The approximate CNDOL Fockian, together with the configuration interaction of single excitations (CIS|CNDOL/21), is applied to investigate the electronic properties of three different kinds of donors ...(D) considered suitable for photovoltaic devices, either as isolated systems or complexed with fullerene (C
60
) as potential acceptors (A). Calculated charge maps, together with the Coulomb-exchange term of CIS lowest transitions, are used to understand the electronic topology and possible behaviour of D-A excitons. The effects of varying donor structures are compared. The lowest excitation energies of the donor-C
60
complexes arise from electron densities localised at the central ring units in the donors. Nevertheless, C
60
does not always participate in electron sharing upon excitation. It sometimes acts only as a structural companion for enhancing or not the exciton capability to provide adequate photoelectric power conversion efficiencies. The CIS|CNDOL/21 method is validated as a valuable tool for modelling structure-related properties of molecular excitons and for predicting the performance of D-A materials in relatively big supramolecular systems. It is shown that multi-electron CIS wavefunctions are at least as useful as one-electron molecular orbitals to describe charge-transfer properties of excitons and provide a physical picture of the whole electron density.
Clustering Molecular Dynamics trajectories is a common analysis that allows grouping together similar conformations. Several algorithms have been designed and optimized to perform this routine task, ...and among them, Quality Threshold stands as a very attractive option. This algorithm guarantees that in retrieved clusters no pair of frames will have a similarity value greater than a specified threshold, and hence, a set of strongly correlated frames are obtained for each cluster. In this work, it is shown that various commonly used software implementations are flawed by confusing Quality Threshold with another simplistic well-known clustering algorithm published by Daura et al. (Daura, X.; van Gunsteren, W. F.; Jaun, B.; Mark, A. E.; Gademann, K.; Seebach, D. Peptide Folding: When Simulation Meets Experiment. Angew. Chemie Int. Ed. 1999, 38 (1/2), 236–240). Daura’s algorithm does not impose any quality threshold for the frames contained in retrieved clusters, bringing unrelated structural configurations altogether. The advantages of using Quality Threshold whenever possible to explore Molecular Dynamic trajectories is exemplified. An in-house implementation of the original Quality Threshold algorithm has been developed in order to illustrate our comments, and its code is freely available for further use by the scientific community.
We have developed two ligand- and receptor-based computational approaches to study the physicochemical properties relevant to the biological activity of vasopressin V2 receptor (V2R) antagonist and ...eventually to predict the expected binding mode to V2R. The obtained quantitative structure activity relationship (QSAR) model showed a correlation of the antagonist activity with the hydration energy (E
H2O
), the polarizability (P), and the calculated partial charge on atom N7 (q6) of the common substructure. The first two descriptors showed a positive contribution to antagonist activity, while the third one had a negative contribution. V2R was modeled and further relaxed on a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocoline (POPC) membrane by molecular dynamics simulations. The receptor antagonist complexes were guessed by molecular docking, and the stability of the most relevant structures was also evaluated by molecular dynamics simulations. As a result, amino acid residues Q96, W99, F105, K116, F178, A194, F307, and M311 were identified with the probably most relevant antagonist-receptor interactions on the studied complexes. The proposed QSAR model could explain the molecular properties relevant to the antagonist activity. The contributions to the antagonist-receptor interaction appeared also in agreement with the binding mode of the complexes obtained by molecular docking and molecular dynamics. These models will be used in further studies to look for new V2R potential antagonist molecules.
1,3 Dipolar Cycloaddition of Münchnones: Factors behind the Regioselectivity Bocalandro, Meylin; González Armesto, Juan J; Montero-Cabrera, Luis A ...
The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory,
2023-Jan-26, 2023-01-26, 20230126, Letnik:
127, Številka:
3
Journal Article
Recenzirano
The 1,3 dipolar cycloaddition reactions of münchnones and alkenes provide an expedite synthetic way to substituted pyrroles, an exceedingly important structural motif in the pharmaceutical and ...material science fields of research. The factors governing their regioselectivity rationalization are not well understood. Using several approaches, we investigate a set of 14 reactions (featuring two münchnones, 12 different alkenes, and two alkynes). The Natural Bond Theory and the Non-Covalent Interaction Index analyses of the noncovalent interaction energies fail to predict the experimental major regioisomer. Employing global cDFT descriptors or local ones such as the Fukui function and dual descriptor yields similarly inaccurate predictions. Only the local softness pairing, within Pearson's Hard and Soft Acids and Bases principle, constitutes a reliable predictor for the major reaction product. By taking into account an estimator for the steric effects, the correct regioisomer is predicted. Steric effects play a major role in driving the regioselectivity, as was corroborated by energy decomposition analysis of the transition states.
Cardiovascular disease (CVD) continues as the most important cause of mortality. Better risk screening and prediction are needed to reduce the cardiovascular disease burden. The aim of the study was ...to assess the role of serum biomarkers in the prediction of CVD among asymptomatic middle-aged adults with no prior CVD history. A systematic review and meta-analysis were carried out using literature from PubMed and following PRISMA reporting guidelines. Twenty-five studies met our inclusion criteria and were included in the systematic review. The most commonly studied biomarker was high-sensitivity C reactive protein (hs-CRP) (10 studies), which showed that higher hs-CRP levels are associated with an increased risk of subsequent CVD events and mortality. In addition, several less-studied biomarkers (N-terminal pro-brain natriuretic peptide (NT-proBNP), fibrinogen, gamma-glutamyl transferase (GGT), and others) also showed significant associations with greater future risk of CVD. A meta-analysis was possible to perform for hs-CRP and NT-proBNP, which showed statistically significant results for the ability of hs-CRP (hazard ratio (HR) 1.19, (95% CI: 1.09−1.30), p < 0.05) and NT-proBNP (HR 1.22, (1.13−1.32), p < 0.05) to predict incident CVD among middle-aged adults without a prior CVD history or symptoms. Several serum biomarkers, particularly hs-CRP and NT-proBNP, have the potential to improve primary CVD risk prevention among asymptomatic middle-aged adults.
Spectroscopic properties of molecules hold great importance for the description of the molecular response under the effect of UV/vis electromagnetic radiation. Computationally expensive ab initio ...(e.g., MultiConfigurational SCF, Coupled Cluster) or TDDFT methods are commonly used by the quantum chemistry community to compute these properties. In this work, we propose a (supervised) Machine Learning approach to model the absorption spectra of organic molecules. Several supervised ML methods have been tested such as Kernel Ridge Regression (KRR), Multiperceptron Neural Networs (MLP), and Convolutional Neural Networks. Ramakrishnan et al. J. Chem. Phys. 2015, 143, 084111. Ghosh et al. Adv. Sci. 2019, 6, 1801367. The use of only geometrical-atomic number descriptors (e.g., Coulomb Matrix) proved to be insufficient for an accurate training. Ramakrishnan et al. J. Chem. Phys. 2015, 143, 084111. Inspired by the TDDFT theory, we propose to use a set of electronic descriptors obtained from low-cost DFT methods: orbital energy differences (Δϵ ia = ϵ a – ϵ i ), transition dipole moment between occupied and unoccupied Kohn–Sham orbitals (⟨ϕ i |r|ϕ a ⟩), and when relevant, charge-transfer character of monoexcitations (R ia ). We demonstrate that with these electronic descriptors and the use of Neural Networks we can predict not only a density of excited states but also get a very good estimation of the absorption spectrum and charge-transfer character of the electronic excited states, reaching results close to chemical accuracy (∼2 kcal/mol or ∼0.1 eV).
Abstract
There are knowledge gaps regarding healthy lifestyle (HLS) interventions in fire academy settings and also concerning the impacts of the pandemic on training. We enrolled fire recruits from ...two fire academies (A and B) in New England in early 2019 as the historical control group, and recruits from academies in New England (B) and Florida (C), respectively, during the pandemic as the intervention group. The three academies have similar training environments and curricula. The exposures of interest were a combination of (1) an HLS intervention and (2) impacts of the pandemic on training curricula and environs (i.e. social distancing, masking, reduced class size, etc.). We examined the health/fitness changes throughout training. The follow-up rate was 78%, leaving 92 recruits in the historical control group and 55 in the intervention group. The results show an HLS intervention improved the effects of fire academy training on recruits healthy behaviors (MEDI-lifestyle score, 0.5 ± 1.4 vs. − 0.3 ± 1.7), systolic blood pressure (− 7.2 ± 10.0 vs. 2.9 ± 12.9 mmHg), and mental health (Beck Depression score, − 0.45 ± 1.14 vs. − 0.01 ± 1.05) (all P < 0.05). The associations remained significant after multivariable adjustments. Moreover, a 1-point MEDI-lifestyle increment during academy training is associated with about 2% decrement in blood pressures over time, after multivariable adjustments (P < 0.05). Nonetheless, the impacts of pandemic restrictions on academy procedures compromised physical fitness training, namely in percent body fat, push-ups, and pull-ups.
To assess the title issue, 38 hydrogen transfer barrier heights and 38 non‐hydrogen transfer barrier heights/isomerizations extracted from extensive databases have been considered, in addition to 4 2 ...p‐isomerization reactions and 6 others for large organic molecules. All Kohn–Sham DFT calculations have employed the popular M06‐2X functional, whereas the correlated molecular orbital (MO)‐based ones are from single‐reference MP2 and CCSD(T) methods. They have all utilized the same basis sets, with raw MO energies subsequently extrapolated to the complete basis set limit without additional cost. MP2 calculations are found to be as cost‐effective as DFT ones and often slightly more, while showing a satisfactory accuracy when compared with the reference data. Although the focus is on barrier heights, the results may bear broader implications, in that one may see successes and difficulties of DFT when compared with traditional MO theories for the same data.
Counting the cost: To assess different computational methods, 38 hydrogen transfer barrier heights and 38 non‐hydrogen transfer barrier heights/isomerizations extracted from extensive databases have been considered. MP2 calculations are as cost‐effective as DFT ones and often slightly more, while showing a satisfactory accuracy when compared with the reference data (see figure).
Dipolar cycloaddition reactions involving munchnönes and simple dipolarophiles provide a versatile synthetic route toward pyrrole derivatives. However, despite their widespread use, there are still ...debates regarding the factors governing the regio‐selectivity of these reactions. In this contribution, we study the regio‐selectivity of 1,3‐dipolar cycloadditions of munchnönes and alkenes, and the ability of conceptual density functional theory (c‐DFT) descriptors to correctly study these processes. We base our analysis on the variation of different reactivity descriptors along the reaction path, calculated for the whole reacting complex, and for the isolated species, with the strained geometries they present within this supra‐molecular aggregate. The study of several global descriptors indicates that the path leading to the preferred product proceeds via an asynchronous mechanism, with the maximum extent of charge transfer occurring after the transition state. This helps to understand why several reactivity principles fail to correctly account for the position of the transition state in this case. This also explains why local c‐DFT descriptors fail to predict the observed majoritarian regio‐isomer. These results highlight the fundamental role of the distortion effects for determining the extent of charge transfer between the reactants, and thus their impact on the reactivity and regio‐selectivity in these reactions.
Dipolar cycloadditions involving munchnönes are a powerful tool in the synthesis of many heterocyclic compounds. Therefore, there is recent increasing interest in the elucidation of the factors governing their regio‐selectivity. First‐principles calculations show that the geometrical distortion of the reactants, and the charge transfer between them, must be taken into account to accurately predict the formation of the preferred regio‐isomer.
The aim of this work is to describe the molecular inclusion of chlordecone with α-, β-, and γ-cyclodextrin in aqueous solution using quantum mechanics. The guest–host complexes of chlordecone and ...cyclodextrins are modeled in aqueous solution using the multiple minima hypersurface methodology with a PM6-D3H4X semiempirical Hamiltonian, and the lowest energy minima obtained are reoptimized using the M06-2X density functional and the intermolecular interactions described using quantum theory of atoms in molecules (QTAIM). The studied complexes are classified according to the degree of inclusion, namely, total occlusion, partial occlusion, and external interaction. More stable complexes are obtained when γ-CD is used as the host molecule. The interactions characterized through QTAIM analysis are all of electrostatic nature, predominantly of dispersive type. In this work, a method based on the counterpoise correction is also discussed to mitigate the basis set superposition error in density functional theory calculations when using an implicit solvation model.
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