Determination of the gas-phase acidity of methylthioacetic acid using the Cooks’ kinetic method

We determined the gas-phase acidity of methylthioacetic acid (MTA) in a triple-quadrupole mass spectrometer using the Cooks’ kinetic method with the consideration of entropy effects. The negatively charged proton-bound dimers were generated by electrospray ionization. Collision-induced dissociation was applied to the dimer ions and the product ion ratios were measured at four different collision energies. The gas-phase acidity (ΔH _acid) of MTA was determined to be 340.0±1.7 kcal/mol using the extended kinetic method and 339.8±1.7 kcal/mol using the standard kinetic method. The entropy term is insignificant in this case and can be ignored. The standard kinetic method yielded a free energy of deprotonation of MTA (ΔG _acid) of 333.0±1.7 kcal/mol. The entropy of the acid dissociation, ΔS _acid, was estimated to be 22.8 cal/mol K. Theoretical prediction at the B3LYP/6-31+G* level of theory gives a similar value for ΔH _acid of 338. 9 kcal/mol. In the gas-phase, MTA is a stronger acid than methoxyacetic acid, although in solution, MTA is a weaker one.     

The chemist’s concept of molecular structure

The concept of molecular structure is fundamental to the practice and understanding of chemistry, but the meaning of this term has evolved and is still evolving. The Born–Oppenheimer separation of electronic and nuclear motions lies at the heart of most modern quantum chemical models of molecular structure. While this separation introduces a great computational and practical simplification, it is neither essential to the conceptual formulation of molecular structure nor universally valid. Going beyond the Born–Oppenheimer approximation introduces new paradigms, bringing fresh insight into the chemistry of fluxional molecules, proteins, superconductors and macroscopic dielectrics, thus opening up new avenues for exploration. But it requires that our ideas of molecular structure need to evolve beyond simple ball-and-stick-type models.

The curious case of 12-hydroxystearic acid — the Dr. Jekyll & Mr. Hyde of molecular gelators

A comprehensive review of the features driving self-assembly of 12-hydroxystearic acid (12-HSA), a low-molecular-weight gelator, and its applications in drug delivery and as other soft innovative materials are presented herein. 12-HSA is obtained via hydrogenation of ricinoleic acid naturally found in high concentrations in castor oil. The ability of 12-HSA to self-assemble is associated with the presence, position, and enantiomeric purity of the hydroxy group along the fatty acid chain. The polarity and position of the hydroxyl group facilitates more interaction possibilities leading to its exceptional self-assembly behavior giving rise to fibers, ribbons, and tubes in a variety of solvents. Upon self-assembly, 12-HSA undergoes crystallization resulting in the formation of high aspect ratio fibrillar structures due to noncovalent, intermolecular interactions forming self-spanning, three-dimensional networks (called self-assembled fibrillar networks) in both aqueous and organic solvents. Herein, emphasis is placed on emerging applications of 12-HSA supramolecular assemblies (i.e. responsive aqueous foams, gelled complex fluids, drug delivery systems, hydrogels, organogels, xerogels, and aerogel). The vast literature is compiled associated with 12-HSA self-assembly exploring supramolecular assemblies based on one ambidextrous gelator capable of assembling in aqueous and nonaqueous solvent.     

Comparison of hydrophobicity studies of silica aerogels using contact angle measurements with water drop method and adsorbed water content measurements made by Karl Fischer’s titration method

Hydrophobic silica aerogels possesses potential applications as insulating materials for refrigerators, furnaces and thermos flasks. In such applications, aerogel materials may get exposed for longer time to atmosphere and the adsorbed water content from surroundings may deteriorate its properties. Therefore, hydrophobicity of the arogels becomes crucial parameter and needs to be evaluated critically. In the present works, silica alcogels were prepared using the mixture of tetramethoxysilane and methyltrimethoxysilane (MTMS) as precursor chemicals for silica. The concentration of MTMS, which is used as hydrophobic reagent, in the said mixture of silicon alkoxide was varied between 0 and 100% in steps of 25%. After gelation, the alcogels were dried supercritically by solvent extraction method. Resulted aerogels were exposed to relative humidity of 90% for a period of one month which were then characterized to assess hydrophobicity by the contact angle using water drop method and adsorbed water content measurements by Karl Fischer’s Titration method. Observed contact angle and water content measurements were compared and the results are reported in the present research paper.     

Acylation of Meldrum’s acid with arylacetic acid imidazolides as a convenient method for the synthesis of 4-aryl-3-oxobutanoates

C-Acylation of Meldrum’s acid by (het)arylacetic acids in ethanol in the presence of 1,1′-carbonyldiimidazole leads to ethyl 4-(het)aryl-3-oxobutanoates in high yields.     

Do ion tethered functional groups affect IL solvent properties? The case of sulfoxides and sulfones

The covalent incorporation of functional groups-specifically sulfoxide and sulfone-into the cation of imidazolium ionic liquids leads to significant, quantifiable changes in solvent parameters which in turn have important effects on the bulk properties of the materials.     

Can quantum-mechanical calculations yield reasonable estimates of hydrogen-bonding acceptor strength? The case of hydrogen-bonded complexes of methanol

The thermodynamics and some vibrational properties of hydrogen-bonded complexes of methanol with 23 hydrogen-bond acceptors (HBAs) have been determined in CCl(4) by FTIR spectrometry. The experimental sample contains carbon, nitrogen, oxygen, sulfur, fluorine, and chlorine organic bases and covers an energetic range of 13 kJ mol(-1) in the basicity scale (-ΔG), 22 kJ mol(-1) in the affinity scale (-ΔH), and 400 cm(-1) in the spectroscopic scale (Δν((OH))) (from benzene to trimethylphosphane oxide and amines). The experimental results in CCl(4) are compared to those computed in the gas phase at various levels of theory. Ninety five percent of the variance of the red shift and 89% of the variance of the intensification of the OH stretching upon hydrogen bonding are explained by gas-phase B3LYP/6-31+G(d,p) calculations. However, this level does not satisfactorily explain the thermodynamic properties. Only 68% of the variance of the methanol affinity (-ΔH) is taken into account. MP2/aug-cc-pVTZ//B3LYP/6-31+G(d,p) affinity calculations raise the explanation to 77% for all HBAs and to 93% when three outliers (Me(2)SO, Me(3)PO, and tetrahydrothiophene) are excluded. Discrepancies are analyzed in terms of experimental errors, calculation approximations, and solvation.     

How does it become possible to treat delocalized and/or open-shell systems in fragmentation-based linear-scaling electronic structure calculations? The case of the divide-and-conquer method

The authors have developed a fragmentation-based linear-scaling electronic structure calculation strategy named the divide-and-conquer (DC) method, which has been implemented into the Gamess program package. Although there are many sorts of fragmentation-based linear-scaling schemes, most of them require the charge and spin multiplicity of each fragment a priori. Therefore, their applications to delocalized and/or open-shell systems have been limited. However, the DC method is a notable exception because the distribution of electrons in the entire system is automatically determined by the universal Fermi level. In this perspective, the authors have summarized the performance of the linear-scaling self-consistent field (SCF) and post-SCF calculations of delocalized and/or open-shell systems based on the DC method. Furthermore, some future prospects of the method have been discussed.     

An alignment-free method to find similarity among protein sequences via the general form of Chou’s pseudo amino acid composition

In this paper, we propose a method to create the 60-dimensional feature vector for protein sequences via the general form of pseudo amino acid composition. The construction of the feature vector is based on the contents of amino acids, total distance of each amino acid from the first amino acid in the protein sequence and the distribution of 20 amino acids. The obtained cosine distance metric (also called the similarity matrix) is used to construct the phylogenetic tree by the neighbour joining method. In order to show the applicability of our approach, we tested it on three proteins: 1) ND5 protein sequences from nine species, 2) ND6 protein sequences from eight species, and 3) 50 coronavirus spike proteins. The results are in agreement with known history and the output from the multiple sequence alignment program ClustalW, which is widely used. We have also compared our phylogenetic results with six other recently proposed alignment-free methods. These comparisons show that our proposed method gives a more consistent biological relationship than the others. In addition, the time complexity is linear and space required is less as compared with other alignment-free methods that use graphical representation. It should be noted that the multiple sequence alignment method has exponential time complexity.     

The composition of some Roman medicines: evidence for Pliny’s Punic wax?

Residues from medicine containers in the collections of the British Museum have been investigated as part of a wider programme of scientific work on Roman surgical instruments. The cylindrical bronze containers are often described as instrument cases, but some contain materia medica, ranging from extensive extant remains of ancient preparations to possible minor deposits on the interior surfaces of the containers. Samples from seven residues have been analysed by gas chromatography–mass spectrometry (GC-MS) to identify lipid, resin and carbohydrate components and by X-ray fluorescence and Raman spectroscopy to characterise inorganic materials. The results have provided evidence for ointments and powders or pills consistent with a medical purpose. The ingredients identified include beeswax, fat, conifer resin and gum-derived sugars, plus elemental carbon and lead and zinc salts. Particularly significant were the varied compositions of residues from four sections of a multi-compartment container. In one of these compartments, the beeswax seems to have been prepared as the ‘Punic wax’ described by Pliny. Experimental preparation of Punic wax following Pliny’s method was undertaken in the laboratory and the product analysed to compare with the ointment residues. This paper discusses the GC-MS results of both the experimental material and the archaeological residues and their significance for the interpretation of the past intended applications of the medicines and the use of the containers.     

Can the bis(diboranyl) structure of B(4)H(10) be observed? The story continues

Pathways for the conversion of the unknown bis(diboranyl) isomer of tetraborane(10) (B(4)H(10)) to the known arachno isomer have been determined for the first time with the use of an electron correlation ab initio quantum chemical method and without the use of constraints in determination of the transition structures. Two isomers of tetraborane(10), one new, with a pentacoordinated boron atom have been found on the theoretical potential energy surface. Several other pathways for molecular rearrangement of tetraborane(10) have also been characterized. The theoretical method was MP2 theory with the 6-31G(d,p) basis set. The most likely pathway for the conversion of the bis(diboranyl) isomer of tetraborane(10) to the arachno isomer is a concerted pathway with two pentacoordinated intermediates. The highest energy transition state for this pathway lies 27.7 kcal/mol above the bis(diboranyl) isomer. At the same level of the theory, the bis(diboranyl) isomer lies 9.2 kcal/mol above the known arachno isomer. The two isomers with a pentacoordinated boron atom lie 12.5 and 13.1 kcal/mol above the arachno isomer.     

Can TD‐DFT calculations accurately describe the excited states behavior of stacked nucleobases? The cytosine dimer as a test case

By using calculations rooted in the time dependent density functional theory (TD-DFT) we have investigated how the lowest energy excited states of a face-to-face pi-stacked cytosine dimer vary with the intermonomer distance (R). The perfomances of different density functionals have been compared, focussing mainly on the lowest energy single excited state of the dimer (S(1))(2). TD-PBE0, TD-LC-omegaPBE, and TD-M05-2X provide a picture very similar to that obtained at the CASPT2 level by Merchan et al. (J Chem Phys 2006, 125, 231102), predicting that (S(1))(2) has a minimum for R approximately 3 A, with a binding energy of approximately 0.5 eV, whereas TD-B3LYP, TD-CAM-B3LYP, and TD-PBE understimate the binding energy. However, independently of the functional employed, no low-energy spurious charge transfer transitions are predicted by TD-DFT calculations, also when a nonsymmetric dimer is investigated, providing encouraging indications for the use of TD-DFT for studying the excited state of pi-stacked nucleobases.     

Can octahedral t2g6 complexes substitute associatively? The case of the isoelectronic ruthenium(II) and rhodium(III) hexaaquaions

For the low-spin t2g6 Ru(OH2)6(2+) (delta V++ = -0.4 cm3 mol-1) and Rh(OH2)6(3+) (delta V++ = -4.2 cm3 mol-1) hexaaquaions, the respective Id and Ia water exchange mechanisms had been assigned, mainly on the basis of activation volumes delta V++ and entering ligands effects for water substitution. For Ru(II) the near-zero delta V++ was supposed to be due to the compensation between a positive contribution (the loss of a water molecule) and a negative one (the contraction of the bonds of the five spectator ligands at the transition state). Recently, it has been suggested that Rh(III), because of its higher positive charge, could promote further spectator ligands bond contraction sufficient to change the sign of delta V++ to a negative value. If true, this would be an example of limitation in the use of delta V++ for a direct diagnosis of the mechanism. Quantum chemical calculations including hydration effects show that the activation energies for the water exchange on Rh(OH2)6(3+) via the Ia (114.8 kJ mol-1) and the D pathways is 21.8 kJ mol-1 in favor of the former. In the case of Ru(OH2)6(2+) all attemps to compute a transition state for an interchange mechanism failed, but the calculated delta E++ for the D mechanism (71.9 kJ mol-1) is close to both experimental delta G298++ and delta H298++ values. The calculated delta sigma d(M-O) values of -0.53 A for rhodium(III) and +1.25 A for ruthenium(II) agree with the experimented delta V++ values and suggest Ia and D (or Id) mechanisms, respectively. In the case of Ru(OH2)6(2+) the shortening of the bonds of the five spectator ligands to reach the transition states corresponds to a volume change of -1.7 cm3 mol-1. For Rh(OH2)6(3+) these spectator ligands' volume decrease is much smaller (maximum of -0.8 cm3 mol-1) and the bond lengths of the two exchanging ligands at the transition state are characteristic of an interchange pathway with a small "a" character. Because of the strong RhIII-O bonds, water exchange on Rh(OH2)6(3+) proceeds via the Ia pathway with retention of the configuration, whereas the same reaction of Ru(OH2)6(2+), which has considerably weaker RuII-O bonds, follows the Id or the D mechanism.     

Termolecular ion-molecule reactions in Titan’s atmosphere. II: The structure of the association adducts of HCNH+ with C2H2 and C2H4

The ion-molecule reactivity of the products formed in the association reactions of HCNH+ with C2H2 (C3H4N+) and C2H4 (C3H6N+) has been investigated to provide information on the structures of the adducts thus formed. The C3H4N+ and C3H6N+ adducts were formed in the reaction flow tube of a flowing afterglow sourced-selected ion flow tube (FA-SIFT) and their reactivity with a neutral molecular "probe" examined. The reactivity of possible known structural isomers for the C3H4N+ and C3H6N+ ions was investigated in both the FA-SIFT and an ion cyclotron resonance spectrometer (ICR). Ab initio investigations of the potential energy surfaces for both structures at the G2(MP2) level have also been performed and structures corresponding to local minima on both surfaces have been identified and evaluated. The results of these experimental and theoretical studies show that at room temperature, the C3H4N+ adduct ion contains two isomers; a less reactive one that is likely to be a four-membered cyclic covalent isomer (approximately 70%) and a faster reacting component that is probably an electrostatic complex (approximately 30%). The C3H6N+ adduct ion formed from HCNH+ + C2H4 at room temperature is a single isomer that is likely to be the four-membered covalently bound cyclic CH2CH2CHNH+ species.