Comprehensive Basis-Set Testing of Extended Symmetry-Adapted Perturbation Theory and Assessment of Mixed-Basis Combinations to Reduce Cost

An efficient method by combining different basis sets and SAPT levels

In symmetry-adapted perturbation theory (SAPT), accurate calculations on non-covalent interaction (NCI) for large complexes with more than 50 atoms are time-consuming using large basis sets. More efficient ones with smaller basis sets usually result in poor prediction in terms of dispersion and overall energies. In this study, we propose two composite methods with baseline calculated at SAPT2/aug-cc-pVDZ and SAPT2/aug-cc-pVTZ with dispersion term corrected at SAPT2+ level using bond functions and smaller basis set with δ MP2 corrections respectively. Benchmark results on representative NCI data sets, such as S22, S66, and so forth, show significant improvements on the accuracy compared to the original SAPT Silver standard and comparable to SAPT Gold standard in some cases with much less computational cost.

Assessing the domain-based local pair natural orbital (DLPNO) approximation for non-covalent interactions in sizable supramolecular complexes

The titular domain-based local pair natural orbital (DLPNO) approximation is the most widely used method for extending correlated wave function models to large molecular systems, yet its fidelity for intermolecular interaction energies in large supramolecular complexes has not been thoroughly vetted. Non-covalent interactions are sensitive to tails of the electron density and involve nonlocal dispersion that is discarded or approximated if the screening of pair natural orbitals (PNOs) is too aggressive. Meanwhile, the accuracy of the DLPNO approximation is known to deteriorate as molecular size increases. Here, we test the DLPNO approximation at the level of second-order Møller-Plesset perturbation theory (MP2) and coupled-cluster theory with singles, doubles, and perturbative triples [CCSD(T)] for a variety of large supramolecular complexes. DLPNO-MP2 interaction energies are within 3% of canonical values for small dimers with ≲10 heavy atoms, but for larger systems, the DLPNO approximation is often quite poor unless the results are extrapolated to the canonical limit where the threshold for discarding PNOs is taken to zero. Counterpoise correction proves to be essential in reducing errors with respect to canonical results. For a sequence of nanoscale graphene dimers up to (C96H24)2, extrapolated DLPNO-MP2 interaction energies agree with canonical values to within 1%, independent of system size, provided that the basis set does not contain diffuse functions; these cause the DLPNO approximation to behave erratically, such that results cannot be extrapolated in a meaningful way. DLPNO-CCSD(T) calculations are typically performed using looser PNO thresholds as compared to DLPNO-MP2, but this significantly impacts accuracy for large supramolecular complexes. Standard DLPNO-CCSD(T) settings afford errors of 2-6 kcal/mol for dimers involving coronene (C24H12) and circumcoronene (C54H18), even at the DLPNO-CCSD(T1) level.

Enhanced selectivity towards melanoma cells with zinc(II)-Schiff bases containing imidazole derivatives

Zinc(II)-complexes with the general formula [Zn(L)2] containing 8-hydroxyquinoline Schiff bases functionalized with 1-(3-aminopropyl)imidazole or 1-(3-aminopropyl)-2-methyl-1H-imidazole on 2-position and their respective ligands (HL1 or HL2) were synthesized and characterized by NMR, UV-Vis, FTIR and CD spectroscopies as well as ESI-MS spectrometry. Single crystals of HL2 and [Zn(L1)2]n were analysed by SC-XRD. [Zn(L1)2]n shows a 1D polymeric chain structure of alternating Zn(II) cations and bridging Schiff base ligands, in contrast to previously reported monomeric structures of analogous complexes. DFT calculations were performed to rationalize the polymeric X-ray structure of Zn(L1)2. Results showed that the ligands can bind as bi- or tridentate to Zn(II) and there is the possibility of a dynamic behavior for the complexes in solution. Both ligands and complexes present limited stability in aqueous media, however, in the presence of bovine serum albumin the complexes are stable. Molecular docking simulations and circular dichroism spectroscopic studies suggest binding to this protein in close proximity to the Trp213 residue. Biological studies on a panel of cancer cells revealed that the Zn(II)-complexes have a lower impact on cell viability than cisplatin, except for triple-negative breast cancer cells in which they were comparable. Notwithstanding, they display much higher selectivity towards cancer cells vs. normal cells, than cisplatin. They induce the generation of ROS and DNA double-strand breaks, primarily through apoptosis as the mode of cell death. Overall, the novel Zn(II)-complexes demonstrate improved induction of apoptosis and higher selectivity, particularly for melanoma cells, compared to previously reported analogues, making them promising candidates for clinical application.

Unraveling environmental effects in the absorption and fluorescence spectra of p-methoxyphenylpiperazine derivatives

The p-methoxyphenylpiperazine motif can be found in many biologically active molecules, including approved drugs. It is characterized by a relatively weak fluorescence, which can be employed in different types of studies involving molecules with this motif. In this work, a thorough analysis of the absorption, excitation and emission spectra of the diphenyl(aminomethyl)phosphine and tris(aminomethyl)phosphine derivatives of p-methoxyphenylpiperazine, supported by the DFT calculations (ωB97XD/6-311++G(d,p)) with NBO and QTAIM analysis also for different model molecules (e.g. 1-(4-methoxyphenyl)-4-methylpiperazine) enabled determination of the mechanisms underlying beneath the electronic transitions and allowed to rationalize mixed solvent effects observed in electronic spectra of the studied compounds. Electronic transition from the ground state to the first excited state can be regarded as the n,π → π* transition with no solvatochromic effects, however the hydrogen bonds between the HBD solvent molecules and the nitrogen atom bound directly to the aromatic ring (N(4)) are shifting strongly the 1st absorption or excitation band maxima to the higher energies. Fluorescence band, as a result of the electron transition from the equilibrated 1st excited state to the ground state, can be described as the π*→π with positive solvatochromism. N(4) in the excited states adopts a sp2 hybridization and is no longer able to form HBs. On the other hand, increased electron density on the aromatic ring makes the emission processes vulnerable to its direct environment.

Visualizing and characterizing excited states from time-dependent density functional theory

Time-dependent density functional theory (TD-DFT) is the most widely-used electronic structure method for excited states, due to a favorable combination of low cost and semi-quantitative accuracy in many contexts, even if there are well recognized limitations. This Perspective describes various ways in which excited states from TD-DFT calculations can be visualized and analyzed, both qualitatively and quantitatively. This includes not just orbitals and densities but also well-defined statistical measures of electron-hole separation and of Frenkel-type exciton delocalization. Emphasis is placed on mathematical connections between methods that have often been discussed separately. Particular attention is paid to charge-transfer diagnostics, which provide indicators of when TD-DFT may not be trustworthy due to its categorical failure to describe long-range electron transfer. Measures of exciton size and charge separation that are directly connected to the underlying transition density are recommended over more ad hoc metrics for quantifying charge-transfer character.

Applying Large Graph Neural Networks to Predict Transition Metal Complex Energies Using the tmQM_wB97MV Data Set

Machine learning (ML) methods have shown promise for discovering novel catalysts but are often restricted to specific chemical domains. Generalizable ML models require large and diverse training data sets, which exist for heterogeneous catalysis but not for homogeneous catalysis. The tmQM data set, which contains properties of 86,665 transition metal complexes calculated at the TPSSh/def2-SVP level of density functional theory (DFT), provided a promising training data set for homogeneous catalyst systems. However, we find that ML models trained on tmQM consistently underpredict the energies of a chemically distinct subset of the data. To address this, we present the tmQM_wB97MV data set, which filters out several structures in tmQM found to be missing hydrogens and recomputes the energies of all other structures at the ωB97M-V/def2-SVPD level of DFT. ML models trained on tmQM_wB97MV show no pattern of consistently incorrect predictions and much lower errors than those trained on tmQM. The ML models tested on tmQM_wB97MV were, from best to worst, GemNet-T > PaiNN ≈ SpinConv > SchNet. Performance consistently improves when using only neutral structures instead of the entire data set. However, while models saturate with only neutral structures, more data continue to improve the models when including charged species, indicating the importance of accurately capturing a range of oxidation states in future data generation and model development. Furthermore, a fine-tuning approach in which weights were initialized from models trained on OC20 led to drastic improvements in model performance, indicating transferability between ML strategies of heterogeneous and homogeneous systems.

Anticandidal Cu(I) complexes with neocuproine and 1-(4-methoxyphenyl)piperazine based diphenylaminomethylphosphine: Is Cu-diimine moiety a pharmacophore?

The studies on metal complexes as potential antifungals are of growing interest because they may be the answer to increasingly effective defense mechanisms. Herein we present two new copper(I) iodide or thiocyanide complexes with 2,9-dimethyl-1,10-phenanthroline (dmp) and diphenylphosphine derivative of 1-(4-methoxyphenyl)piperazine (4MP): [CuI(dmp)4MP] (1-4MP) and [CuNCS(dmp)4MP] (2-4MP) - their synthesis, as well as structural and spectroscopic characteristics. Interestingly, while 4MP and its oxide derivative (4MOP) show a very low or no activity against all tested Candida albicans strains (MIC50 ≥ 200 μM against CAF2-1 - laboratory control strain, DSY1050 - mutant without transporters Cdr1, Cdr2, Mdr1; isogenic for CAF2-1, and fluconazole resistant clinical isolates), for 1-4MP and 2-4MP MIC50 values were 0.4 μM, independently on the complex and strain tested. Determination of the viability of NHDF-Ad (Normal Adult Human Dermal Fibroblasts) cell line treated with 1-4MP and 2-4MP showed that for both complexes there was only a 20% reduction in the concentration range ¼ to 2 × MIC50 and the 70% at 4 × MIC50. Subsequently, the MLCT based luminescence of the complexes in aqueous media allowed to record the confocal micrographs of 1-4MP in the cells. The results show that it is situated most likely in the vacuoles (C. albicans) or lysosomes (NHDF-Ad).

Accurate three-body noncovalent interactions: the insights from energy decomposition

An impressive collection of accurate two-body interaction energies for small complexes has been assembled into benchmark databases and used to improve the performance of multiple density functional, semiempirical, and machine learning methods. Similar benchmark data on nonadditive three-body energies in molecular trimers are comparatively scarce, and the existing ones are practically limited to homotrimers. In this work, we present a benchmark dataset of 20 equilibrium noncovalent interaction energies for a small but diverse selection of 10 heteromolecular trimers. The new 3BHET dataset presents complexes that combine different interactions including π-π, anion-π, cation-π, and various motifs of hydrogen and halogen bonding in each trimer. A detailed symmetry-adapted perturbation theory (SAPT)-based energy decomposition of the two- and three-body interaction energies shows that 3BHET consists of electrostatics- and dispersion-dominated complexes. The nonadditive three-body contribution is dominated by induction, but its influence on the overall bonding type in the complex (as exemplified by its position on the ternary diagram) is quite small. We also tested the extended SAPT (XSAPT) approach which is capable of including some nonadditive interactions in clusters of any size. The resulting three-body dispersion term (obtained from the many-body dispersion formalism) is mostly in good agreement with the supermolecular CCSD(T)-MP2 values and the nonadditive induction term is similar to the three-body SAPT(DFT) data, but the overall three-body XSAPT energies are not very accurate as they are missing the first-order exchange terms.

Fragment-Based Calculations of Enzymatic Thermochemistry Require Dielectric Boundary Conditions

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

Birth of the Hydrated Electron via Charge-Transfer-to-Solvent Excitation of Aqueous Iodide

A primary means to generate hydrated electrons in laboratory experiments is excitation to the charge-transfer-to-solvent (CTTS) state of a solute such as I^-(aq), but this initial step in the genesis of e^-(aq) has never been simulated directly using ab initio molecular dynamics. We report the first such simulations, combining ground- and excited-state simulations of I^-(aq) with a detailed analysis of fluctuations in the Coulomb potential experienced by the nascent solvated electron. What emerges is a two-step picture of the evolution of e^-(aq) starting from the CTTS state: I^-(aq) + hν → I^-*(aq) → I^•(aq) + e^-(aq). Notably, the equilibrated ground state of e^-(aq) evolves from I^-*(aq) without any nonadiabatic transitions, simply as a result of solvent reorganization. The methodology used here should be applicable to other photochemical electron transfer processes in solution, an important class of problems directly relevant to photocatalysis and energy transfer.

Systematic Evaluation of Counterpoise Correction in Density Functional Theory

A widespread belief persists that the Boys-Bernardi function counterpoise (CP) procedure "overcorrects" supramolecular interaction energies for the effects of basis-set superposition error. To the extent that this is true for correlated wave function methods, it is usually an artifact of low-quality basis sets. The question has not been considered systematically in the context of density functional theory, however, where basis-set convergence is generally less problematic. We present a systematic assessment of the CP procedure for a representative set of functionals and basis sets, considering both benchmark data sets of small dimers and larger supramolecular complexes. The latter include layered composite polymers with ∼150 atoms and ligand-protein models with ∼300 atoms. Provided that CP correction is used, we find that intermolecular interaction energies of nearly complete-basis quality can be obtained using only double-ζ basis sets. This is less expensive as compared to triple-ζ basis sets without CP correction. CP-corrected interaction energies are less sensitive to the presence of diffuse basis functions as compared to uncorrected energies, which is important because diffuse functions are expensive and often numerically problematic for large systems. Our results upend the conventional wisdom that CP "overcorrects" for basis-set incompleteness. In small basis sets, CP correction is mandatory in order to demonstrate that the results do not rest on error cancellation.