Halogen Bonding： An AIM Analysis of the Weak Interactions

A series of complexes formed between halogen-containing molecules and ammonia have been investigated by means of the atoms in molecules （AIM） approach to gain a deeper insight into halogen bonding. The existence of the halogen bond critical points （XBCP） and the values of the electron density （Pb） and Laplacian of electron density （V2pb） at the XBCP reveal the closed-shell interactions in these complexes. Integrated atomic properties such as charge, energy, polarization moment, volume of the halogen bond donor atoms, and the corresponding changes （△） upon complexation have been calculated. The present calculations have demonstrated that the halogen bond represents different AIM properties as compared to the well-documented hydrogen bond. Both the electron density and the Laplacian of electron density at the XBCP have been shown to correlate well with the interaction energy, which indicates that the topological parameters at the XBCP can be treated as a good measure of the halogen bond strength In addition, an excellent linear relationship between the interatomic distance d（X…N） and the logarithm of Pb has been established.     

Computational studies of σ-type weak interactions between NCO/NCS radicals and XY(X = H,Cl;Y = F,Cl,and Br)

The triatomic radicals NCO and NCS are of interest in atmospheric chemistry,and both the ends of these radicals can potentially serve as electron donors during the formation of σ-type hydrogen/halogen bonds with electron acceptors XY(X = H,Cl;Y = F,Cl,and Br).The geometries of the weakly bonded systems NCO/NCS···XY were determined at the MP2/aug-cc-pVDZ level of calculation.The results obtained indicate that the geometries in which the hydrogen/halogen atom is bonded at the N atom are more stable than those where it is bonded at the O/S atom,and that it is the molecular electrostatic potential(MEP)-not the electronegativity-that determines the stability of the hydrogen/halogen bond.For the same electron donor(N or O/S) in the triatomic radical and the same X atom in XY,the bond strength decreases in the order Y = F > Cl > Br.In the hydrogen/halogen bond formation process for all of the complexes studied in this work,transfer of spin electron density from the electron donor to the electron acceptor is negligible,but spin density rearranges within the triatomic radicals,being transferred to the terminal atom not interacting with XY.     

Study on the Cation-π Interactions between Ammonium Ion and Aromatic π Systems

The nature and strength of the cation-π interactions between NH4^＋ and toluene, p-cresol, or Me-indole were studied in terms of the topological properties of molecular charge density and binding energy decomposition. The results display that the diversity in the distribution pattern of bond and cage critical points reflects the profound influence of the number and nature of substituent on the electron density of the aromatic rings. On the other hand, the energy decomposition shows that dispersion and repulsive exchange forces play an important role in the organic cation （NH4^＋）-π interaction, although the electrostatic and induction forces dominate the interaction. In addition, it is intriguing that there is an excellent correlation between the electrostatic energy and ellipticity at the bond critical point of the aromatic π systems, which would be helpful to further understand the electrostatic interaction in the cation-π complexes.     

Investigation of the Substituent Effects on π-Type Pnicogen Bond Interaction

Intermolecular interactions between PH_2Cl and Ar–R(R = H,OH,NH_2,CH_3,Br,Cl,F,CN,NO_2) were calculated by using MP2/aug-cc-p VDZ quantum chemical method.It has been shown from our calculations that the aromatic rings with electron-withdrawing groups represent much weaker binding affinities than those with electron-donating groups.The charge-transfer interaction between PH_2Cl and Ar–R plays an important role in the formation of pnicogen bond complexes,as revealed by NBO analysis.Nevertheless,AIM analysis shows that the nature of the interactions between PH_2Cl and Ar–R is electrostatic,and the interaction energies of the complexes are correlated positively with the electron densities in the bond critical points(BCPs).RDG/ELF graphical analyses were performed to visualize the positions and strengths of the pnicogen bonding,as well as the spatial change of the electron localization upon the formation of complexes.The π-type halogen bond was also calculated,and it has been revealed that the π-type pnicogen bond systems are more stable than the halogen bond ones.     

Rapid and accurate evaluation of the binding energies and the individual N-H···O=C, N-H···N, C-H···O=C, and C-H···N interaction energies for hydrogen-bonded peptide-base complexes

The binding energies of thirty-six hydrogen-bonded peptide-base complexes, including the peptide backbone-ase complexes and amino acid side chain-base complexes, are evaluated using the analytic potential energy function established in our lab recently and compared with those obtained from MP2, AMBER99, OPLSAA/L, and CHARMM27 calculations. The comparison indicates that the analytic potential energy function yields the binding energies for these complexes as reasonable as MP2 does, much better than the force fields do. The individual N H…O=C, N H…N, C H…O=C, and C H…N attractive interaction energies and C=O…O=C, N H…H N, C H…H N, and C H…H C repulsive interaction energies, which cannot be easily obtained from ab initio calculations, are calculated using the dipole-dipole interaction term of the analytic potential energy function. The individual N H…O=C, C H…O=C, C H…N attractive interactions are about 5.3±1.8, 1.2±0.4, and 0.8 kcal/mol, respectively, the individual N H … N could be as strong as about 8.1 kcal/mol or as weak as 1.0 kcal/mol, while the individual C=O…O=C, N H…H N, C H…H N, and C H…H C repulsive interactions are about 1.8±1.1, 1.7±0.6, 0.6±0.3, and 0.35±0.15 kcal/mol. These data are helpful for the rational design of new strategies for molecular recognition or supramolecular assemblies.     

Theoretical Studies on the Intermolecular Interactions of Aza-calix[2]arene[2]-triazines with RDX

Six fully optimized structures of the aza-calix[2]arene[2]-triazines/RDX supramo-lecular complexes have been obtained at the DFT-B3LYP/6-311++G** level,and the corresponding intermolecular interactions have been investigated using the B3LYP,mPWPW91 and MP2 methods at the 6-311++G** level,respectively.The natural bond orbital(NBO) and atoms in molecules(AIM) analyses have been performed to reveal the origin of interactions.To our interest,the result indicates that the strongest interaction is up to -22.34 kJ/mol after basis set superposition error(BSSE) and zero point energy(ZPE) correction at the MP2/6-311++G** level.Furthermore,the intermolecular interactions between aza-calix[2]arene[2]-triazines with the substituted amidos and RDX are stronger than those of other complexes.Thus,the complexes with amidos can be used as the candidates to increase the stability of explosive and eliminate the explosive wastewater.     

The open-close mechanism of M2 channel protein in influenza A virus:A computational study on the hydrogen bonds and cation-π interactions among His37 and Trp41

The M2 protein from influenza A virus is a tetrameric ion channel. It was reported that the permeation of the ion channel is correlated with the hydrogen bond network among His37 residues and the cation-π interactions between His37 and Trp41. In the present study,the hydrogen bonding network of 4-methyl-imidazoles was built to mimic the hydrogen bonds between His37 residues,and the cation-π interactions between 4-methyl-imidazolium and indole systems were selected to represent the interac-tions between His37 and Trp41. Then,quantum chemistry calculations at the MP2/6-311G level were carried out to explore the properties of the hydrogen bonds and the cation-π interactions. The calcula-tion results indicate that the binding strength of the N-H···N hydrogen bond between imidazole rings is up to -6.22 kcal·mol-1,and the binding strength of the strongest cation-π interaction is up to -18.8 kcal·mol-1(T-shaped interaction) or -12.3 kcal·mol-1(parallel stacking interaction). Thus,the calcu-lated binding energies indicate that it is possible to control the permeation of the M2 ion channel through the hydrogen bond network and the cation-π interactions by altering the pH values.     

Substituent Effects on the Hydrogen Bonding between 4-Substituted Phenols and HF, H2O, NH3

Density function theory UB3LYP/6-31 g(d) calculations were performed to study the hydrogen bonds between para-substituted phenols and HF, H2O, or NH3. It revealed that many properties of the non-covalent complexes, such as the interaction energies, donor-acceptor distances, bond lengths and vibration frequencies, showed well-defined substituent effects. Therefore, from the substituent effects not only the mechanism of a certain non-covalent interaction can be better understood, but also the interaction energies and structures of a certain non-covalent complex, which otherwise might be very hard or resource-consuming to estimate, can be easily predicted.     

Theoretical study of bifurcated bent blue-shifted hydrogen bonds CH_2…Y

Ab initio quantum chemistry methods were applied to study the bifurcated bent hydrogen bonds Y… H2CZ (Z = O, S, Se) and Y…H2CZ2 (Z = F, Cl, Br) (Y = Cl-, Br-) at the MP2/6-311 G(d,p) and MP2/6-311 G(2df,2p) levels. The results show that in each complex there are two equivalent blue-shifted H-bonds Y…H—C, and that the interaction energies and blue shifts are large, the energy of each Y…H—C H-bond is 15-27 kJ/mol, and Δr(CH) = -0.1 - -0.5 pm and Δv(CH) = 30 - 80 cm-1. The natural bond orbital analysis shows that these blue-shifted H-bonds are caused by three factors: large rehybridization; small direct intermolecular hyperconjugation and larger indirect intermolecular hy- perconjugation; large decrease of intramolecular hyperconjugation. The topological analysis of elec- tron density shows that in each complex there are three intermolecular critical points: there is one bond critical point between the acceptor atom Y and each hydrogen, and there is a ring critical point inside the tetragon YHCH, so these interactions are exactly H-bonding.     

Theoretical Investigations on the Structures and Properties of the Side-on Complexes B_2(N_2)_2 and Monocyclic B_n(N_2)_n~m (n=3～6,m=-1～+2)

The structures and energies of the side-on complexes B2(N2)2 and monocyclic Bn(N2)nm (n = 3～6,m = -1～+2) between N2 (1∑+g) and B (2P) have been investigated by the DFT-B3LYP and MP2 methods at the 6-311+G(2d) and aug-cc-pVTZ levels. The analyses of NICS (Nucleus Independent Chemical Shifts),NBO (nature bond orbital),AIM (atoms in molecules) and frontal orbitals have been used to reveal the origin of coordination bond between the π-electron donor N2 group and B atom,accompanied by the comparison with the end-on complexes. The results have indicated that the side-on coordination complexes can be formed due to the relative strong fluidity of the π-electrons,and the nature of the coordination bond has been exposed to be that the N2 group offers 1πu electron to the 2p orbital of boron. The coordinate energies of the side-on complexes are less than those of the end-on complexes. Furthermore,the aromaticity of side-on coordination complex is weaker than that of the corresponding end-on coordination complex.     

Structural Probing on the Sn-C_(C5 ring) Bond of the Sn(Ⅱ) Metallocenes in Both the Solid State and the Temperature-dependent Solution Relaxation State

Various bond modes of the M-C_(C5 ring) exist in metallocene compounds of group 14 heavier elements,mostly due to an intricate interaction between the lone electron pairs at the M center and the 6 p-electrons of the C_5 ring.The tin(Ⅱ) metallocene complexes LSn R(L = HC[CMe(N-2,6-iPr_2C_6H_3)]_2,R = cyclopentadienyl,C_5H_5(1); indenyl,C_9H_7(2); fluorenyl,C_(13)H_9(3)) stabilized by the β-diketiminato ligand were prepared and utilized in the study on their solid and solution state structures.X-ray single-crystal diffraction data revealed an η~1-mode of the Sn-C_(C5 ring) bond in each 1~3.However,the room temperature ~1H NMR spectral studies disclosed such a fluxional bonding mode in solution.The 119 Sn NMR studies suggested a quadruple coordination nature of the Sn center in 1 while the triple coordination manner was for the Sn atom in both 2 and 3.Then the variable-temperature(25~–75 ℃) ~1H NMR spectral studies for each 1~3 were performed,which detected the relaxation state structures of 1~3 at lower temperature.All of these results indicate a stereochemical activity of the lone electron pairs at the tin(Ⅱ) atom that definitely has an electronic interaction with the 6 p-electrons of the C_5 ring.The observed Sn-C_(C5 ring) bond modes appear influenced by either the metallocene size or the compound state existed.     

Theoretical study of the N—H···O red-shifted andblue-shifted hydrogen bonds

Theoretical calculations are performed to study the nature of the hydrogen bonds in complexes HCHO···HNO, HCOOH···HNO, HCHO···NH3, HCOOH···NH3, HCHO···NH2F and HCOOH···NH2F. The geomet- ric structures and vibrational frequencies of these six complexes at the MP2/6-31 G(d,p), MP2/6-311 G(d,p), B3LYP/6-31 G(d,p) and B3LYP/6-311 G(d,p) levels are calculated by standard and counterpoise-corrected methods, respectively. The results indicate that in complexes HCHO···HNO and HCOOH···HNO the N—H bond is strongly contracted and N—H···O blue-shifted hydrogen bonds are observed. While in complexes HCHO···NH3, HCOOH···NH3, HCHO···NH2F and HCOOH···NH2F, the N—H bond is elongated and N—H···O red-shifted hydrogen bonds are found. From the natural bond orbital analysis it can be seen that the X—H bond length in the X—H···Y hydrogen bond is controlled by a balance of four main factors in the opposite directions: hyperconjugation, electron density redistribu- tion, rehybridization and structural reorganization. Among them hyperconjugation has the effect of elongating the X—H bond, and the other three factors belong to the bond shortening effects. In complexes HCHO···HNO and HCOOH···HNO, the shortening effects dominate which lead to the blue shift of the N—H stretching frequencies. In complexes HCHO···NH3, HCOOH···NH3, HCHO···NH2F and HCOOH···NH2F where elongating effects are dominant, the N—H···O hydrogen bonds are red-shifted.     

Theoretical study of the N-H…O red-shifted and blue-shifted hydrogen bonds

Theoretical calculations are performed to study the nature of the hydrogen bonds in complexes HCHO…HNO, HCOOH…HNO, HCHO…NH3, HCOOH…NH3, HCHO…NH2F and HCOOH…NH2F. The geometric structures and vibrational frequencies of these six complexes at the MP2/6-31 G(d,p), MP2/6-311 G(d,p), B3LYP/6-31 G(d,p) and B3LYP/6-311 G(d,p) levels are calculated by standard and counterpoise-corrected methods, respectively. The results indicate that in complexes HCHO…HNO and HCOOH…HNO the N-H bond is strongly contracted and N-H…O blue-shifted hydrogen bonds are observed. While in complexes HCHO…NH3, HCOOH…NH3, HCHO…NH2F and HCOOH…NH2F, the N-H bond is elongated and N-H…O red-shifted hydrogen bonds are found. From the natural bond orbital analysis it can be seen that the X-H bond length in the X-H…Y hydrogen bond is controlled by a balance of four main factors in the opposite directions hyperconjugation, electron density redistribution, rehybridization and structural reorganization. Among them hyperconjugation has the effect of elongating the X-H bond, and the other three factors belong to the bond shortening effects. In complexes HCHO…HNO and HCOOH…HNO, the shortening effects dominate which lead to the blue shift of the N-H stretching frequencies. In complexes HCHO…NH3, HCOOH…NH3, HCHO…NH2F and HCOOH…NH2F where elongating effects are dominant, the N-H…O hydrogen bonds are red-shifted.     

Density Functional Investigation of Methanethiol and Dimethyl Sulfide Adsorption on Zeolite

The density functional theory and cluster model methods have been employed to investigate the interactions between methanethiol, dimethyl sulfide and zeolites. The molecular complexes formed by adsorption of methanethiol or dimethyl sulfide on silanol H3SiOSi(OH)2OSiH3 with five coordination forms or four coordination forms, and complexes formed by interactions of Bronsted acid sites of bridging hydroxyl H3Si(OH)Al(OH)2OSiH3 with methanethiol or dimethyl sulfide have been investigated. Full optimization and frequency analysis of all cluster models have been carried out using the B3LYP hybrid method at 6-31 G (d,p) basis set level for hydrogen, silicon, aluminum, oxygen, carbon, and sulfur atoms. The structures and energy changes of different coordination forms between methanethiol and H3Si(OH)Al(OH)2OSiH3, dimethyl sulfide and H3Si(OH)Al(OH)2OSiH3, methanethiol and H3SiOSi(OH)2OSiH3, dimethyl sulfide and H3SiOSi(OH)2OSiH3 complexes have been comparatively studied. The calculated results showed the nature of interactions that led to the formation of all complexes was van der Waals force confirmed by an insignificant change of geometric structures and properties. The conclusions that methanethiol and dimethyl sulfide molecules were adsorbed on bridging hydroxyl group prior to silanol group were obtained on the basis of adsorption heat, the most stable adsorption models of a 6 ring structure for interaction between bridging hydroxyl and methanethiol, and a 7 ring structure for interaction between bridging hydroxyl and dimethyl sulfide.     

Substituent Effects on the Blue—Shifting Hydrogen Bonds between X—C≡C—CF2—H and Water

MP2／6－31 g(d) calculations were performed verifying the existences of blue-shifting X-C≡C-CF2-H…OH2 hydrogen bonds.Detailed analyses revealed that the interaction energy and donor-acceptor distance had good correlations with the substituent Hammett constants.However,the extent of C-H bond contraction and the blue shift of the C-H stretching vibration did not show any good correlation with the traditional substituent constants,indicating that certain more complicated mechanisms might be involved in the present systems.Nevertheless,it was found that highly electron-with-drawing susbtituents were not favorable to the C-H bond contraction,and it was suggested that the attractive interaction between water and the carbon of -CF2H probably played an important role in the blue shift.     

Ab initio studies on the thermolysis of azetidine

The reaction mechanism of the thermolysis of azetidine to form ethylene and methylen-imine has been studied by ab initio SCF MO method at STO--3G and 3-21G levels. Two possible step-wise pathways are explored. One is the breaking of C--C bond as the first step, while the other is thebreaking of C--N bond. All the stationary points on the potential energy surface (PES) are fully optimiz-ed. MP2 / 3-21G single point calculations on all stationary points and MCSCF / STO-3G computationsfor some stationary points are also carried out. The calculations indicate that azetidine decomposesvia biradicaloid intermediates and the cleavage of C--N bond is preferable to that of C--C bond.     

An MP2 study on pre-reactive complexes (CH_2)_2O … XY (X,Y = H,F,Cl,Br,I)

The structures, energies, atomic chaiges and IR spectra of complexes (CH2)2O…XY (X, Y = H, F, Cl, Br, and I) have been examined by means of ab initio molecular orbital theory at the second-order level of Moller-Plesset perturbation correction. It is found that the hydrogen bond O…H-X is non-linear. The attraction between X and the H atoms in oxirane ring causes O…H-X bond bending. The hydrogen bond slighdy weakens the bond strength of C-O, and leads the bending and stretching mode of IR to shift to the red. The calculation results show that there is no evidence of a significant extent of proton transfer to give (CH2)2OH …X- in the isolated complexes.     

Theoretical Studies on the Cu-Cu Interaction and Stability of [Cu_a(Ph_2Ppy)_b(CH_3CN)_c]~(a+) (a=1～2,b=1～3,c=0～2)

To study the Cu-Cu interaction and stability of the title complexes,the structures of complexes [Cu(Ph2Ppy)(CH3CN)]+ 1,[Cu(Ph2Ppy)]+ 2,[Cu2(Ph2Ppy)2(CH3CN)2]2+ 3,[Cu2(Ph2Ppy)2(CH3CN)]2+ 4,[Cu2(Ph2Ppy)2]2+ 5 and [Cu2(Ph2Ppy)3(CH3CN)]2+ 6 were calculated by density functional theory PBE0 method,and the following conclusions can be drawn:(1) There is no orbital overlapping between two Cu atoms,indicating no Cu-Cu orbital interaction exists in complexes 3～6.Due to a breakdown of the closed shell configuration of Cu atoms,the weak Cu-Cu interactions result from the 3dCu → 4sCu' charge-transfer in 4～6.The Cu-Cu interaction strength follows 5 6 4,implying that there are stronger Cu-Cu interactions in the complexes with fewer CH3CN or more Ph2Ppy ligands.(2) The calculated interaction energies suggest that the coordination of Cu to Ph2Ppy is stronger than that to CH3CN.In 3～6,there are weaker interactions between Cu and CH3CN or Ph2Ppy in the complexes with more CH3CN or Ph2Ppy ligands.(3) The P-Cu and N-Cu interactions are much stronger than the Cu-Cu interaction,so we mainly attribute the stabilities of the binuclear complexes to the eight-membered rings Cu2P2N2C2.     

Theoretical study of the interaction mechanism of single-electron halogen bond complexes H_3C…Br-Y(Y=H,CN,NC,CCH,C_2H_3)

The characteristics and structures of single-electron halogen bond complexes H3C…Br-Y(Y = H,CCH,CN,NC,C2H3) have been investigated by theoretical calculation methods.The geometries were optimized and frequencies calculated at the B3LYP/6-311++G level.The interaction energies were corrected for basis set superposition error(BSSE) and the wavefunctions obtained by the natural bond orbital(NBO) and atom in molecule(AIM) analyses at the MP2/6-311++G level.For each H3C…Br-Y complex,a single-electron Br bond is f...     

Synthesis and Molecular Structure of Phosphorus-Sulfur Hybrid Atom Ligand and Their Palladium Complexes With the Studies on the C—H Bond Activation and Photochemical Carbonylation Reaction of Benzene

In this paper, a novel and ideal synthetic method of the phosphorus and sulfur hybrid atom ligand is reported. The speciality of this method is that the by-products of some reactions could be used circularly as starting materials in the synthetic route. Further, we synthesized a series of organopalladium complexes containing these hybrid atom chelate ligands, among them the molecular structures of novelorganopalladium complexes Pd((i-Pr)_2-P(CH_2)_2SEt)Cl_2, Pd(Et_2P(CH_2)_2SEt)Cl_2 and Pd(Ph_2P(CH_2)_2SEt)Cl_2 were determined by using the X-ray single crystal diffraction method. We first used the organotransition metal complexes containing phosphorus and sulfur hybrid atom ligands to activate the σ-C—H bond, and researched the catalytic activity, i.e. the photochemical carbonylation of benzene was catalyzed by these palladium complexes.