Dynamic Properties of Local Structures in Aqueous Model Systems

A method for describing structural and dynamic inhomogeneity in aqueous model systems is proposed. The method is based on the construction of ranked distributions of measured quantities (lifetime of hydrogen bonds and local configurations of water molecules). Asymptotic estimates were obtained for the lifetimes of hydrogen bonds and local configurations of hydrogenbonded water molecules selected by a dynamic criterion for hydrogen bonds.     

H/D isotopic recognition in hydrogen bonded systems: H/D isotopic self-organization effects in the IR spectra of the hydrogen bond in 2-methylimidazole crystals

Polarized IR spectra of H12(3)45 2-methylimidazole and of its H1D2(3)45, D1H2(3)45 and D12(3)45 deuterium derivative crystals are reported and interpreted within the limits of the "strong-coupling" theory. The spectra interpretation facilitated the recognition of the H/D isotopic "self-organization" phenomenon, which depends on a non-random distribution of protons and deuterons in the lattices of isotopically diluted crystal samples. The H/D isotopic "self-organization" mechanism engaged all four hydrogen bonds from each unit cell. These effects basically resulted from the dynamical co-operative interactions involving adjacent hydrogen bonds in each hydrogen bond chain. A weaker exciton coupling involved the closely spaced hydrogen bonds; each belonging to a different chain of associated 2-methylimidazole molecules. The high intensity of the narrow band at ca. 1880cm(-1) was interpreted as the result of coupling between the γ(N-H?N) proton bending "out of plane" vibration overtone and the ν(N-H) proton stretching vibration.     

Superhydrophobic 3D Microstructures Assembled From 1D Nanofibers of Polyaniline

Superhydrophobic dandelion‐like 3D microstructures self‐assembled from 1D nanofibers of PANI were prepared by a self‐assembly process in the presence of perfluorosebacic acid (PFSEA) as a dopant. The dandelion‐like microspheres (about 5 µm) are composed of uniform Y‐shaped junction nanofibers of about 210 nm average diameter and several micrometers in length, as measured by SEM. The dandelion‐like microstructure is coreless with a hollow cavity, and the shell thickness is about one third of the sphere diameter, as measured by TEM. Since PFESA dopant has a low surface energy perfluorinated carbon chain and two hydrophilic  COOH end groups, it has dopant, is a “soft‐template” and brings about superhydrophobic functions at the same time. Moreover, it is proposed that the self‐assembly of PANI 1D nanofibers, driven by a combined interaction of hydrogen bonding, π‐π stacking and hydrophobic interactions, leads to the formation of the 3D microstructures.

     

Solid state self-assembly of triptycene-based catechol derivatives by multiple O-H…O hydrogen bonds

Single crystals of two triptycene-based catechol derivatives 1 and 2 were obtained,and their X-ray crystal structural studies showed that the two tecton molecules had different conformations in the solid state,and they could self-assemble into interesting 3D networks with solvent molecules included inside, in which multiple O-H…O hydrogen bonds played important roles.     

Modulation of ionization and structural properties of weak polyelectrolytes due to 1D, 2D,and 3D confinement

What is the impact of reducing the space available to molecules onto their properties is a fundamental question for capillary systems, molecular biology and transport, protein and material sciences. Possibly influenced by space restriction, ionization degree has rarely been studied for confined polyelectrolytes; Monte Carlo titrations and coarse‐grained models are thus used to investigate structural and ionization changes induced on a single polyelectrolyte chain by confinement into slit (1D), cylindrical (2D), or spherical (3D) cavities. Four polyelectrolyte models differing in chain stiffness and the possible formation of charged hydrogen bonds (c? H? bonds) are studied. Low pH effective ionization constants (pK_a ) of confined chains are lower than for the free species if c? H? bonds can be formed. This is especially evident for 3D‐confined stiff chains, a finding rationalized by the impact of global compression onto chain conformations. If no c? H? bonds are allowed, chain ionization is largely unaffected by 1D or 2D confinement, while it is depressed by 3D. Chain confinement Helmholtz energy (ΔA _conf) was computed as a function of both pH and confining width (W) to gauge the impact of ionization‐induced stiffening onto ΔA _conf versus W behavior, the partition coefficient governing absorption, and the average number of c? H? bond formed. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2017 , 55 , 1088–1102     

Effect of the orientation of the water molecules in the system of hydrogen bonds in the crystal hydrate of m-bromo-N′-(5-nitrofurylidene)benzohydrazide on its sensitivity to light

On the basis of a crystal-chemical analysis of the structure of the investigated benzohydrazides, the structural characteristics typical of light-sensitive crystal hydrates of this type were formulated: the formation of intermolecular polar chains of hydrogen bonds of the C=O...H₂O...H-N type with the water molecules; head-to-tail stacking of the molecules. It was shown that the investigated m-bromo-N-(5-nitrofurylidene)benzohydrazide forms 12 crystal hydrates. The dimeric associates of the water molecules link the benzohydrazide molecules in the stacks by hydrogen bonds. Polar chains of hydrogen bonds, along which intermolecular N O-phototransfer of a proton occur, are formed between the stacks with the participation of one of the water molecules. An assignment was made of the bands for the OH stretching vibrations of the water molecules in the investigated crystal hydrate.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 3, pp. 567–572, March, 1990.     

Intermolecular Interactions of 3,5-Di-tert-butyl-4-hydroxybenzyl Acetate in Crystal and in Solutions

The molecular and crystal structure of 3,5-di-tert-butyl-4-hydroxybenzyl acetate was studied by single-crystal X-ray diffraction. The molecules form infinite chains in the crystals via hydrogen bonds between the hydroxy and carbonyl groups. The interchain bonding is provided by CH- interactions. In carbon tetrachloride, the molecules of the title compound form weak associates via hydrogen bonds between the hydroxy and carbonyl groups.     

H/D isotopic recognition in hydrogen-bonded systems: strong dynamical coupling effects in the polarized IR spectra of 3-methylthioacetanilide and 4-methylthioacetanilide crystals

This paper presents the investigation results of the polarized IR spectra of the hydrogen bond in crystals of 3- and 4-methylthioacetanilide. The spectra were measured at 293 and 77 K by a transmission method, with the use of polarized light. The main spectral properties of the crystals can be interpreted satisfactorily in terms of the "strong-coupling" theory, on the basis of the hydrogen bond centrosymmetric dimer model. The spectra revealed that the strongest vibrational exciton coupling involved the closely spaced hydrogen bonds, each belonging to a different chain of associated 3- and 4-methylthioacetanilide molecules. A weaker exciton coupling involved the adjacent hydrogen bonds in each individual chain. It was proven that a nonrandom distribution of the protons and deuterons took place in the lattices of isotopically diluted crystalline samples of 3- and 4-methylthioacetanilide. In each case, the H/D isotopic "self-organization" mechanism involved all four hydrogen bonds from each unit cell.     

An inequality for 3D database searching and its use in evaluating the treatment of conformational flexibility

Summary A mathematical formula is introduced for predicting the number of hits that should be observed in a flexible 3D database search, based on the results of a set of related queries. The projected number of hits is always greater than or equal to the actual number of hits, the discrepancy being due to imperfect treatment of conformational flexibility of the molecules. Hence, the difference between the projected and actual number of hits, , serves to measure how well conformational flexibility is being treated, in a manner that is objective, easy for a user to quickly verify, and independent of the particular algorithm for flexible 3D database search. It is shown that is a function both of how well conformational flexibility is treated and of the precision of the query. When the distance constraint is defined only to a precision of ±2.0 Å, in a single-conformer database of drug-like molecules values of only 0.03 are found, while in a single-conformer database of di- and tripeptides, is 0.15. At increased precision, a flexible 3D database search becomes critical. For a single-conformer database, using a query of precision ±0.2 Å, applied to a database of drug-like molecules, is 0.97; applied to a database of di- and tripeptides, is 2.21. By contrast, treating conformational flexibility by storing up to 100 conformers per molecule, at this precision, applied to a database of drug-like molecules, is 0.002; applied to a database of di- and tripeptides, is 0.07. This inequality, and hence , is defined only for database queries containing a single distance constraint; how the inequality may generalize to higher-dimensional queries is still unclear.     

Crystal Structures and Photoluminescence of Two Inorganic–Organic Hybrids of Anderson Anions

Two supramolecular compounds (Hbipy)₂[Cr(OH)₆Mo₆O₁₈H](bipy) (1) and (Hbipy)₃[Al(OH)₆Mo₆O₁₈]·3H₂O (2) were synthesized and their crystal structures were analyzed with x-ray diffraction technique. In 1 the Anderson anion with six hydroxyl groups forms six hydrogen bonds with bipy molecules, forming a supramolecular layer, the layers are linked by hydrogen bonds between anions. In 2 the Anderson anion with three hydroxyl groups and terminal/bridging oxygen atoms forms six hydrogen bonds with bipy molecules, and lattice water molecules and the anions form also hydrogen bonds, constructing a supramolecular architecture. The intensive emission in 650–740 nm of 1 is attributed to R-lines of Cr³⁺ and the high intensity may be caused by energy transfer of bipy molecules through hydrogen bonds. In contrast, 2 gives only the π* → π emission of bipy molecules at 460 nm.     

Synthesis and Crystal Structures of [(Nicotinic Acid)2H]+I-, [(2-Amino-6-methylpyridine)H]+(NO3)-, and the 1:1 Complex Between 1-Isoquinoline Carboxylic Acid (Zwitter Ion) and L-Ascorbic Acid Assembled via Hydrogen Bonds

Three new complexes, namely [(nicotinic acid)₂H]⁺I^–, [(2-amino-6-methylpyridine)H]⁺ (NO₃)^–, and the 1:1 complex between 1-isoquinoline carboxylic acid (zwitter ion form) and L-ascorbic acid were synthesized. The IR spectra revealed different types of hydrogen bonds in these compounds. The X-ray structure determination has shown the first compound to consist of a packing of [(nicotinic acid)₂H]⁺ cations and I^– anions. In the dimeric cation the two nicotinic acid molecules (zwitter ions) are connected through hydrogen bonds (O–HO). Each dimer is further engaged in other hydrogen bonds with adjacent dimers giving 2D layers. The I^– ion is located at the inversion center. In the second compound the cation and anion are connected via hydrogen bonds formed between oxygen atoms of the NO₃ ^– anion and NH and NH₂ of the cation generating a layer structure. All atoms are coplanar on mirror planes. In the 1:1 complex the two molecules are connected through hydrogen bonds formed between the two oxygen atoms of the carboxylate group of 1-isoquinoline carboxylic acid (zwitter ion) and the oxygen atoms of the two adjacent hydrogen groups of the L-ascorbic acid molecule. These complex molecules are engaged in other hydrogen bonds with each other forming a 2D system normal to the long b-axis of the unit cell.     

Synthesis and Crystal Structures of [(Nicotinic Acid)2H]+I-, [(2-Amino-6-methylpyridine)H]+(NO3)-, and the 1:1 Complex Between 1-Isoquinoline Carboxylic Acid (Zwitter Ion) and L-Ascorbic Acid Assembled via Hydrogen Bonds

Summary. Three new complexes, namely [(nicotinic acid)₂H]⁺I^–, [(2-amino-6-methylpyridine)H]⁺ (NO₃)^–, and the 1:1 complex between 1-isoquinoline carboxylic acid (zwitter ion form) and L-ascorbic acid were synthesized. The IR spectra revealed different types of hydrogen bonds in these compounds. The X-ray structure determination has shown the first compound to consist of a packing of [(nicotinic acid)₂H]⁺ cations and I^– anions. In the dimeric cation the two nicotinic acid molecules (zwitter ions) are connected through hydrogen bonds (O–HO). Each dimer is further engaged in other hydrogen bonds with adjacent dimers giving 2D layers. The I^– ion is located at the inversion center. In the second compound the cation and anion are connected via hydrogen bonds formed between oxygen atoms of the NO₃ ^– anion and NH and NH₂ of the cation generating a layer structure. All atoms are coplanar on mirror planes. In the 1:1 complex the two molecules are connected through hydrogen bonds formed between the two oxygen atoms of the carboxylate group of 1-isoquinoline carboxylic acid (zwitter ion) and the oxygen atoms of the two adjacent hydrogen groups of the L-ascorbic acid molecule. These complex molecules are engaged in other hydrogen bonds with each other forming a 2D system normal to the long b-axis of the unit cell.     

NMR and X-ray analyses of triethyl 3,7,11-triphenylcyclonona[1,2-b;4,5-b′;7,8-b″]tripyrrole-2,6,10-tricarboxylate: reinvestigation of crown vs saddle conformation of cyclononatripyrroles

From X-ray analyses of 3,7,11-triphenylcyclonona[1,2-b;4,5-b′;7,8-b″]tripyrrole-2,6,10-tricarboxylate (CNTP 1), the molecules existed as saddle forms in both crystals of 1·3ClPh and 1·1/2CHCl₃. In the former crystal, hydrogen bonds between pyrrolic hydrogen and ester carbonyl oxygen spread two-dimensionally, forming molecular sheets, between which the solvent molecules were included, while two independent molecules were bounded three-dimensionally by the hydrogen bonds in the latter. In CDCl₃, CNTP was observed to adopt a crown form, while interconversion of the conformers was observed in C₅D₅N.     

X-ray and IR studies of

Summary A homology model building study of cytochrome P450 2D6 has been carried out based on the crystal structure of cytochrome P450 101. The primary sequences of P450 101 and P450 2D6 were aligned by making use of an automated alignment procedure. This alignment was adjusted manually by matching -helices (C, D, G, I, J, K and L) and -sheets (3/4) of P450 101 that are proposed to be conserved in membrane-bound P450s (Ouzounis and Melvin [Eur. J. Biochem., 198 (1991) 307]) to the corresponding regions in the primary amino acid sequence of P450 2D6. Furthermore, -helices B, B and F were found to be conserved in P450 2D6. No significant homology between the remaining regions of P450 101 and P450 2D6 could be found and these regions were therefore deleted. A 3D model of P450 2D6 was constructed by copying the coordinates of the residues from the crystal structure of P450 101 to the corresponding residues in P450 2D6. The regions without a significant homology with P450 101 were not incorporated into the model. After energy-minimization of the resulting 3D model of P450 2D6, possible active site residues were identified by fitting the substrates debrisoquine and dextrometorphan into the proposed active site. Both substrates could be positioned into a planar pocket near the heme region formed by residues Val³⁷⁰, Pro³⁷¹, Leu³⁷², Trp³¹⁶, and part of the oxygen binding site of P450 2D6. Furthermore, the carboxylate group of either Asp¹⁰⁰ or Asp³⁰¹ was identified as a possible candidate for the proposed interaction with basic nitrogen atom(s) of the substrates. These findings are in accordance with a recently published predictive model for substrates of P450 2D6 [Koymans et al., Chem. Res. Toxicol., 5 (1992) 211].     

A preliminary 3D model for cytochrome P450 2D6 constructed by homology model building

Summary A homology model building study of cytochrome P450 2D6 has been carried out based on the crystal structure of cytochrome P450 101. The primary sequences of P450 101 and P450 2D6 were aligned by making use of an automated alignment procedure. This alignment was adjusted manually by matching -helices (C, D, G, I, J, K and L) and -sheets (3/4) of P450 101 that are proposed to be conserved in membrane-bound P450s (Ouzounis and Melvin [Eur. J. Biochem., 198 (1991) 307]) to the corresponding regions in the primary amino acid sequence of P450 2D6. Furthermore, -helices B, B and F were found to be conserved in P450 2D6. No significant homology between the remaining regions of P450 101 and P450 2D6 could be found and these regions were therefore deleted. A 3D model of P450 2D6 was constructed by copying the coordinates of the residues from the crystal structure of P450 101 to the corresponding residues in P450 2D6. The regions without a significant homology with P450 101 were not incorporated into the model. After energy-minimization of the resulting 3D model of P450 2D6, possible active site residues were identified by fitting the substrates debrisoquine and dextrometorphan into the proposed active site. Both substrates could be positioned into a planar pocket near the heme region formed by residues Val³⁷⁰, Pro³⁷¹, Leu³⁷², Trp³¹⁶, and part of the oxygen binding site of P450 2D6. Furthermore, the carboxylate group of either Asp¹⁰⁰ or Asp³⁰¹ was identified as a possible candidate for the proposed interaction with basic nitrogen atom(s) of the substrates. These findings are in accordance with a recently published predictive model for substrates of P450 2D6 [Koymans et al., Chem. Res. Toxicol., 5 (1992) 211].     

Structure of dilignol,β-O-4-[1-(4-hydroxyphenyl)-2-(2-methoxyphenoxy)-1-ethanol] in crystal and in solution

The structure of dilignol, 1-(4-hydroxyphenyl)-2-(2-methoxyphenoxy)-1-ethanol was studied by x-ray diffraction structural analysis and¹H PMR spectroscopy. The dilignol molecules crystallize in an extended conformation with trans-Ar-C-C-O and trans-C-C-O-Ar structures: the angle between the plane of the aromatic systems was 74.0°. This conformation was stabilized by intermolecular hydrogen bonds, which linked the molecules into chains. Weak Y-shaped hydrogen bonds were found between molecules of adjacent chains. These results were compared with the literature data on the crystal structure of -O-4 dilignols. A similar conformation of dilignol stabilized by an intramolecular hydrogen bond, whose existence was indicated by IR spectroscopy, was found to predominate in acetone and chloroform solutions. A conclusion was drawn concerning the conformational mobility of -O-4 dilignols and the factors determining the conformational composition of dilignols in solution were discussed.S. M. Kirov Leningrad Forest Technology Institute, Institute of Wood Chemistry, Academy of Sciences of the Latvian SSR. Institute of Organic Synthesis, Academy of Sciences of the Latvian SSR. Translated from Zhurnal Strukturnoi Khimii, Vol. 30, No. 5, pp. 135–141, September–October, 1989.     

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.     

Effect of intermolecular hydrogen bonding on the molecular structures of imidazole and 1,2,4-triazole: A study by ab initio molecular orbital calculations

The effect of intermolecular hydrogen bonding in the solid state on the molecular structures of imidazole and 1,2,4-triazole has been studied by SCF ab initio molecular orbital calculations at the HF/6-31G^* level. The crystals of these species contain endless chains of molecules, connected by unusually strong N-H N hydrogen bonds. Our simulation of the crystal field, based on two simple models, unequivocally shows that hydrogen bond formation not only lengthens the N-H bond but also causes a concerted change in the length of two N-C bonds. The change indicates that the contribution of a polar canonical form to the structure of the molecule increases in going from the gaseous phase to the crystal. This provides a rationale for the strong intermolecular hydrogen bond occurring in the solid state. We have also optimized the geometry of the free molecules at the MP2/6-31G^* level, to investigate the effect that correcting for electron correlation has on the equilibrium structure of these systems.     

On the use of LUDI to search the Fine Chemicals Directory for ligands of proteins of known three-dimensional structure

Summary It is shown that the computer program LUDI can be used to search large databases of three-dimensional structures for putative ligands of proteins with known 3D structure. As an example, a subset of 30 000 small molecules (with less than 40 atoms and 0–2 rotatable bonds) from the Fine Chemicals Directory has been used in the search for possible novel ligands for four different proteins (trypsin, streptavidin, purine nucleoside phosphorylase and HIV protease). For trypsin and streptavidin, known ligands or substructures of known ligands are retrieved as top-scoring hits. In addition, a number of new interesting structures are found in all considered cases. Therefore, the method holds promise to retrieve automatically protein ligands from a 3D database if the 3D structure of the target protein is known.