scholarly journals Computational Estimation of the Acidities of Pyrimidines and Related Compounds

Molecules ◽  
2022 ◽  
Vol 27 (2) ◽  
pp. 385
Author(s):  
Rachael A. Holt ◽  
Paul G. Seybold
Keyword(s):  
Density Functional ◽  
Parent Compound ◽  
Density Functional Theory Calculations ◽  
Energy Difference ◽  
Quantitative Structure Activity Relationship ◽  
Computational Estimation ◽  
Aqueous Solvent ◽  
Solvent Model ◽  
Variation Parameter ◽  
Living Organisms

Pyrimidines are key components in the genetic code of living organisms and the pyrimidine scaffold is also found in many bioactive and medicinal compounds. The acidities of these compounds, as represented by their pKas, are of special interest since they determine the species that will prevail under different pH conditions. Here, a quantum chemical quantitative structure–activity relationship (QSAR) approach was employed to estimate these acidities. Density-functional theory calculations at the B3LYP/6-31+G(d,p) level and the SM8 aqueous solvent model were employed, and the energy difference ∆EH2O between the parent compound and its dissociation product was used as a variation parameter. Excellent estimates for both the cation → neutral (pKa1, R2 = 0.965) and neutral → anion (pKa2, R2 = 0.962) dissociations were obtained. A commercial package from Advanced Chemical Design also yielded excellent results for these acidities.

scholarly journals Breakdown of chiral recognition of amino acids in reduced dimensions

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Yongchan Jeong ◽  
Hyo Won Kim ◽  
JiYeon Ku ◽  
Jungpil Seo
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Self Assembly ◽  
Density Functional ◽  
Chiral Recognition ◽  
Density Functional Theory Calculations ◽  
The Self ◽  
Reduced Dimensions ◽  
Tunnelling Microscopy ◽  
Living Organisms

Abstract The homochirality of amino acids in living organisms is one of the great mysteries in the phenomena of life. To understand the chiral recognition of amino acids, we have used scanning tunnelling microscopy to investigate the self-assembly of molecules of the amino acid tryptophan (Trp) on Au(111). Earlier experiments showed only homochiral configurations in the self-assembly of amino acids, despite using a mixture of the two opposite enantiomers. In our study, we demonstrate that heterochiral configurations can be favored energetically when l- and d-Trp molecules are mixed to form self-assembly on the Au surface. Using density functional theory calculations, we show that the indole side chain strongly interacts with the Au surface, which reduces the system effectively to two-dimension, with chiral recognition disabled. Our study provides important insight into the recognition of the chirality of amino acid molecules in life.

Insights into the Adsorption of Water and Oxygen on the Cubic CsPbBr3 Surfaces: A First-Principle Study

2021 ◽  
Author(s):  
Xin Zhang ◽  
Ruge Quhe ◽  
Ming Lei
Keyword(s):  
Adsorption Energy ◽  
Density Functional ◽  
Degradation Mechanism ◽  
Perovskite Solar Cells ◽  
Density Functional Theory Calculations ◽  
Adsorbed Water ◽  
Energy Difference ◽  
Device Fabrication ◽  
Water Molecules ◽  
Inorganic Perovskite

Abstract The degradation mechanism of the all-inorganic perovskite solar cells in the ambient environment remains unclear. In this paper, water and oxygen molecule adsorptions on the all-inorganic perovskite (CsPbBr3) surface are studied by density-functional theory calculations. In terms of the adsorption energy, the water molecules are more susceptible than the oxygen molecules to be adsorbed on the CsPbBr3 surface. The water molecules can be adsorbed on both the CsBr- and PbBr-terminated surfaces, but the oxygen molecules tend to be selectively adsorbed on the CsBr-terminated surface instead of the PbBr-terminated one due to the significant adsorption energy difference. While the adsorbed water molecules only contribute deep states, the oxygen molecules introduce interfacial states inside the bandgap of the perovskite, which would significantly impact the chemical and transport properties of the perovskite. Therefore, special attention should be paid to reduce the oxygen concentration in the environment during the device fabrication process so as to improve the stability and performance of the CsPbBr3 based devices.

A density functional theory study on the structural and electronic properties of PbxSbySez (x + y + z = 2, 3) clusters

2018 ◽  
Vol 32 (03) ◽  
pp. 1850024
Author(s):  
Rengi̇n Peköz ◽  
Şaki̇r Erkoç
Keyword(s):  
Density Functional Theory ◽  
Electronic Properties ◽  
Density Functional ◽  
Ground States ◽  
Density Functional Theory Calculations ◽  
Energy Difference ◽  
Binding Energies ◽  
Functional Theory ◽  
Structural And Electronic Properties ◽  
Scalene Triangle

The structural and electronic properties of neutral ternary PbxSbySez clusters (x + y + z = 2, 3) in their ground states have been explored by means of density functional theory calculations. The geometric structures and binding energies are systematically explored and for the most stable configurations of each cluster type vibrational frequencies, charges on atoms, energy difference between highest occupied and lowest unoccupied molecular orbitals, and the possible dissociations channels have been analyzed. Depending on being binary or ternary cluster and composition, the most energetic structures have singlet, doublet or triplet ground states, and trimers prefer to form isosceles, equilateral or scalene triangle structure.

Density Functional Calculations on the Metal-Polymer Interfaces

1993 ◽  
Vol 304 ◽  
Author(s):  
A. Selmani ◽  
A. Ouhlal ◽  
A. Yelon
Keyword(s):  
Density Functional ◽  
Vibrational Analysis ◽  
Density Functional Theory Calculations ◽  
Energy Difference ◽  
Stable Configuration ◽  
Polymer Interfaces ◽  
Functional Theory ◽  
Model Molecule ◽  
Spin Polarisation ◽  
Metal Polymer

AbstractBonding of chromium to the polyimide, PMDA-ODA, surface is still subject to debate. In an attempt to clarify this problem, we have performed density functional theory calculations on a model molecule, phthalimide, which contains the most reactive functionalities of the polyimide PMDA part. Considering only the low spin case, we find that chromium bonds preferentially to the phenyl ring. However, when we release the spin polarisation and optimise the structure, we find that the absolute stable configuration is that of chromium in a quintet state at a carbonyl group. The energy difference is 0.30 eV. The complete optimised structures are determined. The infrared spectrum have been calculated for phthalimide and compared to experimental spectra. The agreement is excellent. A vibrational analysis for the Cr/phthalimide system, in both configurations (Cr on C=O and Cr on phenyl), in their stable spin states, is presented.

scholarly journals Theoretical Study of the Effect of Water Clusters on the Enol Content of Acetone as a Model for Understanding the Effect of Water on Enolization Reaction

2021 ◽  
Author(s):  
Zahra Tohidi Nafe ◽  
Nematollah Arshadi
Keyword(s):  
Carbonyl Compounds ◽  
Density Functional ◽  
Water Clusters ◽  
Experimental Studies ◽  
Density Functional Theory Calculations ◽  
Energy Difference ◽  
Biochemical Processes ◽  
Small Water ◽  
Effect Of Water ◽  
Practical Conclusion

Abstract The enolization of simple carbonyl compounds is a key reaction for many chemical and biochemical processes. Numerous theoretical and experimental studies have been done to probe aspects of the mechanism of this reaction. In this work, the effect of small water clusters, (H2O)n: n=1-9, on the enol content of acetone is investigated by using density functional theory calculations at the M06 level of theory in the gas and solution phases. The calculations indicated that the formation of hydrogen-bonded assemblies between water clusters and both tautomers of acetone affect the enolization reaction. Among them, the trimeric water cluster has the highest binding energy difference (DEb) in the solution phase and greatly shift the equilibrium in the favor of the enol form. The results also shown that under this condition, the enol content of acetone increased by decreasing the polarity of the solvent. The practical conclusion of this study is that the enol content of carbonyl compounds can be maximized only by addition a defined amount of water.

scholarly journals Density functional theory calculations of merohedric twinning in KLiSO4

2019 ◽  
Vol 234 (4) ◽  
pp. 211-217
Author(s):  
Hans Grimmer ◽  
Bernard Delley
Keyword(s):  
Density Functional Theory ◽  
Aqueous Solutions ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Energy Difference ◽  
Boundary Plane ◽  
Temperature Phase ◽  
Functional Theory ◽  
Transformation Twins ◽  
Polysynthetic Twin

Abstract Density functional theory (DFT) calculations have been performed on five models of periodic, polysynthetic twin interfaces in the ambient-temperature phase of KLiSO4, which has space group P63. The models represent the three merohedric twin laws (m||z, 2⊥z and 1̅) with boundary plane (1 0 1̅ 0), also with boundary plane (0 0 0 1) in case of m, and with boundary plane (1 2̅ 1 0) in case of 1̅. The models satisfy stoichiometry at the boundary plane and maintain the fourfold coordination of the Li and S atoms and the twofold coordination of the oxygen atoms. Relaxed lattice parameters and atomic positions were determined by DFT, using the DMol3 code with functional PBEsol. The energy difference between polysynthetic twin and single crystal per primitive cell of the twin is 0.0009 eV for m(0 0 0 1), 0.09 eV for 1̅(1 0 1̅ 0), 0.58 eV for m(1 0 1̅ 0) and 0.55 eV for 2(1 0 1̅ 0). In KLiSO4 crystals grown from aqueous solutions the first twin was frequently observed, similarly also the second twin in Cr-doped crystals, whereas the third twin appeared only rarely and the fourth was not observed. Not only for KLiSO4 but also for quartz, the energy of twins and the frequency of their occurrence are closely connected for crystals grown from aqueous solutions, whereas for the formation of transformation twins the availability of twin nuclei plays a major role.

Keto, thione, selone, and tellone carotenoids — Changing antioxidants to antireductants

2013 ◽  
Vol 91 (7) ◽  
pp. 621-627 ◽  
Author(s):  
Ana Martínez
Keyword(s):  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Free Radical Scavengers ◽  
Oxygen Quenching ◽  
Functional Theory ◽  
Electron Transfer Mechanism ◽  
Singlet Oxygen Quenching ◽  
Vertical Ionization Energy ◽  
Vertical Electron Affinity ◽  
Living Organisms

Heterocarotenoids can be considered as xenobiotic compounds as they are foreign to living organisms. Thione carotenoids are heterocarotenoids that are particularly interesting because the presence of sulfur shifted the absorption to longer wavelengths than the corresponding keto carotenoids. This may be important for further applications such as the development of new pigments. Keto carotenoids are well-known antiradical molecules, however, nothing is known about heterocarotenoids acting as free radical scavengers. Thus, the main goal of this investigation is to study the antiradical properties of some heterocarotenoids, such as thione, selone, and tellone carotenoids. For this purpose, the energy differences between singlets and triplets are used to analyze the singlet oxygen quenching mechanism, and the electron transfer mechanism is investigated, taking into account that these may constitute antiradical molecules either donating or accepting electrons (antioxidants or antireductants). To analyze these mechanisms, vertical ionization energy (I), vertical electron affinity (A), and electrodonating (χ−) and electroaccepting (χ+) electronegativities were evaluated by applying density functional theory calculations. The investigated heterocarotenoids are as effective as keto carotenoids in terms of being either electron donors or acceptors, and therefore, they have a similar capacity for scavenging free radicals. Changing the C=O group to C=S, C=Se, or C=Te converts an antioxidant to an antireductant.

scholarly journals Screening of II-IV-V2 Materials for Photovoltaic Applications Based on Density Functional Theory Calculations

Crystals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 883
Author(s):  
Byeong-Hyeon Jeong ◽  
Minwoo Jeong ◽  
Youbin Song ◽  
Kanghyeon Park ◽  
Ji-Sang Park
Keyword(s):  
Density Functional Theory ◽  
Band Gap ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Energy Difference ◽  
Stacking Sequence ◽  
Electronic Band ◽  
Functional Theory ◽  
Photovoltaic Applications ◽  
Calculation Results

The relative stability of polymorphs and their electronic structure was investigated for II-IV-V2 materials by using first-principles density functional theory calculations. Our calculation results show that, for Zn-, Cd-, and Be-containing compounds, nitrides favor the 2H polymorph with AB stacking sequence; however, phosphides, arsenides, and antimonides are more stable in the 3C polymorph with the ABC stacking sequence. The electronic band gap of materials was calculated by using hybrid density functional theory methods, and then materials with an ideal band gap for photovoltaic applications were chosen. The experimental synthesis of the screened materials is reported, except for CdSiSb2, which was found to be unstable in our calculation. The absorption coefficient of the screened materials, especially ZnGeAs2, was high enough to make thin-film solar cells. The higher stacking fault energy in ZnGeAs2 than the others is consistent with the larger formation energy difference between the 2H and 3C polymorphs.

scholarly journals Density-Functional-Theory Calculations of Formation Energy of the Nitrogen-Doped Diamond

2018 ◽  
Vol 18 (4) ◽  
pp. 749 ◽  
Author(s):  
Sholihun Sholihun ◽  
Hana Pratiwi Kadarisman ◽  
Pekik Nurwantoro
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Formation Energy ◽  
Geometry Optimization ◽  
Density Functional Theory Calculations ◽  
Energy Difference ◽  
Stable Configuration ◽  
Functional Theory ◽  
Substitutional Site ◽  
Nitrogen Doped

The geometry optimization of the nitrogen-doped diamond has been carried out by the density functional theory (DFT) calculations. We model the defective diamond of substitutional and interstitial nitrogen atoms by using a simple-cubic supercell. Atoms in the supercell are relaxed by allowing them to move so that the atomic forces are less than 5.0 × 10-3 eV/Å. We calculate the formation energy for substitutional and interstitial sites. We find that the formation energy for the substitutional defect is10.89 eV. We check the convergence of the calculation with respect to the k×k×k - Monkhorst-Pack grids. We show that the energy difference between k = 4 and 6 is very small (7.0 meV). We also check the calculations by using a 216-sites supercell and find that the energy difference is 0.10 eV. Thus, the calculations of the formation energy converge well. As for the interstitial defect, we model some possible configurations and find that the smallest formation energy is 21.88 eV. Therefore, the most stable configuration of the nitrogen-doped diamond belongs to the substitutional site.

scholarly journals Using the Isalos platform to develop a (Q)SAR model that predicts metal oxide toxicity utilizing facet-based electronic, image analysis-based, and periodic table derived properties as descriptors

2021 ◽  
Author(s):  
M. M. Thwala ◽  
A. Afantitis ◽  
A. G. Papadiamantis ◽  
A. Tsoumanis ◽  
G. Melagraki ◽  
...  
Keyword(s):  
Metal Oxide ◽  
Metal Oxides ◽  
Density Functional ◽  
Chemical Potential ◽  
Metal Oxide Nanoparticles ◽  
Experimental Studies ◽  
Density Functional Theory Calculations ◽  
Quantitative Structure Activity Relationship ◽  
Engineered Nanoparticles ◽  
Metal Oxide Nanoparticle

AbstractEngineered nanoparticles (NPs) are being studied for their potential to harm humans and the environment. Biological activity, toxicity, physicochemical properties, fate, and transport of NPs must all be evaluated and/or predicted. In this work, we explored the influence of metal oxide nanoparticle facets on their toxicity towards bronchial epithelial (BEAS-2B), Murine myeloid (RAW 264.7), and E. coli cell lines. To estimate the toxicity of metal oxide nanoparticles grown to a low facet index, a quantitative structure–activity relationship ((Q)SAR) approach was used. The novel model employs theoretical (density functional theory calculations) and experimental studies (transmission electron microscopy images from which several particle descriptors are extracted and toxicity data extracted from the literature) to investigate the properties of faceted metal oxides, which are then utilized to construct a toxicity model. The classification mode of the k-nearest neighbour algorithm (EnaloskNN, Enalos Chem/Nanoinformatics) was used to create the presented model for metal oxide cytotoxicity. Four descriptors were identified as significant: core size, chemical potential, enthalpy of formation, and electronegativity count of metal oxides. The relationship between these descriptors and metal oxide facets is discussed to provide insights into the relative toxicities of the nanoparticle. The model and the underpinning dataset are freely available on the NanoSolveIT project cloud platform and the NanoPharos database, respectively.

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