Abstract

The unrestricted Hartree-Fock method is extended to correlation calculation within the density-matrix functional theory. The method is derived from an entropic cumulant functional for the correlation energy. The eigenvalue equations for the spin-orbitals are modified by the orbital occupation numbers. The Euler equation for the occupation numbers results in the Fermi-Dirac distribution, which is very efficient to update as soon as the orbital eigenvalue equations are solved. The method is demonstrated on the ground state of O2$$ {}_2 $$.

The structure, stability, and bonding characteristics of 1,1- and 1,2-ethenediol, their radical cations, and their protonated and deprotonated species were investigated using high-level ab initio G4 calculations.

Abstract

The structure, stability, and bonding characteristics of 1,1- and 1,2-ethenediol, their radical cations, and their protonated and deprotonated species were investigated using high-level ab initio G4 calculations. The electron density of all the neutral and charged systems investigated was analyzed using the QTAIM, ELF, and NBO approaches. The vertical ionization potential (IP) of the five stable tautomers of 1,2-ethenediol and the two stable tautomers of 1,1-ethenediol go from 11.81 to 12.27 eV, whereas the adiabatic ones go from 11.00 to 11.72 eV. The adiabatic ionization leads to a significant charge delocalization along the O-C-C-O skeleton. The most stable protonated form of (Z)-1,2-ethenediol can be reached by the protonation of both the anti-anti and the syn-anti conformers, whereas the most stable deprotonated form arises only from the syn-anti one. Both charged species are extra-stabilized by the formation of an O-H···O intramolecular hydrogen bond (IHB) which is not found in the neutral system. (Z)-1,2-ethenediol is predicted to be less stable, less basic, and more acidic than its cis-glycolaldehyde isomer. The most stable protonated species of (E)-1,2-ethenediol comes from its syn-syn conformer, although the anti-anti conformer is the most basic one. Contrarily, the three conformers yield a common deprotonated species, so their acidity follows exactly their relative stability. Again, the (E)-1,2-ethenediol is predicted to be less stable, less basic, and more acidic than its trans-glycolaldehyde isomer. Neither the neutral nor the protonated or the deprotonated forms of 1,1-ethenediol show the formation of any O-H···O IHB. The most stable protonated species is formed by the protonation of any of the two tautomers, but the most stable deprotonated form arises exclusively from the syn-anti neutral conformer. The conformers of 1,1-ethenediol are much less stable and significantly less basic than their isomer, acetic acid, and only slightly more acidic.

Abstract

Using full configuration interaction (FCI) and multi-reference configuration interaction methods (MRCI), reliable geometrical and energetic references for B _n (n = 1–4) clusters were established. The accuracy of the computed results was confirmed by comparison with available experimental data. Benchmark calculations indicated that B97D3, B97D, VSXC, HCTH407, BP86 and CCSD(T) methods provided reasonable results for structural parameters, with mean absolute error (MAEs) within 0.020 Å. Among the tested density functional theory (DFT) methods, the VSXC functional showed the best performance in predicting the relative energies of B₁B₄ with a MAE of 12.8 kJ mol⁻¹. Besides, B1B95, B971, TPSS, B3LYP, and BLYP functionals exhibited reasonable performance with MAE values of less than 15.0 kJ mol⁻¹. T ₁ diagnostic values between 0.035 and 0.109 at the CCSD(T) level revealed strong correlations in B₂B₄ clusters, highlighting the need for caution in using CCSD(T) as an energy reference for small boron clusters. The methods of CCSDT, CCSDT(Q) and CCSDT[Q], which incorporate three-electron and four-electron excitations, effectively improved the accuracy of the energy calculations.

The ethane C1-C2 bond critical point (BCP) Hessian of ρ(r) eigenvector-trajectories T(s) for the for the clockwise (CW, [+1]) (red) and counter-clockwise (CCW, [−1]) (blue) circularly laser pulse polarized in yz plane 60 femtoseconds after the pulses are switched off. The end of each T(s) is denoted by a cube marker. The most (±e₂) and least (±e₁) preferred eigenvector directions of the total charge density accumulation ρ(r_b). The inset is the view down the ethane C1-C2 BCP bond-path, showing the Cartesian yz axes, where the BCPs are represented by undecorated green spheres.

Abstract

A pair of simulated left and right circularly polarized ultra-fast laser pulses of duration 20 femtoseconds that induce a mixture of excited states are applied to ethane. The response of the electron dynamics is investigated within the next generation quantum theory of atoms in molecules (NG-QTAIM) using third-generation eigenvector-trajectories which are introduced in this work. This enables an analysis of the mechanical and chiral properties of the electron dynamics of ethane without needing to subject the C-C bond to external torsions as was the case for second-generation eigenvector-trajectories. The mechanical properties, in particular, the bond-flexing and bond-torsion were found to increase depending on the plane of the applied laser pulses. The bond-flexing and bond-torsion, depending on the plane of polarization, increases or decreases after the laser pulses are switched off. This is explainable in terms of directionally-dependent effects of the long-lasting superpositions of excited states. The chiral properties correspond to the ethane molecule being classified as formally achiral consistent with previous NG-QTAIM investigations. Future planned investigations using ultra-fast circularly polarized lasers are briefly discussed.

Overtones of the bending mode of triplet methylene predicted from the developed ab initio PES

Abstract

In this work, we report rovibrational energy levels for four isotopologues of methylene (CH₂, CHD, CD₂, and ¹³CH₂) in their ground triplet electronic state (X~$$ \overset{\sim }{X} $$³ B ₁) from variational calculation up to ~10,000 cm⁻¹ and using a new accurate ab initio potential energy surface (PES). Triplet methylene exhibits a large-amplitude bending vibration and can reach a quasilinear configuration due to its low barrier (~2000 cm⁻¹). To construct the ab initio PES, the Dunning's augmented correlation-consistent core-valence orbital basis sets were employed up to the sextuple-ζ quality [aug-cc-pCVXZ, X = T, Q, 5, and 6] combined with the single- and double-excitation unrestricted coupled cluster approach with a perturbative treatment of triple excitations [RHF-UCCSD(T)]. We have shown that the accuracy of the ab initio energies is further improved by including the corrections due to the scalar relativistic effects, DBOC and high-order electronic correlations. For the first time, all the available experimental rovibrational transitions were reproduced with errors less than 0.12 cm⁻¹, without any empirical corrections. Unlike more “traditional” nonlinear triatomic molecules, we have shown that even the energies of the ground vibrational state (000) with rather small rotational quantum numbers are strongly affected by the very pronounced rovibrational resonance interactions. Accordingly, the polyad structure of the vibrational levels of CH₂ and CD₂ was analyzed and discussed. The comparison between the energy levels obtained from the effective Watson A-reduced Hamiltonian, from the generating-function approach and from a variational calculation was given.

The aromaticity and stability of benzynes in the ground and first triplet states have been studied using unrestricted DFT methods. The results using multiple aromaticity criteria and CCSD(T) calculations show that aromaticity is conserved while stability is reversed from the ground to the excited state.

Abstract

In this work, we have revisited the aromaticity of benzyne isomers at the unrestricted density functional theory level (UDFT) using the energetic, magnetic, and delocalization criteria. In addition, this last criterion has also been analyzed employing complete active space (CASSCF) calculations. The results show conservation of aromaticity in these monocycles. Additionally it is observed that this trend is maintained in polycyclic aromatic hydrocarbon derivatives such as biradical didehydrophenanthrenes. Do these results imply a violation of Baird's rule? The answer is No, because this conservation in aromaticity is due to the loss of hydrogen atoms affects only the electronic σ skeleton and exerts a minor influence on the π cloud. Additionally, we have analyzed the relative stability of benzyne isomers and their relationship with experimental ΔE _S-T values. According to the literature, the stability of the benzynes in the singlet state is due to an effective interaction between the electrons of the biradical centers; however, this effect is completely reversed in the triplet state, which explains why the para isomer has the lowest ΔE _S-T gap.

Basicity of Phosphoryl Group: The study examines the role of orbital overlap, dispersion interactions, charge transfer, and dipole moments of the resulting complexes, in understanding the increasing U(VI) extraction behavior across the ligand series phosphate → phosphonate → phosphinate → phosphine oxide.

Abstract

The conventional argument that extraction efficiency depends on the “basicity of the phosphoryl oxygen” is thoroughly examined in this study. The analysis involves studying the electronic structures of various ligands, such as phosphate, phosphonate, phosphinate, and phosphine oxide, as well as variations in their alkyl chain length, and their corresponding uranium complexes. The studies revealed a significant amount of destabilizing strain and steric repulsion for ligands having longer alkyl chains upon complexation. A considerable amount of stabilizing orbital and dispersion interactions compensate for these repulsions, forming stable complexes. Dispersion interactions become more significant upon chain elongation and are mainly responsible for the preference for U(VI) metal ions by ligands with lengthy alkyl chain units. The preference of phosphine oxide ligands for U(VI) is analyzed within the context of enhanced orbital interactions resulting from the energetically close donor (ligand) and acceptor (metal nitrate) orbitals. Additionally, dispersion-based interactions also become significant, especially with larger chain lengths. The electronegative environment around the phosphorus atom, along with the existence of low-dipole moment structures, is also examined in relation to their possible role in solvent extraction and their influence on the selectivity of ligands for uranyl species.

Antimicrobial resistance has become a global health concern because of the rapid evolution of multidrug-resistant microbes and the delayed development of new medications. Microbes have a variety of molecular resistance mechanisms; one of them is the presence of efflux pumps. Considering E. coli as a model organism, we have identified potential AcrAB-TolC inhibitors by performing molecular docking and density functional theory (DFT) calculations to get insight into the binding model. These identified compounds could pose a better inhibitor and provide a potential approach for stimulating the actions of antibiotics in resistant bacteria.

Abstract

Multidrug resistance pathogens causing infections and illness remain largely untreated clinically. Efflux pumps are one of the primary processes through which bacteria develop resistance by transferring antibiotics from the interior of their cells to the outside environment. Inhibiting these pumps by developing efficient derivatives appears to be a promising strategy for restoring antibiotic potency. This investigation explores literature-reported inhibitors of E. coli efflux pump fusion proteins AcrB-AcrA and identify potential chemical derivatives of these inhibitors to overcome the limitations. Using computational and structure-guided approaches, a study was conducted with the selected inhibitors (AcrA:25-AcrB:59) obtained by data mining and their derivatives (AcrA:857-AcrB:3891) to identify their inhibitory effect on efflux pump using virtual screening, molecular docking and density functional theory (DFT) calculations. The finding indicates that Compound 2 (ZINC000072136376) has shown better binding and a significant inhibitory effect on AcrA, while Compound 3 (ZINC000072266819) has shown stronger binding and substantial inhibition effect on both non-mutant and mutated AcrB subunits. The identified derivatives could exhibit a better inhibitor and provide a potential approach for restoring the actions of resistant antibiotics.

Mapping the chemical interactions in pyrite enabled the development of molecular cluster models for mineral surface sites. These models serve as computational nano-reactors for exploring the atomic-scale mechanism of pyrite reactivity. The maquettes of surface sites are composed of a layer of magnetic iron sites that are connected with bridging persulfides and wrapped around a non-magnetic bulk iron core. Incompleteness of iron site chemical environment enables binding of reductants, interconversion of pyrite to an intermediate surface-associated iron-sulfur phase, and ultimately to mackinawite nanoparticles upon abiotic and biotic reductive dissolution.

Abstract

The recent discovery that anaerobic methanogens can reductively dissolve pyrite and utilize dissolution products as a source of iron and sulfur to meet their biosynthetic demands for these elements prompted the development of atomic-scale nanoparticle models, as maquettes of reactive surface sites, for describing the fundamental redox steps that take place at the mineral surface during reduction. The given report describes our computational approach for modeling n(FeS₂) nanoparticles originated from mineral bulk structure. These maquettes contain a comprehensive set of coordinatively unsaturated Fe^(II) sites that are connected via a range of persulfide (S₂ ²⁻) ligation. In addition to the specific maquettes with n = 8, 18, and 32 FeS₂ units, we established guidelines for obtaining low-energy structures by considering the pattern of ionic, covalent, and magnetic interactions among the metal and ligand sites. The developed models serve as computational nano-reactors that can be used to describe the reductive dissolution mechanism of pyrite to better understand the reactive sites on the mineral, where microbial extracellular electron-transfer reactions can occur.

Employing the bioisosterism strategy enables the conception of new drug candidates from biologically active molecules whose safety and efficacy are already established. In this sense, gaining selectivity to SARS-CoV-2 cysteine proteases is a powerful step towards creating a chemical arsenal against COVID-19, especially when drug resistance is in vogue.

Abstract

SARS-CoV-2 cysteine proteases are essential nonstructural proteins due to their role in the formation of the virus multiple enzyme replication-transcription complex. As a result, those functional proteins are extremely relevant targets in the development of a new drug candidate to fight COVID-19. Based on this fact and guided by the bioisosterism strategy, the present work has selected 126 out of 1050 ligands from DrugBank website. Subsequently, 831 chemical analogs containing bioisosteres, some of which became structurally simplified, were created using the MB-Isoster software, and molecular docking simulations were performed using AutoDock Vina. Finally, a study of physicochemical properties, along with pharmacokinetic profiles, was carried out through SwissADME and ADMETlab 2.0 platforms. The promising results obtained with the molecules encoded as DB00549_BI_005, DB04868_BI_003, DB11984_BI_002, DB12364_BI_006 and DB12805_BI_004 must be confirmed by molecular dynamics studies, followed by in vitro and in vivo empirical tests that ratify the advocated in-silico results.