Frontier Orbitals and Charges Approaches in Electrophilic Aromatic Substitution: The Cases of Anisole and Benzaldehyde

Spectroscopic (FT-IR, FT-Raman, UV, NMR, NLO) investigation, molecular docking and molecular simulation dynamics on 1-Methyl-3-Phenylpiperazine

Spectroscopic (FT-IR, FT-Raman, UV, NMR, NBO, NLO) investigation and molecular docking study of (R)-2-Methylamino-1-Phenylethanol (Halostachine)

Spectroscopic (FT-IR, FT-Raman, UV, NMR, NLO) investigation and molecular docking study of 1-(4-Methylbenzyl) piperazine

Spectroscopic (FT-IR, FT-Raman, UV, NMR, NBO) investigation and molecular docking study of (R)-2-Amino-1-PhenylEthanol

Influence of basis sets on electron affinities (EAs) of DNA and RNA bases has been investigated using density functional method (B3LYP functional) with different basis sets (6-31G, TZVP and 6-311+ + G**). Effect of some PBE functionals namely, PBEOP, PBELYP and PBEVWN, on EA values of the nucleobases was studied using basis set which predicted the most reliable values with B3LYP functional. Observation of the trends in the values of EA and dipole moment of the molecules enable us to identify the features of a basis set that shows the presence of dipole-bound state of some of the nucleobases. The vertical electron affinities with B3LYP and PBEOP functionals are close to the experimental values. The adiabatic electron affinities of uracil and thymine were found to be positive for basis set with diffuse functions using B3LYP functional. Adenine does not have a stable covalently bound anion at all levels of basis sets and functionals. The sign of adiabatic electron affinity value of cytosine is inconsistent with that of experimental value but in agreement with previous theoretical results. For guanine the adiabatic electron affinity value with 6-311+ + G** basis set was found to be very high as comparison with other two basis sets confirming the formation of mixed covalent-dipole character.

A comparative study of structure and electrostatic potential of hydrogen-bonded clusters of neutral ammonia, (NH 3) n ( n=2–6)

The pKa's of substituted thiols are important for understanding their properties and reactivities in applications in chemistry, biochemistry, and material chemistry. For a collection of 175 different density functionals and the SMD implicit solvation model, the average errors in the calculated pKa's of methanethiol and ethanethiol are almost 10 pKa units higher than for imidazole. A test set of 45 substituted thiols with pKa's ranging from 4 to 12 has been used to assess the performance of 8 functionals with 3 different basis sets. As expected, the basis set needs to include polarization functions on the hydrogens and diffuse functions on the heavy atoms. Solvent cavity scaling was ineffective in correcting the errors in the calculated pKa's. Inclusion of an explicit water molecule that is hydrogen bonded with the H of the thiol group (in neutral) or S(-) (in thiolates) lowers error by an average of 3.5 pKa units. With one explicit water and the SMD solvation model, pKa's calculated with the M06-2X, PBEPBE, BP86, and LC-BLYP functionals are found to deviate from the experimental values by about 1.5-2.0 pKa units whereas pKa's with the B3LYP, ωB97XD and PBEVWN5 functionals are still in error by more than 3 pKa units. The inclusion of three explicit water molecules lowers the calculated pKa further by about 4.5 pKa units. With the B3LYP and ωB97XD functionals, the calculated pKa's are within one unit of the experimental values whereas most other functionals used in this study underestimate the pKa's. This study shows that the ωB97XD functional with the 6-31+G(d,p) and 6-311++G(d,p) basis sets, and the SMD solvation model with three explicit water molecules hydrogen bonded to the sulfur produces the best result for the test set (average error -0.11 ± 0.50 and +0.15 ± 0.58, respectively). The B3LYP functional also performs well (average error -1.11 ± 0.82 and -0.78 ± 0.79, respectively).

A Green's function formalism incorporating broadened density of states (DOS) is proposed for the calculation of electrical conductance. In cluster-molecule-cluster systems, broadened DOS of the clusters are defined as continuous DOS of electrodes and used to calculate Green's function of electrodes. This approach combined with density functional theory is applied to the electrical transmission of gold atomic wires and molecular wires consisting of benzene-1,4-dithiolate, benzene-1,4-dimethanethiolate, 4,4(')-bipyridine, hexane dithiolate, and octane dithiolate. The B3LYP, B3PW91, MPW1PW91, SVWN, and BPW91 functionals with the LANL2DZ, CEP, and SDD basis sets are employed in the calculation of conductance. The width parameter was successfully determined to reproduce the quantum unit of conductance 2e(2)/h in gold atomic wires. The combination of the B3LYP hybrid functional and the CEP-31G basis set is excellent in reproducing measured conductances of molecular wires by Tao et al. [Science 301, 1221 (2003); J. Am. Chem. Soc. 125, 16164 (2003); Nano Lett. 4, 267 (2004)].

In this work, electrophilic substitution and oxidation reactions with benzeneselenyl bromide (BSB) and benzeneselenyl chloride (BSC) were applied in peptide synthesis. Using the electrophilic substitution reaction, BSB and BSC modified the cysteine (Cys) residue to generate a (phenylselenenyl)sulfide group in the peptide. This group then reacted with the Cys residue of another peptide, affording either an asymmetric or symmetric intermolecular disulfide bond. Furthermore, both BSB and BSC can react with either two acetamidomethyl (Acm)-protected Cys residues (Cys(Acm)) or one 1,3-thiazolidine-4-carbonyl (Thz) group and one Cys(Acm) residue in acidic media. This reaction proceeds via the electrophilic substitution to form two (phenylselenenyl)sulfide groups in the peptide. These groups subsequently disproportionated to form an intramolecular disulfide bond. By utilization of the oxidation reaction, a pair of free Cys residues were oxidized to generate the intramolecular disulfide bond in the peptide. By combining the electrophilic substitution and oxidation reaction, two disulfide bonds were chemoselectively and regioselectively constructed in a-conotoxin IMI, a-conotoxin SI, a methionine-containing peptide, and apamin via a one-pot manner. Excellent yields of these peptides were achieved. Moreover, no oxidation reactions occurred on tryptophan (Trp), methionine (Met), or tyrosine (Tyr) residues in peptides.

This article presents an experimental investigation and theoretical analysis of the electronic absorption spectra of the indicator nitrazine yellow (NY) in aqueous solutions. Quantum chemical modeling of electronically excited states is performed within the framework of time-dependent density functional theory (TD-DFT). A variety of approaches and basis sets are explored, particularly focusing on the B3LYP and CAM-B3LYP functionals. The standard 6-31+G(d,p) basis set is employed, along with combinations using pseudopotential basis sets for Na and S atoms. In the first variant of calculations, the LanL2DZ basis set (and corresponding pseudopotential) is used for all atoms within the molecules. In the second variant, the LanL2DZ basis set is applied exclusively to Na and S atoms, while the standard valence double-zeta split basis set 6-31+G(d,p) is utilized for the remaining elements (H, C, N, O). Solvent effects on the absorption spectra are incorporated using the polarizable continuum model, employing the linear response method. Calculations are performed on three forms of NY. Two of these forms (A and B) correspond to azo-hydrazone tautomerism, while the third form (C) represents the deprotonated state. Ground state geometry calculations indicate that the π-conjugated part of form A is largely planar and stabilized by an intramolecular hydrogen bond O-H...N. The tautomeric form B is also characterized by a high degree of planarity in its conjugation system. In contrast, the deprotonated form C shows significant rotation of the 2,4-dinitrophenyl group and the nitro group in the ortho position of the benzene ring. Analysis of excited-state calculations for the three forms of NY reveals that both variants (B3LYP/LanL2DZ and B3LYP/LanL2DZ/6-31+G(d,p)) require minimal computational resources while producing results that correspond well with the experimentally observed absorption bands.

Assessment of the performance of commonly used DFT functionals vs. MP2 in the study of IL-Water, IL-Ethanol and IL-(H2O)3 clusters

This paper undertakes the synthesis by slow evaporation method at room temperature of a new organic–inorganic hybrid material with the general formula [C12H13N2O]H2AsO4. The newly developed hybrid is characterized by X-ray single crystal diffraction, Infrared, Raman spectroscopy and density functional theory (DFT) calculations. At ambient temperature, this compound crystallizes in the non-centrosymmetric space group P212121 of the orthorhombic system. The structural arrangement is formed by infinite anionic chains extending parallel to the direction [100]. The organic entities are linked to these chains by N–H···O type hydrogen bonds which play an important role in the cohesion of the one-dimensional network. The optimized molecular structure, vibrational spectra and the optical properties were calculated by the DFT method using the B3LYP function with the LanL2DZ basis set. The vibrational wavenumbers were evaluated for this compound by using transferable scale factor. The first hyperpolarizability value βtot of the title compound is equal to 15.94 × 10−31 esu. Hence, the large β value calculated by the B3LYP method shows that the studied compound is a good NLO material and is suitable for future non-linear optical studies. The HOMO–LUMO energy gap and other related molecular properties are going to be discussed and reported later.

Molecular structure, X-ray crystallography, spectroscopic characterization, solvent effect, NLO, NBO, FMO analysis of [Cu(bpabza)] complexe

Conventional image resizing problems demand hard conditions on size and aspect ratio, which must be met with no tolerance. In this paper, a generalized optimization framework is presented, which can handle soft conditions as well as the hard ones. The soft condition can be given by an allowable range of the image parameter, which is incorporated as an inequality condition in the constrained optimization framework. Given the soft constraints, the proposed framework seeks to find the set of image parameters that minimize the cost function. A constrained optimization via a linear programming framework is employed to manage a diverse combination of soft and hard conditions for the target image. The optimization is based on the image line, which optimally selects a set of image lines (columns and rows) to be deleted for size reduction in accordance with the cost function and the constraints. As a case study, the line-based optimal image resizing method based on the linear programming framework is applied for the pre-processing of VGG-19 convolutional neural network (CNN). Although the target input size is a hard condition of $224\times 224$ for the VGG-19 CNN, the proposed optimization framework with a soft condition on the image size firstly finds an optimal near-square image with a tradeoff against the saliency level of image features. Then, the optimal near-square image is linearly scaled to the final image size to meet the hard condition.

Structural and spectroscopic analysis of the Cis-Trans isomers of the captopril in the gaseous and aqueous phases