Investigations of molecular interactions in propionic acid–N,N-dimethyl formamide binary system—FTIR study

FTIR spectra of propionic acid (PA), N,N-dimethyl formamide (DMF) and its binary mixtures with varying molefractions of the PA were recorded in the region 500–3500 cm⁻¹, to investigate the formation of hydrogen bonded complexes in a mixed system. The observed features in ν(CO), δ(OC–N) and ν_as(CN) of DMF, ν(CO) and ν(CO) of PA have been explained in terms of the hydrogen bonding interactions between DMF and PA and dipole–dipole interaction. The intrinsic bandwidth for the vibrational modes ν_as(CN) and ν(CO) has been elucidated using Bondarev and Mardaeva model.     

Theoretical Study on the Hydrogen Bonding Interactions in Complexes of 5‐Hydroxytryptamine with Water

The energies, geometries and harmonic vibrational frequencies of 1:1 5‐hydroxytryptamine‐water (5‐HT‐H₂O) complexes are studied at the MP2/6‐311++G(d,p) level. Natural bond orbital (NBO), quantum theory of atoms in molecules (QTAIM) analyses and the localized molecular orbital energy decomposition analysis (LMO‐EDA) were performed to explore the nature of the hydrogen‐bonding interactions in these complexes. Various types of hydrogen bonds (H‐bonds) are formed in these 5‐HT‐H₂O complexes. The intermolecular C4H5^5‐HT···O^w H‐bond in HTW3 is strengthened due to the cooperativity, whereas no such cooperativity is found in the other 5‐HT‐H₂O complexes. H‐bond in which nitrogen atom of amino in 5‐HT acted as proton donors was stronger than other H‐bonds. Our researches show that the hydrogen bonding interaction plays a vital role on the relative stabilities of 5‐HT‐H₂O complexes.     

1,2,4-三氮杂苯-(H2O)n复合物氢键相互作用的密度泛函理论研究

用密度泛函理论方法在B3LYP/6-31++G**水平上对1,2,4-三氮杂苯-(H₂O)_n (n＝1, 2, 3)氢键复合物的基态进行了结构优化和能量计算, 结果表明复合物之间存在较强的氢键作用, 所有稳定复合物结构中形成一个N…H—O氢键并终止于弱O…H—C氢键的氢键水链的构型最稳定. 同时, 用含时密度泛函理论方法(TD-DFT)在TD-B3LYP/6-31++G**水平上计算了1,2,4-三氮杂苯单体及其氢键复合物的单重态第一¹(n, π^*)垂直激发能.     

Theoretical study of the interaction of a proton with the O, F and Cl atoms of enflurane (CHFCl–CF2–O–CHF2)

Ab initio MP2 and density functional B3LYP calculations were performed to investigate the interaction of a proton with the O, F and Cl atoms of enflurane (CHFCl–CF₂–O–CHF₂) in the gas phase. The study included the optimized structures, proton affinities, interactions energies and thermodynamic properties of protonated enflurane. The proton affinities (PAs) of the O and Cl atoms are 154.5 and 139.8 kcal mol⁻¹, respectively, whereas PAs of five of the fluorine atoms are between 143.6 and 165.5 kcal mol⁻¹ (MP2 results). In contrast to protonation at the O and Cl atoms, protonation at each of the F atoms of enflurane reveals a striking result, it leads to a cleavage of the C–F bond and formation of an ion–dipole complex between the enfluranyl cation and neutral hydrogen fluoride. The [(enfluranyl)⁺FH] complexes are weakly bound, the SAPT-calculated interaction energy varies between −12.5 and −11.7 kcal mol⁻¹. The long range attraction in these complexes is dominated by the electrostatic term (70%), whereas the induction and dispersion components contribute by about 15% each. Protonation at the chlorine atom of enflurane does not lead to a cleavage of the C–Cl bond. For the O-protonated enflurane the results from the natural bond orbital analysis (NBO) are discussed in details.     

Hydrogen bond strength in chromates with kröhnkite-type chains, K2Me(CrO4)2·2H2O (Me = Mg, Co, Ni, Zn, Cd)

Infrared spectra of the title compounds with kröhnkite-type infinite octahedral–tetrahedral chains, K₂Me(CrO₄)₂·2H₂O (Me = Mg, Co, Ni, Zn, Cd), are presented in the regions of the uncoupled O–D stretching modes of matrix-isolated HDO molecules (isotopically dilute samples) and water librations. The strengths of the hydrogen bonds are discussed in terms of the respective O_wO bond distances, the Me–water interactions (synergetic effect), the proton acceptor capability of the chromate oxygen atoms as deduced from Brown's bond valence sum of the oxygen atoms. The spectroscopic experiments reveal that hydrogen bonds of medium strength are formed in the chromates. The hydrogen bond strengths decrease in the order Cd > Zn > Ni > Co in agreement with the decreasing covalency of the respective Me–OH₂ bonds in the same order, i.e. decreasing acidity of the water molecules. The infrared band positions corresponding to the water librations confirm the claim that the hydrogen bonds in K₂Cd(CrO₄)₂·2H₂O are stronger than those formed in K₂Mg(CrO₄)₂·2H₂O on one hand, and on the other—the hydrogen bonds in K₂Ni(CrO₄)₂·2H₂O are stronger than those in K₂Co(CrO₄)₂·2H₂O.     

Olefin epoxidation catalyzed by [Ru(TDL)(tmeda)H2O] complexes (TDL = tridentate Schiff-base ligand; tmeda = tetramethylethylenediamine)

Mixed-chelate complexes of ruthenium have been synthesized using tridentate Schiff-base ligands (TDLs) derived from condensation of 2-aminophenol or 2-aminobenzoic acid with aldehydes (salicyldehyde, 2-pyridinecarboxaldehyde), and tmeda (tetramethylethylenediamine). [Ru^III(hpsd)(tmeda)(H₂O)]⁺ (1), [Ru^III(hppc)(tmeda)(H₂O)]²⁺ (2), [Ru^III(cpsd)(tmeda)(H₂O)]⁺ (3) and [Ru^III(cppc)(tmeda)(H₂O)]²⁺ (4) complexes (where hpsd²⁻ = N-(hydroxyphenyl)salicylaldiminato); hppc⁻ = N-(2-hydroxyphenylpyridine-2-carboxaldiminato); cpsd²⁻ = (N-(2-carboxyphenyl)salicylaldiminato); cppc⁻ = N-2-carboxyphenylpyridine-2-carboxaldiminato) were characterized by microanalysis, spectral (IR and UV–vis), conductance, magnetic moment and electrochemical studies. Complexes 1–4 catalyzed the epoxidation of cyclohexene, styrene, 4-chlorostyrene, 4-methylstyrene, 4-methoxystyrene, 4-nitrostyrene, cis- and trans-stilbenes effectively at ambient temperature using tert-butylhydroperoxide (t-BuOOH) as terminal oxidant. On the basis of Hammett correlation (log k_rel vs. σ⁺) and product analysis, a mechanism involving intermediacy of a [Ru–O–OBu^t] radicaloid species is proposed for the catalytic epoxidation process.     

Theoretical investigation of C–HM interactions in organometallic complexes: A natural bond orbital (NBO) study

The nature of C–HM agostic interactions in model metal complexes [M²⁺(CH₂CH₃)(PH₃)_nCl] (where M = Sc, Ti, V, Ti, Cr, Mn, Fe, Co, Ni, Cu, Zn; n = 1, 2, 3, 4) was studied with the natural bond orbital analysis (NBO) approach using density functional theory (DFT) optimized geometries at the B3LYP/6-31G(d,p) level of theory. The effect of nature of metal, coordination number, oxidation state and ligand field effects on the agostic interaction is examined. A set of 20 crystal structures of organometallic complexes taken from the Cambridge Structural Database (CSD) was studied computationally employing AIM theory and NBO analysis, and the applicability of these methods was critically accessed in demarcating the two types of interaction.     

A novel tubular hydrogen‐bond pattern in a new diazaphosphole oxide: a combination of X‐ray crystallography and theoretical study of hydrogen bonds

In the structure of 2‐(4‐chloroanilino)‐1,3,2λ⁴‐diazaphosphol‐2‐one, C₁₂H₁₁ClN₃OP, each molecule is connected with four neighbouring molecules through (N—H)₂…O hydrogen bonds. These hydrogen bonds form a tubular arrangement along the [001] direction built from R ³₃(12) and R ₄³(14) hydrogen‐bond ring motifs, combined with a C (4) chain motif. The hole constructed in the tubular architecture includes a 12‐atom arrangement (three P, three N, three O and three H atoms) belonging to three adjacent molecules hydrogen bonded to each other. One of the N—H groups of the diazaphosphole ring, not co‐operating in classical hydrogen bonding, takes part in an N—H…π interaction. This interaction occurs within the tubular array and does not change the dimension of the hydrogen‐bond pattern. The energies of the N—H…O and N—H…π hydrogen bonds were studied by NBO (natural bond orbital) analysis, using the experimental hydrogen‐bonded cluster of molecules as the input file for the chemical calculations. In the ¹H NMR experiment, the nitrogen‐bound proton of the diazaphosphole ring has a high value of 17.2 Hz for the ²J _H–P coupling constant.     

A theoretical study of the C–HN hydrogen bond in the methane–ammonia complex

The C–HN hydrogen bond in the methane–ammonia complex is studied by determining its bond dissociation energy (BDE) and the n(N)→σ^*(C–H) interaction. At the MP2(Full)/6-311++G(3df,2p) level of theory with basis set superposition error (BSSE) correction, the BDE was determined to be 2.5 kJ mol⁻¹. The n(N)→σ^*(C–H) interaction at this level of theory was found to be 3.7 kJ mol⁻¹ by natural bond orbital (NBO) analysis. It was also found that the NBO values are in general higher than the BDE values with BSSE correction when they are compared at the same level of theory.     

Density Functional Theory Study on Hydrogen Bonding Interaction of Catechin-(H2O)n

Density functional theory B3LYP method with 6‐31G* basis set has been used to optimize the geometries of the catechin, water and catechin‐(H₂O)_n complexes. The vibrational frequencies have been studied at the same level to analyze these complexes. Six and eleven stable structures for the catechin‐H₂O and catechin‐(H₂O)₂ have been found, respectively. Theories of atoms in molecules (AIM) and natural bond orbital (NBO) have been utilized to investigate the hydrogen bonds involved in all the systems. The interaction energies of all the complexes corrected by basis set superposition error, are from ?13.27 to ?83.56 kJ/mol. All calculations also indicate that there are strong hydrogen‐bonding interactions in catechin‐water complexes. The strong hydrogen‐bonding contributes to the interaction energies dominantly. The O–H stretching motions in all the complexes are red‐shifted relative to that of the monomer.     

Structures,vibrational frequencies,topologies, and energies of hydrogen bonds in cysteine‐formaldehyde complexes

The hydrogen bonding interactions between cysteine (Cys) and formaldehyde (FA) were studied with density functional theory regarding their geometries, energies, vibrational frequencies, and topological features of the electron density. The quantum theory of atoms in molecules and natural bond orbital analyses were employed to elucidate the interaction characteristics in the Cys‐FA complexes. The intramolecular hydrogen bonds (H‐bonds) formed between the hydroxyl and the N atom of cysteine moiety in some Cys‐FA complexes were strengthened because of the cooperativity. Most of intermolecular H‐bonds involve the O atom of cysteine/FA moiety as proton acceptors, while the strongest H‐bond involves the O atom of FA moiety as proton acceptor, which indicates that FA would rather accept proton than providing one. The H‐bonds formed between the CH group of FA and the S atom of cysteine in some complexes are so weak that no hydrogen bonding interactions exist among them. In most of complexes, the orbital interaction of H‐bond is predominant during the formation of complex. The electron density (ρ_b) and its Laplace (?²ρ_b) at the bond critical point significantly correlate with the H‐bond parameter δR, while a linearly relationship between the second‐perturbation energy E(2) and ρ_b has been found as well. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Theoretical studies of uracil–(H2O)n (n = 1–7) clusters by ab initio and ABEEMσπ/MM fluctuating charge model

Uracil–(H₂O)_n (n = 1–7) clusters were systemically investigated by ab initio methods and the newly constructed ABEEMσπ/MM fluctuating charge model. Water molecules have been gradually placed in an average plane containing uracil. The geometries of 38 uracil–water complexes were obtained using B3LYP/6-311++G** level optimizations, and the energies were determined at the MP2/6-311++G** level with BSSE corrections. The ABEEMσπ/MM potential model gives reasonable properties of these clusters when comparing with the present ab initio data. For interaction energies, the root mean square deviation is 0.96 kcal/mol, and the linear coefficient reaches 0.997. Furthermore, the ABEEMσπ charges changed when H₂O interacted with the uracil molecule, especially at the sites where the hydrogen bond form. These results show that the ABEEMσπ/MM model is fine giving the overall characteristic hydration properties of uracil–water systems in good agreement with the high-level ab initio calculations.     

Effect of Ethylene Glycol on the Molecular Organization of H2O in Comparison with Methanol and Glycerol: A Calorimetric Study

Excess partial molar enthalpies of ethylene glycol, H ^E _EG, in binary ethylene glycol–H₂O, and those of 1-propanol, H ^E _IP, in ternary 1-propanol–ethylene glycol (or methanol)–H₂O were determined at 25°C. From these data, the solute–solute interaction functions, H ^E _EG–EG = N(H ^E _EG/n _EG) and H ^E _1P–1P = N(H ^E _1P/n _1P), were calculated by graphical differentiation without resorting to curve fitting. Using these, together with the partial molar volume data, the effect of ethylene glycol on the molecular organization of H₂O was investigated in comparison with methanol and glycerol. We found that there are three concentration regions, in each of which the mixing scheme is qualitatively different from the other regions. Mixing scheme III operative in the solute-rich region is such that the solute molecules are in a similar situation as in the pure state, most likely in clusters of its own kind. Mixing scheme II, in the intermediate region, consists of two kinds of clusters each rich in solute and in H₂O, respectively. Thus, the bond percolation nature of the hydrogen bond network of liquid H₂O is lost. Mixing scheme I is a progressive modification of liquid H₂O by the solute, but the basic characteristics of liquid H₂O are still retained. In particular, the bond percolation of the hydrogen bond network is still intact. Similar to glycerol, ethylene glycol participates in the hydrogen bond network of H₂O via-OH groups, and reduces the global average of the hydrogen bond probability and the fluctuations inherent in liquid H₂O. In contrast to glycerol, there is also a sign of a weak hydrophobic effect caused by ethylene glycol. However, how these hydrophobic and hydrophilic effects of ethylene glycol work together in modifying the molecular organization of H₂O in mixing scheme I is yet to be elucidated.     

Synthesis, structure and DNA binding studies of mononuclear copper(II) complexes with mixed donor macroacyclic ligands, 2,6-bis({N-[2&3-(phenylselenato)alkyl]}benzimidoyl)-4-methylphenol

Two new phenol based macroacyclic Schiff base ligands, 2,6-bis({N-[2-(phenylselenato)ethyl]}benzimidoyl)-4-methylphenol (bpebmpH, 1) and 2,6-bis({N-[3-(phenylselenato)propyl]}benzimidoyl)-4-methylphenol (bppbmpH, 2) of the Se₂N₂O type have been prepared by the condensation of 4-methyl-2,6-dibenzoylphenol (mdbpH) with the appropriate (for specific reactions) phenylselenato(alkyl)amine. These ligands with Cu(II) acetate monohydrate in a 2:1 molar ratio in methanol form complexes of the composition [(C₆H₂(O)(CH₃){(C₆H₅)CN(CH₂)_nSe(C₆H₅)}{(C₆H₅)CO}₂Cu] (3 (n = 2), 4 (n = 3)) with the loss of phenylselenato(alkyl)amine and acetic acid. In both these complexes, one arm of the ligand molecule undergoes hydrolysis, and links with Cu(II) in a bidentate (NO) fashion, as confirmed by single crystal X-ray crystallography of complex 3. The selenium atoms do not form part of the copper(II) distorted square planar coordination sphere which has a trans-CuN₂O₂ core. The average Cu–N and Cu–O distances are, respectively, 1.973(3) and 1.898(2) Å. The N–Cu–N and O–Cu–O angles are, respectively, 167.4(11)° and 164.5(12)°. The compounds 1–4 have been characterized by elemental analysis, conductivity measurements, mass spectrometry, IR, electronic, ¹H and ⁷⁷Se{¹H} NMR spectroscopy and cyclic voltammetry. The interaction of complex 3 with calf thymus DNA has been investigated by a spectrophotometric method and cyclic voltammetry.     

Comparative analysis of blue‐shifted hydrogen bond versus conventional hydrogen bond in methyl radical complexes

Methyl radical complexes H₃C…HCN and H₃C…HNC have been investigated at the UMP2(full)/aug‐cc‐pVTZ level to elucidate the nature of hydrogen bonds. To better understand the intermolecular H‐bond interactions, topological analysis of electron density at bond critical points (BCP) is executed using Bader's atoms‐in‐molecules (AIM) theory. Natural bond orbital (NBO) analysis has also been performed to study the orbital interactions and change of hybridization. Theoretical calculations show that there is no essential difference between the blue‐shift H‐bond and the conventional one. In H₃C…HNC complex, rehybridization is responsible for shortening of the N? H bond. The hyperconjugative interaction between the single electron of the methyl radical and N? H antibonding orbital is up to 7.0 kcal/mol, exceeding 3.0 kcal/mol, the upper limit of hyperconjugative n(Y)→σ*(X–H) interaction to form the blue‐shifted H‐bond according to Alabugin's theory. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Fermi resonance and strong anharmonic effects in the absorption spectra of the ν-OH (ν-OD) vibration of solid H- and D-benzoic acid

The vibrational spectra of polycrystalline benzoic acid (BA) and its deuterated derivative were studied over the wide frequency region 4000–10 cm⁻¹ by IR and Raman methods. A theoretical analysis of the hydrogen bond frequency region and calculations at the B3LYP/6-311++G(2d, 2p) level for the benzoic acid cyclic dimer in the gas phase were made. In order to study the dynamics of proton transfer two formalisms were applied: Car–Parrinello Molecular Dynamics (CPMD) and Path Integrals Molecular Dynamics (PIMD). It was shown that the experimentally observed very broad ν-OH band absorption is the result of complex anharmonic interaction: Fermi resonance between the OH-stretching and bending vibrations and strong interaction of the ν-OH stretching with the low frequency phonons. The theoretical analysis in the framework of such an approach gave a good correlation with experiment. From the CPMD calculations it was confirmed that the O–HO bridge is not rigid, with the OO distance being described by a large amplitude motion. For the benzoic acid dimer we observed stepwise (asynchronous) proton transfer.     

Specific crystal structure of poly(3-hydroxybutyrate) thin films studied by infrared reflection–absorption spectroscopy

Infrared reflection–absorption (IR-RAS) and transmission spectra were measured for poly(3-hydroxybutyrate) (PHB) thin films to explore its specific crystal structure in the surface region. As IR-RAS is sensitive to the vibration mode of perpendicular orientation of the surface, differences between IR-RAS and transmission spectra indicate an orientation of the lamella structure in the surface of PHB thin films. The relative intensity of the crystalline CO stretching band in the IR-RAS spectrum is significantly weaker than that in the transmission spectrum. It may be concluded that the transient dipole moment of the CO stretching mode of the crystalline state is not oriented perpendicular but nearly parallel to the substrate surface. On the other hand, the relative intensity of the band at 3009 cm⁻¹ due to the C–H stretching mode of the C–HOC hydrogen bonding is similar between the IR-RAS and transmission spectra, suggesting that the C–H bond is oriented neither perpendicular nor parallel to the substrate surface but in an intermediate direction. Since the CO group of the C–HOC hydrogen bonding is oriented nearly parallel to the surface and its C–H group is in the intermediate direction, it is very likely that the C–HOC hydrogen bonding has a somewhat bent structure. These results are in good agreement with our previous conclusion that the C–HOC hydrogen bonding of PHB exists along the a-axis (not the b-axis) between the CH₃ group of one helix and the CO group of another helix.     

Facile hydrosilylation of norbornadiene by silanes R3SiH and R2SiH2 with molybdenum catalysts

Photochemically activated [Mo(CO)₆] and [Mo(CO)₄(η⁴-nbd)] have been demonstrated to be very effective catalysts for hydrosilylation of norbornadiene (nbd) by tertiary (Et₃SiH, Cl₃SiH) and secondary (Et₂SiH₂ and Ph₂SiH₂) silanes to give 5-silyl-2-norbornene, which under the same reaction conditions transform in ring-opening metathesis polymerization (ROMP) to unsaturated polymers and to a double hydrosilylation product, 2,6-bis(silyl)norbornane. The yield of a particular reaction depends very strongly on the kind of silane involved. The reaction products were identified by means of chromatography (GC–MS) and ¹H and ¹³C NMR spectroscopy. In photochemical reaction of [Mo(CO)₄(η⁴-nbd)] and Ph₂SiH₂ in cyclohexane-d₁₂, η²-coordination of the SiH bond to the molybdenum atom is supported by ¹H NMR spectroscopy due to the detection of two equal-intensity doublets with ²J_HH = 5.4 Hz at δ 6.12 and −5.86 ppm.     

An unprecedented Cu–Schiff base complex existing as two different trinuclear units with strong antiferromagnetic couplings

A new tetradentate N₂O₂ donor Schiff base ligand [OHC₆H₄CHNCH₂CH₂CH(CH₂CH₃)NCHC₆H₄OH = H₂L ] was obtained by 1:2 condensation of 1,3-diaminopentane with salicylaldehyde and has been used to synthesise an unusual copper(II) complex whose asymmetric unit presents two structurally different almost linear trinuclear units [Cu₃(μ-L)₂(ClO₄)₂] [Cu₃(μ-L)₂(H₂O)(ClO₄)₂] (1). The ligand and the complex were characterised by elemental analysis, FT-IR, ¹H NMR and UV–Vis spectroscopy in addition electrochemical and single crystal X-ray diffraction studies were performed for the complex. The magnetic properties of 1 reveal the presence of strong intra-trimer (J₁ = −202(3) cm⁻¹ and J₂ = −233(3) cm⁻¹) as well as very weak inter-trimer (zJ′ = −0.11(1) cm⁻¹) antiferromagnetic interactions.     

An ab initio study of the structures and enthalpies of the hydrogen-bonded complexes of the acids H2O,H2S,HCN, and HCl with the anions OH−, SH−, CN−, and Cl−

Ab initio calculations at second-order Møller-Plesset perturbation theory with the 6-31 + G(d,p) basis set have been performed to determine the equilibrium structures and energies of a series of negative-ion hydrogen-bonded complexes with H₂O, H₂S, HCN, and HCl as proton donors and OH^–, SH^–, CN^–, and Cl^– as proton acceptors. The computed stabilization enthalpies of these complexes are in agreement to within the experimental error of 1 kcal mol^–1 with the gas-phase hydrogen bond enthalpies, except for HOHOH^–, in which case the difference is 1.8 kcal mol^–1. The structures of these complexes exhibit linear hydrogen bonds and directed lone pairs of electrons except for complexes with H₂O as the proton donor, in which cases the hydrogen bonds deviate slightly from linearity. All of the complexes have equilibrium structures in which the hydrogen-bonded proton is nonsymmetrically bound, although the symmetric structures of HOHOH^– and ClHCl^– are only slightly less bound than the equilibrium structures. MP2/6-31 + G(d,p) hydrogen bond energies calculated at optimized MP2/B-31 + G(d,p) and at optimized HF/6-31G(d) geometries are similar. Using HF/6-31G(d) frequencies to evaluate zero-point and thermal vibrational energies does not introduce significant error into the computed hydrogen bond enthalpies of these complexes provided that the hydrogen-bonded proton is definitely nonsymmetrically bound at both Hartree-Fock and MP2.