Chemphyschem最新文献

We performed a hierarchical ab initio benchmark study of the gas-phase radical addition reactions of X⋅+C₂H₂ and X⋅+C₂H₄ (X⋅ = CH₃⋅, NH₂⋅, OH⋅, SH⋅). The hierarchical series of ab initio methods (HF, MP2, CCSD, CCSD(T)) were paired with a hierarchal series of Dunning basis sets with and without diffuse functions ((aug)-cc-pVDZ, (aug)-cc-pVTZ, (aug)-cc-pVQZ). The HF ground-state wavefunctions were transformed into quasi-restricted orbital (QRO) reference wavefunctions to address spin contamination. Following extrapolation to the CBS limit, the energies from our highest- QRO-CCSD(T)/CBS+ level converged within 0.0-3.4 kcal mol^-1 and 0.0-1.0 kcal mol^-1 concerning the ab initio method and basis set, respectively. Our QRO-CCSD(T)/CBS+ reference data was used to evaluate the performance of 98 density functional theory (DFT) approximations. The MAE of the best functionals for reaction barriers and energies were: OLYP (1.9 kcal mol^-1), BMK (1.0 kcal mol^-1), M06-2X (0.9 kcal mol^-1), MN12-SX (0.8 kcal mol^-1) and CAM-B3LYP (0.8 kcal mol^-1). These functionals also accurately reproduce key geometrical parameters of the stationary points within an average 2 % deviation from the reference QRO-CCSD(T)/cc-pVTZ level.

Intermolecular interactions and adsorbate coverage on a metal electrode's surface/interface play an important role in CO₂ reduction reaction (CO₂RR). Herein, the activity and selectivity of CO₂RR on bimetallic electrode, where a full monoatomic Cu layer covers on Ag surface (Cu_ML/Ag) are investigated by using density functional theory calculations. The surface geometric and electronic structure results indicate that there is high electrocatalytic activity for CO₂RR on the Cu_ML/Ag electrode. Specifically, the Cu_ML/Ag surface can accelerate the H₂O and CO₂ adsorption and hydrogenation while lowering the reaction energy of the rate-determining step. The structure parameters of chemisorbed CO₂ with and without H₂O demonstrate that activated H₂O not only promotes the C-O dissociation but also provides the protons required for CO₂RR on the Cu_ML/Ag electrode surface. Furthermore, the various reaction mechanism diagrams indicate that the Cu_ML/Ag electrode has high selectivity for CO₂RR, and the efficiency of products can be regulated by modulating the reaction's electric potential.

Quinoline represents a promising scaffold for developing potential drugs because of the wide range of biological and pharmacological activities that it exhibits. In the present study, quinoline derivatives obtained from CADMA-Chem docking protocol were investigated in the mean of molecular dynamics simulations as potential inhibitors of acetylcholinesterase enzyme. The examined species can be partitioned between neutral, dq815 (2,3 dihydroxyl-quinoline-4-carbaldehyde), dq829 (2,3 dihydroxyl-quinoline-8-carboxylic acid methane ester), dq1356 (3,4 dihydroxyl-quinoline-6-carbaldehyde), dq1368 (3,4 dihydroxyl-quinoline-8-carboxylic acid methane ester) and dq2357 (5,6 dihydroxyl-quinoline-8-carboxylic acid methane ester), and deprotonated, dq815_dep, dq829_dep, dq1356_dep and dq2357_dep. Twelve molecular dynamics simulations were performed including those of natural acetylcholine, of the well-known donepezil inhibitor and of the founder quinoline chosen as reference. Key intermolecular interactions were detected and discussed to describe the different dynamic behavior of all the considered species. Binding energies calculation from MMPBSA well accounts for the dynamic behavior observed in the simulation time proposing dq1368 as promising candidate for the inhibition of acetylcholinesterase. Retrosynthetic route for the production of the investigated compounds is also proposed.

Amyloid fibril formation by some peptides leads to several neurogenetic disorders. This limits their biological activity and increases cytotoxicity. Human calcitonin (hCT), 32 residue containing peptide, known for regulating calcium and phosphate concentration in the blood tends to form amyloids in aqueous medium. Polyphenols are very effective in inhibiting fibril formation. As part of our research, we have taken Magnolol (Mag), which is extracted from the Chinese herb Magnolia officinalis. To evaluate its effectiveness as an inhibitor in preventing hCT aggregation, we conducted an all-atom classical molecular dynamics simulation with varying concentrations of Mag. In presence of Mag, hCT maintains its helical conformation in higher order. Magnolol primarily interacts with hCT via van der Waals interaction. Asp15 residue of hCT, resides in the amyloid region (D₁₅FNKF₁₉) forms strong hydrogen bonding interaction with Mag. Moreover, aromatic residues of hCT interact with Mag through π-π stacking interactions. Our work gives insights into the molecular mechanism of Magnolol in the inhibition of hCT fibril formation to use it as a potential candidate for medicinal purpose.

Catalytic reactions running in an adsorbed overlayer on metallic alloy nanoparticles are of high interest in the context of applications in the chemical industry. The understanding of the corresponding kinetics is, however, still limited. One of the reasons of this state of the art is the interplay between adsorption and adsorbate-influenced segregation of metal atoms inside alloy nanoparticles. I scrutinize this interplay by using a generic field model of segregation and the mean-field approximation in order to describe adsorption, desorption, and elementary catalytic reactions. Under steady-state conditions, the segregation is demonstrated to be manifested in the change of the dependence of the activation energies of desorption or elementary reactions on coverage, and the sign of this change is positive. The effect of this change on the apparent reaction orders is briefly discussed as well.

It is shown, by examining the variations in off-nucleus isotropic magnetic shielding around a molecule, that thiophene which is aromatic in its electronic ground state (S₀) becomes antiaromatic in its lowest triplet state (T₁) and then reverts to being aromatic in T₂. Geometry relaxation has an opposite effect on the aromaticities of the ππ* vertical T₁ and T₂: The antiaromaticity of T₁ is reduced whereas the aromaticity of T₂ is enhanced. The shielding picture around T₂ is found to closely resemble those around certain second singlet ππ* excited states (S₂), for example, those of benzene and cyclooctatetraene, thought to be "strongly aromatic" because of their very negative nucleus-independent chemical shift (NICS) values. It is argued that while NICS values correctly follow the changes in aromaticity along the potential energy surface of a single electronic state, the use of NICS values for the purpose of quantitative comparisons between the aromaticities of different electronic states cannot be justified theoretically and should be avoided. "Strongly aromatic" S₂ and T₂ states should be referred to simply as "aromatic" because detailed comparisons between the properties of these states and those of the corresponding S₀ states do not suggest higher levels of aromaticity.

The protonation state of molecules and surfaces is pivotal in various disciplines, including (electro-)catalysis, geochemistry, biochemistry, and pharmaceutics. Accurately and efficiently determining acidity constants is critical yet challenging, particularly when explicitly considering the electronic structure, thermal fluctuations, anharmonic vibrations, and solvation effects. In this research, we employ thermodynamic integration accelerated by committee Neural Network potentials, training a single machine learning model that accurately describes the relevant protonated, deprotonated, and intermediate states. We investigate two deprotonation reactions at the BiVO₄ (010)-water interface, a promising candidate for efficient photocatalytic water splitting. Our results illustrate the convergence of the required ensemble averages over simulation time and of the final acidity constant as a function of the Kirkwood coupling parameter. We demonstrate that simulation times on the order of nanoseconds are required for statistical convergence. This time scale is currently unachievable with explicit ab-initio molecular dynamics simulations at the hybrid DFT level of theory. In contrast, our machine learning workflow only requires a few hundred DFT single point calculations for training and testing. Exploiting the extended time scales accessible, we furthermore asses the effect of commonly applied bias potentials. Thus, our study significantly advances calculating free energy differences with ab-initio accuracy.

Light patternable colorless liquid crystalline (LC) polymers are promising materials for functional photonic devices with broad applications in optical communication, diffractive optics, and displays. This work reports photoinduced optical anisotropy in thin films of azobenzene-containing (Azo) LC block copolymer supramolecular complexes, which can be decolorized after light patterning providing colorless patterned birefringent polymer films. The supramolecular complexes are prepared via intermolecular pyridine-phenol hydrogen bonding between a low-molecular-weight Azo phenol and host LC AB diblock and ABA triblock copolymers consisted of LC phenylbenzoate (PhM) blocks and poly(vinylpyridine) units. The molecular architecture of the host polymers and the morphological pattern formed by the complexes can affect orientational behavior of Azo groups under irradiation with linearly polarized light. Photoorientation of hydrogen-bonded Azo groups is accompanied by the cooperative orientation of non-photochromic PhM units, which form individual microphases and stabilize the orientation of Azo groups. This effect is specific for block copolymer complexes and it is absent for random copolymer complex, which is used as a reference sample. Optical anisotropy induced in films of the block copolymer complexes can be amplified by heating above the glass transition temperature and subsequent rinsing with diethyl ether allows colorless birefringent polymer films to be prepared.

We provide here a comprehensive investigation spectroscopic of the controlled hydration of Re₂O₇ using Raman, Fourier-Transform Infrared (FTIR) and X-Rays Absorption (XAS) techniques in complement with ab initio modelling for confirming the spectral assignments. Hence, the Raman signature of Re₂O₇.2H₂O was obtained, and the evolution kinetics was investigated to provide a detailed description of the hydration process.

Cyclopentanone is a potential bio-fuel which can be produced from bio-mass. Its gas phase dissociation chemistry has attracted several experimental and theoretical investigations. In the photochemical and thermal decomposition studies of cyclopentanone, ethylene and carbon monoxide were found to be dominant reaction products along with several other compounds in smaller quantities. For the formation of ethylene and carbon monoxide, a concerted mechanism has been proposed as the primary reaction pathway. In addition, a step-wise mechanism involving ring-opened radical intermediate has also been considered. The present work reports gas phase thermal decomposition of cyclopentanone at high temperatures investigated using electronic structure theory methods, Rice-Ramsperger-Kassel-Marcus (RRKM) rate constant calculations, and Born-Oppenheimer direct classical trajectory simulations. The trajectory calculations were performed on density functional PBE96/6-31+G* potential energy surface using initial conditions selected from fixed energy normal mode distributions. Simulations showed that ethylene and carbon monoxide formed primarily via the concerted mechanism confirming the earlier predictions. In addition, step-wise pathways were also observed for the same products in lower fraction of trajectories. Furthermore, several other reaction products in smaller quantities and new mechanistic pathways were observed. The computed RRKM rate constants and simulation data are in agreement with experimental results and detailed atomic level dissociation mechanisms presented.