Best-Practice DFT Protocols for Basic Molecular Computational Chemistry

Cp* non-innocence and the implications of (η4-Cp*H)Rh intermediates in the hydrogenation of CO2, NAD+, amino-borane, and the Cp* framework - a computational study

In hydrogenation mediated by half-sandwich complexes of Rh, Cp*Rh(III)-H intermediates are critical hydride-delivery agents. For bipyridine-supported complexes, a unique transformation named 'Cp* non-innocence' leads to the appearance of (Cp*H)Rh(I) intermediates, which are purported to exhibit enhanced hydride-delivery capabilities. In this work, DFT calculations performed to compare the role of these complexes in hydrogenation reveal that (Cp*H)Rh(I) intermediates do not compete with the conventional pathway (involving Cp*Rh(III)-H); instead they can lead to sequential hydrogenation of the Cp* framework, and potentially, catalyst degradation. Thus, caution is warranted when invoking the truly homogeneous nature of hydrogenation catalysis mediated by this popular class of complexes.

The computational road to reactivity scales

Reactivity scales are useful research tools for chemists, both experimental and computational. However, to determine the reactivity of a single molecule, multiple measurements need to be carried out, which is a time-consuming and resource-intensive task. In this Tutorial Review, we present alternative approaches for the efficient generation of quantitative structure-reactivity relationships that are based on quantum chemistry, supervised learning, and uncertainty quantification. First published in 2002, we observe a tendency for these relationships to become not only more predictive but also more interpretable over time.

ωB97X-3c: A composite range-separated hybrid DFT method with a molecule-optimized polarized valence double-ζ basis set

A new composite density functional theory (DFT) method is presented. It is based on ωB97X-V as one of the best-performing density functionals for the GMTKN55 thermochemistry database and completes the family of "3c" methods toward range-separated hybrid DFT. This method is consistently available for all elements up to Rn (Z = 1-86). Its further key ingredients are a polarized valence double-ζ (vDZP) Gaussian basis set, which was fully optimized in molecular DFT calculations, in combination with large-core effective core potentials and a specially adapted D4 dispersion correction. Unlike most existing double-ζ atomic orbital sets, vDZP shows only small basis set superposition errors (BSSEs) and can compete with standard sets of triple-ζ quality. Small residual BSSE effects are efficiently absorbed by the D4 damping scheme, which overall eliminates the need for an explicit treatment or empirical corrections for BSSE. Thorough tests on a variety of thermochemistry benchmark sets show that the new composite method, dubbed ωB97X-3c, is on par with or even outperforms standard hybrid DFT methods in a quadruple-zeta basis set at a small fraction of the computational cost. Particular strengths of this method are the description of non-covalent interactions and barrier heights, for which it is among the best-performing density functionals overall.

Synthesis of D-π-A'-π-A Chromophores with Quinoxaline Core as Auxiliary Acceptor and Effect of Various Silicon-Substituted Donor Moieties on Thermal and Nonlinear Optical Properties at Molecular and Material Level

Novel D-π-A'-π-A chromophores with quinoxaline cores as auxiliary acceptors and various donor moieties (aniline, carbazole, phenothiazine, tetrahydroquinoline) containing bulky tert-butyldimethylsilyloxy (TBDMSO) groups and tricyanofuranyl (TCF) acceptors with bulky cyclohexylphenyl substituents were synthesized via eight- to nine-step procedures, and their photo-physical and thermal properties were investigated. The values of the chromophores' first hyperpolarizabilities were calculated in the framework of DFT at the M06-2X/aug-cc-pVDZ computational level; the effect of the introduction of the TBDMSO group into the donor fragment is shown to be inessential, as this group is not coupled to the π-conjugated system of the chromophore. The chromophore with the tetrahydroquinoline donor has a first hyperpolarizability value of 937 × 10^-30 esu, which is the highest for the studied chromophores. Atomistic modeling of composite materials with the studied chromophores as guests demonstrated that the presence of bulky substituent in the donor fragment prevents notable aggregation of chromophores, even at high chromophore content (40 wt.%). The nonlinear optical performance of guest-host materials with 25 and 40 wt.% of suggested chromophore content was studied using a second harmonic generation technique to give the NLO coefficient, d₃₃ up to 52 pm/V.

Angewandte Chemie: A Team Effort

While the number of submissions to the journal continued to increase in 2022, the Editorial Team also implemented a number of changes with support of the GDCh and the journal's advisory bodies. For example, "Team Profiles" are author profiles that celebrate joint efforts as the basis of an inclusive research culture. In looking forward, two new members will join the International Advisory Board in 2023.

Calcium Hydride Cation Dimer Catalyzed Hydrogenation of Unactivated 1-Alkenes and H2 Isotope Exchange: Competitive Ca-H-Ca Bridges and Terminal Ca-H Bonds

Recently, it was shown that the double Ca-H-Ca bridged calcium hydride cation dimer complex [LCaH₂ CaL]²⁺ (macrocyclic ligand L=NNNN-tetradentate Me₄ TACD) exhibited remarkable activity in catalyzing the hydrogenation of unactivated 1-alkenes as well as the H₂ isotope exchange under mild conditions, tentatively via the terminal Ca-H bond of cation monomer LCaH⁺ . In this DFT mechanistic work, a novel substrate-dependent catalytic mechanism is disclosed involving cooperative Ca-H-Ca bridges for H₂ isotope exchange, competitive Ca-H-Ca bridges and terminal Ca-H bonds for anti-Markovnikov addition of unactivated 1-alkenes, and terminal Ca-H bonds for Markovnikov addition of conjugation-activated styrene. THF-coordination plays a key role in favoring the anti-Markovnikov addition while strong cation-π interactions direct the Markovnikov addition to terminal Ca-H bonds.

Design, Molecular Modeling, MD Simulations, Essential Dynamics, ADMET, DFT, Synthesis, Anti-proliferative, and Apoptotic Evaluations of a New Anti-VEGFR-2 Nicotinamide Analogue

OBJECTIVES

This study aims to design and evaluate (in silico and in vitro) a new nicotinamide derivative as an inhibitor of VEGFR-2, a major mediator of angiogenesis Methods: The following in silico studies were performed; DFT calculations, molecular modelling, MD simulations, MM-GBSA, PLIP, and PCAT studies. The compound's in silico (ADMET) analysis was also conducted. Subsequently, the compound ((E)-N-(4-(1-(2-(4-(4-Chlorobenzamido)benzoyl)hydrazono)ethyl) phenyl)nicotinamide) was successfully synthesized and designated as compound X. In vitro, VEGFR-2 inhibition and cytotoxicity of compound X against HCT-116 and A549 cancer cell lines and normal Vero cell lines were conducted. Apoptosis induction and migration assay of HCT-116 cell lines after treatment with compound X were also evaluated.

RESULTS

DFT calculations assigned stability and reactivity of compound X. Molecular docking and MD simulations indicated its excellent binding against VEGFR-2. Furthermore, MM-GBSA analysis, PLIP experiments, and PCAT studies confirmed compound X's correct binding with optimal dynamics and energy. ADMET analysis expressed its general likeness and safety. The in vitro assays demonstrated that compound X effectively inhibited VEGFR-2, with an IC50 value of 0.319 ± 0.013 μM and displayed cytotoxicity against HCT-116 and A549 cancer cell lines, with IC50 values of 57.93 and 78.82 μM, respectively. Importantly, compound X exhibited minimal toxicity towards the non-cancerous Vero cell lines, (IC50 = 164.12 μM). Additionally, compound X significantly induced apoptosis of HCT-116 cell lines and inhibited their potential to migrate and heal.

CONCLUSION

In summary, the presented study has identified compound X as a promising candidate for the development of a novel apoptotic lead anticancer drug.

Origin of the Ligand Ring-Size Effect on the Catalytic Activity of Cationic Calcium Hydride Dimers in the Hydrogenation of Unactivated 1-Alkenes

Recently, it was shown that the double Ca-H-Ca-bridged calcium hydride cation dimer [LCaH₂ CaL]²⁺ when stabilized by a larger macrocyclic N,N',N'',N''',N''''-pentadentate ligand showed evidently higher activity than when stabilized by a smaller N,N',N'',N'''-tetradentate ligand in the catalytic hydrogenation of unactivated 1-alkenes. In this DFT-mechanistic work, the origin of the observed ring-size effect is examined in detail using 1-hexene, CH₂ =CH₂ and H₂ as substrates. It is shown that, at room temperature, both the N,N',N'',N''',N''''-stabilized dimer and the monomer are not coordinated by THF in solution, while the corresponding N,N',N'',N'''-stabilized structures are coordinated by one THF molecule mimicking the fifth N-coordination. Catalytic 1-alkene hydrogenation may occur via anti-Markovnikov addition over the terminal Ca-H bonds of transient monomers, followed by faster Ca-C bond hydrogenolysis. The higher catalytic activity of the larger N,N',N'',N''',N''''-stabilized dimer is due to not only easier formation of but also due to the higher reactivity of the catalytic monomeric species. In contrast, despite unfavorable THF-coordination in solution, the smaller N,N',N'',N'''-stabilized dimer shows a 3.2 kcal mol^-1 lower barrier via a dinuclear cooperative Ca-H-Ca bridge for H₂ isotope exchange than the large N,N',N'',N''',N''''-stabilized dimer, mainly due to less steric hindrance. The observed ring-size effect can be understood mainly by a subtle interplay of solvent, steric and cooperative effects that can be resolved in detail by state-of-the-art quantum chemistry calculations.

Diastereoselective Synthesis of Novel Spiro-Phosphacoumarins and Evaluation of Their Anti-Cancer Activity

Herein we present the regio- and diastereoselective synthesis of novel pyrrolidine-fused spiro-dihydrophosphacoumarins via intermolecular [3 + 2] cycloaddition reaction. The presented approach is complementary to existing ones and provides an easy entry to the otherwise inaccessible derivatives. Additionally, the unprecedented pathway of the reaction of 4-hydroxycoumarin with azomethine ylides is described. The anti-cancer activity of the obtained compounds was tested in vitro, the most potent compound being 2.6-fold more active against the HuTu 80 cell line than the reference 5-fluorouracil, with a selectivity index > 32.