Triangular Halogen Bond and Hydrogen Bond Supramolecular Complex Consisting of Carbon Tetrabromide,Halide, and Solvent Molecule： A Theoretical and Spectroscopic Study

The theoretical calculation and spectroscopic experiments indicate a kind of triangular three bonding supramolecular complexes CBr4…X^-…-H-C, which consist of carbon tetrabromide, halide, and protic solvent molecule （referring to dichloromethane, chloroform and acetonitrile）, can be formed in solution. The strength of halogen and hydrogen bonds in the triangular complexes using halide as common acceptor obeys the order of iodide〉bromide〉chloride. The halogen and hydrogen bonds work weak-cooperatively. Charge transfer bands of halogen bonding complexes between CBra and halide are observed in UV-Vis absorption spectroscopy in three solvents, and then the stoichiometry of 1：1, formation constants K and molar extinction coefficients ε of the halogen bonding complexes are obtained by Benesi-Hildebrand method. The K and ε show a dependence on the solvent dielectric constant and, on the whole, obey an order of iodide〉bromide〉chloride in the same solvents. Furthermore, the C-H vibrational frequencies of solvent molecules vary obviously with the addition of halide, which indicates the C-H…X- interaction. The experimental data indicate that the halogen bond and hydrogen bond coexist by sharing a common halide acceptor as predicted by calculation.     

Theoretical Investigation on Interaction between Guanine and Luteolin

The interacting patterns of the luteolin and guanine have been investigated by using the density functional theory B3LYP method with 6-31＋G＊ basis set. Eighteen stable structures for the luteolin-guanine complexes have been found respectively. The results indicate that the complexes are mainly stabilized by the hydrogen bonding interactions. Meanwhile, both the number and strength of hydrogen bond play important roles in determining the stability of the complexes which can form two or more hydrogen bonds. Theories of atoms in molecules and natural bond orbital have also been utilized to investigate the hydrogen bonds involved in all the systems. The interaction energies of all the complexes which were corrected by basis set superposition error are 6.04-56.94 kJ/mol. The calculation results indicate that there are strong hydrogen bonding interactions in the luteolin-guanine complexes. We compared the interaction between luteolin and four bases of DNA, and found luteolin-thymine was the strongest and luteolin-adenine was the weakest. The interaction between luteolin and DNA bases are all stronger than luteolin-water.     

Theoretical Study on Dihydrogen Bonds of NH3BH3 with Several Small Molecules

The dihydrogen bonds B-H...H-X （X= the complexes of NH3BH3 with HF, HCl, F, Cl, Br, C, O, N） in the dimer （NH3BH3）2 and HBr, H2CO, H20, and CH3OH were theoretically studied. The results show that formation of the dihydrogen bond leads to elongation and stretch frequency red shift of the BH and XH bonds, except that in the H2CO system, the CH bond blue shifts. For （NH3BH3）2 and the complexes of the halogenides, red shifts of the XH bonds are caused by the intermolecular hyperconjugation σ（BH）→σ^＊ （XH）. For the system of H2CO, a blue shift of the CH bond is caused by a decrease of the intramolecular hyperconjugation n（O→σ^＊ （CH）. In the other two systems, the red shift of OH bond is a secondary effect of the stronger traditional red-shifted H-bonds N-H... O. In all these systems, red shifts of the BH bonds are caused by two factors： negative repolarization and negative rehybridization of the BH bond, and decrease of occupancy on σ（BH） caused by the intermolecular hyperconjugation σ（BH）→σ^＊ （XH）.     

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.     

Thermodynamic Properties and Relative Stability of Polyhydroxylated Dibenzo-p dioxins Calculated by Density Functional Theory

In this work, partial thermodynamic properties of polyhydroxylated dibenzo-p-dioxins (PHODDs) are calculated by density functional theory (DFT) with the Gaussian 03 program at the B3LYP/6-311G** level. By comparing the total energy Eθ values, it is found that two types of hydrogen bonds exist in PHODDs, one between a hydroxyl and the parent compound (dibenzop-dioxin) with bond energy of approximate 15.7 kJ/mol and the other between two ortho hydroxyl groups with higher bond energy of about 18.3 kJ/mol. Hydrogen bonds have an effect on the conformation stability. On the basis of evaluating the strength of these two types of hydrogen bonds, 75 most stable congeners are ascertained. The relations of calculated thermodynamic parameters (total energy Eθ, zero-point vibrational energy ZPE, correction value of thermal energy Ethθ, heat capacity at constant volume CVθ) with the number and position of hydroxyl substitution (NPHOS) are also discussed. The results show that the NPHOS models can be used to predict the thermodynamic properties for PHODD congeners. In addition, the values of molar heat capacities at constant pressure (Cp,m) from 200 to 1000 K for PHODD congeners are calculated, and the temperature dependence relation of Cp,m is obtained with the least-squares method.     

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.     

Theory Studies on the Intermolecular Interactions of Urea Nitrate with RDX

Six fully optimized geometries of urea nitrate cation and RDX complexes have been obtained with DFT-B3LYP and MP2 methods at the 6-311++G** level. The intermolecular interaction energies have been calculated with basis set superposition error (BSSE) and zero point energy (ZPE) correction. The nature of intermolecular interaction has been revealed by the analysis of AIM and NBO. The results indicate that the greatest binding energy of urea nitrate with RDX is –82.47kJ/mol. The O–H…O and N–H…O hydrogen bonds are important intermolecular interactions of urea nitrate cation with RDX, and the origin of hydrogen bonds is the oxygen atom offering its lone-pair electrons to the σ(O-H)* or σ(O-H)* antibonding orbital. The intermolecular interactions strengthen the N–NO2 bond, leading to the reduced sensitivity of urea nitrate and RDX mixture explosive.     

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.     

Syntheses,Crystal Structures and Intermolecular Interactions of Cu（II） Complexes with Methyl- benzoic Acid （MBA） and 1,10-Phenanthroline

Two cupric complexes containing methylbenzoic acid have been prepared and crystallized by solvent evaporation method in DMF. The single-crystal X-ray crystallographic analysis reveals that they are dicaryon complexes. Complex I with formula of [Cu2（m- MBA）4DMF2] crystallizes in monoclinic with space group of P21/c and complex 2 with formula of [Cuz（o-MBA）ffo-phen）2]·NO3·H2O crystallizes in triclinic with space group of P I. The weak interactions including C-H...O hydrogen bonds, C-H…π interactions and π-π stacking in the structures of two complexes are observed from the X-ray crystallographic data. In addition, there are still classical hydrogen bonds in 2. The different strength of intermolecular interaction in the structure is reflected on their different thermal stability measured by thermal gravimetric analysis and 2D-1R correlation spectroscopy of two complexes. The study of weak interactions is meaningful to provide supporting data for supramolecular chemistry theory and potential applications in molecular biology.     

Structure of cis-[Pt(NH_3)(2-picoline)]~(2+) and DNA adduct and its bonding characteristics

Several methods including molecular mechanics, molecular dynamics, ONIOM that combines quantum chemistry with molecular mechanics and standard quantum chemistry are used to study the configuration and electron structures of an adduct of the DMA segment d(ATACATG*G*TACATA)-d(TATGTACCATGTAT) with cis-[Pt(NH3)(2-Picoline)]2+. The investigation shows that the configuration optimized by ONIOM is similar to that determined by NMR. Strong chemical bonds between Pt of the complex and two N7s of neighboring guanines in the DNA duplex and hydrogen bond between the NH3of the complex and O6 of a nearby guanine have a large impact on the configuration of the adduct. Chemical bonds, the aforementioned hydrogen bond, and the interaction between a methyl of the complex and a methyl of the base in close proximity are critical for the complex to specifically recognize DNA.     

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.     

Effects of Anions and Cations on π-Complexation Between Olefin and Metal Halide

An ab initio molecular orbital study was performed to determine the effects of anions and cations on the π-complexation of C2H4 on MX(M=Ag, Cu; X=F, Cl). The calculated results show the following order of adsorption strength: F-＞Cl- for anions; Cu ＞Ag for cations. The results can be explained by the detailed analysis of atomic charge, orbital energy and orbital population by using the natural bond orbital(NBO) theory: (1) anions with stronger electronegativity can attract more electrons from the s orbital of M, while at the same time it does not obviously weaken the d orbital occupation of M, thus the nearly vacant s orbital and the sufficiently filled d orbitals of M help with forming σ-donation and d-π* backdonation with the π orbital and the π* orbital of olefin, respectively; (2) a smaller energy gap of symmetry-adapted orbitals between olefin and a cation can favor the electron transfer, that is why Cu forms stronger adsorption with olefin than Ag does.     

Ab Initio Calculations on Halogen Bond Between N——Br and Electron-donating Groups

Ab initio calculations of complexes formed between N-bromosuccinimide and a series of electron-donating groups were performed at the level of MP2/Lanl2DZ to gain a deeper insight into the nature of the N—Br halogen bonding. For the small complexes, H3C—Br…NH3 and H2N—Br…NH3, the primary calculation has demonstrated that the N—Br in H2N—Br…NH3 can form a much stronger halogen-bonding complex than the C—Br. A comparison of neutral hydrogen bond complex series reveals that the electron-donating capacities of the atoms decrease in the order, N>O>S; O(sp3)>O(sp2), which is adequate for the C—Br halogen bonding. Interaction energies, in conjunction with the geometrical parameters show that the affinitive capacity of trihalide anions X-3 with N-bromosuccinimide are markedly lower than that of the corresponding X- with N-bromosuccinimide, even lower than those of neutral molecules with N-bromosuccinimide. AIM analyses further confirmed the above results.     

Synthesis and Crystal Structure of N-（1′-H-Pyrrol- 2′-ylcarbonyl）-5-amino- 1,10-phenanthroline

The title compound, N-（1′-H-pyrrol-2′-ylcarbonyl）-5-amino-1,10-phenanthroline, was synthesized by the reaction of a-pyrrolyl carbonyl chloride and 5-amino-1,10-phenanthroline in pyridine. Determined by X-ray structure analysis, it crystallizes in triclinic system, space group P1 with the following crystallographic data： C20H21N5O3, Mr = 379.42, a = 7.8559（4）, b = 9.1681（6）, c = 14.6818（9） A, α= 73.254（10）,β= 88.938（15）, γ= 68.080（10）°, V= 934.66（10） A3, Z = 2, F（000） = 400, Dc = 1.348 g/cm^3 and p = 0.094 mm-1. The final R = 0.0680 and wR = 0.1419 for 2142 observed reflections with I 〉 2σ（/）, and R = 0.1084 and wR = 0.1643 for all reflections. Two aromatic ring planes （pyrrole and phenanthroline rings） are connected by the amide plane. Two different types of intermolecular hydrogen bonds, O-H…N and N-H…O, exist in the crystal. The title complex molecules are connected through hydrogen bonds and weak π-π stacking interactions to generate a 3-D supramolecule.     

Synthesis,Crystal Structure and Antibacterial Activity of （E）-N1,N4-Bis（2,3,4-trimethoxy-6- methylbenzylidene）butane- 1,4-diamine

The title compound （E）-N1,N4-bis（2,3,4-trimethoxy-6-methylbenzylidene） butane- 1,4- diamine （C26H36N2O6, Mr = 472.57） was synthesized and characterized by elemental analysis, IR spectra and single-crystal X-ray diffraction. The crystal belongs to triclinic, space group C2/c with a = 36.102（4）, b = 5.6620（11）, c = 13.015（2）A,β = 105.491 （2）°, V = 2563.7（7）A3, Z = 4, Dc = 1.224 g/cm3, 2 = 0.71073 A,μ（MoKα） = 0.087 mm^-1, F（000） = 1016, the final R = 0.0456 and wR = 0.1257 for 2255 observed reflections with I 〉 2σ（I）. X-ray diffraction analysis reveals that the molecule adopts an E configuration about the central C=N functional bond. The phenyl rings of two 2,3,4-trimethoxy-6-methylbenzaldehyde groups are parallel by symmetry. The molecules are linked through π-π and C-H…π stacking interactions and C-H…O hydrogen bonding interactions. The title compound possesses moderate antibacterial activity.     

CO2 capture through halogen bonding: A theoretical perspective

Halogen bonding interactions between several halogenated ion pairs and CO2 molecules have been investigated by means of density functional theory calculations. To account for the influence of solvent environment, the implicit polarized continuum model was also employed. The bromide and iodide cations of ionic liquids (ILs) under study can interact with CO2 molecules via X O interactions, which become much stronger in strength than those in the complexes of iodo-perfluorobenzenes, very effective halogen bond donors, with CO2 molecules. Such interactions, albeit somewhat weaker in strength, are also observed between halogenated ion pairs and CO2 molecules. Thus, the solubility of CO2 may be improved when using halogenated ILs, as a result of the formation of X O halogen bonds. Under solvent effects, the strength of the interactions tends to be weakened to some degree, with a concomitant elongation of intermolecular distances. The results presented here would be very useful in the design and synthesis of novel and potent ILs for CO2 physical absorption.     

Orbital Interaction of Epoxidation on the Same Curvature Bonds of Single-walled Carbon Nanotubes

The epoxidation of different bonds with the same bond curvature in one nano-tube including armchair,zigzag and chiral tubes was studied. The calculated results showed that for the adducts with opened C–O–C configuration,the magnitude of the binding energies was related with their corresponding bonding characteristics in HOMO,and the larger binding energies were attributed to stronger orbital interaction between one O atom and the nanotube; whereas for the adducts with 3MR structures,the binding energies were related with the changes of C–C bond length and independent of the frontier orbital interaction before and after epoxidation.     

Theoretical Investigation on the Geometries and Properties of Guanine-BX3 （X = F, Cl） Complex

Geometries and binding energies were predicted at the B3LYP/6-311+G* level for the guanine-BX3 (X = F, Cl) systems and four isomers with no imaginary frequencies have been obtained for both guanine-BF3 and guanine-BCl3, respectively. Single energy calculations using much larger basis sets (6-311+G(2df,p) and aug-cc-pVDZ were carried out as well. It was found that the most stable isomer of guanine-BF3 is BF3 connected to N3 of guanine with the stabilization energy of –19.93 kcal/mol (BSSE corrected), while that of guanine-BCl3 is BCl3 connected to O10 of guanine having stabilization energy of –15.02 kcal/mol at the same level. The analyses for the combining interaction between BX3 and guanine with the atom-in-molecules theory (AIM) and natural bond orbital (NBO) methods have been performed. The results indicated that all the isomers are formed with σ-p type interactions between guanine and BX3, in which pyridine-type nitrogen or carbonyl oxygen or nitrogen atom of amino group offers its lone pair electrons to the empty p orbital of boron atom and the concomitance of charge transfer from guanine to BX3 has occurred. Still, one or two hydrogen bonds exist in some isomers of guanine-BX3 system and contribute to the stability of complex systems. Frequency analysis suggested that the stretching vibration of BX3 undergoes a red shift in complexes. Guanine-BF3 complex is more stable than guanine-BCl3 although the B–Y (Y=N, O) bond distance in the latter is shorter.     

脱铁伴清蛋白两结合位点不同酪氨酸氢键的特性

The interaction of gallium（Ⅲ） with the ligands containing phenolic group（s）, such as salicylic acid, 8-hydroxyquinoline, N,N＇-bis（2-hydroxybenzyl）ethylenediamine-N,N＇diacetic acid （HBED）, N,N＇-ethylenebis[2-（o- hydroxyphenyl）glycine （EHPG）, and ovotransferrin, was studied, respectively, by means of fluorescence in 0.01 mol/L Hepes at pH 7.4 and room temperature. Fluorescence intensity showed an increase when gallium（Ⅲ） was bound to 8-hydroxyquinoline and HBED. In contrast, it was decreased with the interaction of gallium（Ⅲ） with salicylic acid and EHPG. At pH 7.4, there was N…H-O type intramolecular hydrogen bond in the former, and the latter existed O…H-O type intramolecular hydrogen bond. Fluorescence titration of apoovotransferrin with gallium（Ⅲ） displayed that the fluorescence intensity was decreased at the N-terminal binding site, while enhanced at the C-terminal binding site. It can account for the O…H-O type intramolecular hydrogen bonds for the phenolic groups of Tyr92 and Tyr191 residues at the N-terminal binding site. And there are N…H-O type intramolecular hydrogen bonds for Tyr431 and Tyr524 residues at the C-terminal binding site. In addition, under the same conditions, the conditional binding constant of gallium（Ⅲ） with EHPG or HBED determined by fluorescence method is lg KGa-EHPG=19.18 or lg KGa-HBED= 19.08.     

Theoretical Study on lntramolecular Proton Transfer of Perylenequinonoid Derivatives

Intramolecular proton transfer of hypomycin A in the ground state So and singlet excited state S1 were calculated by high level quantum chemical method in this letter. It was found that the IPT barriers for Ⅰ→TS1 are 38.56 kJ/mol in So and 8.19 kJ/mol in S1, while those for Ⅰ→TS4 get approximately 17 kJ/mol higher in So and 28 kJ/mol higher in S1. The calculation of IPT rate constants suggests that the experiment observed process of PQD is in S1. The height of the IPT barriers correlate not only with the variance of charge for labile hydrogen, the change of H-bond‘s length, the change of O-H bond‘s length and the change of O-O distance, but also with the reactant molecular H-bond‘s length. Moreover, the correlations are the same for S0 and S1.