Search Results (3)

Recently, we reported a new approach to develop pairwise analytical corrections to improve the description of noncovalent interactions, by approximate methods of electronic structures, such as semiempirical quantum mechanical (SQM) methods. In particular, and as a proof of concept, we used the PM6 Hamiltonian and we named the method PM6-FGC, where the FGC acronym, corresponding to Functional Group Corrections, emphasizes the idea that the corrections work for specific functional groups rather than for individual atom pairs. The analytical corrections were derived from fits to B3LYP-D3/def2-TZVP (reference). PM6 interaction energy differences, evaluated for a reduced set of small bimolecular complexes, were chosen as representatives of saturated hydrocarbons, carboxylic, amine and, tentatively, amide functional groups. For the validation, the method was applied to several complexes of well-known databases, as well as to complexes of diglycine and dialanine, assuming the transferability of amine group corrections to amide groups. The PM6-FGC method showed great potential but revealed significant inaccuracies for the description of some interactions involving the –NH₂ group in amines and amides, caused by the inadequate selection of the model compound used to represent these functional groups (an NH₃ molecule). In this work, methylamine and acetamide are used as representatives of amine and amide groups, respectively. This new selection leads to significant improvements in the calculation of noncovalent interactions in the validation set. Full article

The influence of nitrogen-containing surface groups (SGs) onto activated carbon (AC) over the adsorption of chlordecone (CLD) and β-hexachlorocyclohexane (β-HCH) was characterized by a molecular modelling study, considering pH (single protonated SGs) and hydration effect (up to three water molecules). The interactions of both pollutants with amines and pyridine as basic SGs of AC were studied, applying the multiple minima hypersurface (MMH) methodology and using PM7 semiempirical Hamiltonian. Representative structures from MMH were reoptimized using the M06-2X density functional theory. The quantum theory of atoms in molecules (QTAIM) was used to characterize the interaction types in order understanding the adsorption process. A favorable association of both pesticides with the amines and pyridine SGs onto AC was observed at all pH ranges, both in the absence and presence of water molecules. However, a greater association of both pollutants with the primary amine was found under an acidic pH condition. QTAIM results show that the interactions of CLD and β-HCH with the SGs onto AC are governed by Cl···C interactions of chlorine atoms of both pesticides with the graphitic surface. Electrostatic interactions (H-bonds) were observed when water molecules were added to the systems. A physisorption mechanism is suggested for CLD and β-HCH adsorption on nitrogen-containing SGs of AC. Full article

We investigate the modeling capabilities of sets of coupled classical harmonic oscillators (CHO) in the form of a modeling game. The application of the simple but restrictive rules of the game lead to conditions for an isomorphism between Lie-algebras and real Clifford algebras. We show that the correlations between two coupled classical oscillators find their natural description in the Dirac algebra and allow to model aspects of special relativity, inertial motion, electromagnetism and quantum phenomena including spin in one go. The algebraic properties of Hamiltonian motion of low-dimensional systems can generally be related to certain types of interactions and hence to the dimensionality of emergent space-times. We describe the intrinsic connection between phase space volumes of a 2-dimensional oscillator and the Dirac algebra. In this version of a phase space interpretation of quantum mechanics the (components of the) spinor wavefunction in momentum space are abstract canonical coordinates, and the integrals over the squared wave function represents second moments in phase space. The wave function in ordinary space-time can be obtained via Fourier transformation. Within this modeling game, 3+1-dimensional space-time is interpreted as a structural property of electromagnetic interaction. A generalization selects a series of Clifford algebras of specific dimensions with similar properties, specifically also 10- and 26-dimensional real Clifford algebras. Full article