Short Intermolecular Hydrogen Bonds Research Articles

Complexes of the “proton sponge” 1,8-bis(dimethylamino)naphthalene (DMAN) Part 7. The occurrence of a very short asymmetric intermolecular hydrogen bond in the 100 K structure of [DMANH] +·[ d-hydrogentartrate] −·trihydrate

The structure of the complex of 1,8-bis(dimethylamino)naphthalene with d-tartaric acid, [DMANH] +·[ d-hydrogentartrate] −·3H 2O, has been determined by X-ray diffraction methods at 100 K. The crystals are orthorhombic, space group P2 12 12 1 with a = 7.0849(3), b = 12.2115(3), c = 24.089(1) Å, V = 2084.1(1) Å 3 and Z = 4. The structure, solved by direct methods, refined to R = 0.0315 for 2327 unique reflections with I >/ 2.5σ( I). As in other [DMANH] + complexes, a proton is transferred to the DMAN residue, which results in a strong intramolecular [NH⋯N] + H-bond (N⋯N 2.610(3) Å). The H atom in this intramolecular H-bond was found to be disordered over two positions at distances of 0.91(5) and 0.84(12) Å from the N atoms. The H-bond scheme primarily d-hydrogentartrate fragments and water molecules. One H-bond between carboxyl and carboxylate groups is extremely short (O⋯O 2.463(2) Å), but nevertheless asymmetric.

Conformation and hydrogen bonding of N‐formylpeptides: crystal and molecular structure of N‐formyl‐l‐alanyl‐l‐aspartic acid†

Crystals of N-formyl-L-alanyl-L-aspartic acid (C8H11N2O6) grown from aqueous methanol solution are orthorhombic, space group, P2(1)2(1)2(1) with cell parameters at 294K of a = 13.619(2), b = 8.567(2), c = 9.583(3)A, V = 1118.1A3, M.W. = 232.2, Z = 4, Dm = 1.38 g/cm3 and Dx = 1.378 g/cm3. The crystal structure was solved by the application of direct methods and refined to an R value of 0.075 for 1244 reflections with I greater than or equal to 3 sigma collected on a CAD-4 diffractometer. The structure contains two short intermolecular hydrogen bonds: (i) between the C-terminal carboxyl OH and the N-acyl oxygen (2.624(3)A), a characteristic feature found in many N-acyl peptides and (ii) between the aspartic carboxyl OH. and the peptide oxygen OP1 (2.623(3)A). The peptide is nonplanar (omega = 165.5(6) degrees). The molecule takes up a folded conformation in contrast to N-formyl peptides which form extended beta-sheets; the values of phi 1, psi 1, phi 2, psi 2(1), and psi 2(2) are, respectively -65.7(6), 152.0(5), -107.2(5), 30.9(5), and -150.3(6). The aspartic acid side chain conformation is g- with chi 1 = 73.1(5). The formyl group, as expected, is transplanar [OF-CF-N1-CA1 = -4.0(8) degrees]. The presence of the short O-H ... O hydrogen bond emerges as a structural feature common to this peptide and several other N-formyl peptides. There are no C-H ... O hydrogen bonds in this structure.

Spectres de vibration et liaison hydrogène du cyclobutane 1-1 dicarboxylate acide de potassium

The crystal structure of potassium hydrogen cyclobutane 1-1 dicarboxylate has been determined by X-ray analysis. This acid salt has a short unsymmetrical intermolecular hydrogen bond with O … O = 2,53 Å, but the carboxylic residues show only small differences in dimensions. Polycrystalline samples of CB(COO) 2HK-1,1 and its O-deuterated analog have been studied by i.r. and Raman spectroscopy. An assignment of the bands is given, the details of the hydrogen bond bands are discussed; in particular the isotopic ettect (νOH/ νOD ∼ 1), the combination bands in the region 1900–2500 cm −1 and the carbonyl region. It suggested that the acid salt belongs to Speakman's pseudo A type.

Untersuchungen zur struktur des adduktes aus hydrochinon und N-methylpyrrolidon-(2)

The 1:2 adduct between quinol and N-methyl-pyrrolidone-(2) was synthesized and its composition confirmed by NMR-data. However, X-ray data showed a 1:1 stoicheiometry after recrystallisation; this apparent discrepancy is discussed. In the 1:1 adduct the pyrrolidone is twofold disordered, without however affecting the pattern of short intermolecular hydrogen bonds [OH··OH 2.690(3), OH··O=2.575(4) Å]. The special significance of the hydrogen bonding between phenols and amides is demonstrated.

Neutron diffraction studies of potassium hydrogen diformate, KH(HCOO)2, at 120 and 295 K

Mr= 130.144, orthorhombic, Pbca, Z = 8; at 120 K a = 17.705 (8), b = 7.349 (4), c = 7.302 (3)/k, V = 950.1 (8) ~3, D~, = 1.820 (1) g cm-3; at 295K a=17.7079(9), b=7.5096(4), c= 7.3774 (4) ,~, V= 981.05 (9) /k 3, Dx=l.7623(2)g cm -3. The crystal structure has been investigated by neutron diffraction at 120 K (2 = 0.7228/k) and 295 K (2= 1.210/~); final R(F 2) values are 0.041 (1418 reflections) and 0.065 (1365 reflections), respectively. The short intermolecular O...O hydrogen bond (2.437 (1),~ at 120 K) is found to be asymmetrical (O-H 1.167 (1), H...O 1.270 (1) A) even though the bonding situations around the two formate groups are quite similar. Introduction. The main purpose of this investigation is to study the geometry and electron density in the very short intermolecular hydrogen bond (O..-O: 2.437 (1)/k at 120 K) between the two formate groups in KH(HCOO) 2. The crystal structure was determined previously from room-temperature single-crystal X-ray data by Larsson & Nahringbauer (1968). Most of the very short hydrogen bonds investigated by diffraction methods are either of an intramolecular type or they have a symmetry restriction on the bond, which makes it difficult to distinguish between a disordered non- centred bond and a centred bond with a large proton thermal vibration. This is not the case in potassium hydrogen diformate, where the two formate ions, hydrogen-bonded to form a dimer, are crystal- lographically non-equivalent. In the present paper neutron diffraction studies at 120 and 295 K will be presented. The deformation electron density distribution at 120 K will be described in a later publication. Experimental. Crystal growth: KH(HCOO) 2 was pre- pared from formic acid and potassium hydroxide and recrystallized several times from an aqueous solution containing a small amount of formic acid. A large crystal was grown in a quartz-glass tube (Q ~3-5 mm) with the zone-melting technique. A cylinder-shaped 0108-2701/83/111507-04501.50

Molecular and crystal structure ofl-phosphinothricin (2-ammonio-4-methylphosphinico-butyrate)

l-Phosphinothricin crystallizes in the monoclinic space group P21 with two molecules in the cell. At least in the crystalline state the α-carbon atom and the phosphorous are chiral, they have the S- and the R-configuration respectively. There is a very short intermolecular oxygen-oxygen hydrogen bond of 2.427 Å.

Electron density in the water molecule in α-oxalic and dihydrate and the nature of short hydrogen bonds

The experimental electron density in α-oxalic acid dihydrate indicates a perturbation of the water molecule density due to the short intermolecular hydrogen bond. The dipole moment of the water molecule in the crystal is slightly higher than the isolated-molecule value and displaced significantly out of the molecular plane.

SPECIFIC CONFIGURATIONS OF HYDROGEN BONDING

From a reexamination of the X-ray studies of the crystal structures of 27 N-acylamino acids, peptides and their derivatives and 30 linear peptides, it is concluded that specific formation of short intermolecular hydrogen bonds (2,5 to 2.6 A) from the carboxyl OH to the N-acyl oxygen is an important feature for N-acylamino acids. For N-acyl-N-amides, the formation of hydrogen bonds 2.7 to 2.9A long between N(acyl-H...O(amide) is strongly preferred. The dihedral angle delta between the N-acyl and carboxyl groups or adjacent amide groups shows a preference for values near 20 degrees or 90 degrees for N-acylamino acids and 90 degrees for N-acyl-N-amides.