Contribution of the intramolecular hydrogen bond to the shift of the pKa value and the oxidation potential of phenols and phenolate anions

Intramolecularly OHO[double bond, length as m-dash]C hydrogen bonded phenols, 2-HO-C6H2-3,5-(t-Bu)2-CONH-t-Bu (1-OH), 2-HO-C6H2-5-t-Bu-1,3-(CONH-t-Bu)2 (2-OH) and 2-HO-C6H2-3,5-(t-Bu)2-NHCO-t-Bu (4-OH), were synthesized and their phenolate anions were prepared as tetraethylammonium salts (-1O-(NEt4+), 2-O-(NEt4+) and 4-O-(NEt4+)) with intramolecular NHO(oxyanion) hydrogen bonds. 4-HO-C(6)H(2)-3,5-t-Bu(2)-CONH-t-Bu (3-OH) and its phenolate anion, 3-O-(NEt4+), were synthesized as non-hydrogen bonded references. The presence of intramolecular hydrogen bonds was established through the crystallographic analysis and/or (1)H NMR spectroscopic results. Intramolecular NHO(phenol) hydrogen bonds shift the pK(a) of the phenol to a more acidic value. The results of cyclic voltammetry show that the intramolecular OH...O=C hydrogen bond negatively shifts the oxidation potential of the phenol. In contrast, the intramolecular NHO(oxyanion) hydrogen bond positively shifts the oxidation potential of the phenolate anion, preventing oxidation. These contributions of the hydrogen bond to the pKa value and the oxidation potentials probably play an important role in the formation of a tyrosyl radical in photosystem II.     

Marine natural products: Deodactol,antineoplastic sesquiterpenoid from the sea hare aplysia dactylomela

Deodactol, a halogenated bisabolene-type sesquiterpene alcohol, has been isolated from the sea hare Aplysia dactylomela, and its structure and absolute configuration have been determined by X-ray diffraction. The compound crystallizes in the monoclinic system with the following crystal data: a=6.723(2), b = 11.838(1), c= 10.962(2) Å, β=99.41(2)°, V= 860.7; ?x= 1.669 g cm^?3 at ?135±2°C; space group P2₁. The structure was solved by the heavy-atom method from 3-dimensional diffractometer data collected at ?135±2°C using CuK_α radiation. The final R factor for 1854 reflections is 0.029. The absolute configuration of the molecule was determined by the “R Method” of Hamilton. Deodactol has a strong intramolecular OHO hydrogen bond bridging its tetrahydropyranyl and cyclohexanol rings. The alcohol shows moderate cytotoxic activity. The absolute configuration of deodactol corresponds to that of several halogenated chamigrenes and supports the proposed biogenetic hypothesis linking halogenated bisabolenes and chamigrenes.     

Novel photosystem involving protonation and deprotonation processes modelled on a PYP photocycle

The synthesis of novel ortho-coumaric acid derivatives, with an amide group linked with an olefin moiety, which introduced photoinduced switching of the intramolecular hydrogen bonds is presented. An intramolecular OH...O=C hydrogen bond formed in a Z-phenol compound was switched to an intramolecular NH...O hydrogen bond in Z phenolate state via deprotonation. The pK(a) value of the Z-phenol derivative was lower than that of E-phenol, and a novel photocycle system involving protonation and deprotonation processes was achieved.     

Synthesis and Crystal Structure of (4R, 5R)(5-Hydroxymethyl-2,2-dimethyl- [1,3]dioxolan-4-yl)-bis-(4-methoxy-phenyl)-methanol

1　ＩＮＴＲＯＤＵＣＴＩＯＮＴｈｅα ,α ,α′,α′ ｔｅｔｒａａｒｙｌ 1 ,3 ｄｉｏｘｏｌａｎｅ 4,5 ｄｉｍｅｔｈａｎｏｌｓ (ＴＡＤＤＯＬＳ)ｄｉｏｌｓｗｈｉｃｈａｒｅｒｅａｄｉｌｙａｖａｉｌａｂｌｅｆｒｏｍａｌｋｙｌｔａｒｔｒａｔｅｓ ,ｈａｖｅｂｅｅｎｗｉｄｅｌｙｕｓｅｄａｓｃｈｉｒａｌｌｉｇａｎｄｓｉｎｅｎａｎｔｉｏｓｅｌｅｃｔｉｖｅａｄｄｉｔｉｏｎｒｅａｃｔｉｏｎｓｏｆｃａｒｂｏｎ ｃｅｎｔｅｒｅｄｎｕｃｌｅｏｐｈｉｌｅｓｔｏａｌｄｅｈｙ ｄｅｓ[1 ] ,ｉｎ [2 +2 ]ｃｙｃｌｏａｄｄｉｔｉｏｎｓ[2 ] …     

Crystal Structure of Ethoxyethyl 3-(2-Chloro-5-pyridyl methylamino)-2-cyano-4-methylpent-2-enoate

1 INTRODUCTION The nature and topography of the herbicide binding site in the reaction center of photosystem Ⅱ (PSⅡ) have been the subject of intense interest for many years. Among several commercially important herbicides with different structures such as atrazine and polypeptide of the PSII reaction center[1], the cyanoacrylates with general structure 1 have proved hightly potent and useful as probes[2, 3] of the receptor because their activities as inhibitors of photosynthetic ele…     

(Z)-2-羟基-3-苯甲酰丙烯酸甲酯的合成及晶体结构

标题化合物C11H10O4的晶体结构用X-射线单晶衍射法测定。晶体属单斜晶系, P21/c空间群, 晶胞参数a = 12.136(1), b = 5.559(1), c = 14.615(2) ? b = 96.758(3), V = 979.1(3) ?, Z = 4, Mr = 206.19, Dc = 1.399 g/cm3, F(000) = 432, m(MoKa) = 0.107 mm-1。晶体结构用直接法解出, 经全矩阵最小二乘法对原子参数进行修正, 最终的偏离因子为R = 0.0453, wR = 0.0990。标题化合物形成了1个大的共轭体系, 含有1个稳定的烯醇结构。结构测定表明还存在着1个分子内氢键的结构, 它使烯醇结构更加稳定。     

Synthesis and Crystal Structure of 1-（Trifluoromethyl）-1-（propioloyl）-（E）-3-oxo-（2-thienyl）-（2-naphthylamine）

1INTRODUCTIONTheSchiffbasesderivedfromb-diketonesandaliphaticamineshavebeenshowntoexistastheketo-amines.However,ifsubstituentseitherattheketooraminogrouparearomatic,itmaybeexpectedtheenoliminewillbethefavoredtautomericform[1].Recently,someSchiffbasesderivedfromTTA(4,4,4-trifluoro-1-(2-thienyl)-1,3-butanedione)andPMBPhavebeenstudiedbyWang[2]andYu[3]etal.Inordertostudytherelationshipbetweenthestructuresandperformancesofthesecompounds,thetitlecom-poundwillbereportedherein.2EXPERIMENT…     

Synthesis and Structure of N-（1,5-Dihydro-1-phenyl-3-methyl-4-benzoyl）-3-chloroaniline

1 INTRODUCTION 4-Acyl-5-pyrazolone, a family of flexible b- diketonate, is widely used as extract[1] and well known for its applications as analgesics, antipyre- tics, anti-inflammatory and insecticides[2]. Therefore the study on the derivation of 4-acyl-5-pyrazolone is the focus of many research groups working in the fields of coordination chemistry, biomedicine and pharmaceutical chemistry. In order to study the rela- tionship between the structure and performance of these compounds, w…     

ISOLATION AND X-RAY STRUCTURE CHARACTERIZATION OF (+)-ONONITOL FROM CHINESE CAESALPINIA CRISTAL

<正> The compound (+)-Ononitol was isolated from Chinese Caesalpinia Cristal and identified by X-ray structure analysis to be 4-0-methyl-myo-inositol-hydrate. C7H1406·H2O,Mr=212.2, triclinic, space group Pl,a=5.074 (1), b = 6.599(1), c = 7.750(1)A,α=106.02(1),β=93.47(1),γ= 109.09(2)°,V = 232.5 A3,Z=1, Dc=1.516 gcm-3, u(MoKa)=1.28 cm-1, R=0.034 for 1431 observed reflections. There is no intramolecular hydrogen bond in (+)-Ononitol, but intermolecular hydrogen bonds exist between water molecule and hydroxy group as well as between hydroxy groups.     

Synthesis and Structure Analysis of N-（Dehydroabietyl）maleamic Acid

N-(Dehydroabietyl)maleamic acid was synthesized from dehydroabietylamine and maleic anhydride.Its structure was characterized by IR,1 H-and 13 C-NMR spectra.The stereo structure of the title compound was also unambiguously confirmed by X-ray crystal structure analysis.The white crystal crystallizes in the monoclinic system,space group P2 1 with a=12.075(2),b=10.377(2),c=17.840(4),β=100.31(3) °,V=2199.3(8) 3,R=0.0618 and wR=0.1437.Two crystallographically independent molecules with different conformations co-exist in the unit.In each molecule,the two cyclohexane rings form a trans ring junction with chair and half-chair conformations,respectively.The C=C double bond between two carbonyl groups is in a Z configuration.Intermolecular and intramolecular hydrogen bonds coexist to stabilize the structure.     

Synthesis and Crystal Structure of Cis-syn Cyclobutane 1-（Carboxyethyl）thymine Dimer Monopentyl Amide Monotryptophan Methyl Ester Amide

The crystal structure of the title compound (C34H47N7O9, Mr = 697.79) has been determined by single-crystal X-ray diffraction. The crystal belongs to monoclinic, space group P21 with a = 9.000(8), b = 11.360(10), c = 17.841(15) , β = 97.083(14)°, V = 1810(3) 3, Z = 2, F(000) = 744, Dc = 1.280 g/cm3, μ = 0.094 mm-1, the final R = 0.0721 and wR = 0.1942 for 2479 observed reflections with I > 2σ(I). The two methyl groups attached to the cyclobutane ring are cis oriented. An intramolecular hydrogen bond (N(6)-H(6)…O(8)) introduces rigidity into the title molecule and the crystal structure is stabilized by intermolecular N-H…O hydrogen bonds.     

Synthesis and Crystal Structure of Cis 2-（6-Chloro-3-pyridylmethylamino）-4-chlorophenyl- 5,5-dimethyl- 1,3,2-dioxaphosphinane 2-Oxides

1 INTRODUCTION Neonicotinioid insecticides as nicotinic acetyl-choline receptor inhibitors have attracted increasingattention because of its safety, low toxicity, wide andhigh activities[1, . A lot of new insecticides such as 2]imidacloprid, acetamiprd and nitenpyram have beencommercialized. It is found that most biologicallyactive nicotinic compounds contain 3-aminomethyl-pyridine moiety[3]. Due to their wide biological acti-vities, organic phosphorus heterocyclic compoundsplay an import…     

Investigating the effect of hydrogen bonding environments in amide cleavage reactions at zinc(II) complexes with intramolecular amide oxygen co-ordination

Amide oxygen co-ordination to a zinc(II) ion around a hydrogen bonding microenvironment is a common structural/functional feature of metalloproteases. We report two strategies to position hydrogen bonding groups in the proximity of a zinc(II)-bound amide oxygen, and we investigate their effect on the stability of the amide group. Polydentate tripodal ligands (6-R1-2-pyridylmethyl)-R2 (R1= NHCOtBu, R2= N(CH2-py-6-X)2 X = H L1, X = NH2, H L2, X = NH2 L3) form [(L)Zn]2+ cations (L =L1, 1; L2, 2; L3, 3) with intramolecular amide oxygen co-ordination (1-3), and intramolecular N-H...O=C(amide) hydrogen bonding (2, 3) rigidly fixed by the ligand framework. 1-3 undergo cleavage of the tert-butyl amide upon addition of Me4NOH.5H2O (1 equiv.) in methanol at 50(1) degrees C. Under these conditions the half-life, t(1/2), of the amide bond is 0.4 h for 1, 9 h for 2 and 320 h for 3. Mononuclear zinc(II) complexes of (6-NHCOtBu-2-pyridylmethyl)-R2(R2= N(CH2CH2)2S) L4 and chelating N2 ligands without hydrogen bonding groups (1,10-phenanthroline L5, 2-(aminomethyl)pyridine L6) as control compounds, and with an amino hydrogen bonding group (6-amino-2-(aminomethyl)pyridine L7) have been synthesised. Amide cleavage is in this case faster at the zinc(II) complex with the amino hydrogen bonding group. Thus, hydrogen bonding environments can both accelerate and slow down amide bond cleavage reactions at zinc(II) sites. Importantly, the magnitude of the effect exerted by the hydrogen bonding environments was found to be significant; 800-fold rate difference. This result highlights the importance of hydrogen bonding environments around metal centres in amide cleavage reactions, which may be relevant to the chemistry of natural metalloproteases and applicable to the design of more efficient artificial protein cleaving agents.     

Synthesis and Crystal Structure of 2-(4''-Methylphenoxy)-5,8,9-trimethyl-3-phenyl Thieno[3'',2'':5,6]pyrido[4,3-d]pyrimidin-4-(3H)-one Hydrochloride

The title compound 2-(4′-methylphenoxy)-5,8,9-trimethyl-3-phenyl thieno[3′,2′:5,6]pyrido[4,3-d]pyrimidin-4(3H)-one hydrochloride (C26H23Cl4N3O2S, Mr = 583.33) has been deter- mined by single-crystal X-ray diffraction. The crystal belongs to monoclinic, space group P21/c with a = 14.8442(11), b = 11.5131(8), c = 17.2010(13) (A), β = 113.7250(10)o, V = 2691.3(3) (A)3, Z = 4, Dc = 1.440 g/cm3, S = 1.094, μ = 0.547 mm-1, F(000) = 1200, the final R = 0.0571 and wR = 0.1458. X-ray analysis reveals that the title compound combines with a molecule of dichloromethane by an intramolecular hydrogen bond. The thienopyridine ring is almost coplanar, and the dihedral angle between the thiophene plane and the pyridine plane is 0.6o.     

Neutral and ionic hydrogen bonding in Schiff bases

Low-temperature, high-resolution X-ray studies of charge distributions in the three Schiff bases, the dianil of 2-hydroxy-5-methylisophthaldehyde, 3,5-dinitro-N-salicylidenoethylamine and 3-nitro-N-salicylidenocyclohexylamine, have been carried out. These structures exhibit interesting weak interactions, including two extreme cases of intramolecular hydrogen bonds that are ionic N(+)-H...O- and neutral O-H...N in nature. These two types of hydrogen bond reflect differences in geometrical parameters and electron density distribution. At the level of geometry, the neutral O-H...N hydrogen bond is accompanied by an increase in the length of the C(1)-O(1) bond, opening of the ipso-C(1) angle, elongation of the aromatic C-C bonds, shortening of the C(7)-N(2) bond and increased length of the C(1)-C(7) bond, relative to the ionic hydrogen bond type. According to the geometrical and critical point parameters, the neutral O-H...N hydrogen bond seems to be stronger than the ionic ones. There are also differences between charge density parameters of the aromatic rings consistent with the neutral hydrogen bond being stronger than the ionic ones, with a concomitant reduction in the aromaticity of the ring. Compounds with the ionic hydrogen bonds show a larger double-bond character in the C-O bond than appears in the compound containing a neutral hydrogen bond; this suggests that the electronic structure of the former pair of compounds includes a contribution from a zwitterionic canonical form. Furthermore, in the case of ionic hydrogen bonds, the corresponding interaction lines appear to be curved in the vicinity of the hydrogen atoms. In the 3-nitro-N-salicylidenocyclohexylamine crystal there exists, in addition to the intramolecular hydrogen bond, a pair of intermolecular O...H interactions in a centrosymmetric dimer unit.     

Contribution of intramolecular C=O...H-N hydrogen bonding to the solvent-induced reentrant phase separation of poly(N-isopropylacrylamide)

Changes in the local environment around amide groups of poly(N-isopropylacrylamide) (PNiPA) during a solvent-induced reentrant phase separation have been investigated by infrared spectroscopy combined with quantum chemical calculations. The addition of methanol or tetrahydrofuran as a cosolvent to an aqueous solution of PNiPA causes spectral changes in the amide I regions. By preparing a dimer model compound for PNiPA, we can establish the assignment of the amide I bands for the polymer in solutions. Hydrogen-deuterium exchange experiments of the amide protons of PNiPA and its dimer models have revealed that the amide groups of PNiPA form an intramolecular C=O...H-N hydrogen bond even in a good solvent. The result has suggested that the change in the amide I envelope of PNiPA observed during the solvent-induced phase transition reflects the modification of the intramolecular C=O...H-N hydrogen bond of PNiPA as well as the variation in solvation state of the amide groups. On the basis of the assignment, we have discussed contributions of the intramolecular C=O...H-N hydrogen bond to the phase behavior of PNiPA.     

Synthesis and Crystal Structure of (E)-Ethyl (9-bromo-5-oxo-4-phenyl-1,10b-dihydro-5H-pyrano [3,4-c] chromen-2-ylidene) Acetate

The crystal structure of the title compound (C22H17BrO5 , Mr = 441.27) has been determined by single-crystal X-ray diffraction. The crystal is of orthorhombic system, space group Pna21 with a = 11.76(1), b = 14.58(1), c = 11.52(1), V = 1973.93 , Z = 4, Dc = 1.485 g/cm3 , F(000) = 896, μ(MoKα) = 2.113 mm-1 , the final R = 0.0394 and wR = 0.0809 for 3918 observed reflections (Ⅰ > 2 (Ⅰ)). The single-crystal X-ray diffraction data indicate that the C=C bond is in an E-configuration. The intramolecular C(10)-H(10B)···O(4) and intermolecular C(17)-H(17)···O(4) hydrogen bonds contribute to the stability of the structure.     

二茂铁基正庚基β-二酮的合成及晶体结构

在氢化钠存在下,用乙酰基二茂铁与正辛酸乙酯进行缩合反应,合成了标题化合物FeCOCH2COC7H15(Fc=C5H5FeC5H4).X射线衍射测定其晶体学数据为:C20H26FeO2,空间群P21/n,a=0.5790(1)nm,b=4.1634(4)nm,c=0.7635(1)nm,β=101.39(1)°,Z=4.最终的偏离因子R=0.050.结构分析表明,该化合物分子以烯醇式形式存在,通过分子内氢键,形成六元环,环中O…H氢键距离为0.146nm.β-二羰基中与正庚基相连接的羰基易于烯醇化。     

The crystal structure of 5-amino-6-chloro-4-nitro-2-(β-D-ribofuranosyl)-2H-pyridazin-3-one

The nucleoside, 5-amino-6-chloro-4-nitro-2-β-D-ribofuranosyl-2H-pyridazin-3-one ( 4 ), was synthesized as part of a study to prepare potential chemotherapeutic compounds. An X-ray crystal structure study of the compound was initiated in order to substantiate its formula and to examine its conformation and absolute configuration. The structure was determined using direct methods and refined to an R of 0.020 (R_w = 0.024). The compound has a glycosyl torsion angle of 71.2°. The structure contains three intermolecular hydrogen bonds and one intramolecular hydrogen bond.     

Shape of 4S- and 4R-hydroxyproline in gas phase

The alpha-amino acids 4(S)-hydroxyproline and 4(R)-hydroxyproline have been studied under isolation conditions in gas phase using laser-ablation molecular-beam Fourier transform microwave spectroscopy. Two conformers of each molecule have been detected in the jet-cooled rotational spectrum. The most stable conformer in both molecules exhibits an intramolecular N...H-O hydrogen bond (configuration 1) between the hydrogen atom of the carboxylic group and the nitrogen atom. The second conformer is characterized by an intramolecular N-H...O=C hydrogen bond (configuration 2). The conformers of 4(R)-hydroxyproline adopt a C(gamma)-exo puckering, while those of 4(S)-hydroxyproline present a C(gamma)-endo ring conformation. These ring conformations, which show the same propensity observed in collagen-like peptides, are stabilized by additional intramolecular hydrogen bonds involving the 4-hydroxyl group, with the exception of the most stable form of 4(S)-hydroxyproline for which a n-pi interaction between the oxygen atom of the 4-hydroxyl group and the carboxyl group carbon seems to be established. A gauche effect could be also contributing to stabilize the observed conformers.