Minimally Empirical Double-Hybrid Functionals Trained against the GMTKN55 Database: revDSD-PBEP86-D4, revDOD-PBE-D4, and DOD-SCAN-D4

Water-carbon disulfide dimers: observation of a new isomer and ab initio structure theory

The weakly bound dimer water-carbon disulfide is studied by ab initio structure theory and high-resolution infrared spectroscopy. The calculations yield three stable minima in the potential energy surface, all planar. The most stable, isomer 1, was observed previously by microwave spectroscopy. It has C2v symmetry, an S-O bond, and a linear O-S-C-S backbone. Isomer 2, the next most stable, has not been considered previously by theory or experiment. It also has C2v symmetry, but with a side-by-side structure. Isomer 3, which is slightly less stable, is side-by-side with one O-H bond pointing toward an S atom. The first gas phase water-CS2 infrared spectra are reported. For isomer 1, H2O-, HDO-, and D2O-CS2 are observed in the CS2ν1 + ν3 region, H2O-CS2 in the H2O ν2 bend region, and D2O-CS2 in the D2O ν1 and ν3 stretch regions. The latter ν3 spectrum enables an experimental determination of the A rotational parameter, which turns out to be larger than expected. The new isomer 2 is observed by means of a band in the H2O ν2 region, confirming its C2v symmetry and calculated structure.

The structure of the Lujo virus spike complex

Lujo virus (LUJV) is a human pathogen that was the cause of a deadly hemorrhagic fever outbreak in Africa. LUJV is a divergent member of the Arenaviridae with some similarities to both the "Old World" and "New World" serogroups, but it uses a cell-entry receptor, neuropilin-2 (NRP2), that is distinct from the receptors of OW and NW viruses. Though the receptor binding domain of LUJV has been characterized structurally, the overall organization of the trimeric spike complex and how NRP2 is recognized in this context were unknown. Here, we present the structure of the membrane-embedded LUJV spike complex determined by cryo-electron microscopy. Analysis of the structure suggested that a single NRP2 molecule is bound at the apex of the trimeric spike and that multiple subunits of the trimer contact the receptor. The binding of NRP2 involves an intriguing arginine-methionine interaction, which we analyzed using quantum mechanical modeling methods. We compare the LUJV spike structure with the only other available structure of a complete arenaviral spike, which is the Lassa virus. The similarities and differences between them shed light on Arenavirus evolution, inform vaccine design, and provide information that will be useful in combating future Arenavirus outbreaks.

Histidine in Proteins: pH-Dependent Interplay between π-π, Cation-π, and CH-π Interactions

Histidine (His) stands out as the most versatile natural amino acid due to its side chain's facile propensity to protonate at physiological pH, leading to a transition from aromatic to cationic characteristics and thereby enabling diverse biomolecular interactions. In this study, our objective was to quantify the energetics and geometries of pairwise interactions involving His at varying pH levels. Through quantum chemical calculations, we discovered that His exhibits robust participation in both π-π and cation-π interactions, underscoring its ability to adopt a π or cationic nature, akin to other common residues. Of particular note, we found that the affinity of protonated His for aromatic residues (via cation-π interactions) is greater than the affinity of neutral His for either cationic residues (also via cation-π interactions) or aromatic residues (via π-π interactions). Furthermore, His frequently engages in CH-π interactions, and notably, depending on its protonation state, we found that some instances of hydrogen bonding by His exhibit greater stability than is typical for interamino acid hydrogen bonds. The strength of the pH-dependent pairwise energies of His with aromatic residues is supported by the abundance of pairwise interactions with His of low and high predicted pKa values. Overall, our findings illustrate the contribution of His interactions to protein stability and its potential involvement in conformational changes despite its relatively low abundance in proteins.

Harmonic and anharmonic vibrational computations for biomolecular building blocks: Benchmarking DFT and basis sets by theoretical and experimental IR spectrum of glycine conformers

Advanced vibrational spectroscopic experiments have reached a level of sophistication that can only be matched by numerical simulations in order to provide an unequivocal analysis, a crucial step to understand the structure-function relationship of biomolecules. While density functional theory (DFT) has become the standard method when targeting medium-size or larger systems, the problem of its reliability and accuracy are well-known and have been abundantly documented. To establish a reliable computational protocol, especially when accuracy is critical, a tailored benchmark is usually required. This is generally done over a short list of known candidates, with the basis set often fixed a priori. In this work, we present a systematic study of the performance of DFT-based hybrid and double-hybrid functionals in the prediction of vibrational energies and infrared intensities at the harmonic level and beyond, considering anharmonic effects through vibrational perturbation theory at the second order. The study is performed for the six-lowest energy glycine conformers, utilizing available "state-of-the-art" accurate theoretical and experimental data as reference. Focusing on the most intense fundamental vibrations in the mid-infrared range of glycine conformers, the role of the basis sets is also investigated considering the balance between computational cost and accuracy. Targeting larger systems, a broad range of hybrid schemes with different computational costs is also tested.

Evaluating Noncovalent Interactions in Halogenated Molecules with Double-Hybrid Functionals and a Dedicated Small Basis Set

We present here an extension of our recently developed PBE-QIDH/DH-SVPD basis set to halogen atoms, with the aim of obtaining, for weakly interacting halogenated molecules, interaction energies close to those provided by a large basis set (def2-TZVPP) coupled to empirical dispersion potential. The core of our approach is the split-valence basis set, DH-SVPD, that has been developed for F, Cl, Br, and I atoms using a self-consistent formula, containing only energy terms computed for dimers and the corresponding monomers at the same level of theory. The basis set developed considering four systems, one for each halogen atoms, has been then tested on the X40, X4 × 10 benchmarks as well as on other two, less standard, data sets. Finally, a large system (380 atoms) has been also considered as a "crash" test. Our results show that the simple and nonempirical PBE-QIDH/DH-SVPD approach is able to provide accurate results for interaction energies of all the considered systems and can thus be considered as a cheaper alternative to DH functionals paired with empirical dispersion corrections and a large basis set of triple-ζ quality.

Assessment of the applicability of DFT methods to [Cp*Rh]-catalyzed hydrogen evolution processes

The present computational study provides a benchmark of density functional theory (DFT) methods in describing hydrogen evolution processes catalyzed by [Cp*Rh]-containing organometallic complexes. A test set was composed of 26 elementary reactions featuring chemical transformations and bonding situations essential for the field, including the emerging concept of non-innocent Cp* behavior. Reference values were obtained from a highly accurate 3/4 complete basis set and 6/7 complete PNO space extrapolated DLPNO-CCSD(T) energies. The performance of lower-level extrapolation procedures was also assessed. We considered 84 density functionals (DF) (including 13 generalized gradient approximations (GGA), nine meta-GGAs, 33 hybrids, and 29 double-hybrids) and three composite methods (HF-3c, PBEh-3c, and r2SCAN-3c), combined with different types of dispersion corrections (D3(0), D3BJ, D4, and VV10). The most accurate approach is the PBE0-DH-D3BJ (MAD of 1.36 kcal mol-1) followed by TPSS0-D3BJ (MAD of 1.60 kcal mol-1). Low-cost r2SCAN-3c composite provides a less accurate but much faster alternative (MAD of 2.39 kcal mol-1). The widely used Minnesota-family M06-L, M06, and M06-2X DFs should be avoided (MADs of 3.70, 3.94, and 4.01 kcal mol-1, respectively).

The Semiexperimental Approach at Work: Equilibrium Structure of Radical Species

The so-called semiexperimental (SE) approach is a powerful technique for obtaining highly accurate equilibrium structures for isolated systems. This Featured Article describes its extension to open-shell species, thus providing the first systematic investigation on radical equilibrium geometries to be used for benchmarking purposes. The small yet significant database obtained demonstrates that there is no reduction in accuracy when moving from closed-shell species to radicals. We also provide an extension of the applicability of the SE approach to medium-/large-sized radicals by exploiting the so-called "Lego-brick" approach, which is based on the assumption that a molecular system can be seen as formed by smaller fragments for which the SE equilibrium structure is available. In this Featured Article we show that this model can be successfully applied also to open-shell species.

Theoretical investigation of the OH-initiated atmospheric degradation mechanism of CX2CHX (X = H, F, Cl) by advanced quantum chemical and transition state theory methods

Halogenated olefins are anthropogenic compounds with many industrial applications but at the same time raising many environmental and health concerns. Gas-phase electrophilic addition of the OH radical to the olefinic CC bond represents the primary sink for these chemicals in the atmosphere, with the degree and type of halogenation playing a significant role in their overall reactivity. In this work, we present a theoretical investigation of the reaction mechanisms and kinetics for the reactions between the OH radical and CH2CH2 (ethylene, ETH), CF2CHF (trifluoroethylene, TFE) and CCl2CHCl (trichloroethylene, TCE), simulated by state-of-the-art protocols and methods, with the aim of providing a detailed interpretation of the available experimental results, as well as new data of relevance to tropospheric chemistry. Specifically, potential energy surfaces (PESs) are obtained using the jun-Cheap (jChS) composite scheme, whereas temperature and pressure dependent rate coefficients and product distributions in the 100-600 K temperature range are calculated within the Rice-Ramsperger-Kassel-Marcus/master equation (RRKM/ME) framework. The rates for barrierless channels are obtained from variable reaction coordinate-variational transition state theory (VRC-VTST) combined with the two transition state model. While the reactions with ETH and TFE proceed mainly via the formation of addition adducts at P = 1 atm and T = 298 K, the dominant channel for TCE is the Cl-elimination reaction. Global rate constants for the two halogenated olefins, TFE and TCE, are found to be pressure-independent, contrary to the case of ETH. The computed rate constants, as well as their temperature and pressure dependence, are in remarkable agreement with the available experimental data, and they are used to derive atmospheric lifetimes (τ) for both TFE and TCE as a function of altitude (h) in the atmosphere, by taking into account variations in the rate coefficients (k (T, P)) and [OH] concentration.

Antiaromaticity of Cycloheptatrienyl Anions: Structure, Acidity, and Magnetic Properties

Investigations of the nature and degree of antiaromaticity of cycloheptatrienyl anion derivatives using both experimental and computational tools are presented. The ground state of cycloheptatrienyl anion in the gas phase is triplet, planar and Baird-aromatic. In DMSO, it assumes a singlet distorted allylic form with a paratropic ring current. The other derivatives in both phases assume either allylic or diallylic conformations depending on the substituent pattern. A combination of experimental and computational methods was used to determine the pKa values of 16 derivatives in DMSO, which ranged from 36 to -10.7. We revealed that the stronger stabilization of the anionic system, which correlates with acidity, does not necessarily imply a lower degree of antiaromaticity in terms of magnetic properties. Conversely, the substitution pattern first affects the geometry of the ring through the bulkiness of the substituents and their better conjugation with a more distorted system. Consequently, the distortion reduces the cyclic conjugation in the π-system and thereby decreases the paratropic current in a magnetic field, which manifests itself as a decrease in the NICS. The triplet-state geometries and magnetic properties are nearly independent on the substitution pattern, which is typical for simple aromatic systems.

How do spin-scaled double hybrids designed for excitation energies perform for noncovalent excited-state interactions? An investigation on aromatic excimer models

Time-dependent double hybrids with spin-component or spin-opposite scaling to their second-order perturbative correlation correction have demonstrated competitive robustness in the computation of electronic excitation energies. Some of the most robust are those recently published by our group (M. Casanova-Páez, L. Goerigk, J. Chem. Theory Comput. 2021, 20, 5165). So far, the implementation of these functionals has not allowed correctly calculating their ground-state total energies. Herein, we define their correct spin-scaled ground-state energy expressions which enables us to test our methods on the noncovalent excited-state interaction energies of four aromatic excimers. A range of 22 double hybrids with and without spin scaling are compared to the reasonably accurate wavefunction reference from our previous work (A. C. Hancock, L. Goerigk, RSC Adv. 2023, 13, 35964). The impact of spin scaling is highly dependent on the underlying functional expression, however, the smallest overall errors belong to spin-scaled functionals with range separation: SCS- and SOS- ω PBEPP86, and SCS-RSX-QIDH. We additionally determine parameters for DFT-D3(BJ)/D4 ground-state dispersion corrections of these functionals, which reduce errors in most cases. We highlight the necessity of dispersion corrections for even the most robust TD-DFT methods but also point out that ground-state based corrections are insufficient to completely capture dispersion effects for excited-state interaction energies.

Synthesis of Thiourea and Thioamide S-Oxides via SO Transfer from a Thiirane S-Oxide onto N-Heterocyclic Carbenes

Thiourea S-oxides are labile compounds that suffer from a quick overoxidation when directly prepared from thioureas. Therefore, we have developed an alternative route on the basis of the SO transfer from a thiirane S-oxide onto sterically encumbered N-heterocyclic carbenes, including imidazole- and imidazoline-ylidenes, and a cyclic alkyl amino carbene. Reaction conditions and DFT computations suggest a concerted SO transfer mechanism. Thiourea S-oxides are nucleophiles adding to dimethyl acetylenedicarboxylate under fission of the S-O bond.

Accurate structures and rotational constants of bicyclic monoterpenes at DFT cost by means of the bond-corrected Pisa composite scheme (BPCS)

The structural, conformational, and spectroscopic properties in the gas phase of 20 bicyclic monoterpenes and monoterpenoids have been analyzed by a new accurate, reduced-cost computational strategy. In detail, the revDSD-PBEP86 double-hybrid functional in conjunction with the D3BJ empirical dispersion corrections and a suitable triple-zeta basis set provides accurate geometrical parameters, whence equilibrium rotational constants, which are further improved by proper account of core-valence correlation. Average deviations within 0.1% between computed and experimental rotational constants are reached when taking into account the vibrational corrections obtained by the B3LYP functional in conjunction with a double-zeta basis set in the framework of second-order vibrational perturbation theory. In addition to their intrinsic interest, the studied terpenes further extend the panel of systems for which the proposed strategy has provided accurate results at density functional theory cost. Therefore, a very accurate yet robust and user-friendly tool is now available for systematic investigations of the role of stereo-electronic effects on the properties of large systems of current technological and/or biological interest by experimentally oriented researchers.

Carbamic acid and its dimer: A computational study

A recent work by Marks et al. on the formation of carbamic acid in NH3 $$ {}_3 $$ -CO2 $$ {}_2 $$ interstellar ices pointed out its stability in the gas phase and the concomitant production of its dimer. Prompted by these results and the lack of information on these species, we have performed an accurate structural, energetic and spectroscopic investigation of carbamic acid and its dimer. For the former, the structural and spectroscopic characterization employed composite schemes based on coupled cluster (CC) calculations that account for the extrapolation to the complete basis set limit and core correlation effects. A first important outcome is the definitive confirmation of the nonplanarity of carbamic acid, then followed by an accurate estimate of its rotational and vibrational spectroscopy parameters. As far as the carbamic acid dimer is concerned, the investigation started from the identification of its most stable forms. For them, structure and vibrational properties have been evaluated using density functional theory, while a composite scheme rooted in CC theory has been employed for the energetic characterization. Our results allowed us to provide a better interpretation of the feature observed in the recent experiment mentioned above.

A new chapter in the never ending story of cycloadditions: The puzzling case of SO2 and acetylene

A comprehensive study of the different classes of cycloaddition reactions ([3+2], [2+2], and [2+1]) of SO2 to acetylene and ethylene has been performed using density functional theory (DFT) and composite wavefunction methods. The [3+2] cycloaddition reaction, that was previously explored in the context of the cycloaddition of thioformaldehyde S-methylide (TSM) to ethylene and acetylene, proceeds in a concerted way to the formation of stable heterocycles. In this paper, we extend our study to the [2+2] and [2+1] cycloadditions of SO2 to acetylene, which would produce 1,1-oxathiete-2-oxide and thiirene-1,1-dioxide, respectively. One of the main conclusions is that cyclic 1,1-oxathiete-2-oxide can open through a relatively easy breaking of the SO single bond and rearrange toward sulfinyl acetaldehyde (SA). The SA molecule can easily undergo several internal rearrangements, which eventually lead to sulfenic acid and sulfoxide derivatives of ethenone, 1,2,3-dioxathiole, and CO plus sulfinylmethane. The most probable path, however, produces 2-thioxoacetic acid, whose derivatives (or those of the corresponding acetate) are usually obtained by Willgerodt-Kindler-type sulfuration of acetates. This product can in turn decompose, leading to the final products CO2 and H2CS. Comparison of this decomposition path with that of 2-amino-2-thioxoacetic acid shows that the process occurs through different H-transfer processes.

Norcaradiene-Cycloheptatriene Equilibrium: A Heavy-Atom Quantum Tunneling Case

The equilibrium between norcaradiene and cycloheptatriene, which has captivated chemists for more than half a century, is revisited by state-of-the-art quantum chemical calculations. Our theoretical data significantly deviate from the experimental results (J. Am. Chem. Soc., 1981, 26, 7791-7792), especially at low temperatures, where isomerization is dominated by heavy-atom tunneling. This effect results in an extremely short half-life for norcaradiene, rendering it undetectable. This work sheds light on this equilibrium, updating the kinetic and thermodynamic data while also expanding the repertoire of organic reactions controlled by this exotic quantum effect.

Hydroboration and hydrosilylation of alkenes catalyzed by an unsymmetrical magnesium methyl complex

The hydroboration and hydrosilylation of alkenes catalyzed by the unsymmetrical β-diketiminate magnesium methyl complex [(DippXylNacnac)MgMe (THF)] (1) have been reported. When complex 1 was employed as a highly efficient catalyst in the hydroboration of various alkenes with HBpin, only the anti-Markovnikov hydroboration products were obtained in high yields and with high regioselectivities under mild reaction conditions (60 °C). To our surprise, it showed different regioselectivities in the hydrosilylation of a range of alkenes with PhSiH3. Aromatic alkene substrates afforded the corresponding branched Markovnikov hydrosilylation products in high yields and with high regioselectivities; conversely, aliphatic alkenes produced the linear anti-Markovnikov products in moderate yields. This is completely consistent with the corresponding density functional theory (DFT) calculations. In addition, the practical utility was demonstrated via scale-up reactions of boronate esters and a preliminary plausible mechanism of hydroboration and hydrosilylation have been investigated as well.

The synthesis of N,1,4-tri(alkoxy-hydroxybenzyl)-1,4-diazepane-amines: investigations on reaction characteristics and mechanism

1,4-Diazepane-6-amine (DAZA) can be alkylated with three 2-hydroxybenzyl pendant arms, resulting in hexadentate chelators suitable for coordination of radiometals like 68Ga. These chelators, N,1,4-tri(alkoxy-2-hydroxybenzyl)-DAZA, can be produced via a one-pot synthesis, with the first step being a carbonyl amine condensation of DAZA with two respective 4-alkoxy-2-hydroxybenzaldehydes, followed by reductive amination with sodium borohydride. While the first step of this reaction is predictable, the subsequent reductive amination can result in either mono-, di- or tri(alkoxy-hydroxybenzyl)-DAZA compounds. Seeking to identify dependencies that might allow a specific reaction control towards the formation of either of the three possible products, and particularly towards the favoured trialkylated DAZA compounds, a variety of synthesis trials were performed. Additionally, computational methods were employed to evaluate the underlying reaction mechanism. Synthesis trials verified that the trialkylated DAZA compounds are formed via direct reductive amination of the dialkylated DAZA compounds. Subsequently, a synthetic method was established, leading to an increase in the percentage of the trialkylated DAZA compounds, which allowed the successful isolation of those hexadentate chelators. Additionally, an alternative pathway proceeding via aminal C-N bond insertion of an attacking third carbonyl moiety was evaluated by means of quantum chemical calculations but so far remains entirely hypothetical.

Toward Accurate Quantum Chemical Methods for Molecules of Increasing Dimension: The New Family of Pisa Composite Schemes

The new versions of the Pisa composite scheme introduced in the present paper are based on the careful selection of different quantum chemical models for energies, geometries, and vibrational frequencies, with the aim of maximizing the accuracy of the overall description while retaining a reasonable cost for all the steps. In particular, the computation of accurate electronic energies has been further improved introducing more reliable complete basis set extrapolations and estimation of core-valence correlation, together with improved basis sets for third-row atoms. Furthermore, the reduced-cost frozen natural orbital (FNO) model has been introduced and validated for large molecules. Accurate molecular structures can be obtained avoiding complete basis set extrapolation and evaluating core-valence correlation at the MP2 level. Unfortunately, analytical gradients are not available for the FNO version of the model. Therefore, for large molecules, an accurate reduced-cost alternative is offered by evaluation of valence contributions with a double-hybrid functional in conjunction with the same MP2 contribution for core-valence correlation or by means of a one-parameter approximation. The same double-hybrid functional and basis set are employed to evaluate zero-point energies and partition functions. After the validation of the new models for small systems, a panel of molecular bricks of life has been used to analyze their performances for problems of current fundamental or technological interest. The fully black-box implementation of the computational workflow paves the way toward the accurate yet not prohibitively expensive study of medium- to large-sized molecules also by experimentally oriented researchers.

Ruthenium/η5-Phenoxo-Catalyzed Amination of Phenols with Amines

Ruthenium(II) complexes are known to form η6-arene complexes with benzene-containing compounds through π-coordination, a property extensively utilized to initiate reactions not typically observed with free arenes. A prime example is nucleophilic aromatic substitution, where ruthenium-complexed aryl halides undergo nucleophilic attack, allowing the direct synthesis of diverse aromatic compounds by displacing halides with nucleophiles. However, this activation relies on the electron-withdrawing effect of the Ru(II) species, as well as is hindered by the resistance of η6-arenes to arene exchange. In the previous pursuit of catalysis, the emphasis of ligand design has centered on promoting arene exchange. In this study, we extended the ruthenium activation strategy to umpolung substitution reactions of phenols. The amination proceeds through a direct condensation between phenols and amines, with a key intermediate identified as [bis(η5-phenoxo)Ru], which is in situ generated from a commercially available ruthenium catalyst. In comparison with the well-studied cyclopentadienyl (Cp) type ligands, we demonstrated that an η5-phenoxo motif, as a superior alternative to Cp, contributes to the amination of phenols in two crucial ways: its less electron-donating nature enhances the withdrawing effect of the ruthenium unit, facilitating substitution on the phenol complex; its distinctive behavior in arene exchange allows for conducting the amination with a catalytic amount of metal. Additionally, hydrogen bonding, wherein the phenoxo serves as the acceptor, was found to be important for the substitution. The versatility of this ruthenium-catalyzed amination was validated by performing reactions with a diverse array of phenols exhibiting various electronic properties, in combination with a wide range of primary amines. This work exemplifies the expansion of the scope of π-coordination activation in catalysis through innovative ligand development.

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.

On the sensitivity of computed partial charges toward basis set and (exchange-)correlation treatment

Partial charges are a central concept in general chemistry and chemical biology, yet dozens of different computational definitions exist. In prior work [Cho et al., ChemPhysChem 21, 688-696 (2020)], we showed that these can be reduced to at most three 'principal components of ionicity'. The present study addressed the dependence of computed partial charges q on 1-particle basis set and (for WFT methods) n -particle correlation treatment or (for DFT methods) exchange-correlation functional, for several representative partial charge definitions such as QTAIM, Hirshfeld, Hirshfeld-I, HLY (electrostatic), NPA, and GAPT. Our findings show that semi-empirical double hybrids can closely approach the CCSD(T) 'gold standard' for this property. In fact, owing to an error compensation in MP2, CCSD partial charges are further away from CCSD(T) than is MP2. The nonlocal correlation is important, especially when there is a substantial amount of nonlocal exchange. Employing range separation proves to be "mostly" not advantageous, while global hybrids perform optimally for 20%-30% Hartree-Fock exchange across all charge types. Basis set convergence analysis shows that an augmented triple-zeta heavy-aug-cc-pV(T+d)Z basis set or a partially augmented jun-cc-pV(T+d)Z basis set is sufficient for Hirshfeld, Hirshfeld-I, HLY, and GAPT charges. In contrast, QTAIM and NPA display slower basis set convergence. It is noteworthy that for both NPA and QTAIM, HF exhibits markedly slower basis set convergence than the correlation components of MP2 and CCSD. Triples corrections in CCSD(T), denoted as CCSD(T)-CCSD, exhibit even faster basis set convergence.

XMECP: Reaching State-of-the-Art MECP Optimization in Multiscale Complex Systems

The Python-based program, XMECP, is developed for realizing robust, efficient, and state-of-the-art minimum energy crossing point (MECP) optimization in multiscale complex systems. This article introduces the basic capabilities of the XMECP program by theoretically investigating the MECP mechanism of several example systems including (1) the photosensitization mechanism of benzophenone, (2) photoinduced proton-coupled electron transfer in the cytosine-guanine base pair in DNA, (3) the spin-flip process in oxygen activation catalyzed by an iron-containing 2-oxoglutarate-dependent oxygenase (Fe/2OGX), and (4) the photochemical pathway of flavoprotein adjusted by the intensity of an external electric field. MECPs related to multistate reaction and multistate reactivity in large-scale complex biochemical systems can be well-treated by workflows suggested by the XMECP program. The branching plane updating the MECP optimization algorithm is strongly recommended as it provides derivative coupling vector (DCV) with explicit calculation and can equivalently evaluate contributions from non-QM residues to DCV, which can be nonadiabatic coupling or spin-orbit coupling in different cases. In the discussed QM/MM examples, we also found that the influence on the QM region by DCV can occur through noncovalent interactions and decay with distance. In the example of DNA base pairs, the nonadiabatic coupling occurs across the π-π stacking structure formed in the double-helix system. In contrast to general intuition, in the example of Fe/2OGX, the central ferrous and oxygen part contribute little to the spin-orbit coupling; however, a nearby arginine residue, which is treated by molecular mechanics in the QM/MM method, contributes significantly via two hydrogen bonds formed with α-ketoglutarate (α-KG). This indicates that the arginine residue plays a significant role in oxygen activation, driving the initial triplet state toward the productive quintet state, which is more than the previous knowledge that the arginine residue can bind α-KG at the reaction site by hydrogen bonds.

Theoretical Study of the Temperature- and Pressure-Dependent Rate Constants for Nine Reactions between COn (n = 0-4), Om (m = 1-3), C2O, and C3O2 during the Radiolysis of Carbon Dioxide

We investigate the reaction pathways of nine important CO2-related reactions using the revDSD-PBEP86-D3(BJ)/jun-cc-pV(T+d)Z level and simultaneously employ an accurate composite method (jun-Cheap) based on coupled-cluster (CC) theory. Subsequently, the Rice-Ramsperger-Kassel-Marcus/master equation (RRKM/ME) is solved to calculate the temperature- and pressure-dependent rate constants. This work investigates reactions involving transition states that have been overlooked in previous literature, including the dissociation of singlet-state C3O2, the triple channel formation of C2O + CO to form C3O2, and the formation of O3 + CO. The results show that CO3 is highly prone to dissociation at high temperatures. Finally, the kinetic data show that over a wide temperature range, our calculations are consistent with previous experimental measurements. The majority of the reaction rate constants studied exhibit significant pressure dependence, while the O3 + CO reaction is pressure-independent at low temperatures. These results are instrumental in the development of detailed kinetic models for the CO2 radiolysis reaction network.

Isomerism of CH 2 SO : Accurate structural, energetic, and spectroscopic characterization

A recent work [Ye et al. Mon. Not. R. Astron. Soc. 2023, 525, 1158] on the gas-phase formation of t-HC(O)SH, already detected in the interstellar medium, pointed out that the trans form of HC(S)OH is a potential candidate for astronomical observations. Prompted by these results, theCH 2 SO family of isomers has been investigated from an energetic point of view using a double-hybrid density functional in combination with a partially augmented triple-zeta basis set. This preliminary study showed that the most stable species of the family are the cis and trans forms of HC(O)SH and HC(S)OH. For their structural and spectroscopic characterization, a composite scheme based on coupled cluster (CC) calculations that incorporates up to the quadruple excitations and accounts for the extrapolation to the complete basis set limit and core correlation effects has been employed. This approach opens to the prediction of rotational constants with an accuracy of 0.1%. A hybrid scheme, based on harmonic frequencies computed using the CC singles, doubles and a perturbative treatment of triples method (CCSD(T)) in conjunction with a quadruple-zeta basis set, allowed us to obtain fundamental vibrational frequencies with a mean absolute error of about 1%.

Unbiased Comparison between Theoretical and Experimental Molecular Structures and Properties: Toward an Accurate Reduced-Cost Evaluation of Vibrational Contributions

The tremendous development of hardware and software is constantly increasing the role of quantum chemical (QC) computations in the assignment and interpretation of experimental results. However, an unbiased comparison between theory and experiment requires the proper account of vibrational averaging effects. In particular, high-resolution spectra in the gas phase are now available for molecules containing up to about 50 atoms, which are too large for a brute-force approach with the available QC methods of sufficient accuracy. In the present paper, we introduce hybrid approaches, which allow the accurate evaluation of vibrational averaging effects for molecules of this size beyond the harmonic approximation, with special attention being devoted to rotational constants. After the validation of new tools for relatively small molecules, the β-estradiol hormone and a prototypical molecular motor have been considered to witness the feasibility of accurate computations for large molecules.

Accurate Structures and Rotational Constants of Steroid Hormones at DFT Cost: Androsterone, Testosterone, Estrone, β-Estradiol, and Estriol

A comprehensive analysis of the structural, conformational, and spectroscopic properties in the gas phase has been performed for five prototypical steroid hormones, namely, androsterone, testosterone, estrone, β-estradiol, and estriol. The revDSD-PBEP86 double-hybrid functional in conjunction with the D3BJ empirical dispersion and a suitable triple-ζ basis set provides accurate conformational energies and equilibrium molecular structures, with the latter being further improved by proper account of core-valence correlation. Average deviations within 0.1% between computed and experimental ground state rotational constants are reached when adding to those equilibrium values vibrational corrections obtained at the cost of standard harmonic frequencies thanks to the use of a new computational tool. Together with the intrinsic interest of the studied hormones, the accuracy of the results obtained at DFT cost for molecules containing about 50 atoms paves the way toward the accurate investigations of other flexible bricks of life.

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.

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

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

Structural confirmation of position isomers 2-(2-methylaminoprolyl)benzofuran and 5-(2-methylaminopropyl)benzofuran: a combined mass spectrometric and computational study

RATIONALE

Phenylethylamines are one of the most common types of new psychoactive substances, following synthetic cannabinoids and synthetic cathinones. They are regulated in many countries because of their strong hallucinogenic effects, which can cause serious nerve damage. There is a wide variety of phenylethylamines, exhibiting rapid renewal and extremely similar structures, therefore accurate qualitative analysis of isomers is a difficult problem in current drug analysis.

METHODS

The dissociation pathways of the position isomers 2-(2-methylaminoprolyl)benzofuran (2-MAPB) and 5-(2-methylaminopropyl)benzofuran (5-MAPB) were investigated by gas chromatography-mass spectrometry and liquid chromatography coupled to high-resolution quadrupole Orbitrap MS. The dissociation patterns of the phenethylamine-based designer drugs 2-MAPB and 5-MAPB were explored and extended in this work based on MS combined with density functional theory studies.

RESULTS

For electron ionization mass spectrometry (EI-MS) analysis, the dissociation patterns of 2-MAPB were similar to those of 5-MAPB. For electrospray ionization mass spectrometry (ESI-MSn ) analysis, the hydrogen atom on amino group was facile to form a intramolecular hydrogen bond with the oxygen atom on the parent nucleus of benzofuran in the structure of 2-MAPB, leading to higher abundance of the product ion at m/z 58. However, there was a conjugated system between the positive charge formed by the cleavage of the 5-MAPB side chain and the benzofuran ring, enabling the 5-MAPB to generate a product ion at m/z 131. Computational study showed that energy barrier and spin density difference distribution jointly control the selective dissociation in EI-MS, while different types of orbital interaction induced by intramolecular hydrogen bond led to different dissociation results in ESI-MSn .

CONCLUSIONS

These different dissociation patterns could be used to distinguish 2-MAPB from 5-MAPB. This could assist forensic laboratories in the differentiation and characterization of potential isomers in these kinds of compounds, especially in mixtures.

Accurate Geometries of Large Molecules by Integration of the Pisa Composite Scheme and the Templating Synthon Approach

An effective yet reliable computational workflow is proposed, which permits the computation of accurate geometrical structures for large flexible molecules at an affordable cost thanks to the integration of machine learning tools and DFT models together with reduced scaling computations of vibrational averaging effects. After validation of the different components of the overall strategy, a panel of molecules of biological interest have been analyzed. The results confirm that very accurate geometrical parameters can be obtained at reasonable cost for molecules including up to about 50 atoms, which are the largest ones for which comparison with high-resolution rotational spectra is possible. Since the whole computational workflow can be followed employing standard electronic structure codes, accurate results for large-sized molecules can be obtained at DFT cost also by nonspecialists.

Theoretical Prediction of the Reaction Probabilities of H, O, and OH Radicals on the Polypropylene Surface

To determine the H-abstraction reaction probabilities of H/O/OH radicals with a polypropylene (PP) surface, a first-principles calculation was performed based on the DLPNO-CCSD(T)/CBS//M06-2X-D3/def-TZVP theory level. The PP chain model used in this study was 2,4,6-trimethylheptane. The rate constants of the H/O/OH radicals with the isolated PP chain model were calculated based on the conventional transition-state theory. By comparing the experimental values and considering the error factors and their compensation, it was concluded that the orders of magnitude of the predicted rate constants were accurate. The resulting rate constants were converted to reaction probabilities between the H/O/OH radicals and the PP surface. The method used in this study is applicable for obtaining theoretical values of surface reaction probabilities based on first-principles calculations. The calculation at the DLPNO-CCSD(T)/CBS theory level has high accuracy but consumes a large amount of computational resources. The study also demonstrated that the double-hybrid functionals, wB97x-2-D3(BJ) and rev-DSD-PBEP86-D3(BJ), with a 3-ζ or 4-ζ basis set, could reproduce the electronic energy values obtained from DLPNO-CCSD(T)/CBS while using only approximately 1/100 of the computational resources required by the latter under our computer configuration.

Quantum chemistry meets high-resolution spectroscopy for characterizing the molecular bricks of life in the gas-phase

Computation of accurate geometrical structures and spectroscopic properties of large flexible molecules in the gas-phase is tackled at an affordable cost using a general exploration/exploitation strategy. The most distinctive feature of the approach is the careful selection of different quantum chemical models for energies, geometries and vibrational frequencies with the aim of maximizing the accuracy of the overall description while retaining a reasonable cost for all the steps. In particular, a composite wave-function method is used for energies, whereas a double-hybrid functional (with the addition of core-valence correlation) is employed for geometries and harmonic frequencies and a cheaper hybrid functional for anharmonic contributions. A thorough benchmark based on a wide range of prototypical molecular bricks of life shows that the proposed strategy is close to the accuracy of state-of-the-art composite wave-function methods, and is applicable to much larger systems. A freely available web-utility post-processes the geometries optimized by standard electronic structure codes paving the way toward the accurate yet not prohibitively expensive study of medium- to large-sized molecules by experimentally-oriented researchers.

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.

Doubling down on density-functional theory

In a recent paper, Becke et al. [J. Chem. Phys. 158, 151103 (2023)] presented a novel double hybrid density functional, "DH23," whose terms are based on good physics. Its 12 coefficients were trained on the GMTKN55 (general main-group thermochemistry, kinetics, and noncovalent interactions) chemical database of Goerigk et al. [Phys. Chem. Chem. Phys. 19, 32184 (2017)]. The lowest GMTKN55 "WTMAD2" error to date for any hybrid or double hybrid density functional was obtained (1.76 kcal/mol). Here, we make some revisions to DH23 and test its efficacy on reference data beyond GMTKN55, namely, organometallic reaction energies and barrier heights. The results confirm that DH23 is robust outside its training set. In the process, a slightly smaller GMTKN55 WTMAD2 of 1.73 kcal/mol is achieved.

Hunting for Complex Organic Molecules in the Interstellar Medium: The Role of Accurate Low-Cost Theoretical Geometries and Rotational Constants

A new approach to computation at affordable cost of accurate geometrical structures and rotational constants for medium-sized molecules in the gas phase is further improved and applied to a large panel of interstellar complex organic molecules. The most distinctive feature of the new model is the effective inclusion of core-valence correlation and vibrational averaging effects in the framework of density functional theory (DFT). In particular, a double-hybrid functional in conjunction with a quadruple-ζ valence/triple-ζ polarization basis set is employed for geometry optimizations, whereas a cheaper hybrid functional in conjunction with a split-valence basis set is used for the evaluation of vibrational corrections. A thorough benchmark based on a wide range of prototypical systems shows that the new scheme approaches the accuracy of state-of-the-art wave function methods with the computational cost of the standard methods (DFT or MP2) routinely employed in the interpretation of microwave spectra. Since the whole computational workflow involves the postprocessing of the output of standard electronic structure codes by a new freely available web utility, the way is paved for the accurate yet not prohibitively expensive study of medium- to large-sized molecules also by nonspecialists.

Core-Shell Reactor Partitioning Enzyme and Prodrug by ZIF-8 for NADPH-Sensitive In Situ Prodrug Activation

Enzyme-prodrug therapies have shown unique advantages in efficiency, selectivity, and specificity of in vivo prodrug activation. However, precise spatiotemporal control of both the enzyme and its substrate at the target site, preservation of enzyme activity, and in situ substrate depletion due to low prodrug delivery efficiency continue to be great challenges. Here, we propose a novel core-shell reactor partitioning enzyme and prodrug by ZIF-8, which integrates an enzyme with its substrate and increases the drug loading capacity (DLC) using a prodrug as the building ligand to form a Zn-prodrug shell. Cytochrome P450 (CYP450) is immobilized in ZIF-8, and the antitumor drug dacarbazine (DTIC) is coordinated and deposited in its outer layer with a high DLC of 43.6±0.8 %. With this configuration, a much higher prodrug conversion efficiency of CYP450 (36.5±1.5 %) and lower IC50 value (26.3±2.6 μg/mL) are measured for B16-F10 cells with a higher NADPH concentration than those of L02 cells and HUVECs. With the tumor targeting ability of hyaluronic acid, this core-shell enzyme reactor shows a high tumor suppression rate of 96.6±1.9 % and provides a simple and versatile strategy for enabling in vivo biocatalysis to be more efficient, selective, and safer.

Noncovalently bound excited-state dimers: a perspective on current time-dependent density functional theory approaches applied to aromatic excimer models

Excimers are supramolecular systems whose binding strength is influenced by many factors that are ongoing challenges for computational methods, such as charge transfer, exciton coupling, and London dispersion interactions. Treating the various intricacies of excimer binding at an adequate level is expected to be particularly challenging for time-dependent Density Functional Theory (TD-DFT) methods. In addition to well-known limitations for some TD-DFT methods in the description of charge transfer or exciton coupling, the inherent London dispersion problem from ground-state DFT translates to TD-DFT. While techniques to appropriately treat dispersion in DFT are well-developed for electronic ground states, these dispersion corrections remain largely untested for excited states. Herein, we aim to shed light on current TD-DFT methods, including some of the newest developments. The binding of four model excimers is studied across nine density functionals with and without the application of additive dispersion corrections against a wave function reference of SCS-CC2/CBS(3,4) quality, which approximates select CCSDR(3)/CBS data adequately. To our knowledge, this is the first study that presents single-reference wave function dissociation curves at the complete basis set level for the assessed model systems. It is also the first time range-separated double-hybrid density functionals are applied to excimers. In fact, those functionals turn out to be the most promising for the description of excimer binding followed by global double hybrids. Range-separated and global hybrids-particularly with large fractions of Fock exchange-are outperformed by double hybrids and yield worse dissociation energies and inter-molecular equilibrium distances. The deviation between each assessed functional and reference increases with system size, most likely due to missing dispersion interactions. Additive dispersion corrections of the DFT-D3(BJ) and DFT-D4 types reduce the average errors for TD-DFT methods but do so inconsistently and therefore do not offer a black-box solution in their ground-state parametrised form. The lack of appropriate description of dispersion effects for TD-DFT methods is likely hindering the practical application of the herein identified more efficient methods. Dispersion corrections parametrised for excited states appear to be an important next step to improve the applicability of TD-DFT methods and we hope that our work assists with the future development of such corrections.

Improved Description of Intra- and Intermolecular Interactions through Dispersion-Corrected Second-Order Møller-Plesset Perturbation Theory

ConspectusThe quantum chemical modeling of organic crystals and other molecular condensed-phase problems requires computationally affordable electronic structure methods which can simultaneously describe intramolecular conformational energies and intermolecular interactions accurately. To achieve this, we have developed a spin-component-scaled, dispersion-corrected second-order Møller-Plesset perturbation theory (SCS-MP2D) model. SCS-MP2D augments canonical MP2 with a dispersion correction which removes the uncoupled Hartree-Fock dispersion energy present in canonical MP2 and replaces it with a more reliable coupled Kohn-Sham treatment, all evaluated within the framework of Grimme's D3 dispersion model. The spin-component scaling is then used to improve the description of the residual (nondispersion) portion of the correlation energy.The SCS-MP2D model improves upon earlier corrected MP2 models in a few ways. Compared to the highly successful dispersion-corrected MP2C model, which is based solely on intermolecular perturbation theory, the SCS-MP2D dispersion correction improves the description of both inter- and intramolecular interactions. The dispersion correction can also be evaluated with trivial computational cost, and nuclear analytic gradients are computed readily to enable geometry optimizations. In contrast to earlier spin-component scaling MP2 models, the optimal spin-component scaling coefficients are only mildly sensitive to the choice of training data, and a single global parametrization of the model can describe both thermochemistry and noncovalent interactions.The resulting dispersion-corrected, spin-component-scaled MP2 (SCS-MP2D) model predicts conformational energies and intermolecular interactions with accuracy comparable to or better than those of many range-separated and double-hybrid density functionals, as is demonstrated on a variety of benchmark tests. Among the functionals considered here, only the revDSD-PBEP86-D3(BJ) functional gives consistently smaller errors in benchmark tests. The results presented also hint that further improvements of SCS-MP2D may be possible through a more robust fitting procedure for the seven empirical parameters.To demonstrate the performance of SCS-MP2D further, several applications to molecular crystal problems are presented. The three chosen examples all represent cases where density-driven delocalization error causes GGA or hybrid density functionals to artificially stabilize crystals exhibiting more extended π-conjugation. Our pragmatic strategy addresses the delocalization error by combining a periodic density functional theory (DFT) treatment of the infinite lattice with intramolecular/conformational energy corrections computed with SCS-MP2D. For the anticancer drug axitinib, applying the SCS-MP2D conformational energy correction produces crystal polymorph stabilities that are consistent with experiment, in contrast to earlier studies. For the crystal structure prediction of the ROY molecule, so named for its colorful red, orange, and yellow crystals, this approach leads to the first plausible crystal energy landscape, and it reveals that the lowest-energy polymorphs have already been found experimentally. Finally, in the context of photomechanical crystals, which transform light into mechanical work, these techniques are used to predict the structural transformations and extract design principles for maximizing the work performed.

Synthesis of tetrazoles through a domino reaction: A molecular electron density theory study of energetics, selectivities, and molecular mechanistic aspects

This study corresponds to a molecular electron density theory (MEDT) investigation to shed light on the energetics, selectivities, and molecular mechanistic aspects of an experimental domino reaction. Theoretical evidences at the M06-2X/6-31G(d) level indicates that this domino reaction includes three different successive steps and is initialized by a stepwise HCl elimination from precursor chlorohydrazone NPCH to yield nitrile imine NI-2. A subsequent stepwise and highly regioselective [3 + 2] cycloaddition (32CA) reaction of NI-2 toward tetramethylguanidine TMG-3 affords corresponding formal [3 + 2] cycloadduct CA-1 as the sole product. Finally, a stepwise HNMe2 elimination experienced by CA-1 leads to amino triazole ATA as an aromatic five-membered target product. Computed rate constants reveal that the HCl elimination step should be considered as the bottleneck of this domino reaction. However, a topological analysis of electron localization function (ELF) of NI-2 demonstrates a zwitterionic type (zw-type) 32 C A reaction is expected between NI-2 and TMG-3. This 32CA reaction also displays an almost noticeable polar character arising from moderate electrophilicity and strong nucleophilicity of NI-2 and TMG-3, respectively. The regioselectivity of 32CA reaction can be explained via analysis of Parr functions values calculated at the reactive sites of reagents. The molecular mechanism of the 32CA reaction was explored through portraying bond forming/breaking patterns involved in this polar, stepwise, and zw-type reaction by means of the ELF analysis. Indeed, formation of both C-N single bonds along the first and second steps takes place through coupling of the corresponding pseudoradical centers.

Accurate Force Fields for Atomistic Simulations of Oxides, Hydroxides, and Organic Hybrid Materials up to the Micrometer Scale

The simulation of metals, oxides, and hydroxides can accelerate the design of therapeutics, alloys, catalysts, cement-based materials, ceramics, bioinspired composites, and glasses. Here we introduce the INTERFACE force field (IFF) and surface models for α-Al2O3, α-Cr2O3, α-Fe2O3, NiO, CaO, MgO, β-Ca(OH)2, β-Mg(OH)2, and β-Ni(OH)2. The force field parameters are nonbonded, including atomic charges for Coulomb interactions, Lennard-Jones (LJ) potentials for van der Waals interactions with 12-6 and 9-6 options, and harmonic bond stretching for hydroxide ions. The models outperform DFT calculations and earlier atomistic models (Pedone, ReaxFF, UFF, CLAYFF) up to 2 orders of magnitude in reliability, compatibility, and interpretability due to a quantitative representation of chemical bonding consistent with other compounds across the periodic table and curated experimental data for validation. The IFF models exhibit average deviations of 0.2% in lattice parameters, <10% in surface energies (to the extent known), and 6% in bulk moduli relative to experiments. The parameters and models can be used with existing parameters for solvents, inorganic compounds, organic compounds, biomolecules, and polymers in IFF, CHARMM, CVFF, AMBER, OPLS-AA, PCFF, and COMPASS, to simulate bulk oxides, hydroxides, electrolyte interfaces, and multiphase, biological, and organic hybrid materials at length scales from atoms to micrometers. The nonbonded character of the models also enables the analysis of mixed oxides, glasses, and certain chemical reactions, and well-performing nonbonded models for silica phases, SiO2, are introduced. Automated model building is available in the CHARMM-GUI Nanomaterial Modeler. We illustrate applications of the models to predict the structure of mixed oxides, and energy barriers of ion migration, as well as binding energies of water and organic molecules in outstanding agreement with experimental data and calculations at the CCSD(T) level. Examples of model building for hydrated, pH-sensitive oxide surfaces to simulate solid-electrolyte interfaces are discussed.

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.

Modeling-Experiment-Theory Analysis of Reactions Initiated from Cl + Methyl Formate

Methyl formate (MF; CH3OCHO) is the smallest representative of esters, which are common components of biodiesel. The present study characterizes the thermal dissociation kinetics of the radicals formed by H atom abstraction from MF─CH3OCO and CH2OCHO─through a combination of modeling, experiment, and theory. For the experimental effort, excimer laser photolysis of Cl2 was used as a source of Cl atoms to initiate reactions with MF in the gas phase. Time-resolved species profiles of MF, Cl2, HCl, CO2, CH3, CH3Cl, CH2O, and CH2ClOCHO were measured and quantified using photoionization mass spectrometry at temperatures of 400-750 K and 10 Torr. The experimental data were simulated using a kinetic model, which was informed by ab initio-based theoretical kinetics calculations and included chlorine chemistry and secondary reactions of radical decomposition products. We calculated the rate coefficients for the H-abstraction reactions Cl + MF → HCl + CH3OCO (R1a) and Cl + MF → HCl + CH2OCHO (R1b): k1a,theory = 6.71 × 10-15·T1.14·exp(-606/T) cm3/molecule·s; k1b,theory = 4.67 × 10-18·T2.21·exp(-245/T) cm3/molecule·s over T = 200-2000 K. Electronic structure calculations indicate that the barriers to CH3OCO and CH2OCHO dissociation are 13.7 and 31.6 kcal/mol and lead to CH3 + CO2 (R3) and CH2O + HCO (R5), respectively. The master equation-based theoretical rate coefficients are k3,theory (P = ∞) = 2.94 × 109·T1.21·exp(-6209/T) s-1 and k5,theory (P = ∞) = 8.45 × 108·T1.39·exp(-15132/T) s-1 over T = 300-1500 K. The calculated branching fractions into R1a and R1b and the rate coefficient for R5 were validated by modeling of the experimental species time profiles and found to be in excellent agreement with theory. Additionally, we found that the bimolecular reactions CH2OCHO + Cl, CH2OCHO + Cl2, and CH3 + Cl2 were critical to accurately model the experimental data and constrain the kinetics of MF-radicals. Inclusion of the kinetic parameters determined in this study showed a significant impact on combustion simulations of larger methyl esters, which are considered as biodiesel surrogates.

Rotational spectra and semi-experimental structures of furonitrile and its water cluster

Rotational spectroscopy represents an invaluable tool for several applications: from the identification of new molecules in interstellar objects to the characterization of van der Waals complexes, but also for the determination of very accurate molecular structures and for conformational analyses. In this work, we used high-resolution rotational spectroscopic techniques in combination with high-level quantum-chemical calculations to address all these aspects for two isomers of cyanofuran, namely 2-furonitrile and 3-furonitrile. In particular, we have recorded and analyzed the rotational spectra of both of them from 6 to 320 GHz; rotational transitions belonging to several singly-substituted isotopologues have been identified as well. The rotational constants derived in this way have been used in conjunction with computed rotation-vibration interaction constants in order to derive a semi-experimental equilibrium structure for both isomers. Moreover, we observed the rotational spectra of four different intermolecular adducts formed by furonitrile and water, whose identification has been supported by a conformational analysis and a theoretical spectroscopic characterization. A semi-experimental determination of the intermolecular parameters has been achieved for all of them and the results have been compared with those obtained for the analogous system formed by benzonitrile and water.

Chemically accurate singlet-triplet gaps of organic chromophores and linear acenes by the random phase approximation and σ-functionals

Predicting the energy differences between different spin-states is challenging for many widely used ab initio electronic structure methods. We here assess the ability of the direct random phase approximation (dRPA), dRPA plus two different screened second-order exchange (SOX) corrections, and σ-functionals to predict adiabatic singlet-triplet gaps. With mean absolute deviations of below 0.1 eV to experimental reference values, independent of the Kohn-Sham starting point, dRPA and σ-functionals accurately predict singlet-triplet gaps of 18 organic chromophores. The addition of SOX corrections to dRPA considerably worsens agreement with experiment, adding to the mounting evidence that dRPA+SOX methods are not generally applicable beyond-RPA methods. Also for a series of linear acene chains with up to ten fused rings, dRPA, and σ-functionals are in excellent agreement with coupled-cluster single double triple reference data. In agreement with advanced multi-reference methods, dRPA@PBE and σ-functional@PBE predict a singlet ground state for all chain lengths, while dRPA@PBE0 and σ-functional@PBE0 predict a triplet ground state for longer acenes. Our work shows dRPA and σ-functionals to be reliable methods for calculating singlet-triplet gaps in aromatic molecules.

Toward an Accurate Black-Box Tool for the Kinetics of Gas-Phase Reactions Involving Barrier-less Elementary Steps

An enhanced computational protocol has been devised for the accurate characterization of gas-phase barrier-less reactions in the framework of the reaction-path (RP) and variable reaction coordinate variational transition-state theory. In particular, the synergistic combination of density functional theory and Monte Carlo sampling to optimize reactive fluxes led to a reliable yet effective computational workflow. A black-box strategy has been developed for selecting the most suited density functional with reference to a high-level one-dimensional reference potential. At the same time, different descriptions of hindered rotations are automatically selected, depending on the corresponding harmonic frequencies along the RP. The performance of the new tool is investigated by means of two prototypical reactions involving different degrees of static and dynamic correlation, namely, H2S + Cl and CH3 + CH3. The remarkable agreement of the computed kinetic parameters with the available experimental data confirms the accuracy and robustness of the proposed approach. Together with their intrinsic interest, these results also pave the way toward systematic investigations of gas-phase reactions involving barrier-less elementary steps by a reliable, user-friendly tool, which can be confidently used also by nonspecialists.

Exploring α-electron-deficiency-induced [1,2]-fluorine migration

The present study investigates the standard model of [1,2]-fluorine migration and that triggered by the rearrangement of cyclopropyl-substituted fluoroepoxides. The [1,2]-fluorine migration reaction proceeds via a synchronous concerted, tight-ion-pair mechanism. When coupled with other reaction coordinates, the whole reaction follows an asynchronous mechanism, while the [1,2]-fluorince migration unit still retains its tight-ion-pair feature and the reaction coordinates of two C-F distances vary synchronously. A general reaction program for α-electron-deficiency-induced [1,2]-fluorine migration is proposed through an analysis of the intermediates generated from nucleophilic addition. The reaction mechanisms associated with α-electron deficiency and the rearrangement are scrutinized using computational chemistry. Two additional reaction programs for [1,2]-fluorine migration are identified. The Gibbs free energy change of [1,2]-fluorine migration exhibits a linear dependence on the value of the Fukui function of the substrate, which could lead to the production of the desired α-monofluoroketone and enhance the utilization of fluorine atoms.

Solvent and Substituent Size Influence on the Cyclochiral Rigidity of Aminomethylene Derivatives of Resorcin[4]arene

Resorcin[4]arenes (R[4]A) are a group of macrocyclic compounds whose peculiar feature is the presence of eight hydroxyl groups in their structure. The directional formation of intramolecular hydrogen bonds with their participation leads to the formation of a cyclochiral racemic mixture of these compounds. Their stability strongly depends on the substituent and especially the environment in which they are located. The paper discusses the cyclochiral nature of aminomethylene derivatives of R[4]A (AMD-R[4]A). Their cyclochiral rigidity in non-polar solvents has been shown. The influence of the size of the alkyl groups in the amino substituents of AMD-R[4]A on their cyclochiral nature was noted. To calculate the reaction paths for their racemization, the nudged elastic band (NEB) method was employed using the semi-empirical DFT (GFN1-xTB) approach. The calculated activation barrier energies for their racemization in chloroform, obtained through various semi-empirical quantum chemical methods (SE), Hartree-Fock (HF), and density functionals theory (DFT), show good correlation with experimental observations. Among the tested methods, the B38LYP-D4 method is highly recommended due to its fast computational speed and accuracy, which is comparable to the time-consuming double-hybrid DH-revDSD-PBEP86 approach.

Bimolecular Reaction of Methyl-Ethyl-Substituted Criegee Intermediate with SO2

Methyl-ethyl-substituted Criegee intermediate (MECI) is a four-carbon carbonyl oxide that is formed in the ozonolysis of some asymmetric alkenes. MECI is structurally similar to the isoprene-derived methyl vinyl ketone oxide (MVK-oxide) but lacks resonance stabilization, making it a promising candidate to help us unravel the effects of size, structure, and resonance stabilization that influence the reactivity of atmospherically important, highly functionalized Criegee intermediates. We present experimental and theoretical results from the first bimolecular study of MECI in its reaction with SO2, a reaction that shows significant sensitivity to the Criegee intermediate structure. Using multiplexed photoionization mass spectrometry, we obtain a rate coefficient of (1.3 ± 0.3) × 10-10 cm3 s-1 (95% confidence limits, 298 K, 10 Torr) and demonstrate the formation of SO3 under our experimental conditions. Through high-level theory, we explore the effect of Criegee intermediate structure on the minimum energy pathways for their reactions with SO2 and obtain modified Arrhenius fits to our predictions for the reaction of both syn and anti conformers of MECI with SO2 (ksyn = 4.42 × 1011 T-7.80exp(-1401/T) cm3 s-1 and kanti = 1.26 × 1011 T-7.55exp(-1397/T) cm3 s-1). Our experimental and theoretical rate coefficients (which are in reasonable agreement at 298 K) show that the reaction of MECI with SO2 is significantly faster than MVK-oxide + SO2, demonstrating the substantial effect of resonance stabilization on Criegee intermediate reactivity.

Accurate Thermochemical and Kinetic Parameters at Affordable Cost by Means of the Pisa Composite Scheme (PCS)

A new strategy for the computation at an affordable cost of geometrical structures, thermochemical parameters, and rate constants for medium-sized molecules in the gas phase is proposed. The most distinctive features of the new model are the systematic use of cc-pVnZ-F12 basis sets, the addition of MP2 core-valence correlation in geometry optimizations by a double-hybrid functional, the separate extrapolation of MP2 and post-MP2 contributions, and the inclusion of anharmonic contributions in zero-point energies and thermodynamic functions. A thorough benchmark based on a wide range of prototypical systems shows that the new scheme outperforms the most well-known model chemistries without the need for any empirical parameter. Additional tests show that the computed zero-point energies and thermal contributions can be confidently used for obtaining accurate thermochemical and kinetic parameters. Since the whole computational workflow is translated in a black-box procedure, which can be followed with standard electronic structure codes, the way is paved for the accurate yet not prohibitively expensive study of medium- to large-sized molecules also by nonspecialists.

Rhodium-Catalyzed Addition of (Trialkylsilyl)arenes to Electrophiles via π-Coordination-Driven C-Si Bond Activation

Aromatic organosilicon compounds serve as valuable synthons due to their diverse reactivities, excellent compatibility with various functional groups, and ready availability. However, (trialkylsilyl)arenes, despite their potential utility, are generally considered unsuitable substrates for transition-metal-catalyzed cross-coupling due to the low polarity of their covalent C(aryl)-Si bonds and the significant steric hindrance imposed by alkyl substituents. These factors render them inert toward reactions with transition metals, such as transmetalation and oxidative addition. In this study, we present a method for the rhodium-catalyzed addition of (trialkylsilyl)arenes to electrophiles via π-coordination-driven desilylation. We propose that a dicationic rhodium species activates the unbiased C(aryl)-Si bond, increasing its polarity by forming an η6-arene complex, thereby facilitating heterolysis. The resulting phenyl anion complex readily engages in addition reactions with external electrophiles, effectively forming C-C bonds. Through comprehensive computational studies, we have unraveled an unexpected stepwise pathway for desilylation with fluoride. This pathway involves the addition of fluoride to the aromatic ring, followed by a 1,2-migration of fluoride, ultimately culminating in the departure of fluorotrimethylsilane.