Hydrogen bonding in the urea dimers and adenine–thymine DNA base pair: anharmonic effects in the intermolecular H-bond and intramolecular H-stretching vibrations

The equilibrium structures, binding energies, vibrational harmonic frequencies, and the anharmonic corrections for two different (cyclic and asymmetric) urea dimers and for the adenine–thymine DNA base pair system have been studied using the second-order Møller–Plesset perturbation theory (MP2) method and different density functional theory (DFT) exchange–correlation (XC) functionals (BLYP, B3LYP, PBE, HCTH407, KMLYP, and BH and HLYP) with the D95V, D95V**, and D95V++** basis sets. The widely used a posteriori Boys–Bernardi or counterpoise correction scheme for basis set superposition error (BSSE) has been included in the calculations to take into account the BSSE effects during geometry optimization (on structure), on binding energies and on the different levels of approximation used for calculating the vibrational frequencies. The results obtained with the ab initio MP2 method are compared with those calculated with different DFT XC functionals; and finally the suitability of these DFT XC functionals to describe intermolecular hydrogen bonds as well as harmonic frequencies and the anharmonic corrections is assessed and discussed.     

From a Network of Computed Reaction Enthalpies to Atom‐Based Thermochemistry (NEAT)

A simple and fast, weighted, linear least‐squares refinement protocol and code is presented for inverting the information contained in a network of quantum chemically computed 0 K reaction enthalpies. This inversion yields internally consistent 0 K enthalpies of formation for the species of the network. The refinement takes advantage of the fact that the accuracy of computed enthalpies depends strongly on the quantum‐chemical protocol employed for their determination. Different protocols suffer from different sources of error; thus, the reaction enthalpies computed by them have “random” residual errors. Since it is much more natural for quantum‐chemical energy and enthalpy results, including reaction enthalpies, to be based on the electronic ground states of the atoms and not on the historically preferred elemental states, and since these two possible protocols can be converted into each other straightforwardly, it is proposed that first‐principles thermochemistry should employ the ground electronic states of atoms. In this scheme, called atom‐based thermochemistry (AT), the enthalpy of formation of a gaseous compound corresponds simply to the total atomization energy of the species; it is always positive, and it reflects the bonding strength within the molecule. The inversion protocol developed and based on AT is termed NEAT, which represents the fact that the protocol proceeds from a network of computed reaction enthalpies toward atom‐based thermochemistry, most directly to atom‐based enthalpies of formation. After assembling a database that consisted of 361 ab initio reactions and reaction enthalpies involving 188 species, collected from 31 literature sources, the following dependable 0 K atom‐based enthalpies of formation, Δ_f${H{{{\rm AT}\hfill \atop 0\hfill}}}$ , all in kJ mol^?1, have been obtained by means of NEAT: H₂=432.07(0), CH=334.61(15), NH=327.69(25), OH=425.93(21), HF=566.13(31), CO=1072.08(28), O₂=493.51(34), CH₂=752.40(21), H₂O=918.05(20), HO₂=694.53(32), CO₂=1597.77(40), CH₃=1209.64(29), NH₃=1157.44(33), C₂H₂=1625.78(40), and CH₄=1641.68(40), in which the uncertainty values given in parentheses represent 95 % confidence intervals. The average deviation of these values from the well‐established active thermochemical tables (ATcT) values is a mere 0.25 kJ mol^?1, with a maximum deviation of 0.7 kJ mol^?1. This shows that the use of a large number of ab initio reaction enthalpies within a NEAT‐type protocol has considerable advantages over the sequential utilization of the ab initio information.     

Paddling mode of forward flight in insects

By analyzing high-speed video of the fruit fly, we discover a swimminglike mode of forward flight characterized by paddling wing motions. We develop a new aerodynamic analysis procedure to show that these insects generate drag-based thrust by slicing their wings forward at low angle of attack and pushing backwards at a higher angle. Reduced-order models and simulations reveal that the law for flight speed is determined by these wing motions but is insensitive to material properties of the fluid. Thus, paddling is as effective in air as in water and represents a common strategy for propulsion through aquatic and aerial environments.     

Pure Cognitivism and Beyond

The article begins with Jonathan Dancy’s attempt to refute the Humean Theory of Motivation. It first spells out Dancy’s argument for his alternative position, the view he labels ‘Pure Cognitivism’, according to which what motivate are always beliefs, never desires. The article next argues that Dancy’s argument for his position is flawed. On the one hand, it is not true that desire always comes with motivation in the agent; on the other, even if this was the case, it would still not follow that desire is identical with the state of being motivated. When this negative work is done, the article turns to some positive, albeit admittedly tentative remarks about what sort of cognitivist theory of motivation one should endorse. The aim at this point is not to present a brand new theory, but rather to sketch an alternative that stems from what Dancy himself says and is in line with many of his endorsed commitments in other areas. In this way, by moving beyond Pure Cognitivism, the paper sketches a different, but still ‘Dancyesque’ theory of motivation.     

Weakly separative weakly commutative semigroups

A semigroup S is called a weakly commutative semigroup if, for every a,b∈S, there is a positive integer n such that (ab) ⁿ ∈Sa∩bS. A semigroup S is called archimedean if, for every a,b∈S, there are positive integers m and n such that a ⁿ ∈SbS and b ^m ∈SaS. It is known that every weakly commutative semigroup is a semilattice of weakly commutative archimedean semigroups. A semigroup S is called a weakly separative semigroup if, for every a,b∈S, the assumption a ²=ab=b ² implies a=b. In this paper we show that a weakly commutative semigroup is weakly separative if and only if its archimedean components are weakly cancellative. This result is a generalization of Theorem 4.16 of Clifford and Preston (The Algebraic Theory of Semigroups, Am. Math. Soc., Providence, 1961).     

Forbidden Configurations and Product Constructions

A simple matrix is a (0,1)-matrix with no repeated columns. For a (0,1)-matrix F, we say that a (0,1)-matrix A has F as a configuration if there is a submatrix of A which is a row and column permutation of F (trace is the set system version of a configuration). Let \({\|A\|}\) denote the number of columns of A. We define \({{\rm forb}(m, F) = {\rm max}\{\|A\| \,:\, A}\) is m-rowed simple matrix and has no configuration F. We extend this to a family \({\mathcal{F} = \{F_1, F_2, \ldots , F_t\}}\) and define \({{\rm forb}(m, \mathcal{F}) = {\rm max}\{\|A\| \,:\, A}\) is m-rowed simple matrix and has no configuration \({F \in \mathcal{F}\}}\) . We consider products of matrices. Given an m ₁ × n ₁ matrix A and an m ₂ × n ₂ matrix B, we define the product A × B as the (m ₁ + m ₂) × n ₁ n ₂ matrix whose columns consist of all possible combinations obtained from placing a column of A on top of a column of B. Let I _k denote the k × k identity matrix, let \({I_k^{c}}\) denote the (0,1)-complement of I _k and let T _k denote the k × k upper triangular (0,1)-matrix with a 1 in position i, j if and only if i ≤ j. We show forb(m, {I ₂ × I ₂, T ₂ × T ₂}) is \({\Theta(m^{3/2})}\) while obtaining a linear bound when forbidding all 2-fold products of all 2 × 2 (0,1)-simple matrices. For two matrices F, P, where P is m-rowed, let \({f(F, P) = {\rm max}_{A} \{\|A\| \,:\,A}\) is m-rowed submatrix of P with no configuration F}. We establish f(I ₂ × I ₂, I _m/2 × I _m/2) is \({\Theta(m^{3/2})}\) whereas f(I ₂ × T ₂, I _m/2 × T _m/2) and f(T ₂ × T ₂, T _m/2 × T _m/2) are both \({\Theta(m)}\) . Additional results are obtained. One of the results requires extensive use of a computer program. We use the results on patterns due to Marcus and Tardos and generalizations due to Klazar and Marcus, Balogh, Bollobás and Morris.     

Asymmetric epoxidation of substituted chalcones and chalcone analogues catalyzed by α-d-glucose- and α-d-mannose-based crown ethers

The chiral monoaza-15-crown-5 lariat ethers annellated to methyl-4,6-O-benzylidene-α-d-glucopyranoside-1 or mannopyranoside 2 have been applied as phase-transfer catalysts in the epoxidation of substituted chalcones and chalcone analogues with tert-butylhydroperoxide resulting in significant asymmetric induction. It was found that the position of the substituents in the aromatic ring of the chalcone had an influence both on the chemical yields and enantiomeric excesses. The lowest enantioselectivities (62–83% ee) were found in the case of ortho-substituted model compounds. The highest ee values (ee of 83–97%) were obtained in the case of para-substituted models. From among the chalcone analogues, the maximum ee (90–92%) was detected for the model compound having α-tert-butyl- and β-aryl groups. Using glucose-based crown ether 1, formation of the (?)-enantiomer was preferred, while applying mannose-based 2 as the catalyst, the (+)-enantiomer was in excess.     

LC-UV Assay of Tolperisone HCl from Sustained Release Matrix Tablets

Tolperisone HCl is a central muscle relaxant, which was incorporated in a matrix system formulated with poly(ethylene oxide)–PEO, in order to achieve adequate gastric residence time. This tablet presents considerable analytical difficulties in the quantitative determination of the drug, because the PEO matrix causes significant increase of viscosity in the samples. Our purpose was to develop a reproducible sample preparation method, which is adapted from parameters of the in vitro dissolution test and validate an LC-UV analytical method, which allows good recovery of the drug (99.97%). The developed analytical method was suitable for quantitative analysis of tolperisone HCl in matrix tablets.     

Theoretical study of hyaluronan oligosaccharides

The structure and energetics of hyaluronan oligomers from di- to decasaccharides have been studied by density functional theory calculations at the B3LYP/6-31G** level. The study covered selected conformers of the sodium salt, anionic disaccharides, and neutral acids in the isolated state and in aqueous solution using the PCM model approach. We investigated the structural changes of the hyaluronan chain when the Na⁺ ion is removed or replaced by proton. These processes result in some characteristic changes in the glycosidic torsional angles and hydrogen bonding interactions. We evaluated the folding for the hyaluronan chains and obtained values between 2.2 and 3.2, somewhat smaller than reported for the crystals. We found a contraction of the hyaluronan chains upon enlargement in most derivatives attributed partly to the helical character of hyaluronan. The energy consequences of the enlargement have been modeled by isodesmic reactions. The enlargement processes proved to be exothermal and the energies consistent within the gradual enlargement.