Hydro­gen‐bonded adducts of ferrocene‐1,1′‐diyl­bis­(di­phenyl­methanol): monomeric and polymeric adducts with 1,2‐bis(4‐pyridyl)­ethene and 1,6‐di­amino­hexane

In the adduct ferrocene‐1,1′‐diyl­bis­(di­phenyl­methanol)–1,2‐bis(4‐pyridyl)­ethene (1/1), [Fe(C₁₈H₁₅O)₂]·C₁₂H₁₀N₂, there is an intramolecular O—H?O hydrogen bond in the ferro­cene­diol component and a single O—H?N hydrogen bond linking the diol to the di­amine, which is disordered over two sets of sites, so forming a finite monomeric adduct. In the adduct ferrocene‐1,1′‐diyl­bis­(di­phenyl­methanol)–1,6‐di­amino­hexane (2/1), 2[Fe(C₁₈H₁₅O)₂]·C₆H₁₆N₂, the amine lies across a centre of inversion in space group P. There is an intramolecular O—H?O hydrogen bond in the ferrocenediol, and the molecular components are linked by O—H?N and N—H?O hydrogen bonds, one of each type, into a C(13)[R(12)] chain of rings.     

Intramolecular Hydrogen Bonding In N-(2-Amino-2-Deoxy-β-D-Glucopyranoside)-N'-Carbamoyl-L-Dipeptidylesters: An Infrared And 1H Nmr Study

ABSTRACT

Ten N-(2-amino-2-deoxy-β-D-glucopyranoside)-N'-carbamoyl-L-dipeptidylesters with different amino acid sequences in the dipeptide unit were studied by means of IR and ¹H NMR spectroscopy. In the IR spectra three bands at 3453, 3420 and 3390 cm^-1 were observed which could be assigned to the free NH, the intramolecularly hydrogen bonded NH species forming five-membered, C₅, and seven-membered, C₇, rings, respectively. Comparing the NH band positions which correspond to the C₇ rings of the Gly-Xaa and the Xaa-Gly dipeptidylesters, the signals of the Xaa-Gly sequence were shifted by 10 cm^-1 to lower wave numbers indicating stronger hydrogen bonds. The temperature effect dv/dT was an order of magnitude larger for the C₇ associates than for C₅ showing the highest enthalpy of the C₇ hydrogen bond. The ¹H NMR spectra give three separate signals for the NH groups. The temperature coefficient ?δ/?T was the largest for N-1-H indicating the formation of less stable hydrogen bonds (C₇). The solvent induced changes of the chemical shift of the NH signals was lowest for the N-3-H signal. Obviously the deshielding properties on this function do not vary in dependence of the solvent polarity. The hydrogen/deuterium exchange rate was lowest for the N-6-H proton indicating the lower accessibility of this proton. Combining the results of both spectroscopic methods it can be concluded that the N-1-H forms only C₇ rings whereas N-6-H can participate in C₅ and C₇ intramolecular hydrogen bonds. The strength of the formed C₇ associates depends on the amino acid sequence in the dipeptide residue.     

Hydro­gen‐bonded adducts of ferrocene‐1,1′‐diyl­bis­(di­phenyl­methanol): a finite cyclic 1:1 adduct with 2,2′‐dipyridyl­amine

In ferrocene‐1,1′‐diyl­bis­(di­phenyl­methanol)–2,2′‐dipyridyl­amine (1/1), [Fe(C₁₈H₁₅O)₂]·C₁₀H₉N₃, (I), there is an intramolecular O—H?O hydrogen bond [H?O 2.03 Å, O?O 2.775 (2) Å and O—H?O 147°] in the ferrocenediol component, and the two neutral molecular components are linked by one O—H?N hydrogen bond [H?N 1.96 Å, O?N 2.755 (2) Å and O—H?N, 157°] and one N—H?O hydrogen bond [H?O 2.26 Å, N?O 3.112 (2) Å and N—H?O 164°] forming a cyclic R(8) motif. One of the pyridyl N atoms plays no part in the intermolecular hydrogen bonding, but participates in a short intramolecular C—H?N contact [H?N 2.31 Å, C?N 2.922 (2) Å and C—H?N 122°].     

Relationships between the acidity of the Z and E isomers of N-Nitroso-N-alkyl-α-amino acids and their conformations

The acidity constants of both Z and E conformational isomers of five N-nitroso-N-alkyl-α-amino acids, ON? N(R₁)? CH(R₂)? COOH, are determined by the observation of selected pH titrated ¹H NMR signals. For two glycine derivatives (1, R₁?CH₃, R₂?H, ON? Sar; 2, R₁?C₂H₅, R₂?H, ON? EtGly) and two alanine derivatives (3, R₁?CH₃, R₂?CH₃, ON? MeAla; 4, R₁?C₂H₅, R₂?CH₃, ON? EtAla) the E isomers appear to be stronger acids than the Z while for the third alanine derivative (5, R₁?n-C₃H₇, R₂?CH₃, ON? PrAla) the opposite is observed. These results, also including anisotropy effects associated with the N? NO group, are discussed in terms of conformations. A 7-membered ring conformation with an ? NO…HOOC? intramolecular hydrogen bond is proposed to be statistically important in the Z isomers of 1, 2, 3 and, to a lesser extent, 4.     

Intramolecular hydrogen bond in the hydroxycyclohexadienyl peroxy radicals

The hydroxycyclohexadienyl peroxy radicals (HO? C₆H₆? O₂) produced from the reaction of OH‐benzene adduct with O₂ were studied with density functional theory (DFT) calculations to determine their characteristics. The optimized geometries, vibrational frequencies, and total energies of 2‐hydroxycyclohexadienyl peroxy radical II_s and 4‐hydroxycyclohexadienyl peroxy radical III_s were calculated at the following theoretical levels, B3LYP/6‐31G(d), B3LYP/6‐311G(d,p), and B3LYP/6‐311+G(d,p). Both were shown to contain a red‐shifted intramolecular hydrogen bond (O? H … O? H bond). According to atoms‐in‐molecules (AIM) analysis, the intramolecular hydrogen bond in the 2‐hydroxycyclohexadienyl peroxy radical II_s is stronger than that one in 4‐hydroxycyclohexadienyl peroxy radical III_s, and the former is the most stable conformation among its isomers. Generally speaking, hydrogen bonding in these radicals plays an important role to make them more stable. Based on natural bond orbital (NBO) analysis, the stabilization energy between orbitals is the main factor to produce red‐shifted intramolecular hydrogen bond within these peroxy radicals. The hyperconjugative interactions can promote the transfer of some electron density to the O? H antibonding orbital, while the increased electron density in the O? H antibonding orbital leads to the elongation of the O? H bond and the red shift of the O? H stretching frequency. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Hydrogen bonding in C‐substituted nitroanilines: molecular ladders in 2‐trifluoromethyl‐4‐nitroaniline and sheets of R(12) and R(32) rings in 3‐trifluoromethyl‐4‐nitroaniline

In 2‐tri­fluoro­methyl‐4‐nitro­aniline, C₇H₅F₃N₂O₂, (I), the mol­ecules lie across a mirror plane in space group Pnma. The mol­ecules are linked by paired N—H?O hydrogen bonds to form a C(8)[R(6)] chain of rings, pairs of which are linked into a molecular ladder by a single C—H?O hydrogen bond. The isomeric 3‐tri­fluoro­methyl‐4‐nitro­aniline, (II), has Z′ = 2 in space group P2₁/c. Each mol­ecule is linked to four others by N—H?O hydrogen bonds to form sheets built from alternating R(12) and R(32) rings.     

N‐(tert‐Butoxycarbonyl)‐α‐aminoisobutyryl‐α‐aminoisobutyric acid methyl ester: two polymorphic forms in the space group P21/n

The title compound (systematic name: methyl 2‐{2‐[(tert‐butoxycarbonyl)amino]‐2‐methylpropanamido}‐2‐methylpropanoate), C₁₄H₂₆N₂O₅, (I), crystallizes in the monoclinic space group P2₁/n in two polymorphic forms, each with one molecule in the asymmetric unit. The molecular conformation is essentially the same in both polymorphs, with the α‐aminoisobutyric acid (Aib) residues adopting ϕ and ψ values characteristic of α‐helical and mixed 3₁₀‐ and α‐helical conformations. The helical handedness of the C‐terminal residue (Aib2) is opposite to that of the N‐terminal residue (Aib1). In contrast to (I), the closely related peptide Boc‐Aib‐Aib‐OBn (Boc is tert‐butoxycarbonyl and Bn is benzyl) adopts an α_L‐P_II backbone conformation (or the mirror image conformation). Compound (I) forms hydrogen‐bonded parallel β‐sheet‐like tapes, with the carbonyl groups of Aib1 and Aib2 acting as hydrogen‐bond acceptors. This seems to represent an unusual packing for a protected dipeptide containing at least one α,α‐disubstituted residue.     

Surfing π Clouds for Noncovalent Interactions: Arenes versus Alkenes

A comparative study of molecular balances by NMR spectroscopy indicates that noncovalent functional‐group interactions with an arene dominate over those with an alkene, and that a π‐facial intramolecular hydrogen bond from a hydroxy group to an arene is favored by approximately 1.2 kJ mol^?1. The strongest interaction observed in this study was with the cyano group. Analysis of the series of groups CH₂CH₃, CH?CH₂, C?CH, and C?N shows a correlation between conformational free‐energy differences and the calculated charge on the C^α atom of these substituents, which is indicative of the electrostatic nature of their π interactions. Changes in the free‐energy differences of conformers show a linear dependence on the solvent hydrogen bond acceptor parameter β.     

Methyl 2‐benzamido‐4‐(3,4‐dimethoxyphenyl)‐5‐methylbenzoate and N‐{5‐benzoyl‐2‐[(Z)‐2‐methoxyethenyl]‐4‐methylphenyl}benzamide

Methyl 2‐benzamido‐4‐(3,4‐dimethoxyphenyl)‐5‐methylbenzoate, C₂₄H₂₃NO₅, (Ia), and N‐{5‐benzoyl‐2‐[(Z)‐2‐methoxyethenyl]‐4‐methylphenyl}benzamide, C₂₄H₂₁NO₃, (IIa), were formed via a Diels–Alder reaction of appropriately substituted 2H‐pyran‐2‐ones and methyl propiolate or (Z)‐1‐methoxybut‐1‐en‐3‐yne, respectively. Each of these cycloadditions might yield two different regioisomers, but just one was obtained in each case. In (Ia), an intramolecular N—H...O hydrogen bond closes a six‐membered ring. A chain is formed due to aromatic π–π interactions, and a three‐dimensional framework structure is formed by a combination of C—H...O and C—H...π(arene) hydrogen bonds. Compound (IIa) was formed not only regioselectively but also chemoselectively, with just the triple bond reacting and the double bond remaining unchanged. Compound (IIa) crystallizes as N—H...O hydrogen‐bonded dimers stabilized by aromatic π–π interactions. Dimers of (IIa) are connected into a chain by weak C—H...π(arene) interactions.     

Hydrogen‐bonded sheets of R22(10) and R44(24) rings in 1‐deoxy‐1‐morpholino‐d‐fructopyranose

In the title compound, C₁₀H₁₉NO₆, both rings adopt almost perfect chair conformations and their mutual orientation is influenced by an intramolecular O—H...N hydrogen bond. The molecules are linked by three independent O—H...O hydrogen bonds into sheets containing equal numbers of R₂²(10) and R₄⁴(24) rings.     

Hydro­gen‐bonded chains in N‐(2‐nitrophenyl)phenylamine

Molecules of the title compound, C₁₂H₁₀N₂O₂, are markedly non‐planar. There is an intramolecular N—H?O hydrogen bond, and the mol­ecules are linked into zigzag chains by a single C—H?O hydrogen bond. Comparisons are made with the supramolecular aggregation in isomeric amino–nitro derivatives, and in some N‐methylnitro­anilines.     

Nonmerohedrally twinned 6‐amino‐3‐methyluracil‐5‐carbaldehyde: a hydrogen‐bonded ribbon containing four types of ring

In the title compound [systematic name: 6‐amino‐5‐formyl‐3‐methylpyrimidine‐2,4(1H,3H)‐dione], C₆H₇N₃O₃, the intramolecular dimensions provide evidence for some polarization of the electronic structure. There is an intramolecular N—H...O hydrogen bond; this and a combination of three intermolecular N—H...O hydrogen bonds generate an almost planar ribbon containing S(6), R₂²(4), R₂¹(6) and R₄⁴(16) rings. These ribbons are linked into sheets by a dipolar carbonyl–carbonyl interaction. The structure was refined as a nonmerohedral twin, with twin fractions 0.7924 (1) and 0.2076 (10).     

μ‐1,4‐Benzenedicarboxylato‐bis[trans‐aqua(1,4,8,11‐tetraazacyclotetradecane)nickel(II)] diperchlorate forms a three‐dimensional hydrogen‐bonded framework

The title compound, [Ni₂(C₈H₄O₄)(C₁₀H₂₄N₄)₂(H₂O)₂](ClO₄)₂, contains two independent octahedral Ni^II centres with trans‐NiN₄O₂ chromophores. The bridging benzene­dicarboxyl­ate ligand is bonded to the two Ni atoms, each via one O atom of each carboxyl­ate, while the other O atom participates in an intramolecular N—H?O hydrogen bond, forming an S(6) motif. The cations are linked to the perchlorate anions via O—H?O and N—H?O hydrogen bonds [O?O 2.904 (6) and 2.898 (6) Å; O—H?O 158 (6) and 165 (6)°; N?O 3.175 (7) and 3.116 (7) Å; N—H?O 168 and 166°] to form molecular ladders. These ladders are linked by further O—H?O and N—H?O hydrogen bonds [O?O 2.717 (6) and 2.730 (5) Å; O—H?O 170 (4) and 163 (6)°; N?O 3.373 (7) and 3.253 (7) Å; N—H?O 163 and 167°] to form a continuous three‐dimensional framework. The perchlorate anions both participate in three hydrogen bonds, and both are thus fully ordered.     

丙氨酸二肽分子二级结构与振动光谱特性

利用从头算方法探索蛋白质模型分子——丙氨酸二肽的二级结构布居特性以及体系势能变化. 引入对分子结构敏感的振动探针(酰胺振动吸收带), 借助其光谱表象, 寻求振动光谱参数与分子结构之间的联系. 研究结果表明: 丙氨酸二肽分子处于C_7eq构型(Φ/Ψ=-80°/80°)时具有最低能量值, 且分子易形成β折叠、PP_II、C₅及C₇等能量较低的稳定构型. 通过简正模式分析, 得到分子3N-6 个振动模式的吸收光谱, 并通过势能分布分析方法对分子骨架上酰胺振动吸收带的特征振动模式进行了指认. 重点考察分子骨架上酰胺-I带振动光谱参数与分子构型变化之间的相关性, 建立振动光谱参数与蛋白质二级结构之间的联系, 为在化学键水平上研究蛋白质的结构及其发挥作用的机制提供科学依据.     

Design of peptides with α,β‐de­hydro residues: pseudo‐tripeptide N‐benzyl­oxy­carbonyl–ΔLeu–l‐Ala–l‐Leu–OCH3

The title peptide N‐benzyl­oxy­carbonyl–ΔLeu–l ‐Ala–l ‐Leu–OCH₃ [methyl N‐(benzyl­oxy­carbonyl)‐α,β‐de­hydro­leucyl‐l ‐alanyl‐l ‐leucinate], C₂₄H₃₅N₃O₆, was synthesized in the solution phase. The peptide adopts a type II′β‐turn conformation which is stabilized by an intramolecular 4 1 N—H?O hydrogen bond. The crystal packing is stabilized by two intermolecular N—H?O hydrogen bonds.     

A new ‘hydrogen‐bond rule' applied to the structure of l‐seryl‐l‐alanine and pairs of dipeptide retroanalogues

A new `rule' for the association of hydrogen‐bond donors and acceptors in crystal structures is presented. It implies that ranks are assigned to each donor and each acceptor (1 is best, 2 is next best etc.), and that hydrogen bonds should be formed between donors and acceptors in rank order. l ‐Ser‐l ‐Ala, C₆H₁₂N₂O₄, is used together with its retroanalogue, l ‐Ala‐l ‐Ser, and three other pairs of dipeptide retroanalogues to illustrate this rule and the reasons why it may not always be followed.     

Transition metal complexes with ­thiosemicarbazide‐based ligands. XLIII.

In the title compound, [ZnCl(C₂H₇N₃S)₂]Cl, the Zn^II ion is five‐coordinated in a distorted trigonal–bipyramidal arrangement, with the hydrazine N atoms located in the apical positions. The structure is stabilized by N—H?Cl hydrogen bonds, which involve both the Cl atoms and all the hydrogen donors, except for one of the two thio­amide N atoms. A comparison of the geometry of thio­semicarbazide and S‐­methyl­iso­thio­semicarbazide complexes with Zn^II, Cu^II and Ni^II shows the pronounced influence of the hydrogen‐bond network on the coordination geometry of Zn^II compounds.     

Conformational structure of peptides containing dehydroalanine: Formation of β‐bend ribbon structure

α,β‐Unsaturated amino acids (dehydroamino acids) have been found in naturally occurring antibiotics of microbial origin and in some proteins. Due to the presence of the C_αC_β double bond, the dehydroamino acids influence the main‐chain and the side‐chain conformations. The lowest‐energy conformational state of the model tripeptides, Ac–X–ΔAla–NHMe, (X=Ala, Val, Leu, Abu, or Phe) corresponds to ϕ₁=−30°, ψ₁=120° and ϕ₂=ψ₂=30°. This structure is stabilized by the hydrogen bond between CO of the acetyl group and the NH of the amide group, resulting in the formation of a 10‐membered ring. In the model heptapeptide containing ΔAla at alternate position with Ala, Abu, and Leu, the lowest‐energy conformation corresponds to ϕ=−30° and ψ=120° for all the Ala, Abu, and Leu residues and ϕ=ψ=30° for all ΔAla residues. A graphical view of the molecule in this conformation reveals the formation of three hydrogen bonds involving the CO moiety of the ith residue and the NH moiety of the i+3th residue, resulting in a 10‐membered ring formation. In this structure, only alternate peptide bonds are involved in the intramolecular hydrogen‐bond formation unlike the helices and it has been named the β‐bend ribbon structure. The helical structures were predicted to be the most stable structures in the heptapeptide Ac–(Aib–ΔAla)₃–NHMe with ϕ=±30°, ψ=±60° for Aib residues and ϕ=ψ=±30° for ΔAla residues. The computational results reveal that the ΔAla residue does not induce an inverse γ‐turn in the preceding residue. It is the competitive interaction of small solvent molecules with the hydrogen‐bonding sites of the peptide which gives rise to the formation of an inverse γ‐turn (ϕ₁=−54°, ψ₁=82°; ϕ₂=44°, ψ₂=3°) in the preceding residue to ΔAla. The computational studies for the positional preference of ΔAla in the peptide containing one ΔAla and nine Ala residues reveals the formation of a 3₁₀ helical structure in all the cases with the terminal preferences for ΔAla, consistent with the position of ΔAla in the natural antibiotics. The extended structures is found to be the most stable for poly‐ΔAla. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 72: 15–23, 1999     

Channel‐forming solvates of 6‐chloro‐2,5‐dihydroxypyridine and its solvent‐free tautomer 6‐chloro‐5‐hydroxy‐2‐pyridone

On crystallization from CHCl₃, CCl₄, CH₂ClCH₂Cl and CHCl₂CHCl₂, 6‐chloro‐5‐hydroxy‐2‐pyridone, C₅H₄ClNO₂, (I), undergoes a tautomeric rearrangement to 6‐chloro‐2,5‐dihydroxypyridine, (II). The resulting crystals, viz. 6‐chloro‐2,5‐dihydroxypyridine chloroform 0.125‐solvate, C₅H₄ClNO₂·0.125CHCl₃, (IIa), 6‐chloro‐2,5‐dihydroxypyridine carbon tetrachloride 0.125‐solvate, C₅H₄ClNO₂.·0.125CCl₄, (IIb), 6‐chloro‐2,5‐dihydroxypyridine 1,2‐dichloroethane solvate, C₅H₄ClNO₂·C₂H₄Cl₂, (IIc), and 6‐chloro‐2,5‐dihydroxypyridine 1,1,2,2‐tetrachloroethane solvate, C₅H₄ClNO₂·C₂H₂Cl₄, (IId), have I4₁/a symmetry, and incorporate extensively disordered solvent in channels that run the length of the c axis. Upon gentle heating to 378 K in vacuo, these crystals sublime to form solvent‐free crystals with P2₁/n symmetry that are exclusively the pyridone tautomer, (I). In these sublimed pyridone crystals, inversion‐related molecules form R²₂(8) dimers via pairs of N—H...O hydrogen bonds. The dimers are linked by O—H...O hydrogen bonds into R⁴₆(28) motifs, which join to form pleated sheets that stack along the a axis. In the channel‐containing pyridine solvate crystals, viz. (IIa)–(IId), two independent host molecules form an R²₂(8) dimer via a pair of O—H...N hydrogen bonds. One molecule is further linked by O—H...O hydrogen bonds to two 4₁ screw‐related equivalents to form a helical motif parallel to the c axis. The other independent molecule is O—H...O hydrogen bonded to two related equivalents to form tetrameric R⁴₄(28) rings. The dimers are π–π stacked with inversion‐related dimers, which in turn stack the R⁴₄(28) rings along c to form continuous solvent‐accessible channels. CHCl₃, CCl₄, CH₂ClCH₂Cl and CHCl₂CHCl₂ solvent molecules are able to occupy these channels but are disordered by virtue of the site symmetry within the channels.     

A pipecolic acid (Pip)‐containing dipeptide,Boc‐d‐Ala‐l‐Pip‐NHiPr

The title dipeptide, 1‐(tert‐butoxy­carbonyl‐d ‐alanyl)‐N‐iso­propyl‐l ‐pipecol­amide or Boc‐d ‐Ala‐l ‐Pip‐NHⁱPr (H‐Pip‐OH is pipecolic acid or piperidine‐2‐carboxylic acid), C₁₇H₃₁N₃­O₄, with a d –l heterochiral sequence, adopts a type II′β‐­turn conformation, with all‐trans amide functions, where the C‐terminal amide NH group interacts with the Boc carbonyl O atom to form a classical i+3 i intramolecular hydrogen bond. The C^α substituent takes an axial position [H^α (Pip) equatorial] and the trans pipecolamide function is nearly planar.