Theoretical Chemistry Accounts最新文献

Abstract

This study investigates the supramolecular interactions between perylene diimides (PDI) and nucleotides, specifically adenosine monophosphate (AMP) and cytidine monophosphate (CMP). Ten complexes (complex 1 (l-ala-PDI-AMP), complex 2 (B-ala-PDI-AMP), complex 3 (GLY-PDI-AMP), complex 4 (IMI-PDI-AMP), complex 5 (PYR-PDI-AMP, complex 6 (l-ala-PDI-CMP), complex 7 (B-ala-PDI-CMP), complex 8 (GLY-PDI-CMP), complex 9 (IMI-PDI-CMP), and complex 10 (PYR-PDI-CMP), were simulated using the B3LYP/6-31G(d,p) level of DFT method. The study explores NMR, IR, UV, hyperpolarizabilities, frontier molecular orbitals (FMOs), density of states (DOS), noncovalent interactions (NCI), iso-surface analysis, atom in molecule (AIM), dipole moment (µ), electron density distribution map (EDDM), transition density matrix (TDM), molecular electrostatic potential (MEP), and electron–hole analysis (EHA) using differential functional theory (DFT). The weak bonds formed were visualized using Discovery Studio Visualizer. The electronic properties of the complexes were examined through natural bond orbital (NBO) and natural population analysis (NPA), leading to nonlinear optics (NLO) study. Complex 6 demonstrates the highest NLO activity with γ static of 17,424,700.00, and complex 10 exhibits the weakest NLO activity with second dipole hyperpolarizability (γ static) at 25,116.10. Moreover, global reactivity factors for complexes 1–5 show EA ranging from 6.53 to 7.7, and ionization potential (IP) spans 7.8–8.8. Global hardness values highlight complex 4 as the hardest (η = 0.55) and complex 1 as the softest (η = 0.51). Electronegativity (X) varies from 7.28 to 8.25, with complex 3 being the most electronegative. Chemical potential (μ) ranges from − 7.9 to − 8.25, global softness (σ) identifies complex 1 as the softest (0.2575) and complex 4 as the hardest (0.435). Electrophilicity (ω) ranges from 33.30 to 61.87. Complexes 6–10 show EA from 6.7 to 7.53. IP values range from 8.4 to 8.6, with complexes 7 and 10 highest. Global hardness spans 0.53 to 0.85. X ranges from 7.55 to 8.06, with complex 7 the most electronegative. μ varies from − 7.55 to − 8.06, and complex 7 has the lowest. From σ values, complexes 9 and 10 are the softest. ω ranges from 35.53 to 60.78, with complex 7 the most electrophilic.

The anti (a) to syn (s) isomerization pathway of the deprotonated form of the dimer with two nickel(II) 15-membered octaazamacrocyclic units connected via a carbon–carbon (C–C) σ bond was investigated. For the initial anti (a) structure, a deprotonation of one of the bridging (sp³ hybridized) carbon atoms is suggested to allow for an a to s geometry twist. A 360° scan around the bridging C–C dihedral angle was performed first to find an intermediate geometry. Subsequently, the isomerization pathway was explored via individual steps using a series of mode redundant geometry optimizations (internal coordinates potential energy surface scans) and geometry relaxations leading to the s structure. The prominent geometries (intermediates) of the isomerization pathway are chosen and compared to the a and s structures, and geometry relaxations of the protonated forms of selected intermediates are considered.

The tri-nuclear heterometallic tetrahedral cluster [Mo–Ru–Co(µ₃–S)(CO)₈(Cp)COOCH₃] (Cp = η⁵-C₅H₄) was studied employing quantum theory of atoms in molecules (QTAIM) to examine bonding interactions, including metal–metal (M–M), metal–sulfur (M–S), metal–carbonyl (M–CO), and metal–cyclopentadienyl (M–Cp) interactions. The electron density of bonding interactions within the cluster has its topological properties calculated based on this theory. Interestingly, the computed local topological characteristics for the Mo–Ru bond show notable distinctions in comparison to the parameters for interactions involving Mo–Co and Ru–Co, since for the latter, critical points and paths were not observed. The distribution of electron density was notably affected by the presence of bridging sulfide ligands in Mo…Co, Ru…Co interactions, much more than in the Mo–Ru bond. The characteristics of the latter bond exhibited attributes typical of interactions between open-shell metals. These features included slightly positive values for ρ_(b) and ∇²ρ_(b), along with small negative values of H_(b)/ρ_(b) approaching zero. Additionally, using the source function (SF) and electron localization function (ELF) methods, more focus has been given to the Mo–Ru bond. The core part, [Mo–Ru–Co(µ₃–S)], was found to have a multicenter 4c–6e interaction. In this core, the three M–S bonds between the metal atoms and the sulfide ligand showed similar topological parameters that were typical of open-shell (covalent) interactions. Substantial π–back donation from CO to M was identified through the execution of δ(M…O_CO) delocalization index calculations.

Abstract

In the realm of studying supramolecular polymers using computer simulations, the task of generating appropriate initial structures poses a significant challenge, primarily owing to the extensive range of potential configurations. In this study, we introduce StackGen, an open-source framework designed to efficiently create energy-optimized one-dimensional supramolecular polymer structures with minimal computational overhead. This tool utilizes the particle swarm optimization (PSO) algorithm in conjunction with a semiempirical quantum mechanical approach to identify low-energy supramolecular stack configurations from a diverse set of possibilities. These configurations result from the translational and rotational adjustments of adjacent molecules around monomers along various axes. The tool also considers various structural factors, including the presence of functional side groups and the extent of intermolecular (pi) – (pi) stacking interactions. Extensive testing across different molecules demonstrates StackGen’s ability to produce low-energy structures with negligible computational costs. Additionally, the tool incorporates features for optimizing PSO hyperparameters in real-time, thus improving convergence. The tool provides a convenient means of generating structures suitable for both molecular simulations and quantum mechanical calculations.

Cyclotrisilenes can pursue four types of reaction pathways with unsaturated substrates: π-addition, σ-insertion, exocyclic σ-insertion, and ring-opening reactions. A computational investigation of all these reaction pathways of 1,2,3,3-tetramethyl cyclotrisilene c-Si₃Me₄ (I) and 1,2-bis(trimethylsilyl)-3,3-dimethyl cyclotrisilene c-Si₃Me₂(SiMe₃)₂ (II) with phenylacetylene (R1) and benzaldehyde (R2) is carried out. The reaction pathways are found to be significantly influenced by the substituents attached to the cyclotrisilene ring. Both the π-addition and the σ-insertion reactions proceed with moderate activation energy and high exoergicity, and the electronic nature of the functional group is crucial in deciding the favorable pathway. The exocyclic σ-insertion reactions are found to possess a huge energy barrier, irrespective of the steric and electronic nature of cyclotrisilenes and the substrates. While the course of the reaction and the viability of the ring-opening reaction with phenylacetylene are impacted by the nature of cyclotrisilene, the ring-opening reactions of I and II with benzaldehyde are both highly endoergic.

NH₃ is the most basic raw material in industrial and agricultural production, and it is also an excellent hydrogen carrier. The high energy consumption and pollution of traditional NH₃ synthesis methods limit their further development. As an environmentally friendly and efficient industrial technology, electrocatalysis has important application value in the field of green energy storage and conversion. Therefore, the development of electrocatalysts with high activity, good stability and low cost is the key to improve the efficiency of the nitrogen reduction reaction (NRR) to generate NH₃. Herein, a series of transition metal clusters loaded onto the di-vacancy graphene (X_mY_n@Gra(X, Y = Fe, Co and Ni; m + n = 3)) as electrocatalysts were designed. By calculating the free energy of the first and last hydrogenation steps, it was found that NiCo₂@Gra and FeCo₂@Gra had the best catalytic activity. The first hydrogenation process from *N₂ to *N₂H was potential-determining step, and the corresponding limiting potentials were − 0.57 and − 0.51 V, respectively. In addition, the reasons for the high catalytic activity of NiCo₂@Gra and FeCo₂@Gra were further elucidated by analyzing the electronic properties. This study provides a new strategy for the use of cluster catalysts in NRR process and a new idea for the fixation and conversion of N₂.

This study focuses on conducting a comparative study of the extraction capacities of alizarin-oxalate (AR-Ox) ligands with La³⁺ and Nd³⁺ in acidic, neutral, and alkaline mediums. Density functional theory calculations at ωB97X-D/6-311++G(d,p)/SDD level have been performed for structural, thermochemical, frontier-orbital (highest occupied molecular orbitals and lowest unoccupied molecular orbitals), natural bond orbital, reduced density gradient (RDG), and density of state analysis for alizarin-oxalate-La(III) (AR-Ox-La) and alizarin-oxalate-Nd(III) (AR-Ox-Nd) complexes. The bonding characteristics of La³⁺ & Nd³⁺ ions with alizarin-oxalate ligand have been analysed using the quantum theory of atoms in molecules, revealing the presence of an intermediate type of bond between closed-shell and shared-shell electrons in (La/Nd)-O, (La/Nd)-C. The reduced density gradient (RDG) and iso-surface generated through the Multiwfn program shows mostly hydrogen-like and van der Waals interaction between La³⁺/Nd³⁺ and oxygen atoms of alizarin-oxalate ligand except for some of the complexes showing the presence of non-bonded/repulsive (La/Nd)-O interaction. Thermochemical, DOS, and natural bond orbital analysis reveals alizarin-oxalate-(La³⁺/Nd³⁺) complexes in the alkaline medium is more stable than in neutral and acidic medium, and the stability of AR-Ox-Nd complexes is more than AR-Ox-La complexes. It is observed that participation of oxygen atoms from both alizarin and oxalate in bond formation with lanthanides enhances the stability of alizarin-oxalate-lanthanide complexes, emphasizing the pivotal role of ligand coordination modes. This work illustrates the subtle differences in chelating properties of alizarin-oxalate ligands with La³⁺ and Nd³⁺ for designing new ligands for efficient selective lanthanide separation.

The atomic-scale structures of Al–Si eutectics and hypereutectic are studied by using global structure searching method combined with ab initio density functional theories. The chemical components Al₇Si, Al₆Si and Al₄Si, with silicon contents of 12.9, 14.7 and 20.6 wt%, are set for searching the lowest-energy structures. The global search results show that all of the low-energy structures demonstrate the fcc structure feature of pure aluminum crystal; while, the alloy structures distort slightly due to the addition of silicon. In the term of binding energy, the stabilities of the alloys enhance with increasing the silicon contents. The binding energies are approximated as the sum of the bond energies, and the least square fitting results give the Al–Al, Al–Si and Si–Si bond energies as − 0.624, − 0.731 and − 0.819 eV, respectively. Forming two Al–Si bonds sacrifices one Si–Si and one Al–Al bonds, and the Al–Si alloys have an energy gain of − 0.019 eV. It suggests that dispersion of silicon atoms in the alloys is favorable for the stability. The mechanical properties of the structures are calculated. While the bulk moduli of the alloys are very close, the shear and Young’s moduli are quite different for different structures with different distributions of silicon atoms.

Abstract

We performed several types of ab initio calculations, from Hartree-Fock to Complete-Active-Space second-order perturbation theory and Coupled Cluster, on compact clusters of stoichiometry X (_4) Y (_4) , where X and Y are atoms belonging to the second row of the periodic table. More precisely, we considered the “cubic” structures of three isoelectronic groups, having a total of 48, 52, and 56-electrons, respectively. Notice that the highly symmetric cubic clusters of type X (_8) are characterized by an (O_h) symmetry group, while the X (_4) Y (_4) structures, with X (ne) Y, have at most a (T_d) symmetry. Binding energies and wave function analysis of these clusters have been performed, in order to investigate the nature, and the electron delocalization of these systems and establish a comparison between them. To this purpose, we also computed the Total-Position Spread tensor for each structure, a quantity which is related to the multi-reference nature of a system wave function.

This study focuses on investigating the spring properties of helicenes through DFT theoretical calculations. The energy change during stretching was observed by incrementally scanning the distance between both ends of the helicene from its stable state. The stiffness (k value) of each helicene was also determined at different stretching states. Interestingly, the k value was found to be non-constant during stretching, suggesting that helicenes do not behave as ideal springs. Furthermore, the effects of heteroatom doping and lateral π-extension on [6]helicene were examined, indicating that these factors have minimal impact on the spring nature of helicenes. Additionally, the study extended to longer helicenes, namely [12] and [18]helicenes. It was observed that the stiffness at the middle part of the helicene is greater than at the terminal parts, and the helical structures begin to collapse when the stretching length reaches approximately 2.5 times the stable state. We expected this work could bring innovative concept in future design of molecular devices.