Are calculated enthalpies of formation sometimes more reliable than experimental? A test on alkyl substituted benzoic acids

Energies of 20 alkyl-substituted benzoic acids were calculated at the levels B3LYP/6-311+G(d,p)//B3LYP/6-311+G(d,p) and MP2/6-311+G(d,p)//MP2/6-311+G(d,p); the pertinent enthalpies at 298 K were calculated at the same levels. Comparison with experimental enthalpies of formation Delta(f)H degrees (g)(298) was carried out in terms of isodesmic reactions, that is, in the relative values. Of the four calculated quantities, the DFT enthalpies yielded best correlation with the standard deviation of 2.1 kJ mol(-1), near to the experimental uncertainty; the DFT energies are only slightly worse and the MP2 enthalpies or energies much worse. However, the DFT method overestimated systematically the substituent effects and had to be calibrated. Comparison with the experimental gas-phase acidities was less telling and the fit was worse because both methods overestimated the substituent effects. Extending the base in selected examples did not give better results. Although the systematic deviations are evidently due to the imperfections of the theoretical models, individual big deviations should be attributed to experimental errors or to the abnormal behavior of certain compounds at the experimental conditions. From this point of view, three examples of the so-called long-range effect claimed in the case of different benzoic acid derivatives, always for substituents in the meta position, must be refused as unproven because the experimental energies were not confirmed by calculations.     

Are Hetero-metallapentalenes Aromatic or Not? A DFT Investigation

Aromaticity is one of the most basic concepts in organic chemistry. The planar Möbius aromatic metallapentalynes and metallapentalenes have attracted considerable attention in the past few years. However, the aromaticity of metallapentalenes containing heteroatoms (such as B, N, and O), termed as hetero-metallapentalenes, is rarely studied. Herein, the stability and aromaticity of a series of hetero-metallapentalenes are theoretically investigated. The results reveal lower aromaticity in metallaborapentalene, comparable aromaticity in metallazapentalene, and nonaromaticity in metalloxapentalene relative to that of metallapentalene. Moreover, the effect of Lewis bases on the aromaticity and stability of metallaborapentalene is discussed. These results provide useful information for experimental chemists to realize more hetero-metallapentalenes.     

Are hydroxyl-containing biomolecules important in biosilicification? A model study

To understand the roles of hydroxyl-containing biomolecules in biosilicification, theoretical and experimental studies of silica formation utilizing biological and model organic additives have been undertaken. However, the role of hydroxyl functionalized biomolecules in silica formation is still not fully understood. To address this problem, we performed a systematic in vitro study of silica formation in the presence of two proteins rich in hydroxyl-containing amino acids (native sericin proteins extracted from Bombyx mori and a recombinant sericin precursor peptide) and a range of small alkanediols. The data obtained suggest the following hypotheses for the role of hydroxyl-containing organic molecules in silica formation. In the first case, hydroxyl-containing organic molecules are not at all involved chemically in the formation of silica. Instead, they may be only assisting in rendering stability and solubility to the organic molecules found occluded in silica. The second possibility is that if we assume that hydroxyl-containing organic molecules affect silica formation, then the environments of silicic acid polymerization could be highly deficient in water to increase the effects of hydroxyl functional groups of proteins in silica formation. These results and their implications are discussed in the context of biosilicification and biomineralization.     

A comparison of the FAST,Premi® and KIS™ tests for screening antibiotic residues in beef kidney juice and serum

Three microbial inhibition-based screening methods, the fast antimicrobial screening test (FAST), the Premi test, and the kidney inhibition swab (KIS) test, were evaluated using penicillin G, sulfadimethoxine, oxytetracyline, tylosin, danofloxacin, streptomycin, neomycin, and spectinomycin at a range of fortified concentrations in beef kidney juice and beef serum. Each antibiotic was individually tested simultaneously using the different assays in replicate experiments. Detection threshold concentrations for each analyte in each screening assay were determined for the different matrices. Each assay gave a different detectability profile for the different antibiotics, with the largest differences related to neomycin, which was more sensitively detected by the FAST, and penicillin G, which was detected at lower levels by the Premi and KIS tests. In addition to practical considerations, analysts can use the information presented in this study to evaluate each kit for applicability to their monitoring needs.     

A2A Adenosine Receptor Antagonists: Are Triazolotriazine and Purine Scaffolds Interchangeable?

The A_2A adenosine receptor (A_2AAR) is one of the four subtypes activated by nucleoside adenosine, and the molecules able to selectively counteract its action are attractive tools for neurodegenerative disorders. In order to find novel A_2AAR ligands, two series of compounds based on purine and triazolotriazine scaffolds were synthesized and tested at ARs. Compound 13 was also tested in an in vitro model of neuroinflammation. Some compounds were found to possess high affinity for A_2AAR, and it was observed that compound 13 exerted anti-inflammatory properties in microglial cells. Molecular modeling studies results were in good agreement with the binding affinity data and underlined that triazolotriazine and purine scaffolds are interchangeable only when 5- and 2-positions of the triazolotriazine moiety (corresponding to the purine 2- and 8-positions) are substituted.     

Are there reliable DFT approaches for 13C NMR chemical shift predictions of fullerene C60 derivatives?

The relationships between experimental and theoretical ¹³C NMR chemical shifts of a pristine fullerene C₆₀, monoadducts from [2 + n] cycloaddition (n = 1–3), and one [2 + 1] bis‐adduct are systematically analyzed for the first time by using diverse quantum‐chemical levels of theory. These levels involved B3LYP, B3PW91, B97‐2, mPW1PW91, PBE1PBE, and X3LYP hybrid functionals combined with 3‐21G, 6‐31G, 6‐31G(d), 6‐31G(d,p), 6‐31G(d,2p), LanL2DZ, and SDDAll basis sets. X3LYP/6‐31G approach is determined to have the lowest deviations from the ¹³C NMR experimental data compared to the other methods for all the fullerene compounds (mean absolute error value is 0.856 ppm and root mean squared error value is 1.197 ppm). The highest deviations are characteristic for α (sp² C2/C5/C8/C10) and β (sp² C6/C7/C11/C12) carbon atoms relative to a functionalization site and for those (sp³ C1/C9) directly attached with a side fragment in the [2 + n] monoadducts (n = 1–3). A probable reason of such deviation is that the approaches do not take into account a contribution of paramagnetic ring currents to ¹³C NMR chemical shifts. The results will be useful in design of novel fullerene derivatives and in performing unambiguous ¹³C NMR chemical shift assignments with modern quantum chemistry calculations.     

How Stable Are Epoxides? A Novel Synthesis of Epothilone B

Remarkable stability of the oxirane function is displayed over a number of synthetic operations in a novel synthesis of the antitumor compound epothilone B (see scheme). The cis-epoxide, generated very early by dihydroxylation of an (E)-olefin, was resistant to more than ten synthetic steps under a wide variety of reaction conditions. TBS=tert-butyldimethylsilyl.     

Are electrophilicity and electrofugality related concepts? A density functional theory study

It is proposed that the electrofugality of a fragment within a molecule is determined by its group nucleophilicity. The variation of electrofugality should be tightly related to the electron releasing ability of the substituent attached to the electrofuge moiety. This contribution closes the set of relationships between philicity and fugality quantities: while nucleofugality appears related to the group electrophilicity of the leaving group, electrofugality is related to the group nucleophilicity of the permanent group.     

Are isolated nucleic acid bases really planar? A Car-Parrinello molecular dynamics study

Car-Parrinello molecular dynamics simulations of the flexibility of isolated DNA bases have been carried out. The comparison of lowest ring out-of-plane vibrations calculated by using MP2/cc-pvdz and BLYP/PW methods reveals that the DFT method with the plane wave basis set reasonably reproduces out-of-plane deformability of the pyrimidine ring in nucleic acid bases and could be used for reliable modeling of conformational flexibility of nucleobases. The conformational phase space of pyrimidine rings in thymine, cytosine, guanine, and adenine has been investigated by using the ab initio Car-Parrinello molecular dynamics method. It is demonstrated that all nucleic acid bases are highly flexible molecules and possess a nonplanar effective conformation of the pyrimidine ring despite the fact that the planar geometry corresponds to a minimum on the potential energy surface. The population of the planar geometry of the pyrimidine ring does not exceed 30%. Among the nonplanar conformations of the pyrimidine rings, the boat-like and half-chair conformations are the most populated.     

How Good Are Coarse‐Grained Polymer Models? A Comparison for Atactic Polystyrene

This review provides an overview of the various coarse‐grained models that have been developed in the past few years for amorphous polystyrene. Different techniques to develop the force fields and different mapping schemes lead to models that perform differently depending on the properties investigated. This review collects and compares the models to guide the reader in the choice of the best model for the application of interest. It is expected that the central features of the various coarse‐graining procedures will also apply to systems other than polystyrene and that some of the conclusions about different coarse‐graining strategies are general.     

Are the asserted advantages of organic solvents in capillary electrophoresis real? A critical discussion

Background electrolytes (BGEs) prepared in pure organic solvents are common alternatives to aqueous BGEs in capillary electrophoresis. Several general advantages of organic solvents over water have been asserted in the literature, namely (i) organic solvents increase the separation selectivity; (ii) organic solvents increase the separation efficiency; (iii) high separation voltages and/or high BGE ionic strengths can be used in organic solvents due to lower electric current compared to water. Related assumptions are that (iv) due to higher field strengths applicable in organic solvents the analysis time is shorter than in aqueous BGEs, and (v) the solubility and/or stability of components (either analytes or BGE chemicals) is higher/better in organic solvents. In the present work, these asserted advantages were critically evaluated based on the physical principles of ion transport and zone dispersion in solution. The result was that many of the above-mentioned general advantages are overestimated or even inexistent; often they have no fundamental basis.     

Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements

Recent hardware and software advances have enabled simulation studies of protein systems on biophysically-relevant timescales, often revealing the need for improved force fields. Although early force field development was limited by the lack of direct comparisons between simulation and experiment, recent work from several labs has demonstrated direct calculation of NMR observables from protein simulations. Here we quantitatively evaluate recent molecular dynamics force fields against a suite of 524 chemical shift and J coupling ((3)JH(N)H(α), (3)JH(N)C(β), (3)JH(α)C', (3)JH(N)C', and (3)JH(α)N) measurements on dipeptides, tripeptides, tetra-alanine, and ubiquitin. Of the force fields examined (ff96, ff99, ff03, ff03*, ff03w, ff99sb*, ff99sb-ildn, ff99sb-ildn-phi, ff99sb-ildn-nmr, CHARMM27, OPLS-AA), two force fields (ff99sb-ildn-phi, ff99sb-ildn-nmr) combining recent side chain and backbone torsion modifications achieve high accuracy in our benchmark. For the two optimal force fields, the calculation error is comparable to the uncertainty in the experimental comparison. This observation suggests that extracting additional force field improvements from NMR data may require increased accuracy in J coupling and chemical shift prediction. To further investigate the limitations of current force fields, we also consider conformational populations of dipeptides, which were recently estimated using vibrational spectroscopy.     

Is nontarget screening of emerging contaminants by LC-HRMS successful? A plea for compound libraries and computer tools

This review focuses on the possibilities and limits of nontarget screening of emerging contaminants, with emphasis on recent applications and developments in data evaluation and compound identification by liquid chromatography-high-resolution mass spectrometry (HRMS). The general workflow includes determination of the elemental composition from accurate mass, a further search for the molecular formula in compound libraries or general chemical databases, and a ranking of the proposed structures using further information, e.g., from mass spectrometry (MS) fragmentation and retention times. The success of nontarget screening is in some way limited to the preselection of relevant compounds from a large data set. Recently developed approaches show that statistical analysis in combination with suspect and nontarget screening are useful methods to preselect relevant compounds. Currently, the unequivocal identification of unknowns still requires information from an authentic standard which has to be measured or is already available in user-defined MS/MS reference databases or libraries containing HRMS spectral information and retention times. In this context, we discuss the advantages and future needs of publicly available MS and MS/MS reference databases and libraries which have mostly been created for the metabolomic field. A big step forward has been achieved with computer-based tools when no MS library or MS database entry is found for a compound. The numerous search results from a large chemical database can be condensed to only a few by in silico fragmentation. This has been demonstrated for selected compounds and metabolites in recent publications. Still, only very few compounds have been identified or tentatively identified in environmental samples by nontarget screening. The availability of comprehensive MS libraries with a focus on environmental contaminants would tremendously improve the situation.     

Are isatin and isatoic anhydride antiaromatic and aromatic respectively? A combined experimental and theoretical investigation

This paper reports the results of our thermochemical/calorimetric determination of the enthalpies of combustion, phase change, and formation of isatin, isatoic anhydride, and N-methylisatin. The density functional calculations accompanied by vibrational and thermal corrections were also performed for these compounds and N-methylisatoic anhydride. Through a combination of theoretical calculations and associated isodesmic reactions, we have deduced that isatin has some antiaromatic character and isatoic anhydride enjoys some aromatic stabilization.     

Are biosensor arrays in one membrane possible? A combination of multifrequency impedance measurements and chemometrics

A novel concept of a membrane-based micro-array biosensor is presented. The methodology is based on a single lipid membrane interrogated with electrochemical impedance techniques followed by multivariate data analysis. A single membrane is designed so that relaxation processes with a range of time constants can be probed at different potentials. A range of other approaches cited in the literature is reviewed.     

Are insertion compounds of CH2CHF and the rare gases stable? A computational study

Ab initio calculations, using second-order M?ller-Plesset perturbation theory with a 6-311+ +G(2d,2p) basis set, predict the stability of two novel compounds of monofluoroethene, CH2CHF, with the rare-gas atoms Ar and Kr. The dissociation energies to the lowest-energy fragmentation products, CH2CHF + Rg (Rg = Ar,Kr), were computed to be -528 and -449 kJ mol(-1), respectively, at the coupled-cluster singles, doubles, and triples level of theory. Possible transition states (at second-order M?ller-Plesset theory) via a C-Rg-F bending mode for these fragmentation reactions were also located with barrier heights of about 76 and 106 kJ mol(-1), for the Ar- and Kr-containing species, respectively. However, the Ar-containing species may not exist at all as it is less stable than the fragments CH2CH + F + Ar at the higher level of theory and may possibly dissociate via this route.     

Are metal-organic frameworks able to provide a new generation of solid-phase microextraction coatings? – A review

Solid-phase microextraction (SPME) is a powerful technique commonly used in sample preparation for extraction/preconcentration of analytes from a wide variety of samples. Among the trends in improving SPME applications, current investigations are focused on the development of novel coatings able to improve the extraction efficiency, sensitivity, and thermal and mechanical stability, within other properties, of current commercial SPME fibers. Metal-organic frameworks (MOFs) merit to be highlighted as promising sorbent materials in SPME schemes. MOFs are porous hybrid materials composed by metal ions and organic linkers, presenting the highest surface areas known, with ease synthesis and high tuneability, together with adequate chemical and thermal stability. For MOF based-SPME fibers, it results important to pretreat adequately the SPME supports to ensure the correct formation of the MOF onto the fiber or the attachment MOF-support. This, in turn, will increase the final stability of the fiber while generating uniform coatings. This review provides a critical overview of the current state of the use of MOFs as SPME coatings, not only highlighting the advantages of these materials versus commercial SPME coatings in terms of stability, selectivity, and sensitivity; but also insightfully describing the current methods to obtain reproducible MOF-based SPME coatings.     

A rapid UPLC–MS/MS method for simultaneous separation of 48 acylcarnitines in dried blood spots and plasma useful as a second-tier test for expanded newborn screening

Acylcarnitine profiling in dried blood spots (DBS) is a useful method for high-throughput newborn screening of metabolic disorders, but differentiation of isobaric and isomeric compounds is not achievable. Chromatographic methods for separation have already been reported but are specific for short-chain acylcarnitines or time-consuming. The aim of this work was to develop a fast ultraperformance liquid chromatography (UPLC)-tandem mass spectrometry (MS/MS) method for separation and quantification of a large number of acylcarnitines, including dicarboxylic acylcarnitines and hydroxyacylcarnitines, in DBS and plasma samples. Acylcarnitines from DBS and plasma were converted to their butyl esters and analyzed by electrospray ionization MS/MS. Chromatographic separation was achieved using a UPLC system equipped with an ethylene-bridged hybrid C(18) column. The correlation coefficients of the calibration curves (r(2)) ranged from 0.990 to 0.999. The limit of detection ranged from 0.002 and 0.063 μM for all compounds, and the limit of quantification ranged from 0.004 and 0.357 μM. Precision ranged from 0.8 to 8.8% and the mean recovery was 103%. Profiles of acylcarnitine isomers were investigated in specimens obtained from patients diagnosed with different inborn errors of metabolism. Acylcarnitine concentrations were also measured in 58 term newborns and compared with flow injection analysis measurements. With this newly developed UPLC-MS/MS method, the simultaneous detection of 61 (13 of these labeled) acylcarnitines in DBS and plasma can be achieved in 15 min including postrun equilibration. The method has been validated and can be used as an important component of newborn screening methods as a second-tier test for discrimination and to confirm diagnosis.     

Are electrocyclization reactions of (3Z)-1,3,5-hexatrienone and nitrogen derivatives pseudopericyclic? A DFT study

[reactions: see text] Electrocyclization reactions of (3Z)-1,3,5-hexatrienone and nitrogen derivatives were studied by performing density functional theory (DFT) calculations together with the 6-31+G* basis set. Reactants, products, and transition states for each reaction were localized and the IRC connecting reactants and products was also obtained. Magnetic properties were evaluated along the reaction path to elucidate the characteristics of the reactions studied. As obtained from the calculations, electrocyclization of (3Z)-1,3,5-hexatrienone is a pericyclic process, as indicated by a variety of indexes, such as Nucleus Independent Chemical Shift (NICS), anisotropy of the magnetic susceptibility, or anisotropy of the current-induced density (ACID). This reaction presents characteristics of pericyclic reactions despite the activation energy lowering relative to the electrocyclization of (4Z)-1,2,4,6-heptatetraene, and the relatively small NICS values observed in the transition state. Magnetic properties indicate that an enhancement of the aromaticity relative to reactants and products occurs revealing the absence of orbital disconnections on the cyclic loop of interacting orbitals. Only two reactions among those studied exhibit pseudopericyclic character due to the in-plane attack of the lone pair on nitrogen. In these cases, the reactions showed no barrier for the electrocyclization process, and no aromaticity enhancement was observed.