Hydrogen Rearrangement Research Articles

Dimensionality Switching Through a Thermally Induced Reversible Single-Crystal-to-Single-Crystal Phase Transition in a Cyanide Complex

The heterometallic hexanuclear cyanide-bridged complex {[Mn(bpym)(H(2)O)](2)[Fe(HB(pz)(3))(CN)(3)](4)} (1), its C(15)N and D(2)O enriched forms {[Mn(bpym)(H(2)O)](2)[Fe(HB(pz)(3))(C(15)N)(3)](4)} (2) and {[Mn(bpym)(D(2)O)](2)[Fe(HB(pz)(3))(CN)(3)](4)} (3), and the hexanuclear derivative complex {[Mn(bpym)(H(2)O)](2)[Fe(B(pz)(4))(CN)(3)](4)}·4H(2)O (4) [bpym = 2,2'-bipyrimidine, HB(pz)(3)(-) = hydrotris(1-pyrazolyl)borate, B(pz)(4)(-) = tetra(1-pyrazolyl)borate] have been synthesized. Their structures have been determined through single-crystal X-ray crystallography at different temperatures. Whereas 3 and 4 maintain a discrete hexanuclear motif during the entire temperature range investigated (down to 95 K), 1 and 2 exhibit a thermally induced reversible single-crystal to single-crystal phase transition driven by a remarkable concerted rearrangement of hydrogen and cyanide coordination bonds. While hexanuclear complexes are observed in the high temperature phases (noted 1a and 2a) above 200 K, the low temperature phases are composed of one-dimensional coordination polymers noted 1b and 2b. The magnetic properties of the four compounds have been investigated in the 2-300 K range, and they reveal the occurrence of an overall antiferromagnetic behavior. The thermal dependence of the optical reflectivity and the FT-IR absorbance have been studied for 1 in the range 10-300 K and 130-300 K, respectively. A comparative analysis of the structural and electronic properties for 1-4 clearly underlines the major role of the intermolecular interactions in the topological and dimensional rearrangement observed during the structural phase transition. This result opens new perspectives in the design of cyanide-based switchable magnetic materials using coordination bonds rearrangements.

Characterization and identification of steroidal alkaloids in Fritillaria species using liquid chromatography coupled with electrospray ionization quadrupole time-of-flight tandem mass spectrometry

Liquid chromatography coupled with electrospray ionization quadrupole time-of-flight tandem mass spectrometry (LC/ESI-QTOF-MS/MS) was performed to study the fragmentation behaviors of steroidal alkaloids from Fritillaria species, the antitussive and expectorant herbs widely used in traditional Chinese medicine. We propose, herein, a strategy that combining key diagnostic fragment ions and the relative abundances and amounts of major fragment ions (the ions exceeding 10% in abundance) to distinguish different sub-classes of Fritillaria alkaloids (FAs). It was found that hydrogen rearrangement and induction effects result in ring cleavage of the basic skeletons occurred in the MS/MS process and produced characteristic fragment ions, which are useful for structural elucidation. This method was finally used to investigate the primary steroidal alkaloids in the extracts of eight major Fritillaria species. As a result, 41 steroidal alkaloids (29 cevanine type, 1 jervine type, 6 veratramine type and 5 secosolanidine type alkaloids) were selectively identified in these Fritillaria species. Twenty-six compounds were unambiguously identified by comparing with the reference compounds and 15 compounds were tentatively identified or deduced according to their MS/MS data. Logical fragmentation pathways for different types of FAs have been proposed and are useful for the identification of these types of steroidal alkaloids in natural products especially when there are no reference compounds available.

Solution behavior of methyl cellulose mixtures with poly(N-vinylformamide) in water and dimethyl sulfoxide

The rheological properties of diluted and moderately concentrated solutions of methyl cellulose mixtures with poly(N-vinylformamide) in water and dimethyl sulfoxide are investigated. Negative deviations of the viscosities of these solutions from the additive values are observed and explained by different mechanisms of solvation of macromolecules with water and dimethyl sulfoxide. Incompatibility of the polymers in a common solvent is discovered. This circumstance leads to the formation of a new system of hydrogen bonds and rearrangement of the structural organization of solutions.

The Lighter Side of a Sweet Reaction

The unique advantage of neutrons as biological probes is the ability to visualize hydrogen atoms in macromolecules. In this issue, Kovalevsky et al. (2010) solved an ensemble of xylose isomerase structures by neutron crystallography, and the determination of hydrogen atom rearrangements during the catalytic cycle provides insight into the enzyme's mechanism.

Characterization of protostane triterpenoids in Alisma orientalis by ultra‐performance liquid chromatography coupled with quadrupole time‐of‐flight mass spectrometry

A reliable and sensitive ultra-performance liquid chromatography/quadrupole time-of-flight mass spectrometry (UPLC/Q-TOF-MS) method has been optimized and established for analysis of protostane triterpenoids in a commonly used traditional Chinese herbal medicine Alisma orientalis (Sam.) Juzep. The separation of crude extract of A. orientalis was achieved on a Waters ACQUITY HSS T3 column (100 mm x 2.1 mm, 1.8 microm) eluting with 0.1% (v/v) formic acid/acetonitrile. A total of 20 protostane triterpenoids including 19 known compounds and a new one were well separated within 7 min. The collision-induced dissociation (CID) tandem mass spectrometric (MS/MS) fragmentation patterns of protostane triterpenoids was firstly reported in this study. The hydrogen rearrangement at the C-23-OH leads to dissociation of the bond between C-23 and C-24 in the protostane triterpenoid skeleton during the CID process. This dissociation was the characteristic CID fragmentation pathway of this class of triterpenoids, and was useful for further differentiation of some positional isomers which contain an acetyl unit on the C-23 or C-24 position. The identities of isolated compounds were identified by comparing their retention times and CID fragmentation behaviors with those of reference standards or tentatively assigned by matching the empirical molecular formulae with those reported in the literature. It is concluded that this newly established UPLC/Q-TOF-MS method is a powerful approach for structural elucidation of protostane triterpenoids isolated from A. orientalis.

CoH n ( n = 1–3): Classical and non-classical cobalt polyhydride

UB3LYP calculations with the TZVP, DGDZVP and 6-31+G(2d,p) basis sets have been used to explore the potential energy surfaces of CoH n ( n = 1–3). A hydrogen rearrangement process with a low activation energy was found in the H–Co⋯H–H complex. This process requires elongation of the H–H bond and a concomitant shortening of the distance between the hydride and the vicinal hydrogen of the H 2 ligand. In addition, we present a classification of cobalt–hydrogen interactions in the CoH n complexes based on topological parameters of the charge density.

Specific fragmentation of the K-shell excited/ionized pyridine derivatives studied by electron impact: 2-, 3- and 4-methylpyridine

Fragmentation of the pyridine ring upon K-shell excitation/ionization has been studied with gaseous 2-, 3- and 4-methylpyridine by the electron-impact method. Ab initio molecular orbital (MO) calculations were also carried out to explore electronic states correlating with specific fragments. Some specific fragmentation channels were identified from the ionic fragments enhanced characteristically at the N 1s edge. Yields of the C(2)HN(+) and C(5)H(5)(+)/C(5)H(6)(+) ions show that the fission of the N-C2 and C4-C5/C5-C6 bonds of the ring is likely to occur after the N 1s excitation and ionization. Ab initio MO calculations for the 2-methylpyridine molecule indicate that the dissociation channels to produce these ions are only accessible through the excited states of the parent molecular dication, which can be formed by Auger decays after the N 1s ionization. Fragment ions via hydrogen rearrangement are produced as well, but the rearrangement is not a phenomenon specific to the K-shell excitation/ionization.

PH-sensitive hydrogels based on bovine serum albumin for anticancer drug delivery

Protein conjugates consisting of hydroxyethyl methacrylate and acrylic acid monomers in the presence of bovine serum albumin (BSA) were prepared by gamma irradiation to examine the potential use of these hydrogels in the controlled drug release systems. The study parameter was the BSA content in the as-prepared conjugates. Polymers were characterized with FTIR, scanning electron microscopy (SEM), and swelling studies. The polymerization reaction caused the rearrangement of the BSA carbonyl hydrogen bonding and finally led to the modification of the BSA secondary structure as proved by FTIR. SEM proved that the prepared conjugates matrices are porous, with a three-dimensional interconnected microstructure. The swelling kinetics of the hydrogels and the release dynamics of an anticancer model drug (flutamide) have been studied. High equilibrium swelling values, up to 1550%, could be observed and were correlated with the increase in pH, temperature, and BSA content. The mechanism of swelling changed from Fickian to non-Fickian by reducing the acidity of the medium. This study proved that there is a direct relationship between the protein content in the conjugates and both the loaded and the released drug. These pH responsive conjugates may be exploited for the delivery of flutamide. © 2009 Wiley Periodicals, Inc. J Appl Polym Sci, 2010

Gas Chromatography Electron Ionization Mass Spectrometric Analysis of O-Alkyl Methylphosphinates for Verification of Chemical Weapons Convention

We describe the gas chromatography/mass spectrometric (GC/MS) analysis of O-alkyl methylphosphinates (AMPs), which are included in schedule 2B4 chemicals in the Chemical Weapons Convention (CWC). GC/MS analysis of variety of AMPs and their deuterated analogues revealed that their fragmentations were determined by alpha-cleavages, McLafferty +1 and hydrogen rearrangements. Based on the obtained electron ionization mass spectra of AMPs the fragmentation routes were rationalized, which were substantiated by the GC/MS analysis of deuterated analogues.

Negative Ion Electrospray Ionization Mass Spectrometry and Computational Studies on Substituted 7-Hydroxycoumarins

Twenty-two substituted 7-hydroxycoumarins were studied by negative ion electrospray ionization collision- induced dissociation (CID) mass spectrometry. Fragmentation pathways were also investigated by computation method using the B3LYP density functional theory. In general, the most important fragmentations of the 7- hydroxycoumarin [M - H](-) ions were the elimination of CO(2) and CO which agreed with the calculated energies of the proposed fragmentation reactions. In most cases, methyl group elimination was also favorable. Methyl group elimination occurred in three different ways, the most interesting being hydrogen rearrangement from a neighboring alkyl group to a ring carbon, which led to a benzyl radical formation. In some cases, CH(2)CO elimination was observed as well. Isomeric compounds gave rise to different CID spectra.

High‐throughput approaches towards the definitive identification of pharmaceutical drug metabolites. 2. An example of how unexpected dissociation behaviour could preclude correct assignment of sites of metabolism

S-oxidation is a common metabolic route for sulfur-containing compounds. Whilst investigating the dissociation of a series of chemically synthesised model S-oxide metabolites, two unexpected losses of 62 m/z units were observed in the collision-induced dissociation (CID) product ion spectrum of protonated 3-dimethylaminomethyl-4-(4-methanesulfinyl-3-methylphenoxy)benzenesulfonamide. A single loss was initially assigned using the low-resolution product ion spectrum, acquired by electrospray ionisation quadrupole ion trap mass spectrometry (ESI-QIT-MS), as methanethial, S-oxide via a charge-remote, four-centred rearrangement. This assignment was consistent with well-documented hydrogen rearrangements in the literature. Further, the loss was not observed for the parent compound. Thus, it was inferred that the site of metabolism was involved in the dissociation and the attractive nature of the four-centred rearrangement meant that the loss of methanethial, S-oxide was a logical assignment. However, deuterium-labelling experiments and accurate mass measurements, performed using electrospray ionisation Fourier transform ion cyclotron resonance mass spectrometry (ESI-FT-ICR-MS), showed that the nominal loss of 62 m/z units occurs via two distinct dissociation pathways. Neither of these losses was of methanethial, S-oxide as initially hypothesised from the low-resolution product ion spectrum of the protonated molecule. Mechanisms consistent with the experimental findings are postulated. An MS(3) spectrum of the fully exchanged, deuterated species supported the proposed mechanisms by suggesting that 3-dimethylaminomethyl-4-(4-methanesulfinyl-3-methylphenoxy)benzenesulfonamide has multiple sites of protonation in the gas phase. The planar structures of the posited product ions are likely to provide the driving force for the rearrangements. The relevance of the observations with regards to pharmaceutical drug metabolite identification is discussed.

Thermal activation energy for the passivation of the n-type crystalline silicon surface by hydrogenated amorphous silicon

Excellent surface passivation of crystalline silicon wafers is known to occur following post-deposition thermal annealing of intrinsic a-Si:H thin-film layers deposited by plasma-enhanced chemical vapor deposition. In this work, layer thicknesses ranging from 5 to 50 nm were used to indirectly study the surface passivation mechanism by sequentially measuring the effective carrier lifetime as a function of annealing time and temperature. From this, an activation energy of 0.7±0.1 eV was calculated, suggesting that surface passivation is reaction-limited and not determined by a bulk hydrogen diffusion process. We conclude that the primary surface reaction stems from surface rearrangement of hydrogen already near the interface.

Microsynthesis and gas chromatography/electron ionization mass spectrometric and tandem mass spectrometric analysis of cyclic alkylphosphonates for verification of the Chemical Weapons Convention

We describe the microsynthesis and gas chromatography/mass spectrometric (GC/MS) analysis of cyclic alkylphosphonates (CAPs), which are included in schedule 2B4 chemicals in the Chemical Weapons Convention (CWC). The reported microsynthesis is efficient in comparison with traditional synthesis. GC/MS and GC/tandem mass spectrometric (MS/MS) analysis of a variety of CAPs revealed that their fragmentations were dominated by alpha-cleavages, alkene eliminations and hydrogen rearrangements. Based on the obtained mass spectra and precursor and product ion analysis of five-, six- and seven-membered cyclic alkylphosphonates, the proposed fragmentation routes rationalize most of the characteristic ions.

Atmospheric pressure photoionization mass spectrometry of per-O-methylated oligosaccharides related to d-xylans

Three d-xylan type per-O-methylated trisaccharides with various types of linkages between the d-xylopyranose units were examined by atmospheric pressure photoionization (APPI) mass spectrometry in the positive ion mode. The most interesting feature of a thermospray mass spectrum using the APPI source with UV lamp switched off, is the exclusive production of [M+Na] + adduct ions. [M+Na] + cationized ions are the most abundant species in the case of APPI mass spectrometry. The second ionization process has no analogy in the case of substances studied using APPI to date. This aspect involves the addition of a water molecule to the molecular ion of a per-O-methylated saccharide, giving rise to [M+H 2O] + adduct ions. The [M+H 2O] + species are readily detected at m/ z 544, and are clearly visible for all three isomers studied. The MS/MS spectrum of [M+Na] + ions contains a base peak at m/ z 375, produced by a Y-type cleavage of the trisaccharide, along with a hydrogen rearrangement on the terminal interglycosidically linkage glycosidic oxygen atom. The [M+H 2O] + species fragment largely give rise to ions at m/ z 175, 143 and, as a result, the m/ z 111 ion is unique to nonreducing terminal units.

Last Step of the Para Route of the Kolbe−Schmitt Reaction

This work is an extension of our investigations of the Kolbe--Schmitt reaction mechanism. The last step in the para route of the carboxylation reaction of alkali metal phenoxides is investigated at the B3LYP/LANL2DZ level of theory. Among several examined pathways, two mechanisms are proposed: the one involving a successive rearrangement of hydrogen and the other one based on the formation of free radicals. The former pathway is energetically comparable to the last step of the carboxylation reaction in the ortho position, whereas the latter pathway requires higher activation energy. Bearing in mind that the Kolbe--Schmitt reaction is performed at high temperatures, we assume that both reaction paths are plausible.

Coherent-states dynamics of the H + + HF reaction at ELab = 30 eV: A complete electron nuclear dynamics investigation

Results of a complete investigation of the H + + HF reaction at E Lab = 30 eV with the electron nuclear dynamics (END) and the coherent-states dynamics (CSD) theories are herein presented. Current END–CSD methodology employs frozen Gaussian wave packet in the semiclassical limit of ℏ → 0 for the nuclei, and a single-determinantal Thouless coherent state (CS) for the electrons. The simulated 400 CS trajectories from five independent HF target orientations provide a complete description of the reactive processes in this system, including: non-charge-transfer scattering (NCTS), charge-transfer scattering (CTS), hydrogen fluoride dissociation (H–F D), and hydrogen rearrangement (HR). Several aspects of the reactions dynamics, such as mechanistic details and rainbow angles effects, are discussed. Differential and integral cross sections are evaluated via a novel CS formulation of those properties in conjunction with semiclassical techniques. The calculated total differential cross section shows an excellent agreement with available experimental results.

Intramolecular ring rearrangements in the mass spectrometric fragmentation of 1-( N-ethoxycarbonylamino)arylmethylphosphonic monoesters under electrospray ionization conditions

The mass spectrometric fragmentation of 1-( N-ethoxycarbonylamino)arylmethylphosphonic monoesters has been investigated under positive ion electrospray ionization conditions. All protonated title compounds predominantly eliminate a phosphite monoester via a four-membered ring hydrogen rearrangement to yield protonated N-ethoxycarbonyl arylmethylimines, which could further undergo four-, six-, or eight-membered ring rearrangements to produce mainly N-substituted/unsubstituted arylmethylimine ions by loss of carbon dioxide, ethene, and cyanic acid alone or together. It is interesting to note that the protonation of 1-( N-ethoxycarbonylamino)arylmethylphosphonic monoesters should be occurred in their arene rings.

Reassessment of the molecular mechanisms for H2 thermal desorption pathways from Si(1−x)Gex(001)-(2×1) surfaces

One of the aims of temperature-programmed desorption experiments is to facilitate identification of molecular pathways for desorption. The authors provide a rigorous assessment of the difficulty of doing this for H(2)/Si((1-x))Ge(x)(100)-(2x1). An extensive series of density functional calculations using both cluster and slab methods is performed. The resulting desorption barriers are used to compute thermal desorption spectra. A mean-field approximation is used to treat the populations of the various adsites present on the surface. The authors find a number of significant results. First, slab and cluster calculations do not appear to predict consistent differences in desorption barriers between intradimer and interdimer channels. Second, they find that a germanium atom affects the desorption barrier significantly only if it is present at the adsite. A germanium atom adjacent to an adsite or in the second layer influences the desorption barrier negligibly. Both cluster and slab calculations consistently predict a decrease of approximately 0.3-0.4 eV per germanium atom at the adsite. Third, current analysis of thermal desorption spectra in the literature, although yielding good fits to experimental data, is not rigorous. The authors' calculated spectra can be fitted rather well by assuming, as in current analysis of experimental data, three independent second-order channels, even though the underlying molecular pathways used to calculate the spectra are considerably different. Fourth, the authors' results highlight the importance of treating the rearrangement of hydrogen and germanium atoms at the surface during the thermal desorption process. This is generally not taken into account in kinetics modeling of desorption spectra.

Distinguishing glucuronic from iduronic acid in glycosaminoglycan tetrasaccharides by using electron detachment dissociation.

Distinguishing the epimers iduronic acid (IdoA) and glucuronic acid (GlcA) has been a long-standing challenge for the mass spectrometry analysis of glycosaminoglycan (GAG) oligosaccharides. In this work, electron detachment dissociation (EDD) and Fourier transform ion cyclotron resonance mass spectrometry is shown to provide mass spectral features that can distinguish GlcA from IdoA in heparan sulfate (HS) tetrasaccharides. EDD of HS tetrasaccharide dianions produces a radical species that fragments to produce information-rich glycosidic and cross-ring product ions which can be used to determine the sites of acetylation/sulfation. More significantly, EDD of HS tetrasaccharide epimers produces diagnostic product ions that can be used to distinguish IdoA from GlcA. These diagnostic product ions are not observed in the tandem mass spectra obtained by collisionally activated dissociation or infrared multiphoton dissociation of the tetrasaccharides, suggesting a radical-initiated mechanism for their formation. Differences in the observed product ions obtained by EDD of the tetrasaccharide epimers can be rationalized by simple alpha-cleavage of an oxy radical located at C2 or C3 or a radical at C3 or C4. These radicals are proposed to arise from a hydrogen rearrangement in which a hydrogen atom is transferred from the C2 or C3 hydroxyl group or C3 or C4 to a carboxy radical at C5. This hydrogen transfer depends on the proximity of the carboxy radical to the hydroxyl group on C2 or C3 or the hydrogen on C3 or C4 and is thus influenced by C5 stereochemistry. These epimer-sensitive fragmentations should allow this approach to be applied to the structural analysis of a wide variety of GAG oligosaccharides.

Direct-Dynamics VTST Study of the [1,7] Hydrogen Shift in 7-Methylocta-1,3(Z),5(Z)-triene. A Model System for the Hydrogen Transfer Reaction in Previtamin D3

Direct-dynamics canonical variational transition-state theory calculations with microcanonically optimized multidimensional transmission coefficient (CVT/muOMT) for tunneling were carried out at the MPWB1K/6-31+G(d,p) level to study the [1,7] sigmatropic hydrogen rearrangement in 7-methylocta-1,3(Z),5(Z)-triene. This compound has seven conformers, of which only one leads to products, although all of them have to be included in the theoretical treatment. The calculated CVT/muOMT rate constants are in good agreement with the available experimental data. To try to understand the role of tunneling in the hydrogen shift reaction, we have also calculated the thermal rate constants for the monodeuterated compound in the interval T = 333.2-388.2 K. This allowed us to evaluate primary kinetic isotope effects (KIEs) and make a direct comparison with the experiment. Our calculations show that both the large measured KIE and the large measured difference in the activation energies between the deuterated and root compounds are due to the quantum tunneling. The tunneling contribution to the KIE becomes noticeable only when the coupling between the reaction coordinate and the transverse modes is taken into account. Our results confirm previous experimental and theoretical works, which guessed that the obtained kinetic parameters pointed to a reaction with an important contribution due to tunneling. The above conclusion would be essentially valid for the case of the [1,7] hydrogen shift in previtamin D3 because of the similarity to the studied model system.