In this work, we report rovibrational energy levels for four isotopologues of methylene (CH2 , CHD, CD2 , and 13 CH2 ) in their ground triplet electronic state ( X~ 3 B1 ) 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.

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 ΔES-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 ΔES-T gap.

The nudged elastic band (NEB) method has been widely employed for reaction path (RP) finding; however, certain NEB calculations do not converge to the minimum energy paths (MEPs) because of the occurrence of kinks, which are caused by the free bending of bands. Thus, we propose an extension of the NEB method, called the nudged elastic stiffness band (NESB) method, which adds the stress of stiffness using a beam theory. Here we present results from three examples: the NFK potential, the RPs of the Witting reaction, and finding saddle points for a set of five chemical reaction benchmarks. The results showed that the NESB method has three advantages: to decrease the number of iterations, shrink the length of the pathways from reducing unnecessary fluctuations, and find TS structures by converging to paths close to the MEPs for systems that have sharp curves on the MEPs.

The knowledge of individual hydrogen bond (HB) strength in molecular clusters is indispensable to get insights into the bulk properties of condensed systems. Recently, we have developed the molecular tailoring approach based (MTA-based) method for the estimation of individual HB energy in molecular clusters. However, the direct use of this MTA-based method to large molecular clusters becomes progressively difficult with the increase in the size of a cluster. To overcome this caveat, herein, we propose the use of linear scaling method (such as the original MTA method) for the estimation of single-point (SP) energies of large-sized parent molecular cluster and their respective fragments. Because the fragments of the MTA-based method, for the estimation of HB energy, are further fragmented, this proposed strategy is called as Fragments-in-Fragments (Frags-in-Frags) method. The SP energies of fragments and parent cluster calculated by the Frags-in-Frags approach were utilized to estimate the individual HB energy. The estimated individual HB energies, in various molecular clusters, by Frags-in-Frags method are found to be in excellent linear agreement with their MTA-based counterparts (R2  = 0.9975 of 348 data points). The difference being less than 0.5 kcal/mol in most of the cases. Furthermore, RMSD is 0.43 kcal/mol, MAE is 0.33 kcal/mol, and the standard deviation is 0.44 kcal/mol. Importantly, the Frags-in-Frags method not only enables the reliable estimation of HB energy in large molecular clusters but also requires less computational time and can be possible even with off-the-shelf hardware.

The presence of carboxyl groups in a molecule delivers an affinity to metal cations and a sensitivity to the chemical environment, especially for an environment that can give rise to intermolecular hydrogen bonds. Carboxylate groups can also induce intramolecular interactions, such as the formation of hydrogen bonds with donor groups, leading to an impact on the conformational space of biomolecules. In the latter case, the protonation state of the amino groups plays an important role. In order to provide an accurate description of the modifications induced in a carboxylated molecule by the formation of hydrogen bonds, one needs a compromise between a quantum chemical description of the system and the necessity to take into account explicit solvent molecules. In this work, we propose a bottom-up approach to study the conformational space and the carboxylate stretching band of (bio)organic anions. Starting from the anions in a continuum solvent, we then move to calculations using a microsolvation approach including one explicit water molecule per polar group, immersed in a continuum. Finally, we run QM/MM molecular dynamics simulations to analyze the solvation properties and to explore the anions conformational space. The results thus obtained are in good agreement with the description given by the microsolvation approach and they bring a more detailed description of the solvation shell and of the intermolecular hydrogen bonds.

This article presents detailed structural, electronic, magnetic, and thermoelectric properties of two experimentally existing isostructural variant perovskite compounds Tl2 NbX6 (X = Cl, Br) with the help of first principles calculations. As per requirement of stability in the device applications, the structural and thermodynamic stabilities were, respectively verified by tolerance factor and negative formation energies. The structural parameters in ferromagnetic phase were calculated and found in close agreement with the available experimental results. The electronic nature was found as half metallic from spin polarized calculations of electronic band structures and density of states, where the semiconductor nature was found in the spin down states and metallic nature in the spin up states. The magnetic moments of both the compounds were calculated as 1 μB majorly contributed by Nb atom. The Boltzmann transport theory was implemented via BoltzTraP for calculating the spin resolved thermoelectric parameters, such as Seebeck coefficient, electronic and thermal conductivities, and figure of merit. Overall, both the compounds were found suitable for use in spintronics and spin Seebeck effect for energy applications.

The accuracy of quantum mechanics (QM) simulations depends heavily on the quality of initial input files. Despite the popularity of QM simulation packages, achieving precise results still heavily relies on the user's proficiency in preparing the QM simulation systems. In this work, we present an easy-to-use tool called GUIDE, a YASARA plugin to assist researchers in quantum chemistry workflow automation using ORCA and MOPAC simulation packages. GUIDE lets users compute complex QM calculation workflows via an automated graphical window system. It allows for a more integrated and streamlined research process, as researchers can easily access all the necessary tools within one software without switching between multiple programs. This tool can save time and increase efficiency in computational chemistry methods. GUIDE is written in Python and is freely available for download at https://github.com/YAMACS-SML/GUIDE. The plugin is released under a GPL-3.0 license and is supported on Windows and Linux.

The numerical ill-conditioning associated with approximating an electron density with a convex sum of Gaussian or Slater-type functions is overcome by using the (extended) Kullback-Leibler divergence to measure the deviation between the target and approximate density. The optimized densities are non-negative and normalized, and they are accurate enough to be used in applications related to molecular similarity, the topology of the electron density, and numerical molecular integration. This robust, efficient, and general approach can be used to fit any non-negative normalized functions (e.g., the kinetic energy density and molecular electron density) to a convex sum of non-negative basis functions. We present a fixed-point iteration method for optimizing the Kullback-Leibler divergence and compare it to conventional gradient-based optimization methods. These algorithms are released through the free and open-source BFit package, which also includes a L2-norm squared optimization routine applicable to any square-integrable scalar function.

Understanding the molecular basis for protein stability requires a thermodynamic analysis of protein folding. Thermodynamic analysis is often performed by sampling many atomistic conformations using molecular simulations that employ either explicit or implicit water models. However, it remains unclear to what extent thermodynamic results from different solvation models are reliable at the molecular level. In this study, we quantify the influence of both solvation models on folding stability at the individual backbone and side chain resolutions. We assess the residue-specific folding free energy components of a β-sheet protein and a helical protein using trajectories resulting from TIP3P explicit and generalized Born/surface area implicit solvent simulations of model proteins. We found that the thermodynamic discrepancy due to the implicit solvent mostly originates from charged side chains, followed by the under-stabilized hydrophobic ones. In contrast, the contributions of backbone residue in both proteins were comparable for explicit and implicit water models. Our study lays out the foundation for detailed thermodynamic assessment of solvation models in the context of protein simulation.

We have investigated the NMR chemical shift of 205 Tl in several thallium compounds, ranging from small covalent Tl(I) and Tl(III) molecules to supramolecular complexes with large organic ligands and some thallium halides. NMR calculations were run at the ZORA relativistic level, with and without spin-orbit coupling using few selected GGA and hybrid functionals, namely BP86, PBE, B3LYP, and PBE0. We also tested solvent effects both at the optimization level and at the NMR calculation step. At the ZORA-SO-PBE0 (COSMO) level of theory we find a very good performance of the computational protocol that allows to discard or retain possible structures/conformations based on the agreement between the calculated chemical shift and the experimental value.

The surfaces of waimirite β- YF3 have been studied for their fluorine and chlorine versus water affinity. Bonding patterns of HF, HCl, and H2O chemically adsorbed onto surfaces of (010), (100), (011), and (101) have been quantified by density functional theory applying energy decomposition analysis. We found that the adsorption of H2O is dominated by about 65% of electrostatics, which causes a low surface sensitivity and weak interactions. On the contrary, the adsorptions of HF and HCl are driven by strong hydrogen bonds resulting in a highly surface-dependent ratio of 30-60% electrostatic versus orbital contribution. Among the stoichiometric surfaces, the shortest and strongest hydrogen bonds and consequently most covalent bonding patterns are found within YF3 ·  HCl. However, when including the preparation energy, each surface favors the adsorption of HF over HCl, which reproduces the higher affinity of yttrium towards fluoride over chloride, previously known for solutions, also for the solid state.

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.

DFT calculations and kinetic analysis have been employed to comprehensively explore the possibility to prepare epoxides by one-step method using the in-situ generated peroxy radicals or hydroperoxides as epoxidizing agents. Computational studies demonstrated that the selectivities for the reaction systems of O2 /R2/R1, O2 /CuH/R1, O2 /CuH/styrene, O2 /AcH/R1 were 68.2%, 69.6%, 100% and 93.3%, respectively. The in-situ generated peroxide radicals, such as HOO˙, CuOO˙ and AcOO˙, could react with R1 or styrene by attacking the CC double bond to form a CO bond and subsequently undergoing a cleavage of OO bond to yield epoxides. Peroxide radicals could abstract a hydrogen atom from methyl group on R1, forming unwanted by-products. It should be noted that the hydrogen atoms of HOO˙ is easy to be abstracted by CC double bond and simultaneously the oxygen atom is connected to the CH moiety to form an alkyl peroxy radical (Rad11), greatly limiting the selectivity. The comprehensive mechanistic studies provide a deep understanding on preparing epoxides by one-step method.

We performed a theoretical analysis of the BIPS photochemical cycle using an extensive set of forty hybrid functionals and taking into account a highly polar solvent (methanol). The functionals with a small fraction of the exact Hartree-Fock exchange (%HF) showed the predominant S0  → S2 transition with the strengthening of the Cspiro O bond. At the same time, functionals with medium and high %HF (including those with long-range correction) gave a dominant S0  → S1 transition with weakening or breaking of the Cspiro O bond, which corresponds to the experimental results. The influence of a highly polar solvent on the photochemical electrocyclic transformations of BIPS turned out to be significant. The number of functionals causing dissociation of the Cspiro O bond decreased from 10 to 7 compared to the gas phase. The magnitude of the oscillator strength has increased by approximately one and a half times. Structural distortions of the BIPS molecule during excitation (both with and without Cspiro O bond cleavage) significantly decreased in methanol compared to the gas phase. The two strong hydrogen bonds of methanol molecules with the oxygen and nitrogen atoms of spiropyran also have a significant effect on its excitation. They lead to a change in the predominant transition from S0  → S2 to S0  → S1 for five functionals. The number of functionals giving dissociation of the Cspiro O bond decreased from seven to four (M08HX, M052X, CAM-B3LYP, and M11). After the opening of the excited BIPS molecule, both of its strong H-bonds with methanol are preserved. Of this set of four functionals, only M052X and CAM-B3LYP exhibited the dominant HOMO-1 → LUMO configuration observed in high-level computations by other authors. Therefore, both of these functionals are recommended for modeling the photochemical cycle of this spiropyran. The photochemical cycle of BIPS was theoretically analyzed. The redistribution of the electron density in this cycle was quantitatively described using the differences in NPA of the atomic charges. The most important result of this analysis was the electrostatic mechanism of the approach of Cspiro and oxygen atoms at the fourth stage, which causes further reduction of the Cspiro O bond.

The possibilities and problems to predict excited-state acidities and basicities in water with electronic structure calculations combined with a continuum solvation model are investigated for a test set of photoacids and photobases. Different error sources, like errors in the ground-state pKa values, the excitation energies in solution for the neutral and (de-)protonated species, basis set effects, and contributions beyond implicit solvation are investigated and their contributions to the total error in pKa∗ are discussed. Density functional theory in combination with the conductor like screening model for real solvents and an empirical linear Gibbs free energy relationship are used to predict the ground-state pKa values. For the test set, this approach gives more accurate pKa values for the acids than for the bases. Time-dependent density-functional theory (TD-DFT) and second-order wave function methods in combination with the conductor like screening model are applied to compute excitation energies in water. Some TD-DFT functionals fail for several species to predict correctly the order of the lowest excitations. Where experimental data for absorption maxima in water is available, the implicit solvation model leads with the applied electronic structure methods in most cases for the excitation energies in water to an overestimation for the protonated and to an underestimation for the deprotonated species. The magnitude and sign of the errors depend on the hydrogen bond donating and accepting ability of the solute. We find that for aqueous solution this results generally in an underestimation in the pKa changes from the ground to the excited state for photoacids and an overestimation for photobases.

A new genetic algorithm has been proposed focusing on direct ab initio potential energy surface (PES) global minima search. Besides the commonly used operators, this new approach uses an operator to: improve the initial cluster generation, classify and compare all generated clusters, and use machine learning to model the quantum PES used in parallel optimization. Part of the validation process for this methodology was done with CunAum ( n + m ≤ X for X = 14, 19, 38, 55 ) and AunAgn ( n = 10, 20, 30, 40, 50, 60, 70 , and 75). The results are in fair agreement with the literature and led to a new global minimum for Cu12Au7 . A search has been done for the lowest energies of Lin nanoclusters with 2-8 atoms using the DFT approach and for Li3, Li4, Li2H , Li3H using DLPNO-CCSD(T) approach. NQGA successfully performed the MP2 optimizations for (H2O)11 cluster. In all cases, the proposed genetic algorithm located the previously reported global minima with very efficient performance. The new proposed methodology makes it possible to optimize cluster geometries directly using high-level ab initio methods relinquishing any bias introduced by a classical approach. Our results show that this proposed method has great potential applications due to its flexibility and efficiency in identifying global minima in the tested atomic systems.

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.

Using full configuration interaction (FCI) and multi-reference configuration interaction methods (MRCI), reliable geometrical and energetic references for Bn (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 . T1 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 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.

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.