Consistent structures and interactions by density functional theory with small atomic orbital basis sets

Low-lying LUMO Boosts Conductance in Antiaromatic Dibenzopentalene Versus Aromatic Analogues

Antiaromaticity is a fundamental concept in chemistry, but the study of molecular wires incorporating antiaromatic units is limited. Despite initial predictions, very few studies show that antiaromaticity has a beneficial effect on electron transport. Dibenzo[a,e]pentalene (DBP) is a stable structure that displays appreciable antiaromaticity within the five-membered rings of the pentalene core. We have investigated derivatives of DBP furnished with pyridyl (Py) and F4-pyridyl (PyF4) anchor groups, and compared the conductance with purely aromatic phenyl and anthracene analogues. We find that the low-bias conductance of DBP-Py is approximately 60 % larger than that of the anthracene analogue Anth-Py and 250 % larger compared to the phenyl derivative Ph-Py. This is due to a better alignment of the LUMO with the gold Fermi level, which we confirm by conductance-voltage spectroscopy where the conductance of DBP-Py shows the greatest voltage-dependence. The F4-pyridyl compounds, which have lower LUMO energies compared to the pyridyl analogues, did not, however, form detectable molecular junctions. The strongly electron-withdrawing fluorine atoms reduce the donor capability of the nitrogen lone-pair to the point where stable N-Au bonds no longer form.

Theoretical Study of Structural and Electronic Trends of the Sulfonylurea Herbicides Family

The sulfonylurea herbicide family has been extensively studied using computational techniques. The most stable conformer structures of the 34 molecules analyzed in gaseous, aqueous, and octanol phases have been determined. The study employed CREST conformational search methods along with the CENSO script to explore all possible conformational structures. Additional evaluations conducted at the B3LYP-D3/6-311+G(d,p) level have enabled the identification of intramolecular stability patterns across the various compounds. It has been discovered that stability is primarily determined by two factors: intramolecular hydrogen bonding involving an NH group adjacent to the sulfonyl group with either N donors or the nearby carbonyl group and potential π-π interactions between the aromatic rings of the molecules. These have been characterized through QTAIM and NCI population analyses. Furthermore, with the goal of developing predictive models for the physicochemical properties of pesticides that include the sulfonylurea family, a statistical analysis among the different properties of the studied molecules has been conducted. Significant correlations have been found between various properties, predicting a promising future for the prediction of characteristics that could assist laboratories in selecting among different pesticides.

Ab initio investigation of the geometrical behavior in solution and electronic structure of the anion complexes [bis(1,3-dithiole-2-thione-4,5-dithiolate)M], for M = Bi(III), Sb(III), and Zn(II)

CONTEXT

1,3-Dithiole-2-thione-4,5-dithiolate (dmit) ligands are known for their conductive and optical properties. Dmit compounds have been assessed for use in sensor devices, information storage, spintronics, and optical material applications. Associations with various metallic centers endow dmit complexes with magnetic, optical, conductive, and antioxidant properties. Optical doping can facilitate the fabrication of magnetic conductor materials from ground-state nonmagnetic cations. While most studied complexes involve transition-metal centers due to their diverse chemistry, compounds with representative elements are less explored in the literature. This study investigated the structural and electronic properties of bisdmit complexes with representative Bi(III), Sb(III), and Zn(II) cations. AIMD calculations revealed two new geometries for Bi(III) and Zn(II) complexes, diverging from the isolated geometry typically used in quantum chemical calculations. The coordination of acetonitrile molecules to the cationic centers of the complexes resulted in unstable structures, while the dimerization of the complexes was stable. SA-CASSCF/NEVPT2 calculations were applied to the structures of the isolated complexes and stable dimers, confirming the multireference character of the electronic structure of the three systems and the multiconfigurational character of the Bi(III) complex. The electronic spectra simulated by the STEOM-DLPNO-CCSD calculations accurately reproduced the experimental UV‒Vis spectra indicating the participation of the isolated Bi(III) dmit complex and its dimeric form in solution.

METHODOLOGY

AIMD calculations of the dmit salts were conducted using the GFN2-xTB method with 60 explicit acetonitrile molecules as the solvent at 300 K for a total simulation time of 50.0 ps, with printing intervals of 0.5 fs. The final geometries were optimized employing the PBEh-3c compound method, incorporating implicit conductor-like polarizable continuum model (CPCM) solvation for acetonitrile. Local energy decomposition (LED) analysis at the DLPNO-CCSD(T)/Def2-TZVP level of theory was utilized to investigate the stability of the complex geometries identified by AIMD. The electronic structures of the complexes were assessed using the SA-CASSCF/NEVPT2/Def2-TZVP method to confirm the multiconfigurational and multireference nature of their electronic structures. Electronic spectra were analyzed using the STEOM-DLPNO-CCSD/Def2-TZVP method, with CPCM used to simulate an acetonitrile medium.

Electric nuclear quadrupole coupling reveals dissociation of HCl with a few water molecules

Investigating the dissociation of acids in the presence of a limited number of water molecules is crucial for understanding various elementary chemical processes. In our study, focusing on HCl(H2O)n clusters (where HCl is hydrogen chloride and H2O is water) formed in a cold and isolated jet expansion, we used the nuclear quadrupole coupling tensor obtained through rotational spectroscopy to decipher the nature of the hydrogen-chlorine (H-Cl) chemical bond in a microaqueous environment. For n = 1 to 4, the H-Cl bond is covalent. At n = 5 and 7, the contact ion pair of H3O+Cl- is spontaneously formed within the hydrogen bond networks of book and cube acid-water clusters, respectively.

Ferrocene-Based N-Heterocyclic Silylenes: Monomeric Silanechalcogenones, Silanimines, Silirenes, and Insertion Products with P4

The stable ferrocene-based N-heterocyclic silylenes fc[(N{B})2Si] (A; fc=1,1'-ferrocenylene, {B}=(HCNDipp)2B, Dipp=2,6-diisopropylphenyl) and fc[(NDipp)2Si] (B) are compared in a study focussing on their reactivity towards a range of small to moderately sized molecular substrates, viz. P4, S8, Se8, MesN3 (Mes=mesityl), RC≡CH, and RC≡CR (R=Ph, SiMe3). The Dipp-substituted congener B exhibits a more pronounced ambiphilicity and is sterically less congested than its 1,3,2-diazaborolyl-substituted relative A, in line with the higher reactivity of the former. The difference in reactivity is obviously due more to electronic than to steric reasons, as is illustrated by the fact that both A and B react with the comparatively bulky substrate MesN3 under mild conditions to afford the corresponding silanimine fc[(N{B})2Si=NMes] and fc[(NDipp)2Si=NMes], respectively. The heavier ketone analogues fc[(N{B})2Si=E] (E=S, Se, Te) are readily available from A and the corresponding chalcogen. In contrast, the reaction of the more reactive silylene B with elemental sulfur or selenium is unspecific, affording product mixtures. However, fc[(NDipp)2Si=Se] is selectively prepared from B and (Et2N)3PSe; the Te analogue is also accessible, but crystallises as head-to-tail dimer.

Detection and Characterization of Hydride Ligands in Copper Complexes by Hard X-Ray Spectroscopy

Transition metal complexes, particularly copper hydrides, play an important role in various catalytic processes and molecular inorganic chemistry. This study employs synchrotron hard X-ray spectroscopy to gain insights into the geometric and electronic properties of copper hydrides as potential catalysts for CO2 hydrogenation. The potential of high energy resolution X-ray absorption near-edge structure (HERFD-XANES) and valence-to-core X-ray emission (VtC-XES) is demonstrated with measurement on Stryker's reagent (Cu6H6) and [Cu3(μ3-H)(dpmppe)2](PF6)2 (Cu3H), alongside a non-hydride copper compound ICu(dtbppOH) (Cuy-I). The XANES analysis reveals that coordination geometries strongly influence the spectra, providing only indirect details about hydride coordination. The VtC-XES analysis exhibits a distinct signal around 8975 eV, offering a diagnostic tool to identify hydride ligands. Theoretical calculations support and extend these findings by comparing hydride-containing complexes with their hydride-free counterparts.

Predicting redox potentials by graph-based machine learning methods

The evaluation of oxidation and reduction potentials is a pivotal task in various chemical fields. However, their accurate prediction by theoretical computations, which is a complementary task and sometimes the only alternative to experimental measurement, may be often resource-intensive and time-consuming. This paper addresses this challenge through the application of machine learning techniques, with a particular focus on graph-based methods (such as graph edit distances, graph kernels, and graph neural networks) that are reviewed to enlighten their deep links with theoretical chemistry. To this aim, we establish the ORedOx159 database, a comprehensive, homogeneous (with reference values stemming from density functional theory calculations), and reliable resource containing 318 one-electron reduction and oxidation reactions and featuring 159 large organic compounds. Subsequently, we provide an instructive overview of the good practice in machine learning and of commonly utilized machine learning models. We then assess their predictive performances on the ORedOx159 dataset through extensive analyses. Our simulations using descriptors that are computed in an almost instantaneous way result in a notable improvement in prediction accuracy, with mean absolute error (MAE) values equal to 5.6 kcal mol- 1 $$ {}^{-1} $$ for reduction and 7.2 kcal mol- 1 $$ {}^{-1} $$ for oxidation potentials, which paves a way toward efficient in silico design of new electrochemical systems.

Combining low-cost electronic structure theory and low-cost parallel computing architecture

The computational efficiency of low-cost electronic structure methods can be further improved by leveraging heterogenous computing architectures. The software package TeraChem has been developed since 2008 to make use of graphical processing units (GPUs), particularly their strong single-precision performance, for the acceleration of quantum chemical calculations. Here, we present the implementation of three low-cost methods, namely HF-3c, PBEh-3c, and the recently introduced ωB97X-3c. We show that these can benefit in terms of performance when combined with "consumer grade" GPUs by leveraging the mixed precision integral handling in TeraChem. The current limitation of the latter's GPU integral library is that Gaussian integrals only for functions with angular momentum l < 3 can be computed, which generally restricts the achievable accuracy in terms of the one-particle basis set. Particularly, the implementation of the ωB97X-3c method now enables higher accuracy with this setting which, in turn, provides the most efficient implementation accessible with consumer-grade hardware. We furthermore show that the implemented 3c methods can be combined with the hh-TDA formalism. This gives new and efficient low-cost multi-configurational excited states methods, which are benchmarked for the description of lowest vertical excitation energies in this work. All in all, the combination of these efficient electronic structure theory methods with affordable highly parallelized computing hardware provides an optimal computational and monetary cost to accuracy ratio.

Enhancing the charge transport and luminescence properties of ethyl 4-[(E)-(2-hydroxy-4-methoxyphenyl)methyleneamino]benzoate through complexation: a DFT and TD-DFT study

Organic light emitting diode (OLED) and organic solar cell (OSC) properties of ethyl 4-[(E)-(2-hydroxy-4-methoxyphenyl)methyleneamino]benzoate (EMAB) and its Pt2+, Pd2+, Ni2+, Ir3+, Rh3+, and Zn2+ complexes have been theoretically studied herein. Geometry optimizations have been performed via the r2SCAN-3c composite method while single-point calculations have been carried out at the PBE0-D3(BJ)/def2-TZVP level of theory. Results have shown that complexation with selected metal ions improves hole and electron transfer rates in Pt[EMAB]2 and Rh[EMAB]2 +. Specifically, the hole transport rate of Pt[EMAB]2, (k ct(h) = 6.15 × 1014 s-1), is found to be 44 times greater than that of [EMAB], (k ct(h) = 1.42 × 1013 s-1), whereas electron transport rate of Pt[EMAB]2, (k ct(e) = 4.6 × 1013 s-1) is 4 times that of EMAB (k ct(e) = 1.1 × 1013 s-1). Charge mobility for holes and electrons are equal to 19.182 cm2 V-1 s-1 and 1.431 cm2 V-1 s-1 respectively for Pt[EMAB]2, and equal to 4.11 × 10-1 cm2 V-1 s-1 and 3.43 × 10-1 cm2 V-1 s-1 for EMAB respectively. These results show that, charge transport in EMAB can be tuned for better performance through complexation with transition metals such as Pt2+. OSC properties of the complexes were also studied by comparing their HOMO/LUMO energies with those of (6,6)-phenyl-C61-butyric acid methyl ester (PCBM) and poly(3-hexylthiophene) (P3HT). It turned out that the energy gap of EMAB reduced significantly upon complexation from 2.904 eV to 0.56 eV in [Rh(EMAB)2]+ and to a lesser extent in the other complexes. The energy values of the HOMOs remained higher than those of PCBM while those of the LUMOs were found to be greater than that of P3HT with the exception of [Rh(EMAB)2]+. These findings show that the aforementioned species are good electron donors to PCBM. The open circuit voltage, V OC, of the compounds ranged between 0.705 × 10-19 V and 6.617 × 10-19 V, values that are good enough for practical usage in OSC applications. The UV-visible absorption spectra revealed absorption maxima well below 900 nm in all compounds, vital in the efficient functioning of solar cells. In general, this study has shown that platinoid complexation of EMAB can successfully modify both its OLED and OSC properties, making them better precursors in the electronic industry.

Limiting factors in the accuracy of DFT calculation for redox potentials

In the present study, we have investigated factors affecting the accuracy of computational chemistry calculation of redox potentials, namely the gas-phase ionization energy (IE) and electron affinity (EA), and the continuum solvation effect. In general, double-hybrid density functional theory methods yield IEs and EAs that are on average within ~0.1 eV of our high-level W3X-L benchmark, with the best performing method being DSD-BLYP/ma-def2-QZVPP. For lower-cost methods, the average errors are ~0.2-0.3 eV, with ωB97X-3c being the most accurate (~0.15 eV). For the solvation component, essentially all methods have an average error of ~0.3 eV, which shows the limitation of the continuum solvation model. Curiously, the directly calculated redox potentials show errors of ~0.3 eV for all methods. These errors are notably smaller than what can be expected from error propagation with the two components (IE and EA, and solvation effect). Such a discrepancy can be attributed to the cancellation of errors, with the lowest-cost GFN2-xTB method benefiting the most, and the most accurate ωB97X-3c method benefiting the least. For organometallic species, the redox potentials show large deviations exceeding ~0.5 eV even for DSD-BLYP. The large errors are attributed to those for the gas-phase IEs and EAs, which represents a major barrier to the accurate calculation of redox potentials for such systems.

Development of a multi-step screening procedure for redox active molecules in organic radical polymer anodes and as redox flow anolytes

Benzo[d]-X-zolyl-pyridinyl (XO, S, NH) radicals represent a promising class of redox-active molecules for organic batteries. We present a multistep screening procedure to identify the most promising radical candidates. Experimental investigations and highly correlated wave function-based calculations are performed to determine benchmark redox potentials. Based on these, the accuracies of different methods (semi-empirical, density functional theory, wave function-based), solvent models, dispersion corrections, and basis sets are evaluated. The developed screening procedure consists of three steps: First, a conformer search is performed with CREST. The molecules are selected based on the redox potentials calculated using GFN2-xTB. Second, HOMO energies calculated with reparametrized B3LYP-D3(BJ) and the def2-SVP basis set are used as selection criteria. The final molecules are selected based on the redox potentials calculated from Gibbs energies using BP86-D3(BJ)/def2-TZVP. With this multistep screening approach, promising molecules can be suggested for synthesis, and structure-property relationships can be derived.

In Search of the Best Low-Cost Methods for Efficient Screening of Conformers

Locating the lowest energy conformer is crucial for the accurate computation of equilibrium properties of molecular systems. This paper examines the performance of efficient low-cost methods in terms of the alignment and relative energies of their energy minima against the benchmark revDSD-PBEP86-D4/def2-TZVPP//MP2/cc-pVTZ potential energy surface. The low-cost methods considered include GFN-FF, GFN2-xTB, DFTB3, HF-3c, B97-3c, PBEh-3c, and r2SCAN-3c composite methods against a diverse test set of 20 compounds including alkanes, perfluoroalkyl molecules, peptides, open-shell radicals, and Zn(II) complexes of varying sizes. The "3c" composite methods are generally more accurate, but are at least 2-3 orders of magnitude more expensive than tight-binding methods which have energy minima that align well with the benchmark potential energy surface. The findings of this paper were further exploited to introduce a simple strategy involving Grimme's CENSO energy-sorting algorithm that resulted in up to an order of magnitude reduction in computational time for locating the lowest energy conformer on the revDSD-PBEP86-D4/def2-TZVPP//MP2/cc-pVTZ surface.

Facilitating Electron Transfer by Resizing Cyclocarbon Acceptor from C18 to C16

Recent advances in synthetic methods, combined with tip-induced on-surface chemistry, have enabled the formation of numerous cyclocarbon molecules. Here, we investigate computationally the experimentally studied C16 and C18 molecules as well as their van der Waals (vdW) complexes with several typical donor and acceptor molecules. Our results demonstrate a remarkable electron-withdrawing ability of cyclocarbon molecules. The vdW complexes of C16 and C18 exhibit a thermodynamically favorable photoinduced electron transfer (ET) from the donor partner to the cyclocarbons that occurs on a picosecond time scale. The lower reorganization energy of C16 compared to C18 leads to a significant acceleration of the ET reactions.

Structure and isomerization behavior relationships of new push-pull azo-pyrrole photoswitches

A family of stilbenyl-azopyrroles compounds 2a-d and 3a-d was efficiently obtained via a Mizoroki-Heck C-C-type coupling reaction between 2-(4'-iodophenyl-azo)-N-methyl pyrrole (1a) and different vinyl precursors. The influence of the π-conjugated backbone and the effect of the pyrrole moiety were correlated with their optical properties. Studies via UV-Visible spectrophotometry revealed that the inclusion of EWG or EDG favors a red-shift of the main absorption band in these azo compounds compared with their non-substituted analogues. Furthermore, there is a clear influence between the half-life of the Z isomer formed by irradiation with white light and the push-pull behavior of the molecules. In several cases, the stilbenyl-azopyrroles led to the formation of J-type aggregates in binary MeOH : H2O solvents, which are of interest for water compatible applications.

Stepping-Stone CBH: Benchmark and Application of a Multilayered Isodesmic-Based Correction Scheme

We present a generalization of the connectivity-based hierarchy (CBH) of isodesmic-based correction schemes to a multilayered fragmentation platform for overall cost reduction while retaining high accuracy. The newly developed multilayered CBH approach, called stepping-stone CBH (SSCBH), is benchmarked on a diverse set of 959 medium-sized organic molecules. Applying SSCBH corrections to the PBEh-D3 density functional resulted in an average error of 0.76 kcal/mol for the full test set compared to accurate CCSD(T)-quality enthalpies and an even lower error of 0.44 kcal/mol on a subset containing only acyclic molecules. These results rival the traditional CBH-3 approach at a greatly reduced cost, allowing larger fragment corrections to be made at the MP2 level of theory rather than with G4. Our SSCBH approach will enable more widespread applications of CBH methods to a broader range of organic and biomolecular systems.

The p-block challenge: assessing quantum chemistry methods for inorganic heterocycle dimerizations

The elements of the p-block of the periodic table are of high interest in various chemical and technical applications like frustrated Lewis-pairs (FLP) or opto-electronics. However, high-quality benchmark data to assess approximate density functional theory (DFT) for their theoretical description are sparse. In this work, we present a benchmark set of 604 dimerization energies of 302 "inorganic benzenes" composed of all non-carbon p-block elements of main groups III to VI up to polonium. This so-called IHD302 test set comprises two classes of structures formed by covalent bonding and by weaker donor-acceptor (WDA) interactions, respectively. Generating reliable reference data with ab initio methods is challenging due to large electron correlation contributions, core-valence correlation effects, and especially the slow basis set convergence. To compute reference values for these dimerization reactions, after thorough testing, we applied a computational protocol using state-of-the-art explicitly correlated local coupled cluster theory termed PNO-LCCSD(T)-F12/cc-VTZ-PP-F12(corr.). It includes a basis set correction at the PNO-LMP2-F12/aug-cc-pwCVTZ level. Based on these reference data, we assess 26 DFT methods in combination with three different dispersion corrections and the def2-QZVPP basis set, five composite DFT approaches, and five semi-empirical quantum mechanical methods. For the covalent dimerizations, the r2SCAN-D4 meta-GGA, the r2SCAN0-D4 and ωB97M-V hybrids, and the revDSD-PBEP86-D4 double-hybrid functional are found to be the best-performing methods among the evaluated functionals of the respective class. However, since def2 basis sets for the 4th period are not associated to relativistic pseudo-potentials, we obtained significant errors in the covalent dimerization energies (up to 6 kcal mol-1) for molecules containing p-block elements of the 4th period. Significant improvements were achieved for systems containing 4th row elements by using ECP10MDF pseudopotentials along with re-contracted aug-cc-pVQZ-PP-KS basis sets introduced in this work with the contraction coefficients taken from atomic DFT (PBE0) calculations. Overall, the IHD302 set represents a challenge to contemporary quantum chemical methods. This is due to a large number of spatially close p-element bonds which are underrepresented in other benchmark sets, and the partial covalent bonding character for the WDA interactions. The IHD302 set may be helpful to develop more robust and transferable approximate quantum chemical methods in the future.

Sorting drug conformers in enzyme active sites: the XTB way

In the present study, we have used the MEI196 set of interaction energies to investigate low-cost computational chemistry approaches for the calculation of binding between a molecule and its environment. Density functional theory (DFT) methods, when used with the vDZP basis set, yield good agreement with the reference energies. On the other hand, semi-empirical methods are less accurate as expected. By examining different groups of systems within MEI196 that contain species of a similar nature, we find that chemical similarity leads to cancellation of errors in the calculation of relative binding energies. Importantly, the semi-empirical method GFN1-xTB (XTB1) yields reasonable results for this purpose. We have thus further assessed the performance of XTB1 for calculating relative energies of docking poses of substrates in enzyme active sites represented by cluster models or within the ONIOM protocol. The results support the observations on error cancellation. This paves the way for the use of XTB1 in parts of large-scale virtual screening workflows to accelerate the drug discovery process.

How do microplastics alter molluscicidal activity? Effects of weathered microplastics and niclosamide in developing freshwater snails

Despite the wide distribution and persistence of microplastics (MPs), their interactive effects with molluscicides are unknown. Schistosomiasis, a neglected tropical disease, affects 236.6 million people worldwide. Niclosamide (NCL) is the only molluscicide recommended by the World Health Organization (WHO) and it is used to control the population of Schistosoma spp.'s intermediate host. Thus, this study aimed to evaluate of the interaction between polyethylene (PE) MPs and NCL, and their associated toxicity in the freshwater snail Biomphalaria glabrata (Say 1818). Weathered PE MPs were characterized and theoretical analysis of NCL-MP adsorption nature was made using quantum mechanical calculations. The toxicity of NCL isolated (0.0265 to 0.0809 mg L-1) and under interaction with PE MPs (3400 μg L-1) in B. glabrata embryos and newly hatched snails was analyzed. In silico analysis confirmed the adsorption mechanisms of NCL into PE MPs. PE MPs decreased the NCL toxicity to both B. glabrata developmental stages, increasing their survival and NCL lethal concentrations, indicating concerns regarding NCL use as molluscicide in aquatic environments polluted by MPs. In conclusion, MPs may change the efficiency of chemicals used in snail control programs.

Predicting valence tautomerism in diverse cobalt-dioxolene complexes: elucidation of the role of ligands and solvent

The ability of molecular switches to reversibly interconvert between different forms promises potential applications at the scale of single molecules up to bulk materials. One type of molecular switch comprises cobalt-dioxolene compounds that exhibit thermally-induced valence tautomerism (VT) interconversions between low spin Co(iii)-catecholate (LS-CoIII-cat) and high spin Co(ii)-semiquinonate (HS-CoII-sq) forms. Two families of these compounds have been investigated for decades but have generally been considered separately: neutral [Co(diox)(sq)(N2L)] and cationic [Co(diox)(N4L)]+ complexes (diox = generic dioxolene, N2L/N4L = bidentate/tetradentate N-donor ancillary ligand). Computational identification of promising new candidate compounds prior to experimental exploration is beneficial for environmental and cost considerations but requires a thorough understanding of the underlying thermochemical parameters that influence the switching. Herein, we report a robust approach for the analysis of both cobalt-dioxolene families, which involved a quantitative density functional theory-based study benchmarked with reliable quasi-experimental references. The best-performing M06L-D4/def2-TZVPP level of theory has subsequently been verified by the synthesis and experimental investigation of three new complexes, two of which exhibit thermally-induced VT, while the third remains in the LS-CoIII-cat form across all temperatures, in agreement with prediction. Valence tautomerism in solution is markedly solvent-dependent, but the origin of this has not been definitively established. We have extended our computational approach to elucidate the correlation of VT transition temperature with solvent stabilisation energy and change in dipole moment. This new understanding may inform the development of VT compounds for applications in soft materials including films, gels, and polymers.

An N-Heterocyclic Quinodimethane: A Strong Organic Lewis Base Exhibiting Diradical Reactivity

We report the preparation of a new organic σ-donor with a C6H4-linker between an N-heterocyclic carbene (NHC) and an exocyclic methylidene group, which we term N-heterocyclic quinodimethane (NHQ). The aromatization of the C6H4-linker provides a decisive driving force for the reaction of the NHQ with an electrophile and renders the NHQ significantly more basic than analogous NHCs or N-heterocyclic olefins (NHOs), as shown by DFT computations and competition experiments. In solution, the NHQ undergoes an unprecedented dehydrogenative head-to-head dimerization by C-C coupling of the methylidene groups. DFT computations indicate that this reaction proceeds via an open-shell singlet pathway revealing the diradical character of the NHQ. The product of this dimerization can be described as conjugated N-heterocyclic bis-quinodimethane, which according to cyclic voltammetry is a strong organic reducing agent (E1/2=-1.71 V vs. Fc/Fc+) and exhibits a remarkable small singlet-triplet gap of ΔES→T=4.4 kcal mol-1.

Correlating Structure with Spectroscopy in Ascorbate Peroxidase Compound II

Structural and spectroscopic investigations of compound II in ascorbate peroxidase (APX) have yielded conflicting conclusions regarding the protonation state of the crucial Fe(IV) intermediate. Neutron diffraction and crystallographic data support an iron(IV)-hydroxo formulation, whereas Mössbauer, X-ray absorption (XAS), and nuclear resonance vibrational spectroscopy (NRVS) studies appear consistent with an iron(IV)-oxo species. Here we examine APX with spectroscopy-oriented QM/MM calculations and extensive exploration of the conformational space for both possible formulations of compound II. We establish that irrespective of variations in the orientation of a vicinal arginine residue and potential reorganization of proximal water molecules and hydrogen bonding, the Fe-O distances for the oxo and hydroxo forms consistently fall within distinct, narrow, and nonoverlapping ranges. The accuracy of geometric parameters is validated by coupled-cluster calculations with the domain-based local pair natural orbital approach, DLPNO-CCSD(T). QM/MM calculations of spectroscopic properties are conducted for all structural variants, encompassing Mössbauer, optical, X-ray absorption, and X-ray emission spectroscopies and NRVS. All spectroscopic observations can be assigned uniquely to an Fe(IV)═O form. A terminal hydroxy group cannot be reconciled with the spectroscopic data. Under no conditions can the Fe(IV)═O distance be sufficiently elongated to approach the crystallographically reported Fe-O distance. The latter is consistent only with a hydroxo species, either Fe(IV) or Fe(III). Our findings strongly support the Fe(IV)═O formulation of APX-II and highlight unresolved discrepancies in the nature of samples used across different experimental studies.

The reduction behavior of sulfurized polyacrylonitrile (SPAN) in lithium-sulfur batteries using a carbonate electrolyte: a computational study

Lithium-sulfur batteries (LSBs) have attracted attention due to their high theoretical energy density. This and various other advantages, such as the availability and non-toxicity of sulfur, raise interest in LSBs against the background of the energy revolution. However, a polysulfide shuttle mechanism can adversely affect the electrochemical performance of the cell. The sulfur redox properties are influenced, for example, by the electrolyte and the cathode material. Here, a computational study of the discharge process of an LSB with sulfurized poly(acrylonitrile) (SPAN) as the cathode material in combination with a carbonate electrolyte is presented. The nucleation of produced solid Li2S is compared to soluble Li2S. Dominating species are determined by comparing the Gibbs free energy of several species. We found that multiple lithiation steps occur before each Li2S detachment, preventing longer-chain polysulfide cleavage and a polysulfide shuttle. Through nucleating on the nitrogen-rich backbone of SPAN, Li2S units are stabilized by interactions with each other and with the nitrogen atoms. Experimental data show a potential drop and plateau during discharge, which is consistent with the calculated discharge profiles of SPAN with both soluble and nucleated Li2S, and hints at a direct solid-solid transition in the Li-SPAN cell during discharge when using carbonate-based electrolytes.

Basis Set Requirements of σ-Functionals for Gaussian- and Slater-Type Basis Functions and Comparison with Range-Separated Hybrid and Double Hybrid Functionals

σ-Functionals belong to the class of Kohn-Sham (KS) correlation functionals based on the adiabatic-connection fluctuation-dissipation theorem and are technically closely related to the random phase approximation (RPA). They have the same computational demand as the latter, with the computational effort of an energy evaluation for both methods being lower than that of a preceding hybrid DFT calculation for typical systems but yield much higher accuracy, reaching chemical accuracy of 1 kcal/mol for quantities such as reactions and transition energies in main group chemistry. In previous work on σ-functionals, rather large Gaussian basis sets have been used. Here, we investigate the actual basis set requirements of σ-functionals and present three setups that employ smaller Gaussian basis sets ranging from quadruple-ζ (QZ) to triple-ζ (TZ) quality and represent a good compromise between accuracy and computational efficiency. Furthermore, we introduce an implementation of σ-functionals based on Slater-type basis sets and present two setups of QZ and TZ quality for this implementation. We test the accuracy of these setups on a large database of various physical properties and types of reactions, as well as equilibrium geometries and vibrational frequencies. As expected, the accuracy of σ-functional calculations becomes somewhat lower with a decreasing basis set size. However, for all setups considered here, calculations with σ-functionals are clearly more accurate than those within the RPA and even more so than those of the conventional KS methods. For the smallest setup using Gaussian-type basis functions and Slater-type basis functions, we introduce a reparametrization that reduces the loss in accuracy due to the basis set error to some extent. A comparison with the range-separated hybrid ωB97X-V and the double hybrid DSD-BLYP-D3 shows that σ functionals outperform in accuracy both of these accurate and, for their class, representative functionals.

Systematic QM/MM Study for Predicting 31P NMR Chemical Shifts of Adenosine Nucleotides in Solution and Stages of ATP Hydrolysis in a Protein Environment

NMR (nuclear magnetic resonance) spectroscopy allows for important atomistic insights into the structure and dynamics of biological macromolecules; however, reliable assignments of experimental spectra are often difficult. Herein, quantum mechanical/molecular mechanical (QM/MM) calculations can provide crucial support. A major problem for the simulations is that experimental NMR signals are time-averaged over much longer time scales, and since computed chemical shifts are highly sensitive to local changes in the electronic and structural environment, sufficiently large averages over representative structural ensembles are essential. This entails high computational demands for reliable simulations. For NMR measurements in biological systems, a nucleus of major interest is 31P since it is both highly present (e.g., in nucleic acids) and easily observable. The focus of our present study is to develop a robust and computationally cost-efficient framework for simulating 31P NMR chemical shifts of nucleotides. We apply this scheme to study the different stages of the ATP hydrolysis reaction catalyzed by p97. Our methodology is based on MM molecular dynamics (MM-MD) sampling, followed by QM/MM structure optimizations and NMR calculations. Overall, our study is one of the most comprehensive QM-based 31P studies in a protein environment and the first to provide computed NMR chemical shifts for multiple nucleotide states in a protein environment. This study sheds light on a process that is challenging to probe experimentally and aims to bridge the gap between measured and calculated NMR spectroscopic properties.

CREST-A program for the exploration of low-energy molecular chemical space

Conformer-rotamer sampling tool (CREST) is an open-source program for the efficient and automated exploration of molecular chemical space. Originally developed in Pracht et al. [Phys. Chem. Chem. Phys. 22, 7169 (2020)] as an automated driver for calculations at the extended tight-binding level (xTB), it offers a variety of molecular- and metadynamics simulations, geometry optimization, and molecular structure analysis capabilities. Implemented algorithms include automated procedures for conformational sampling, explicit solvation studies, the calculation of absolute molecular entropy, and the identification of molecular protonation and deprotonation sites. Calculations are set up to run concurrently, providing efficient single-node parallelization. CREST is designed to require minimal user input and comes with an implementation of the GFNn-xTB Hamiltonians and the GFN-FF force-field. Furthermore, interfaces to any quantum chemistry and force-field software can easily be created. In this article, we present recent developments in the CREST code and show a selection of applications for the most important features of the program. An important novelty is the refactored calculation backend, which provides significant speed-up for sampling of small or medium-sized drug molecules and allows for more sophisticated setups, for example, quantum mechanics/molecular mechanics and minimum energy crossing point calculations.

Persistent guaiazulene arylmethylium ions as electrophilic traps for metal enolates

Guaiazulene-stabilized cations reacted with metal enolates affording carbonyl compounds with an azulene moiety. Metal enolates generated by asymmetric conjugate addition of organometallic reagents led to enantioenriched products. Additionally, guaiazulene-substituted cations efficiently react with silyl enol ethers. DFT calculations allowed estimation of the electrophilicities of the carbocations. Reaction progress was monitored by a decrease in the reactant's Vis-light absorption and an increase in the product's anti-Kasha emission.

Understanding Alkene Interaction with Metal-Modified Zeolites: Thermodynamics and Mechanism of Bonding in the π-Complex

Zeolites modified with metal cations are perspective catalysts for converting light alkenes to valuable chemicals. A crucial step of the transformation is an alkene interaction with zeolite to afford π-complex with metal cations. The mechanism of alkene bonding with cations is still unclear. To address this problem, propene adsorption on H+ (Bro̷nsted acid site), Na+, Ca2+, Zn2+, Co2+, Cu2+, Cu+, and Ag+ cationic sites in ZSM-5 zeolite has been studied by quantum chemical calculations in terms of adsorption enthalpy, νC═C frequency, and natural bond orbital (NBO) analysis together with natural energy decomposition analysis (NEDA). It is revealed that the conventional concept of σ- and π-bonding is only partially applicable to alkene interaction with metal cations in zeolites. The orbital interaction between an alkene molecule and a metal site is more complex. Several different bonding mechanisms have been identified depending on the nature and electron configuration of the metal cation. This finding explains the complex correlations observed for propene π-complex stability and νC═C frequency shift or charge transfer from the alkene molecule. The results provide the basis for further understanding the interactions between alkenes and inorganic solid Bro̷nsted and Lewis acids.

Conformational energies of biomolecules in solution: Extending the MPCONF196 benchmark with explicit water molecules

A prerequisite for the computational prediction of molecular properties like conformational energies of biomolecules is a reliable, robust, and computationally affordable method usually selected according to its performance for relevant benchmark sets. However, most of these sets comprise molecules in the gas phase and do not cover interactions with a solvent, even though biomolecules typically occur in aqueous solution. To address this issue, we introduce a with explicit water molecules solvated version of a gas-phase benchmark set containing 196 conformers of 13 peptides and other relevant macrocycles, namely MPCONF196 [J. Řezáč et al., JCTC 2018, 14, 1254-1266], and provide very accurate PNO-LCCSD(T)-F12b/AVQZ' reference values. The novel solvMPCONF196 benchmark set features two additional challenges beyond the description of conformers in the gas phase: conformer-water and water-water interactions. The overall best performing method for this set is the double hybrid revDSDPBEP86-D4/def2-QZVPP yielding conformational energies of almost coupled cluster quality. Furthermore, some (meta-)GGAs and hybrid functionals like B97M-V and ω B97M-D with a large basis set reproduce the coupled cluster reference with an MAD below 1 kcal mol- 1  . If more efficient methods are required, the composite DFT-method r2 SCAN-3c (MAD of 1.2 kcal mol- 1 ) is a good alternative, and when conformational energies of polypeptides or macrocycles with more than 500-1000 atoms are in the focus, the semi-empirical GFN2-xTB or the MMFF94 force field (for very large systems) are recommended.

Exploring Chemical Space Using Ab Initio Hyperreactor Dynamics

In recent years, first-principles exploration of chemical reaction space has provided valuable insights into intricate reaction networks. Here, we introduce ab initio hyperreactor dynamics, which enables rapid screening of the accessible chemical space from a given set of initial molecular species, predicting new synthetic routes that can potentially guide subsequent experimental studies. For this purpose, different hyperdynamics derived bias potentials are applied along with pressure-inducing spherical confinement of the molecular system in ab initio molecular dynamics simulations to efficiently enhance reactivity under mild conditions. To showcase the advantages and flexibility of the hyperreactor approach, we present a systematic study of the method's parameters on a HCN toy model and apply it to a recently introduced experimental model for the prebiotic formation of glycinal and acetamide in interstellar ices, which yields results in line with experimental findings. In addition, we show how the developed framework enables the study of complicated transitions like the first step of a nonenzymatic DNA nucleoside synthesis in an aqueous environment, where the molecular fragmentation problem of earlier nanoreactor approaches is avoided.

Correlation consistent basis sets designed for density functional theory: Third-row atoms (Ga-Br)

The correlation consistent basis sets (cc-pVnZ with n = D, T, Q, 5) for the Ga-Br elements have been redesigned, tuning the sets for use for density functional approximations. Steps to redesign these basis sets for an improved correlation energy recovery and efficiency include truncation of higher angular momentum functions, recontraction of basis set coefficients, and reoptimization of basis set exponents. These redesigned basis sets are compared with conventional cc-pVnZ basis sets and other basis sets, which are, in principle, designed to achieve systematic improvement with respect to increasing basis set size. The convergence of atomic energies, bond lengths, bond dissociation energies, and enthalpies of formation to the Kohn-Sham limit is improved relative to other basis sets where convergence to the Kohn-Sham limit is typically not observed.

Electronic Structures of Radical-Pair-Forming Cofactors in a Heliobacterial Reaction Center

Photosynthetic reaction centers (RCs) are membrane proteins converting photonic excitations into electric gradients. The heliobacterial RCs (HbRCs) are assumed to be the precursors of all known RCs, making them a compelling subject for investigating structural and functional relationships. A comprehensive picture of the electronic structure of the HbRCs is still missing. In this work, the combination of selective isotope labelling of 13C and 15N nuclei and the utilization of photo-CIDNP MAS NMR (photochemically induced dynamic nuclear polarization magic-angle spinning nuclear magnetic resonance) allows for highly enhanced signals from the radical-pair-forming cofactors. The remarkable magnetic-field dependence of the solid-state photo-CIDNP effect allows for observation of positive signals of the electron donor cofactor at 4.7 T, which is interpreted in terms of a dominant contribution of the differential relaxation (DR) mechanism. Conversely, at 9.4 T, the emissive signals mainly originate from the electron acceptor, due to the strong activation of the three-spin mixing (TSM) mechanism. Consequently, we have utilized two-dimensional homonuclear photo-CIDNP MAS NMR at both 4.7 T and 9.4 T. These findings from experimental investigations are corroborated by calculations based on density functional theory (DFT). This allows us to present a comprehensive investigation of the electronic structure of the cofactors involved in electron transfer (ET).

Development of a universal method for vibrational analysis of the terminal alkyne C≡C stretch

The terminal alkyne C≡C stretch has a large Raman scattering cross section in the "silent" region for biomolecules. This has led to many Raman tag and probe studies using this moiety to study biomolecular systems. A computational investigation of these systems is vital to aid in the interpretation of these results. In this work, we develop a method for computing terminal alkyne vibrational frequencies and isotropic transition polarizabilities that can easily and accurately be applied to any terminal alkyne molecule. We apply the discrete variable representation method to a localized version of the C≡C stretch normal mode. The errors of (1) vibrational localization to the terminal alkyne moiety, (2) anharmonic normal mode isolation, and (3) discretization of the Born-Oppenheimer potential energy surface are quantified and found to be generally small and cancel each other. This results in a method with low error compared to other anharmonic vibrational methods like second-order vibrational perturbation theory and to experiments. Several density functionals are tested using the method, and TPSS-D3, an inexpensive nonempirical density functional with dispersion corrections, is found to perform surprisingly well. Diffuse basis functions are found to be important for the accuracy of computed frequencies. Finally, the computation of vibrational properties like isotropic transition polarizabilities and the universality of the localized normal mode for terminal alkynes are demonstrated.

Diaryltriazolium Photoswitch: Reaching a Millisecond Cycloreversion with High Stability and NIR Absorption

The exceptional thermal stability of diarylethene closed isomers enabled many applications but also prevented utilization in photochromic systems that require rapid thermal reversibility. Herein, we report the diaryltriazolium (DAT+ ) photoswitch undergoing thermal cycloreversion within a few milliseconds and absorption of the closed form in the near-infrared region above 900 nm. Click chemistry followed by alkylation offers modular and fast access to the electron-deficient DAT+ scaffold. In addition to excellent fatigue resistance, the introduced charge increases water solubility, rendering this photoswitch an ideal candidate for exploring biological applications.

Juggling Optoelectronics and Catalysis: The Dual Talents of Bench Stable 1,4-Azaborinines

Boron- and nitrogen-doped polycyclic aromatic hydrocarbons (B-PAHs) have established a strong foothold in the realm of organic electronics. However, their catalytic potential remains largely untapped. In this study, we synthesise and characterise two bench stable B,N-doped PAH derivatives based on a 1,4-azaborinine motif. Most importantly, the anthracene derived structure is an efficient catalyst in the reduction of various carbonyls and imines. These results underscore the potential of B,N-PAHs in catalytic transformations, setting the stage for deeper exploration in this chemical space.

Confined Lewis Pairs: Investigation of the X- →Si20 Interaction in Halogen-Encapsulating Silafulleranes

A joint theoretical and experimental study on 32 endohedral silafullerane derivatives [X@Si20 Y20 ]- (X=F-I; Y=F-I, H, Me, Et) andT h ${T_h }$ -[Cl@Si20 H12 Y8 ]- (Y=F-I) is presented. First, we evaluated the structure-determining template effect of Cl- in a systematic series of concave silapolyquinane model systems. Second, we investigated the X- →Si20 interaction energy (E int ${E_{{\rm{int}}} }$ ) as a function of X- and Y and found the largestE int ${E_{{\rm{int}}} }$ values for electron-withdrawing exohedral substituents Y. Given that X- ions can be considered as Lewis bases and empty Si20 Y20 clusters as Lewis acids, we classify our inseparable host-guest complexes [X@Si20 Y20 ]- as "confined Lewis pairs". Third, 35 Cl NMR spectroscopy proved to be highly diagnostic for an experimental assessment of the Cl- →Si20 interaction as the paramagnetic shielding and, in turn, δ ${\delta }$ (35 Cl) of the endohedral Cl- ion correlate inversely withE int ${E_{{\rm{int}}} }$ . Finally, we disclose the synthesis of [PPN][Cl@Si20 Y20 ] (Y=Me, Et, Br) and provide a thorough characterization of these new silafulleranes.

Enhanced reversal of ABCG2-mediated drug resistance by replacing a phenyl ring in baicalein with a meta-carborane

Success of chemotherapy is often hampered by multidrug resistance. One mechanism for drug resistance is the elimination of anticancer drugs through drug transporters, such as breast cancer resistance protein (BCRP; also known as ABCG2), and causes a poor 5-year survival rate of human patients. Co-treatment of chemotherapeutics and natural compounds, such as baicalein, is used to prevent chemotherapeutic resistance but is limited by rapid metabolism. Boron-based clusters as meta-carborane are very promising phenyl mimetics to increase target affinity; we therefore investigated the replacement of a phenyl ring in baicalein by a meta-carborane to improve its affinity towards the human ABCG2 efflux transporter. Baicalein strongly inhibited the ABCG2-mediated efflux and caused a fivefold increase in mitoxantrone cytotoxicity. Whereas the baicalein derivative 5,6,7-trimethoxyflavone inhibited ABCG2 efflux activity in a concentration of 5 μm without reversing mitoxantrone resistance, its carborane analogue 5,6,7-trimethoxyborcalein significantly enhanced the inhibitory effects in nanomolar ranges (0.1 μm) and caused a stronger increase in mitoxantrone toxicity reaching similar values as Ko143, a potent ABCG2 inhibitor. Overall, in silico docking and in vitro studies demonstrated that the modification of baicalein with meta-carborane and three methoxy substituents leads to an enhanced reversal of ABCG2-mediated drug resistance. Thus, this seems to be a promising basis for the development of efficient ABCG2 inhibitors.

Decorrelated singlet and triplet exciton delocalization in acetylene-bridged Zn-porphyrin dimers

The controlled delocalization of molecular excitons remains an important goal towards the application of organic chromophores in processes ranging from light-initiated chemical transformations to classical and quantum information processing. In this study, we present a methodology to couple optical and magnetic spectroscopic techniques and assess the delocalization of singlet and triplet excitons in model molecular chromophores. By comparing the steady-state and time-resolved optical spectra of Zn-porphyrin monomers and weakly coupled dimers, we show that we can use the identity of substituents bound at specific positions of the macromolecules' rings to control the inter-ring delocalization of singlet excitons stemming from their B states through acetylene bridges. While broadened steady-state absorption spectra suggest the presence of delocalized B state excitons in mesityl-substituted Zn-tetraphenyl porphyrin dimers (Zn2U-D), we confirm this conclusion by measuring an enhanced ultrafast non-radiative relaxation from these inter-ring excitonic states to lower lying electronic states relative to their monomer. In contrast to the delocalized nature of singlet excitons, we use time-resolved EPR and ENDOR spectroscopies to show that the triplet states of the Zn-porphyrin dimers remain localized on one of the two macrocyclic sub-units. We use the analysis of EPR and ENDOR measurements on unmetallated model porphyrin monomers and dimers to support this conclusion. The results of DFT calculations also support the interpretation of localized triplet states. These results demonstrate researchers cannot conclude triplet excitons delocalize in macromolecular based on the presence of spatially extended singlet excitons, which can help in the design of chromophores for application in spin conversion and information processing technologies.

Dinitrogen Activation Mediated by the (P2PPh)Fe Complex: Electronic Structure, Dimerization Mechanism, and Magnetic Coupling

Herein, we report the estimation of the extent of dinitrogen activation by different charged and structural forms of (P2PPh)Fe biomimetic catalysts, which, in the presence of light, exhibit significant yield in the N2-to-NH3 conversion. Complete active space self-consistent field (CASSCF) calculations have been used to determine the electronic structure of different reduced forms of the mononuclear complexes: the neutral (P2PPh)Fe(N2)2 adduct and the anionic [(P2PPh)Fe(N2)]- and [(P2PPh)Fe(N2)]2- complexes. These calculations also revealed that the extent of reduction of a dinitrogen molecule reaches up to one electron (N21-) due to the back-bonding from the Fe center, in agreement with the changes observed in the vibration frequency of the N-N bond in these complexes. In addition, the energy profile of the dimerization of the mononuclear (P2PPh)Fe(N2)2 complex to the dinuclear mono-N2-bridged [(P2PPh)Fe]2(μ-N2) complex has been determined by means of density functional theory (DFT) calculations. A three-step mechanism has been proposed for the dimerization, favored by both kinetics and thermodynamics criteria. Finally, the magnetic coupling constant in the diiron (μ-N2) complex is estimated from CASSCF/NEVPT2 calculations. Such a dinuclear complex presents a strong antiferromagnetic coupling resulting from the interaction between two S = 1 d6 Fe2+ ions, bridged by a highly activated dinitrogen molecule (N22-) with two electrons on the π* orbitals.

Metal-Free B-B Dehydrocoupling Reaction of a Simple Borane Adduct: Convenient Access to a Nucleophilic Diborane(4)

The selective formation of homonuclear bonds is of key importance in synthetic chemistry. Especially, dehydrocoupling reactions are attractive as ecologically and economically friendly alternatives to established reductive bond forming reactions, since they do not require the use of stoichiometric amounts of a reducing reagent and produce only valuable dihydrogen as by-product. Here, we report on a metal-free B-B dehydrocoupling reaction that starts directly from a simple, easily accessible BH3 adduct, providing convenient access to a new nucleophilic dihydridodiborane in excellent yield. The dihydridodiborane in turn activates dihydrogen, allowing to obtain quantitatively the dideuteridodiborane from the dihydridodiborane by D2 activation. On the basis of detailed quantum-chemical calculations, the mechanism of this unprecedented reaction is elucidated. Some key points that are essential for metal-free dehydrocoupling are disclosed, paving the way for their systematic evaluation and application.

Triiron Complex with N-Ferrocenyl Aminocarbyne Ligand Bridging a Diiron Core: DFT, Electrochemical, and Biological Insights

The first N-ferrocenyl aminocarbyne complex, [Fe2Cp2(CO)2(μ-CO){μ-CN(Me)(Fc)}]CF3SO3 ([2]CF3SO3), was synthesized with an 88% yield from [Fe2Cp2(CO)4], isocyanoferrocene (CNFc), and methyl triflate. The synthesis proceeded through the intermediate formation of [Fe2Cp2(CO)3(CNFc)], 1. Multinuclear NMR experiments revealed the presence of cis and trans isomers for [2]CF3SO3 in organic solvents, in agreement with DFT outcomes. Electrochemical and spectroelectrochemical studies demonstrated one reduction process occurring prevalently at the diiron core and one oxidation involving the ferrocenyl substituent. The oxidation process is expected to favor the redox activation of [2]+ in a biological environment. Both [2]CF3SO3 and its phenyl analogue [Fe2Cp2(CO)2(μ-CO){μ-CN(Me)(Ph)}]CF3SO3 ([3]CF3SO3), prepared for comparison, exerted moderate antiproliferative activity against the human cancer cell lines A431, HCT-15, PSN-1, 2008, and U1285. However, [2]CF3SO3 exhibited a higher cytotoxicity than [3]CF3SO3, showed a substantial ability to induce intracellular ROS production, and outperformed cisplatin in a three-dimensional SCLC cell model.

Exploring CPS-Extrapolated DLPNO-CCSD(T1) Reference Values for Benchmarking DFT Methods on Enzymatically Catalyzed Reactions

Domain-based local pair natural orbital coupled-cluster singles doubles with perturbative triples [DLPNO-CCSD(T)] is regularly used to calculate reliable benchmark reference values at a computational cost significantly lower than that of canonical CCSD(T). Recent work has shown that even greater accuracy can be obtained at only a small additional cost through extrapolation to the complete PNO space (CPS) limit. Herein, we test two levels of CPS extrapolation, CPS(5,6), which approximates the accuracy of standard TightPNO, and CPS(6,7), which surpasses it, as benchmark values to test density functional approximations (DFAs) on a small set of organic and transition-metal-dependent enzyme active site models. Between the different reference levels of theory, there are changes in the magnitudes of the absolute deviations for all functionals, but these are small and there is minimal impact on the relative rankings of the tested DFAs. The differences are more significant for the metalloenzymes than the organic enzymes, so we repeat the tests on our entire ENZYMES22 set of organic enzyme active site models [Wappett, D. A.; Goerigk, L. J. Phys. Chem. A 2019, 123, 7057-7074] to confirm that using the CPS extrapolations for the reference values has negligible impact on the benchmarking outcomes. This means that we can particularly recommend CPS(5,6) as an alternative to standard TightPNO settings for calculating reference values, increasing the applicability of DLPNO-CCSD(T) in benchmarking reaction energies and barrier heights of larger models of organic enzymes. DLPNO-CCSD(T1)/CPS(6,7) energies for ENZYMES22 are finally presented as updated reference values for the set, reflecting the recent improvements in the method.

Multimer Embedding Approach for Molecular Crystals up to Harmonic Vibrational Properties

Accurate calculations of molecular crystals are crucial for drug design and crystal engineering. However, periodic high-level density functional calculations using hybrid functionals are often prohibitively expensive for the relevant systems. These expensive periodic calculations can be circumvented by the usage of embedding methods in which, for instance, the periodic calculation is only performed at a lower-cost level and then monomer energies and dimer interactions are replaced by those of the higher-level method. Herein, we extend such a multimer embedding approach to enable energy corrections for trimer interactions and the calculation of harmonic vibrational properties up to the dimer level. We evaluate this approach for the X23 benchmark set of molecular crystals by approximating a periodic hybrid density functional (PBE0+MBD) by embedding multimers into less expensive calculations using a generalized-gradient approximation functional (PBE+MBD). We show that trimer interactions are crucial for accurately approximating lattice energies within 1 kJ/mol and might also be needed for further improvement of lattice constants and hence cell volumes. Finally, the vibrational properties are already very well captured at the monomer and dimer level, making it possible to approximate vibrational free energies at room temperature within 1 kJ/mol.

Power of the Disulfide Bond: An Ideal Random Copolymerization of Biodegradable Redox-Responsive Hyperbranched Polyglycerols

The development of copolymerization techniques that can randomly incorporate biodegradable moieties into the hyperbranched polyglycerol backbone is an option to prevent its bioaccumulation in vivo. In this study, redox-responsive and biocompatible hyperbranched polyglycerol copolymers of glycidol and 1,4,5-oxadithiepan-2-one were synthesized with an adjustable molecular weight and a defined disulfide bond content through anionic and coordination-insertion ring-opening polymerization. A truly random incorporation of the monomers was achieved under both copolymerization mechanisms. The copolymers were further characterized in terms of their aggregation behavior in solution, degradability, in vitro cell viability, and blood compatibility for potential future biomedical applications. Transmission electron microscopy revealed that the copolymer assembled into nanoparticles with a size range of 20 nm. The copolymers underwent degradation when incubated with two different reducing agents, resulting in smaller fragments of the polymer with thiol end groups. The copolymers demonstrated good biocompatibility, making them suitable for further investigation in biomedical applications.

Improved Sampling of Adaptive Path Collective Variables by Stabilized Extended-System Dynamics

Because of the complicated multistep nature of many biocatalytic reactions, an a priori definition of reaction coordinates is difficult. Therefore, we apply enhanced sampling algorithms along with adaptive path collective variables (PCVs), which converge to the minimum free energy path (MFEP) during the simulation. We show how PCVs can be combined with the highly efficient well-tempered metadynamics extended-system adaptive biasing force (WTM-eABF) hybrid sampling algorithm, offering dramatically increased sampling efficiency due to its fast adaptation to path updates. For this purpose, we address discontinuities of PCVs that can arise due to path shortcutting or path updates with a novel stabilization algorithm for extended-system methods. In addition, we show how the convergence of simulations can be further accelerated by utilizing the multistate Bennett's acceptance ratio (MBAR) estimator. These methods are applied to the first step of the enzymatic reaction mechanism of pseudouridine synthases, where the ability of path WTM-eABF to efficiently explore intricate molecular transitions is demonstrated.

Symmetrical and Mixed Tris(acyl)phosphines: Synthesis, Oxidation and Photochemistry

Herein, we present a convenient synthesis for symmetrical and mixed substituted tris(acyl)phosphines (TAPs) starting from red phosphorus. All TAPs exhibit a phosphaalkene-acylphosphine equilibrium, which was investigated in detail by variable-temperature (VT) NMR spectroscopy supported by density-functional theory (DFT) calculations. Depending on the substituents, two phosphaalkene derivatives and ten acylphosphine derivatives could be isolated. NMR spectroscopy and single-crystal X-ray crystallography enabled a clear structural assignment of these compounds. Oxidation of selected TAPs led to the formation of the corresponding tris(acyl)phosphine oxides (TAPOs). Furthermore, their spectroscopic properties as well as their photochemistry was investigated. Especially, the TAPO compounds were evaluated for their suitability as photoinitiators by CIDNP spectroscopy, photobleaching measurements and by storage stability tests.

Improved Configurational Sampling Protocol for Large Atmospheric Molecular Clusters

The nucleation process leading to the formation of new atmospheric particles plays a crucial role in aerosol research. Quantum chemical (QC) calculations can be used to model the early stages of aerosol formation, where atmospheric vapor molecules interact and form stable molecular clusters. However, QC calculations heavily depend on the chosen computational method, and when dealing with large systems, striking a balance between accuracy and computational cost becomes essential. We benchmarked the binding energies and structures and found the B97-3c method to be a good compromise between the accuracy and computational cost for studying large cluster systems. Further, we carefully assessed configurational sampling procedures for targeting large atmospheric molecular clusters containing up to 30 molecules (approximately 2 nm in diameter) and proposed a funneling approach with highly improved accuracy. We find that several parallel ABCluster explorations lead to better guesses for the cluster global energy minimum structures than one long exploration. This methodology allows us to bridge computational studies of molecular clusters, which typically reach only around 1 nm, with experimental studies that often measure particles larger than 2 nm. By employing this workflow, we searched for low-energy configurations of large sulfuric acid-ammonia and sulfuric acid-dimethylamine clusters. We find that the binding free energies of clusters containing dimethylamine are unequivocally more stable than those of the ammonia-containing clusters. Our improved configurational sampling protocol can in the future be applied to study the growth and dynamics of large clusters of arbitrary compositions.

Benchmarking Density Functional Theory Methods for Metalloenzyme Reactions: The Introduction of the MME55 Set

We present a new benchmark set of metalloenzyme model reaction energies and barrier heights that we call MME55. The set contains 10 different enzymes, representing eight transition metals, both open and closed shell systems, and system sizes of up to 116 atoms. We use four DLPNO-CCSD(T)-based approaches to calculate reference values against which we then benchmark the performance of a range of density functional approximations with and without dispersion corrections. Dispersion corrections improve the results across the board, and triple-ζ basis sets provide the best balance of efficiency and accuracy. Jacob's ladder is reproduced for the whole set based on averaged mean absolute (percent) deviations, with the double hybrids SOS0-PBE0-2-D3(BJ) and revDOD-PBEP86-D4 standing out as the most accurate methods for the MME55 set. The range-separated hybrids ωB97M-V and ωB97X-V also perform well here and can be recommended as a reliable compromise between accuracy and efficiency; they have already been shown to be robust across many other types of chemical problems, as well. Despite the popularity of B3LYP in computational enzymology, it is not a strong performer on our benchmark set, and we discourage its use for enzyme energetics.

Metal-ligand interactions in a redox active ligand system. Electrochemistry and spectroscopy of [M(dipyvd)2]n+ (M=Zn, Ni, n=0, 1, 2)

Reaction of nickel and zinc triflates with the tridentate leucoverdazyl 1-isopropyl-3,5-di (2'-pyridyl)-6-oxo-2H-tetrazine (dipyvdH) and triethylamine resulted in the neutral coordination compounds M(dipyvd)2 (M = Ni,Zn). In acetonitrile, both compounds undergo two one electron oxidation processes, Zn (dipyvd)2 at -0.28 V and -0.12 V and Ni(dipyvd)2 at -0.32 V and -0.15 V vs ferrocene/ferricenium. Oxidations are ligand based resulting in an intermediate mixed valence species and a cationic bis(verdazyl) compound respectively. Oxidation of the ligand changes a localized, antiaromatic, non-planar 8π electron anion to a planar, delocalized 7π electron radical. The change in ligand structure results in an increase in the octahedral ligand field splitting from 10,500 cm-1 to ∼13,000 cm-1, suggesting an increase in the pi acceptor character of the ligand. In the mixed valence species, spectroscopic data suggests minimal interaction between ligands mediated by the metal center; i.e., these are class I-II systems in the Robin-Day classification.

Deposition products predicted from conceptual DFT: The hydrolysis reactions of MoF6, WF6, and UF6

Metal hexafluorides hydrolyze at ambient temperature to deposit compounds having fluorine-to-oxygen ratios that depend upon the identity of the metal. Uranium-hexafluoride hydrolysis, for example, deposits uranyl fluoride (UO2F2), whereas molybdenum hexafluoride (MoF6) and tungsten hexafluoride deposit trioxides. Here, we pursue general strategies enabling the prediction of depositing compounds resulting from multi-step gas-phase reactions. To compare among the three metal-hexafluoride hydrolyses, we first investigate the mechanism of MoF6 hydrolysis using hybrid density functional theory (DFT). Intermediates are then validated by performing anharmonic vibrational simulations and comparing with infrared spectra [McNamara et al., Phys. Chem. Chem. Phys. 25, 2990 (2023)]. Conceptual DFT, which is leveraged here to quantitatively evaluate site-specific electrophilicity and nucleophilicity metrics, is found to reliably predict qualitative deposition propensities for each intermediate. In addition to the nucleophilic potential of the oxygen ligands, several other contributing characteristics are discussed, including amphoterism, polyvalency, fluxionality, steric hindrance, dipolar strength, and solubility. To investigate the structure and composition of pre-nucleation clusters, an automated workflow is presented for the simulation of particle growth. The workflow entails a conformer search at the density functional tight-binding level, structural refinement at the hybrid DFT level, and computation of a composite free-energy profile. Such profiles can be used to estimate particle nucleation kinetics. Droplet formation is also considered, which helps to rationalize the different UO2F2 particle morphologies observed under varying levels of humidity. Development of predictive methods for simulating physical and chemical deposition processes is important for the advancement of material manufacturing involving coatings and thin films.

Assessment of DLPNO-MP2 Approximations in Double-Hybrid DFT

The unfavorable scaling (N5) of the conventional second-order Møller-Plesset theory (MP2) typically prevents the application of double-hybrid (DH) density functionals to large systems with more than 100 atoms. A prominent approach to reduce the computational demand of electron correlation methods is the domain-based local pair natural orbital (DLPNO) approximation that is successfully used in the framework of DLPNO-CCSD(T). Its extension to MP2 [Pinski P.; Riplinger, C.; Valeev, E. F.; Neese, F. J. Chem. Phys. 2015, 143, 034108.] paved the way for DLPNO-based DH (DLPNO-DH) methods. In this work, we assess the accuracy of the DLPNO-DH approximation compared to conventional DHs on a large number of 7925 data points for thermochemistry and 239 data points for structural features, including main-group and transition-metal systems. It is shown that DLPNO-DH-DFT can be applied successfully to perform energy calculations and geometry optimizations for large molecules at a drastically reduced computational cost. Furthermore, PNO space extrapolation is shown to be applicable, similar to its DLPNO-CCSD(T) counterpart, to reduce the remaining error.