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In this study, we present an accurate protocol for the fast prediction of p's of carboxylic acids based on the linear relationship between computed atomic charges of the anionic form of the carboxylate fragment and their experimental p values. Five charge descriptors, three charge models, three solvent models, gas-phase calculations, several DFT methods (a combination of eight DFT functionals and fifteen basis sets), and four different semiempirical approaches were tested. Among those, the best combination to reproduce experimental p's is to compute the natural population analysis atomic charge using the solvation model based on density model at the M06L/6-311G(d,p) level of theory and selecting the maximum atomic charge on the carboxylic oxygen atoms ( = 0.955). The applicability of the suggested protocol and its stability along geometrical changes are verified by molecular dynamics simulations performed for a set of aspartate, glutamate, and alanine peptides. By reporting the calculated atomic charge of the carboxylate form into the linear relationship derived in this work, it should be possible to accurately estimate the amino acid's p's in a protein environment.
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http://dx.doi.org/10.1021/acs.jcim.1c00059 | DOI Listing |
J Phys Chem C Nanomater Interfaces
December 2024
Department of Materials Science, University of Milano-Bicocca, Via Roberto Cozzi 55, 20125 Milano, Italy.
The adsorption of (X = Ni, Pd, and Pt) nanoclusters is simulated by using first-principles methods on MgO(100) and on a MgO monolayer supported on Ag(100), considering the presence of interfacial oxygen. On both the free-standing MgO surface and MgO/Ag, all clusters exhibit robust adhesion and negative charge transfer. molecular dynamics calculations at 200 K demonstrate the stability of the nanoparticles on the MgO/Ag support.
View Article and Find Full Text PDFJ Phys Chem C Nanomater Interfaces
December 2024
Department of Chemical and Process Engineering, University of Strathclyde, 75 Montrose Street, Glasgow G1 1XJ, U.K.
Chitosan is a nontoxic biopolymer with many potential biomedical and material applications due to its biodegradability, biocompatibility, and antimicrobial properties. Here, fully atomistic molecular dynamics simulations and enhanced sampling methods have been used to study the adsorption mechanism of chitosan oligomers on a silica surface from an aqueous solution. The free energy of adsorption of chitosan on a silica surface was calculated to be 0.
View Article and Find Full Text PDFAngew Chem Int Ed Engl
December 2024
Chinese Academy of Sciences, State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350608, P. R. China., CHINA.
Coordination polymers (CPs) are promising for direct X-ray detection and imaging owing to higher designability and outstanding stability, however, it remains a challenge to achieve highly X-ray detection performance, particularly both high sensitivity and low detection limit at the same operating voltage. Herein, we construct a new conjugated CP {[Co(BPTTz)(DIPA)] DMA}n (1, BPTTz = 2,5-bis(pyridine-4-yl)thiazolo[5,4-d]thiazole, H2DIPA = 2,5-diiodoterephthalic acid, DMA = N, N'-dimethylacetamide), with multi-channel charge transfer by regulating the linker mediated electronic-state, which reduces carrier losses resulting from recombination or quenching, enhances the efficiency of charge separation and transfer, thus further optimizes X-ray detection performance. The semiconductor prepared based on this strategy achieves record values including the highest mobility-lifetime product (μτ, 8.
View Article and Find Full Text PDFJ Phys Chem A
December 2024
DTU Chemistry, Technical University of Denmark, Kemitorvet Bldg. 206, 2800 Kgs., Lyngby 2800, Denmark.
We present a new theory for partitioning simulations of periodic and solid-state systems into physically sound atomic contributions at the level of Kohn-Sham density functional theory. Our theory is based on spatially localized linear combinations of crystalline Gaussian-type orbitals and, as such, capable of exposing local features within periodic electronic structures in a more intuitive and robust manner than alternatives based on the spatial distribution of atomic basis functions alone. Early decomposed cohesive energies of both molecular polymers and different crystalline polymorphs demonstrate how the atomic properties yielded by our theory convincingly align with the expected charge polarization in these systems, also whenever partial charges and Madelung energies may lend themselves somewhat ambiguous to interpretation.
View Article and Find Full Text PDFLangmuir
December 2024
School of Materials, Sun Yat-sen University, Shenzhen 518107, China.
Hydrogen sulfide (HS), carbonyl sulfide (COS), and dimethyl sulfide (DMS) are the primary sulfur compounds found in seawater, which cause pitting corrosion on the oxide passivation film of titanium, known as "the marine metals". In this study, density functional theory (DFT) was used to analyze the adsorption and surface electronic properties of these three small molecules on the anatase TiO(101) surface. The analysis was conducted through adsorption energy, work function, Mulliken charge population, and density of states (DOS).
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