Journal of Computational Chemistry

doi: 10.1002/jcc.26679pmid: N/A

Luise, Davide; D'Alterio, Massimo Christian; Talarico, Giovanni; Ciofini, Ilaria; Labat, Frédéric

doi: 10.1002/jcc.26955pmid: 35762850

The absorption spectra of polymers derived from ortho, meta and para phenylenediamines (o‐PDA, m‐PDA and p‐PDA) have been simulated combining periodic density functional theory (DFT) calculations with time‐dependent DFT simulations. These latter have been carried out on finite clusters embedded in a set of point charges devised to exactly reproduce the electrostatic potential of the periodic chains. The results are compared with those obtained for solvated o‐PDA, m‐PDA and p‐PDA oligomers of increasing sizes extracted from the periodic structures. The electronic transitions involved have been investigated by a qualitative analysis based on isodensity maps completed by a quantitative analysis based on the density‐based index (DCT). For poly‐(o)‐ and poly‐(p)‐ phenylenediamines the agreement with the experimental data is achieved already by modeling solvated dimers whereas the inclusion of long‐range electrostatic effects is mandatory for poly‐(m)‐phenylenediamine highlighting the importance of an accurate treatment of the electrostatic environment when a finite cluster approach is considered.

Kong, Linghan; Bryce, Richard A.

doi: 10.1002/jcc.27000pmid: 36165294

Pyranose ring pucker is a key coordinate governing the structure, interactions and reactivity of carbohydrates. We assess the ability of the machine learning potentials, ANI‐1ccx and ANI‐2x, and the GFN2‐xTB semiempirical quantum chemical method, to model ring pucker conformers of five monosaccharides and oxane in the gas phase. Relative to coupled‐cluster quantum mechanical calculations, we find that ANI‐1ccx most accurately reproduces the ring pucker energy landscape for these molecules, with a correlation coefficient r2 of 0.83. This correlation in relative energies lowers to values of 0.70 for ANI‐2x and 0.60 for GFN2‐xTB. The ANI‐1ccx also provides the most accurate estimate of the energetics of the 4C1‐to‐1C4 minimum energy pathway for the six molecules. All three models reproduce chair more accurately than non‐chair geometries. Analysis of small model molecules suggests that the ANI‐1ccx model favors puckers with equatorial hydrogen bonding substituents; that ANI‐2x and GFN2‐xTB models overstabilize conformers with axially oriented groups; and that the endo‐anomeric effect is overestimated by the machine learning models and underestimated via the GFN2‐xTB method. While the pucker conformers considered in this study correspond to a gas phase environment, the accuracy and computational efficiency of the ANI‐1ccx approach in modeling ring pucker in vacuo provides a promising basis for future evaluation and application to condensed phase environments.

Monti, Marta; Stener, Mauro; Aschi, Massimiliano

doi: 10.1002/jcc.27001pmid: 36134712

The present study consists in a novel computational protocol to model the UV‐circular dichroism spectra of solvated species. It makes use of quantum‐chemical calculations on a series of conformations of a flexible chromophore or on a series of chromophore/solvent clusters extracted from molecular dynamic simulations. The protocol is described and applied to the aqueous cationic tripeptide GAG+ and to the aqueous neutral decapeptide (GVGVP)2. The protocol has proven able to: (i) properly consider the conformational motion of solute in the given environment; (ii) give the actual statistical weight of each conformational state; (iii) provide a reliable quantum mechanical method able to reproduce the spectral features. Temperature effects on conformations and spectral properties are properly taken into account. The role of explicit solvent on the conformational analysis and the spectra calculation is discussed. The comparison of the calculated circular dichroism spectra with experimental ones recorded at different temperatures represents a strict validation test of the method.

De Simone, Bruna Clara; Mazzone, Gloria; Toscano, Marirosa; Russo, Nino

doi: 10.1002/jcc.27002pmid: 36129210

The main photophysical properties, useful for establishing whether hypericin in anionic form and some of its derivatives containing heavy atoms such as iodine, can be proposed for their use in photodynamic therapy, were determined using density functional based computations. The results showed that in the anionic form and in the iodinated derivatives, the absorption wavelength undergoes a bathochromic shift, the singlet‐triplet energy gap assumes values ​that allow to excite the oxygen molecule from its ground to the excited singlet state, and that the spin–orbit couplings between singlet and triplet states significantly increase.