Robust and Efficient Implicit Solvation Model for Fast Semiempirical Methods

Complexes of resorcin[4]arene with secondary amines: synthesis, solvent influence on "in-out" structure, and theoretical calculations of non-covalent interactions

Resorcin[4]arenes (R[4]A) are macrocyclic compounds with a cavity structure. Despite a relatively small cavity, these compounds are capable of forming complexes with small organic molecules. The current paper focuses on the synthesis of complexes between R[4]A and secondary aliphatic amines (sec-amines). Through NMR spectroscopy, it was observed that "in-out" complexes are formed depending on the solvent. It was also found that the stoichiometry of the formed complexes depends on the size of the amine molecule. The automated interaction sites screening (aISS) made it possible to generate molecular ensembles of complexes. The geometry of the ensembles was first optimized with the r2scan-3c functional and, finally, the structure with the lowest energy, with the functional PBE0-D4/mTZVPP/CPCM. The Hartree-Fock plus London dispersion (HFLD) method was used for the study of non-covalent interactions (NCI). The calculations lead to the conclusion that a reduction in electrostatic interactions and an increase in exchange and dispersion interactions in CHCl3 in relation to DMSO are the driving forces behind the placement of sec-amine molecules into the R[4]A cavity and the formation of "in" type complexes.

Infrared Spectroscopy of Liquid Solutions as a Benchmarking Tool of Semiempirical QM Methods: The Case of GFN2-xTB

The accurate description of large molecular systems has triggered the development of new computational methods. Due to the computational cost of modeling large systems, the methods usually require a trade-off between accuracy and speed. Therefore, benchmarking to test the accuracy and precision of the method is an important step in their development. The typical gold standard for evaluating these methods is isolated molecules, because of the low computational cost. However, the advent of high-performance computing has made it possible to benchmark computational methods using observables from more complex systems such as liquid solutions. To this end, infrared spectroscopy provides a suitable set of observables (i.e., vibrational transitions) for liquid systems. Here, IR spectroscopy observables are used to benchmark the predictions of the newly developed GFN2-xTB semiempirical method. Three different IR probes (i.e., N-methylacetamide, benzonitrile, and semiheavy water) in solution are selected for this purpose. The work presented here shows that GFN2-xTB predicts central frequencies with errors of less than 10% in all probes. In addition, the method captures detailed properties of the molecular environment such as weak interactions. Finally, the GFN2-xTB correctly assesses the vibrational solvatochromism for N-methylacetamide and semiheavy water but does not have the accuracy needed to properly describe benzonitrile. Overall, the results indicate not only that GFN2-xTB can be used to predict the central frequencies and their dependence on the molecular environment with reasonable accuracy but also that IR spectroscopy data of liquid solutions provide a suitable set of observables for the benchmarking of computational methods.

When catchers meet - a computational study on the dimerization of the Buckycatcher

We study the dimerization of the buckycatcher in gas phase and in toluene. We created an extensive library of 36 different complexes, which were characterized at semi-empirical and DFT levels. Semi-empirical geometries and dimerization energies compare well against reference data or Density Functional Theory calculations we performed. Born-Oppenheimer molecular dynamics was used to understand what happens when two molecules of the buckycatcher meet, allowing us to infer on the lack of kinetic barriers when dimers form. Thermodynamically, it is possible that room temperature solutions contain dimerized buckycatcher. Using a very simple exchange model, it is shown, however, that dimerization cannot compete thermodynamically against complexation with fullerenes, which accounts for experimental observations.

Combined molecular dynamics and coordinate driving method for automatically searching complicated reaction pathways

The combined molecular dynamics and coordinate driving (MD/CD) method is updated and generalized in this work to broaden its applications in automatically searching reaction pathways for complicated reactions. In this updated version, MD simulations are performed with the GFN's family of methods to systematically sample conformers for almost any systems with atomic numbers Z ≤ 86. The improved CD procedure is greatly accelerated by applying a pre-screening stage at the semiempirical GFN2-xTB level. An automatic module based on the Marcus theory and its improved version (the Wolynes theory) is designed to include single electron transfer (SET) processes into reaction pathways. The capabilities of this method are demonstrated by exploring the most possible reaction pathways of three experimentally reported reactions: the organophosphine-catalyzed trans phosphinoboration, the Fe(II) complex-mediated C(sp2)-H borylation reaction, and the SET-triggered deaminative radical cross-coupling reaction. Comprehensive reaction networks are obtained for all three reactions with reasonable computational costs. Detailed mechanisms for these reactions can account for the reported experimental facts.

Solvent-controlled formation of alkali and alkali-earth-secured cucurbituril/guest trimers

Cucurbit[7]uril (CB[7]) encapsulates adamantyl and trimethylsilyl substituents of positively charged guests in dimethyl sulfoxide (DMSO). Unlike in water or deuterium oxide, addition of a selection of alkali and alkali-earth cations with van der Waals radii between 1.0 and 1.4 Å (Na+, K+, Ca2+, Sr2+, Ba2+ and Eu3+) to the CB[7]/guest complexes triggers their cation-mediated trimerization, a process that is very slow on the nuclear magnetic resonance (NMR) time scale. Smaller (Li+, Mg2+) or larger cations (Rb+, Cs+ or NH4+) are inert. The trimers display extensive CH-O interactions between the equatorial and pseudo-equatorial hydrogens of CB[7] and the carbonyl rim of the neighboring CB[7] unit in the trimer, and a deeply nested cation between the three interacting carbonylated CB[7] rims; a counteranion is likely perched in the shallow cavity formed by the three outer walls of CB[7] in the trimer. Remarkably, a guest must occupy the cavity of CB[7] for trimerization to take place. Using a combination of semi-empirical and density functional theory techniques in conjunction with continuum solvation models, we showed that trimerization is favored in DMSO, and not in water, because the penalty for the partial desolvation of three of the six CB[7] portals upon aggregation into a trimer is less unfavorable in DMSO compared to water.

PyConSolv: A Python Package for Conformer Generation of (Metal-Containing) Systems in Explicit Solvent

We introduce PyConSolv, a freely available Python package that automates the generation of conformers of metal- and nonmetal-containing complexes in explicit solvent, through classical molecular dynamics simulations. Using a streamlined workflow and interfacing with widely used computational chemistry software, PyConSolv is an all-in-one tool for the generation of conformers in any solvent. Input requirements are minimal; only the geometry of the structure and the desired solvent in xyz (XMOL) format are needed. The package can also account for charged systems, by including arbitrary counterions in the simulation. A bonded model parametrization is performed automatically, utilizing AmberTools, ORCA, and Multiwfn software packages. PyConSolv provides a selection of preparametrized solvents and counterions for use in classical molecular dynamics simulations. We show the applicability of our package on a number of (transition-metal-containing) systems. The software is provided open source and free of charge.

Tweaking the conjugation effects on a pair of new triazene compounds by targeted deprotonation: a spectroscopic and theoretical overview

CONTEXT

Triazene compounds (-NNN(H)-) exhibit versatility in biological, physical, and chemical applications. In their anionic form (-NNN-)(-), they can act as coordinating sites for metals, forming metallic complexes. In this study, two new isomeric triazene compounds with meta- and para-substituents in their neutral and anionic forms were investigated. A combination of detailed experimental spectroscopic characterization and computational chemistry analyses were employed. The new compounds, 1-(2-benzamide)-3-(3-nitrophenyl) triazene (m-TZN) and 1-(2-benzamide)-3-(4-nitrophenyl) triazene (p-TZN), were compared to 1,3-diphenyltriazene (dph-TZN) to understand the effects of functionalization and targeted triazene deprotonation. The anionic forms are stable, and our investigation suggests that these new compounds are suitable tridentate ligands that can act as chelating agents for metallic cations in stable complexes, similar to those found in vitamin B12.

METHODS

The absorption, vibrational, and electronic properties of the newly synthesized triazene compounds were extensively characterized using FT-IR/FT-Raman and UV-Vis spectroscopy. Their distinct molecular properties, intramolecular hydrogen bond effects, stability, and electronic transitions were investigated using the ORCA software. These analyses involved DFT and TD-DFT calculations at the ωB97X-D3/Def2-TZVP level of theory with THF CPCM implicit solvation to determine the molecular topology and electronic structure. The advanced STEOM-DLPNO-CCSD method for excited states was employed, enabling an in-depth analysis of ground and excited-state chemistry, accounting for precise electronic correlation and solvation effects. Explicit THF solvation was tested on the full TD-DFT ωB97X-D3/Def2-TZVP level and using ONIOM on the STEOM calculation. Reactivity was studied using Fukui functions, and action as chelating agents was investigated using GFN-xTB2 and DFT.

Extended Conductor-like Polarizable Continuum Solvation Model (CPCM-X) for Semiempirical Methods

We have developed a new method to accurately account for solvation effects in semiempirical quantum mechanics based on a polarizable continuum model (PCM). The extended conductor-like polarizable continuum model (CPCM-X) incorporates a computationally efficient domain decomposition conductor-like screening model (ddCOSMO) for extended tight binding (xTB) methods and uses a post-processing approach based on established solvation models, like the conductor-like screening model for real solvents (COSMO-RS) and the universal solvent model based on solute electron density (SMD). According to various benchmarks, the approach performs well across a broad range of systems and applications, including hydration free energies, non-aqueous solvation free energies, and large supramolecular association reactions of neutral and charged species. Our method for computing solvation free energies is much more accurate than the current methods in the xtb program package. It improves the accuracy of solvation free energies by up to 40% for larger supramolecular association reactions to match even the accuracy of higher-level DFT-based solvation models like COSMO-RS and SMD while being computationally more than 2 orders of magnitude faster. The proposed method and the underlying ddCOSMO model are readily available for a wide variety of solvents and are accessible in xtb for use in various computational applications.

as a Versatile and Predictable Chiral Stationary Phase for the Resolution of Racemic Mixtures

Metal-organic frameworks (MOFs) have become promising materials for multiple applications due to their controlled dimensionality and tunable properties. The incorporation of chirality into their frameworks opens new strategies for chiral separation, a key technology in the pharmaceutical industry as each enantiomer of a racemic drug must be isolated. Here, we describe the use of a combination of computational modeling and experiments to demonstrate that high-performance liquid chromatography (HPLC) columns packed with TAMOF-1 as the chiral stationary phase are efficient, versatile, robust, and reusable with a wide array of mobile phases (polar and non-polar). As proof of concept, in this article, we report the resolution with TAMOF-1 HPLC columns of nine racemic mixtures with different molecular sizes, geometries, and functional groups. Initial in silico studies allowed us to predict plausible separations in chiral compounds from different families, including terpenes, calcium channel blockers, or P-stereogenic compounds. The experimental data confirmed the validity of the models and the robust performance of TAMOF-1 columns. The added value of in silico screening is an unprecedented achievement in chiral chromatography.

Chemoinformatic modelling of the antioxidant activity of phenolic compounds

BACKGROUND

Antioxidants are chemicals used to protect foods from deterioration by neutralizing free radicals and inhibiting the oxidative process. One approach to investigate the antioxidant activity is to develop quantitative structure-activity relationships (QSARs).

RESULTS

A curated database of 165 structurally heterogeneous phenolic compounds with the Trolox equivalent antioxidant capacity (TEAC) was developed. Molecular geometries were optimized by means of the GFN2-xTB semiempirical method and diverse molecular descriptors were obtained afterwards. For model development, V-WSP unsupervised variable reduction was used before performing the genetic algorithms-variable subset selection (GAs-VSS) to construct the best five-descriptor multiple linear regression model. The coefficient of determination and the root mean square error were used to measure the performance in calibration (R²  = 0.789 and RMSEC = 0.381), and test set prediction (Q²  = 0.748 and RMSEP = 0.416), along several cross-validation criteria. To thoroughly understand the TEAC prediction, a fully explained mechanism of action of the descriptors is provided. In addition, the applicability domain of the model defined a theoretical chemical space for reliable predictions of new phenolic compounds.

CONCLUSION

This in silico model conforms to the five principles stated by the Organisation for Economic Co-operation and Development. The model might be useful for virtual screening of the antioxidant chemical space and for identifying the most potent molecules related to an experimental measurement of TEAC activity. In addition, the model could assist chemists working on computer-aided drug design for the synthesis of new targets with improved activity and potential uses in food science. © 2023 Society of Chemical Industry.

Hybrid Machine Learning Approach to Predict the Site Selectivity of Iridium-Catalyzed Arene Borylation

The borylation of aryl and heteroaryl C-H bonds is valuable for the site-selective functionalization of C-H bonds in complex molecules. Iridium catalysts ligated by bipyridine ligands catalyze the borylation of the C-H bond that is most acidic and least sterically hindered in an arene, but predicting the site of borylation in molecules containing multiple arenes is difficult. To address this challenge, we report a hybrid computational model that predicts the Site of Borylation (SoBo) in complex molecules. The SoBo model combines density functional theory, semiempirical quantum mechanics, cheminformatics, linear regression, and machine learning to predict site selectivity and to extrapolate these predictions to new chemical space. Experimental validation of SoBo showed that the model predicts the major site of borylation of pharmaceutical intermediates with higher accuracy than prior machine-learning models or human experts, demonstrating that SoBo will be useful to guide experiments for the borylation of specific C(sp2)-H bonds during pharmaceutical development.

Borane-Catalyzed C-F Bond Functionalization of gem-Difluorocyclopropenes Enables the Synthesis of Orphaned Cyclopropanes

Herein, we disclose an approach to synthesize tert-alkyl cyclopropanes by leveraging C-F bond functionalization of gem-difluorocyclopropenes using tris(pentafluorophenyl)borane catalysis. The reaction proceeds through the intermediacy of a fluorocyclopropenium ion, which was confirmed by the isolation of [Ph2(C6D5)C3]+[(C6F5)3BF]-. We found that silylketene acetal nucleophiles were optimal reaction partners with fluorocyclopropenium ion intermediates yielding fully substituted cyclopropenes functionalized with two α-tert-alkyl centers (63-93% yield). The regioselectivity of the addition to cyclopropenium ions is controlled by their steric and electronic properties and enables access to 3,3-bis(difluoromethyl)cyclopropenes in short order. The resulting cyclopropene products are readily reduced to the corresponding orphaned cyclopropanes under hydrogenation conditions. Quantum chemical calculations reveal the nature of the C-F bond cleavage steps and provide evidence for catalysis by boron and not silylated oxonium ions, though Si-F bond formation is the enthalpic driving force for the reaction.

Revisiting Homochiral versus Heterochiral Interactions through a Long Detective Story of a Useful Azobis-Nitrile and Puzzling Racemate

This paper documents and reinvestigates the solid-state and crystal structures of 4,4'-azobis-4-cyanopentanoic acid (ACPA), a water-soluble azobis-nitrile of immense utility as a radical initiator in living polymerizations and a labile mechanophore that can be embedded within long polymer chains to undergo selective scission under mechanical activation. Surprisingly, for such applications, both the commercially available reagent and their derivatives are used as "single initiators" when this azonitrile is actually a mixture of stereoisomers. Although the racemate and meso compounds were identified more than half a century ago and their enantiomers were separated by classical resolution, there have been confusing narratives dealing with their characterization, the existence of a conglomeratic phase, and fractional crystallization. Our results report on the X-ray crystal structures of all stereoisomers for the first time, along with further details on enantiodiscrimination and the always intriguing arguments accounting for the stability of homochiral versus heterochiral crystal aggregates. To this end, metadynamic (MTD) simulations on stereoisomer molecular aggregates were performed to capture the incipient nucleation events at the picosecond time scale. This analysis sheds light on the driving homochiral aggregation of ACPA enantiomers.

DFT-based analysis of siderophore-metal ion interaction for efficient heavy metal remediation

Siderophores have great application potential in metal pollutant remediation because of their effective cost and friendly impact on the environment. However, the practical use of siderophores in the remediation of specific metals is rather limited because of the weak nonspecific interactions between the siderophores and different metals. Thus, screening for a siderophore with optimal interaction with a specific metal would be necessary. In this study, the interaction between metal ions and moieties that donate the oxygen ligands for the coordination of four types of siderophore (hydroxamates, catecholates, phenolates, and carboxylates) was modeled and analyzed. As revealed by DFT-based analysis, the four types of siderophore generally exhibited selection preference for different metal ions in the order Ga3+  > Al3+  > Fe3+  > Cr3+  > Ni2+  > Cu2+  > Zn2+  > Co2+  > Mn2+  > Hg2+  > Pb2+  > Cd2+, which was determined mainly by the electronegativity of the siderophore functional groups, the electronegativity of the metals, and the ionic radius of the metals, as well as the interaction between the siderophores and the metals. Moreover, the effect of linear or nonlinear (cyclic) structure on the affinity of each siderophore for different metal ions was evaluated. In most situations, metal-bound cyclic siderophores were found to be more stable than their linear counterparts. Thus, proper siderophores for the remediation of metal pollution may be rapidly screened using this model.

ONIOM meets : efficient, accurate, and robust multi-layer simulations across the periodic table

The computational treatment of large molecular structures is of increasing interest in fields of modern chemistry. Accordingly, efficient quantum chemical approaches are needed to perform sophisticated investigations on such systems. This engaged the development of the well-established "Our own N-layered integrated molecular orbital and molecular mechanics" (ONIOM) multi-layer scheme [L. W. Chung et al., Chem. Rev., 2015, 115, 5678-5796]. In this work, we present the specific implementation of the ONIOM scheme into the xtb semi-empirical extended tight-binding program package and its application to challenging transition-metal complexes. The efficient and broadly applicable GFNn-xTB and -FF methods are applied in the ONIOM framework to elucidate reaction energies, geometry optimizations, and explicit solvation effects for metal-organic systems with up to several hundreds of atoms. It is shown that an ONIOM-based combination of density functional theory, semi-empirical, and force-field methods can be used to drastically reduce the computational costs and thus enable the investigation of huge systems at almost no significant loss in accuracy.

Measurement of Water Saturation in Soybean Oil

In a previous study, it was observed that survivability was low when attempting to cryopreserve sperm cells in a nanoliter-sized droplet protected under soybean oil, in stark contrast to the high survival rates in milliliter-sized droplets. In this study, infrared spectroscopy was used to provide an estimate of the saturation concentration of water in soybean oil. By following the time evolution of the infrared absorption spectrum of water-oil mixtures, the saturation of water in soybean oil was found to reach equilibrium after 1 h. From the absorption spectra of neat water and neat soybean oil and the application of the Beer-Lambert law to an estimation of the absorption of a mixture from its individual components, it was estimated that the saturation concentration of water is 0.010 M. This estimate was supported by molecular modeling using the latest semiempirical methods (in particular, GFN2-xTB). While for most applications the very low solubility has little impact, the implications in those exceptions were discussed.

Intramolecular and intermolecular hole delocalization rules the reducer character of isolated nucleobases and homogeneous single-stranded DNA

The use of DNA strands as nanowires or electrochemical biosensors requires a deep understanding of charge transfer processes along the strand, as well as of the redox properties. These properties are computationally assessed in detail throughout this study. By applying molecular dynamics and hybrid QM/continuum and QM/QM/continuum schemes, the vertical ionization energies, adiabatic ionization energies, vertical attachment energies, one-electron oxidation potentials, and delocalization of the hole generated upon oxidation have been determined for nucleobases in their free form and as part of a pure single-stranded DNA. We show that the reducer ability of the isolated nucleobases is explained by the intramolecular delocalization of the positively charged hole, while the enhancement of the reducer character when going from aqueous solution to the strand correlates very well with the intermolecular hole delocalization. Our simulations suggest that the redox properties of DNA strands can be tuned by playing with the balance between intramolecular and intermolecular charge delocalization.

NDIPhos as a platform for chiral supramolecular ligands in rhodium-catalyzed enantioselective hydrogenation

Chiral naphthalene diimide ligands (NDIPhos) were exploited in rhodium-catalyzed enantioselective hydrogenation. The key feature of these ligands is their ability to self-assemble via π-π interactions to mimic bidentate ligands, offering a complementary method to traditional supramolecular strategies. This concept was further substantiated by computations with the composite electronic-structure method r²SCAN-3c.

Fragment-Based Calculations of Enzymatic Thermochemistry Require Dielectric Boundary Conditions

Electronic structure calculations on enzymes require hundreds of atoms to obtain converged results, but fragment-based approximations offer a cost-effective solution. We present calculations on enzyme models containing 500-600 atoms using the many-body expansion, comparing to benchmarks in which the entire enzyme-substrate complex is described at the same level of density functional theory. When the amino acid fragments contain ionic side chains, the many-body expansion oscillates under vacuum boundary conditions but rapid convergence is restored using low-dielectric boundary conditions. This implies that full-system calculations in the gas phase are inappropriate benchmarks for assessing errors in fragment-based approximations. A three-body protocol retains sub-kilocalorie per mole fidelity with respect to a supersystem calculation, as does a two-body calculation combined with a full-system correction at a low-cost level of theory. These protocols pave the way for application of high-level quantum chemistry to large systems via rigorous, ab initio treatment of many-body polarization.

The Interplay of Weakly Coordinating Anions and the Mechanical Bond: A Systematic Study of the Explicit Influence of Counterions on the Properties of (Pseudo)rotaxanes

Weakly coordinating anions (WCAs) have attracted much attention in recent years due to their ability to stabilise highly reactive cations. It may well be argued, however, that a profound understanding of what truly defines a WCA is still lacking, and systematic studies to unravel counterion effects are scarce. In this work, we investigate a supramolecular pseudorotaxane formation reaction, subject to a selection of anions, ranging from strongly to weakly coordinating, which not only aids in fostering our knowledge about anion coordination properties, but also provides valuable theoretical insight into the nature of the mechanical bond. We employ state-of-the-art DFT-based methods and tools, combined with isothermal calorimetry and 1H NMR experiments, to compute anion-dependent Gibbs free association energies ΔGa, as well as to evaluate intermolecular interactions. We find correlations between ΔGa and the anions’ solvation energies, which are exploited to calculate physico-chemical reaction parameters in the context of coordinating anions. Furthermore, we show that the binding situation within the (pseudo)rotaxanes can be mostly understood by straight-forward electrostatic considerations. However, quantum-chemical effects such as dispersion and charge-transfer interactions become more and more relevant when WCAs are employed.

Silmitasertib (CX-4945), a Clinically Used CK2-Kinase Inhibitor with Additional Effects on GSK3β and DYRK1A Kinases: A Structural Perspective

A clinical casein kinase 2 inhibitor, CX-4945 (silmitasertib), shows significant affinity toward the DYRK1A and GSK3β kinases, involved in down syndrome phenotypes, Alzheimer's disease, circadian clock regulation, and diabetes. This off-target activity offers an opportunity for studying the effect of the DYRK1A/GSK3β kinase system in disease biology and possible line extension. Motivated by the dual inhibition of these kinases, we solved and analyzed the crystal structures of DYRK1A and GSK3β with CX-4945. We built a quantum-chemistry-based model to rationalize the compound affinity for CK2α, DYRK1A, and GSK3β kinases. Our calculations identified a key element for CK2α's subnanomolar affinity to CX-4945. The methodology is expandable to other kinase selectivity modeling. We show that the inhibitor limits DYRK1A- and GSK3β-mediated cyclin D1 phosphorylation and reduces kinase-mediated NFAT signaling in the cell. Given the CX-4945's clinical and pharmacological profile, this inhibitory activity makes it an interesting candidate with potential for application in additional disease areas.

A Buckycatcher in Solution-A Computational Perspective

In this work, we study the buckycatcher (C₆₀H₂₈) in solution using quantum chemical models. We investigate the conformational equilibria in several media and the effects that molecules of solvent might have in interconversion barriers between the different conformers. These are studied in a hypothetical gas phase, in the dielectric of a solvent, as well as with hybrid solvation. In the latter case, due to a disruption of π-stacking interactions, the transition states are destabilized. We also evaluate the complexation of the buckycatcher with solvent-like molecules. In most cases studied, there should be no adducts formed because the enthalpy driving force cannot overcome entropic penalties.

Theoretical and Experimental Investigation of Autoxidation Propensity of Selected Drugs in Solution State

The C-H bond dissociation energy (BDE) of drug molecules is often used to estimate their relative propensities to undergo autoxidation. BDE calculations based on electronic structures provide a convenient means to estimate the risk for a given compound to degrade via autoxidation. This study aimed to verify the utility of calculated C-H BDEs of a range of drug molecules in predicting their autoxidation propensities, in the solution state. For the autoxidation study, 2,2'-azobis (2-methylpropionitrile) was employed as the solution state stressor, and the experimental reaction rate constants were determined employing ultraperformance liquid chromatographic (UPLC) methods. Reaction rates in the solution state were compared to the calculated C-H BDE values of the respective compounds. The results indicated a poor correlation for compounds in the solution state, and their relative stabilities could not be explained with C-H BDE. On the other hand, a favorable relationship was observed between the relative extent of ionization and the autoxidation rates of the selected compounds. In the solution state, factors such as the type and extent of drug ionization, degree and type of solvation have been shown to contribute to differences in reactivity. By applying the computational method involving the effect of H-atom abstraction and potential ionization sites in the molecule, the calculated C-H BDE should relate better to the experimental autoxidation rates.

ESIPT-based benzazole-pyromellitic diimide derivatives. A thermal, electrochemical, and photochemical investigation

This study describes the synthesis of new pyromellitic diimide (PMDI) derivatives obtained in good yields from the reaction between pyromellitic dianhydride and aminobenzazoles reactive to proton-transfer in the excited state (ESIPT). In this investigation, a non-ESIPT PMDI was also prepared for comparison. These compounds presented absorption maxima in the ultraviolet region attributed to the allowed ¹π-π* electronic transitions. Redshifted absorptions were observed for the ESIPT compounds (3b-3c) due to their π-extended conjugation if compared to the non-ESIPT dye (3a). The compounds presented fluorescence emissions between 300 and 600 nm, dependent on the solvent polarity and their chemical structures. While compound 3a presents a single emission, a dual fluorescence could be observed for compounds 3b-3c. As expected for ESIPT compounds, the emission at higher energies could be related to the excited enol conformer (E*), and the emission with a large Stokes shift was attributed to the keto tautomer (K*). All compounds presented fluorescence emission in the solid state, whereas the ESIPT derivatives presented redshifted emissions with a large Stokes shift, as expected. Cyclic voltammetry was employed to investigate the electrochemical properties of these compounds. The HOMO and LUMO energy levels were estimated at -5.40 to -5.00 eV and -2.84 to -2.62 eV, and good thermal stability (T_d > 150 °C) was observed. Quantum chemical calculationsusingTD-DFT and DFT were performed to investigate the electronic and photophysical features of the molecules.

DFT and ONIOM Simulation of 1,3-Butadiene Polymerization Catalyzed by Neodymium-Based Ziegler-Natta System

Using modern methods of quantum chemistry, a theoretical substantiation of the high cis-stereospecificity of 1,3-butadiene polymerization catalyzed by the neodymium-based Ziegler-Natta system was carried out. For DFT and ONIOM simulation, the most cis-stereospecific active site of the catalytic system was used. By analyzing the total energy, as well as the enthalpy and Gibbs free energy of the simulated catalytically active centers, it was found that the coordination of 1,3-butadiene in the trans-form was more favorable than in the cis-form by 11 kJ/mol. However, as a result of π-allylic insertion mechanism modeling, it was found that the activation energy of cis-1,3-butadiene insertion into the π-allylic neodymium-carbon bond of the terminal group on the reactive growing chain was 10-15 kJ/mol lower than the activation energy of trans-1,3-butadiene insertion. The activation energies did not change when both trans-1,4-butadiene and cis-1,4-butadiene were used for modeling. That is, 1,4-cis-regulation was due not to the primary coordination of 1,3-butadiene in its cis-configuration, but to its lower energy of attachment to the active site. The obtained results allowed us to clarify the mechanism of the high cis-stereospecificity of 1,3-butadiene polymerization by the neodymium-based Ziegler-Natta system.

Nucleation of zeolitic imidazolate frameworks: from molecules to nanoparticles

We have studied the clusters involved in the initial stages of nucleation of Zeolitic Imidazolate Frameworks, employing a wide range of computational techniques. In the pre-nucleating solution, the prevalent cluster is the ZnIm₄ cluster (formed by a zinc cation, Zn²⁺, and four imidazolate anions, Im^-), although clusters such as ZnIm₃, Zn₂Im₇, Zn₂Im₇, Zn₃Im₉, Zn₃Im₁₀, or Zn₄Im₁₂ have energies that are not much higher, so they would also be present in solution at appreciable quantities. All these species, except ZnIm₃, have a tetrahedrally coordinated Zn²⁺ cation. Small Zn_xIm_y clusters are less stable than the ZnIm₄ cluster. The first cluster that is found to be more stable than ZnIm₄ is the Zn₄₁Im₈₈ cluster, which is a disordered cluster with glassy structure. Bulk-like clusters do not begin to be more stable than glassy clusters until much larger sizes, since the larger cluster we have studied (Zn₁₄₄Im₂₈₈) is still less stable than the glassy Zn₄₁Im₈₈ cluster, suggesting that Ostwald's rule (the less stable polymorph crystallizes first) could be fulfilled, not for kinetic, but for thermodynamic reasons. Our results suggest that the first clusters formed in the nucleation process would be glassy clusters, which then undergo transformation to any of the various crystal structures possible, depending on the kinetic routes provided by the synthesis conditions. Our study helps elucidate the way in which the various species present in solution interact, leading to nucleation and crystal growth.

Multifaceted View on the Mechanism of a Photochemical Deracemization Reaction

Upon irradiation in the presence of a chiral benzophenone catalyst (5 mol %), a racemic mixture of a given chiral imidazolidine-2,4-dione (hydantoin) can be converted almost quantitatively into the same compound with high enantiomeric excess (80-99% ee). The mechanism of this photochemical deracemization reaction was elucidated by a suite of mechanistic experiments. It was corroborated by nuclear magnetic resonance titration that the catalyst binds the two enantiomers by two-point hydrogen bonding. In one of the diastereomeric complexes, the hydrogen atom at the stereogenic carbon atom is ideally positioned for hydrogen atom transfer (HAT) to the photoexcited benzophenone. Detection of the protonated ketyl radical by transient absorption revealed hydrogen abstraction to occur from only one but not from the other hydantoin enantiomer. Quantum chemical calculations allowed us to visualize the HAT within this complex and, more importantly, showed that the back HAT does not occur to the carbon atom of the hydantoin radical but to its oxygen atom. The achiral enol formed in this process could be directly monitored by its characteristic transient absorption signal at λ ≅ 330 nm. Subsequent tautomerization leads to both hydantoin enantiomers, but only one of them returns to the catalytic cycle, thus leading to an enrichment of the other enantiomer. The data are fully consistent with deuterium labeling experiments and deliver a detailed picture of a synthetically useful photochemical deracemization reaction.

Glyphosate mimics 17β-estradiol effects promoting estrogen receptor alpha activity in breast cancer cells

Glyphosate, the active ingredient in several broad-spectrum herbicide formulations, has been validated and widely used throughout the world. Recent reports have questioned its safety, showing that glyphosate may act as an endocrine disruptor by promoting estrogenic activity. However, the molecular mechanism involved in this phenomenon remains unclear. Therefore, here we aimed to elucidate the mechanism by which glyphosate induces estrogenic activity using estrogen-sensitive breast cancer cell line models. Our results show that glyphosate mimics the cell effects of 17β-estradiol (E2), promoting estrogen receptor α (ERα) phosphorylation, its degradation, and transcriptional activity at high concentrations. The molecular mechanism seems involved in the ERα ligand-binding domain (LBD). Molecular simulations suggest a plausible interaction between glyphosate and the LBD through a coordinated complex involving divalent cations such as Zn (II). In addition, glyphosate exposure alters the level of Cyclin-dependent kinase 7 that contribute to ERα phosphorylation. Finally, glyphosate increases cell proliferation rate and levels of cell cycle regulators, accompanied by an increase in anchorage-independent growth capacity. These findings suggest that glyphosate at high concentrations, induces estrogen-like effects through an ERα ligand binding site-dependent mechanism, leading to cellular responses resulting from a complex interplay of genomic and non-genomic events.

Supramolecular Optimization of Sensory Function of a Hemicurcuminoid through Its Incorporation into Phospholipid and Polymeric Polydiacetylenic Vesicles: Experimental and Computational Insight

This work presents the synthesis of a new representative of hemicurcuminoids with a nonyloxy substituent (HCur) as a fluorescent amphiphilic structural element of vesicular aggregates based on phosphatidylcholine (PC), phosphatidylserine (PS), and 10,12-pentacosadiynoic acid (PCDA). Both X-ray diffraction analysis of the single crystal and ¹H NMR spectra of HCur in organic solvents indicate the predominance of the enol-tautomer of HCur. DFT calculations show the predominance of the enol tautomer HCur in supramolecular assemblies with PC, PS, and PCDA molecules. The results of the molecular modeling show that HCur molecules are surrounded by PC and PS with a rather weak exposure to water molecules, while an exposure of HCur molecules to water is enhanced under its supramolecular assembly with PCDA molecules. This is in good agreement with the higher loading of HCur into PC(PS) vesicles compared to PCDA vesicles converted into polydiacetylene (PDA) ones by photopolymerization. HCur molecules incorporated into HCur-PDA vesicles exhibit greater planarity distortion and hydration effect in comparison with HCur-PC(PS) ones. HCur-PDA is presented as a dual fluorescence-chromatic nanosensor responsive to a change in pH within 7.5-9.5, heavy metal ions and polylysine, and the concentration-dependent fluorescent response is more sensitive than the chromatic one. Thus, the fluorescent response of HCur-PDA allows for the distinguishing between Cd²⁺ and Pb²⁺ ions in the concentration range 0-0.01 mM, while the chromatic response allows for the selective sensing of Pb²⁺ over Cd²⁺ ions at their concentrations above 0.03 mM.

Geometrical benchmarking and analysis of redox potentials of copper(I/II) guanidine-quinoline complexes: Comparison of semi-empirical tight-binding and DFT methods and the challenge of describing the entatic state (part III)

Copper guanidine-quinoline complexes are an important class of bioinorganic complexes that find utilization in electron and atom transfer processes. By substitution of functional groups on the quinoline moiety the electron transfer abilities of these complexes can be tuned. In order to explore the full substitution space by simulations, the accurate theoretical description of the effect of functional groups is essential. In this study, we compare three different methods for the theoretical description of the structures. We use the semi-empirical tight-binding method GFN2-xTB, the density functional TPSSh and the double-hybrid functional B2PLYP. We evaluate the methods on five different complex pairs (Cu(I) and Cu(II) complexes), and compare how well calculated energies can predict the redox potentials. We find even though B2PLYP and TPSSh yield better accordance with the experimental structures. GFN2-xTB performs surprisingly well in the geometry optimization at a fraction of the computational cost. TPSSh offers a good compromise between computational cost and accuracy of the redox potential for real-life complexes.

How well do semiempirical QM methods describe the structure of proteins?

Semiempirical quantum-mechanical (QM) computational methods are an increasingly popular tool for the study of biomolecular systems. They were, however, developed and tested mostly on small model molecules. In this work, we explore one topic fundamental to these applications: the ability of the methods to describe the structure of proteins. In a set of 19 proteins for which a crystal structure with very high resolution is available, we analyze the properties of the protein geometries optimized using several semiempirical QM methods including PM6-D3H4, PM7, and GFN2-xTB. Some of the methods provide a very good description of the general structural features of the protein, yielding results better than or comparable to the AMBER ff03 force field. However, PM7 and PM6-D3H4 optimizations introduce artificial close contacts in the structure, which is partially remediated by reparameterization.

Automated and Efficient Generation of General Molecular Aggregate Structures

Modeling intermolecular interactions of complex non-covalent structures is important in many areas of chemistry. To facilitate the generation of reasonable dimer, oligomer, and general aggregate geometries, we introduce an automated computational interaction site screening (aISS) workflow. This easy-to-use tool combines a genetic algorithm employing the intermolecular force-field xTB-IFF for initial search steps with the general force-field GFN-FF and the semi-empirical GFN2-xTB method for geometry optimizations. Compared with the alternative CREST program, aISS yields similar results but with computer time savings of 1-3 orders of magnitude. This allows for the treatment of systems with thousands of atoms composed of elements up to radon, e.g., metal-organic complexes, or even polyhedra and zeolite cut-outs which were not accessible before. Moreover, aISS can identify reactive sites and provides options like site-directed (user-guided) screening.

Estimating hydroxyl/epoxy ratio in graphene oxide through adsorption experiment and semiempirical GFN2-xTB quantum method

CONTEXT

The reactivity of graphene oxide (GO) with amines is related to the ring-opening of the epoxy groups in its basal surface, as addressed experimentally. Therefore, discussing the hydroxyl/epoxy ratio for GO is relevant to improve the characterization of such material. As the adsorption of Methylene Blue into GO is related to a graphene derivative's oxidation degree (OD), we combined adsorption experimental information and theoretical data to estimate the hydroxyl/epoxy ratio. The theoretical data were compared to the experimental adsorption of Methylene Blue and Indigo Carmine into GO synthesized in our department. Our results show GO systems with hydroxyl/epoxy ratios equal to 0.7, 0.8, and 0.9 are the most representative in which the most coherent model corresponds to OH/EP=0.8 for our GO previously synthesized.

METHODS

The GO-MODEL software was developed in the present work to obtain cartesian coordinates of GO systems. We investigated 204 systems comprising models with 486 carbon atoms with the GFN2-xTB semiempirical quantum method. The supramolecular arrangements were constructed with the recently developed UD-APARM program.

Multifunctional Organocatalysts - Singly-Linked and Macrocyclic Bisphosphoric Acids for Asymmetric Phase-Transfer and Brønsted-Acid Catalysis

The linking of phosphoric acids via covalent or mechanical bonds has proven to be a successful strategy for the design of novel organocatalysts. Here, we present the first systematic investigation of singly-linked and macrocyclic bisphosphoric acids, including their synthesis and their application in phase-transfer and Brønsted acid catalysis. We found that the novel bisphosphoric acids show dramatically increased enantioselectivities in comparison to their monophosphoric acid analogues. However, the nature, length and number of linkers has a profound influence on the enantioselectivities. In the asymmetric dearomative fluorination via phase-transfer catalysis, bisphosphoric acids with a single, rigid bisalkyne-linker give the best results with moderate to good enantiomeric excesses. In contrast, bisphosphoric acids with flexible linkers give excellent enantioselectivities in the transfer-hydrogenation of quinolines via cooperative Brønsted acid catalysis. In the latter case, sufficiently long linkers are needed for high stereoselectivities, as found experimentally and supported by DFT calculations.

What the Heck?-Automated Regioselectivity Calculations of Palladium-Catalyzed Heck Reactions Using Quantum Chemistry

We present a quantum chemistry (QM)-based method that computes the relative energies of intermediates in the Heck reaction that relate to the regioselective reaction outcome: branched (α), linear (β), or a mix of the two. The calculations are done for two different reaction pathways (neutral and cationic) and are based on r ²SCAN-3c single-point calculations on GFN2-xTB geometries that, in turn, derive from a GFNFF-xTB conformational search. The method is completely automated and is sufficiently efficient to allow for the calculation of thousands of reaction outcomes. The method can mostly reproduce systematic experimental studies where the ratios of regioisomers are carefully determined. For a larger dataset extracted from Reaxys, the results are somewhat worse with accuracies of 63% for β-selectivity using the neutral pathway and 29% for α-selectivity using the cationic pathway. Our analysis of the dataset suggests that only the major or desired regioisomer is reported in the literature in many cases, which makes accurate comparisons difficult. The code is freely available on GitHub under the MIT open-source license: https://github.com/jensengroup/HeckQM.

A kinetic study of the photolysis of sulfamethoxazole with special emphasis on the photoisomer

Abstract

The previously not studied photochemical degradation of sulfamethoxazole (SMX) to the isomer of SMX (ISO) was measured via a polychromatic (Xe) and a monochromatic (Hg) light source and accompanied by quantum chemical DFT calculations. In addition to the $$\mathrm{p}K_\mathrm{a} = \;7.0 \pm 0.1$$ p K a = 7.0 ± 0.1 of ISO, tautomer-dependent properties such as the $$K_\mathrm{OW}$$ K OW were measured and theoretically confirmed by DFT. The kinetics in solutions below and above the $$\mathrm{p}K_\mathrm{a} = 5.6$$ p K a = 5.6 of SMX were studied for the available and quantifiable products SMX, ISO, 3-amino-5-methylisoxazole (AMI), 2-amino-5-methyloxazole (AMO), and sulfanilic acid (SUA). The quantum yields of the neutral ($$\Phi _\mathrm{N}$$ Φ N ) and anionic $$\Phi _\mathrm{A}$$ Φ A ) forms of SMX ($$\Phi _\mathrm{A} = 0.03 \pm 0.001$$ Φ A = 0.03 ± 0.001 , $$\Phi _\mathrm{N} = 0.15 \pm 0.01$$ Φ N = 0.15 ± 0.01 ) and ISO ($$\Phi _\mathrm{A} = 0.05 \pm 0.01$$ Φ A = 0.05 ± 0.01 and $$\Phi _\mathrm{N} = 0.06 \pm 0.02$$ Φ N = 0.06 ± 0.02 ) were found to be wavelength-independent. In a competitive reaction to the formation of ISO from SMX, the degradation product TP271 is formed. Various proposed structures for TP271 described in the literature have been studied quantum mechanically and can be excluded for thermodynamic reasons. In real samples in a northern German surface water in summer 2021 mean concentrations of SMX were found in the range of 120 ng/L. In agreement with the pH-dependent yields, concentrations of ISO were low in the range of 8 ng/L.

Graphical abstract

SOMAS: a platform for data-driven material discovery in redox flow battery development

Aqueous organic redox flow batteries offer an environmentally benign, tunable, and safe route to large-scale energy storage. The energy density is one of the key performance parameters of organic redox flow batteries, which critically depends on the solubility of the redox-active molecule in water. Prediction of aqueous solubility remains a challenge in chemistry. Recently, machine learning models have been developed for molecular properties prediction in chemistry and material science. The fidelity of a machine learning model critically depends on the diversity, accuracy, and abundancy of the training datasets. We build a comprehensive open access organic molecular database "Solubility of Organic Molecules in Aqueous Solution" (SOMAS) containing about 12,000 molecules that covers wider chemical and solubility regimes suitable for aqueous organic redox flow battery development efforts. In addition to experimental solubility, we also provide eight distinctive quantum descriptors including optimized geometry derived from high-throughput density functional theory calculations along with six molecular descriptors for each molecule. SOMAS builds a critical foundation for future efforts in artificial intelligence-based solubility prediction models.

Quantum chemical calculation of the vapor pressure of volatile and semi volatile organic compounds

The vapor pressure is a specific and temperature-dependent parameter that describes the volatility of a substance and thus its driving force for evaporation or sublimation into the gas phase. Depending on the magnitude of the vapor pressure, there are different methods for experimental determination. However, these are usually associated with a corresponding amount of effort and become less accurate as the vapor pressure decreases. For purposes of vapor pressure prediction, algorithms were developed that are usually based on quantitative structure-activity relationships (QSAR). The quantum mechanical (QM) approach followed here applies an alternative, much less empirical strategy, where the change in Gibbs free energy for the transition from the condensed to the gas phase is obtained from conformer ensembles computed for each phase separately. The results of this automatic, so-called CRENSO workflow are compared with experimentally determined vapor pressures for a large set of environmentally relevant compounds. In addition, comparisons are made with the single structure-based COSMO-RS QM approach, linear-free-energy relationships (LFER) as well as results from the SPARC program. We show that our CRENSO workflow is superior to conventional prediction models and provides reliable vapor pressures for liquids and sub-cooled liquids over a wide pressure range.

Mutactimycin AP, a New Mutactimycin Isolated from an Actinobacteria from the Atacama Desert

Bacteria belonging to the phylum Actinobacteria are a very good source of antibiotics, and indeed dominate the current clinical antibiotic space. This paper reports Mutactimycin AP, a new compound belonging to an anthracycline-type family of antibiotics, isolated from a Saccharothrix sp. This actinobacterial strain was isolated from the rhizosphere of lupine plants growing in the extreme hyper-arid Atacama Desert. Structural characterization was carried out using electrospray ionization-mass spectrometry (ESI-MS) and NMR spectroscopy in combination with molecular modelling. The compound was tested against the ESKAPE pathogens, where it showed activity against MRSA and five strains associated with bovine mastitis, where it showed activity against Enterococcus pseudoavium and Staphylycoccus Aureus subsp. Aureus.

Best-Practice DFT Protocols for Basic Molecular Computational Chemistry

Nowadays, many chemical investigations are supported by routine calculations of molecular structures, reaction energies, barrier heights, and spectroscopic properties. The lion's share of these quantum-chemical calculations applies density functional theory (DFT) evaluated in atomic-orbital basis sets. This work provides best-practice guidance on the numerous methodological and technical aspects of DFT calculations in three parts: Firstly, we set the stage and introduce a step-by-step decision tree to choose a computational protocol that models the experiment as closely as possible. Secondly, we present a recommendation matrix to guide the choice of functional and basis set depending on the task at hand. A particular focus is on achieving an optimal balance between accuracy, robustness, and efficiency through multi-level approaches. Finally, we discuss selected representative examples to illustrate the recommended protocols and the effect of methodological choices.

Fast Screening of Minimum Energy Crossing Points with Semiempirical Tight-Binding Methods

The investigation of photochemical processes is a highly active field in computational chemistry. One research direction is the automated exploration and identification of minimum energy conical intersection (MECI) geometries. However, due to the immense technical effort required to calculate nonadiabatic potential energy landscapes, the routine application of such computational protocols is severely limited. In this study, we will discuss the prospect of combining adiabatic potential energy surfaces from semiempirical quantum mechanical calculations with specialized confinement potential and metadynamics simulations to identify S₀/T₁ minimum energy crossing point (MECP) geometries. It is shown that MECPs calculated at the GFN2-xTB level can provide suitable approximations to high-level S₀/S₁ab initio conical intersection geometries at a fraction of the computational cost. Reference MECIs of benzene are studied to illustrate the basic concept. An example application of the presented protocol is demonstrated for a set of photoswitch molecules.

Direct Electrochemical CO2 Capture Using Substituted Anthraquinones in Homogeneous Solutions: A Joint Experimental and Theoretical Study

Electrochemical capture of carbon dioxide (CO2) using organic quinones is a promising and intensively studied alternative to the industrially established scrubbing processes. While recent studies focused only on the influence of substituents having a simple mesomeric or nucleophilicity effect, we have systematically selected six anthraquinone (AQ) derivatives (X-AQ) with amino and hydroxy substituents in order to thoroughly study the influence thereof on the properties of electrochemical CO2 capture. Experimental data from cyclic voltammetry (CV) and UV-Vis spectroelectrochemistry of solutions in acetonitrile were analyzed and compared with innovative density functional tight binding computational results. Our experimental and theoretical results provide a coherent explanation of the influence of CO2 on the CV data in terms of weak and strong binding nomenclature of the dianions. In addition to this terminology, we have identified the dihydroxy substituted AQ as a new class of molecules forming rather unstable [X-AQ-(CO2) n ]2- adducts. In contrast to the commonly used dianion consideration, the results presented herein reveal opposite trends in stability for the X-AQ-CO2 •- radical species for the first time. To the best of our knowledge, this study presents theoretically calculated UV-Vis spectra for the various CO2-AQ reduction products for the first time, enabling a detailed decomposition of the spectroelectrochemical data. Thus, this work provides an extension of the existing classification with proof of the existence of X-AQ-CO2 species, which will be the basis of future studies focusing on improved materials for electrochemical CO2 capture.

Carbon Nanodots from an In Silico Perspective

Carbon nanodots (CNDs) are the latest and most shining rising stars among photoluminescent (PL) nanomaterials. These carbon-based surface-passivated nanostructures compete with other related PL materials, including traditional semiconductor quantum dots and organic dyes, with a long list of benefits and emerging applications. Advantages of CNDs include tunable inherent optical properties and high photostability, rich possibilities for surface functionalization and doping, dispersibility, low toxicity, and viable synthesis (top-down and bottom-up) from organic materials. CNDs can be applied to biomedicine including imaging and sensing, drug-delivery, photodynamic therapy, photocatalysis but also to energy harvesting in solar cells and as LEDs. More applications are reported continuously, making this already a research field of its own. Understanding of the properties of CNDs requires one to go to the levels of electrons, atoms, molecules, and nanostructures at different scales using modern molecular modeling and to correlate it tightly with experiments. This review highlights different in silico techniques and studies, from quantum chemistry to the mesoscale, with particular reference to carbon nanodots, carbonaceous nanoparticles whose structural and photophysical properties are not fully elucidated. The role of experimental investigation is also presented. Hereby, we hope to encourage the reader to investigate CNDs and to apply virtual chemistry to obtain further insights needed to customize these amazing systems for novel prospective applications.

Atomically Precise Platinum Carbonyl Nanoclusters: Synthesis, Total Structure, and Electrochemical Investigation of [Pt27(CO)31]4- Displaying a Defective Structure

The molecular Pt nanocluster [Pt27(CO)31]4- (14-) was obtained by thermal decomposition of [Pt15(CO)30]2- in tetrahydrofuran under a H2 atmosphere. The reaction of 14- with increasing amounts of HBF4·Et2O afforded the previously reported [Pt26(CO)32]2- (32-) and [Pt26(CO)32]- (3-). The new nanocluster 14- was characterized by IR and UV-visible spectroscopy, single-crystal X-ray diffraction, direct-current superconducting quantum interference device magnetometry, cyclic voltammetry, IR spectroelectrochemistry (IR SEC), and electrochemical impedance spectroscopy. The cluster displays a cubic-close-packed Pt27 framework generated by the overlapping of four ABCA layers, composed of 3, 7, 11, and 6 atoms, respectively, that encapsulates a fully interstitial Pt4 tetrahedron. One Pt atom is missing within layer 3, and this defect (vacancy) generates local deformations within layers 2 and 3. These local deformations tend to repair the defect (missing atom) and increase the number of Pt-Pt bonding contacts, minimizing the total energy. The cluster 14- is perfectly diamagnetic and displays a rich electrochemical behavior. Indeed, six different oxidation states have been characterized by IR SEC, unraveling the series of 1n- (n = 3-8) isostructural nanoclusters. Computational studies have been carried out to further support the interpretation of the experimental data.

Exhaustive Mapping of the Conformational Space of Natural Dipeptides by the DFT-D3//COSMO-RS Method

We extensively mapped energy landscapes and conformations of 22 (including three His protonation states) proteinogenic α-amino acids in trans configuration and the corresponding 484 (22²) dipeptides. To mimic the environment in a protein chain, the N- and C-termini of the studied systems were capped with acetyl and N-methylamide groups, respectively. We systematically varied the main chain dihedral angles (ϕ, ψ) by 40° steps and all side chain angles by 90° or 120° steps. We optimized the molecular geometries with the GFN2-xTB semiempirical (SQM) method and performed single point density functional theory calculations at the BP86-D3/DGauss-DZVP//COSMO-RS level in water, 1-octanol, N,N-dimethylformamide, and n-hexane. For each restrained (nonequilibrium) structure, we also calculated energy gradients (in water) and natural atomic charges. The exhaustive and unprecedented QM-based sampling enabled us to construct Ramachandran plots of quantum mechanical (QM(BP86-D3)//COSMO-RS) energies calculated on SQM structures, for all 506 (484 dipeptides and 22 amino acids) studied systems. We showed how the character of an amino acid side chain influences the conformational space of single amino acids and dipeptides. With clustering techniques, we were able to identify unique minima of amino acids and dipeptides (i.e., minima on the GFN2-xTB potential energy surfaces) and analyze the distribution of their BP86-D3//COSMO-RS conformational energies in all four solvents. We also derived an empirical formula for the number of unique minima based on the overall number of rotatable bonds within each peptide. The final peptide conformer data set (PeptideCs) comprises over 400 million structures, all of them annotated with QM(BP86-D3)//COSMO-RS energies. Thanks to its completeness and unbiased nature, the PeptideCs can serve, inter alia, as a data set for the validation of new methods for predicting the energy landscapes of protein structures. This data set may also prove to be useful in the development and reparameterization of biomolecular force fields. The data set is deposited at Figshare (10.25452/figshare.plus.19607172) and can be accessed using a simple web interface at http://peptidecs.uochb.cas.cz.

ULYSSES: An Efficient and Easy to Use Semiempirical Library for C+

We introduce ULYSSES, a user-friendly and robust C++ library for semiempirical quantum chemical calculations. In its current version, ULYSSES is equipped with a large set of different semiempirical models, most of which are based on the Neglect of Diatomic Differential Overlap (NDDO) approximation. Empirical corrections for dispersion and hydrogen bonding are available for most methods, so that higher quality is achieved in the calculation of energies of nonbonded complexes. The library is furthermore equipped with geometry optimization, as well as modules for calculating molecular properties of general interest. Ideal gas thermodynamics is available and allows single structure as well as conformer (multistructure) averaged properties to be calculated. We offer the possibility to use several vibrational partition functions according to the nature of interactions being studied: for covalent systems, the traditional harmonic oscillator approximation is available; for nonbonded complexes, we systematically extended the partition function proposed by Grimme for all thermodynamic functions. The library is also capable of running Born-Oppenheimer molecular dynamics.

Anthraquinone and its derivatives as sustainable materials for electrochemical applications - a joint experimental and theoretical investigation of the redox potential in solution

Anthraquinone (AQ) has long been identified as a highly promising lead structure for various applications in organic electronics. Considering the enormous number of possible substitution patterns of the AQ lead structure, with only a minority being commercially available, a systematic experimental screening of the associated electrochemical potentials represents a highly challenging and time consuming task, which can be greatly enhanced via suitable virtual pre-screening techniques. In this work the calculated electrochemical reduction potentials of pristine AQ and 12 hydroxy- or/and amino-substituted AQ derivatives in N,N-dimethylformamide have been correlated against newly measured experimental data. In addition to the calculations performed using density functional theory (DFT), the performance of different semi-empirical density functional tight binding (DFTB) approaches has been critically assessed. It was shown that the SCC DFTB/3ob parametrization in conjunction with the COSMO solvation model provides a highly adequate description of the electrochemical potentials also in the case of the two-fold reduced species. While the quality in the correlation against the experimental data proved to be slightly inferior compared to the employed DFT approach, the highly advantageous cost-accuracy ratio of the SCC DFTB/3ob/COSMO framework has important implications in the formulation of hierarchical screening strategies for materials associated with organic electronics. Based on the observed performance, the low-cost method provides sufficiently accurate results to execute efficient pre-screening protocols, which may then be followed by a DFT-based refinement of the best candidate structures to facilitate a systematic search for new, high-performance organic electronic materials.