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.     

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）.     

On the Correlation between the Blue Shift of Hydrogen Bonding and the Proton Donor-Proton Acceptor Distance

It is demonstrated that in all types of hydrogen bonds (X—H…Y) there is a balance between the long-range attractive orbital interactions and short-range Pauli/nucleus repulsions. When the proton acceptor approaches the proton donor from distance, the hydrogen bonding energy becomes more negative at relatively large distance, goes through a minimum, and then starts to become less negative when the short-range repulsive forces come into effect.Meanwhile, the X--H bond length increases at relatively large distances, goes through a maximum and starts to shorten when the short-range repulsive forces come into effect. Whether the hydrogen bond is red or blue shifted is dictated by the energy minimum position. If at the energy minimum position the X—H bond length is shorter than that for the free monomer, the hydrogen bond is blue shifted and vice versa. Further studies demonstrate that the recent report about the correlation of C—H bond lengths with proton donor-acceptor distance in F3C—H…OH2 and F3C—H…Cl^- is not fully correct because the authors conducted an inappropriate comparison. Furthermore, it is shown for the first time that the Pauli/nucleus repulsion theory is applicable to the blue-shifted hydrogen bonds in the X—H…π complexes and the blue-shifted lithium bonds in the X—Li…Y complexes.     

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.     

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.     

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.     

Trimer formation of 6-methyl-1,3,5-triazine-2,4-diamine in salt with organic and inorganic acids:analysis of supramolecular architecture

Although the numbers of co-crystals,salts,polymorphs,hydrates,and solvates are growing steadily,trimers that contain both inorganic and organic acids are still very rare in the Cambridge Structural Database(CSD).When 3,5-dihydroxybenzoic acid was crystallized readily with 6-methyl-1,3,5-triazine-2,4-diamine in a 4:3 ratio of ethanol and water by adding a few drops of nitric acid upon slow evaporation in ambient conditions,6-methyl-1,3,5-triazine-2,4-diamine and 3,5-dihydroxybenzoic acid with the nitric acid form of 1:1:1 an inorganic-organic salt formulated as[(C4H8N5+)·(NO3-)·(C7H6O4)].The supramolecular architecture,which is quite elegant and simple,appeared as stacking of a 3D network in adduct.Proton transfer from the HNO3to 6-methyl-1,3,5-triazine-2,4-diamine N acceptor(triazine N)occurred in the organic salt and led to the ionic heterosynthon in the structure.Cooperation among the–COOH,–OH,NO3–,and–NH–functional groups for the observed hydrogen bond synthon was examined in the structure.In adduct,recognition among the constituents is established through N–H···O,O–H···N,and O–H···O hydrogen bonds.The agomelatine molecules are linked through the intermolecular hydrogen bonding interactions(O–H···O)to form a 1D chain.In addition,the nitric acid anions and base cations act as donors and acceptors of hydrogen bonds and interlink,almost to co-planarity,the hydrogen-bonded chains through interchain N–H···O,O–H···N,as well as O–H···O interactions into a 2D sheet structure.Persistent N–H···O interactions were found to play an important role in the formation of the final 3D array.The salt was characterized by elemental analysis,IR,thermogravimetric analysis,and singlecrystal X-ray diffraction,to better understand how intermolecular interactions influence its supramolecular assembly.     

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.     

Multi-component hydrogen-bonding salts formed between imidazole and aromatic acids: Synthons cooperation and crystal structures

Imidazole base was crystallized with different aromatic carboxylic acids 2,4-dihydroxybenzoic acid, 5-chlorosalicylic acid, and 1,8-naphthalic acid, affording three new binary molecular organic salts of [(C 3 H 5 N 2 + )·(C 7 H 5 O 4 )] (1), [(C 3 H 5 N 2 + )·(C 7 H 4 O 3 Cl )] C 7 H 5 O 3 Cl (2), and [(C 3 H 5 N 2 + ) (C 12 H 7 O 4 )] (3). Proton transfer occurs from the COOH of carboxylic acid to nitrogen of imidazole in all complexes (1-3), leading to the hydrogen bond N-H…O in all structures. To our knowledge, the recognition pattern between the carboxylic acid group and imidazole (acid-imidazole synthon) is less well-studied so far. The cooperation among COOH, COO and imidazolium cation functional groups for the observed hydrogen bond synthons is examined in the three structures. Generally, the strong N-H…O and O-H…O hydrogen bonds define supramolecular architecture and connectivity within chains, while weaker C-H…O hydrogen bonds play the dominant role in controlling the interactions between layers in these novel organic salts. Thermal stability of these compounds has been investigated by thermogravimetric analysis (TGA) of mass loss.     

4-Amino-3-（p-chlorophenyl）-5-（p-methoxybenzyl）-4H-1,2,4-triazole：X-ray and DFT-calculated Structures

The title compound, 4-amino-3-(p-chlorophenyl)-5-(p-methoxybenzyl)-4H-1,2,4- triazole I , C16H15ClN4O), has been determined using X-ray diffraction techniques and the molecular structure has also been optimized at the B3LYP/6-31 G(d, p) level using density functional theory (DFT). The triazole ring exhibits dihedral angles of 41.61(15)o and 80.73(11)o with the phenyl rings. The molecules are linked principally by N–H…N hydrogen bonds involving the amino NH2 group and a triazole N atom, forming C(5) chains which are further linked to give a two-dimensional network of molecules. The N–H…N hydrogen bonding is supported by C–H…N hydrogen bond and C–H…π interaction. Intermolecular N–H…N and C–H…N hydrogen bonds produce R22(9), R44(10) and R44(20) rings.     

Syntheses,Crystal Structures and Antibacterial Activities of Cobalt(Ⅱ) and Manganese(Ⅱ) Complexes with Schiff Base Ligand Derived from Tryptamine

Two new mononuclear complexes, namely [Co(L)_2](1) and [Mn(L)_2](2)(HL = N-(3-methylsalicylidene)tryptamine), have been synthesized by the reactions of the ligand with cobalt acetate or manganese acetate in anhydrous ethanol. The crystal structures of the complexes were characterized by IR spectrum, elemental analysis, PXRD and single-crystal X-ray diffraction analysis. Complex 1 crystallizes in monoclinic, space group C2/c, with a = 23.146(2), b = 9.4864(10), c = 13.9261(15) ?, β = 102.898(2)°, V = 2980.6(5) ?3, Z = 4, Dc = 1.367 g/cm3, F(000) = 1284 and μ = 0.616 mm-1. Complex 2 crystallizes in monoclinic, space group P21/n, with a = 14.807(11), b = 13.118(10), c = 16.663(13) ?, β = 111.237(14)°, V = 3017(4) ?3, Z = 4, Dc = 1.342 g/cm~3, F(000) = 1276 and μ = 0.477 mm-1. The units of complex 1 are linked by intermolecular N–H···π hydrogen bonds into infinite 1D chains, which are further extended into a 3D supramolecular structure by a series of π···π stacking interactions. The units of complex 2 are linked by intermolecular N–H···π hydrogen bonds and C–H···π hydrogen bonds into an infinite 3D supramolecular structure. Meanwhile, the antibacterial activities of the ligand and its complexes have been tested against four kinds of bacteria. The results show that the three compounds all have excellent antibacterial activities and that 1 and 2 possess stronger inhibiting effects against the bacteria than the Schiff base.     

Hydrogen-bonding Networks in Cocrystal of Melamine and 4-Fluoro-benzoic Acid

A novel interpenetrating structure [(HMA + )(FB – )]·2H 2 O of melamine(MA) with 4-fluoro-benzoic acid (HFB) was synthesized. It crystallized in the monoclinic system with space group P2 1 /c. The complex has a interpenetrating 2D structure with hydrogen-bonded grid networks. Carboxylic acid to melamine proton transfer occurs in the complex. The adjacent HMA + cations related by an inverse center form cationic [HMA + ] ∞ ribbons via a pair of N―H···N hydrogen bonds. Adjacent FB – anions are paired by C―H···F hydrogen bonds to form dimers, which are connected to [HMA + ] ∞ ribbons through N―H···O interactions. The supramolecular features in the complex are guided by control of strong N―H···N, N―H···O and O―H···O hydrogen bonds, as well as highly directional weak C―H···F interactions and aromatic π···π stacking interactions.     

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 into the Intermolecular Hydrogen-bonding Interactions between Azacyclopentane-2-one and N-Methylol Ethanone

The structures of the complexes formed between N-methylol ethanone(model molecule of ceramide) and azacyclopentane-2-one(the model molecule of azone) have been fully optimized at the B3LYP/6-311++G** level.The intermolecular hydrogen bonding interaction energies have been calculated by using the B3LYP/6-311++G**,B3LYP/6-311++G(2df,2p),MP2(full)/6-311++G** and MP2(full)/6-311++G(2df,2p) methods,respectively.The results show that strong O–H···O=C,N–H···O=C and C–H···O=C hydrogen bonds could exist between azacyclopentane-2-one and N-methylol ethanone.The formation of the complexes might change the conformation of ceramide molecule and thus cause better percutaneous permeation for the drugs.This is perhaps the origin of the permeation enhances the activity of azone for medicament,as is in accordance with the experimental results.The hydrogen-bonding interactions follow the order of(a) (c) (b) (d) (g) ≈(e) ≈(i) (h) (f).The analyses of frequency,NBO,AIM and electron density shift are used to further reveal the nature of the complex formation.In the range of 263.0~328.0 K,the complex is formed via an exothermic reaction,and the solvent with lower temperature and dielectric constant is favorable to this process.     

Unraveling weak interactions in aniline-pyrrole dimer clusters

Weak intermolecular interactions in aniline-pyrrole dimer clusters have been studied by the dispersion-corrected density functional theory(DFT) calculations. Two distinct types of hydrogen bonds are demonstrated with optimized geometric structures and largest interaction energy moduli. Comprehensive spectroscopic analysis is also addressed revealing the orientation-dependent interactions by noting the altered red-shifts of the infrared and Raman activities. Then we employ natural bond orbital(NBO)analysis and atom in molecules(AIM) theory to have determined the origin and relative energetic contributions of the weak interactions in these systems. NBO and AIM calculations confirm the V-shaped dimer cluster is dominated by N.H···N and C.H···π hydrogen bonds, while the J-aggregated isomer is stabilized by N.H···π, n→π* and weak π···π* stacking interactions.The noncovalent interactions are also demonstrated via energy decomposition analysis associated with electrostatic and dispersion contributions.     

SYNTHESIS AND STRUCTURE OF [4Ni(SALEN)·GGH] CLO_4· EtOH·H_2O (GG=Glycylglyciae)

The complex of [4Ni(salen)·GGH] CLO_4·EtOH·H_2O has been synthesized and studied by X-ray single crystal analysis. The results show that there are both intra-unit hydrogen bonds in the [4Ni(salen)·GGH]~+ and inter-unit hydrogen bonds between the two [4Ni(salen)·GGH]~+. Ni(salen) in the unit are still centrosymmetric dimers with planar structure. Imide N(10)—H(10) in the [GGH]~+ bonds with one phenolic oxygen 0(7) of Ni(salen) dimer in the same unit. Two H atoms of amino group N(9)— H [H(A), H(C)] in the glycylglycine perchlorate interact with phenolic oxygen [0(3), 0(5)] of [4Ni(salen)·GGH]~+ through two strong hydrogen bonds respectively.     

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.     

Synthesis,crystal structures and luminescence properties of europium and terbium picolinamide complexes

The novel coordination structures of europium and terbium chloride-picolinamide complexes （EuCl3-（C6H6N2O）2.5H2O, Eu-pa and TbCl3.（C6H6N2O）2.5H2O, Tb-pa） are reported. The crystal structures in the solid state are characterized by X-ray single crystal diffraction, FTIR, Raman, FIR, THz and luminescence spectroscopy. In the crystal structures, the pyridyl nitrogen and carbonyl oxygen atoms in picolinamide are coordinated to the metal ions to form a five-membered ring structure. The experimental results indicate the similar coordination structures of Eu and Tb-pa complexes and the changes of hydrogen bonds and conformation provide models for the coordination structures of the ligands induced by complexation. The results of lanthanide ions with ligands having amide groups.     

Theoretical Studies on the Hydrogen Bonds of Different Position Action Mechanisms of Thymine with Uracil

In this research, the hydrogen bonds Y···H-X(X = C, N; Y = N, O) of thymine and uracil have been theoretically studied. The results show that hydrogen bond leads to bond length elongation and stretches the frequency red-shift of N-H···Y. Meanwhile, the C-H···O bonds shorten and stretch the frequency blue-shift. They all belong to traditional hydrogen bonds. The intermolecular charge transfer caused by the intermolecular hyperconjugation ρ*(N–H) →n(Y) and intramolecular charge redistribution by intramolecular hyperconjugation ρ(C-H)→ρ*(C-N) play important roles in the formation of hydrogen bonds. According to the judgment standards proposed by Bader and Popelier, these hydrogen bonds have typical electron density topological properties. Electrostatic surface potential(ESP) is a useful physicochemical property of a molecule that provides insights into inter- and intramolecular associations, as well as the prediction of likely sites of electrophilic and nucleophilic metabolic attack.     

Crystal Structures and Theoretical Calculation of Zn（Ⅱ） and Cu（Ⅱ） Supramolecular Complexes Based on Macrocyclic Triamine Ligand 1,4,7-Triazacyclodecane （tacd）

Two supramolecular complexes [Zn（tacd）2]（C6H8O4）·6H2O（1） and [Cu（tacd）2]Cl2·4H2O（2） were synthesized and characterized by elemental analysis, IR spectra, TGA and single-crystal X-ray diffraction analysis. The crystal structure showed that the metal ions in complexes 1 and 2 had similar coordination circumstance. But for the complex 2, it formed a novel two-dimensional supramolecular network with 12-membered rings and four-membered rings via hydrogen bond interaction. The thermal gravimetric analyses indicated that the two complexes had similar steps of weight-loss. On the basis of experiment, the two complexes were calculated by DFT-B3LYP/6-31G（d） in Gaussian 03. The results of calculation are in good agreement with the experiment.