Atomic charges derived from a fast and accurate method for electrostatic potentials based on modified AM1 calculations

Quantum-Classical Protocol for Efficient Characterization of Absorption Lineshape and Fluorescence Quenching upon Aggregation: The Case of Zinc Phthalocyanine Dyes

A quantum-classical protocol that incorporates Jahn-Teller vibronic coupling effects and cluster analysis of molecular dynamics simulations is reported, providing a tool for simulations of absorption spectra and ultrafast nonadiabatic dynamics in large molecular photosystems undergoing aggregation in solution. Employing zinc phthalocyanine dyes as target systems, we demonstrated that the proposed protocol provided fundamental information on vibronic, electronic couplings and thermal dynamical effects that mostly contribute to the absorption spectra lineshape and the fluorescence quenching processes upon dye aggregation. Decomposing the various effects arising upon dimer formation, the structure-property relations associated with their optical responses have been deciphered at atomistic resolution.

Conformational study of the electronic interactions and nitric oxide release potential of new S‑nitrosothiols esters derivatives of ibuprofen, naproxen and phenyl acids substituted (SNO-ESTERS): Synthesis, infrared spectroscopy analysis and theoretical calculations

The conformational study on the new S‑nitrosothiols esters (SNO-ESTERS): para-substituted (X = H, OMe, Cl and NO₂) S‑nitrosothiol derivatives 2‑methyl‑2‑(sulfanyl)propyl phenylacetates (R1), 2‑(4‑isobutylphenyl)propanoate (ibuprofen, R2), and 2‑(4‑isobutylphenyl)propanoate of 2‑methyl‑2‑(nitrososulfanyl)propyl (naproxen, R3) was performed using infrared spectroscopy (IR) in solvents with increasing polarity (CCl₄, CH₃Cl, and CH₃CN), and theoretical calculations, to determine the preferential conformer and the potential of these compounds to release nitric oxide (NO). S‑Nitrosothiols were synthesized by esterification reactions, using chlorides of the corresponding carboxylic acids, with good yields (~60%). IR results showed that these compounds presented only one conformation, and the experimental data were supported by the theoretical results obtained by density functional theory (DFT) calculations using the 6311+G (2df, 2p) basis set. The calculations revealed that all S‑nitrosothiols presented one preferential anticlinal (ac) geometric conformation, which agrees with the data obtained experimentally in CCl₄. These conformers are stabilized by intramolecular hydrogen bonds. Examination of the geometry with regard to the RSNO group revealed that these compounds are preferentially in the trans (anti) conformation. The calculation of the orbital interactions using the Natural Bond Orbital (NBO) method showed that the n_O(NO) → σ_(SN)^∗ hyper-conjugative interaction increases the SN bond length. The strong n_S → π_(NO)^∗ interaction and electronic delocalization induces a partial π character to the SN bond. The weak σ_SN bond indicates strong delocalization of the electron pair in O (NO) by the n_O(NO) → σ_(SN)^∗ interaction, thereby increasing the capacity of NO release from SNO-ESTERS.

Benchmark of different charges for prediction of the partitioning coefficient through the hydrophilic/lipophilic index

A few different theoretical methods for assigning the partial atomic charges were benchmarked for calculation of the hydrophilic/lipophilic index (HLI). The coefficients were selected to produce the best correlation of the HLI values with the experimental octanol-water partition. Different parameters were checked in calculations of partial charges to get the best performance of the HLI values obtained. Thus, four partitioning schemes (Coulson, Mulliken, Merz-Kollman, Ford-Wang) were benchmarked for calculations of atomic charges with six semiempirical methods (AM1, PM3, RM1, PM6, PM6-D3H4, PM7). Moreover, five distinct types of partial atomic charges (Mulliken, Hirshfeld, Löwdin, CHELPG, NPA), obtained at the Hartree-Fock and DFT levels of theory with three basis sets, were tested for their ability to produce the HLI values with the best correlation to experimental logP coefficients of 50 mono-charged organic anions. In the case of the semiempirical methods, the best correlation between the HLI and logP values (the correlation coefficient r = 0.9216) was obtained with the AM1 Ford-Wang parametric electrostatic potential charges. The Mulliken and Coulson charges calculated with the PM7 method can be used as an alternative to AM1, with the r values of 0.9107 and 0.8984, respectively. In the case of the DFT, the PBE/def2-TZVP natural population analysis charges produce the best correlation (r = 0.9220). Nevertheless, in spite of a marginally lower performance (r = 0.9159), the NPA charges computed at the PBE/def2-SVP level are more robust and can be regarded as the optimum choice for calculating the HLI values. Graphical abstract The hydrophilic/lipophilic index (HLI).

Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometric and semi-empirical calculations study of five isoflavone aglycones

Five isoflavones, daidzein, genistein, formononetin, prunetin and biochanin A, known for their biological properties, are investigated by electrospray ionization mass spectrometry in the positive ion mode. The most probable protonation sites are determined taking into account semi-empirical calculations using the PM6 Hamiltonian. Fragmentation mechanisms are proposed based on accurate mass measurements, MS(3) experiments and supported by the semi-empirical calculations. Some of the fragmentation pathways were found to be dependent on the substitution pattern of the B-ring and the ions afforded by these fragmentations can be considered as diagnostic. It was possible to distinguish between prunetin and biochanin A, two isobaric isoflavone aglycones included in this study. Furthermore, a comparison of the fragmentation patterns of genistein and biochanin A, two isoflavones, with those of their flavone counterparts, apigenin and acacetin, enabled us to identify some key ions mainly due to structural features, allowing distinction to be made between these two classes of compounds.

Pharmacophore mapping of arylbenzothiophene derivatives for MCF cell inhibition using classical and 3D space modeling approaches

Considering the worth of developing non-steroidal estrogen analogs, the present study explores the pharmacophore features of arylbenzothiophene derivatives for inhibitory activity to MCF-7 cells using classical QSAR and 3D space modeling approaches. The analysis shows that presence of phenolic hydroxyl group and ketonic linkage in the basic side chain of 2-arylbenzothiophene core of raloxifene derivatives are crucial. Additionally piperidine ring connected through ether linkage is favorable for inhibition of breast cancer cell line. These features for inhibitory activity are also highlighted through 3D space modeling approach that explored importance of critical inter features distance among HB-acceptor lipid, hydrophobic and HB-donor features in the arylbenzothiophene scaffold for activity.

Optimization of parameters for semiempirical methods V: modification of NDDO approximations and application to 70 elements

Several modifications that have been made to the NDDO core-core interaction term and to the method of parameter optimization are described. These changes have resulted in a more complete parameter optimization, called PM6, which has, in turn, allowed 70 elements to be parameterized. The average unsigned error (AUE) between calculated and reference heats of formation for 4,492 species was 8.0 kcal mol(-1). For the subset of 1,373 compounds involving only the elements H, C, N, O, F, P, S, Cl, and Br, the PM6 AUE was 4.4 kcal mol(-1). The equivalent AUE for other methods were: RM1: 5.0, B3LYP 6-31G*: 5.2, PM5: 5.7, PM3: 6.3, HF 6-31G*: 7.4, and AM1: 10.0 kcal mol(-1). Several long-standing faults in AM1 and PM3 have been corrected and significant improvements have been made in the prediction of geometries.