A combination of virtual screening, molecular dynamics simulation, MM/PBSA, ADMET, and DFT calculations to identify a potential DPP4 inhibitor.

DPP4 inhibitors can control glucose homeostasis by increasing the level of GLP-1 incretins hormone due to dipeptidase mimicking. Despite the potent effects of DPP4 inhibitors, these compounds cause unwanted toxicity attributable to their effect on other enzymes. As a result, it seems essential to find novel and DPP4 selective compounds. In this study, we introduce a potent and selective DPP4 inhibitor via structure-based virtual screening, molecular docking, molecular dynamics simulation, MM/PBSA calculations, DFT analysis, and ADMET profile. The screened compounds based on similarity with FDA-approved DPP4 inhibitors were docked towards the DPP4 enzyme. The compound with the highest docking score, ZINC000003015356, was selected. For further considerations, molecular docking studies were performed on selected ligands and FDA-approved drugs for DPP8 and DPP9 enzymes. Molecular dynamics simulation was run during 200 ns and the analysis of RMSD, RMSF, Rg, PCA, and hydrogen bonding were performed. The MD outputs showed stability of the ligand-protein complex compared to available drugs in the market. The total free binding energy obtained for the proposed DPP4 inhibitor was more negative than its co-crystal ligand (N7F). ZINC000003015356 confirmed the role of the five Lipinski rule and also, have low toxicity parameter according to properties. Finally, DFT calculations indicated that this compound is sufficiently soft.

Mesoporous cobalt-manganese layered double hydroxides promote the activation of calcium sulfite for degradation and detoxification of metronidazole.

Metronidazole (MNZ), a commonly used antibiotic, poses risks to water bodies and human health due to its potential carcinogenic, mutagenic, and genotoxic effects. In this study, mesoporous cobalt-manganese layered double hydroxides (CoxMny-LDH) with abundant oxygen vacancies (Ov) were successfully synthesized using the co-precipitation method and used to activate calcium sulfite (CaSO3) with slight soluble in water for MNZ degradation. The characterization results revealed that Co2Mn-LDH had higher specific areas and exhibited good crystallinity. Co2Mn-LDH/CaSO3 exhibited the best catalytic performance under optimal conditions, achieving a remarkable MNZ degradation efficiency of up to 98.1 % in only 8 min. Quenching experiments and electron paramagnetic resonance (EPR) tests showed that SO4•- and 1O2 played pivotal roles in the MNZ degradation process by activated CaSO3, while the redox cycles of Co2+/Co3+ and Mn3+/Mn4+ on the catalyst surface accelerated electron transfer, promoting radical generation. Three MNZ degradation routes were put forward based on the density functional theory (DFT) and liquid chromatography-mass spectrometer (LC-MS) analysis. Meanwhile, the toxicity analysis result demonstrated that the toxicity of intermediates post-catalytic reaction was decreased. Furthermore, the Co2Mn-LDH/CaSO3 system displayed excellent stability, reusability, and anti-interference capability, and achieved a comparably high removal efficiency across various organic pollutant water bodies. This study provides valuable insights into the development and optimization of effective heterogeneous catalysts for treating antibiotic-contaminated wastewater.

The influence of model building schemes and molecular dynamics sampling on QM-cluster models: the chorismate mutase case study.

Most QM-cluster models of enzymes are constructed based on X-ray crystal structures, which limits comparison to in vivo structure and mechanism. The active site of chorismate mutase from Bacillus subtilis and the enzymatic transformation of chorismate to prephenate is used as a case study to guide construction of QM-cluster models built first from the X-ray crystal structure, then from molecular dynamics (MD) simulation snapshots. The Residue Interaction Network ResidUe Selector (RINRUS) software toolkit, developed by our group to simplify and automate the construction of QM-cluster models, is expanded to handle MD to QM-cluster model workflows. Several options, some employing novel topological clustering from residue interaction network (RIN) information, are evaluated for generating conformational clustering from MD simulation. RINRUS then generates a statistical thermodynamic framework for QM-cluster modeling of the chorismate mutase mechanism via refining 250 MD frames with density functional theory (DFT). The 250 QM-cluster models sampled provide a mean ΔG‡ of 10.3 ± 2.6 kcal mol-1 compared to the experimental value of 15.4 kcal mol-1 at 25 °C. While the difference between theory and experiment is consequential, the level of theory used is modest and therefore "chemical" accuracy is unexpected. More important are the comparisons made between QM-cluster models designed from the X-ray crystal structure versus those from MD frames. The large variations in kinetic and thermodynamic properties arise from geometric changes in the ensemble of QM-cluster models, rather from the composition of the QM-cluster models or from the active site-solvent interface. The findings open the way for further quantitative and reproducible calibration in the field of computational enzymology using the model construction framework afforded with the RINRUS software toolkit.

Deconvolution and Analysis of the 1H NMR Spectra of Crude Reaction Mixtures.

Nuclear magnetic resonance (NMR) spectroscopy is an important analytical technique in synthetic organic chemistry, but its integration into high-throughput experimentation workflows has been limited by the necessity of manually analyzing the NMR spectra of new chemical entities. Current efforts to automate the analysis of NMR spectra rely on comparisons to databases of reported spectra for known compounds and, therefore, are incompatible with the exploration of new chemical space. By reframing the NMR spectrum of a reaction mixture as a joint probability distribution, we have used Hamiltonian Monte Carlo Markov Chain and density functional theory to fit the predicted NMR spectra to those of crude reaction mixtures. This approach enables the deconvolution and analysis of the spectra of mixtures of compounds without relying on reported spectra. The utility of our approach to analyze crude reaction mixtures is demonstrated with the experimental spectra of reactions that generate a mixture of isomers, such as Wittig olefination and C-H functionalization reactions. The correct identification of compounds in a reaction mixture and their relative concentrations is achieved with a mean absolute error as low as 1%.

Cinnamic Acid: A Low-Toxicity Natural Bidentate Ligand for Uranium Decorporation.

Uranium accumulation in the kidneys and bones following internal contamination results in severe damage, emphasizing the pressing need for the discovery of actinide decorporation agents with efficient removal of uranium and low toxicity. In this work, cinnamic acid (3-phenyl-2-propenoic acid, CD), a natural aromatic carboxylic acid, is investigated as a potential uranium decorporation ligand. CD demonstrates markedly lower cytotoxicity than that of diethylenetriaminepentaacetic acid (DTPA), an actinide decorporation agent approved by the FDA, and effectively removes approximately 44.5% of uranyl from NRK-52E cells. More importantly, the results of the prompt administration of the CD solution remove 48.2 and 27.3% of uranyl from the kidneys and femurs of mice, respectively. Assessments of serum renal function reveal the potential of CD to ameliorate uranyl-induced renal injury. Furthermore, the single crystal of CD and uranyl compound (C9H7O2)2·UO2 (denoted as UO2-CD) reveals the formation of uranyl dimers as secondary building units. Thermodynamic analysis of the solution shows that CD coordinates with uranyl to form a 2:1 molar ratio complex at a physiological pH of 7.4. Density functional theory (DFT) calculations further show that CD exhibits a significant 7-fold heightened affinity for uranyl binding in comparison to DTPA.

Unveiling the synergy: a combined experimental and theoretical study of ß-cyclodextrin with melatonin.

Melatonin (MT) is a vital hormone controlling biorhythms, and optimizing its release in the human body is crucial. To address MT's unfavorable pharmacokinetics, we explored the inclusion complexes of MT with ß-cyclodextrin (ß-CD). Nano spray drying was applied to efficiently synthesize these complexes in three molar ratios (MT : ß-CD = 1 : 1, 2 : 1, and 1 : 2), reducing reagent use and expediting inclusion. The complex powders were characterized through thermal analyses (TGA and DSC), Fourier transform infrared spectroscopy (FTIR), and in vitro MT release measurements via high-performance liquid chromatography (HPLC). In parallel, computational studies were conducted, examining the stability of MT : ß-CD complexes by means of unbiased semi-empirical conformational searches refined by DFT, which produced a distribution of MT : ß-CD binding enthalpies. Computational findings highlighted that these complexes are stabilized by specific hydrogen bonds and non-specific dispersive forces, with stronger binding in the 1 : 1 complex, which was corroborated by in vitro release data. Furthermore, the alignment between simulated and experimental FTIR spectra demonstrated the quality of both the structural model and computational methodology, which was crucial to enhance our comprehension of optimizing MT's release for therapeutic applications.

Sorting drug conformers in enzyme active sites: the XTB way.

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

Periodic DFT calculations for the heterogeneous formation of 2-chlorothiophenoxy radical from 2-chlorothiophenol on Cu(111) surface in fly ash.

Copper plays a crucial role in the heterogenous dissociation of chlorothiophenols (CTPs) to form chlorothiophenoxy radicals (CTPRs), which is the initial and critical step in the formation of polychlorinated thianthrenes/dibenzothiophenes (PCTA/DTs). Here, first-principles calculations were performed to investigate the activity of Cu(111) surface towards the formation of adsorbed 2-CTPR from 2-CTP. The interaction between 2-CTP and Cu(111) surface was explored to find stable adsorption configurations. Besides, the decomposition routes of 2-CTP on the Cu(111) surface were further explored. Moreover, the effects of water on the formation of absorbed 2-CTPR on the Cu(111) surface were examined. Our results demonstrate that the flat adsorption of 2-CTP on the surface with adsorption energy in the range of -33.21 kcal/mol to -28.37 kcal/mol is more stable than the vertical adsorption with adsorption energy ranging from -23.53 kcal/mol to -13.38 kcal/mol. The Cu(111) surface catalyzes the conversion of 2-CTP into the adsorbed 2-CTPR with a modest energy barrier of 9.46 kcal/mol. Furthermore, water molecules exhibit stronger catalytic activity in this process with a decreased energy barrier of 5.87 kcal/mol through "water bridge" and hydrogen bonding. Specifically, the water accepts the hydrogen atom from 2-CTP and donates another hydrogen to the surface via "water bridge". This research provides a molecular-level understanding of the heterogeneous formation of PCTA/DTs by fly ash, suggesting novel approaches for control strategy and legislation of dioxin analogues.

Copper-mediated cyclization of thiosemicarbazones leading to 1,3,4-thiadiazoles: Structural elucidation, DFT calculations, in vitro biological evaluation and in silico evaluation studies.

Cancer's global impact necessitates innovative and less toxic treatments. Thiosemicarbazones (TSCs), adaptable metal chelators, offer such potential. In this study, we have synthesized N (4)-substituted heterocyclic TSCs from syringaldehyde (TSL1, TSL2), and also report the unexpected copper-mediated cyclization of the TSCs to form thiadiazoles (TSL3, TSL4), expanding research avenues. This work includes extensive characterization and studies such as DNA/protein binding, molecular docking, and theoretical analyses to demonstrate the potential of the as-prepared TSCs and thiadiazoles against different cancer cells. The DFT results depict that the thiadiazoles exhibit greater structural stability and reduced reactivity compared to the corresponding TSCs. The docking results suggest superior EGFR inhibition for TSL3 with a binding constant value of - 6.99 Kcal/mol. According to molecular dynamics studies, the TSL3-EGFR complex exhibits a lower average RMSD (1.39 nm) as compared to the TSL1-EGFR complex (3.29 nm) suggesting that both the thiadiazole and thiosemicarbazone examined here can be good inhibitors of EGFR protein, also that TSL3 can inhibit EGFR better than TSL1. ADME analysis indicates drug-likeness and oral availability of the thiadiazole-based drugs. The DNA binding experiment through absorption and emission spectroscopy discovered that TSL3 is more active towards DNA which is quantitatively calculated with a Kb value of 4.74 × 106 M-1, Kq value of 4.04 × 104 M-1and Kapp value of 5 × 106 M-1. Furthermore, the BSA binding studies carried out with fluorescence spectroscopy showed that TSL3 shows better binding capacity (1.64 × 105 M-1) with BSA protein. All the compounds show significant cytotoxicity against A459-lung, MCF-7-breast, and HepG2-liver cancer cell lines; TSL3 exhibits the best cytotoxicity, albeit less effective than cisplatin. Thiadiazoles demonstrate greater cytotoxicity than the TSCs. Overall, the promise of TSCs and thiadiazoles in cancer research is highlighted by this study. Furthermore, it unveils unexpected copper-mediated cyclization of the TSCs to thiadiazoles.

Novel manganese and nitrogen co-doped biochar based on sodium bicarbonate activation for efficient removal of bisphenol A: Mechanism insight and role analysis of manganese and nitrogen by combination of characterizations, experiments and density functional theory calculations.

A novel porous manganese and nitrogen co-doped biochar (Mn-N@SBC) was synthesized via one-step pyrolysis, utilizing loofah agricultural waste as the precursor and NaHCO3 as the activator. The behavior of bisphenol A adsorbed on Mn-N@SBC was evaluated using static batch adsorption experiments. Compared to direct manganese-nitrogen co-doping, co-doping based on NaHCO3 activation significantly increased the specific surface area (231 to 1027 m2·g-1) and adsorption capacity (15 to 351 mg·g-1). Wide pH (2-10) and good resistance to cation/anion, humic acid and actual water demonstrated the robust adaptability of Mn-N@SBC to environmental factors. The significantly reduced specific surface area after adsorption, adverse effects of ethanol and phenanthrene on the removal of bisphenol A, and theoretically predicted interaction sites indicated the primary adsorption mechanisms involved pore filling, hydrophobicity, and π-π-electron-donor-acceptor interaction. This work presented an approach to create high-efficiency adsorbents from agricultural waste, offering theoretical and practical guidance for the removal of pollutants.

Solid state NMR study of the bioenhancer piperine, supported by GIPAW DFT calculations.

Piperine, an alkaloid found in black pepper fruits, has the properties of promoting the absorption of other substances (e.g. curcumin), therefore it is used in solid forms of dietary supplements as an additive increasing bioavailability. The aim of the study was to analyze piperine in a solid state and then to use it in the analysis of solid dietary supplements with the addition of piperine as an absorption promoter. The 13C CP MAS NMR spectra were recorded using variable contact time and dipolar dephasing experiment. The calculation of theoretical chemical shift values for three polymorphic forms of piperine allowed us to create a database of NMR parameters enabling the identification of polymorphic forms based on the analysis of the 13C CP MAS NMR spectrum. Additionally, the analysis of cross-polarization kinetics parameters was performed. Then, the 13C CP MAS NMR technique was used to confirm the authenticity and determine the presence of curcumin in dietary supplements containing curcumin with the addition of piperine. The presence of piperine could be confirmed even when the mass content of piperine was 70 times lower than that of curcumin. This method can be used to test the quality of dietary supplements containing the addition of piperine as an absorption promoter.

Combined Experimental and Density Functional Theory Study on the Mechanism of the Selective Catalytic Reduction of NO with NH3 over Metal-Free Carbon-Based Catalysts.

Metal-free carbon-based catalysts are attracting much attention in the low-temperature selective catalytic reduction of NOx with NH3 (NH3-SCR). However, the mechanism of the NH3-SCR reaction on carbon-based catalysts is still controversial, which severely limits the development of carbon-based SCR catalysts. Herein, we successfully reconstructed carbon-based catalysts through oxidation treatment with nitric acid, thereby enhancing their low-temperature activity in NH3-SCR. Combining experimental results and density functional theory (DFT) calculations, we proposed a previously unreported NH3-SCR reaction mechanism over carbon-based catalysts. We demonstrated that C-OH and C-O-C groups not only effectively activate NH3 but also remarkedly promote the decomposition of intermediate NH2NO. This study enhances the understanding of the NH3-SCR mechanism on carbon-based catalysts and paves the way to develop low-temperature metal-free SCR catalysts.

Prediction of Base-Catalyzed Hydrolysis Kinetics of Polychlorinated Dibenzo-p-Dioxins by Density Functional Theory Calculations.

Polychlorinated dibenzo-p-dioxins (PCDDs), comprising 75 congeners, have gained considerable attention from the general public and the scientific community owing to their high toxic potential. The base-catalyzed hydrolysis of PCDDs is crucial for the assessment of their environmental persistence. Nonetheless, owing to the substantial number of congeners and low hydrolysis rates of PCDDs, conducting hydrolysis experiments proves to be exceedingly time-consuming and financially burdensome. Herein, density functional theory and transition state theory were employed to predict the base-catalyzed hydrolysis of PCDDs in aquatic environments. Findings reveal that PCDDs undergo base-catalyzed hydrolysis in aquatic environments with two competing pathways: prevailing dioxin ring-opening and reduced reactivity in the hydrolytic dechlorination pathway. The resultant minor products include hydroxylated PCDDs, which exhibit thermodynamic stability surpassing that of the principal product, chlorinated hydroxydiphenyl ethers. The half-lives (ranging from 17.10 to 1.33 × 1010 h at pH = 8) associated with the base-catalyzed hydrolysis of PCDDs dissolved in water were shorter compared to those within the water-sediment environmental system. This observation implies that hydroxide ions can protect aquatic environments from PCDD contamination. Notably, this study represents the first attempt to predict the base-catalyzed hydrolysis of PCDDs by using quantum chemical methods.

Exploring Molecular Energy Landscapes by Coupling the DFTB Potential with a Tree-Based Stochastic Algorithm: Investigation of the Conformational Diversity of Phthalates.

Exploring the global energy landscape of relatively large molecules at the quantum level is a challenging problem. In this work, we report the coupling of a nonredundant conformational space exploration method, namely, the robotics-inspired iterative global exploration and local optimization (IGLOO) algorithm, with the quantum-chemical density functional tight binding (DFTB) potential. The application of this fast and efficient computational approach to three close-sized molecules of the phthalate family (DBP, BBP, and DEHP) showed that they present different conformational landscapes. These differences have been rationalized by making use of descriptors based on distances and dihedral angles. Coulomb interactions, steric hindrance, and dispersive interactions have been found to drive the geometric properties. A strong correlation has been evidenced between the two dihedral angles describing the side-chain orientation of the phthalate molecules. Our approach identifies low-energy minima without prior knowledge of the potential energy surface, paving the way for future investigations into transition paths and states.

Integrating density functional theory and chemical ionization mass spectrometry techniques to assess benzophenone derivatives in food packaging: implications for enhancing food quality and safety.

Benzophenone and related derivatives are widely used as photoinitiators for food packaging to cure inks or lacquers with ultraviolet (UV) light on cardboard and paper. However, there are concerns about the potential health risks of their migration into food. Knowing the physical and chemical properties of benzophenone and its derivatives could play a significant role in their quantification and analysis using chemical ionization mass spectrometry (CI-MS) methods. These parameters are evaluated using B3LYP/6-311++** density functional theory (DFT) implemented on Gaussian code. Ion-molecule chemistry through the selection of reagent ions, reaction energetics and kinetics, thermodynamic stability, and reactivity of molecules deemed to foster VOC identification and quantification via CI-MS techniques. The VOCs under study are expected to undergo exothermic reactions from H3 O+ , NH4 + , NO+ , and O2 + ions, except endothermic proton transfer from NH4 + to 2-hydroxy-4-methoxybenzophenone and 2,3,4-trihydroxy benzophenone. These compounds possess less proton affinities than NH3 and are least stable in their protonated forms. The DFT computed properties provide the basis for developing reliable and accurate methods to detect and measure the presence of benzophenone and its derivatives in packaging materials and food products.

Dual Emissive Zn(II) Naphthalocyanines: Synthesis, Structural and Photophysical Characterization with Theory-Supported Insights towards Soluble Coordination Compounds with Visible and Near-Infrared Emission.

Metal phthalocyaninates and their higher homologues are recognized as deep-red luminophores emitting from their lowest excited singlet state. Herein, we report on the design, synthesis, and in-depth characterization of a new class of dual-emissive (visible and NIR) metal naphthalocyaninates. A 4-N,N-dimethylaminophen-4-yl-substituted naphthalocyaninato zinc(II) complex (Zn-NMe2Nc) and the derived water-soluble coordination compound (Zn-NMe3Nc) exhibit a near-infrared fluorescence from the lowest ligand-centered state, along with a unique push-pull-supported luminescence in the visible region of the electromagnetic spectrum. An unprecedentedly broad structural (2D-NMR spectroscopy and mass spectrometry) as well as photophysical characterization (steady-state state and time-resolved photoluminescence spectroscopy) is presented. The unique dual emission was assigned to two independent sets of singlet states related to the intrinsic Q-band of the macrocycle and to the push-pull substituents in the molecular periphery, respectively, as predicted by TD-DFT calculations. In general, the elusive chemical aspects of these macrocyclic compounds are addressed, involving both reaction conditions, thorough purification, and in-depth characterization. Besides the fundamental aspects that are investigated herein, the photoacoustic properties were exemplarily examined using phantom gels to assess their tomographic imaging capabilities. Finally, the robust luminescence in the visible range arising from the push-pull character of the peripheral moieties demonstrated a notable independence from aggregation and was exemplarily implemented for optical imaging (FLIM) through time-resolved multiphoton micro(spectro)scopy.

Predicting Spin-Dependent Phonon Band Structures of HKUST-1 Using Density Functional Theory and Machine-Learned Interatomic Potentials.

The present study focuses on the spin-dependent vibrational properties of HKUST-1, a metal-organic framework with potential applications in gas storage and separation. Employing density functional theory (DFT), we explore the consequences of spin couplings in the copper paddle wheels (as the secondary building units of HKUST-1) on the material's vibrational properties. By systematically screening the impact of the spin state on the phonon bands and densities of states in the various frequency regions, we identify asymmetric -COO- stretching vibrations as being most affected by different types of magnetic couplings. Notably, we also show that the DFT-derived insights can be quantitatively reproduced employing suitably parametrized, state-of-the-art machine-learned classical potentials with root-mean-square deviations from the DFT results between 3 cm-1 and 7 cm-1. This demonstrates the potential of machine-learned classical force fields for predicting the spin-dependent properties of complex materials, even when explicitly considering spins only for the generation of the reference data used in the force-field parametrization process.

Photostimulus-Responsive Peptide Dot-Centered Covalent Organic Polymers: Effective Pesticide Sensing via Enhancing Accessibility.

Pesticide detection and monitoring are necessary for human health as the overapplication has serious consequences for environmental pollution. Herein, a proper modulation strategy was implemented to construct the photostimulus-responsive peptide-dot-centered covalent organic polymer (P-PCOP) nanoarchitecture for selective sensing of pesticides. The as-constructed P-PCOP was prepared at room temperature by using amino-containing peptide dots as a building block instead of common organic molecules, and the merits of P-PCOP enable it to reduce the steric hindrance of recognition, enhance the interfacial contact of the target, and facilitate the accessibility of sites, which promises to improve the sensitivity. The P-PCOF exhibited a low detection limit of 0.38 µg L-1 to cartap over the range of 1-80 µg L-1 (R2 = 0.9845), and the recoveries percentage in real samples was estimated to be 93.39-105.82%. More importantly, the DFT calculation confirmed the selective recognition ability of P-PCOP on chemical pesticides. In conjunction with a smartphone-integrated portable reading device, on-site chemical sensing is achieved. The proper modulation strategy of fixing a functional guest on the COP system contributes to the advanced structure-chemical properties that are conducive to their applications in chemical sensing.

Decoding Van der Waals Impact on Chirality Transfer in Perovskite Structures: Density Functional Theory Insights.

Chiral organic-inorganic perovskites exhibit unique physicochemical properties driven by the symmetry of monovalent organic cations. However, an atomistic understanding of how chiral cations transfer their chirality to the inorganic framework and the role played by van der Waals (vdW) interactions in this process is still incomplete. In this work, we report a theoretical investigation, based on density functional theory calculations within the Perdew-Burke-Ernzerhof (PBE) formulation for the exchange-correlation functional, into the role of the vdW interactions in the chirality transfer process. For that, we selected several vdW corrections, namely, Grimme (D2, D3, D3(BJ)), Tkatchenko-Scheffler (TS, TS+SCS, TS+HSI), density-dependent energy correction (dDsC), and many-body scattering (MBD) energy method correction. For the chiral perovskite systems, we selected a set of chiral organic-inorganic perovskites with several dimensions, namely, from zero-dimensional to three-dimensional, each having enantiomers with R and S configurations. Based on a statistical treatment of the relative errors of all lattice parameters with respect to experimental data, we found that D3, D3(BJ), TS, TS+SCS, TS+HSI, and MBD vdW are the most accurate corrections to describe the equilibrium structural properties of chiral perovskites using the PBE method. We identify chirality-induced sequential asymmetries of distorted octahedrons and propose angular descriptors to quantify them, where the orientations of these distortions depend on the R or S nature of the chiral cations. Furthermore, we demonstrate the importance of accurate vdW interactions in precisely describing these asymmetric distortions. By means of binding energies and charge-transfer analysis, we show that the impact of vdW corrections on the charge distribution leads to a subtle strengthening of hydrogen bonds between chiral cations and inorganic octahedra, resulting in an increase in the binding energy. Finally, we identified that the Rashba-Dresselhaus effect in two-dimensionality is refined by vdW interactions.

Reconciling TD-DFT and CASPT2 electronic structure methods for describing the photophysics of DNA.

Time-dependent density functional theory (TD-DFT) and multiconfigurational second-order perturbation theory (CASPT2) are two of the most widely used methods to investigate photoinduced dynamics in DNA-based systems. These methods sometimes give diverse dynamics in physiological environments usually modeled by quantum mechanics/molecular mechanics (QM/MM) protocol. In this work, we demonstrate for the uridine test case that the underlying topology of the potential energy surfaces of electronic states involved in photoinduced relaxation is similar in both electronic structure methods. This is verified by analyzing surface-hopping dynamics performed at the QM/MM level on aqueous solvated uridine at TD-DFT and CASPT2 levels. By constraining the dynamics to remain on π π * state we observe similar fluctuations in energy and relaxation lifetimes in surface-hopping dynamics in both TD-DFT and experimentally validated CASPT2 methods. This finding calls for a systematic comparison of the ES potential energy surfaces of DNA and RNA nucleosides at the single- and multi-reference levels of theory. The anomalous long excited state lifetime at the TD-DFT level is explained by n π * trapping due to the tendency of TD-DFT in QM/MM schemes with electrostatic embedding to underestimate the energy of the π π * state leading to a wrong π π * / n π * energetic order. A study of the FC energetics suggests that improving the description of the surrounding environment through polarizable embedding or by the expansion of QM layer with hydrogen-bonded waters helps restore the correct state order at TD-DFT level. Thus by combining TDDFT with an accurate modeling of the environment, TD-DFT is positioned as the standout protocol to model photoinduced dynamics in DNA-based aggregates and multimers.