Theoretical study of X- · 1 · YF (1 = triazine,X = Cl,Br and I,Y = H,Cl, Br,I, PH2 and AsH2): noncovalently electron-withdrawing effects on anion-arene interactions

The ternary complexes X^- · 1 · YF (1 = triazine, X = Cl, Br and I, Y = H, Cl, Br, I, PH₂ and AsH₂) have been investigated by MP2 calculations to understand the noncovalently electron-withdrawing effects on anion-arene interactions. The results indicate that in binary complexes (1 · X^-), both weak σ-type and anion-π complexes can be formed for Cl^- and Br^-, but only anion-π complex can be formed for I^-. Moreover, the hydrogen-bonding complex is the global minimum for all three halides in binary complexes. However, in ternary complexes, anion-π complex become unstable and only σ complex can retain in many cases for Cl^- and Br^-. Anion-π complex keeps stable only when YF = HF. In contrast with binary complexes, σ complex become the global minimum for Cl^- and Br^- in ternary complexes. These changes in binding mode and strength are consistent with the results of covalently electron-withdrawing effects. However, in contrast with the covalently electron-withdrawing substituents, Cl^- and Br^- can attack the aromatic carbon atom to form a strong σ complex when the noncovalently electron-withdrawing effect is induced by halogen bonding. The binding behavior for I^- is different from that for Cl^- and Br^- in two aspects. First, the anion-π complex for I^- can also keep stable when the noncovalent interaction is halogen bonding. Second, the anion-π complex for I^- is the global minimum when it can retain as a stable structure.     

The cooperativity between hydrogen and halogen bond in the XY···HNC···XY (X,Y = F,Cl, Br) complexes

The cooperativity between hydrogen and halogen bonds in XY···HNC···XY (X, Y = F, Cl, Br) complexes was studied at the MP2/aug-cc-pVTZ level. Two hydrogen-bonded dimers, five hydrogen-bonded dimers, and ten trimers were obtained. The hydrogen- and halogen-bonded interaction energies in the trimers were larger than those in the dimers, indicating that both the hydrogen bonding interaction and the halogen bonding interaction are enhanced. The binary halogen bonding interaction plays the most important role in the ternary system. The hydrogen donor molecule influences the magnitude of the halogen bonding interaction much more than the hydrogen bonding interaction in the trimers with respect to the dimers. Our calculations are consistent with the conclusion that the stronger noncovalent interaction has a bigger effect on the weaker one. The variation in the vibrational frequency in the HNC molecule was considered. The NH antisymmetry vibration frequency has a blue shift, whereas the symmetry vibration frequency has a red shift. A dipole moment enhancement is observed upon formation of the trimers. The variation in topological properties at bond critical points was obtained using the atoms in molecules method, and was consistent with the results of the interaction energy analysis.     

A comprehensive analysis of P···π pnicogen bonds: substitution effects and comparison with Br···π halogen bonds

Journal of Molecular Modeling - Ab initio calculations were carried out in a systematic investigation of P···π pnicogen-bonded complexes XH2P···C2H2/C2H4 and...     

Comparison of the directionality of the halogen,hydrogen, and lithium bonds between HOOOH and XF (X = Cl,Br, H,Li)

Detailed electrostatic potential (ESP) analyses were performed to compare the directionality of halogen bonds with those of hydrogen bonds and lithium bonds. To do this, the interactions of HOOOH with the molecules XF (X?=?Cl, Br, H, Li) were investigated. For each molecule, the percentage of the van der Waals (vdW) molecular surface that intersected with the ESP surface was used to roughly quantify the directionality of the halogen/hydrogen/lithium bond associated with the molecule. The size of the region of intersection was found to increase in the following order: ClF?<?BrF?<?HF?<?LiF. The maximum ESP in the region of intersection, V _{S, max}, was observed to become more positive according to the sequence ClF?<?BrF?<?HF?<?LiF. For ClF and BrF, the positive electrostatic potential was concentrated in a very small region of the vdW molecular surface. On the other hand, for HF and LiF, the positive electrostatic potential was more diffusely scattered across the vdW surface than for ClF and BrF. Also, the optimized geometries of the dipolymers HOOOH···?XF (X?=?Cl, Br, H, Li) indicated that halogen bonds are more directional than hydrogen bonds and lithium bonds, consistent with the results of ESP analyses.

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Graphical abstract Electrostatic potential (ESP) contour maps in the xz plane of ClF and BrF

     

Formation of the Si-B bond: insertion reactions of silylenes into B-X(X = F,Cl, Br,O, and N) bonds

The insertion reactions of the silylene H₂Si with H₂BXH_n-1 (X?=?F, Cl, Br, O, N; n?=?1, 1, 1, 2, 3) have been studied by DFT and MP2 methods. The calculations show that the insertions occur in a concerted manner, forming H₂Si(BH₂)(XH_n-1). The essences of H₂Si insertions with H₂BXH_n-1 are the transfers of the σ electrons on the Si atom to the positive BH₂ group and the electrons of X into the empty p orbital on the Si atom in H₂Si. The order of reactivity in vacuum shows the barrier heights increase for the same-family element X from up to down and the same-row element X from right to left in the periodic table. The energies relating to the B-X bond in H₂BXH_n-1, and the bond energies of Si-X and Si-B in H₂Si(BH₂)(XH_n-1) may determine the preference of insertions of H₂Si into B-X bonds for the same-column element X or for the same-row element X. The insertion reactions in vacuum are similar to those in solvents, acetone, ether, and THF. The barriers in vacuum are lower than those in solvents and the larger polarities of solvents make the insertions more difficult to take place. Both in vacuum and in solvents, the silylene insertions are thermodynamically exothermic.

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Graphical Abstract The insertion process of H₂Si and H₂BXH_n-1(X?=?F, Cl, Br, O, and N; n?=?1, 1 , 1, 2, 3).

     

Theoretical investigations of the H···π and X (X = F,Cl, Br,I)···π complexes between hypohalous acids and benzene

The H···π and X (X = F, Cl, Br, I)···π interactions between hypohalous acids and benzene are investigated at the MP2/6-311++G(2d,2p) level. Four hydrogen-bonded and three halogen-bonded complexes were obtained. Ab initio calculations indicate that the X···π interaction between HOX and C₆H₆ is mainly electrostatically driven, and there is nearly an equal contribution from both electrostatic and dispersive energies in the case of XOH–C₆H₆ complexes. Natural bond orbital (NBO) analysis reveals that there exists charge transfer from benzene to hypohalous acids. Atom in molecules (AIM) analysis locates bond critical points (BCP) linking the hydrogen or halogen atom and carbon atom in benzene.     

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.

Cα-H···O=C hydrogen bonds contribute to the specificity of RGD cell-adhesion interactions

Background  

The Arg-Gly-Asp (RGD) cell adhesion sequence occurs in several extracellular matrix molecules known to interact with integrin cell-surface receptors. Recently published crystal structures of the extracellular regions of two integrins in complex with peptides containing or mimicking the RGD sequence have identified the Arg and Asp residues as key specificity determinants for integrin recognition, through hydrogen bonding and metal coordination interactions. The central Gly residue also appears to be in close contact with the integrin surface in these structures.     

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.

Theoretical study of noncovalent interactions in XCN···YO<Subscript>2</Subscript>H (X = F,Cl, Br,I; Y = P,As, Sb) complexes

Noncovalent interactions in XCN···YO₂H (X = F, Cl, Br, I; Y = P, As, Sb) complexes were investigated using ab initio calculations at the MP2/aug-cc-pVDZ level of theory. There are four different configurations of these complexes, and the complexes are formed via hydrogen bonds, halogen bonds, π-hole interactions, or dual interactions. An examination of binding distances and interaction energies suggested that π-hole bonds are more stable than the other interactions. Molecular electrostatic potentials, electron densities, second-order stabilization energies, and electron density differences were computed to study the character of these interactions.     

Theoretical potential scans and vibrational spectra of vinyl selenonyl halides CH2=CH–SeO2X (X is F, Cl and Br)

The structure and conformational stability of vinyl selenonyl fluoride, chloride and bromide CH₂=CH–SeO₂X (X is F, Cl and Br) were investigated using density functional B3LYP/6-311+G** and ab initio MP2/6-311+G** calculations. From the calculations the molecules were predicted to exist only in the non-planar gauche conformation with the vinyl C=C group almost eclipsing one of the selenonyl Se=O bonds as a result of conjugation between the two moieties. Single-minimum potential scans were calculated at the DFT level for the molecules. The vibrational frequencies were computed using B3LYP/6-311+G**. Normal coordinate calculations were then carried out and potential energy distributions were calculated for the three molecules in the gauche conformation.Figure Potential function for the asymmetric torsion in vinyl selenonyl fluoride (dotted line), chloride (dashed line) and bromide (solid line) as determined at the DFT-B3LYP/6-311+G** level     

Pulse sequences for detection of NH2···N hydrogen bonds in sheared G⋅A mismatches via remote, non-exchangeable protons

The non-detectability of NH...N hydrogen bonds in nucleic acids due to exchange broadened imino/amino protons has recently been addressed via the use of non-exchangeable protons for detecting internucleotide 2hJ(NN) couplings. In these applications, the appropriate non-exchangeable proton is separated by two bonds from the NH...N bond. In this paper, we extend the scope of this approach to protons which are separated by four bonds from the NH...N moiety. Specifically, we consider the case of the commonly occurring sheared G x A mismatch alignment, in which we use the adenine H2 proton to report on the (A)N6H6(1.2)...N3(G) hydrogen bond, in the presence of undetectable, exchange broadened N6H6(1.2) protons. Two sequences, the 'straight-through' (H6)N6N3H2 and 'out-and-back' H2N6N3 experiments, are presented for observing these correlations in H2O and D2O solution, respectively. The sequences are demonstrated on two uniformly 15N,13C labelled DNA samples: d(G1G2G3T4T5C6A7G8G9)2, containing a G3 x (C6-A7) triad involving a sheared G3 x A7 mismatch, and d(G1G2G3C4A5G6G7T8)4, containing an A5 x (G3 x G6 x G3 x G6) x A5 hexad involving a sheared G3 x A5 mismatch.     

Conformational stability and normal coordinate analyses for 1-halovinyl azides CH<Subscript>2</Subscript>=CX–NNN (X is F,Cl and Br)

The conformational behavior of 1-halovinyl azides CH2=CX-NNN (X=F, Cl and Br) were investigated by DFT-B3LYP and ab initio MP2 calculations with the 6-311++G** basis set. The molecules were predicted to exist predominantly in the trans (the vinyl CH2=CH- and the azide -NNN groups are trans to each other) conformation. The relative energy between cis and trans were calculated to decrease in order: bromide>chloride>fluoride. Full optimization was performed at the ground and transition states in the molecule at both MP2 and B3LYP levels. The barrier to internal rotation around the C-N single bond in the three molecules was calculated to be about 4-5 kcal mol(-1). The vibrational frequencies were computed at the DFT-B3LYP level and the calculated infrared and Raman spectra of the cis- trans mixture of the three molecules were plotted. Complete vibrational assignments were made on the basis of normal coordinate calculations for both stable conformers of the three molecules.     

Synthesis and characterization of triaminecobalt(III) complexes and acid hydrolysis kinetics of fac-[Codpt(H2O)nX3−n]n+ (X = Cl,Br; n = 0,1,2)

The complexes CodptX₃ and [Codpt(H₂O)X₂]ClO₄ (X = Cl, Br; dpt = dipropylenetriamine = NH(CH₂CH₂CH₂NH₂)₂) have been prepared and characterized. Rate constants (s⁻¹) for aqueous solution at 25 °C and μ = 0.5 M (NaClO₄), for the acid-independent sequential ractions.

have been measured spectrophotometrically. For X = Cl: k₁ ⋍ 2 × 10⁻², k₂ = 1.7 × 10⁻⁴ and k₃ = 4.8 × 10⁻⁶, and for X = Br: k₁ ⋍ 2 × 10⁻², k₂ = 5.25 × 10⁻⁴ and k₃ = 2.5 × 10⁻⁵ The primary equation was found to be acid independent, while the secondary and tertiary aquations were acid-inhibited reactions. For the second step, the rate of the reaction was given by the rate equation

where C_t is the complex concentration in the aqua-and hydroxodihalo species, k′₂ is the rate constant for the acid-dependent pathway and K_a is the equilibrium constant between the hydroxo and aqua complex ions. The activation parameters were evaluated, for X = Cl: ΔH^≠₂ = 106.3 ± 0.4 kJ mol⁻¹ and ΔS^≠₂ = 40.2 ± 1.7 J K⁻¹ mol⁻, and for X = Br: ΔH^≠₂ = 91.6 ± 0.4 kJ mol⁻¹ and ΔS^≠₂ = 0.4 ± 1.7 J K⁻¹ mol⁻¹. The results are discussed and detailed comparisons of the reactivities of these complexes with other haloaminecobalt(III) species are presented.     

Competition and interplay between the lithium bonding and hydrogen bonding: R3C···HY···LiY and R3C···LiY···HY triads as a working model (R=H, CH3; Y=CN, NC)

UMP2 calculations with aug-cc-pVDZ basis set were used to analyze intermolecular interactions in R₃C···HY···LiY and R₃C···LiY···HY triads (R=H, CH₃; Y=CN, NC), which are connected via lithium and hydrogen bonds. To better understand the properties of these systems, the corresponding dyads were also studied. Molecular geometries and binding energies of dyads, and triads were investigated at the UMP2/aug-cc-pVDZ computational level. Particular attention was paid to parameters such as cooperative energies, and many-body interaction energies. All studied complexes, with the simultaneous presence of a lithium bond and a hydrogen bond, showed cooperativity with energy values ranging between ?1.71 and ?9.03 kJ mol^?1. The electronic properties of the complexes were analyzed using parameters derived from atoms in molecules (AIM) methodology. Energy decomposition analysis revealed that the electrostatic interactions are the major source of the attraction in the title complexes.     

Reactions of Nb2Cl6(SMe2)3 and Ta2Cl6(SMe2)3 with compounds containing NN single bonds

Ta₂Cl₆(SMe₂)₃ reacts with PhHNNHPh to afford Ta₂Cl₄(μ-Cl)₂(μ-PhN)(PhNH₂)₃ (1) a compound with a Ta^IVTa^IV single bond, with a length of 2.644(1) Å. The compound crystallizes in space group Pnma with unit cell dimensions a = 22.960(8), b = 16.875(4), c = 6.367(3) Å, V = 2467(1) ų, and Z = 4. The reaction of Nb₂Cl₆(SMe₂)₃ with PhHCNNCHPh, merely on mixing at room temperature produced Nb₂Cl₆(SMe₂) [PhHC(N)PhHCNHNCHPh]·C₇H₈ (2) as large red crystals in ca. 50% yield. The molecule consists of two Nb^IV atoms, one six-coordinate and the other seven-coordinate, united by three bridging atoms (Cl, Cl, N) and a NbNb bond of length 2.681(1) Å. The way in which the tridentate triazo ligand is generated is completely obscure. Crystallographic data for 2: space group P2₁/n with a = 11.393(3), b = 11.988(3), c = 27.233(7) Å, β = 100.75(2)°, V = 3654(3) Å, and Z = 4.     

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.