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The metabolism of vitamin D3 includes a parallel C-3 epimerization pathway-in addition to the standard metabolic processes for vitamin D3-reversing the stereochemical configuration of the -OH group at carbon-3 (s→α). While the biological function of the 3α epimer has not been elucidated yet, the additional species cannot be neglected in the analytical determination of vitamin D3, as it has the potential to introduce analytical errors if not properly accounted for. Recently, some inconsistent mass spectral behavior was seen for the 25-hydroxyvitamin D3 (25(OH)D3) epimers during quantification using electrospray LC-MS/MS. The present work extends that of Flynn et al. ( Ann. Clin. Biochem. 2014, 51, 352-559) and van den Ouweland et al. ( J. Chromatogr. B 2014, 967, 195-202), who reported larger electrospray ionization response factors for the 3α epimer of 25(OH)D3 in human serum samples as compared to the regular 3s variant. The present work was concerned with the mechanistic reasons for these differences. We used a combination of electrospray ionization, atmospheric pressure chemical ionization, and density functional theory calculations to uncover structural dissimilarities between the epimers. A plausible mechanism is described based on intramolecular hydrogen bonding in the gas phase, which creates a small difference of proton affinities between the epimers. More importantly, this mechanism allows the explanation of the different ionization efficiencies of the epimers based on kinetic control of the ionization process, where ionization initially takes place at the hydroxyl group with subsequent proton transfer to a basic carbon atom. The barrier for this transfer differs between the epimers and is in direct competition with H2O elimination from the protonated hydroxyl group. The hidden" site of high gas phase basicity was revealed through computational calculations and appears to be inaccessible via direct protonation."

t was discovered that phosphazenyl phosphines (PAPs) can be stronger P‐superbases than the corresponding Schwesinger type phosphazene N‐superbases. A simple synthetic access to this class of PR3 derivatives including their homologization is described. XRD structures, proton affinities (PA), and gas‐phase basicities (GB) as well as calculated and experimental pKurn:x-wiley:14337851:media:anie201903342:anie201903342-math-0001 values in THF are presented. In contrast to their N‐basic counterparts, PAPs are also privileged ligands in transition metal chemistry. In fact, they are currently the strongest uncharged P‐donors known, exceeding classical and more recently discovered ligands such as PtBu3 and imidazolin‐2‐ylidenaminophosphines (IAPs) with respect to their low Tolman electronic parameters (TEPs) and large cone angles.

Molecular dynamics (MD) simulations have been employed for the first time to gain insight into the geometry of glycerol (GOL) bound within the active site of B12 -dependent diol dehydratase (B 12 -dDDH). A peculiar feature of the B 12 -dDDH enzyme is that it undergoes suicidal inactivation by the substrate glycerol. To fully understand the inactivation mechanism, it is crucial to identify all possible interactions between GOL and the surrounding amino acid residues in the enzyme−substrate complex. Particularly important is the orientation of the C3-OH group in GOL since the presence of this OH group is the only difference between GOL and propanediol (PDO), a substrate for B12 - dDDH that does not induce suicidal inactivation. The MD simulations indicate that glycerol can adopt two conformations that differ with respect to the orientation of the C3-OH group ; in one conformer, the C3-OH group is oriented toward Ser301 (C3-OH···Ser301), and in the other toward Asp335 (C3-OH··· Asp335). Although the former configuration is consistent with the crystal structure of B 12 -dDDH crystallized with cyanocobalamin (CNCbl) as the cofactor, MD simulations of this system suggest a substantial predominance of the latter conformer. A similar result with an even higher preference for the latter conformer is obtained for B 12 -dDDH with 5′-deoxyadenosylcobalamin (AdoCbl) as a cofactor. Employing QM/MM calculations it is found that the energy difference between the two conformers of GOL is very small in CNCbl B 12 -dDDH, where the slightly preferred conformer is C3-OH···Ser301. However, in AdoCbl B 12 -dDDH, this energy difference is higher, implying that GOL exists predominantly as the C3-OH···Asp335 conformer. These findings offer a new perspective for investigations of substrate-induced inactivation of the B 12 - dDDH enzyme.

Tissue-specific ion suppression is an unavoidable matrix effect in MALDI mass spectrometry imaging (MALDI-MSI), the negative impact of which on precision and accuracy in quantitative MALDI-MSI can be reduced to some extent by applying isotope internal standards for normalization and matrix-matched calibration routines. The detection sensitivity still suffers, however, often resulting in significant loss of signal for the investigated analytes. An MSI application considerably affected by this phenomenon is the quantitative spatial analysis of central nervous system (CNS) drugs. Most of these drugs are low molecular weight, lipophilic compounds, which exhibit inefficient desorption and ionization during MALDI using conventional polar acidic matrices (CHCA, DHB). Here, we present the application of the (2-[(2E)-3-(4-tert-butylphenyl)-2-methylprop-2-enylidene]malononitrile) matrix for high sensitivity imaging of CNS drugs in mouse brain sections. Since DCTB is usually described as an electron-transfer matrix, we provide a rationale (i.e., computational calculations of gas-phase proton affinity and ionization energy) for an additional proton-transfer ionization mechanism with this matrix. Furthermore, we compare the extent of signal suppression for five different CNS drugs when employing DCTB versus CHCA matrices. The results showed that the signal suppression was not only several times lower with DCTB than with CHCA but also depended on the specific tissue investigated. Finally, we present the application of DCTB and ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry to quantitative MALDI imaging of the anesthetic drug xylazine in mouse brain sections based on a linear matrix-matched calibration curve. DCTB afforded up to 100-fold signal intensity improvement over CHCA when comparing representative single MSI pixels and >440-fold improvement for the averaged mass spectrum of the adjacent tissue sections.

The reactivity of new biologically active thymine derivatives substituted with 2-(arylsulfonamidino)ethyl group at N1 and N3 position was investigated in the gas phase using CID experiments (ESI-MS/MS) and by density functional theory (DFT) calculations. Both derivatives show similar chemistry in the negative mode with a retro-Michael addition (Path A(-)) being the most abundant reaction channel, which correlate well with the fluoride induced retro-Michael addition observed in solution. The difference in the fragmentation of N-3 substituted thymine 5 and N-1 substituted thymine 1 in the positive mode relates to the preferred cleavage of the sulfonyl group (m/z 155, Path B) in N-3 isomer and the formation of the acryl sulfonamidine 3 (m/z 309) via Path A in N-1 isomer. Mechanistic studies of the cleavage reaction conducted by DFT calculations give the trend of the calculated activation energies that agree well with the experimental observations. A mechanism of the retro-Michael reaction was interpreted as a McLafferty type of fragmentation, which includes Hβ proton shift to one of the neighboring oxygen atoms in a 1,5-fashion inducing N1(N3)-Cα bond scission. This mechanism was found to be kinetically favorable over other tested mechanisms. Significant difference in the observed fragmentation pattern of N-1 and N-3 isomers proves the ESI-MS/MS technique as an excellent method for tracking the fate of similar sulfonamidine drugs. Also, the observed N-1 and/or N-3 thymine alkylation with in situ formed reactive acryl sulfonamidine 3 as a Michael acceptor may open interesting possibilities for the preparation of other N-3 substituted pyrimidines.

Investigations on the Staudinger reaction between 1,8-diazidonaphthalene and phosphorous(III) building blocks, a key step in the synthesis of superbasic bisphospha- zene proton sponges, yielded a set of bisphosphazides with a constrained geometry 1,8-disubstituted naphthalene back- bone. This compound class has attracted our interest not only due to their surprisingly high stability, but in particular because of their theoretically predicted basicity in the range of their bisphosphazene analogues that can be referred to the constrained geometry interaction of two highly basic ni- trogen atoms. Eleven new bisphosphazides bearing simple P-amino groups as well as P-guanidino substituents, aza- phosphatrane moieties, P2 building blocks, or chiral P-amino substituents derived from l-proline are presented. They were studied concerning their spectroscopic properties and partly also their chromophoric and structural features. In the case of the pyrrolidino-substituted TPPN(2N2) (TPPN = 1,8- bis(trispyrrolidinophosphazenyl)naphthalene), the stepwise nitrogen elimination is investigated theoretically and experi- mentally, which led to the isolation and structural characteri- zation of TPPN(1N2) bearing a phosphazide and a phospha- zene functionality in one molecule. Attempts to protonate the obtained bisphosphazides and to prove the computa- tionally predicted pKBH + values through NMR titration reac- tions resulted in their decay, which again was rationalized by theoretical calculations. Altogether we present the so far most extensive spectroscopic, structural and theoretical in- vestigation of constrained geometry bisphosphazides and their Bronsted and Lewis basic properties.

We present the up to now strongest chelating neutral pincer ligand for the simplest electrophile of chemistry, the proton. Two novel bisphosphazene proton sponges, 1,8-bis(trispyrrolidinophosphazenyl)naphthalene (TPPN) and its higher homologue P2-TPPN, were obtained via a Staudinger reaction and investigated concerning their structural features and basic properties by experimental and computational means. They exhibit experimental pK(BH)(+) values in acetonitrile of 32.3 and 42.1, respectively, exceeding the existing basicitiy record for proton sponges by more than 10 orders of magnitude. We show that Schwesinger's concept of homologization of phosphazene bases and Alder's concept of proton chelation in a constrained geometry regime of basic centers can be combined in the design of highly basic nonionic superbases of pincer type.

The gas phase basicities and pKa values in acetonitrile of azacalix[3](2,6)pyridine and its derivatives are determined by the B3LYP DFT method. It is found that all compounds of this series are neutral organic superbases. The proton attacks the inner pyridine N(sp2) atom, thus forming a bifurcated intramolecular hydrogen bond. The most powerful superbase is provided by the hexakis(dimethylamino) derivative of the title compound. Its gas phase proton affinity is 296.6 kcal mol-1, its basicity is 291.3 kcal mol-1, and its pKa(MeCN) is 30.9 units. [structure: see text]

It is shown by reliable density functional theory (DFT) calculations that compounds 4 and 6 are very powerful neutral organic superbases as evidenced by the calculated proton affinities in the gas phase 305.4 kcal mol−1 (44.8) and 287.8 kcal mol−1 (37.8), respectively, and the corresponding calculated pKa values in acetonitrile given within parentheses.

The synthesis of novel N, N', N'' tris(3 dimethylaminopropyl)-guanidine 1 is described and the X-ray structure of its hexafluorophosphate salt measured (1H· PF6). The hydrogen bonding in protonated 1 and in 1H· PF6 is also discussed.

The influence of fluorine substitutions on the stability of benzene is examined by using the Hartree-Fock (HF) and MP2 models. It is conclusively demonstrated that homodesmotic reactions based on the open-chain zigzag polyenes are unsatisfactory. A comparison of the intramolecular interactions of educts and products shows that they are not well balanced. Hence, these reactions should be abandoned in discussing aromaticity. A much better vehicle for exploring aromaticity is provided by homostructural reactions, which employ cyclic monoene and diene as reference model compounds. Their heavy atoms are enforced to assume planar geometries to enable sigma/pi separation. The HF/cc-pVTZ calculations show that extrinsic aromaticity of benzene B DeltaE(ease)(B)() arises both from the sigma- and pi-contributions. They are -14.8 and -23.1 in kcal/mol, respectively, if the stockholder energy partitioning scheme is employed. This result implies that both the sigma- and pi-frameworks contribute to the aromatic stabilization of B, the latter being more important. The total aromatic stabilization DeltaE(ease)(B)() is -37.9 kcal/mol. Schleyer's indene-isoindene isomerization approach also strongly indicates that the decisive factor in determining the aromatic stability of the benzene moiety is the pi-electron framework. The origin of extrinsic aromaticity is identified as the increased nuclear-electron attraction of both sigma- and pi-electrons, if 1,3-cyclohexadiene is used as a gauge compound. Further, by using a system of isostructural reactions, it is conclusively demonstrated that fluorobenzenes exhibit a remarkable additivity of the substituent effects, as far as the stability of multiply substituted benzenes is concerned. This additivity rule is so accurate that it enables delineation of the fluorine repulsions and the aromaticity defect DeltaE(AD). It appears that the DeltaE(AD) values increase upon sequential fluorine substitution at the next nearest (vicinal) position thus making multiply fluorinated benzenes less stable.

The aim of this study was to investigate the behavior of the protonated paralytic shellfish poisons saxitoxin (STX) and neosaxitoxin (NEO) in the gas-phase after ion activation using different tandem mass spectrometry techniques. STX and NEO belong to a group of neurotoxins produced by several strains of marine dinoflagellates. Their chemical structures are based on a tetrahydropurine skeleton to which a 5-membered ring is fused. STX and NEO only vary in their substituent at N-1, with STX carrying hydrogen and NEO having a hydroxyl group at this position. The collision-induced dissociation (CID) spectra exhibited an unusually rich variety and abundance of species due to the large number of functional groups within the small skeletal structures. Starting with triple-quadrupole CID spectra as templates, linked ion-trap MSn data were added to provide tentative dissociation schemes. Subsequent high-resolution FTICR experiments gave exact mass data for product ions formed via infrared multiphoton dissociation (IRMPD) from which elemental formulas were derived. Calculations of proton affinities of STX and NEO suggested that protonation took place at the guanidinium group in the pyrimidine ring for both molecules. Most of the observed parallel and consecutive fragmentations could be rationalized through neutral losses of H2O, NH3, CO, CO2, CH2O and different isocyanate, ketenimine and diimine species, many of which were similar for STX and NEO. Several exceptions, however, were noted and differences could be readily correlated with reactions involving NEO's additional hydroxyl group. A few interesting variations between CID and IRMPD spectra are also highlighted in this paper.

The basicity of Verkade's superbase (12) in MeCN solution is considered by a quite accurate theoretical model. It is shown that the corresponding pKa value is 29.0. Hence, its basicity is comparable or higher than that of some other P1 phosphazenes, but it is lower than the basicity of P2 phosphazenes. Structural characteristics of Verkade's superbase and its conjugate acid, as well as the origin of its pronounced basicity, are briefly discussed. Extended Verkade's superbase 13 and some Janus-type phosphazenes are examined too. It is shown that they are very good candidates for even stronger neutral organic superbases. A very useful by-product of the present study are quite accurate estimates of the gas phase proton affinities of some P1, P2, P3 and P4 polyaminophosphazenes obtained by the B3LYP/6-311+G(2df,p)//B3LYP/6-31G* scheme. The latter was successfully tested against G2 results on small molecules. This is of importance, because the experimentally measured gas phase values for phosphazenes are not available, implying that the theoretical data fill this gap with reliable information.

We performed a comparative spectroscopic FTIR and computational study of the vibrational OH stretching frequencies in liquid ethanol–ethanol (I) and liquid ethanol–N-methylimidazole dimers (II). The latter system mimics the hydrogen bond formation between serine and histidine residues, which is the incipient step in the enzymatic activity of the catalytic triads. Complex (I) was studied as a reference system. The infrared spectra revealed the presence of the OH fundamental stretching transitions at 3339 and 3271 cm � 1 for complexes (I) and (II), respectively. This red shift of 68 cm � 1 indicates that the hydrogen bond between ethanol and N-methylimidazole exists and it is favoured over the one occurring in ethanol dimers. It is shown that vibrations exhibit anharmonicity.

The problem of protonation of benzene (B) and cyclobutadiene (CB) is addressed by the ab initio G2 benchmark computations. It appears that the σ-complexes are the most favourable protonated forms in both cases. The proton affinity (PA) of (CB) is higher by 45 kcal/mol than that of B, which is rationalized by a decrease in the antiaromatic destabilization of the four-membered ring and stabilization by the allylic cation formation upon protonation accompanied by the ring puckering, which enables an effective additional homoconjugative interaction. The barrier for the hydrogen ring walk in B is estimated to be 8.6 kcal/mol leading to seven equivalent hydrogens on the NMR time scale. In contrast, this barrier in CB is 43.6 kcal/mol implying that the ring walk is precluded in this cationic system. The ring flipping inversion barrier of the σ-protonated CB is estimated to be 7 kcal/mol thus being in good accordance with experiment. The striking structural features of σ and π-protonated configurations of B and CB involve degrees of pyramidalization and tetrahedral distortions of carbon atoms, which are briefly discussed. Some practical models, alternative to the G2 scheme, designed for studying the PA of aromatic and antiaromatic compounds are examined and recommended.

Several molecular systems which may well serve as potent organic superbases are examined by using ab initio and semiempirical theoretical models. It is found that the imino group attached to the semiquinoid fragment or to a backbone of several quinoid six membered rings exhibits a very high proton affinity (PA). It is found that the reason behind their amplified basicity is appreciable aromatization of the quinoid building blocks upon protonation. The underlying mechanism in extended systems is that of the aromaticity spin-off effect, triggered by the proton attack at the imino N atom and spread along the quinoid ribbon in a typical domino fashion. It yields an increase in the PA as high as roughly 20 kcal/mol per the quinoid ring. Susceptibility toward the proton attack is further amplified by the alkyl substitution at the imino nitrogen atom and by additional substitution of the amino groups at specific positions within the framework of the quinoid building block(s). It is stressed that synthesis of the studied systems might provide very potent organic superbases.

Herbicides are chemical molecules used for destruction of weeds. Massive usage of herbicides has resulted in two global problems: increase in weed resistance and harmful impact of human health [1, 2]. In order to facilitate development of novel, more specific herbicides and of strategies for impeding the weed resistance, we have carried out extensive in silico analysis of the set of herbicides. Herein, we present results revealing links between structural, physicochemical, ADME (Absorption, Distribution, Metabolism, Excretion) and toxic features for herbicides (Figure 1). The analysis has been done by using proper machine learning approaches. References: [1] A. Forouzesh, E. Zand, S. Soufizadeh, S. S. Foroushani, Weed Res. 55 (2015) 334-358. [2] V. I. Lushchak, T. M. Matviishyn, V. V. Husak, J. M. Storey, K. B. Storey, EXCLI J. 17 (2018) 1101-1136.