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At least 19 recordsLinked to original sources
PubMed2006

Crystal engineering of analogous and homologous organic compounds: hydrogen bonding patterns in trimethoprim hydrogen phthalate and trimethoprim hydrogen adipate.

BACKGROUND: Trimethoprim [2,4-diamino-5-(3',4',5'-trimethoxybenzyl)pyrimidine] is an antifolate drug. It selectively inhibits the bacterial dihydrofolate reductase (DHFR) enzyme. RESULTS: In the crystal structures of trimethoprim (TMP)-hydrogen phthalate (1) and trimethoprim-hydrogen adipate (2), one of the N atoms of the pyrimidine ring is protonated and it interacts with the deprotonated carboxylate oxygens through a pair of nearly parallel N-H...O hydrogen bonds to form a fork-like interaction. In the compound 1, the pyrimidine moieties of the TMP cations are centrosymmetrically paired through a pair of N-H...N hydrogen bonds involving 4-amino group and the N (N3) atom of the pyrimidine rings to form a 8-membered hydrogen bonded ring [R2(2)(8)]. The 4-amino group of one TMP moiety and 2-amino group of another TMP moiety (both moieties are members of a base pair) are bridged by the carbonyl oxygen of the phthalate moiety through N-H...O hydrogen bonds forming 8-membered hydrogen-bonded ring [R2(2)(8)]. The characteristic hydrogen-bonded rings observed in the structure aggregate into a supramolecular ladder consisting of a pair of chains, each of which is built up of alternate TMP and hydrogen phthalate ions. In the compound 2, two TMP cations and two hydrogen adipate anions are arranged about an inversion center so that the complementary DDAA (D = donor, A = acceptor) arrays of quadruple hydrogen-bonding patterns are formed. The head-to-tail arrangement of the hydrogen adipate ions leads to a hydrogen-bonded supramolecular chain. From crystal engineering point of view, it is interesting to note that the compound 1 has a hydrogen-bonded network remarkably identical with its aliphatic analogue, trimethoprim hydrogen maleate. Similarly the compound 2, resembles its homolog trimethoprim hydrogen glutarate. CONCLUSION: In the crystal structure of trimethoprim hydrogen phthalate, the hydrogen-bonded network is remarkably identical with its aliphatic analogue, trimethoprim hydrogen maleate. Similarly in the crystal structure of trimethoprim hydrogen adipate the hydrogen bonded network resembles its homolog trimethoprim hydrogen glutarate.

Journal Article↗
PubMed2004

Hydrogen-bonding cooperativity: using an intramolecular hydrogen bond to design a carbohydrate derivative with a cooperative hydrogen-bond donor centre.

Neighbouring groups can be strategically located to polarise HO.OH intramolecular hydrogen bonds in an intended direction. A group with a unique hydrogen-bond donor or acceptor character, located at hydrogen-bonding distance to a particular OH group, has been used to initiate the hydrogen-bond network and to polarise a HO.OH hydrogen bond in a predicted direction. This enhanced the donor character of a particular OH group and made it a cooperative hydrogen-bond centre. We have proved that a five-membered-ring intramolecular hydrogen bond established between an amide NH group and a hydroxy group (1,2-e,a), which is additionally located in a 1,3-cis-diaxial relationship to a second hydroxy group, can be used to select a unique direction on the six-membered-ring intramolecular hydrogen bond between the two axial OH groups, so that one of them behaves as an efficient cooperative donor. Talose derivative 3 was designed and synthesised to prove this hydrogen-bonding network by NMR spectroscopy, and the mannopyranoside derivatives 1 and 2 were used as models to demonstrate the presence in solution of the 1,2-(e,a)/five-membered-ring intramolecular hydrogen bond. Once a well-defined hydrogen-bond is formed between the OH and the amido groups of a pyranose ring, these hydrogen-bonding groups no longer act as independent hydrogen-bonding centres, but as hydrogen-bonding arrays. This introduces a new perspective on the properties of carbohydrate OH groups and it is important for the de novo design of molecular recognition processes, at least in nonpolar media. Carbohydrates 1-3 have shown to be efficient phosphate binders in nonpolar solvents owing to the presence of cooperative hydroxy centres in the molecule.

Journal Article↗
PubMed2001

Asymmetric hydrogen bonds in centrosymmetric environment: neutron study of very short hydrogen bonds in potassium hydrogen dichloromaleate.

The structure of the title compound has been studied by neutron diffraction at 30 and 295 K, with the emphasis on the location of the protons. There are two crystallographically independent H atoms in two very short hydrogen bonds, 2.437 (2) and 2.442 (2) A at 30 K. The structure could be refined successfully in the centrosymmetric space group P1;, with the H atoms located at the centres of symmetry. However, the form of the thermal ellipsoids of hydrogen indicated either asymmetric hydrogen bonds or overlap of two closely spaced, partially occupied positions around the centres of symmetry. Several different types of refinements have then been applied, including unconventional models; with all atoms except hydrogen constrained in P1;, but with hydrogen allowed to refine without any constraints in P1, anisotropic refinement of all atoms resulted in clearly off-centred hydrogen positions. Significance tests clearly showed that the results from this constrained refinement give the most satisfactory description of the structure. This structure may be described as 'pseudo-centrosymmetric with non-centred protons'. The results demonstrate that it is very important to also include refinement models with non-centrosymmetric hydrogen in a centrosymmetric environment when studying very short hydrogen bonds. The shifts of the two H atoms from the centres of symmetry are 0.15 (1) and 0.12 (1) A, respectively, at 30 K, and 0.15 (1) A for both H atoms at room temperature. At 30 K: R(F) = 0.036 for 1485 reflections; at 295 K: R(F) = 0.035 for 1349 reflections.

Journal Article↗
PubMed2005

Hydrogen elimination from a hydroxycyclopentadienyl ruthenium(II) hydride: study of hydrogen activation in a ligand-metal bifunctional hydrogenation catalyst.

At high temperatures in toluene, [2,5-Ph(2)-3,4-Tol(2)(eta(5)-C(4)COH)]Ru(CO)(2)H (3) undergoes hydrogen elimination in the presence of PPh(3) to produce the ruthenium phosphine complex [2,5-Ph(2)-3,4-Tol(2)-(eta(4)-C(4)CO)]Ru(PPh(3))(CO)(2) (6). In the absence of alcohols, the lack of RuH/OD exchange, a rate law first order in Ru and zero order in phosphine, and kinetic deuterium isotope effects all point to a mechanism involving irreversible formation of a transient dihydrogen ruthenium complex B, loss of H(2) to give unsaturated ruthenium complex A, and trapping by PPh(3) to give 6. DFT calculations showed that a mechanism involving direct transfer of a hydrogen from the CpOH group to form B had too high a barrier to be considered. DFT calculations also indicated that an alcohol or the CpOH group of 3 could provide a low energy pathway for formation of B. PGSE NMR measurements established that 3 is a hydrogen-bonded dimer in toluene, and the first-order kinetics indicate that two molecules of 3 are also involved in the transition state for hydrogen transfer to form B, which is the rate-limiting step. In the presence of ethanol, hydrogen loss from 3 is accelerated and RuD/OH exchange occurs 250 times faster than in its absence. Calculations indicate that the transition state for dihydrogen complex formation involves an ethanol bridge between the acidic CpOH and hydridic RuH of 3; the alcohol facilitates proton transfer and accelerates the reversible formation of dihydrogen complex B. In the presence of EtOH, the rate-limiting step shifts to the loss of hydrogen from B.

Catalysis↗
PubMed2004

LZnX complexes of tripodal ligands with intramolecular RN-H hydrogen bonding groups: structural implications of a hydrogen bonding cavity, and of X/R in the hydrogen bonding geometry/strength.

Tripodal ligands N(CH2Py)3-n(CH2Py-6-NHR)n(R=H, n=1-3 L1-3, n=0 tpa; R=CH2tBu, n=1-3 L'1-3) are used to investigate the effect of different hydrogen bonding microenvironments on structural features of their LZnX complexes (X=Cl-, NO3-, OH-). The X-ray structures of [(L2)Zn(Cl)](BPh4)2.0.5(H2O.CH3CN), [(L3)Zn(Cl)](BPh4)3.CH3CN, [(L'1)Zn(Cl)](BPh4) 1', [(L'2)Zn(Cl)](BPh4)2'.CH3OH, and [(L'3)Zn(Cl)](BPh4)3' have been determined and exhibit trigonal bipyramidal geometries with intramolecular (internal) N-HCl-Zn hydrogen bonds. The structure of [(L'2)Zn(ONO2)]NO3 4'.H2O with two internal N-HO-Zn hydrogen bonds has also been determined. The axial Zn-Cl distance lengthens from 2.275 A in [(tpa)Zn(Cl)](BPh4) to 2.280-2.347 A in 1-3, 1'-3'. Notably, the average Zn-N(py) distance is also progressively lengthened from 2.069 A in [(tpa)Zn(Cl)](BPh4) to 2.159 and 2.182 A in the triply hydrogen bonding cavity of 3 and 3', respectively. Lengthening of the Zn-Cl and Zn-N(py) bonds is accompanied by a progressive shortening of the trans Zn-N bond from 2.271 A in [(tpa)Zn(Cl)](BPh4) to 2.115 A in 3 (2.113 A in 3'). As a result of the triply hydrogen bonding microenvironment the Zn-Cl and Zn-N(py) distances of 3 are at the upper end of the range observed for axial Zn-Cl bonds, whereas the axial Zn-N distance is one of shortest among N4 ligands that induce a trigonal bipyramidal geometry. Despite the rigidity of these tripodal ligands, the geometry of the intramolecular RN-HX-Zn hydrogen bonds (X=Cl-, OH-, NO3-) is strongly dependent on the nature of X, however, on average, similar for R=H, CH2tBu.

Journal Article↗
PubMed1985

Faecal hydrogen production in vitro as an indicator for in vivo hydrogen producing capability in the breath hydrogen test.

In the assessment of carbohydrate malabsorption, it is important to determine if a flat breath hydrogen test is a false negative result. Currently, the only reliable way to do this is with a lactulose test. We determined the reliability of assessing faecal hydrogen production as an indicator of an adequate in vivo hydrogen producing colonic bacterial flora. Unfortunately, the results clearly show that the incidence of falsely positive and negative faecal hydrogen production, when compared with in vivo lactulose testing, is so high that the simple faeces screening test is unsuitable for routine use. Until a simpler alternative is found, centres using the breath hydrogen test to determine carbohydrate malabsorption must continue to rely on lactulose breath testing when it is necessary to exclude potential false negative results.

Breath Tests↗
PubMed2006

Computational and empirical trans-hydrogen bond deuterium isotope shifts suggest that N1-N3 A:U hydrogen bonds of RNA are shorter than those of A:T hydrogen bonds of DNA.

Density functional theory calculations of isolated Watson-Crick A:U and A:T base pairs predict that adenine 13C2 trans-hydrogen bond deuterium isotope shifts due to isotopic substitution at the pyrimidine H3, (2h)Delta13C2, are sensitive to the hydrogen-bond distance between the N1 of adenine and the N3 of uracil or thymine, which supports the notion that (2h)Delta13C2 is sensitive to hydrogen-bond strength. Calculated (2h)Delta13C2 values at a given N1-N3 distance are the same for isolated A:U and A:T base pairs. Replacing uridine residues in RNA with 5-methyl uridine and substituting deoxythymidines in DNA with deoxyuridines do not statistically shift empirical (2h)Delta13C2 values. Thus, we show experimentally and computationally that the C7 methyl group of thymine has no measurable affect on (2h)Delta13C2 values. Furthermore, (2h)Delta13C2 values of modified and unmodified RNA are more negative than those of modified and unmodified DNA, which supports our hypothesis that RNA hydrogen bonds are stronger than those of DNA. It is also shown here that (2h)Delta13C2 is context dependent and that this dependence is similar for RNA and DNA.

Adenosine↗
PubMed2001

Final report on the safety assessment of Lard Glyceride, Hydrogenated Lard Glyceride, Lard Glycerides, Hydrogenated Lard Glycerides, Lard and Hydrogenated Lard.

Lard obtained from the rendering of fatty porcine tissue is used in cosmetic products, as are several of its derivatives. These derivatives include Lard Glycerides (mono-, di-, and triglycerides derived from Lard), Lard Glyceride (the monoglycerides only), Hydrogenated Lard Glycerides, Hydrogenated Lard Glyceride, and Hydrogenated Lard. The latter three are produced by controlled hydrogenation of the described precursor. These ingredients function as skin-conditioning agents and, with the exception of Lard, as viscosity-increasing agents in several cosmetic products. No information was available regarding the fate during processing of impurities such as pesticides or heavy metals that may be found in animal tissue. Lard itself is established by the Food and Drug Administration (FDA) as a GRAS (generally recognized as safe) substance. Animal studies report adverse effects expected with the feeding of high fat diets, but other animal toxicity data were not available. Lard was not mutagenic in transgenic mice. Cell proliferation assays showed more proliferation in mice fed Lard compared to those fed plant-source fats, but another study showed no difference. Cocarcinogenic effects were observed when high-fat diets containing Lard were fed, with known carcinogens, to mice, rats, and hamsters. Consistent with the FDA GRAS determination, it was concluded that these ingredients may be used safely in cosmetic formulations. However, it was considered important to limit the presence of heavy metals and/or polychlorinated biphenyl (PCB) or other pesticide contamination. Accordingly, limits were established as follows: lead, not more than 0.1 ppm; arsenic (as As), < or =3 ppm; mercury (as Hg), < or =1 ppm; and total PCB/pesticide contamination, not more than 40 ppm, with not more than 10 ppm for any specific residue.

Administration, Oral↗
PubMed1991

Relative acute toxicities of hydrogen fluoride, hydrogen chloride, and hydrogen bromide in nose- and pseudo-mouth-breathing rats.

Hydrogen fluoride (HF), hydrogen bromide (HBr), and hydrogen chloride (HCl) gases can be generated during the pyrolysis of a variety of materials and they may be encountered in numerous industrial settings. Although injury to the respiratory tract has been characterized following the inhalation of halide gases via the nasal route, essentially no experimental information is currently available about their injurious effects when they are inhaled during mouth breathing. In this study, we simulated mouth breathing by using a pseudo-mouth-breathing (MB) rat model in order to: (1) characterize the profiles and magnitudes of respiratory tract injury that result from the acute inhalation of relatively high mass concentrations of the above halides when the upper airway is bypassed, and (2) assess the relative toxicities of HF, HBr, and HCl when inhaled by way of either the nasal or the oral pathways. Tracheal tubes connected to mouthpieces were inserted into temporarily anesthetized rats, i.e., mouth breathers. Awake rats were placed into whole body flow plethysmographs for pulmonary ventilation studies while they were exposed either to air or to 1300 ppm of HF, HBr, or HCl for 30 min. Similarly pretreated rats were also exposed but without the mouthpiece, i.e., nose breathers (NB). The animals were euthanized 24 hr after exposure for histopathologic analyses of their upper and lower respiratory tracts and for lung gravimetric measurements. Tissue injury following NB exposure to the halides was confined to the nasal region, e.g., epithelial and submucosal necrosis, accumulations of inflammatory cells, exudates, and the extravasation of erythrocytes. MB exposure caused higher mortality rates and major tissue disruption in the trachea, including epithelial, submucosal, glandular, and cartilage necrosis, and accumulations of inflammatory cells and exudates. More peripheral lung damage was manifested by lung gravimetric increases and histopathologic changes primarily in the larger conducting airways. The results of this study demonstrate that the injurious response profiles to HF, HBr, and HCl markedly differ as a function of the route by which they are inhaled. Furthermore, examinations of the magnitudes of injury caused by exposure to the halides during nose or mouth breathing in conjunction with animal ventilatory data obtained during exposure to the halides suggest that HF, HBr, and HCl are quantitatively similar in their toxic effects in the respiratory tract.

Acids↗
PubMed2002

Hydrogen bonding in nitroaniline analogues: hydrogen-bonded sheets in 2-amino-4,6-dimethoxy-5-nitropyrimidine and pi-stacked hydrogen-bonded sheets in 4-amino-2,6-dimethoxy-5-nitropyrimidine.

In 2-amino-4,6-dimethoxy-5-nitropyrimidine, C(6)H(8)N(4)O(4), the molecules are linked by one N-H...N and one N-H...O hydrogen bond to form sheets built from alternating R(2)(2)(8) and R(6)(6)(32) rings. In isomeric 4-amino-2,6-dimethoxy-5-nitropyrimidine, C(6)H(8)N(4)O(4), which crystallizes with Z' = 2 in P-1, the two independent molecules are linked into a dimer by two independent N-H...N hydrogen bonds. These dimers are linked into sheets by a combination of two-centre C-H...O and three-centre C-H...(O)(2) hydrogen bonds, and the sheets are further linked by two independent aromatic pi-pi-stacking interactions to form a three-dimensional structure.

Journal Article↗
PubMed2002

Asymmetric hydrogen bonds in centrosymmetric environment. II. Neutron study of very short hydrogen bonds in potassium hydrogen dichloromaleate at 90 K and 170 K.

In our earlier neutron diffraction study of the title compound at 30 K and 295 K an unconventional strategy in the refinement of hydrogen was applied and the same procedure has now been followed in the present investigation at 170 K and 90 K. There are two short O...H...O hydrogen bonds [2.437 (2) A and 2.442 (2) A at 30 K] and the 'heavy-atom' structure is centrosymmetric (P1) with centres of symmetry in the middle of the O...O bonds. However, statistical significance tests clearly show that an asymmetric location of both H atoms gives the most satisfactory description of the structure at all temperatures. The shift of hydrogen from the centre of symmetry is 0.15, 0.14, 0.15 and 0.15 A for H2 at 30, 90, 170 and 295 K, respectively, and 0.15, 0.15, 0.15 and 0.12 A for H4 (sigma = 0.01 A). Furthermore, the behaviour of H2 is very interesting: at 295 K and 170 K it is located on one side of the symmetry centre but at 90 K and 30 K it is located on the other side. A detailed determination of the unit-cell parameters by X-ray diffraction in the whole temperature range from 30 K to 295 K has revealed that the data points of the cell parameters as a function of temperature fall on two different straight lines with a sudden change in the slope around 135 K. It appears likely that the change in the location of H2 as the temperature is lowered is related to this behaviour. At 170 K, R(F) = 0.029 for 1236 reflections; at 90 K, R(F) = 0.030 for 1457 reflections.

Journal Article↗
PubMed1976

[Single and complex effect of ammonia and hydrogen sulfide in the air on small laboratory animals (rats) under various environmental conditions 2. Effect of hydrogen sulfide alone and hydrogen sulfide with ammonia and dust].

The maximum tolerable concentrations per animal position of hydrogen sulphide alone (5 ppm) and with ammonia (5 ppm H2S; 30 ppm NH3) were established by model experiments under defined environmental conditions. The normal values of the contaminant gas combination were found to be acceptable even with additional dust load on the experimental animals. TGL 29084 should stipulate 5 ppm hydrogen sulphide as the new maximum concentration per animal position.

Ammonia↗
PubMed2003

Hydrogen bonding in diols and binary diol-water systems investigated using DFT methods. II. Calculated infrared OH-stretch frequencies, force constants, and NMR chemical shifts correlate with hydrogen bond geometry and electron density topology. A reevaluation of geometrical criteria for hydrogen bonding.

Although the two hydroxyl groups in 1,2-diols interact as evidenced by NMR and IR spectroscopic shifts, electron density topological analysis has shown a bond critical point (BCP) and atomic bond path to be absent (Klein, R. A.; J Comp Chem 2002, 23, 585-599; J Am Chem Soc 2002, 124, 13931-13937), indicating that no intramolecular hydrogen bond is formed. Here, we demonstrate that small NMR or IR shifts are neither necessarily diagnostic nor sufficient as indicators of hydrogen bond formation; moreover, modified van der Waals atomic radii are needed for estimating maximum nuclear interaction distances and nuclear interpenetration.

Journal Article↗
PubMed2003

(4-nitrophenylsulfinyl)acetic acid, a three-dimensional hydrogen-bonded framework built from a combination of two-centre O-H...O and C-H...O hydrogen bonds and a three-centre C-H...(O)2 hydrogen bond.

Molecules of the title compound, C(8)H(7)NO(5)S, are linked into sheets by a combination of two-centre hydrogen bonds, one of type O-H...O [H...O = 1.81 A, O...O = 2.648 (2) A and O-H...O = 173 degrees ] and three of type C-H...O [H...O = 2.40-2.48 A, C...O = 3.206 (3)-3.391 (3) A and C-H...O = 131-160 degrees ]. These sheets are linked by an unusual three-centre C-H...(O)(2) hydrogen bond [H...O = 2.46 and 2.56 A, C...O = 3.289 (3) and 3.351 (3) A, and C-H...O = 141 and 137 degrees ], in which the two acceptors are carboxyl and sulfoxide O atoms.

Journal Article↗
PubMed1984

Breath hydrogen test for lactose absorption capacity: importance of timing of hydrogen excretion and of high fasting hydrogen concentration.

The breath hydrogen (H2) test for lactose absorption capacity is a simple, noninvasive method for the determination of the adult lactase phenotypes, lactose absorber and malabsorber, in healthy subjects. Two breath H2 tests with a load of 50 g lactose monohydrate were performed on 25 healthy adult lactose malabsorbers in order to determine the validity of simplified versions of the test for field studies. A high variability of peak H2 excretion times, rapid changes in breath H2 concentrations and a significant correlation of intraindividual peak H2 excretion times were observed. High fasting excretion of H2 in breath was a frequent cause of misclassification of probands. It is recommended that at least three breath samples per proband should be collected in field studies of lactose absorption and that special diagnostic criteria be applied in classifying subjects with high initial H2 excretion.

Absorption↗
PubMed1998

Hydrogen bonding in helical polypeptides from molecular dynamics simulations and amide hydrogen exchange analysis: alamethicin and melittin in methanol.

Molecular dynamics simulations of ion channel peptides alamethicin and melittin, solvated in methanol at 27 degrees C, were run with either regular alpha-helical starting structures (alamethicin, 1 ns; melittin 500 ps either with or without chloride counterions), or with the x-ray crystal coordinates of alamethicin as a starting structure (1 ns). The hydrogen bond patterns and stabilities were characterized by analysis of the dynamics trajectories with specified hydrogen bond angle and distance criteria, and were compared with hydrogen bond patterns and stabilities previously determined from high-resolution NMR structural analysis and amide hydrogen exchange measurements in methanol. The two alamethicin simulations rapidly converged to a persistent hydrogen bond pattern with a high level of 3(10) hydrogen bonding involving the amide NH's of residues 3, 4, 9, 15, and 18. The 3(10) hydrogen bonds stabilizing amide NH's of residues C-terminal to P2 and P14 were previously proposed to explain their high amide exchange stabilities. The absence, or low levels of 3(10) hydrogen bonds at the N-terminus or for A15 NH, respectively, in the melittin simulations, is also consistent with interpretations from amide exchange analysis. Perturbation of helical hydrogen bonding in the residues before P14 (Aib10-P14, alamethicin; T11-P14, melittin) was characterized in both peptides by variable hydrogen bond patterns that included pi and gamma hydrogen bonds. The general agreement in hydrogen bond patterns determined in the simulations and from spectroscopic analysis indicates that with suitable conditions (including solvent composition and counterions where required), local hydrogen-bonded secondary structure in helical peptides may be predicted from dynamics simulations from alpha-helical starting structures. Each peptide, particularly alamethicin, underwent some large amplitude structural fluctuations in which several hydrogen bonds were cooperatively broken. The recovery of the persistent hydrogen bonding patterns after these fluctuations demonstrates the stability of intramolecular hydrogen-bonded secondary structure in methanol (consistent with spectroscopic observations), and is promising for simulations on extended timescales to characterize the nature of the backbone fluctuations that underlie amide exchange from isolated helical polypeptides.

Alamethicin↗