Cooperative N–H···N,N–H···O,and O–H···N bonded molecular dimers of two new 3,5-diaryl-1<Emphasis Type="Italic">H</Emphasis>-pyrazoles

Two new 3,5-diaryl-1H-pyrazoles: 3(5)-(4-tert-butylphenyl)-5(3)-(naphthalene-2-yl)-1H-pyrazole (1) and 5-(4-(benzyloxy)phenyl)-3-(furan-2-yl)-1H-pyrazole (2) were synthesized and characterized. Two strong ions peaks [2M]⁺ and [2M + Na]⁺ observed in the ESI–MS spectra are attributed to the dimerization process in solution formed by intermolecular N–H···N hydrogen bonds. The crystal structures have been determined by X-ray crystal structure analysis. Compound 1 exists as a pair of tautomers 1a and 1b, and its dimer [R ₂²(6) motif] is formed by the tautomers 1a and 1b. Compound 2 only exists as a 2a tautomer, and interesting intermolecular N–H···O and O–H···N hydrogen bonds link two pyrazoles and two methanol molecules, leading to the formation of an R ₄⁴(10) dimer motif.     

Novel type of mixed O–H···N/O–H···π hydrogen bonds: monohydrate of pyridine

Investigation of characteristics of hydrogen bonding between pyridine and water by MP2/aug-cc-pvdz method reveals that these two molecules may form three types of hydrogen bonds depending on nature of proton withdrawal site of pyridine. Change of orientation of water with respect to plane of aromatic ring leads to transformation of the O–H···N bond to O–H···π bond via wide region of the potential energy surface where both lone pair of the nitrogen atom and π-system make significant contribution into hydrogen bonding. Hydrogen bond in this intermediate region may be considered as mixed O–H···N/O–H···π bond representing new type of H bonds.     

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.     

Effect of Substituents in Hydrolyzed Cephalosporins on Intramolecular O–H···N Bond

Russian Journal of Physical Chemistry A - Model molecular systems structurally similar to the transition state of the limiting step of the hydrolysis of cephalosporin antibiotics by the L1...     

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.     

Substituent effects on CL···N, S···N, and P···N noncovalent bonds

Cl, S, and P atoms have previously been shown as capable of engaging in a noncovalent bond with the N atom on another molecule. The effects of substituents B on the former atoms on the strength of this bond are examined, and it is found that the binding energy climbs in the order B = CH(3) < NH(2) < CF(3) < OH < Cl < NO(2) < F. However, there is some variability in this pattern, particularly for the NO(2) group. The A···N bonds (A = Cl, S, P) can be quite strong, amounting to as much as 10 kcal/mol. The binding energy arises from approximately equal contributions from its induction and electrostatic components, although the former becomes more dominant for the stronger bonds. The induction energy is due in large measure to the transfer of charge from the N lone pair to a B-A σ* antibonding orbital of the electron-acceptor molecule containing Cl, S, or P. These A···N bonds typically represent the lowest-energy structure on each potential energy surface, stronger than H-bonds such as NH···F, CH···N, or SH···N.     

From a localized H3O radical to a delocalized H3O+···e- solvent-separated pair by sequential hydration

The impact of microhydration on the electronic structure and reactivity of the H(3)O moiety is investigated by ab initio calculations. In the gas phase, H(3)O is a radical with spin density localized on its hydrogen end, which is only kinetically stable and readily decomposes into a water molecule and a hydrogen atom. When solvated by a single water molecule, H(3)O preserves to a large extent its radical character, however, two water molecules are already capable to shift most of the spin density to the solvent. With three solvating water molecules this shift is practically completed and the system is best described as a solvent-separated pair of a hydronium cation and a hydrated electron. The electronic structure of this system and its proton transfer reactivity leading to formation of a hydrogen atom already resemble those of a proton-electron pair in bulk water.     

N–H···O=P hydrogen-bonded dimers as the main structural motif of aminophosphonate diesters

Abstract  

Crystal and molecular structures of three aminophosphonate diesters, diethyl and dibutyl [α-(quinolin-3-ylamino)-N-benzyl]phosphonates (1 and 2) and dibutyl [α-anilino-(quinolin-3-yl)methyl]phosphonate (3) were reported and comparatively discussed. Characteristic structural features for these compounds are strong N–H···O=P hydrogen bonds that connect two organophosphorus molecules in cyclic centrosymmetric dimer. Phosphoryl oxygen forms additional interaction with a C–H donor from the nearby aromatic group. Dimer formation in solution was also confirmed using electrospray ionization mass spectrometry. Mass spectra of six structurally similar aminophosphonate derivatives, 1–3 along with diethyl [α-anilino-(quinolin-3-yl)methyl]phosphonate (4), diethyl and dibutyl [α-anilino-(quinolin-2-yl)methyl]phosphonates (5 and 6) were studied and dimolecular ions [2M + Na]⁺ and [2M + H]⁺ were observed.     

14N16O的LMR光谱测量及其相关同位素分子14N17O和14N18O的光谱分析

采用内脏式ＣＯ激光磁共振（ＬＭＲ）技术测量了~(14)Ｎ~(16)Ｏ的Ｘ~Ｘ Ｚｅｅｍａｎ跃迁谱，并对其进行了标识、在Ｈｕｎｄ情形（ａ）双原子分子结构模型的基础上，采 用先进的同位素分子参数标度函数，对已发表的~(14)Ｎ~mＯ（ｍ＝ １６， １７， １８）光谱实验数据及 测量的 ＬＭＲ光谱数据进行了统一的分析计算，得到~14Ｎ~16Ｏ分子基态的精确结构参数， 其精度比前人的结果提高了 １－ ２个数量级，并由此推导出~(14)Ｎ~(17)Ｏ及~(14)Ｎ~(18)Ｏ等同位素分 子的结构参数．     

Theoretical study of N–H· · ·O hydrogen bonding properties and cooperativity effects in linear acetamide clusters

We investigated geometry, energy, ${\nu_{{\text{N--H}}}}$ harmonic frequencies, ¹⁴N nuclear quadrupole coupling tensors, and ${n_{\rm O}\to \sigma _{{\text{N--H}}}^\ast}$ charge transfer properties of (acetamide) _n clusters, with n = 1 ? 7, by means of second-order Møller-Plesset perturbation theory (MP2) and DFT method. Dependency of dimer stabilization energies and equilibrium geometries on various levels of theory was examined. B3LYP/6-311++G** calculations revealed that for acetamide clusters, the average hydrogen-bonding energy per monomer increases from ?26.85 kJ mol^?1 in dimer to ?35.12 kJ mol^?1 in heptamer; i.e., 31% cooperativity enhancement. The n-dependent trend of ${\nu_{{\text{N--H}}}\,{and}\,^{14}}$ N nuclear quadrupole coupling values were reasonably correlated with cooperative effects in ${r_{{\text{N--H}}}}$ bond distance. It was also found that intermolecular ${n_{\rm O}\to \sigma_{{\text{N--H}}}^\ast}$ charge transfer plays a key role in cooperative changes of geometry, binding energy, ${\nu_{{\text{N--H}}}}$ harmonic frequencies, and ¹⁴N electric field gradient tensors of acetamide clusters. There is a good linear correlation between ¹⁴N quadrupole coupling constants, C _Q (¹⁴N), and the strength of Fock matrix elements (F _ij ). Regarding the ${n_{\rm O}\to \sigma_{{\text{N--H}}}^\ast}$ interaction, the capability of the acetamide clusters for electron localization, at the N–H· · ·O bond critical point, depends on the cluster size and thereby leads to cooperative changes in the N–H· · ·O length and strength, N–H stretching frequencies, and ¹⁴N quadrupole coupling tensors.     

Theoretical Study of the Dehydration Process of MgCl_2·4H_2O to MgCl_2·2H_2O

Density functional theory was employed to study the dehydration mechanism of MgCI_2·4H_2O. Analysis of potential energy surface(PES) of possible pathways indicated that the most possible way was one of the water molecules halfly dissociated with an elongated bond distance with Mg~(2+),where electrostatic interaction played a leading role; another water molecule dissociated sequentially. It was in agreement with the result from differencial thermal analysis. The dehydration process of MgCI_2·4H_2O was clarified theoretically,promoting the theoretical study of dehydration of MgCI_2·2H_2O.     

Conversion of N2O to N2 on MgO （001） Surface with Vacancy： A DFT Study

The adsorption and decomposition of NzO at regular and defect sites of MgO (001) surface have been studied using cluster models embedded in a large array of point charges (PCs) by DFT/B3LYP method. The results indicate that the MgO (001)surface with oxygen vacancies exhibits high catalytic reactivity toward N2O adsorptive-decomposition. It is different from the regular MgO surface or the surface with magnesium vacancies.Much elongation of O—N bond of N2O after adsorption at oxy-gen vacancy site with O end down shows that O—N bond has been broken with concurrent production of N2, leaving a regu-lar site instead of the original oxygen vacancy site (F center ).The MgO (001) surface with magnesium vacancies hardly ex-hibits catalytic reactivity. It can be concluded that N2O dissoci-ation likely occurs at oxygen vacancy sites of MgO (001) sur-face, which is consistent with the generally accepted viewpoint in the experiments. The potential energy surface (PES) reflects that the dissociation process of N2O does not virtually need to surmount a given energy barrier.     

Co-crystal/salt crystal structure disorder of trichloroacetic acid–N-methylurea complex with double system of homo- and heteronuclear O–H···O/N–H···O hydrogen bonds: X-ray investigation, ab initio and DFT studies

The X-ray diffraction studies revealed disorder of a trichloroacetic acid?CN-methylurea complex crystal structure, connected with a proton transfer via O?CH···O hydrogen bond. The observed structure corresponds to a co-existence of ionic (salt) and neutral (co-crystal) forms of the complex in the solid state in ratio 3:1, respectively. The geometrical analysis based on ab initio and density functional theory methods combined with the experimental research indicated that two different N-methylurea molecular conformations, defined by CNCN torsion angle, correspond to the neutral and the ionic form of the complex, respectively. The conformational changes seem to be connected with stabilization of the ionic structure after a proton transfer, as according to theoretical calculations this form of the complex (the ionic one) was unstable in the gas phase. A particular attention was focused on a system of a double intermolecular hydrogen bonds, O?CH···O and N?CH···O which join molecules into the title complex. The analysis of these interactions performed in terms of their geometry, energetic and topological electron density properties let for their classification into strong and medium strength hydrogen bonds. It was also found that the antibonding hydrogen bonding donor orbital occupation corresponded to the stabilization energy resulting from charge transfer in hydrogen bonds. Hence, it is postulated as a possible indicator of interaction strength.     

Negative ion photoelectron spectroscopy of N2O− and (N2O)−2

We have recorded the photoelectron spectra of the gas phase negative ions N₂O⁻ and (N₂O)₂⁻ both of which were prepared in a nozzle ion source. The shift between the maxima of the two spectra is interpreted in terms of the dissociation energy of the dimer ion.     

4[CuCl(C5H5N)4]·[W10O32]·2(C5H5N)·3H2O的合成及晶体结构

标题化合物是通过(NH_4)_2WS_4, CuCl_2·2H_2O在吡咤溶液中反应制得。晶体呈蓝色, 属三斜晶系, 空间群P1, 晶胞参数为:a=1.3555(7), b=1.3666(5), c=1.7860(13) nm, α=69.08(4)°, β=87.39(5)°, γ=70.72(4)。V=2.907(3) nm, Z=1, D_m=2.56 g cm~(-3)。结构由Patterson法和Fourier法测出。对5692个收集到的独立衍射数据进行计算, 最后R=0.046。结构测定表明, 晶体由W_(10)O_(32)~(4-), [CuCl(C_5H_5N)_4]~+, C_5H_5N和H_2O所组成。W_(10)O_(32)~(4-)的结构见图1, W原子处在O原子的八面体配位中, 彼此共边和共顶点相连。[CuCl(C_5H_5N)_4]~+的结构见图2, Cu原子由1个Cl和4个N原子配位, 呈略有变形的四方锥形, 这种离子是首次报导。C_5H_5N和H_2O填入正负离子堆积的空隙中。     

Synthesis,crystal structure,and catalytic performance of two 3-D supramolecular compounds: (C7N2H7)3(C7N2H6) · PMo12O40 · 2H2O and (C7N2H7)3(C7N2H6)2 · AsMo12O40 · 3H2O

Two organic–inorganic compounds based on Keggin building blocks have been synthesized by hydrothermal methods, (C₇N₂H₇)₃(C₇N₂H₆)?·?PMo₁₂O_40?·?2H₂O (1) and (C₇N₂H₇)₃(C₇N₂H₆)_2?·?AsMo₁₂O_40?·?3H₂O (2) (C₇N₂H₆?=?benzimidazole). Single-crystal X-ray analysis revealed that 1 crystallized in the triclinic system, P-1 space group with a?=?9.8980(4)?Å, b?=?11.2893(4)?Å, c?=?25.8933(9)?Å, α?=?93.307(2)°, β?=?90.630(2)°, γ?=?108.330(2)°, V?=?2740.68(18)?ų, Z?=?2, R ₁(F)?=?0.0740, ωR ₂(F ²)?=?0.1511, and S?=?1.037; 2 crystallized in the triclinic system, P-1 space group with a?=?12.3353(4)?Å, b?=?13.2649(4)?Å, c?=?20.2878(6)?Å, α?=?95.6630(10)°, β?=?100.1720(10)°, γ?=?99.3940(10)°, V?=?3195.72(17)?ų, Z?=?2, R ₁(F)?= 0.0329, ωR₂ (F ²)?=?0.1236, and S?=?1.088. The two compounds show a layer framework constructed from Keggin-polyoxoanion clusters and benzimidazole via hydrogen bonds and π–π stacking interactions, resulting in a 3-D supramolecular network. Both have high catalytic activity for oxidation of methanol. When the initial concentration of the methanol is 5.37?g?m^?3 in air and the flow velocity is 4.51?mL?min^?1, methanol is completely eliminated at 150°C for 1 (160°C for 2).     

The first C(O)NHP(O)-based phosphoric triamide structure with an N‒H···π hydrogen bonding: A combination of X-ray crystallography and theoretical study to evaluate the strength of hydrogen bonds

The hydrogen bond pattern of N-(4-methoxybenzoyl)-N′,N″-bis(4-methylbenzyl)-phosphoric triamide, C₂₄H₂₈N₃O₃P, (I), was investigated. In the crystal structure, the molecules are aggregated through N_CP―H···O═P and N_P―H···O═C hydrogen bonds in a one-dimensional arrangement parallel to the c axis (N_CP is the nitrogen atom in the C(O)NHP(O) segment and N_P stands for the two other nitrogen atoms bonded to the P atom). There is also a novel N_P?H···π hydrogen bond in the crystal which extends the aggregation of the molecules to a two-dimensional array parallel to the bc plane. A Cambridge Structural Database (CSD, version 5.37, Feb 2016) analysis shows that the N―H···π hydrogen bond was not observed in any of 156 [RC(O)NH]P(O)[NR¹R² Allen, F. H.; Taylor, R. Chem. Soc. Rev. 2004, 33, 463-475.[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]]₂ (R¹ ≠ H, R² = H or ≠ H) phosphoric triamide structures reported so far. The theoretical calculations at the B3LYP/6-311G^** level of theory (DFT, AIM, and NBO) were performed to evaluate the strengths of N_CP―H···O═P, N_P―H···O═C and N_P―H···π hydrogen bonds, considering two-aggregate molecular assemblies containing these hydrogen bonds. The calculations on the title compound suggest that the intermolecular N_CP―H···O═P hydrogen bond is stronger than N_P―H···O═C and N_P―H···π interactions. The hydrogen bond strength was investigated by NBO, topological analysis, geometry calculation, Hirshfeld surface analysis and experimental spectroscopic results, which are in agreement with each other.     

SH···N and SH···P blue-shifting H-bonds and N···P interactions in complexes pairing HSN with amines and phosphines

Quantum calculations at the MP2/aug-cc-pVDZ level examine complexes pairing HSN with aliphatic amines and phosphines. Complexes are cyclic and contain two attractive interactions. The first is a SH···N/P H-bond in which the S-H covalent bond contracts and shifts its stretching frequency to the blue, more so for amines than for phosphines. The second interaction is different for the amines and phosphines. The amines engage in a NH···N H-bond comparable in strength to the aforementioned SH···N interaction. In contrast, the second interaction in the phosphine complexes is a direct N···P attraction without an intervening H. This interaction is due in part to opposite partial charges on the N and P atoms, as well as covalent forces generated by charge transfer effects.