Racemic dipeptide glycyl‐dl‐leucine at 120 K

The structure of glycyl‐dl ‐leucine, C₈H₁₆N₂O₃, has been determined at 120 K by single‐crystal X‐ray diffraction. In addition to three N—H?O‐type hydrogen bonds of the positively charged RNH₃⁺ group of the zwitterionic mol­ecule, an intermolecular N—H?O contact exists between the peptide bond and the carboxyl­ate group. Four hydrogen‐bond cycles were identified, giving a complex pattern.     

N‐tert‐Butyl‐N′‐[5‐cyano‐2‐(4‐methylphenoxy)phenylsulfonyl]urea,a new TXA2 receptor antagonist

The title compound, C₁₉H₂₁N₃O₄S, crystallizes in the space group P2/c with two molecules in the asymmetric unit. The conformation of both molecules is very similar and is mainly determined by an intramolecular N—H...O hydrogen bond between a urea N atom and a sulfonyl O atom. The O and second N atom of the urea groups are involved in dimer formation via N—H...O hydrogen bonds. The intramolecular hydrogen‐bonding motif and conformation of the C—SO₂—NH(C=O)—NH—C fragment are explored and compared using the Cambridge Structural Database and theoretical calculations. The crystal packing is characterized by π–π stacking between the 5‐cyanobenzene rings.     

Mechanism of Conformational Transition of Silk Fibroin in Alcohol-water Mixtures

Circular dichroism, intrinsic fluorescence of protein and exogenous fluorescence probe of 8‐anilino‐1‐naphtha‐ lenesulfonic acid hemimagnesium salt (ANS) was used to investigate the mechanism of conformational change of silk fibroin (SF) in aqueous alcohol including methanol and ethanol. The conformational transition of SF from random coil to β‐sheet was found to be of a close relationship with the microstructure of the solvent. The alcohol‐water mixture at low concentration had little effect on the solvation of the peptide unit, as the inherent water structure was conserved. At high alcohol concentration, the transition from the tetrahedral‐like water structure to the chain‐like alcohol structure in the mixtures induced a β‐sheet conformation of SF, as a result of the formation of intramolecular hydrogen bond between the peptide units in order to eliminate the thermodynamic unfavorite from the contact to the solvent molecules. Meanwhile, the aggregating of hydrophobic side chains was decreased by the alcohol via the destruction of hydrogen bond network of water by alcohol and the binding of alcohol to hydrophobic group.     

Sodium 2‐oxo‐3‐semicarbazono‐2,3‐dihydro‐1H‐indole‐5‐sulfonate dihydrate

The title compound, Na⁺·C₉H₇N₄O₅S⁻·2H₂O, presents a Z configuration around the imine C=N bond and an E configuration around the C(O)NH₂ group, stabilized by two intra­molecular hydrogen bonds. The packing is governed by ionic inter­actions between the Na⁺ cation and the surrounding O atoms. The ionic unit, Na⁺ and 2‐oxo‐3‐semicarbazono‐2,3‐dihydro‐1H‐indole‐5‐sulfonate, forms layers extending in the bc plane. The layers are connected by hydrogen bonds involving the water mol­ecules.     

脱铁伴清蛋白两结合位点不同酪氨酸氢键的特性

The interaction of gallium（Ⅲ） with the ligands containing phenolic group（s）, such as salicylic acid, 8-hydroxyquinoline, N,N＇-bis（2-hydroxybenzyl）ethylenediamine-N,N＇diacetic acid （HBED）, N,N＇-ethylenebis[2-（o- hydroxyphenyl）glycine （EHPG）, and ovotransferrin, was studied, respectively, by means of fluorescence in 0.01 mol/L Hepes at pH 7.4 and room temperature. Fluorescence intensity showed an increase when gallium（Ⅲ） was bound to 8-hydroxyquinoline and HBED. In contrast, it was decreased with the interaction of gallium（Ⅲ） with salicylic acid and EHPG. At pH 7.4, there was N…H-O type intramolecular hydrogen bond in the former, and the latter existed O…H-O type intramolecular hydrogen bond. Fluorescence titration of apoovotransferrin with gallium（Ⅲ） displayed that the fluorescence intensity was decreased at the N-terminal binding site, while enhanced at the C-terminal binding site. It can account for the O…H-O type intramolecular hydrogen bonds for the phenolic groups of Tyr92 and Tyr191 residues at the N-terminal binding site. And there are N…H-O type intramolecular hydrogen bonds for Tyr431 and Tyr524 residues at the C-terminal binding site. In addition, under the same conditions, the conditional binding constant of gallium（Ⅲ） with EHPG or HBED determined by fluorescence method is lg KGa-EHPG=19.18 or lg KGa-HBED= 19.08.     

Hydrogen bonding in diaquatetrakis(urea‐κO)MII dinitrates,with M = Ni and Co

The isomorphous title compounds, [Ni{(NH₂)₂CO}₄(H₂O)₂](NO₃)₂ and [Co{(NH₂)₂CO}₄(H₂O)₂](NO₃)₂, feature discrete centrosymmetric cations in octahedral coordinations, formed by four urea molecules linked via their O atoms to the central ion in equatorial positions and two water molecules in trans positions. The complexes are packed in a pseudo‐hexagonal manner separated by the nitrate counter‐ions. All H atoms are involved in moderate hydrogen bonds of four types: N—H...O=C, N—H...O—N, O—H...O—N and N—H...O—H. Graph‐set analysis was applied to distinguish the hydrogen‐bond patterns at unitary and higher level graph sets.     

Hydrogen‐Bond Cooperativity in Formamide2–Water: A Model for Water‐Mediated Interactions

The rotational spectrum of formamide₂–H₂O formed in a supersonic jet has been characterized by Fourier‐transform microwave spectroscopy. This adduct provides a simple model of water‐mediated interaction involving the amide linkages, as occur in protein folding or amide‐association processes, showing the interplay between self‐association and solvation. Mono‐substituted ¹³C, ¹⁵N, ¹⁸O, and ²H isotopologues have been observed and their data used to investigate the structure. The adduct forms an almost planar three‐body sequential cycle. The two formamide molecules link on one side through an N?H???O hydrogen bond and on the other side through a water‐mediated interaction with the formation of C=O???H?O and O???H?N hydrogen bonds. The analysis of the quadrupole coupling effects of two ¹⁴N‐nuclei reveals the subtle inductive forces associated to cooperative hydrogen bonding. These forces are involved in the changes in the C=O and C?N bond lengths with respect to pure formamide.     

N‐(4‐Bi­phenyl­yl)­urea

In the crystal structure of the title compound, C₁₃H₁₂N₂O, N—H(anti)?O hydrogen bonds produce the so‐called urea α‐network and the N—H(syn) donor forms an unconventional N—H?π hydrogen bond.     

Different cyclic motifs in phosphoric triamides containing a C(O)NHP(O)(NH)2 skeleton and an R22(10) graph set in three new compounds: a database analysis of hydrogen‐bond strengths based on motifs

In the crystal networks of N,N′‐bis(2‐chlorobenzyl)‐N′′‐(2,6‐difluorobenzoyl)phosphoric triamide, C₂₁H₁₈Cl₂F₂N₃O₂P, (I), N‐(2,6‐difluorobenzoyl)‐N′,N′′‐bis(4‐methoxybenzyl)phosphoric triamide, C₂₃H₂₄F₂N₃O₄P, (II), and N‐(2‐chloro‐2,2‐difluoroacetyl)‐N′,N′′‐bis(4‐methylphenyl)phosphoric triamide, C₁₆H₁₇ClF₂N₃O₂P, (III), C=O...H—N_C(O)NHP(O) and P=O...H—N_amide hydrogen bonds are responsible for the aggregation of the molecules. This is the opposite result from that commonly observed for carbacylamidophosphates, which show a tendency for the phosphoryl group, rather than the carbonyl counterpart, to form hydrogen bonds with the NH group of the C(O)NHP(O) skeleton. This hydrogen‐bond pattern leads to cyclic R₂²(10) motifs in (I)–(III), different from those found for all previously reported compounds of the general formula RC(O)NHP(O)[NR¹R²]₂ with the syn orientation of P=O versus NH [R₂²(8)], and also from those commonly observed for RC(O)NHP(O)[NHR¹]₂ [a sequence of alternate R₂²(8) and R₂²(12) motifs]. In these cases, the R₂²(8) and R₂²(12) graph sets are formed through similar kinds of hydrogen bond, i.e. a pair of P=O...H—N_C(O)NHP(O) hydrogen bonds for the former and two C=O...H—N_amide hydrogen bonds for the latter. This article also reviews 102 similar structures deposited in the Cambridge Structural Database and with the International Union of Crystallography, with the aim of comparing hydrogen‐bond strengths in the above‐mentioned cyclic motifs. This analysis shows that the strongest N—H...O hydrogen bonds exist in the R₂²(8) rings of some molecules. The phosphoryl and carbonyl groups in each of compounds (I)–(III) are anti with respect to each other and the P atoms are in a tetrahedral coordination environment. In the crystal structures, adjacent molecules are linked via the above‐mentioned hydrogen bonds in a linear arrangement, parallel to [010] for (I) and (III) and parallel to [100] for (II). Formation of the N_C(O)NHP(O)—H...O=C instead of the N_C(O)NHP(O)—H...O=P hydrogen bond is reflected in the higher N_C(O)NHP(O)—H vibrational frequencies for these molecules compared with previously reported analogous compounds.     

Impact of Hydrogen Bonding on the Fluorescence of N‐Amidinated Fluoroquinolones

The fluorescence properties of AIE‐active N‐amidinated fluoroquinolones, efficiently obtained by a perfluoroaryl azide–aldehyde–amine reaction, have been studied. The fluorophores were discovered to elicit a highly sensitive fluorescence quenching response towards guest molecules with hydrogen‐bond‐donating ability. This effect was evaluated in a range of protic/aprotic solvents with different H‐bonding capabilities, and also in aqueous media. The influence of acid/base was furthermore addressed. The hydrogen‐bonding interactions were studied by IR, NMR, UV/Vis and time‐resolved fluorescence decay, revealing their roles in quenching of the fluorescence emission. Due to the pronounced quenching property of water, the N‐amidinated fluoroquinolones could be utilized as fluorescent probes for quantifying trace amount of water in organic solvents.     

Anilinium mono­hydrogen dl‐malate

Crystals of the title salt, [(C₆H₅NH₃)]⁺·[(HOOC(CH₂)CH(OH)COO)]⁻ or C₆H₈N⁺·C₄H₅O₅⁻, are built up from protonated anilinium residues and monodissociated dl ‐malate ions. The NH₃⁺ group of the anilinium cation is ordered at room temperature. Rotation of the NH₃⁺ group along the C(aromatic)—Nsp³ bond (often observed at room temperature in other anilinium salts) is prevented by N—H⋯O hydrogen bonds between the NH₃⁺ group and the malate anions. The anions are connected by four O—H⋯O hydrogen bonds into two‐dimensional sheets parallel to the (001) plane. The charged moieties, i.e. the anilinium cations and the sheets of hydrogen‐bonded malate anions, form two‐dimensional layers in which the phenyl rings of the anilinium residues lie perpendicular to the malate‐ion sheets. The conformation of the monodissociated malate ion in the crystal is compared with that obtained from ab initio molecular‐orbital calculations.     

Comparison of the crystal structures of the potent anticancer and anti‐angiogenic agent regorafenib and its monohydrate

Regorafenib {systematic name: 4‐[4‐({[4‐chloro‐3‐(trifluoromethy)phenyl]carbamoyl}amino)‐3‐fluorophenoxy]‐1‐methylpyridine‐2‐carboxamide}, C₂₁H₁₅ClF₄N₄O₃, is a potent anticancer and anti‐angiogenic agent that possesses various activities on the VEGFR, PDGFR, raf and/or flt‐3 kinase signaling molecules. The compound has been crystallized as polymorphic form I and as the monohydrate, C₂₁H₁₅ClF₄N₄O₃·H₂O. The regorafenib molecule consists of biarylurea and pyridine‐2‐carboxamide units linked by an ether group. A comparison of both forms shows that they differ in the relative orientation of the biarylurea and pyridine‐2‐carboxamide units, due to different rotations around the ether group, as measured by the C—O—C bond angles [119.5 (3)° in regorafenib and 116.10 (15)° in the monohydrate]. Meanwhile, the conformational differences are reflected in different hydrogen‐bond networks. Polymorphic form I contains two intermolecular N—H…O hydrogen bonds, which link the regorafenib molecules into an infinite molecular chain along the b axis. In the monohydrate, the presence of the solvent water molecule results in more abundant hydrogen bonds. The water molecules act as donors and acceptors, forming N—H…O and O—H…O hydrogen‐bond interactions. Thus, R₄²(28) ring motifs are formed, which are fused to form continuous spiral ring motifs along the a axis. The (trifluoromethyl)phenyl rings protrude on the outside of these motifs and interdigitate with those of adjacent ring motifs, thereby forming columns populated by halogen atoms.     

Cooperative influence of water binding to peptides by N?H···OH2 and CO···HOH hydrogen bonds: Study by Ab Initio calculations

In this article, the geometry structures of hydrogen bond chains of formamide and N‐methylacetamide and their hydrogen‐bonded complexes with water were optimized at the MP2/6‐31G* level. Then, we performed Møller–Plesset perturbation method with 6‐311++g**, aug‐cc‐pvtz basis sets to study the cooperative influence to the total hydrogen bond energy by the N? H ··· OH₂ and C?O ··· HOH hydrogen bonds. On the basis of our results, we found that the cooperativity of the hydrogen‐bonded complexes become weaker as N? H ··· OH₂ and C?O ··· HOH hydrogen bonds replacing N? H ··· O?C hydrogen bonds in protein and peptide. It means that the N? H and C?O bonds in peptide prefer to form N? H ··· O?C hydrogen bond rather than to form C?O ··· HOH and N? H ··· OH₂. It is significant for understanding the structures and properties of the helical or sheet structures of protein and peptide in biological systems. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Hydrogen‐bonded two‐ and three‐dimensional polymeric structures in the ammonium salts of 3,5‐dinitrobenzoic acid, 4‐nitrobenzoic acid and 2,4‐dichlorobenzoic acid

The structures of ammonium 3,5‐dinitrobenzoate, NH₄⁺·C₇H₃N₂O₆⁻, (I), ammonium 4‐nitrobenzoate dihydrate, NH₄⁺·C₇H₄NO₄⁻·2H₂O, (II), and ammonium 2,4‐dichlorobenzoate hemihydrate, NH₄⁺·C₇H₃Cl₂O₂⁻·0.5H₂O, (III), have been determined and their hydrogen‐bonded structures are described. All three salts form hydrogen‐bonded polymeric structures, viz. three‐dimensional in (I) and two‐dimensional in (II) and (III). With (I), a primary cation–anion cyclic association is formed [graph set R₄³(10)] through N—H...O hydrogen bonds, involving a carboxylate group with both O atoms contributing to the hydrogen bonds (denoted O,O′‐carboxylate) on one side and a carboxylate group with one O atom involved in two hydrogen bonds (denoted O‐carboxylate) on the other. Structure extension involves N—H...O hydrogen bonds to both carboxylate and nitro O‐atom acceptors. With structure (II), the primary inter‐species interactions and structure extension into layers lying parallel to (001) are through conjoined cyclic hydrogen‐bonding motifs, viz.R₄³(10) (one cation, an O,O′‐carboxylate group and two water molecules) and centrosymmetric R₄²(8) (two cations and two water molecules). The structure of (III) also has conjoined R₄³(10) and centrosymmetric R₄²(8) motifs in the layered structure but these differ in that the first motif involves one cation, an O,O′‐carboxylate group, an O‐carboxylate group and one water molecule, and the second motif involves two cations and two O‐carboxylate groups. The layers lie parallel to (100). The structures of salt hydrates (II) and (III), displaying two‐dimensional layered arrays through conjoined hydrogen‐bonded nets, provide further illustration of a previously indicated trend among ammonium salts of carboxylic acids, but the anhydrous three‐dimensional structure of (I) is inconsistent with that trend.     

Co‐templating Ionothermal Synthesis and Crystal Structure of a New Layered Aluminophosphate from a Protic Deep Eutectic Solvent

Protic deep eutectic mixtures are usually composed of organic amine hydrochloride salts and hydrogen bond donors in a specific molar ratio. Ionothermal synthesis of aluminophosphate as an example, herein, was reported for the first time from an urea‐based protic eutectic mixture, consisting of diethylammonium chloride (DEACl) and 1,3‐dimethyl urea (DMU). As a result, a new two dimensional aluminophosphate with 4.8‐network, [CH₃NH₃]₂[(C₂H₅)₂NH₂]Al₃(PO₄)₄, has been successfully synthesized by co‐templating the DEA and methylamine in situ generated from the decomposition of DMU in the absence of HF. Compared to alkyl quaternary ammonium salts with more alkyl‐group connected with N atom, this kind of organic amine salts are more likely as the structure‐directing agents to synthesize aluminophosphates in urea‐based deep eutectic mixtures. It was also found that HF is crucial to the phase selectivity, a known compound with chain‐like structure was obtained with the single methylamine as a structure‐directing agent in the presence of HF. These materials were characterized by powder XRD, SEM, TG‐DSC, ¹³C CP‐MAS NMR and CHN analyses.     

Two polymorphs of bis(2‐carbamoylguanidinium) fluorophosphonate dihydrate

Two polymorphs of bis(2‐carbamoylguanidinium) fluorophosphonate dihydrate, 2C₂H₇N₄O⁺·FO₃P²⁻·2H₂O, are presented. Polymorph (I), crystallizing in the space group Pnma, is slightly less densely packed than polymorph (II), which crystallizes in Pbca. In (I), the fluorophosphonate anion is situated on a crystallographic mirror plane and the O atom of the water molecule is disordered over two positions, in contrast with its H atoms. The hydrogen‐bond patterns in both polymorphs share similar features. There are O—H...O and N—H...O hydrogen bonds in both structures. The water molecules donate their H atoms to the O atoms of the fluorophosphonates exclusively. The water molecules and the fluorophosphonates participate in the formation of R⁴₄(10) graph‐set motifs. These motifs extend along the a axis in each structure. The water molecules are also acceptors of either one [in (I) and (II)] or two [in (II)] N—H...O hydrogen bonds. The water molecules are significant building elements in the formation of a three‐dimensional hydrogen‐bond network in both structures. Despite these similarities, there are substantial differences between the hydrogen‐bond networks of (I) and (II). The N—H...O and O—H...O hydrogen bonds in (I) are stronger and weaker, respectively, than those in (II). Moreover, in (I), the shortest N—H...O hydrogen bonds are shorter than the shortest O—H...O hydrogen bonds, which is an unusual feature. The properties of the hydrogen‐bond network in (II) can be related to an unusually long P—O bond length for an unhydrogenated fluorophosphonate anion that is present in this structure. In both structures, the N—H...F interactions are far weaker than the N—H...O hydrogen bonds. It follows from the structure analysis that (II) seems to be thermodynamically more stable than (I).     

Ethyl N‐[2‐(hydroxy­acetyl)­phenyl]­carbamate,ethyl N‐[2‐(hydroxy­acetyl)‐4‐iodo­phenyl]­carbamate and ethyl N‐[2‐(hydroxy­acetyl)‐4‐methyl­phenyl]­carbamate

In ethyl N‐[2‐(hydroxy­acetyl)phenyl]carbamate, C₁₁H₁₃NO₄, all of the non‐H atoms lie on a mirror plane in the space group Pnma; the mol­ecules are linked into simple chains by a single C—H⋯O hydrogen bond. The mol­ecules of ethyl N‐[2‐(hydroxy­acetyl)‐4‐iodo­phenyl]carbamate, C₁₁H₁₂INO₄, are linked into sheets by a combination of O—H⋯I and C—H⋯O hydrogen bonds and a dipolar I⋯O contact. Ethyl N‐­[2‐(hydroxy­acetyl)‐4‐methyl­phenyl]carbamate, C₁₂H₁₅NO₄, crystallizes with Z′ = 2 in the space group P; pairs of mol­ecules are weakly linked by an O—H⋯O hydrogen bond and these aggregates are linked into chains by two independent aromatic π–π stacking inter­actions.     

Correlated one‐electron wave functions

Using four basis sets, 6‐311G(d,p), 6‐31+G(d,p), 6‐311++G(2d,2p), and 6‐311++G(3df,3pd), the optimized structures with all real frequencies were obtained at the MP2 level for dimers CH₂O? HF, CH₂O? H₂O, CH₂O? NH₃, and CH₂O? CH₄. The structures of CH₂O? HF, CH₂O? H₂O, and CH₂O? NH₃ are cycle‐shaped, which result from the larger bend of σ‐type hydrogen bonds. The bend of σ‐type H‐bond O…H? Y (Y?F, O, N) is illustrated and interpreted by an attractive interaction of a chemically intuitive π‐type hydrogen bond. The π‐type hydrogen bond is the interaction between one of the acidic H atoms of CH₂O and lone pair(s) on the F atom in HF, the O atom in H₂O, or the N atom in NH₃. By contrast with above the three dimers, for CH₂O? CH₄, because there is not a π‐type hydrogen‐bond to bend its linear hydrogen bond, the structure of CH₂O? CH₄ is a noncyclic shaped. The interaction energy of hydrogen bonds and the π‐type H‐bond are calculated and discussed at the CCSD(T)/6‐311++G(3df,3pd) level. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Long‐range π‐type hydrogen bond in dimers CH2?HF,CH2O?H2O,and CH2O?NH3

Using four basis bets, (6‐311G(d,p), 6‐31+G(d,p), 6‐31++G(2d,2p), and 6‐311++G(3df,3pd), the optimized structures with all real frequencies were obtained at the MP2 level for the dimers CH₂O? HF, CH₂O? H₂O, CH₂O? NH₃, and CH₂O? CH₄. The structures of CH₂O? HF, CH₂O? H₂O, and CH₂O? NH₃ are cycle‐shaped, which result from the larger bend of σ‐type hydrogen bonds. The bend of σ‐type H‐bond O…H? Y (Y?F, O, N) is illustrated and interpreted by an attractive interaction of a chemically intuitive π‐type hydrogen bond. The π‐type hydrogen bond is the interaction between one of the H atoms of CH₂O and lone pair(s) on the F atom in HF, the O atom in H₂O, or the N atom in NH₃. In contrast with the above three dimers, for CH₂O? CH₄, because there is not a π‐type hydrogen bond to bend its linear hydrogen bond, the structure of CH₂O? CH₄ is noncyclic shaped. The interaction energy of hydrogen bonds and the π‐type H‐bond are calculated and discussed at the CCSD (T)/6‐311++G(3df,3pd) level. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

DNA/BSA‐binding property and in vitro anticancer activity of a new dicopper(II) complex with N‐(2‐hydroxy‐5‐nitrophenyl)‐N′‐[3‐(diethylamino)propyl]oxamide as bridging ligand: Synthesis and crystal structure

A new oxamido‐bridged dicopper(II) complex formulated as [Cu₂(ndpox)(bpy)(CH₃OH)₂]‐ (ClO₄), where H₃ndpox is N‐(2‐hydroxy‐5‐nitrophenyl)‐N′‐[3‐(diethylamino)propyl]oxamide; and bpy represents 2,2′‐bipyridine, was synthesized and structurally characterized using X‐ray single‐crystal diffraction and other methods. In the molecule, the endo‐ and the exo‐copper(II) ions bridged by the cis ‐ndpox³⁻ ligand are in {N₃O₂} and {N₂O₃} square‐ pyramidal environments, respectively. There is a three‐dimensional hydrogen bonding network dominated by O‐H···O and C‐H···O interactions in the crystal. The reactivity toward DNA/protein bovine serum albumin (BSA) revealed that the complex could interact with herring sperm DNA (HS‐DNA) through the intercalation mode, and effectively quench the intrinsic fluorescence of BSA via a static process. Cytotoxicity studies suggest that the complex displays selective cancer cell antiproliferative activity. The present investigation confirmed that the combined effects of both electron‐withdrawing and hydrophobic groups on the bridging ligand in the dicopper(II) complex systems can increase DNA/BSA‐binding ability and in vitro anticancer activity.