A scheme for rapid prediction of cooperativity in hydrogen bond chains of formamides,acetamides, and N‐methylformamides

A scheme is proposed in this article to predict the cooperativity in hydrogen bond chains of formamides, acetamides, and N‐methylformamides. The parameters needed in the scheme are derived from fitting to the hydrogen bonding energies of MP2/6‐31+G** with basis set superposition error (BSSE) correction of the hydrogen bond chains of formamides containing from two to eight monomeric units. The scheme is then used to calculate the individual hydrogen bonding energies in the chains of formamides containing 9 and 12 monomeric units, in the chains of acetamides containing from two to seven monomeric units, in the chains of N‐methylformamides containing from two to seven monomeric units. The calculation results show that the cooperativity predicted by the scheme proposed in this paper is in good agreement with those obtained from MP2/6‐31+G** calculations by including the BSSE correction, demonstrating that the scheme proposed in this article is reasonable. Based on our scheme, a cooperativity effect of almost 240% of the dimer hydrogen bonding energy in long hydrogen bond formamide chains, a cooperativity effect of almost 190% of the dimer hydrogen bonding energy in long hydrogen bond acetamide chains, and a cooperativity effect of almost 210% of the dimer hydrogen bonding energy in long hydrogen bond N‐methylformamide chains are predicted. The scheme is further applied to some heterogeneous chains containing formamide, acetamide, and N‐methylformamide. The individual hydrogen bonding energies in these heterogeneous chains predicted by our scheme are also in good agreement with those obtained from Møller‐Plesset calculations including BSSE correction. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

N-Substituted α-trifluoromethyl β-nitro amines in the synthesis of fluorine-containing 1,2-diamines, amino alcohols, and β-amino acids

Reactions of 2-diazo-1,1,1-trifluoro-3-nitropropane or 1-trifluoromethyl-2-nitroethenes with amines and amino alcohols afforded N-mono- and N,N-disubstituted α-trifluoromethyl β-nitro amines, which were used to obtain a number of trifluoromethyl-containing 1,2-diamines, amino alcohols, and β-amino acids.     

Evaluation of the individual hydrogen bonding energies in N-methylacetamide chains

The individual hydrogen bonding energies in N-methylacetamide chains were evaluated at the MP2/6-31+G** level including BSSE correction and at the B3LYP/6-311++G(3df,2pd) level including BSSE and van der Waals correction. The calculation results indicate that compared with MP2 results, B3LYP calculations without van der Waals correction underestimate the individual hydrogen bonding energies about 5.4 kJ mol^?1 for both the terminal and central hydrogen bonds, whereas B3LYP calculations with van der Waals correction produce almost the same individual hydrogen bonding energies as MP2 does for those terminal hydrogen bonds, but still underestimate the individual hydrogen bonding energies about 2.5 kJ mol^?1 for the hydrogen bonds near the center. Our calculation results show that the individual hydrogen bonding energy becomes more negative (more attractive) as the chain becomes longer and that the hydrogen bonds close to the interior of the chain are stronger than those near the ends. The weakest individual hydrogen bonding energy is about ?29.0 kJ mol^?1 found in the dimer, whereas with the growth of the N-methylacetamide chain the individual hydrogen bonding energy was estimated to be as large as ?62.5 kJ mol^?1 found in the N-methylacetamide decamer, showing that there is a significant hydrogen bond cooperative effect in N-methylacetamide chains. The natural bond orbital analysis indicates that a stronger hydrogen bond corresponds to a larger positive charge for the H atom and a larger negative charge for the O atom in the N-H?O=C bond, corresponds to a stronger second-order stabilization energy between the oxygen lone pair and the N-H antibonding orbital, and corresponds to more charge transfer between the hydrogen bonded donor and acceptor molecules.     

Four different types of hydrogen bonds observed in 1,2-bis(N-benzenesulfonylamino)benzenes due to conformational properties of the sulfonamide moiety

The crystal structures of 1,2-bis(N-benzenesulfonylamino)benzenes with secondary and/or tertiary sulfonamide groups were determined by X-ray crystallographic analysis. Every Ar-sulfonamide group existed in synclinal conformation in the crystals even though it was secondary or tertiary. Each compound showed different types of hydrogen bonds in the crystal structure. 1,2-Bis(N-benzenesulfonylamino)benzene (1) formed two double hydrogen bonds connected to the next molecules, 1-(N-benzenesulfonylamino)-2-(N-benzenesulfonyl-N-methylamino)benzene (2) contained double hydrogen bond involved by both the sulfonamide moieties, 1,2-bis(N-4-toluenesulfonylamino)benzene (3) had both intra- and intermolecular hydrogen bonds, and 1-(N-methyl-N-4-toluenesulfonylamino)-2-(N-4-toluenesulfonylamino)benzene (4) had one double hydrogen bond involved by only one sulfonamide moiety. Sulfonamides 1 and 3 formed infinite arrays of the molecules, and sulfonamides 2 and 4 formed racemic dimer of their conformational enantiomers via the hydrogen bonds.     

Rapid Prediction of the Hydrogen Bond Cooperativity in N‐methylacetamide Chains

A method is proposed to rapidly predict the hydrogen bond cooperativity in N‐methylacetamide chains. The parameters needed are obtained from the fittings to the hydrogen bonding energies in the formamide chains containing 2 to 8 monomeric units. The scheme is then used to calculate the individual hydrogen bonding energies in N‐methylacetamide chains containing 2 to 7 monomeric units. The cooperativity predicted is in good agreement with those obtained from MP2/6‐31+G** calculations by including the BSSE correction. Our scheme is further employed to predict the individual hydrogen bonding energies in larger N‐methylacetamide chains containing up to 200 monomeric N‐methylacetamide units, to which the MP2 method cannot be applied. Based on our scheme, a cooperative effect of over 170 % of the dimer hydrogen bonding energy in long N‐methylacetamide chains is predicted. The method is also applied to heterogeneous chains containing formamide, acetamide, N‐methylformamide, and N‐methylacetamide. The individual hydrogen bonding energies in these heterogeneous chains are also in good agreement with those obtained from MP2 calculations with the BSSE correction, further demonstrating that our method is reasonable.     

Synthesis, structure and complexation of the fluorinated 1,3-enaminoketones containing at the nitrogen atom substituents with a terminal C≡C bond

The reaction of fluorinated lithium 1,3-diketonates with propargylamine hydrochloride and 1,1,1-trifluorpentane-2,4-dione or 1,1,1-trifluoro-4-methoxypent-3-en-2-one with propargylamine and 3-aminophenylacetylene were performed to obtain fluorinated 1,3-enaminones containing at a nitrogen atom substituents with terminal C≡C bonds: (Z)-1,1,1-trifluoro-4-(2-propynylamino)-3-pentene-2-one, (Z)-1,1,2,2-tetrafluoro-5-(2-propynylamino)-4-hexen-3-one, and 4-(3-ethynylphenylamino)-1,1,1-trifluoropentyl-3-en-2-one. Reactions of 4-(3-ethynyl-phenylamino)-1,1,1-trifluoro-pentyl-3-en-2-one with Cu(II) acetate or nanosized powder of copper or its oxides led to the respective chelate complex. The structure of (Z)-1,1,2,2-tetrafluoro-5-(2-propynylamino)-4-hexen-3-one and a copper complex of 4-(3-etinilphenylamino)-1,1,1-trifluoropenta-3-en-2-one was determined by XRD.     

Hydrogen-Bonding Interaction in a Complex of Amino Acid with <Emphasis Type="Italic">N</Emphasis>,<Emphasis Type="Italic">N</Emphasis>-Dimethylformamide Studied by DFT Calculations

Theoretical studies on hydrogen-bonded complexes between amino acids (glycine, alanine and leucine) and N,N-dimethylformamide (DMF) in gas phase have been carried out using density functional theory (DFT) and ab initio calculations at the B3LYP/6-311++G** and MP2/6-311++G** theory levels. The structures, binding energy, stretching frequency and bond characteristics of the mentioned complexes were calculated. The NH₂ and COOH groups of amino acids form different types of hydrogen bonds with the DMF molecule, as well as alkyl side chains. High binding energy suggests multiple hydrogen bonds present in one complex. The nearly linear OH???O and NH???O contacts are stronger than a conventional hydrogen bond interaction with their H???O separation between 1.74 and 2.14 Å. The weaker CH???O H-bond is also discussed as being a crucial interaction in biological systems involving amino acids. The formation of this interaction results in a blue shift in the CH stretching frequency.     

Density functional theory and topological analysis on the hydrogen bonding interactions in cysteine‐thymine complexes

Hydrogen bonding interactions between amino acids and nucleic acid bases constitute the most important interactions responsible for the specificity of protein binding. In this study, complexes formed by hydrogen bonding interactions between cysteine and thymine have been studied by density functional theory. The relevant geometries, energies, and IR characteristics of hydrogen bonds (H‐bonds) have been systematically investigated. The quantum theory of atoms in molecule and natural bond orbital analysis have also been applied to understand the nature of the hydrogen bonding interactions in complexes. More than 10 kinds of H‐bonds including intra‐ and intermolecular H‐bonds have been found in complexes. Most of intermolecular H‐bonds involve O (or N) atom as H‐acceptor, whereas the H‐bonds involving C or S atom usually are weaker than other ones. Both the strength of H‐bonds and the structural deformation are responsible for the stability of complexes. Because of the serious deformation, the complex involving the strongest H‐bond is not the most stable structures. Relationships between H‐bond length (ΔR_X‐H), frequency shifts (Δv), and the electron density (ρ_b) and its Laplace (?²ρ_b) at bond critical points have also been investigated. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Theoretical Studies on Energetic Property and Stability of Pyrazine and Pyridine Derivatives

Density functional calculations at the B3LYP level with 6‐311G** and aug‐cc‐pVDZ basis sets were performed to predict the heats of formation (HOFs) for two pyrazine derivatives and eight pyridine derivatives. In the isodesmic reactions designed for the computation of heats of formation (HOFs), pyrazine and pyridine were chosen as reference compounds. The N‐oxidations for the ring nitrogen of pyrazine and pyridine derivatives decrease the HOF values when N‐oxide oxygen is neighboring with amino groups, but increase when it neighbors with nitro groups. Thermal stability was evaluated via bond dissociation energies (BDE) at the UB3LYP/6‐311G** level. As a whole, the homolysis of C–NO₂ bonds is the main step for bond dissociation of the title compounds. The BDE values of title compounds are influenced by intramolecular hydrogen bonds. The hydrogen bond effects associated with the length of the H···O bonds were analyzed by the electron density at the critical points and natural bond orbital.     

Study of geometrical parameters in N-H...N type of hydrogen bonds

Geometrical parameters associated with N-H ... N types of hydrogen bonds have been analysed using crystal structure data on nucleic acids, amino acids and related compounds. Histograms depicting the frequency distribution of N-H ... N length (l) and H-N ... N angle (θ) have been drawn and conclusions on the favoured geometry of such bonds have been arrived at. The distribution ofl shows a pronounced maximum in the range between 2.9? and 3.0? with an overall average of 2.98 ?. The θ distribution shows a pronounced maximum for the hydrogen bond angle in the range 0°-10°, with a rapid fall-off in frequency for nonlinear hydrogen bonds. The frequency shows a cos⁶θ dependence as compared to cos²θ dependence term used earlier to predict the angular dependence of hydrogen bond potential energy in proteins and polypeptides.     

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.     

Hydrogen bonded aromatic hydrazide foldamers for the self-assembly of vesicles and gels

This paper describes an investigation of the structural and side-chain factors for the formation of vesicles and gels by hydrogen bonding-mediated aromatic hydrazide foldamers. Six foldamers and one straight analog that bear discrete side chains have been synthesized. SEM and AFM studies reveal that the molecules with the appended 2-(2-(dialkyl-amino)-2-oxoethylamino)-2-oxoethoxyl chains form vesicles, hydrogels or organogels, depending on the solvents. Both the inner amide units and the terminal N,N-dialkylamide units in the chains are revealed to play essential roles in controlling the self-assembly. The former facilitates it by forming the intermolecular hydrogen bonding, while the latter modulates it by providing solubility and balancing the hydrophobicity of the whole molecules in solvents of varying polarity.     

Synthesis and hydrogenation of (E)-γ-aryl-γ-morpholino-α-trifluoromethylated allyl alcohols through the reaction of trifluoroacetaldehyde ethyl hemiacetal with enamines

Treatment of trifluoroacetaldehyde ethyl hemiacetal with enamines, derived from acetophenone derivatives, at room temperature gave (E)-1,1,1-trifluoro-4-morpholino-4-aryl-but-3-en-2-ols, which are intermediates for preparation of the β-trifluoromethylated aldol products, 4,4,4-trifluoro-3-hydroxy-1-aryl-butan-1-ones. The structure of the intermediate (E)-1,1,1-trifluoro-4-morpholino-4-(4-nitrophenyl)-but-3-en-2-ols could be assigned by ¹H, ¹³C NMR, IR, and X-ray crystallography. Furthermore, hydrogenation and reductive deamination of the intermediate (E)-1,1,1-trifluoro-4-morpholino-4-aryl-but-3-en-2-ols with hydrogen in the presence of a catalytic amount (10 mol %) of palladium on carbon in trifluoroethanol proceeded smoothly at room temperature to give 1,1,1-trifluoro-4-aryl-2-butanols in good to excellent yields.     

Where gold meets a hydrogen bond?

This is a short survey of the area of the hydrogen bonding where the noble and coinage metal gold enters its manifold of the proton acceptors. It is largely focused on the nonconventional hydrogen bonds that are formed in the complexes of the auride anion Au⁻ with HF, (HF)₂, H₂O, (H₂O)₂, NH₃, and (NH₃)₂, as mostly experimentally investigated to date. A thorough comparison of the experimental and computational data on these nonconventional hydrogen bonds is the main motif of the present work.     

Copper(II)-saccharinato complexes with piperazine and N-(2-aminoethyl)piperazine ligands

Two copper(II) complexes of the saccharinate anion (sac) with piperazine (ppz) and N-(2-aminoethyl)piperazine (aeppz), namely [Cu(sac)₂(ppz)(H₂O)]_n (1) and trans-[Cu(sac)₂(aeppz)₂] (2), have been synthesized and characterized by elemental analyses, UV–Vis, FT-IR, TGA/DTA, X-ray diffraction and magnetic measurements. The ppz ligands in 1 bridge the copper(II) centers through both nitrogen atoms to form a 1D helical chain structure and the distorted trigonal-bipyramidal coordination geometry at each copper center is completed by an aqua and a pair of N-bonded sac ligands. The helical chains are linked by Ow–H?O hydrogen bonds to build a 2-D network. In complex 2, copper(II) ions are octahedrally coordinated by two sac anions and two neutral aeppz ligands, displaying a distorted octahedral coordination. Sac is O-bonded via the carbonyl group, while ppzea acts as a N,N′-bidentate chelating ligand. The molecules are connected by N–H?N and N–H?O hydrogen bonds, forming a linear chain. In the thermal decomposition of both complexes, the removal of the aqua and ppz or aeppz ligand takes place endothermically in the first stages and the sac moiety undergoes highly exothermic decomposition at higher temperatures to give CuO.     

N,N-二甲基乙酰胺与醇分子间相互作用的理论研究

采用密度泛函理论在B3LYP/6-311＋G*水平上对乙醇、丙醇、丁醇、戊醇与N,N-二甲基乙酰胺形成的1∶1氢键复合物进行计算研究. 结果表明: 醇与N,N-二甲基乙酰胺形成的复合物存在强的氢键, 表现为羰基氧原子的孤对电子与醇羟基反键σ轨道的相互作用. 振动分析显示, 分子间C＝O…H—O氢键的形成使C＝O和H—O伸缩振动频率明显红移. 溶剂对氢键产生较大的影响, 随着溶剂极性的增加, 复合物氢键有蓝移趋势.     

Synthesis, structures and reactions of some metallocene alcohols

E-1-Ferrocenyl-4,4-dimethylpent-2-ene-1-one has been synthesised from the Friedel-Crafts acylation of ferrocene with E-3-tert-butylacryloylchloride and converted to 1-ferrocenyl-3-chloro-4,4-dimethylpentan-1-one using ethereal hydrogen chloride. This new chloro ketone has been converted into three new ferrocene alcohols: 1-ferrocenyl-3,4-dimethyl-4-hydroxypentan-1-one, 1-ferrocenyl-3-chloro-4,4-dimethylpentan-1-ol, and 2,2,6,6-tetramethyl-3-ferrocenyl-5-chloroheptan-3-ol. A new dinuclear ferrocene derivative, E,E-2,2,9,9-tetramethyl-5,6-diferrocenyl-deca-3,7-diene, was isolated after treatment of 1-ferrocenyl-3-chloro-4,4-dimethylpentan-1-ol with acidic alumina; its structure was confirmed by X-ray crystallography, whilst electrochemistry revealed metal-metal interactions of similar magnitude to those seen for other 1,2-bis(ferrocenyl)ethane derivatives. Crystal structures have also been determined for 2,2,6,6-tetramethyl-3-ferrocenyl-5-chloroheptan-3-ol, rac-1-hydroxy[3]ferrocenophane, rac-1S,3S-1,3-diphenyl-1-hydroxy[3]ferrocenophane, and of rac-1,1^′-diphenyl-1,1^′-(1,1^′- ruthenocenediyl)dimethanol and show an intramolecular Cl?H-O hydrogen bond, a tetramer based on O?H-O hydrogen bonds, no hydrogen bonding, and a dimer with inter- and intramolecular O?H-O hydrogen bonds, respectively.     

Spectroscopic and Crystallographic Characterization of the R3N+−C−H⋅⋅⋅X Interaction

As appreciation for nonclassical hydrogen bonds has progressively increased, so have efforts to characterize these interesting interactions. Whereas several kinds of C−H hydrogen bonds have been well-studied, much less is known about the R₃N⁺−C−H⋅⋅⋅X variety. Herein, we present crystallographic and spectroscopic evidence for the existence of these interactions, with special relevance to Selectfluor chemistry. Of particular note is the propensity for Lewis bases to engage in nonclassical hydrogen bonding over halogen bonding with the electrophilic F atom of Selectfluor. Further, the first examples of ¹H NMR experiments detailing R₃N⁺−C−H⋅⋅⋅X (X=O, N) hydrogen bonds are described.     

Stabilizing role of lithium in structures of complex oxide compounds as an instrument for crystal chemical design

Various hydrogen bond lifetime distribution functions, used to describe the breaking and formation dynamics of these bonds in a computer experiment, are examined and relationships between them are found. The procedures for calculating these functions by the molecular dynamics method are described and the results for water models of 3456 molecules at 310 K are reported. The peak of short-lived spurious H-bonds, which results from short-time violations of hydrogen bonding criteria induced by dynamic intermolecular vibrations of molecules, prevails in the types of distributions most often referred to in the literature. A special distribution that appears to have not been used before is proposed. Along with short-lived bonds, it manifests long-lived ones whose lifetime is determined by the genuine, or random, hydrogen bond breaking rather than by dynamic. A technique to exclude dynamic effects and reveal the genuine H-bond breaking is proposed. This allows the evaluation of the average lifetime of “true” H-bonds that turns out to exceed 3 ps.     

氰化物与吡咯复合物氢键强度的理论研究

The R-C≡N…pyrrole (R=H, CH3, CH2F, CHF2, CF3, NH2, BH2, OH, F, CH2Cl, CHCl2, CCl3, Li, Na) complexes were considered as the simple sample for measure of hydrogen bonding strength. Density functional theory B3LYP/6-311 G^** level was applied to the optimization of geometries of complexes and monomers. Measure of hydrogen bonding strength based on geometrical and topological parameters, which were derived from the AIM theory, was analyzed. Additionally, natural bond orbital (NBO) analysis and frequency calculations were performed.From the computation results it was found that the electronic density at N-H bond critical points was also strictly correlated with the hydrogen bonding strength.