³L), whereas dimers of stoichiometry, [Cu₂(μ-X)₂(η¹-S-H²L)₂(Ph₃P)₂] (X = I, 10; Br, 11; Cl, 12) were obtained by the reaction of copper (I) halides with indole-N¹-methyl-3-thiosemicarbazone (HIntsc-N¹-Me, H²L). The synthesized complexes were characterized using NMR (¹H and ¹³C) and single crystal X-ray diffraction (H²L, 3, 7, 8, 10, 11 and 13) as well as elemental analysis. Anti- M. tuberculosis activity of ligands (H¹L-H⁴L) and their metal complexes (1–18) were evaluated against M. tuberculosis H37RV strain ATCC 27294. It has been observed that there is unusual enhancement in anti TB activity of these ligands on complexation with copper (I) and silver (I). Molecular modelling studies in the active binding site are also giving complementary theoretical support for the experimental biological data acquired.     

The structures of solvated methylmercury(II) chlolade,bromide and iodide in pyridine solution; Implications for aqueous solution

The structures of solvated methylmercury(II) halides in pyridine solution were determined by a large angle X-ray scattering technique. Near-linear CH₃HgX (X = Cl, Br and I) species solvated by two weakly-coordinated pyridine molecules are indirectly interpreted. Additional mercury-pyridine interactions, through van der Waals forces, are found at the sum of the van der Waals radii. The HgX bond distances in the methylmercury(II) halides are found to be 2.325(8), 2.480(3) and 2.649(3) Å for chloride, bromide and iodide, respectively. The HgC bond distances are assumed to be ∼2.08 Å. This interaction is indicated in the radial distribution functions. The bond distance between mercury and the two solvating pyridine molecules is ∼2.8 Å, e.g., 2.84(2) Å in methylmercury(II) bromide. The additional mercury interactions with roughly two pyridine molecules at the sum of van der Waals radii are revealed at around 3.15 Å. Comparison between Raman stretching vibrations and the solvated structures of methylmercury(II) complexes found in various solvents indicates a lower limit in solvent donor property for the formation of solvate bonds to mercury for the methylmercury(II) halides.     

Synthesis and characterisation of the halogenated azanonaboranes [(PrNH2)B8H10XNHPr] (X=Cl, Br, I) and their unexpected hydrolysis to hypho-[B5H10(μ-NHPr)]

Treatment of [(ⁱPrNH₂)B₈H₁₁NHⁱPr] with elemental halogen affords the 8-exo-halogen-substituted derivatives [(ⁱPrNH₂)B₈H₁₀XNHⁱPr] (X=Cl, Br, I). The structures of all three compounds are confirmed by NMR spectroscopy and mass spectrometry, and (for X=Br) by an X-ray diffraction study. The bromoazanonaborane undergoes hydrolytic decomposition to the new five-vertex compound [B₅H₁₀(μ-NHⁱPr)] of hypho-type structure.     

Theoretical study on the substitution reactions of the germylenoid H<Subscript>2</Subscript>GeLiF with SiH<Subscript>3</Subscript>X (X = F,Cl, Br)

The substitution reactions of H₂GeLiF (G) with SiH₃X (X = F, Cl, Br) were investigated using calculations performed at the QCISD/6-311++G (d, p)//B3LYP/6-311+G (d, p) level of theory. The results led to the following conclusions. (i) The substitutions are nucleophilic reactions. There are two substitution paths, I and II, which both lead to the germane H₂GeFSiH₃. The enantiomers of this germane are obtained via these two paths if an H in SiH₃X is replaced with a different group or atom. (ii) Both substitution pathways show the same order of barrier heights (SiH₃F > SiH₃Cl > SiH₃Br). The difference between the bond energies of Li–X and Si–X may explain the precedence among the substitution reactions of G with SiH₃X. Path I has a lower activation barrier than path II, indicating that path I is more favorable. (iii) Comparison between the relevant insertion and substitution reactions shows that substitutions are more favorable and that the substitution product H₂GeFSiH₃ predominates over the insertion product. (iv) The substitution reactions of H₂GeLiF with SiH₃X are exothermic.     

A new interaction mechanism of LiNH2 with MgH2: magnesium bond

Quantum chemical calculations were performed for LiNH₂–HMgX (X?=?H, F, Cl, Br, CH₃, OH, and NH₂) complexes to propose a new interaction mechanism between them. This theoretical survey showed that the complexes are stabilized through the combinative interaction of magnesium and lithium bonds. The binding energies are in the range of 63.2–66.5 kcal mol^?1, i.e., much larger than that of the lithium bond. Upon complexation, both Mg–H and Li–N bonds are lengthened. Substituents increase Mg-H bond elongation and at the same time decrease Li-N bond elongation. These cyclic complexes were characterized with the presence of a ring critical point and natural population analysis charges.

Synthesis and structural characterization of (pseudo)-halo adducts of (η-1,5-cyclooctadiene)(1,3-dimethylimidazolin-2-ylidine)rhodium

A series of compounds [(COD)(Me₂Im)RhX] (Me₂Im=1,3-dimethylimidazolin-2-ylidine, X=Cl, Br, I, N₃, NCO, SCN, SeCN) have been prepared and examined using X-ray diffraction and NMR spectroscopy. The synthesis and structure of [(COD)(Me₂Bm)RhCl] (Me₂Bm=1,3-dimethylbenzimidazolin-2-ylidine) are also reported.     

Addition compounds of bis(trifluoromethyl)mercury with tetraphenylphosphonium and tetraphenylarsonium halides and thiocyanates

Addition compounds of Hg(CF₃)₂ with [Ph₄P]X and [Ph₄As]X in the 1:1 ratio for X = Cl, Br, I as well as in the 1:2 ratio for X = SCN, were isolated from aquaeous solution and identified by elemental analysis and infrared spectroscopy. Molar conductance of the thiocyanate compounds in nitrobenzene solution points to its complex-salt nature defined as [Ph₄P]₂[Hg(CF₃)₂(SCN)₂] and [Ph₄As]₂[Hg(CF₃)₂-(SCN)₂], but not for the halide compounds. However, in the monoclinic crystals of the chloride ccompound, as shown by X-ray diffractometry, pairs of [Hg(CF₃)₂ molecules are bridged over by two chlorides in a centro-symmetrical dimer with the CHgC bond angle of 160.5(8)° and the Hg…Cl bond length of 2.823(3) and 2.837(4) Å. The structure was refined to the R factor of 0.053. When X = CN no addition compounds were obtained, the reaction products were HCF₃ and the complex salts [Ph₄P]₂- [Hg(CN)]₄ and [Ph₄As]₂[Hg(CN)]₄, not described so far.     

Theoretical studies on identity SN2 reactions of lithium halide and methyl halide: A microhydration model

Reactions of lithium halide (LiX, X = F, Cl, Br and I) and methyl halide (CH₃X, X = F, Cl, Br and I) have been investigated at the B3LYP/6-31G(d) level of theory using the microhydration model. Beginning with hydrated lithium ion, four or two water molecules have been conveniently introduced to these aqueous-phase halogen-exchange S_N2 reactions. These water molecules coordinated with the center metal lithium ion, and also interacted with entering and leaving halogen anion via hydrogen bond in complexes and transition state, which to some extent compensated hydration of halogen anion. At 298 K the reaction profiles all involve central barriers ΔE _cent which are found to decrease in the order F > Cl > Br > I. The same trend is also found for the overall barriers (ΔE _ovr ) of the title reaction. In the S_N2 reaction of sodium iodide and methyl iodide, the activation energy agrees well with the aqueous conductometric investigation.