Does Z' equal 1 or 2? Enhanced powder NMR crystallography verification of a disordered room temperature crystal structure of a p38 inhibitor for chronic obstructive pulmonary disease

The crystal structure of the Form A polymorph of N-cyclopropyl-3-fluoro-4-methyl-5-[3-[[1-[2-[2-(methylamino)ethoxy]phenyl]cyclopropyl]amino]-2-oxo-pyrazin-1-yl]benzamide (i.e., AZD7624), determined using single-crystal X-ray diffraction (scXRD) at 100 K, contains two molecules in the asymmetric unit (Z' = 2) and has regions of local static disorder. This substance has been in phase IIa drug development trials for the treatment of chronic obstructive pulmonary disease, a disease which affects over 300 million people and contributes to nearly 3 million deaths annually. While attempting to verify the crystal structure using nuclear magnetic resonance crystallography (NMRX), we measured ¹³C solid-state NMR (SSNMR) spectra at 295 K that appeared consistent with Z' = 1 rather than Z' = 2. To understand this surprising observation, we used multinuclear SSNMR (¹H, ¹³C, ¹⁵N), gauge-including projector augmented-wave density functional theory (GIPAW DFT) calculations, crystal structure prediction (CSP), and powder XRD (pXRD) to determine the room temperature crystal structure. Due to the large size of AZD7624 (ca. 500 amu, 54 distinct ¹³C environments for Z' = 2), static disorder at 100 K, and (as we show) dynamic disorder at ambient temperatures, NMR spectral assignment was a challenge. We introduce a method to enhance confidence in NMR assignments by comparing experimental ¹³C isotropic chemical shifts against site-specific DFT-calculated shift distributions established using CSP-generated crystal structures. The assignment and room temperature NMRX structure determination process also included measurements of ¹³C shift tensors and the observation of residual dipolar coupling between ¹³C and ¹⁴N. CSP generated ca. 90 reasonable candidate structures (Z' = 1 and Z' = 2), which when coupled with GIPAW DFT results, room temperature pXRD, and the assigned SSNMR data, establish Z' = 2 at room temperature. We find that the polymorphic Form A of AZD7624 is maintained at room temperature, although dynamic disorder is present on the NMR timescale. Of the CSP-generated structures, 2 are found to be fully consistent with the SSNMR and pXRD data; within this pair, they are found to be structurally very similar (RMSD₁₆ = 0.30 Å). We establish that the CSP structure in best agreement with the NMR data possesses the highest degree of structural similarity with the scXRD-determined structure (RMSD₁₆ = 0.17 Å), and has the lowest DFT-calculated energy amongst all CSP-generated structures with Z' = 2.

Review of footnotes and annotations to the 1949–2013 tables of standard atomic weights and tables of isotopic compositions of the elements (IUPAC Technical Report)

The Commission on Isotopic Abundances and Atomic Weights uses annotations given in footnotes that are an integral part of the Tables of Standard Atomic Weights to alert users to the possibilities of quite extraordinary occurrences, as well as sources with abnormal atomic-weight values outside an otherwise acceptable range. The basic need for footnotes to the Standard Atomic Weights Table and equivalent annotations to the Table of Isotopic Compositions of the Elements arises from the necessity to provide users with information that is relevant to one or more elements, but that cannot be provided using numerical data in columns. Any desire to increase additional information conveyed by annotations to these Tables is tempered by the need to preserve a compact format and a style that can alert users, who would not be inclined to consult either the last full element-by-element review or the full text of a current Standard Atomic Weights of the Elements report. Since 1989, the footnotes of the Tables of Standard Atomic Weights and the annotations in column 5 of the Table of Isotopic Compositions of the Elements have been harmonized by use of three lowercase footnotes, “g”, “m”, and “r”, that signify geologically exceptionally specimens (“g”), modified isotopic compositions in material subjected to undisclosed or inadvertent isotopic fractionation (“m”), and the range in isotopic composition of normal terrestrial material prevents more precise atomic-weight value being given (“r”). As some elements are assigned intervals for their standard atomic-weight values (applies to 12 elements since 2009), footnotes “g” and “r” are no longer needed for these elements.

Solid-state (185/187)Re NMR and GIPAW DFT study of perrhenates and Re2(CO)10: chemical shift anisotropy, NMR crystallography, and a metal-metal bond

Advances in solid-state nuclear magnetic resonance (SSNMR) methods, such as dynamic nuclear polarization (DNP), intricate pulse sequences, and increased applied magnetic fields, allow for the study of systems which even very recently would be impractical. However, SSNMR methods using certain quadrupolar probe nuclei (i.e., I > 1/2), such as (185/187)Re remain far from fully developed due to the exceedingly strong interaction between the quadrupole moment of these nuclei and local electric field gradients (EFGs). We present a detailed high-field (B0 = 21.1 T) experimental SSNMR study on several perrhenates (KReO4, AgReO4, Ca(ReO4)2·2H2O), as well as ReO3 and Re2(CO)10. We propose solid ReO3 as a new rhenium SSNMR chemical shift standard due to its reproducible and sharp (185/187)Re NMR resonances. We show that for KReO4, previously poorly understood high-order quadrupole-induced effects (HOQIE) on the satellite transitions can be used to measure the EFG tensor asymmetry (i.e., ηQ) to nearly an order-of-magnitude greater precision than competing SSNMR and nuclear quadrupole resonance (NQR) approaches. Samples of AgReO4 and Ca(ReO4)2·2H2O enable us to comment on the effects of counter-ions and hydration upon Re(vii) chemical shifts. Calcium-43 and (185/187)Re NMR tensor parameters allow us to conclude that two proposed crystal structures for Ca(ReO4)2·2H2O, which would be considered as distinct, are in fact the same structure. Study of Re2(CO)10 provides insights into the effects of Re-Re bonding on the rhenium NMR tensor parameters and rhenium oxidation state on the Re chemical shift value. As overtone NQR experiments allowed us to precisely measure the (185/187)Re EFG tensor of Re2(CO)10, we were able to measure rhenium chemical shift anisotropy (CSA) for the first time in a powdered sample. Experimental observations are supported by gauge-including projector augmented-wave (GIPAW) density functional theory (DFT) calculations, with NMR tensor calculations also provided for NH4ReO4, NaReO4 and RbReO4. These calculations are able to reproduce many of the experimental trends in rhenium δiso values and EFG tensor magnitudes. Using KReO4 as a prototypical perrhenate-containing system, we establish a correlation between the tetrahedral shear strain parameter (|ψ|) and the nuclear electric quadrupolar coupling constant (CQ), which enables the refinement of the structure of ND4ReO4. Shortcomings in traditional DFT approaches, even when including relativistic effects via the zeroth-order regular approximation (ZORA), for calculating rhenium NMR tensor parameters are identified for Re2(CO)10.

The consistency of the data for neutron fission averaged cross-sections of threshold reactions: a study on the cross-section of 46Ti(n,p)46Sc, 47Ti(n,p)47Sc, 48Ti(n,p)48Sc and 64Zn(n,p)64Cu reactions

The consistency of the published values for fission averaged cross-sections of threshold reactions induced in a nuclear reactor is analyzed. The influence of the literature data involved in the determination of these cross-sections is discussed. Renormalizations based on cross-sections value for the standard reactions, isotopic abundances of the precursors and radiation emission probabilities of the radionuclide under study and the monitor, are applied to the evaluation of the cross-sections for the reactions: (46)Ti(n,p)(46)Sc; (47)Ti(n,p)(47)Sc; (48)Ti(n,p)(48)Sc; and (64)Zn(n,p)(64)Cu.

Definitive solid-state 185/187Re NMR spectral evidence for and analysis of the origin of high-order quadrupole-induced effects for I=5/2

Rhenium-185/187 solid-state nuclear magnetic resonance (SSNMR) experiments using NaReO(4) and NH(4)ReO(4) powders provide unambiguous evidence for the existence of high-order quadrupole-induced effects (HOQIE) in SSNMR spectra. Fine structure, not predicted by second-order perturbation theory, has been observed in the (185/187)Re SSNMR spectrum of NaReO(4) at 11.75 T, where the ratio of the Larmor frequency (ν(0)) to the quadrupole frequency (ν(Q)) is ∼2.6. This is the first experimental observation that under static conditions, HOQIE can directly manifest in SSNMR powder patterns as additional fine structure. Using NMR simulation software which includes the quadrupole interaction (QI) exactly, extremely large (185/187)Re nuclear quadrupole coupling constants (C(Q)) are accurately determined. QI parameters are confirmed independently using solid-state (185/187)Re nuclear quadrupole resonance (NQR). We explain the spectral origin of the HOQIE and provide general guidelines that may be used to assess when HOQIE may impact the interpretation of the SSNMR powder pattern of any spin-5/2 nucleus in a large, axially symmetric electric field gradient (EFG). We also quantify the errors incurred when modeling SSNMR spectra for any spin-5/2 nucleus within an axial EFG using second-order perturbation theory. Lastly, we measure rhenium chemical shifts in the solid state for the first time.

Molecular mass and location of the most abundant peak of the molecular ion isotopomeric cluster

The location of the most abundant peak of the molecular-ion pattern often differs from the molecular mass published in scientific databases. The location is also distinct from the value expected from average atomic masses. The cause of this phenomenon is a large number of atoms of carbon, sulfur, chlorine, bromine, silicon and boron. This due to the natural isotope abundances of some elements forming organic compounds. A parameter called location of the most abundant peak of an isotopometric cluster (LAPIC) denotes the location of the most abundant (the main) peak of an isotopomeric cluster, which is determined, e.g., by mass spectrometry and can be important for medium- and high-molecular mass compounds. The equations for LAPIC calculation are presented for elements usually observed in organic compounds. The LAPIC with elemental formula helps effectively, e.g., in mass spectra interpretation since the prediction of LAPIC allows the correct connection of the main peak of the investigated ion with the expected ion formula and the mass of the ion considered. This solution can be a substitute for the much more complex method of isotopometric analysis applied in mass spectra interpretation. [Figure: see text]. Differences of the most abundant peak location (Delta LAPIC(C)=f(n)) for carbon aggregates C(n).

Determination of inorganic chlorine stable isotopes by continuous flow isotope ratio mass spectrometry

Chlorine stable isotope analyses of inorganic samples were conducted using continuous flow isotope ratio mass spectrometry (CF-IRMS) coupled with gas chromatography (GC). Inorganic chloride was precipitated in the form of silver chloride (AgCl) by using silver nitrate in a standard methodology. Chlorine stable isotope analysis was carried out on methyl chloride (CH3Cl) after converting AgCl into CH3Cl by reacting it with methyl iodide (CH3I). The reaction between AgCl and CH3I took place in 20 mL size vials. Addition of CH3I was performed in a glove bag under helium flow. An Agilent 6890 gas chromatograph equipped with a CTC Analytics CombiPAL autosampler and a DB-5MS 60 m column was used to separate CH3Cl from CH3I. This new technique uses samples as small as 0.2 mg of AgCl (1.4 micromol of Cl-). The chlorine stable isotope analysis using continuous flow technology showed excellent precision and accuracy. The internal precision using pure CH3Cl gas is better than +/-0.04 per thousand (+/-STDV). The external precision using seawater standard is better than +/-0.07 per thousand (+/-STDV) for n=12. Moreover, the sample analysis time is much shorter and many more samples can be analyzed in one day than by using the conventional off-line techniques.

Evaluation of the analyses of tert-butyldimethylsilyl derivatives of naphthenic acids by gas chromatography–electron impact mass spectrometry

Naphthenic acids are a complex mixture of carboxylic acids with the general formula CnH(2n+Z)O2 and they are natural, toxic components of crude oils. GC-MS analyses of tert-butyldimethylsilyl esters of naphthenic acids are used to estimate component distribution within naphthenic acids mixtures. Our evaluations of the GC-MS method showed that ions from column bleed erroneously appear as C14 Z = -4 acids and that correcting for heavy isotopes of C and Si do not significantly affect ion distribution plots. Overall, the GC-MS method appears to overestimate the relative proportion of low-molecular-mass acids.

Anomalous 235U/238U ratios and metal elements detected in the black rain from the Hiroshima A-bomb

Contents of black rain from the A-bomb are important to clarify the health and environmental hazard caused by nuclear warfare. We analyzed the only existing physical remains of the black rain from Hiroshima A-bomb (Little Boy), a plastered wall with black streaks. Excess 137Cs and anomalous 235U/238U ratios detected in the black residues on the wall confirmed that the black streaks on the wall originated from Little Boy. The results also showed that excess 235U could be used as a fingerprint to clarify the distribution of materials discharged from Little Boy into the environment. High concentrations of lead and zinc, which may have caused a degree of heavy metal pollution in the area where the rain fell, were also detected in the black rain sample.

Endogenous alkaloids in man. XXXVIII. "Chiral" and "achiral" determination of the neurotoxin TaClo (1-trichloromethyl-1,2,3,4-tetrahydro-beta-carboline) from blood and urine samples by high-performance liquid chromatography--electrospray ionization tandem mass spectrometry

An improved sensitive assay for the determination of the dopaminergic and serotonergic neurotoxin 1-trichloromethyl-1,2,3,4-tetrahydro-beta-carboline (TaClo) is presented, based upon on-line coupling of high-performance liquid chromatography with electrospray ionization tandem mass spectrometry (HPLC-ESI-MS-MS). Applying synthetic [D4]TaClo as a fourfold deuterated internal standard, TaClo was detected and reliably quantified as a trace constituent of blood samples (0.5 up to 70 ng g(-1) of clot) obtained from six patients orally treated with the hypnotic chloral hydrate. Unambiguous identification of this tricyclic "endogenous alkaloid" was achieved by selected reaction monitoring (SRM) experiments. The molecular ion peaks of TaClo, m/z 289 (for [35Cl3]TaClo) and m/z 291 (for its [37Cl35Cl2]isotopomer), were both monitored to undergo a retro-Diels-Alder fragmentation by loss of a CH2=NH portion (-29 u) as typical of a tetrahydropyrido ring system of tetrahydro-beta-carbolines. Detection of the resulting fragments, m/z 260 and m/z 262, with the expected statistical chlorine isotopic intensities of 100:96 confirmed the identity of the TaClo molecule. In addition, an enantiomer-specific device was developed for TaClo, by employing a chiral reversed-phase HPLC column in combination with circular dichroism (CD) spectroscopy and MS-MS analysis (LC-CD and LC-MS-MS coupling). In a human clot sample, both TaClo enantiomers were found in equimolar concentration (i.e., as a racemate) corroborating a spontaneous, non-enzymatic formation of TaClo from biogenic tryptamine and therapeutically administered chloral. In urine samples of TaClo-treated rats, by contrast, the (S)-antipode was found to predominate, hinting at an enantiomer-differentiating metabolism of the compound.

Multi-isotopic modelling of mass spectra: a procedure for verification of the fragmentation hypothesis for the organometallic and coordination compounds

Interpretations of mass spectra usually depend on explanations of the molecular structure by determination of the fragmentation ions structures. Therefore, identification of fragmentation ions formulas is an initial step of such investigations. It seems that multi-isotopic modelling of all ions proposed in fragmentation data should lead to the theoretical mass spectrum. Good adjustment of experimental and predicted spectra proves the validity of the fragmentation table, whose contents are recognised as fragmentation hypothesis. This means that multi-isotopic modelling is a helpful tool for verification of proposed fragmentation data. Applications of the method are presented for 1,1',2,2',3,3'-hexachloro-ferrocene, C10H4Cl6Fe, and bis(dibutyldithiophosphate)-zinc(II), [(C4H9O)2PS2]2Zn.

Determination of selenium stable isotopes by gas chromatography-mass spectrometry with negative chemical ionisation

A gas chromatography mass spectrometric method using negative chemical ionisation was developed for the determination of stable isotopes of selenium for evaluation of selenium absorption and retention from foods in humans. The method involves an acid digestion to convert all selenium into selenite, which subsequently reacts with 4-nitro-o-phenylene-diamine to form a volatile piazselenole. The piazselenole, after extraction into an organic solvent, was analysed for its isotopic selenium composition by gas chromatography mass spectrometry. Negative chemical ionisation is reported for the first time for the determination of selenium stable isotopes and its analytical characteristics were compared to those of electron impact mass spectrometric ionisation, classically used for the determination of selenium. The negative chemical ionisation technique allowed accurate determination of total selenium by isotope dilution and of selenium isotope ratios in biological samples. The repeatability for total selenium and for stable isotope ratios was good (R.S.D.< or =10%) within the range of 50 to 250 ng selenium. The detection limit for the investigated selenium isotopes was approximately 1 pg (signal to noise ratio at 3). The applicability of the developed stable isotope methodology was demonstrated by the determination of the selenium absorption and retention from foods in a pilot study using one human adult.

Simple and rapid quantitative assay of 13C-labelled urea in human serum using liquid chromatography-atmospheric pressure chemical ionization mass spectrometry

A simple and rapid quantitative method for 13C-labelled urea ([13C]urea) in human serum was developed by using high-performance liquid chromatography-atmospheric pressure chemical ionization mass spectrometry (HPLC-APCI-MS). This method is used to establish and normalize the [13C]urea breath test, which is considered as an effective diagnostic method for Helicobacter pylori infection. HPLC-APCI-MS, involving a simple pretreatment process such as diluting serum with water, was shown to be able to discriminate the extrinsic [13C]urea from intrinsic urea present at high concentration in serum. In addition, a 13C nuclear magnetic resonance spectroscopic quantitative method for [13C]urea in human urine is also described. The precision and accuracy of measured concentrations in these two methods were found to be within the acceptable limit. An application of these methods to investigate the pharmacokinetic profile of orally administered [13C]urea in human serum and urine is also presented.

Dietary fiber in weaning cereals: a study of the effect on stool characteristics and absorption of energy, nitrogen, and minerals in healthy infants

We evaluated the effect of increased dietary fiber (DF) content in weaning cereals based on wheat/soy (8.0 and 1.8% DF) and wheat/milk (5.3 and 2.0% DF) in healthy, formula-fed infants 7-17 weeks old. The study had a cross-over design, each infant acting as his or her own control. Stool characteristics and anthropometry were monitored over 4-week periods in groups of 34 (wheat/soy) and 23 (wheat/milk) infants. Absorption of zinc (Zn) and calcium (Ca) was studied by measuring the fecal excretion of stable isotopes during 72 h (70Zn and 42Ca) in a subgroup of the infants consuming wheat/soy cereals. Iron (Fe) bioavailability was evaluated by analysis of the incorporation of 58Fe into erythrocytes 14 days after administration. Fractional absorption (X +/- SD: 8.0 versus 1.8% DF) was 45.3 +/- 27.5 versus 41.2 +/- 19.4% of 70Zn and 63.4 +/- 15.8 versus 64.4 +/- 10.6% of 42Ca. Bioavailability of 58Fe varied between 1.0% and 5.4% (8.0% DF) and from <0.9% to 9.1% (1.8% DF). No significant difference in energy (95.3 +/- 2.0% versus 95.7 +/- 1.2%) or nitrogen (92.6 +/- 2.3% versus 93.0 +/- 1.6%) apparent absorption from the total diet was found during consumption of cereal with 8.0 and 1.8% DF. The intake of cereal decreased with higher DF content in the wheat/soy product: 34 +/- 23 g/d (8.0% DF) versus 42 +/- 23 g/d (1.8% DF), p < 0.01. While consuming the 8.0% DF product, 11 infants were reported to have "gritty stools"; no other differences were observed between different groups in stool characteristics or anthropometry. These results demonstrate no negative effect on the absorption of energy and nutrients with higher dietary fiber intake in primarily formula-fed infants. The impact of increased dietary fiber levels remains unknown in less well-nourished infants.

An application of nitrogen microwave-induced plasma mass spectrometry to isotope dilution analysis of selenium in marine organisms

Nitrogen microwave-induced plasma mass spectrometry was studied for its applicability to the isotope dilution analysis of selenium in biological samples. Spectroscopic interference by calcium, which is present in high concentrations in biological samples, was investigated. No detectable background spectrum was observed for the major selenium isotopes of 78Se and 80Se. No detectable interferences by sodium, potassium, calcium and phosphorus on the isotope ratio 80Se/78Se were observed up to concentration of 200 mg/ml. The method was applied to the analysis of selenium in biological reference materials of marine organisms. The results showed good agreement between the certified and found values.

Effect of bile/pancreatic secretions on absorption of radioactive or stable zinc. In vivo and in vitro studies

Biliary/pancreatic (B/P) secretions are a major component of endogenous secretions, and endogenously secreted Zn is a primary means of Zn homeostasis. This study examined whether B/P fluid alters the absorption/reabsorption of Zn and, in doing so, whether this contributes to homeostatic control of Zn. Animal experiments utilized rats fed 10 or 300 micrograms Zn/kg diet. An open-ended gut perfusion study in which 65Zn-labeled B/P fluid or 67Zn-labeled and digested diet found significantly decreased Zn absorption from B/P fluid. Although Zn absorption from both sources was less in animals fed diets higher in Zn, there was no interaction of treatment and diet. Further studies utilizing cultured human colon carcinoma cells (CACO-2) as in vitro models of gut enterocytes found that the presence of B/P fluid significantly decreased Zn retention and/or transport and resulted in a redistribution of cellular Zn after 1200 min of incubation. These studies show that a substance in B/P fluid can decrease the absorption of Zn and also suggest that dietary Zn and Zn associated with B/P secretions are absorbed from distinct pools. However, the lack of an interactive effect with diet, and the amount of time required to see differences in CACO-2 cells, suggest that differences in absorption are not a major contributor to Zn homeostasis.