Structural Chemistry最新文献

Density functional theory tight binding molecular dynamics (DFTB-MD) and density functional theory (DFT) are used to study the mechanisms of configuration transformation of ε-2,4,6,8,10,12-hexanitro-2,4,6,6,8,10,12-hexaazaisowurtzitane (ε-CL-20) molecule under the effects of toluene and acetone. DFTB-MD results show that a series of configuration transformations occur to ε-CL-20 molecule in ε-CL-20/toluene solution, which is transformed to γ-CL-20 firstly, then to ζ-CL-20, and finally to ω-CL-20, while ε-CL-20 is transformed to α-CL-20, and finally to ω-CL-20 in ε-CL-20/acetone solution. The DFT calculation results indicate that the ε → γ(α) → ζ → ω transformation of ε-CL-20 molecule is thermodynamically feasible. Because γ(α)-CL-20 molecule is thermodynamically the most stable during γ(α)-, ζ-, and ω-CL-20 molecules, only transformation of ε-CL-20 molecule from configuration ε- to γ(α)- has occurred in experiments. Both Bader’s atoms in molecules (AIM) and independent gradient model (IGM) analyses indicate that the C-H···O type hydrogen bond is the main intermolecular interaction in the CL-20/solvent dimer and plays a major role in the formation of the dimer. This work reveals the configuration transformation mechanism of energetic molecules affected by solvent at the micro level, providing theoretical guidance for the preparation of pure form energetic crystals.

In order to explore novel porphyrins with excellent conductivity and selective light absorption, the influence of metal atom embedding and functional group attachment on the electronic and optical characteristics of porphyrins has been concerned. In this study, the structures, electronic, and optical properties of the 2,7,12,17-tetrakis(pinacolatoboryl) porphyrin and its derivatives have been investigated using density functional theory (DFT). The N–Ni–N bond angles of the derivatives are mostly close to 90.00°, with the exception of the N6-Ni5-N9 bond angle (45.09°) for the Ar and Br co-attached porphyrins (5 porphyrins). Additionally, the calculated ruffling displacements (druf) for the 2, 3, 5, and 6 porphyrins are 1.2691 Å, 1.1427 Å, − 1.2561 Å, and 0.5139 Å, respectively. The lowest frequency out-of-plane (oop) normal deformation of the 4 porphyrins is a waving motion with a displacement of 0.0532 Å. The energy gaps for the 1–6 porphyrins are similar, ranging from 4.44 to 4.80 eV. The presence of Br atoms promotes the Hirshfeld charge transfer between the C atoms within the macro-cycle of the Ar and Br co-attached porphyrins and the Ar functional groups. Furthermore, the Ar attached porphyrins exhibit a 20-nm red-shift compared to the Bpin-attached porphyrins. The addition of Br leads to an additional about 6-nm red-shift compared to the Ar-attached porphyrins. This is advantageous for expanding the application of porphyrins in industrial fields such as sensors and photocatalysts.

Dyes play multiple roles in dye-sensitized solar cells (DSSCs); however, the rational design of efficient dyes is highly challenging due to the sophisticated optoelectronics physics and electrochemistry phenomena. In this work, Ru (II) complexes modified by arylamine groups were used to study the structure-performance relationship. Density functional theory (DFT) and time-dependent DFT methods were employed to calculate the geometries, electronic structures, and optical properties of dyes, while quantum dynamic simulation was conducted to study the interfacial electron transfer (IET) in dye/TiO₂ combined systems. The calculated results suggest that dyes with electron-donating N,N-dibenzyl-aniline and piperidine-modified arylamine groups induce effective intermolecular charge transfer, quickening the IET rate and elevating the TiO₂ conduction band (CB) edge, thus augmenting short-circuit current (J_sc) and open-circuit voltage (V_oc). The N-phenylcarbazol ligand is not suitable for modifying dyes due to weak interfacial electron coupling and invalid IET rate. The simulation highlights the potential of structurally modified Ru-dyes with N,N-dibenzyl-aniline and piperidine ligands, and provides a method for designing and screening high-performance DSSC dyes.

Computational analysis of nine designs of triphenylamine-based sensitizers with donator-π-bridge-acceptor (D-π-A) structure for dye-sensitized solar cells (DSSC) was carried out via density functional theory (DFT). The purpose of this work was the modification of dye CP-II to improve the properties in DSSC with a series of changes using halogens like fluorine and chlorine in the donor group and chalcogens in the π-bridge. M06/6-31G(d) and M06/6-31G(d) + DZVP levels of calculation were utilized to determine ground state geometry optimization, frontier molecular orbitals, and their energy levels. The LUMO levels ranged from − 2.402 to − 2.568 eV, making them suitable for electron injection into the TiO₂ conduction band. Chemical reactivity parameters such as chemical hardness (η), electrophilicity index (ω), electroaccepting power (ω⁺), and electrodonating power (ω⁻) were studied. After their analysis, these values proved suitable for use as sensitizers. The free energy of electron injection (∆G_inject) was calculated with values between 1.203 and 1.683 eV, indicating a sufficient driving force for electron injection. Light-harvesting efficiency (LHE) and excited-state lifetime (τ) were estimated and analyzed. Time-dependent density functional theory (TD-DFT) with M06-2X/6-31G(d) and M06-2X/6-31G(d) + DZVP levels of calculation were used to determine the absorption wavelengths, oscillator strengths, and electron transitions. The incorporation of tellurium and selenium in the π-bridge reduced the HOMO–LUMO gap, enhanced charge transfer, and increased chemical stability. The best-performing sensitizer, MeTTe, exhibited a HOMO–LUMO gap of 2.715 eV, a high electrophilicity index (3.51 eV), and a long excited-state lifetime (9.73 ns).

The FT-IR, FT-Raman, and UV–Vis spectra of bis(benzimidazolium) maleate (BM) were analysed. Quantum computations with the DFT methodology were used for finding the stable conformer and structural optimization deploying the Gaussian '09 software. An X-ray diffraction study on a single crystal revealed that the grown crystal is an orthorhombic system with a space group. To examine the numerous intra- and intermolecular interactions in a molecular system, natural bond orbital (NBO) analysis is performed. After completing normal coordinate analysis to identify the vibrational modes, PED assignments were established. According to vibrational analysis, the stretching wavenumber of hydrogen bond donor NH and hydrogen bond acceptor CO₂ is red-shifted due to interaction. DOS spectral analysis is used to investigate the molecular orbital contributions. The HOMO–LUMO analysis is used to determine the studied compound’s conductivity, reactivity, and stability. The COO⁻ groups are vulnerable to electrophilic attack, whereas the NH group in the benzimidazolium ring is probably nucleophilic, according to the MEP plot, Fukui function, and natural population analysis. The Kirby-Bauer disc diffusion technique was used to determine the antifungal activity of the BM against Candida albicans and Aspergillus niger fungal pathogens. Molecular docking studies were used to elucidate the interaction between ligands and proteins. According to ADME parameter analysis and the Lipinski rule for the BM molecule, the chemical possesses good drug-like qualities and could eventually be developed into an antifungal medication.

In the current work, a novel one-dimensional group VA-VA nanotube material is deployed to adsorb the hazardous amine using the density functional theory (DFT) method. Initially, the phonon band spectrum and formation energy are used to confirm the structural stability of the β-SbP-NT. Furthermore, by using projected-density-of-states (PDOS) maps and band structure, the electronic properties of pristine β-SbP NT are examined. The computed band gap value of pristine β-SbP-NT is 1.969 eV which confirms the semiconducting nature of the material. Owing to the semiconducting nature of β-SbP-NT, it is being used to detect dimethylamine (DMA) and trimethylamine (TMA). The adsorption of DMA and TMA on β-SbP-NT is studied with adsorption energy, Mulliken charge transfer analysis, and relative band gap variation. Based on the findings, it is clear that β-SbP-NT can be used to sense the DMA and TMA in the air environment.

Two possible model reaction mechanisms of trimethylphosphine-catalyzed oxa-Michael addition of phenol and methanol to acrolein, one in which trimethylphosphine acts as a nuclephile and adds to acrolein to generate the enolate anion (mechanism 1) and the other in which trimethylphosphine acts as a base and reacts with the hydroxyl compound to generate PhO⁻ /MeO⁻ anion (mechanism 2), were computed in the gas phase using the B3LYP functional and the ωB97XD functional which incorporates dispersion correction, with the same basis set, 6–31 + G(d). In mechanism 1, the third step involving the attack of PhO⁻ or MeO⁻ on the intermediate, Int.2 accompanied by the loss of Me₃P occurring through TS3 is the rate-determining step. In this case, however, the activation free energy for the attack of PhO⁻ is found to be smaller than for MeO⁻, which is contrary to the experimental results wherein methanol is reported to react faster than phenol. In mechanism 2, the second step involving nucleophilic attack of the PhO⁻ or MeO⁻ anion on C3 of acrolein via TS2’ is the rate-differentiating step vis-à-vis the reactions of phenol and methanol with acrolein. In this case, the activation free energy barrier for PhO⁻ is much higher than for MeO⁻; in fact, the reaction with latter is found to be barrierless. It is in perfect compliance with the experimental results. These results indicate that trimethylphosphine-catalyzed oxa-Michael addition of phenol and methanol with acrolein occurs via the mechanism in which phosphine acts as a base. Acetonitrile is found to lower the activation energies.

Searching for novel materials with high efficiency as electrocatalysts in the field of water splitting is one of the most effective approaches to mitigate energy problems. In this study, we present the impact of transition metal (TM = Mn, Fe, Co, and Ni) decoration on the potential of biphenylene (BP) as a water-splitting electrocatalyst using density functional theory. We first present the structural and electronic properties of the TM-decorated BP monolayers. Our results show that TM decoration can influence the frontier orbitals of pristine BP, leading to a reduced energy gap due to charge transfer from TM to the BP surface. In the hydrogen evolution reaction (HER) section, the lowest ΔG for hydrogen adsorption as an intermediate was obtained for Co@BP at 0.26 eV, which is lower than that of pristine BP and graphene reported in previous studies. On the other hand, evaluating the oxygen evolution reaction (OER) electrocatalytic activity of TM-decorated BP monolayers reveals that Mn decoration is an efficient approach, among the selected transition metals, to improve the catalytic performance of BP. Our study introduces a procedure for the rational design of high-performance single-atom catalyst (SAC) materials.

In this work, we present and test a procedure for generating a chemical virtual library and its subsequent use to select molecular systems with desired properties. The library consists of molecular structures generated from a set of chemical fragments. As an example, we consider two tasks. The first one involves identifying structures with specific spectral properties, particularly concerning the UV–Vis region of the spectrum. To address this, the thiophene cycles with typical donor (dimethylamino) and acceptor (nitro) substituents are chosen as the molecular building blocks. First, the molecules from the derived virtual library are subject to computational screening using the semi-empirical tight binding density-functional method. The primary objective of the screening is to identify molecular structures that exhibit desired spectral properties, especially absorption in the long-wavelength region. Second, for the most promising structures identified in the initial screening, more accurate TD-DFT (B3LYP/cc-pVDZ) calculations are performed. Additionally, the advantage of the developed approach for library generation, aimed at further investigation of biological activity, is illustrated using an example involving papain-like protease (PLpro) inhibitors of the SARS-CoV-2 virus. The calculation scheme used in the considered examples is implemented in the Python program suite QUASAR.