Enhancement of the Tetrel Bond by the Effects of Substituents,Cooperativity, and Electric Field: Transition from Noncovalent to Covalent Bond

The T⋅⋅⋅N tetrel bond (TB) formed between TX₃OH (T=C, Si, Ge; X=H, F) and the Lewis base N≡CM (M=H, Li, Na) is studied by ab initio calculations at the MP2/aug-cc-pVTZ level. Complexes involving TH₃OH contain a conventional TB with interaction energy less than 10 kcal/mol. This bond is substantially strengthened, approaching 35 kcal/mol and covalent character, when fluorosubstituted TF₃OH is combined with NCLi or NCNa. Along with this enhanced binding comes a near equalization of the TB T⋅⋅⋅N and the internal T−O bond lengths, and the associated structure acquires a trigonal bipyramidal shape, despite a high internal deformation energy. This structural transformation becomes more complete, and the TB is further strengthened upon adding an electron acceptor BeCl₂ to the Lewis acid and a base to the NCM unit. This same TB strengthening can be accomplished also by imposition of an external electric field.     

Competition between Inter and Intramolecular Tetrel Bonds: Theoretical Studies Complemented by CSD Survey

Crystal structures document the ability of a TF₃ group (T=Si, Ge, Sn, Pb) situated on a naphthalene system to engage in an intramolecular tetrel bond (TB) with an amino group on the adjoining ring. Ab initio calculations evaluate the strength of this bond and evaluate whether it can influence the ability of the T atom to engage in a second, intermolecular TB with another nucleophile. A very strong CN⁻ anionic base can approach the T either along the extension of a T−C or T−F bond and form a strong TB with an interaction energy approaching 100 kcal/mol, although this bond is weakened a bit by the presence of the internal T⋅⋅⋅N bond. The much less potent NCH base engages in a correspondingly longer and weaker TB, less than 10 kcal/mol. Such an intermolecular TB is weakened by the presence of the internal TB, to the point that it only occurs for the two heavier tetrel atoms Sn and Pb.     

N-Hydroxyurea dimers: A matrix isolation and theoretical study

The dimerization of N-hydroxyurea (NH₂CONHOH) has been investigated by FTIR matrix isolation spectroscopy and DFT(B3LYP)/6-311++G(2d,2p) calculations. The analysis of NH₂CONHOH/Ar matrix spectra and comparison with theoretical ones reveal the formation of two types of dimers with a strong OH⋯O hydrogen bond. There is an additional weak interaction between the oxygen atom of the OH group of the proton donor molecule and the NH or NH₂ group of the proton acceptor in both dimers, respectively. The identified structures correspond to local minima on the PES. The formation of the less stable structures not the most stable ones indicates that the creation of N-hydroxyurea dimers is related to the dipole-dipole interaction at the initial stage of the dimerization process, which favours generation of polar dimers.     

Molecular orbital studies of the NMR hydrogen bond shift

Magnetic shielding constants are calculated for the protons in XOH and XOH…OH₂ (XH, CH₃, NH₂, OH and F) molecules using a slightly extended set of atomic functions modified by gauge factors. These results are used to determine theoretical values for the NMR hydrogen bond shifts in the XOH…OH₂ systems. Such theoretical data are consistent with the few available experimental data. An analysis of the theoretical results reveals that there are three major types of shielding contribution to the NMR hydrogen bond shift; (a) a deshielding change due to the variation of the local currents on the hydrogen bonded proton; (b) a reduction in shielding from currents localized on the oxygen atom of the proton donor; (c) a deshielding contribution from currents induced on the oxygen atom of the proton acceptor. Except for the water dimer, contributions (a), (b) and (c) are of comparable importance for changes in isotropic shielding. For (H₂O)₂ contributions (a) and (c) are somewhat more important than contribution (b). Contribution (c) is almost totally responsible for the changes in the anistropies of the shielding tensors associated with the hydrogen bonded protons. The proton shielding anisotropy changes which occur on hydrogen bond formation are generally much larger than the corresponding variations in the isotropic values of the shielding tensors. This suggests that proton magnetic shielding anisotropies may be more sensitive measures of features of hydrogen bonding than are isotropic proton shielding constants.     

Theoretical study on the gas phase reaction of propargyl alcohol with hydroxyl radical

The reaction of propargyl alcohol with hydroxyl radical has been studied extensively at CCSD(T)/aug‐cc‐pVTZ//MP2/cc‐pVTZ level. This is the first time to gain a conclusive insight into the reaction mechanism and kinetics for this important reaction in detail. Two reaction mechanisms were revealed, namely addition/elimination and hydrogen abstraction mechanism. The reaction mechanism confirms that OH addition to C?C triple bond forms the chemically activated adducts, IM1 (·CHCOHCH₂OH) and IM2 (CHOH·CCH₂OH), and the hydrogen abstraction pathways (? CH₂OH bonded to the carbon atom and alcohol hydrogen) may occur via low barriers. Harmonic model of Rice–Ramsperger–Kassel–Marcus theory and variational transition state theory are used to calculate the overall and individual rate constants over a wide range of temperatures and pressures. The calculated rate constants are in good agreement with the experimental data. At atmospheric pressure with Ar as bath gas, IM1 (·CHCOHCH₂OH) and IM2 (CHOH·CCH₂OH) formed by collisional stabilization are dominant in the low temperature range. The production of CHCCHOH + H₂O via hydrogen abstraction becomes dominate at higher temperature. The fraction of IM3 (CH₂COHCH₂·O) is very significant over the moderate temperature range. © 2014 Wiley Periodicals, Inc.     

Hexacoordinated Tetrel-Bonded Complexes between TF4 (T=Si,Ge, Sn,Pb) and NCH: Competition between σ- and π-Holes

In order to accommodate the approach of two NCH bases, a tetrahedral TF₄ molecule (T=Si, Ge, Sn, Pb) distorts into an octahedral structure in which the two bases can be situated either cis or trans to one another. The square planar geometry of TF₄, associated with the trans arrangement of the bases, is higher in energy than its see-saw structure that corresponds to the cis trimer. On the other hand, the square geometry offers an unobstructed path of the bases to the π-holes above and below the tetrel atom and hence enjoys a higher interaction energy than is the case for the σ-holes approached by the bases in the cis arrangement. When these two effects are combined, the total binding energies are more exothermic for the cis than for the trans complexes. This preference amounts to some 3 kcal mol⁻¹ for Sn and Pb, but is amplified for the smaller tetrel atoms.     

Group 12 Carbonates and their Binary Complexes with Nitrogen Bases and FH2Z Molecules (Z=P,As, Sb): Synergism in Forming Ternary Complexes

MCO₃ (M=Zn, Cd, Hg) forms a spodium bond with nitrogen-containing bases (HCN, NHCH₂, NH₃) and a pnicogen bond with FH₂Z (Z=P, As, Sb). The spodium bond is very strong with the interaction energy ranging from −31 kcal/mol to −56 kcal/mol. Both NHCH₂ and NH₃ have an equal electrostatic potential on the N atom, but the corresponding interaction energy is differentiated by 1.5–4 kcal/mol due to the existence of spodium and hydrogen bonds in the complex with NHCH₂ as the electron donor. The spodium bond is weakest in the HCN complex, which is not consistent with the change of the binding distance. The spodium bond becomes stronger in the CdCO₃<ZnCO₃<HgCO₃ sequence although the positive electrostatic potential on the Hg atom is smallest. This is because the electrostatic interaction is dominant in the spodium-bonded complexes of CdCO₃ and ZnCO₃ but the polarization interaction in that of HgCO₃. The pnicogen bond is much weaker than the spodium bond and the former has a larger enhancement than the latter in the FH₂Z⋅⋅⋅OCO₂M⋅⋅⋅N-base ternary complexes.     

Chalcogen Bond Involving Zinc(II)/Cadmium(II) Carbonate and Its Enhancement by Spodium Bond

Carbonate MCO₃ (M = Zn, Cd) can act as both Lewis acid and base to engage in a spodium bond with nitrogen-containing bases (HCN, NHCH₂, and NH₃) and a chalcogen bond with SeHX (X = F, Cl, OH, OCH₃, NH₂, and NHCH₃), respectively. There is also a weak hydrogen bond in the chalcogen-bonded dyads. Both chalcogen and hydrogen bonds become stronger in the order of F > Cl > OH > OCH₃ > NH₂ > NHCH₃. The chalcogen-bonded dyads are stabilized by a combination of electrostatic and charge transfer interactions. The interaction energy of chalcogen-bonded dyad is less than −10 kcal/mol at most cases. Furthermore, the chalcogen bond can be strengthened through coexistence with a spodium bond in N-base-MCO₃-SeHX. The enhancement of chalcogen bond is primarily attributed to the charge transfer interaction. Additionally, the spodium bond is also enhanced by the chalcogen bond although the corresponding enhancing effect is small.     

Basis set and correlation effects on computed proton affinities of some oxygen and nitrogen bases

Basis set expansion and correlation effects on the computed proton affinities of the oxygen and nitrogen bases CH₃OH, H₂CO, CO, CH₃NH₂, CH₂NH, and HCN have been evaluated. Basis set enhancements lead to systematic changes in computed proton affinities. These effects appear to be additive, and are greater for correlated proton affinities than for Hartree-Fock energies. Inclusion of correlation decreases proton affinities, with fourth-order Møller-Plesset energies bracketed by second and third order energies.     

Investigation of substituent effects in aerogen‐bonding interaction between ZO3 (Z=Kr,Xe) and nitrogen bases

The substituent effects in aerogen bond interactions between ZO₃ (Z = Kr, Xe) and different nitrogen bases are studied at the MP2/aug‐cc‐pVTZ level of theory. The nitrogen bases include the sp bases NCH, NCF, NCCl, NCBr, NCCN, NCOH, NCCH₃ and the sp³ bases NH₃, NH₂F, NH₂Cl, NH₂Br, NH₂CN, NH₂OH, and NH₂CH₃. The nature of aerogen bonds in these complexes is analyzed by means of molecular electrostatic potential, electron localization function, quantum theory atoms in molecules, noncovalent interaction index, and natural bond orbital analyses. The interaction energy (E_int) ranges from ?4.59 to ?9.65 kcal/mol in the O₃Z···NCX complexes and from ?5.30 to ?13.57 kcal/mol in the O₃Z···NH₂X ones. The dominant charge‐transfer interaction in these complexes occurs across the aerogen bond from the nitrogen lone‐pair (n_N) of the Lewis base to the σ*_Z‐O antibonding orbital of the ZO₃. Besides, the formation of aerogen bond tends to decrease the ⁸³Kr or ¹³¹Xe chemical shielding values in these complexes. © 2016 Wiley Periodicals, Inc.     

Noncovalent Bonds between Tetrel Atoms

The pairing of TFH₃ with a TH₂CH₃⁻ anion, where T represents tetrel atoms C, Si, Ge, Sn, Pb, results in a strong direct interaction between the two T atoms. The interaction energy is sensitive to the nature of the two T atoms but can be as large as 90 kcal/mol. The noncovalent bond strength rises quickly as the basic T atom of the anion becomes smaller, or as the Lewis acid T grows larger, although there is less sensitivity to the latter atom. The electrostatic component makes up some 55–70 % of the total attraction energy. This term is well accounted for by simple combination of the maximum and minimum values of the molecular electrostatic potential of the Lewis acid and base units, respectively. The complexation induces a rearrangement in the TFH₃ molecule from tetrahedral to trigonal pyramidal. The associated deformation energy reduces the exothermicity of the complexation reaction. Electron density shift patterns reveal a density loss on the basic T atom, along with accompanying increases on the acidic T and its attached F atom.     

Hydrogen bond vs proton transfer in HZSM5 zeolite. A theoretical study

The interaction of a large set of bases covering a wide range of the basicity scale with HZSM5 medium-size zeolites has been investigated through the use of two model clusters, namely 5T and 7T:63T. The 5T cluster has been treated fully ab initio at the B3LYP level, whereas the 63T cluster has been treated with the ONIOM2 scheme using the B3LYP:MNDO combination for geometry optimizations and B3LYP:HF/3-21G for adsorption energies. The optimized geometries of the different hydrogen bond (HB) and ion pair (IP) complexes obtained with both models are rather similar. However, there are significant dissimilarities as far as the adsorption energies are concerned, in particular when dealing with IP clusters whose intrinsic stability is largely underestimated when the simpler 5T model is used. 5T clusters could be used to obtain reasonable estimates of adsorption energies provided these are scaled by a factor of 1.1 for HB complexes and 1.4 for IP complexes. The zeolite cavity favors the proton transfer process, similarly to that found by third polar partners in gas-phase HB trimers. The intrinsic basicity of the base and its adsorption energy within the zeolite are correlated. From this correlation, is possible to conclude that, in general, bases with proton affinities (PA) larger than 200 kcal mol(-1) should lead to the formation of IPs, whereas bases with PA smaller than this value should form HB complexes.     

Theoretical investigation on mechanism for OH-initiated oxidation of CH2=C(CH3)CH2OH

The mechanism of the gas-phase reaction OH with CH₂=C(CH₃)CH₂OH (2-methyl-2-propen-1-ol) has been elucidated using high-level ab initio method, i.e., CCSD(T)/6-311++g(d,p)//MP2(full)/6-311++g(d,p). Various possible H-abstraction and addition–elimination pathways are identified. The calculations indicate that the addition–elimination mechanism dominates the OH+MPO221 reaction. The addition reactions between OH radicals and CH₂=C(CH₃)CH₂OH begin with the barrierless formation of a pre-reactive complex in the entrance channel, and subsequently the CH₂(OH)C(CH₃)CH₂OH (IM1) and the CH₂C(OH)(CH₃)CH₂OH (IM2) are formed by OH radicals’ electrophilic additions to the double bond. IM1 can easily rearrange to IM2 via a 1,2-OH migration. Subsequently, rearrangement of IM2 to form (CH₃)₂C(OH)CH₂O (IM11) followed by dissociation to HCHO + (CH₃)₂COH (P21) is the most favorable pathway. The decomposition of IM2 to CH₂OH + CH₂=C(OH)CH₃ (P16) is the secondary pathway. The other pathways are not expected to play any important role in forming final products.     

Intra- and intermolecular hydrogen bonding in formohydroxamic acid complexes with water and ammonia: infrared matrix isolation and theoretical study

The complexes of formohydroxamic acid with water and ammonia have been studied using FTIR matrix isolation spectroscopy and MP2 calculations with a 6-311++G(2d,2p) basis set. The analysis of the experimental spectra of the HCONHOH/H₂O(NH₃)/Ar matrixes indicates formation of strongly hydrogen-bonded complexes in which the NH group of formohydroxamic acid acts as a proton donor toward the oxygen atom of water or the nitrogen atom of ammonia. The NH stretching vibration of formohydroxamic acid exhibits 150 cm⁻¹ red shift in the complex with water and 443 cm⁻¹ red shift in the complex with ammonia as compared to the NH stretch of the HCONHOH monomer. The theoretical calculations indicate stability of five isomers for the water complex and three isomers for the ammonia complex. The most stable are the cyclic structures in which the water or ammonia molecules are inserted within the intramolecular hydrogen bond of the formohydroxamic acid molecule and act as proton donors for the CO group and proton acceptors for the OH group of the formohydroxamic acid molecule. In spite of their stability the cyclic structures have not been observed in the matrixes which indicates high energy barrier for their formation, the reaction of complex formation is under kinetic and not thermodynamic control.     

Effects of alkylation upon the proton affinities of nitrogen and oxygen bases

The protonation energies of alkylated derivatives of NH₃ and OH₂ are calculated at the Hartree–Fock level with the split-valence 4-31G basis set. The methyl, dimethyl, and ethyl amines are studied; oxygen bases include methanol, dimethylether, and ethanol. The geometries of each molecule and its protonated analog are fully optimized. It is found that protonation leads to significant changes in the molecular structures. In particular, the bonds to the N and O atoms are substantially elongated, especially when the other atom involved is C rather than H. The calculated absolute proton affinities are somewhat larger than the experimental values. However, the differences in protonation energies of the various molecules relative to one another agree quantitatively with experiment. Replacement of one H atom of the base by a methyl group induces an increase in proton affinity of some 10 kcal/mol. If a second methyl group is added to the N or O atom, a further increment of about 70% this amount is noted. On the other hand, placement of the second C atom on the first methyl group (to form an ethyl substituent) leads to a smaller increase (～30%). The magnitudes of these alkyl substituent effects are somewhat larger for the oxygen bases than for the amines.     

A method for determination of the structure of the intramolecular hydrogen bond in the cations of unsymmetrically substituted 1,8-bis(dimethylamino)naphthalenes in solution

Alkylation of 8-dimethylamino-1-methylamino-4-nitronaphthalene in the CD₃I/KOH/DMSO system afforded a 4-nitro derivative containing the N(CD₃)Me group in position 1. Direct proof of the structure of the intramolecular hydrogen bond in solutions of monoprotonated 4-R-1,8-bis(dimethylamino)naphthalenes was obtained for the first time. ¹H NMR study revealed that the chelated NH proton is shifted to the N(8) atom for R = NO₂ and NH₃ ⁺ and to the N(1) atom for R = NH₂. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 159–162, January, 2006.     

Basicity and Proton Transfer in Proton Sponges and Related Compounds: An Ab Initio Study

Theoretical calculations at the B3LYP/6-31G* level were carried out on a family of 1,8-diR-naphthalenes, which include the proton sponge (1,8-bisdimethylaminonaphthalene, R = NMe₂) and other substituents (R = NH₂, R = OH, R = CH₃, R = F). Their basicity was compared with that of the corresponding monosubstituted benzenes. The dianion of 1,8-dihydroxynaphthalene should be a compound of extraordinary high basicity. The barriers to proton transfer, geometry, and density at the bond critical point of the hydrogen bond have been calculated and compared with experimental data when available.     

Ab initio study of the potential energy surface and product branching ratios for the reaction of O(D) with CH3CH2F

The potential energy surface of O(¹D) + CH₃CH₂F reaction has been studied using QCISD(T)/6-311++G(d,p)//MP2/6-311G(d,p) method. The calculations reveal an insertion–elimination reaction mechanism of the title reaction. The insertion process has two possibilities: one is the O(¹D) atom inserting into C–F bond of CH₃CH₂F produces one energy-rich intermediate CH₃CH₂OF and another is the O(¹D) atom inserting into one of the C–H bonds of CH₃CH₂F produces two energy-rich intermediates, IM1 and IM2. The three intermediates subsequently decompose to various products. The calculations of the branching ratios of various products formed though the three intermediates have been carried out using RRKM theory at the collision energies of 0, 5, 10, 15, 20, 25 and 30 kcal/mol. CH₃CH₂O is the main decomposition product of CH₃CH₂OF. HF and CH₃ are the main decomposition products for IM1; CH₂OH is the main decomposition product for IM2. Since IM1 is more stable and more likely to form than CH₃CH₂OF and IM2, HF and CH₃ are probably the main products of the O(¹D) + CH₃CH₂F reaction. Our computational results can give insight to reaction mechanism and provide probable explanations for future experiments.     

Computational study of structures and proton transfer in hydrogen‐bonded ammonia complexes using semiempirical valence‐bond approach

In this study, the seGVB method was implemented for the N H bonding system, specifically for hydrogen‐bonded ammonia complexes, and the model well reproduces the MP2 geometries and energetics. A comparison between the ammonia dimer and water dimer is given from the viewpoint of valance‐bond structures in terms of the calculated bond energies and pair–pair interactions. The linear hydrogen bond is found to be stronger than the bent bonds in both cases, with the difference in energy between the linear and cyclic structures being comparable in both cases although the NH bonds are generally weaker. The energy decomposition clearly demonstrates that the changes in electronic energy are quite different in the two cases due to the presence of an additional lone pair on the water molecule, and it is this effect which leads to the net stabilization of the cyclic structure for the ammonia dimer. Proton‐transfer profiles for hydrogen‐bonded ammonia complexes [NH₂ H NH₂]⁻ and [NH₃ H NH₃]⁺ were calculated. The barrier for proton transfer in [NH₃ H NH₃]⁺ is larger than that in [NH₂ H NH₂]⁻, but smaller than that in the protonated water dimer. The different bonding structures substantially affect the barrier to proton transfer, even though they are isoelectronic systems. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 73: 357–367, 1999     

Triel–hydride triel bond between ZX3 (Z = B and Al; X = H and Me) and THMe3 (T = Si,Ge and Sn)

Complexes between THMe₃ (T = Si, Ge and Sn) and ZX₃ (Z = B and Al; X = H and Me) have been characterized using MP2/aug‐cc‐pVTZ calculations. These complexes are chiefly stabilized by a triel–hydride triel bond with the T–H bond pointing to the π‐hole on the triel atom. The triel–hydride interaction is mainly attributed to the charge transfer from the T–H bond orbital to the empty p orbital of the triel atom. These complexes are very stable with a large interaction energy (>10 kcal mol^?1) excluding THMe₃···BMe₃ (T = Si and Ge), indicating that the sp²‐hydridized triel atom has a strong affinity for the T–H bond. The formation of THMe₃···BH₃ results in proton transfer, characterized by conversion of orbital interaction and large charge transfer (ca 0.5e). The large deformation is primarily responsible for the abnormally greater interaction energy in THMe₃···BH₃ (>30 kcal mol^?1) than in the AlH₃ analogue. Methyl substitution on the triel atom weakens the triel–hydride interaction and causes a larger interaction energy in THMe₃···AlMe₃ with respect to its BMe₃ counterpart. Most of these interactions possess characteristics of covalent bonds. Polarization makes a contribution to the stability of most complexes nearly equivalent to the electrostatic term.