Revised M06-L functional for improved accuracy on chemical reaction barrier heights, noncovalent interactions, and solid-state physics

Synthetic and theoretical study on novel N-ylidic complexes of mercury as new antibacterial agents

The novel structure of Hg(II) complexes including the pyridinium ylide C5H5NCHC(O)C6H4-m-Br (Y) were synthesized and reported in this study. In the first step, the pyridinium salt C5H5NCH2C(O)C6H4-m-Br (S) was produced by reacting 2,3'-dibromoactophenone and pyridine. then, treatment of S with K2CO3 gave the related pyridinium ylide Y. Finally, the reaction of Y with HgX2 and Hg(NO3)2·H2O leads to the formation of novel binuclear [HgY2][HgX4] (X=Cl (1); X=Br (2); X=I (3)) and polymeric [HgY(NO3)2]n (4) complexes. The structure of complex 2 was also determined by X-ray diffraction analysis. The obtained analyses proved the coordination through the ylidic carbon to metallic center. Additionally, Natural Bond Orbital (NBO), Energy Decomposition Analysis (EDA), and EDA-NOCV studies are also used to investigate the nature of metal-ligand bonding in the complexes. Finally, the antibacterial activity of 1-4 was also examined against Gram positive and negative represented significant levels of inhibitory potency respected to used standards.

Spurious proton transfer in hydrogen bonded dimers

In some hydrogen bonded systems, the proton may translocate along the hydrogen bond (hb) upon geometry optimization with electronic structure methods like density functional theory (DFT). Such proton transfer (pt) events, however, may be spurious. In this work, spurious pt events are investigated in a set of hydrogen bonded dimers formed with molecules HXN, where X stands for C, Si, Ge and Sn. It is found that standard approximations to the electronic exchange and correlation (xc) functional either predict spurious pt events or too strong hbs in all the (HXN)2 dimers except the (HCN)2 one. The latter result is revealed by comparing DFT calculations against wave function methods. Such spurious pt events may be avoided by fine-tuning the percentage of exact exchange (ex) in hybrid xc-functionals. It is shown that the minimum amount of ex to avoid a spurious pt event ranged from 8% to 90%, depending on the system, basis set and xc-functional approximation used. However, these fine-tuned xc-functionals inadequately describe the hb in the (HXN)2 dimers. Moreover, it is determined that the spurious pt event originates from a wrong description of the isolated HXN molecules by xc-functionals that do not include ex or a small amount of it. Therefore, it is argued that one can determine if a pt event is spurious by analyzing the geometry and electronic structure of the isolated molecule.

Machine learning for accuracy in density functional approximations

Machine learning techniques have found their way into computational chemistry as indispensable tools to accelerate atomistic simulations and materials design. In addition, machine learning approaches hold the potential to boost the predictive power of computationally efficient electronic structure methods, such as density functional theory, to chemical accuracy and to correct for fundamental errors in density functional approaches. Here, recent progress in applying machine learning to improve the accuracy of density functional and related approximations is reviewed. Promises and challenges in devising machine learning models transferable between different chemistries and materials classes are discussed with the help of examples applying promising models to systems far outside their training sets.

Small Representative Databases for Testing and Validating Density Functionals and Other Electronic Structure Methods

Broad and diverse sets of accurate data provide useful metrics for assessing the performance of new theoretical methods. However, assessing methods against large databases can be an arduous task. Here, we present 17 representative energetic databases, defined as small databases whose errors and error spreads are representative of larger databases and which therefore can serve as efficient benchmarks for developing and testing electronic structure methods and density functionals. In 15 cases, the representative databases have 6 entries while being representative of larger databases with 14-107 entries, and in the other two cases, they have 14 entries while being representative of larger databases with 418-455 entries. The mean unsigned error (MUE) of 100 electronic structure methods on a given representative database is typically within about 8% of the MUE on its parent database, and the root-mean-square error (RMSE) is typically within about 11% of the RMSE on the parent database. Thus, the representative databases are quite successful in indicating accuracy while maintaining good diversity. The databases include both main-group and transition-metal compounds and reactions, and they include bond energies, reaction energies, barrier heights, noncovalent interactions, ionization potentials, and absolute energies.

DFT Study on the Mechanisms and Selectivities in Rh (III)-Catalyzed [5 + 1] Annulation of 2-Alkenylanilides and 2-Alkylphenols with Allenyl Acetates

The mechanisms and regio-, chemo-, and stereoselectivity were theoretically investigated in the Rh(III)-catalyzed [5 + 1] annulation of 2-alkenylanilides and 2-alkylphenols with allenyl acetates. Two different reactants, 2-alkenylanilides and 2-alkylphenols, were selected as model systems in the density functional theory calculations. The obtained theoretical results show that both these reactants exhibit similar steps, namely, (1) N-H/O-H deprotonation and C-H activation, (2) allenyl acetate migratory insertion, (3) β-oxygen elimination, (4) intramolecular nucleophilic addition of the nitrogen/oxygen-rhodium bond resulting in [5 + 1]-annulation, and (5) protonation with the formation of the desired product and regeneration of the Rh(III) catalyst. The theoretical evidence suggests that the selectivity is determined at the step of allenyl acetate's migratory insertion. Moreover, the regioselectivity is driven by electronic effects, while the interaction energies (C-H···π and C-H···O interactions) play a more imperative role in controlling the stereoselectivity. The obtained theoretical results not only well rationalize the experimental observations but also provide important mechanistic insights for related types of [5 + 1]-annulation reactions.

Ruthenium(II)-Catalyzed Oxidative Annulation of Imidazo[1,5-a]quinolin-2-iums Salts and Internal Alkynes via C-H Bond Activation

Ruthenium(II)-catalyzed synthesis of π-conjugated fused imidazo[1,5-a]quinolin-2-ium derivatives have been achieved via C-H activation of quinoline-functionalized NHC (NHC=N-heterocyclic carbene) and oxidative coupling with internal alkynes. The reaction occurred with high efficiency, broad substrate scope, tolerates a wide range of functional groups and utilized into a gram-scale. Synthetic applications of the coupled product have been exemplified in the late-stage derivatization of various highly functionalized scaffolds. Moreover, most of the annulated products exhibit intense fluorescence and have potential applications in optoelectronic devices. Mechanistic studies have provided insights into the spectroscopic characterization of key five-membered ruthenacycle intermediate and Ru(0) sandwich species. Based on several control experiments, deuterium-kinetic isotope effect, and thermodynamic activation parameters the mechanistic finding demonstrated that fused imidazo-[1,5-a]quinolin-2-ium C(2)-H bond cleavage is the rate-determining step and ruling out the possibility of reductive elimination for controlling the rate of reaction.

Evaluation of DFT methods for predicting geometries and NMR spectra of Bi(III) dithiocarbamate complexes with antitumor properties

CONTEXT

Bismuth complexes with dithiocarbamate ligands have attracted attention because of their biological applications, such as antimicrobial, antileishmanial, and anticancer properties. These complexes have high cytotoxic activity against cancer cells, being more active than the standard drugs cisplatin, doxorubicin, and tamoxifen. In the present study, we investigated the ability of some DFT methods to reproduce the geometries and NMR spectra of the Bi(III) dithiocarbamate complexes, selected based on their proven antitumor activity. Our investigation revealed that the M06-L/def2-TZVP/ECP/CPCM method presented good accuracy in predicting geometries, while the TPSSh/def2-SVP/ECP/CPCM method proved effective in analyzing the 13C NMR spectra of these molecules. In general, all examined methods exhibited comparable performance in predicting 1H NMR signals.

METHODS

Calculations were performed with the Gaussian 09 program using the def2-SVP and def2-TZVP basis sets, employing relativistic effective core potential (ECP) for Bi and using the CPCM solvent model. The exchange-correlation functionals BP86, PBE, OLYP, M06-L, B3LYP, B3LYP-D3, M06-2X, TPSSh, CAM-B3LYP, and ωB97XD were used in the study. Geometry optimizations were started from crystallographic structures available at the Cambridge Structural Database. The theoretical results were compared with experimental data using the mean root-mean-square deviation (RMSD), mean absolute deviations (MAD), and linear correlation coefficient (R2).

Electronic analysis of n-propyl xanthate complexes with group 12 metals: a theoretical-experimental study

CONTEXT

Xanthates are organic compounds of great interest in coordination chemistry due to their different basic sites, which allow them to form complexes with different coordination modes and geometries. These compounds are relevant in the environment and act as heavy metal collectors in aqueous environments. In this theoretical-experimental work, electronic spectroscopy studies of n-propyl xanthate complexes with group 12 metals were performed. This study verified structural differences in these systems, depending on the environment in which they are inserted. In addition, structural differences were observed when the solid was changed to an n-hexane solution. Thus, it was observed that the complexes assume a mononuclear structure in solution, while they present a polymeric form in the solid phase. The electronic spectra obtained through TD-DFT calculations were compared to those of the previously synthesized complexes. In the final theoretical analysis, the main orbitals involved in these transitions were assigned using population analysis calculations. The synthesis of the complexes was confirmed through infrared (MID and FAR), UV‒Vis, Raman, and NMR-1H spectroscopic analyses.

METHODS

The structures of the mononuclear and polymeric complexes were optimized in vacuum and n-hexane. Under vacuum, DFT levels M06L/6-311 + + G** + LANL2TZ and M06L/def2-TZVP were used for the mononuclear complexes, and M06L/LANL2DZ + LANL2 were used for the polymer complexes. For the calculations of the mononuclear complexes in n-hexane, the same level of theory was used for the solid state. TD-DFT calculations for 300 excited states were performed with the same levels of theory and used the optimized structures of the complexes. Furthermore, population analysis was carried out on all the systems studied. Gaussian 09 software was used for the structure optimization, TD-DFT, and population analysis calculations. GaussSum software was used to evaluate the molecular orbitals and electronic spectra.

Theoretical Spectroscopic Study of Normal Raman and Charge Transfer Surface-Enhanced Raman Scattering (SERS) Spectra of the Adsorbed l- and d-Cysteine on the Chiral Au34 and Ag4@Au30 Nanoclusters: Chirality Discrimination

In this work, the discrimination of the enantiomers of cysteine (l- and d-CYS) using the chiral Au34 and Ag4@Au30 clusters was theoretically investigated in the gas phase and water. Two modes were considered for the interaction of each enantiomer with the clusters (via only its S atom or its S atom and NH2 group, simultaneously). The interaction energy (Eint) and adsorption energy (Ead) for the complexation of each enantiomer with the clusters for each interaction mode were calculated. Considering the calculated interaction energies, the interaction of d-CYS with Au34 is stronger than that of l-CYS with the same cluster. Also, it was observed that the substitution of the Au4 core of the Au34 cluster with the Ag4 cluster caused the increase of the interaction energy of l-CYS with the Ag4@Au30 cluster compared to the Au34 cluster, while the reverse trend was observed for d-CYS. Quantum theory of atoms in molecules (QTAIM) analysis was employed to calculate the interaction paths and their related bond critical points (BCPs) between the CYS enantiomers and the clusters to explain the difference between the interaction energy of the enantiomers with the clusters. The IR, normal Raman (NR), and surface-enhanced Raman scattering (SERS) spectra of the enantiomers interacting with the Au34 and Ag4@Au30 clusters were calculated, and the discrimination between l-CYS and d-CYS using the calculated spectra was explained. It was found that the discrimination of the enantiomers based on their interaction with the clusters is controlled by the charge transfer between the enantiomers and the clusters.

Single-and double transition metal atoms anchored C2N as a high-activity catalyst for CO oxidation: A first-principles study

The oxidation of CO has attracted great interest in recent years due to its important role in enhancing the catalyst durability in fuel cells and solving the growing environmental problems caused by CO emissions. Consequently, the catalytic oxidation of CO at double non-noble metal atoms anchored C2N is investigated using density functional theory (DFT) computations. All the screened Ti@C2N and Ti2@C2N are thermodynamically stable based on their binding energy calculations. The electronic characteristics, the natural bond orbital analyses (NBO), Frontier orbital, statistical thermodynamics, projected densities of states (PDOS) characteristics, non-covalent interactions (NCI), and quantum theory of atoms in molecules (QTAIM) descriptors of these systems have been examined to analyze the interaction process. Our comparative study suggested that the newly predicted double-atom catalyst (Ti2@C2N) is highly active for CO oxidation, which is a useful guideline for further development. The calculated static first-order hyperpolarizability (βo) illustrated that the double-atom catalyst under investigation can be considered a potential candidate for non-linear optical behavior and could be used for NLO applications. CO oxidation on Ti2@C2N along the Eley-Rideal (ER) mechanism with a low energy barrier of 0.16 eV, which is smaller than the maximum energy barrier (0.73 eV) of CO oxidation along the Langmuir-Hinshelwood (LH) mechanism. Consequently, the ER mechanism is more favorable both thermodynamically and dynamically. This work can provide useful insights and guidelines for future theoretical and experimental investigations to promote the design and development of highly effective and low-cost non-precious-metal Ti2@C2N nanocatalysts towards CO oxidation at ambient temperature.

Performance of Density Functionals for Excited-State Properties of Isolated Chromophores and Exciplexes: Emission Spectra, Solvatochromic Shifts, and Charge-Transfer Character

This study assesses the performance of various meta-generalized gradient approximation (meta-GGA), global hybrid, and range-separated hybrid (RSH) density functionals in capturing the excited-state properties of organic chromophores and their excited-state complexes (exciplexes). Motivated by their uses in solar energy harvesting and photoredox CO2 reduction, we use oligo-(p-phenylenes) and their excited-state complexes with triethylamine as model systems. We focus on the fluorescence properties of these systems, specifically emission energies. We also consider solvatochromic shifts and wave function characteristics. The latter is described by using reduced quantities such as natural transition orbitals (NTOs) and exciton descriptors. The functionals are benchmarked against the experimental fluorescence spectra and the equation-of-motion coupled-cluster method with single and double excitations. Both in isolated chromophores and in exciplexes, meta-GGA functionals drastically underestimate the emission energies and exhibit significant exciton delocalization and anticorrelation between electron and hole motion. The performance of global hybrid functionals is strongly dependent on the percentage of exact exchange. Our study identifies RSH GGAs as the best-performing functionals, with ωPBE demonstrating the best agreement with experimental results. RSH meta-GGAs often overestimate emission energies in exciplexes and yield larger hole NTOs. Their performance can be improved by optimally tuning the range-separation parameter.

Structure and dynamics of liquid water from ab initio simulations: adding Minnesota density functionals to Jacob's ladder

The accurate representation of the structural and dynamical properties of water is essential for simulating the unique behavior of this ubiquitous solvent. Here we assess the current status of describing liquid water using ab initio molecular dynamics, with a special focus on the performance of all the later generation Minnesota functionals. Findings are contextualized within the current knowledge on DFT for describing bulk water under ambient conditions and compared to experimental data. We find that, contrary to the prevalent idea that local and semilocal functionals overstructure water and underestimate dynamical properties, M06-L, revM06-L, and M11-L understructure water, while MN12-L and MN15-L overdistance water molecules due to weak cohesive effects. This can be attributed to a weakening of the hydrogen bond network, which leads to dynamical fingerprints that are over fast. While most of the hybrid Minnesota functionals (M06, M08-HX, M08-SO, M11, MN12-SX, and MN15) also yield understructured water, their dynamical properties generally improve over their semilocal counterparts. It emerges that exact exchange is a crucial component for accurately describing hydrogen bonds, which ultimately leads to corrections in both the dynamical and structural properties. However, an excessive amount of exact exchange strengthens hydrogen bonds and causes overstructuring and slow dynamics (M06-HF). As a compromise, M06-2X is the best performing Minnesota functional for water, and its D3 corrected variant shows very good structural agreement. From previous studies considering nuclear quantum effects (NQEs), the hybrid revPBE0-D3, and the rung-5 RPA (RPA@PBE) have been identified as the only two approximations that closely agree with experiments. Our results suggest that the M06-2X(-D3) functionals have the potential to further improve the reproduction of experimental properties when incorporating NQEs through path integral approaches. This work provides further proof that accurate modeling of water interactions requires the inclusion of both exact exchange and balanced (non-local) correlation, highlighting the need for higher rungs on Jacob's ladder to achieve predictive simulations of complex biological systems in aqueous environments.

Mesoporous Single Atom-Cluster Fe-N/C Oxygen Evolution Electrocatalysts Synthesized with Bottlebrush Block Copolymer-Templated Rapid Thermal Annealing

Current electrocatalysts for oxygen evolution reaction (OER) are either expensive (such as IrO2, RuO2) or/and exhibit high overpotential as well as sluggish kinetics. This article reports mesoporous earth-abundant iron (Fe)-nitrogen (N) doped carbon electrocatalysts with iron clusters and closely surrounding Fe-N4 active sites. Unique to this work is that the mechanically stable mesoporous carbon-matrix structure (79 nm in pore size) with well-dispersed nitrogen-coordinated Fe single atom-cluster is synthesized via rapid thermal annealing (RTA) within only minutes using a self-assembled bottlebrush block copolymer (BBCP) melamine-formaldehyde resin composite template. The resulting porous structure and domain size can be tuned with the degree of polymerization of the BBCP backbone, which increases the electrochemically active surface area and improves electron transfer and mass transport for an effective OER process. The optimized electrocatalyst shows a required potential of 1.48 V (versus RHE) to obtain the current density of 10 mA/cm2 in 1 M KOH aqueous electrolyte and a small Tafel slope of 55 mV/decade at a given overpotential of 250 mV, which is significantly lower than recently reported earth-abundant electrocatalysts. Importantly, the Fe single-atom nitrogen coordination environment facilitates the surface reconstruction into a highly active oxyhydroxide under OER conditions, as revealed by X-ray photoelectron spectroscopy and in situ Raman spectroscopy, while the atomic clusters boost the single atoms reactive sites to prevent demetalation during the OER process. Density functional theory (DFT) calculations support that the iron nitrogen environment and reconstructed oxyhydroxides are electrocatalytically active sites as the kinetics barrier is largely reduced. This work has opened a new avenue for simple, rapid synthesis of inexpensive, earth-abundant, tailorable, mechanically stable, mesoporous carbon-coordinated single-atom electrocatalysts that can be used for renewable energy production.

DELFI: a computer oracle for recommending density functionals for excited states calculations

Density functional theory (DFT) is the workhorse of computational quantum chemistry. One of its main limitations is that choosing the right functional is a non-trivial task left for human experts. The choice is particularly hard for excited state calculations when using its time-dependent formulation (TD-DFT). This is due to the approximations of the method, but also because the photophysical properties of a molecule are defined by a manifold of states that all need to be properly described. This includes not only the relative energy of the states, but also capturing the correct character, order, and intensity of the transitions. In this work, we developed a neural network to recommend functionals to be used on molecules for TD-DFT calculations, by simultaneously considering all these properties for a manifold of states. This was possible by developing a scoring system to define the accuracy of an excited state's calculation against a higher-accuracy reference. The scoring system is generalizable to any level of theory; we here applied it to evaluate the performance of common functionals of different rungs against a higher accuracy method on a large set of organic molecules. The results are collected in a database that we released and made open, providing four million data points to the community for future applications. The scoring system assigns a value between zero and one hundred to each functional for each molecule, transforming the complicated task of learning photophysical properties into a simpler regression task. We used the dataset to train a graph attention neural network to predict the scores for unseen molecules. We call this oracle DELFI (Data-driven EvaLuation of Functionals by Inference), which can be used to quickly screen and predict the ranking of functionals to calculate the optical properties of organic molecules. We validated DELFI in two in silico experiments: choosing a common functional for a series of spiropyran-merocyanine isomers and a unique functional to screen a large dataset of over 50 000 organic photovoltaic molecules, for which an extensive benchmark would be unfeasible. A corresponding web application allows DELFI to be easily run and the results to be analyzed, alleviating the hurdle of choosing the right functional for TD-DFT calculations.

Investigating the anticancer potential of 4-phenylthiazole derived Ru(II) and Os(II) metalacycles

In this contribution we report the synthesis, characterization and in vitro anticancer activity of novel cyclometalated 4-phenylthiazole-derived ruthenium(II) (2a-e) and osmium(II) (3a-e) complexes. Formation and sufficient purity of the complexes were unambigiously confirmed by 1H-, 13C- and 2D-NMR techniques, X-ray diffractometry, HRMS and elemental analysis. The binding preferences of these cyclometalates to selected amino acids and to DNA models including G-quadruplex structures were analyzed. Additionally, their stability and behaviour in aqueous solutions was determined by UV-Vis spectroscopy. Their cellular accumulation, their ability of inducing apoptosis, as well as their interference in the cell cycle were studied in SW480 colon cancer cells. The anticancer potencies were investigated in three human cancer cell lines and revealed IC50 values in the low micromolar range, in contrast to the biologically inactive ligands.

Modeling Multi-Step Organic Reactions: Can Density Functional Theory Deliver Misleading Chemistry?

Many organic reactions are characterized by a complex mechanism with a variety of transition states and intermediates of different chemical natures. Their correct and accurate theoretical characterization critically depends on the accuracy of the computational method used. In this work, we study a complex ambimodal cycloaddition with five transition states, two intermediates, and three products, and we ask whether density functional theory (DFT) can provide a correct description of this type of complex and multifaceted reaction. Our work fills a gap in that most systematic benchmarks of DFT for chemical reactions have considered much simpler reactions. Our results show that many density functionals not only lead to seriously large errors but also differ from one another in predicting whether the reaction is ambimodal. Only a few of the available functionals provide a balanced description of the complex and multifaceted reactions. The parameters varied in the tested functionals are the ingredients, the treatment of medium-range and nonlocal correlation energy, and the inclusion of Hartree-Fock exchange. These results show a clear need for more benchmarks on the mechanisms of large molecules in complex reactions.

Axial-equatorial equilibrium in substituted cyclohexanes: a DFT perspective on a small but complex problem

In Chemistry, complexity is not necessarily associated to large systems, as illustrated by the textbook example of axial-equatorial equilibrium in mono-substituted cyclohexanes. The difficulty in modelling such a simple isomerization is related to the need for reproducing the delicate balance between two forces, with opposite effects, namely the attractive London dispersion and the repulsive steric interactions. Such balance is a stimulating challenge for density-functional approximations and it is systematically explored here by considering 20 mono-substituted cyclohexanes. In comparison to highly accurate CCSD(T) reference calculations, their axial-equatorial equilibrium is studied with a large set of 48 exchange-correlation approximations, spanning from semilocal to hybrid to more recent double hybrid functionals. This dataset, called SAV20 (as Steric A-values for 20 molecules), allows to highlight the difficulties encountered by common and more original DFT approaches, including those corrected for dispersion with empirical potentials, the 6-31G*-ACP model, and our cost-effective PBE-QIDH/DH-SVPD protocol, in modeling these challenging interactions. Interestingly, the performance of the approaches considered in this contribution on the SAV20 dataset does not correlate with that obtained with other more standard datasets, such as S66, IDISP or NC15, thus indicating that SAV20 covers physicochemical features not already considered in previous noncovalent interaction benchmarks.

Fluorinated Pharmaceutical and Pesticide Photolysis: Investigating Reactivity and Identifying Fluorinated Products by Combining Computational Chemistry,19F NMR, and Mass Spectrometry

Fluorinated breakdown products from photolysis of pharmaceuticals and pesticides are of environmental concern due to their potential persistence and toxicity. While mass spectrometry workflows have been shown to be useful in identifying products, they fall short for fluorinated products and may miss up to 90% of products. Studies have shown that 19F NMR measurements assist in identifying and quantifying reaction products, but this protocol can be further developed by incorporating computations. Density functional theory was used to compute 19F NMR shifts for parent and product structures in photolysis reactions. Computations predicted NMR spectra of compounds with an R2 of 0.98. Computed shifts for several isolated product structures from LC-HRMS matched the experimental shifts with <0.7 ppm error. Multiple products including products that share the same shift that were not previously reported were identified and quantified using computational shifts, including aliphatic products in the range of -80 to -88 ppm. Thus, photolysis of fluorinated pharmaceuticals and pesticides can result in compounds that are polyfluorinated alkyl substances (PFAS), including aliphatic-CF3 or vinyl-CF2 products derived from heteroaromatic-CF3 groups. C-F bond-breaking enthalpies and electron densities around the fluorine motifs agreed well with the experimentally observed defluorination of CF3 groups. Combining experimental-computational 19F NMR allows quantification of products identified via LC-HRMS without the need for authentic standards. These results have applications for studies of environmental fate and analysis of fluorinated pharmaceuticals and pesticides in development.

Altering the Localization of an Unpaired Spin in a Formal Ni(V) Species

The participation of both ligand and the metal center in the redox events has been recognized as one of the ways to attain the formal high valent complexes for the late 3d metals, such as Ni and Cu. Such an approach has been employed successfully to stabilize a Ni(III) bisphenoxyl diradical species in which there exist an equilibrium between the ligand and the Ni localized resultant spin. The present work, however, broadens the scope of the previously reported three oxidized equivalent species by conveying the approaches that tend to affect the reported equilibrium in CH3 CN at 233 K. Various spectroscopic characterization revealed that employing exogenous N-donor ligands like 1-methyl imidazole and pyridine favors the formation of the Ni centered localized spin though axial binding. In contrast, due to its steric hinderance, quinoline favors an exclusive ligand localized radical species. DFT studies shed light on the novel intermediates' complex electronic structure. Further, the three oxidized equivalent species with the Ni centered spin was examined for its hydrogen atom abstraction ability stressing their key role in alike reactions.

M11pz: A Nonlocal Meta Functional with Zero Hartree-Fock Exchange and with Broad Accuracy for Chemical Energies and Structures

The accuracy of Kohn-Sham density functional theory depends strongly on the approximation to the exchange-correlation functional. In this work, we present a new exchange-correlation functional called M11pz (M11 plus rung-3.5 terms with zero Hartree-Fock exchange) that is built on the M11plus functional with the goal of using its rung-3.5 terms without a Hartree-Fock exchange term, especially to improve the accuracy for strongly correlated systems. The M11pz functional is optimized with the same local and rung-3.5 ingredients that are used in M11plus but without any percentage of Hartree-Fock exchange. The performance of M11pz is compared with eight local functionals, and M11pz is found to be in top three when the errors or ranks are averaged over eight grouped and partially overlapping databases: AME418/22, atomic and molecular energies; MGBE172, main-group bond energies; TMBE40, transition-metal bond energies; SR309, single-reference systems; MR54, multireference systems; BH192, barrier heights; NC579, noncovalent interaction energies; and MS20, molecular structures. For calculations of band gaps of solids, M11pz is the second best of the nine tested functionals that have zero Hartree-Fock exchange.

Chemo- and Regioselective Catalytic Cross-Coupling Reaction of Ketones for the Synthesis of β, γ-Disubstituted β, γ-Unsaturated Ketones

C-C bond forming reaction of ketone with aldehyde is well-studied for the synthesis of α, β-unsaturated ketones, however, the reaction with two different ketones to unsaturated carbonyl compound has not yet been systematically studied. Probably due to the relatively low reactivity of ketones as electrophiles (aldol acceptors), its propensity for retro-aldol reaction. The reactions often suffer from unsatisfactory chemoselectivity (self- vs. crossed aldol products) and regioselectivity (thermodynamic vs. kinetic enolate). In this quest, we report here for the first time selective cross-coupling reaction of ketones to β-branched β, γ-unsaturated ketones by using ruthenium catalysis. Interestingly, single crossed aldol condensation products are formed even in reactions where a mixture of products is possible. Reaction is highly chemoselective, regioselective and produces H2 O as the only byproducts making the protocol environmentally benign. Method is compatible with a wide variety of sensitive functional group and applicable for even problematic aliphatic ketones as substrates. Notably, acetone was found as a three-carbon feedstock for the syntheses of simple β, γ-unsaturated ketone compounds. The process can further be extended to the gram-scale reaction and late-stage functionalization of natural products. With the help of DFT calculations, several control experiments, and deuterium-labeling experiments, the mechanistic finding demonstrated that initial aldol-condensation of ketones to a β, β-disubstituted α, β-unsaturated ketone, which further isomerizes to a β, γ- unsaturated ketone via η3 -allyl ruthenium complex.

Doubly Tuned Exchange-Correlation Functionals for Mixed-Reference Spin-Flip Time-Dependent Density Functional Theory

It is demonstrated that significant accuracy improvements in MRSF-TDDFT can be achieved by introducing two different exchange-correlation (XC) functionals for the reference Kohn-Sham DFT and the response part of the calculations, respectively. Accordingly, two new XC functionals of doubly tuned Coulomb attenuated method-vertical excitation energy (DTCAM-VEE) and DTCAM-AEE were developed on the basis of the "adaptive exact exchange (AEE)" concept in the framework of the Coulomb-attenuating XC functionals. The values by DTCAM-VEE are in excellent agreement with those of Thiel's set [mean absolute errors (MAEs) and the interquartile range (IQR) values of 0.218 and 0.327 eV, respectively]. On the other hand, DTCAM-AEE faithfully reproduced the qualitative aspects of conical intersections (CIs) of trans-butadiene and thymine and the nonadiabatic molecular dynamics (NAMD) simulations on thymine. The latter functional also remarkably exhibited the exact 1/R asymptotic behavior of the charge-transfer state of an ethylene-tetrafluoroethylene dimer and the accurate potential energy surfaces (PESs) along the two torsional angles of retinal protonated Schiff base model with six double bonds (rPSB6). Overall, DTCAM-AEE generally performs well, as its MAE (0.237) and IQR (0.41 eV) are much improved as compared to BH&HLYP. The current idea can also be applied to other XC functionals as well as other variants of linear response theories, opening a new way of developing XC functionals.

CRYSTAL23: A Program for Computational Solid State Physics and Chemistry

The Crystal program for quantum-mechanical simulations of materials has been bridging the realm of molecular quantum chemistry to the realm of solid state physics for many years, since its first public version released back in 1988. This peculiarity stems from the use of atom-centered basis functions within a linear combination of atomic orbitals (LCAO) approach and from the corresponding efficiency in the evaluation of the exact Fock exchange series. In particular, this has led to the implementation of a rich variety of hybrid density functional approximations since 1998. Nowadays, it is acknowledged by a broad community of solid state chemists and physicists that the inclusion of a fraction of Fock exchange in the exchange-correlation potential of the density functional theory is key to a better description of many properties of materials (electronic, magnetic, mechanical, spintronic, lattice-dynamical, etc.). Here, the main developments made to the program in the last five years (i.e., since the previous release, Crystal17) are presented and some of their most noteworthy applications reviewed.

Bioinspired Cu(II) Defect Sites in ZIF-8 for Selective Methane Oxidation

Activating the C-H bonds of alkanes without further oxidation to more thermodynamically stable products, CO and CO2, is a long-sought goal of catalytic chemistry. Inspired by the monocopper active site of methane monooxygenase, we synthesized a Cu-doped ZIF-8 metal-organic framework with 25% Cu and 75% Zn in the nodes and activated it by heating to 200 °C and dosing in a stepwise fashion with O2, methane, and steam. We found that it does oxidize methane to methanol and formaldehyde. The catalysis persists through at least five cycles, and beyond the third cycle, the selectivity improves to the extent that no CO2 can be detected. Experimental characterization and analysis were carried out by PXRD, DRUV-vis, SEM, and XAS (XANES and EXAFS). The reaction is postulated to proceed at open-coordination copper sites generated by defects, and the mechanism of methanol production was explicated by density functional calculations with the revMO6-L exchange-correlation functional. The calculations reveal a catalytic cycle of oxygen-activated CuI involving the conversion of two molecules of CH4 to two molecules of CH3OH by a sequence of hydrogen atom transfer reactions and rebound steps. For most steps in the cycle, the reaction is more favored by singlet species than by triplets.

Barrier Heights for Diels-Alder Transition States Leading to Pentacyclic Adducts: A Benchmark Study of Crowded, Strained Transition States of Large Molecules

Theoretical characterization of reactions of complex molecules depends on providing consistent accuracy for the relative energies of intermediates and transition states. Here we employ the DLPNO-CCSD(T) method with core-valence correlation, large basis sets, and extrapolation to the CBS limit to provide benchmark values for Diels-Alder transition states leading to competitive strained pentacyclic adducts. We then used those benchmarks to test a diverse set of wave function and density functional methods for the absolute and relative barrier heights of these transition states. Our results show that only a few of the tested density functionals can predict the absolute barrier heights satisfactorily, although relative barrier heights are more accurate. The most accurate functionals tested are ωB97M-V, M11plus, ωB97X-V, PBE-D3(0), M11, and MN15 with MUDs from best estimates less than 3.0 kcal. These findings can guide selection of density functionals for future studies of crowded, strained transition states of large molecules.

Theoretical studies of Zn2+ complexes with alkyl xanthate ligands: a thermochemical, electronic energy decomposition, and natural bond orbital analysis

CONTEXT

Xanthates are organic compounds that present great interest for coordination chemistry, because they can bond in different ways to the metal ion. Thus, these compounds have several applications, being best known for their environmental application. In fact, xanthates are recognized for their application as heavy metal collector agents in aqueous environments. In view of this application, this study is aimed at showing the thermochemical and electronic parameters obtained for the reactions of substitution water molecules in the aqua zinc complexes, by xanthate ligands (n-propyl, n-butyl, and n-pentyl xanthates). In addition to their environmental application, xanthates have shown biological properties, such as anti-bacterial and anti-cancer. In recent years, xanthates have also been used in the technological area, where it participates as a precursor of sulfides for the manufacture of thin films. Our results showed complexes with distorted octahedral geometries and with negative values of enthalpy and Gibbs free energy, indicating exothermic and spontaneous processes. For all the complexes, it was observed that Zn²⁺ complexes have both an ionic and covalent character. However, the monosubstituted complexes showed a predominance of the ionic character. In addition, high donor-acceptor interaction energies were obtained, indicating a good superposition between the s and p orbitals involved in the Zn-S bond.

METHODS

This work consists in theoretical studies of Zn²⁺ complexes with alkyl xanthate ligands, with different structures, where optimization and normal modes calculations were performed at different DFT levels: M06L, M06-2X, wB97XD, and B3LYP/6-311++G**+LANL2TZ, with Gaussian09 program. The process of substitution of two aqua by two xanthate ligands was analyzed in stages, forming cationic and neutral complexes, in the first and second stages, respectively. In addition, electronic energy decomposition (EDA) and natural bond orbital (NBO) analysis were performed at level M06L/6-311++G**+LANL2TZ with Gamess program.

Comprehensive Theoretical Study on Four Typical Intramolecular Hydrogen Shift Reactions of Peroxy Radicals: Multireference Character, Recommended Model Chemistry, and Kinetics

Intramolecular hydrogen shift reactions in peroxy radicals (RO₂^• → ^•QOOH) play key roles in the low-temperature combustion and in the atmospheric chemistry. In the present study, we found that a mild-to-moderate multireference character of a potential energy surface (PES) is widely present in four typical hydrogen shift reactions of peroxy radicals (RO₂^•, R = ethyl, vinyl, formyl methyl, and acetyl) by a systematic assessment based on the T₁ diagnostic, %TAE diagnostic, M diagnostic, and contribution of the dominant configuration of the reference CASSCF wavefunction (C₀²). To assess the effects of these inherent multireference characters on electronic structure calculations, we compared the PESs of the four reactions calculated by the multireference method CASPT2 in the complete basis set (CBS) limit, single-reference method CCSD(T)-F12, and single-reference-based composite method WMS. The results showed that ignoring the multireference character will introduce a mean unsigned deviation (MUD) of 0.46-1.72 kcal/mol from CASPT2/CBS results by using the CCSD(T)-F12 method or a MUD of 0.49-1.37 kcal/mol by WMS for three RO₂^• reactions (R = vinyl, formyl methyl, and acetyl) with a stronger multireference character. Further tests by single-reference Kohn-Sham (KS) density functional theory methods showed even larger deviations. Therefore, we specifically developed a new hybrid meta-generalized gradient approximation (GGA) functional M06-HS for the four typical H-shift reactions of peroxy radicals based on the WMS results for the ethyl peroxy radical reaction and on the CASPT2/CBS results for the others. The M06-HS method has an averaged MUD of 0.34 kcal/mol over five tested basis sets against the benchmark PESs, performing best in the tested 38 KS functionals. Last, in a temperature range of 200-3000 K, with the new functional, we calculated the high-pressure-limit rate coefficients of these H-shift reactions by the multi-structural variational transition-state theory with the small-curvature tunneling approximation (MS-CVT/SCT) and the thermochemical properties of all of the involved key radicals by the multi-structural torsional (MS-T) anharmonicity approximation method.

Atomic Electronic Structure Calculations with Hermite Interpolating Polynomials

We have recently described the implementation of atomic electronic structure calculations within the finite element method with numerical radial basis functions of the form χ_μ(r) = r^-1B_μ(r), where high-order Lagrange interpolating polynomials (LIPs) were used as the shape functions B_μ(r). In this work, we discuss how χ_μ(r) can be evaluated in a stable manner at small r and also revisit the choice of the shape functions B_μ(r). Three kinds of shape functions are considered: in addition to the C0 continuous LIPs, we consider the analytical implementation of first-order Hermite interpolating polynomials (HIPs) that are C1 continuous, as well as numerical implementations of n-th order (Cn continuous) HIPs that are expressed in terms of an underlying high-order LIP basis. Furnished with the new implementation, we demonstrate that the first-order HIPs are reliable even with large numbers of nodes and that they also work with nonuniform element grids, affording even better results in atomic electronic structure calculations than LIPs with the same total number of basis functions. We demonstrate that discontinuities can be observed in the spin-σ local kinetic energy τ_σ in small LIP basis sets, while HIP basis sets do not suffer from such issues; however, either set can be used to reach the complete basis set limit with smooth τ_σ. Moreover, we discuss the implications of HIPs on calculations with meta-GGA functionals with a number of recent meta-GGA functionals, and we find most Minnesota functionals to be ill-behaved. We also examine the potential usefulness of the explicit control over the derivative in HIPs for forming numerical atomic orbital basis sets, but we find that confining potentials are still likely a better option.

Meta-GGA Density Functional Calculations on Atoms with Spherically Symmetric Densities in the Finite Element Formalism

Density functional calculations on atoms are often used for determining accurate initial guesses as well as generating various types of pseudopotential approximations and efficient atomic-orbital basis sets for polyatomic calculations. To reach the best accuracy for these purposes, the atomic calculations should employ the same density functional as the polyatomic calculation. Atomic density functional calculations are typically carried out employing spherically symmetric densities, corresponding to the use of fractional orbital occupations. We have described their implementation for density functional approximations (DFAs) belonging to the local density approximation (LDA) and generalized gradient approximation (GGA) levels of theory as well as Hartree-Fock (HF) and range-separated exact exchange [Lehtola, S. Phys. Rev. A 2020, 101, 012516]. In this work, we describe the extension to meta-GGA functionals using the generalized Kohn-Sham scheme, in which the energy is minimized with respect to the orbitals, which in turn are expanded in the finite element formalism with high-order numerical basis functions. Furnished with the new implementation, we continue our recent work on the numerical well-behavedness of recent meta-GGA functionals [Lehtola, S.; Marques, M. A. L. J. Chem. Phys. 2022, 157, 174114]. We pursue complete basis set (CBS) limit energies for recent density functionals and find many to be ill-behaved for the Li and Na atoms. We report basis set truncation errors (BSTEs) of some commonly used Gaussian basis sets for these density functionals and find the BSTEs to be strongly functional dependent. We also discuss the importance of density thresholding in DFAs and find that all of the functionals studied in this work yield total energies converged to 0.1 μE_h when densities smaller than 10^-11a₀^-3 are screened out.

Comparison of the Performance of Density Functional Methods for the Description of Spin States and Binding Energies of Porphyrins

This work analyzes the performance of 250 electronic structure theory methods (including 240 density functional approximations) for the description of spin states and the binding properties of iron, manganese, and cobalt porphyrins. The assessment employs the Por21 database of high-level computational data (CASPT2 reference energies taken from the literature). Results show that current approximations fail to achieve the "chemical accuracy" target of 1.0 kcal/mol by a long margin. The best-performing methods achieve a mean unsigned error (MUE) <15.0 kcal/mol, but the errors are at least twice as large for most methods. Semilocal functionals and global hybrid functionals with a low percentage of exact exchange are found to be the least problematic for spin states and binding energies, in agreement with the general knowledge in transition metal computational chemistry. Approximations with high percentages of exact exchange (including range-separated and double-hybrid functionals) can lead to catastrophic failures. More modern approximations usually perform better than older functionals. An accurate statistical analysis of the results also casts doubts on some of the reference energies calculated using multireference methods. Suggestions and general guidelines for users are provided in the conclusions. These results hopefully stimulate advances for both the wave function and the density functional side of electronic structure calculations.

Photodissociation Spectroscopy and Photofragment Imaging to Probe Fe+(Benzene)1,2 Dissociation Energies

Tunable laser photodissociation spectroscopy measurements and photofragment imaging experiments are employed to investigate the dissociation energy of the Fe+(benzene) ion-molecule complex. Additional spectroscopy measurements determine the dissociation energy of Fe+(benzene)2. The dissociation energies for Fe+(benzene) determined from the threshold for the appearance of the Fe+ fragment (48.4 ± 0.2 kcal/mol) and photofragment imaging (≤49.3 ± 3.2 kcal/mol) agree nicely with each other and with the value determined previously by collision-induced dissociation (49.5 ± 2.9 kcal/mol), but they are lower than the values produced by computational chemistry at the density functional theory level using different functionals recommended for transition-metal chemistry. The threshold measurement for Fe+(benzene)2 (43.0 ± 0.2 kcal/mol) likewise agrees with the value (44.7 ± 3.8 kcal/mol) from previous collision-induced dissociation measurements.

Chemical Bonding in Isoelectronic NdO2 and SmO22

Neodymium dioxide (NdO₂) and samarium dioxide cation (SmO₂²⁺) are isoelectronic molecules. Here we used calculations of the spin-orbit-free wave functions to study and compare their geometries, spin states, and bonding. We used Kohn-Sham density functional theory with the B97-1 exchange-correlation functional to optimize the geometries and found that the two molecules have different ground spin states and structures. NdO₂ favors a linear ONdO triplet structure, and SmO₂²⁺ favors a linear SmOO²⁺ quintet structure. We then used state-averaged complete-active-space self-consistent-field (SA-CASSCF) calculations to investigate the bonding characteristics of NdO₂ and SmO₂²⁺ in various geometries. We found that in NdOO, one electron is transferred from Nd to O, while in SmO₂²⁺, there is no electron transfer between Sm and O. The SA-CASSCF calculation also shows that ONdO has a stronger bonding orbital between a 4f orbital of Nd and a p_z orbital of oxygen atoms. We compared three multireference methods, namely, extended multistate complete active space second-order perturbation theory (XMS-CASPT2), extended multistate pair-density functional theory (XMS-PDFT), and compressed multistate pair-density functional theory (CMS-PDFT), for calculating the spin-orbit-free energies of various isomers of both molecules. We found that although XMS-PDFT and CMS-PDFT are at the same cost level as SA-CASSCF, they give results with the same accuracy as given for the much more demanding XMS-CASPT2 calculation. Between the two multistate PDFT methods, CMS-PDFT is better at giving good degeneracies for states that should be degenerate.

Salphen metal complexes as potential anticancer agents: interaction profile and selectivity studies toward the three G-quadruplex units in the KIT promoter

DNA G-rich sequences can organize in four-stranded structures called G-quadruplexes (G4s). These motifs are enriched in significant sites within the human genomes, including telomeres and promoters of cancer related genes. For instance, KIT proto-oncogene promoter, associated with diverse cancers, contains three adjacent G4 units, namely Kit2, SP, and Kit1. Aiming at finding new and selective G-quadruplex binders, we have synthesized and characterized five non-charged metal complexes of Pt(II), Pd(II), Ni(II), Cu(II) and Zn(II) of a chlorine substituted Salphen ligand. The crystal structure of the Pt(II) and Pd(II) complexes was determined by XRPD. FRET measurements indicated that Pt(II) and Pd(II) compounds stabilize Kit1 and Kit2 G4s but not SP, telomeric and double stranded DNA. Spectroscopic investigations (UV-Vis, circular dichroism and fluorescence) suggested the Cu(II) complex as the most G4-selective compound. Interestingly, docking simulations indicate that the synthesized compounds fit groove binding pockets of both Kit1 and Kit2 G4s. Moreover, they exhibited dose-dependent cytotoxic activity in MCF-7, HepG2 and HeLa cancer cells.

Photodissociation Spectroscopy and Photofragment Imaging of the Fe+(Acetylene) Complex

Tunable laser photodissociation spectroscopy in the 700-400 nm region and photofragment imaging experiments are employed to investigate the Fe⁺(acetylene) ion-molecule complex. At energies above a threshold at 679 nm, continuous dissociation is detected throughout the visible wavelength region, with regions of broad structure. Comparison to the spectrum predicted by time-dependent density functional theory (TD-DFT) indicates that the complex has a quartet ground state. The dissociation threshold for Fe⁺(acetylene) at 679 nm provides the dissociation energy on the quartet potential energy surface. Correction for the atomic quartet-sextet spin state energy difference provides an adiabatic dissociation energy of 36.8 ± 0.2 kcal/mol. Photofragment imaging of the Fe⁺ photoproduct produced at 603.5 nm produces significant kinetic energy release (KER). The photon energy and the maximum value of the KER provide an upper limit on the dissociation energy of D₀ ≤ 34.6 ± 3.2 kcal/mol. The dissociation energies determined from the spectroscopy and photofragment imaging experiments agree nicely with the value determined previously by collision-induced dissociation (38.0 ± 2.6 kcal/mol). However, both values are significantly lower than those produced by computational chemistry at the DFT level using different functionals recommended for transition-metal chemistry.

Performance of Screened-Exchange Functionals for Band Gaps and Lattice Constants of Crystals

Kohn-Sham density functional theory is the most widely used method for electronic structure calculations of solid-state systems. The screened-exchange functionals developed following the influential work of Scuseria and co-workers in 2003-2006 have significantly improved the accuracy of the predictions of solid-state properties. This work assesses six screened-exchange density functionals for the prediction of 60 band gaps (database BG60) and 68 lattice constants (database LC68). The band gaps are calculated with both consistently calculated lattice constants and experimental lattice constants. Results for the nonlocal screened-exchange functionals are compared with those for six widely used or recently developed local functionals. The results show that all the screened-exchange functionals have smaller mean absolute errors (MAEs) than any of the local functionals. All the functionals except HLE17 overestimate (on average) the lattice constants, and M06-SX gives the best performance among the compared functionals, with a MAE of 0.051 Å. All the functionals underestimate (on average) the band gaps, and M06-SX outperforms all other functionals, with a MAE of 0.47 eV. M06-SX also has the lowest root-mean-squared error for both LC68 and BG60. For the subdatabases of BG60, M06-SX shows better performance for ionic crystals and systems with large band gaps, while HSE12s gives better results for semiconductors and systems with small band gaps. Overall, M06-SX shows the best performance for solid-state systems, followed by N12-SX and HSE12s. The best-performing local functionals are M06-L, revM06-L, and HLE17 for band gaps and M06-L and revM06-L for lattice constants. We found that M06-SX, revM06-L, and N12-SX not only are well optimized for a broad array of chemical properties but also have very good performance for the databases in this paper, making them well-suited for applications involving heterogeneous chemistry.

Supervised learning of a chemistry functional with damped dispersion

Kohn-Sham density functional theory is widely used in chemistry, but no functional can accurately predict the whole range of chemical properties, although recent progress by some doubly hybrid functionals comes close. Here, we optimized a singly hybrid functional called CF22D with higher across-the-board accuracy for chemistry than most of the existing non-doubly hybrid functionals by using a flexible functional form that combines a global hybrid meta-nonseparable gradient approximation that depends on density and occupied orbitals with a damped dispersion term that depends on geometry. We optimized this energy functional by using a large database and performance-triggered iterative supervised training. We combined several databases to create a very large, combined database whose use demonstrated the good performance of CF22D on barrier heights, isomerization energies, thermochemistry, noncovalent interactions, radical and nonradical chemistry, small and large systems, simple and complex systems and transition-metal chemistry.

Efficient and Accurate Description of Diels-Alder Reactions Using Density Functional Theory

Modeling chemical reactions using Quantum Chemistry is a widely used predictive strategy capable to complement experiments in order to understand the intrinsic mechanisms guiding the chemicals towards the most favorable reaction products. However, at this purpose, it is mandatory to use reliable and computationally tractable theoretical methods. In this work, we focus on six Diels-Alder reactions of increasing complexity and perform an extensive benchmark of middle- to low-cost computational approaches to predict the characteristic reactions energy barriers. We found that Density Functional Theory, using the ωB97XD, LC-ωPBE, CAM-B3LYP, M11 and MN12SX functionals, with empirical dispersion corrections coupled to an affordable 6-31G basis set, provides quality results for this class of reactions, at a small computational effort. Such efficient and reliable simulation protocol opens perspectives for hybrid QM/MM molecular dynamics simulations of Diels-Alder reactions including explicit solvation.

Formation Mechanism of Inter-Crosslink in DNA by Nitrogen Oxides Pollutants through A Diazonium Intermediate

Outdoor air pollution is a mixture of multiple atmospheric pollutants, among which nitrogen oxide (NOx) stands out due to its association with several diseases. NOx reactivity can conduct to DNA damage as severe as interstrand crosslinks (ICL) formation, that in turn is able to block DNA replication and transcription. Experimental studies have suggested that the ICL formation due to NOx is realized through a diazonium intermediate (DI). In this work, we have modeled the DI structure, including a DNA double-strand composed of two base pairs GC/CG, being diazotized as one of the guanine nucleotides. The structural stability of DNA with DI lesion was essayed through 500 ns molecular dynamics simulations. It was found that the DNA structure of the oligonucleotide is stable when the DI is present since the loss of a Guanine-Cytosine hydrogen bond is replaced by the presence of two cation-π interactions. Additionally, we have studied the mechanism of formation of a crosslink between the two guanine nucleobases from the modeled DI by carrying out DFT calculations at the M06-L/DNP+ level of theory. Our results show that the mechanism is thermodynamically favored by a strong stabilization of the ICL product, and the process is kinetically viable since its limiting stage is accessible.

Unusual In-plane Aromaticity Facilitates Intramolecular Hydrogen Transfer in Long-Bonded cis-Isonitrosyl Methoxide

The hydrogen-atom transfer from methoxy radical to nitric oxide, leading to the formation of formaldehyde and nitroxyl, represents a secondary reaction of photodissociation of methyl nitrite, which is used as rocket fuel. In this study, we explored the potential energy profile of the hydrogen-atom transfer using the electronic structure calculations at the DLPNO-CCSD(T)/aug-cc-pVTZ level of theory for two isomeric forms (cis and trans) of the pre-reaction complex. The cis-oriented pre-reaction complex has a weak elongated O─O bond, which gets further elongated in the hydrogen transfer transition state. This O─O bond stabilizes the pre-reaction complex by 32.9 kJ/mol. The O─O-induced stabilization is even greater for the transition state (48.2 kJ/mol), which was unexpected because of the larger O─O distance in the transition state structure. To address this paradox, we performed the electronic structure analysis of the reaction participants using the valence bond (VB) theory, natural resonance theory, topological analysis of the electron density and its derivatives, and analysis of the electron localization function distribution. This combined analysis led to the conclusion that the cis-transition state for hydrogen transfer, instead of being directly stabilized by the O─O interaction, gained substantial stabilization from the in-plane five-center six-electron aromaticity.

Ionic Dynamics and Vibrational Spectral Diffusion of a Protic Alkylammonium Ionic Salt through Intrinsic Cationic N-H Vibrational Probe from FPMD Simulations

We employed density functional theory (DFT)-based molecular dynamics simulations to explore the structure, dynamics, and spectral properties of the protic ionic entity trimethylammonium chloride (TMACl). Structural investigations include calculating the site-site radial distribution functions (RDFs), the distribution of constituent cations and anions in three-dimensional space, and combined distribution functions of the hydrogen-bonded pair RDF versus angle, revealing the structural characteristics of the ionic solvation and the intermolecular interactions within ions. Further, we determined the instantaneous vibrational stretching frequencies of the intrinsic N-H stretch probe modes by applying the time-series wavelet method. The associated ionic dynamics within the protic ionic compound were investigated by calculating the time-evolution of the fluctuating frequencies and the frequency-time correlation functions (FFCFs). The time scale related to the local structural relaxation process and the average hydrogen bond lifetime, ion cage dynamics, and mean squared displacement were investigated. The faster decay component of the FFCFs, depicting the intermolecular motion of intact hydrogen bonds in TMACl, is 0.07 ps for the Perdew-Burke-Ernzerhof (PBE)-based simulation and 0.06 ps for the PBE-D2 representation. The slower time scale of the longer picosecond decay time component of PBE and PBE-D2 representations are 3.13 and 2.87 ps, respectively. These picosecond time scales represent more significant fluctuations of the hydrogen-bonding partners in the ionic entity and hydrogen-bond jump events accompanied by large angular jumps. The longest picosecond time scales represent structural relaxation, including large angular jumps and ion-pair dynamics. Also, ion cage lifetimes correlate with the slowest time scale of the associated dynamics of vibrational spectral diffusion despite the type of DFT functional. This study benchmarks DFT treatments of the exchange-correlation functional with and without the van der Waals (vdW) dispersion correction scheme. The inclusion of vdW interactions to the PBE functional represents a less structured state of the ionic entity and faster dynamics of the molecular motions relative to the one predicted by the PBE system. All the results illustrate the necessity of accurately describing the Coulomb interactions, vdW dispersive interactive forces, and localized hydrogen bonds required to sustain the energetic balance in this ionic salt.

Solid-state performance of a meta-GGA screened hybrid density functional constructed from Pauli kinetic enhancement factor dependent semilocal exchange hole

The semilocal form of the exchange hole is highly useful in developing non-local range-separated hybrid density functionals for finite and extended systems. The way to construct the conventional exact exchange hole model is based on either the Taylor series expansion or the reverse engineering technique from the corresponding exchange energy functional. Although the latter technique is quite popular in context of generalized gradient approximation (GGA) functionals, the same for the meta-GGA functionals is not so much explored. Thus, in this study, we propose a reverse-engineered semilocal exchange hole of a meta-GGA functional, that depends only on the meta-GGA ingredient α (also known as the Pauli kinetic energy enhancement factor). The model is used subsequently to design the short-range-separated meta-GGA hybrid density functional. We show that the present method can be successfully applied for several challenging problems in the context of solids, especially for which the GGA based hybrid fails drastically. This assessment proves that the present functional is quite useful for materials sciences. Finally, we also use this method for several molecular test cases, where the results are also as comparative as its base semilocal functional.

Current Status of Quantum Chemical Studies of Cyclodextrin Host-Guest Complexes

This article aims to review the application of various quantum chemical methods (semi-empirical, density functional theory (DFT), second order Møller-Plesset perturbation theory (MP2)) in the studies of cyclodextrin host-guest complexes. The details of applied approaches such as functionals, basis sets, dispersion corrections or solvent treatment methods are analyzed, pointing to the best possible options for such theoretical studies. Apart from reviewing the ways that the computations are usually performed, the reasons for such studies are presented and discussed. The successful applications of theoretical calculations are not limited to the determination of stable conformations but also include the prediction of thermodynamic properties as well as UV-Vis, IR, and NMR spectra. It has been shown that quantum chemical calculations, when applied to the studies of CD complexes, can provide results unobtainable by any other methods, both experimental and computational.

Recommendation of Orbitals for G0W0 Calculations on Molecules and Crystals

The many-body GW approximation, especially the G₀W₀ method, has been widely used for condensed matter and molecules to calculate quasiparticle energies for ionization, electron attachment, and band gaps. Because G₀W₀ calculations are well-known to have a strong dependence on the orbitals, the goal of the present work is to provide guidance on the choice of density functional used to generate orbitals and to recommend a choice that gives the most broadly accurate results. We have systematically investigated the dependence of G₀W₀ calculations on the orbitals for 100 molecules and 8 crystals by considering orbitals obtained with a diverse set of Kohn-Sham (KS) and generalized KS (GKS) functionals (63 functionals plus Hartree-Fock). The percentage of Hartree-Fock exchange employed in density functionals has been found to have strong influence on the predicted molecular ionization energy and crystal fundamental band gaps (with optimum values between 40 and 56%), but to have less effect on predicting molecular electron affinities. The low cost of the Gaussian implementation, even with hybrid functionals in periodic calculations, the better performance of global hybrids as compared to range-separated hybrids of either than screened exchange or long-range-corrected type, and the relatively low cost of global-hybrid-functional periodic calculations using Gaussians means that one can employ global-hybrid functionals at a very reasonable cost and obtain more accurate band gaps of semiconductors than are obtained by the methods currently widely employed, namely local gradient approximations. We single out three global-hybrid functionals that give especially good results for both molecules (100 in the test set) and crystals (8 in the test set, for all of which our benchmark data are the proper band gap rather than an optical band gap uncorrected for exciton effects).

Revisiting the Performance of Time-Dependent Density Functional Theory for Electronic Excitations: Assessment of 43 Popular and Recently Developed Functionals from Rungs One to Four

In this paper, the performance of more than 40 popular or recently developed density functionals is assessed for the calculation of 463 vertical excitation energies against the large and accurate QuestDB benchmark set. For this purpose, the Tamm-Dancoff approximation offers a good balance between computational efficiency and accuracy. The functionals ωB97X-D and BMK are found to offer the best performance overall with a root-mean square error (RMSE) of around 0.27 eV, better than the computationally more demanding CIS(D) wave function method with a RMSE of 0.36 eV. The results also suggest that Jacob's ladder still holds for time-dependent density functional theory excitation energies, though hybrid meta generalized-gradient approximations (meta-GGAs) are not generally better than hybrid GGAs. Effects of basis set convergence, gauge invariance correction to meta-GGAs, and nonlocal correlation (VV10) are also studied, and practical basis set recommendations are provided.

Spectroscopic and computational studies of the solid state photophysical properties of a biscoumarin dye

The solid state photophysical properties of the 3,3'-paraphenyl bis[6,8-dimethoxy-2H-chromen-2-one] symmetrical biscoumarin material were investigated by optical spectroscopy techniques and by theoretical calculations. Vibrational analysis using IR absorption and Raman scattering techniques carried out together with DFT theoretical calculations have confirmed the structure of this biscoumarin. The geometry optimization using different functionals reveal a nonplanar equilibrium structure with a dihedral between the phenyl and the pyran rings of about 142°. The UV-Visible absorption measurements and the TDDFT simulation show that this biscoumarin is characterized by a bicomponent feature resulting from ππ* electronic transitions and Intramolecular Charge Transfer (ICT). Solid state photoluminescence showed a bright blue-green emission at 506 nm with a large stokes shift estimated at 146 nm, and the temperature dependence study of this emission reveals two thermal evolution regimes. Finally, these good optical properties, as well as the stability of the emission, make this biscoumarin dye of potential interest for optoelectronic applications.