Exploration and Design of Carbon Dot-Based Long Afterglow Materials Using Active Machine Learning and Quantum Chemical Simulations.

Long afterglow materials based on carbon dots (CDs) have attracted extensive attention in the field of optics due to their low cost and nontoxic properties. However, the targeted synthesis of specific properties of complex and unknown structures such as CDs remains a daunting challenge. In this study, the powerful nonlinear fitting ability of machine learning was used to explore the afterglow properties of CDs. The XGBoost algorithm demonstrates high prediction accuracy in determining the optimal excitation wavelength, optimal emission wavelength, and afterglow lifetime. Using Bayesian optimization, we screened and synthesized the CDs-based long afterglow materials with the longest lifetime reported so far by a one-step microwave method. By combining quantum chemical calculations with experimental data, we revealed the structure-function relationship between CDs and their precursors through electron-hole analysis. These results show that machine learning can establish nonlinear correlations between precursors and materials with unknown structures, clarify their intrinsic relationships, simplify the material design process, and thus accelerate the development of advanced materials.

Contrasting conformational behaviors of molecules XXXI and XXXII in the seventh blind test of crystal structure prediction.

Accurate modeling of conformational energies is key to the crystal structure prediction of conformational polymorphs. Focusing on molecules XXXI and XXXII from the seventh blind test of crystal structure prediction, this study employs various electronic structure methods up to the level of domain-local pair natural orbital coupled cluster singles and doubles with perturbative triples [DLPNO-CCSD(T1)] to benchmark the conformational energies and to assess their impact on the crystal energy landscapes. Molecule XXXI proves to be a relatively straightforward case, with the conformational energies from generalized gradient approximation (GGA) functional B86bPBE-XDM changing only modestly when using more advanced density functionals such as PBE0-D4, ωB97M-V, and revDSD-PBEP86-D4, dispersion-corrected second-order Møller-Plesset perturbation theory (SCS-MP2D), or DLPNO-CCSD(T1). In contrast, the conformational energies of molecule XXXII prove difficult to determine reliably, and variations in the computed conformational energies appreciably impact the crystal energy landscape. Even high-level methods such as revDSD-PBEP86-D4 and SCS-MP2D exhibit significant disagreements with the DLPNO-CCSD(T1) benchmarks for molecule XXXII, highlighting the difficulty of predicting conformational energies for complex, drug-like molecules. The best-converged predicted crystal energy landscape obtained here for molecule XXXII disagrees significantly with what has been inferred about the solid-form landscape experimentally. The identified limitations of the calculations are probably insufficient to account for the discrepancies between theory and experiment on molecule XXXII, and further investigation of the experimental solid-form landscape would be valuable. Finally, assessment of several semi-empirical methods finds r2SCAN-3c to be the most promising, with conformational energy accuracy intermediate between the GGA and hybrid functionals and a low computational cost.

Conformational Changes and Coordination Stability of Flexible Tripeptides During Ni(II)-Mediated Self-Assembly.

The rational design of artificial supramolecular structures with specific properties and functions hinges the comprehensive understanding of the coordination and noncovalent interactions driving self-assembly. Herein, the self-assembly of supramolecular systems through octahedral coordination between Ni(II) ions and a flexible tripeptide was theoretically investigated using quantum chemical calculations. These calculations utilized the B3LYP functional with the polarizable continuum model. Our results indicate that tridentate sites have a greater propensity for coordination, and that the presence of chloride anions and conformational shifts enhance bidentate and monodentate coordination. Insights into the effect of counter anions on the stability of octahedral coordination and the prerequisites for self-assembly were gained by determining the stable conformation and potential reaction pathways of the tripeptide before and after adding chloride anions through an efficient automated conformational search. The formation of intramolecular hydrogen bonding interactions during the conformational changes was also studied using model calculations. Possible processes for initial self-assembly of tripeptide were proposed. This study enhances the fundamental understanding of the conformational behavior of building blocks during supramolecular formation and advance the potential for constructing future bioinspired complexes.

Predicting DNA Reactions with a Quantum Chemistry-Based Deep Learning Model.

In this study, a deep learning model based on quantum chemistry is introduced to enhance the accuracy and efficiency of predicting DNA reaction parameters. By integrating quantum chemical calculations with self-designed descriptor matrices, the model offers a comprehensive description of energy variations and considers a broad range of relevant factors. To overcome the challenge of limited labeled data, an active learning method is employed. The results demonstrate that this model outperforms existing methods in predicting DNA hybridization free energies and strand displacement rate constants, thus advancing the understanding of DNA molecular interactions, and aiding in the precise design and optimization of DNA-based systems.

Measurement of coherent vibrational dynamics with X-ray Transient Absorption Spectroscopy simultaneously at the Carbon K- and Chlorine L2,3- edges.

X-ray Transient Absorption Spectroscopy (XTAS) is a powerful probe for ultrafast molecular dynamics. The evolution of XTAS signal is controlled by the shapes of potential energy surfaces of the associated core-excited states, which are difficult to directly measure. Here, we study the vibrational dynamics of Raman activated CCl4 with XTAS targeting the C 1s and Cl 2p electrons. The totally symmetric stretching mode leads to concerted elongation or contraction in bond lengths, which in turn induce an experimentally measurable red or blue shift in the X-ray absorption energies associated with inner-shell electron excitations to the valence antibonding levels. The ratios between slopes of different core-excited potential energy surfaces (CEPESs) thereby extracted agree very well with Restricted Open-Shell Kohn-Sham calculations. The other, asymmetric, modes do not measurably contribute to the XTAS signal. The results highlight the ability of XTAS to reveal coherent nuclear dynamics involving  < 0.01 Å atomic displacements and also provide direct measurement of forces on CEPESs.

Distinguishing Organomagnesium Species in the Grignard Addition to Ketones with X-ray Spectroscopy.

The addition of Grignard reagents to ketones is a well-established textbook reaction. However, a comprehensive understanding of its mechanism has only recently begun to emerge. X-ray spectroscopy, because of its high selectivity and sensitivity, is the ideal tool for distinguishing between an ensemble of competing pathways. With this aim in mind, we investigated the concerted mechanism of the addition of methylmagnesium chloride (CH$_3$MgCl) to acetone in tetrahydrofuran by simulating the X-ray spectra of different molecules in solution. We used electronic structure methods to calculate the X-ray absorption spectra at the Mg K- and L$_1$-edges and the X-ray photoelectron spectra at the Mg K-edge for different organomagnesium species, which coexist in solution due to the Schlenk equilibrium. The simulated spectra show that individual species can be distinguished throughout the different stages of the reaction.Each species has a distinct spectral feature which can be used as a fingerprint in solution. The absorption and photoelectron spectra consistently show a blue shift as the reaction progressed from reagents to products.

Structural and Electronic Properties of Novel Azothiophene Dyes: A Multilevel Study Incorporating Explicit Solvation Effects.

Among azobenzene derivatives, azothiophenes represent a relatively recent family of compounds that exhibit similar characteristics as dyes and photoreactive systems. Their technological applications are extensive thanks to the additional design flexibility conferred by the heteroaromatic ring. In this study, we present a comprehensive investigation of the structural and electronic properties of novel dyes derived from 3-thiophenamine, utilizing a multilevel approach. We thoroughly examined the potential energy surfaces of the E and Z isomers for three molecules, each bearing different substituents on the phenyl ring at the para position relative to the diazo group. This exploration was conducted through quantum chemistry calculations at various levels of theory, employing a continuum solvent model. Subsequently, we incorporated an explicit solvent (a dimethyl sulfoxide-water mixture) to simulate the most stable isomers using classical molecular dynamics, delivering a clear picture of the local solvation structure and intermolecular interactions. Finally, a hybrid quantum mechanics/molecular mechanics (QM/MM) approach was employed to accurately describe the evolution of the solutes' properties within their environment, accounting for finite temperature effects.

Modeling the effect of substituents on the electronically excited states of indole derivatives.

A proper understanding of excited state properties of indole derivatives can lead to rational design of efficient fluorescent probes. The optically active L a $$ {L}_a $$ and L b $$ {L}_b $$ excited states of a series of substituted indoles, where a substituent was placed on position four, were calculated using equation of motion coupled cluster and time dependent density functional theory. The results indicate that most substituted indoles have a brighter second excited state corresponding to experimental absorption maxima, but a few with electron withdrawing substituents absorb more on the first excited state. Absorption on the first excited state may increase their fluorescence quantum yield, making them better probes. Electronic structure methods were found to predict the energies of the systems with electron withdrawing substituents more accurately than those with electron donating substituents. The excited states of both states correlated well with electrophilicity, similar to the experimental trends for the absorption maxima. Overall, these computational studies indicate that theory can be used to predict excited state properties of substituted indoles, when the substituent is an electron withdrawing group.

Theoretical insights into a turn-on fluorescence probe based on naphthalimide for peroxynitrite detection.

Compared with other reactive oxygen species, peroxynitrite (ONOO-) has diversified reactions and transformations in organisms, and its specific action mechanism is not very clear. The study of reactive oxygen species is of great significance in the field of physiology and pathology. Recently an effective on/off fluorescent probe HCA-OH was designed by Liu et al. through tethering p-aminophenol to 1,8-naphthalimide directly. The probe HCA-OH could release the fluorophore HCA-NH2 with good photostability and high fluorescence quantum yield under oxidation of ONOO- via dearylation process. In this work, the sensing mechanism and spectrum character of probe HCA-OH were studied in detail under quantum chemistry calculation. The electronic structures, reaction sites and fluorescent properties of the probe were theoretically analyzed to benefit us for in-depth understanding the principle of detection on reactive oxygen species (ONOO-) with the fluorescent probe HCA-OH. These theoretical results could inspire the medical research community to design and synthesize highly efficient fluorescent probe for reactive oxygen species detection.

How Flexible Is the Hydrogen Sulfide Molecule Structure? Influence of Hydrogen Sulfide Molecule Geometry on Its Hydrogen Bonds.

The geometry of hydrogen sulfide was studied by calculating potential energy surface (PES) with over  1800 configurations. The calculations were performed at very accurate  CCSD(T)/aug-cc-pvz5 level. The most stable geometry on PES has bond angle (H-S-H) of 92.40° and bond length (S-H) of 1.338 Å. PES shows that hydrogen sulfide is a quite flexible molecule. Namely, it can change the bonding angle (H-S-H) in the range of . 15.6° (from 84.6° to 100.2°) and the bond lengths (S-H) in the range of 0.082 Å (from 1.299 Å to 1.381 Å) with an energy increase of only 1.0 kcal/mol. An influence of hydrogen sulfide geometry on its hydrogen bonds was studied on several hydrogen sulfide/hydrogen sulfide and water/hydrogen sulfide dimers. It showed that the change of hydrogen sulfide geometry does not influence the strength of hydrogen bond. Fully optimized geometries in gas and water solution phases revealed structural differences of both monomers and dimers in gas phase and water phase. SAPT analysis of the optimized dimer geometries showed that in all the dimers electrostatic is the most dominant contribution, while, in the dimers with hydrogen sulfide, the influence of dispersion contribution becomes quite pronounced.

The superiority of isomeric, fluorination and curtailed π-conjunction on A-D-A type acceptors for organic photovoltaics.

The performance of organic solar cell (OSC) devices has been significantly enhanced by the dramatic evolution of A-D-A type non-fullerene acceptors (NFAs). Nevertheless, the structure-property-performance relationship of NFAs in the OSC device is unclear. Here, the intrinsic design factors of isomeric, fluorination and π-conjunction curtailing on the photophysical properties of benzodi (thienopyran) (BDTP) (named NBDTP-M, NBDTTP-M, NBDTP-Fin, and NBDTP-Fout)-based NFAs are discussed. The results show that fluorination on the terminal group of NBDTP-Fout could effectively decrease the highest occupied orbital (HOMO) energy level and the lowest unoccupied orbital (LUMO) energy level. And the long π-conjugated donor unit for NBDTTP-M could increase the HOMO energy level and bring a small HOMO-LUMO energy bandgap. Meanwhile, the substitution of external oxygen atoms and the fluorine atoms in the terminal group could introduce positive changes to the electrostatic potential of the NBDTP-Fout, favouring the charge separation at the donor/acceptor interface. Moreover, the structural design of external oxygen atom substitution, fluorination on the terminal group and curtailed π-conjugated donor unit could decrease the electron vibration-coupling of exciton diffusion, exciton dissociation and electronic transfer processes. The suppression of the exciton decay and charge recombination in those high-performance NFAs indicate that the investigated molecular designs could be effective for further improvement of OSCs.

Photolysis of dinotefuran and nitenpyram in water and ice phase: Influence mechanism of temperature over photolysis.

Neonicotinoids are widely used pesticides around the world, but the photolysis of neonicotinoids in cold agricultural region are still in blank. This paper aimed to study the influence of cold temperature over photolysis of neonicotinoids. To this end, the photolysis rates and photoproducts of dinotefuran and nitenpyram in water, ice and freeze-thawing condition were determined. Coupled with quantum chemistry calculation, the influence mechanisms of temperature and medium were investigated. The results showed the photolysis rates of neonicotinoids in water condition slightly declined with the lowered temperature due to the photolysis reactions were endothermic reactions. However, the photolysis rates increased by 89.8 %, 59.2 %, 49.4 % and 9.5 % for dinotefuran and nitenpyram in ice and thawing condition, respectively. This phenomenon was posed by the concentration-enhancing effect and change of photo-chemical properties of neonicotinoids in ice condition, which included lowered bond cleavage energy, lowered first excited singlet state energy and expanded light absorption range. The photolysis pathways of the two neonicotinoids did not change in different medium, but the concentration of carboxyl products was relatively higher than that of water condition due to the more amounts of reactive oxygen species in ice medium, which might increase the secondary pollution risk after ice-off in spring due to the higher ecotoxicity to nontarget organism of these photoproducts. The influence of cold temperature and medium change should be considered for the environmental fate and risk assessment of neonicotinoids in cold agricultural region.

Antioxidant activity of Zuccagnia-type propolis: A combined approach based on LC-HRMS analysis of bioanalytical-guided fractions and computational investigation.

This study reports a combined approach to assess the antioxidant activity of Zuccagnia-type propolis. Fractions exhibiting the highest antioxidant activities evidenced by DPPH, a ß-carotene bleaching and superoxide radical scavenging activity-non-enzymatic assays, were processed by LC-HRMS/MS to characterize the relevant chemical compounds. A computational protocol based on the DFT calculations was used to rationalize the main outcomes. Among the 28 identified flavonoids, caffeic acids derivatives were in the fraction exhibiting the highest antioxidant activity, with 1-methyl-3-(4'-hydroxyphenyl)-propyl caffeic acid ester and 1-methyl-3-(3',4'-dihydroxyphenyl)-propyl caffeic acid ester as major components. Results clearly showed roles of specific chemical motifs, which can be supported by the computational analysis. This is the first report ascribing the antioxidant ability of Zuccagnia-type propolis to its content in specific caffeic acid derivatives, a potential source of radical scavenging phytochemicals. The proposed protocol can be extended to the study of other plant-products to address the most interesting bioactive compounds.

Environment-dependent chlorophyll-chlorophyll charge transfer states in Lhca4 pigment-protein complex.

Photosystem I (PSI) light-harvesting antenna complexes LHCI contain spectral forms that absorb and emit photons of lower energy than that of its primary electron donor, P700. The most red-shifted fluorescence is associated with the Lhca4 complex. It has been suggested that this red emission is related to the inter-chlorophyll charge transfer (CT) states. In this work we present a systematic quantum-chemical study of the CT states in Lhca4, accounting for the influence of the protein environment by estimating the electrostatic interactions. We show that significant energy shifts result from these interactions and propose that the emission of the Lhca4 complex is related not only to the previously proposed a603+-a608- state, but also to the a602+-a603- state. We also investigate how different protonation patterns of protein amino acids affect the energetics of the CT states.

Understanding the Electric Double Layer at the Electrode-Electrolyte Interface: Part I - No Ion Specific Adsorption.

We present a comprehensive mean-field model that takes into account the key components of modern electrical double layer theory at the interface between an electrode and an electrolyte solution. The model considers short-range specific interactions between different species, including electrode-ion repulsion, the hydration of ions, dielectric saturation of solvent (water), and excluded volume (steric) interactions between species. By solving a modified Poisson-Boltzmann equation and using the appropriate results of quantum chemistry calculations on the hydration of ions, we can accurately approximate the differential capacitance profiles of aqueous electrolyte solutions at the boundary with a silver electrode. The specific interactions between the ions and the electrodes in the systems under consideration are assumed to be significantly weaker than their Coulomb interactions. A novel aspect of our research is the investigation of the impact of short-range ion-water interactions on the differential capacitance, which provides new insights into the behavior of the electrical double layer. This model holds the potential to be useful for electrochemical engineers working on the development of supercapacitors and related electrochemical energy storage devices. It serves as a basis for future modeling of electrolyte systems on real electrodes, especially in scenarios where chemical ion-electrode interactions are significant.

Theoretical and experimental studies of cephalexin adsorption on aluminium as a new alternative of removal from wastewater.

Cephalexin (CPX) is an antibiotic widely used to treat many infections. CPX has become an emerging pollutant present in wastewater. On the other hand, it is well known that organic compounds can be adsorbed over metal surfaces when the metal is in active state such as when it is rusting. This work proposes an alternative for the elimination of CPX from wastewater, applying electrochemical principles using a conventional and cheap substrate, aluminium. The first part consisted of obtaining the active states of aluminium electrodes carrying out voltametric curves at different pH (4, 7 and 9) to find the particular condition of interaction between CPX and metal surface. The potential was used in the potentiostatic tests to set the activation potential of metal at different times. After the treatment, electrolyte solutions were analysed using UV-vis spectra, and the aluminium surfaces were studied by optical micrographs and X-ray diffraction. In addition, aluminium-CPX interactions were corroborated by quantum-chemical calculations and adsorption isotherms. All results indicate that it was possible for the CPX removal at basic pH conditions, where the molecule adsorption on the aluminium substrate occurs due to a strong electrostatic interaction.

Molecular Docking of Chiral Drug Enantiomers With Different Bioactivities.

Chirality has an important role in the drug design because enantiomers may exhibit different bioactivity when interacting with macromolecules of a living organism. In our previous work, based on the analysis of a set of 100 chiral drugs, a relationship was established between the sign of chirality of enantiomers and their bioactivity. To understand the reasons for the observed patterns of chiral specificity of drug enantiomers, the interaction of 10 enantiomeric pairs of chiral drugs with the corresponding target proteins has been considered using molecular docking and further postprocessing by quantum chemistry methods. The data obtained confirm that the energetic aspect of the interaction between opposite enantiomers and target protein affects the enantiomer biological activity. In addition, the results show that molecular docking is able to distinguish between bioactive and inactive/less active enantiomers, although many docking programs are not accurate enough to distinguish a weak inhibitor from a strong one.

Theoretical analysis of naproxen reaction with sulfate and hydroxyl radicals in the aqueous phase: Investigating reactive sites and reaction kinetics.

In this study, we have utilized theoretical calculations to predict the reaction active sites of naproxen when reacting with radicals and to further study the thermodynamics and kinetics of the reactions with ·OH and SO4-·. The evidence, derived from the average local ionization energy and electrostatic potential, points to the naphthalene ring as the preferred site of attack, especially for the C2, C6, C9, and C10 sites. The changes in Gibbs free energy and enthalpy of the reactions initiated by ·OH and SO4-· ranged between -19.6 kcal/mol - 26.3 kcal/mol and -22.3 kcal/mol -18.5 kcal/mol, respectively. More in-depth investigation revealed that RA2 pathway for ·OH exhibited the lowest free energy of activation, suggesting this reaction is more inclined to proceed. The second-order rate constant results indicate the ·OH attacking reaction is faster than reactions initiated by SO4·-, yet controlled by diffusion. The consistency between theoretical findings and experimental data underscores the validity of this computational method for our study.

Circular dichroism of relativistically-moving chiral molecules.

Understanding the impact of the relativistic motion of a chiral molecule on its optical response is a prime challenge for fundamental science, but it also has a direct practical relevance in our search for extraterrestrial life. To contribute to these significant developments, we describe a multi-scale computational framework that combines quantum chemistry calculations and full-wave optical simulations to predict the chiral optical response from molecules moving at relativistic speeds. Specifically, the effect of a relativistic motion on the transmission circular dichroism (TCD) of three life-essential biomolecules, namely, B-DNA, chlorophyll a, and chlorophyll b, is investigated. Inspired by previous experiments to detect interstellar chiral molecules, we assume that the molecules move between a stationary observer and a light source, and we study the rotationally averaged TCD as a function of the speed of the molecule.We find that the TCD spectrum that contains the signatures of the molecules shifts with increasing speed to shorter wavelengths, with the effects already being visible for moderate velocities.

Reductive Elimination from Tetra-Alkyl Cuprates [Me n Cu(CF3)4- n ]- (n = 1 - 4): Beyond Simple Oxidation States.

In recent years, the electronic structures of organocuprates in general and the complex [Cu(CF3)4]- in particular have attracted significant interest. A possible key indicator in this context is the reactivity of these species. Nonetheless, this aspect has received only limited attention. Here, we systematically study the series of tetra-alkyl cuprates [MenCu(CF3)4-n]- and their unimolecular reactivity in the gas phase, which includes concerted formal reductive eliminations as well as radical losses. Through computational studies, we characterize the electronic structures of the complexes and show how these are connected to their reactivity. We find that all [MenCu(CF3)4-n]- ions feature inverted ligand fields and that the distinct reactivity patterns of the individual complexes arise from the interplay of different effects.