Quantum Chemical Calculations Research Articles

The first step of cyanine dye self-assembly: Dimerization.

Self-assembling amphiphilic cyanine dyes, such as C8S3, are promising candidates for energy storage and optoelectronic applications due to their efficient energy transport properties. C8S3 is known to self-assemble in water into double-walled J-aggregates. Thus far, the molecular self-assembly steps remain shrouded in mystery. Here, we employ a multiscale approach to unravel the first self-assembly step: dimerization. Our multiscale approach combines molecular dynamics simulations with quantum chemistry calculations to obtain a Frenkel exciton Hamiltonian, which we then use in spectral calculations to determine the absorption and two-dimensional electronic spectra of C8S3 monomer and dimer systems. We model these systems solvated in both water and methanol, validating our model with experiments in methanol solution. Our theoretical results predict a measurable anisotropy decay upon dimerization, which is experimentally confirmed. Our approach provides a tool for the experimental probing of dimerization. Moreover, molecular dynamics simulations reveal that the dimer conformation is characterized by the interaction between the hydrophobic aliphatic tails rather than the π-π stacking previously reported for other cyanine dyes. Our results pave the way for future research into the mechanism of molecular self-assembly in similar light-harvesting complexes, offering valuable insights for understanding and optimizing self-assembly processes for various (nano)technological applications.

Geometrical and Electronic Structure of Fluorinated and Non-fluorinated Platinum(II) Tetraphenylporphyrin Complexes.

The composition of the saturated vapors of two platinum com-plexes with the macrocyclic ligands 5,10,15,20-tetraphenyl-porphyrin (PtTPP) and 5,10,15,20-tetrakis(pentafluoro-phenyl)-por-phyrin (PtTF5PP) and their structures were determined by syn-chronous gas-phase electron diffrac-tion/mass spectrometry (GED/MS). These porphyrin com-plexes are those with the heaviest metal atom in the coordination cavity that have been structurally investigated in the gas phase. The mass spectra confirm the presence of a single molecular form of each, PtTPP (T=629 K) and PtTF5PP (T=597 K). Their structures can serve as references for related com-plexes in the crystalline state or solutions. Differences between the geometries of PtTPP and PtTF5PP in the crystalline and gaseous states include a significant deformation of the tetrapyrrole macro-cycle in solid PtTPP. The experimental Pt-N bond lengths of both complexes are in agreement with quantum chemical calculations (DFT/B97D/ECP(Pt)) taking into account relativistic effects. The effect of lanthanide contraction is evident from the similarity of the Pd-N and Pt-N internuclear distances of analogous compounds. The strong electron density transfer from the porphyrin backbone to the metal ion and the resulting low effective positive charge on the platinum atom, studied by NBO and QTAIM methods, helps to rationalize the high catalytic activity of such platinum compounds.

Rational Design for Antioxidant Diphenylamine Derivatives Using Quantitative Structure-Activity Relationships andQuantum Mechanics Calculations.

Diphenylamine (DPA) derivatives, used as antioxidants in rubber-based products, inhibit autoxidation by donating hydrogen atoms to peroxyl radicals. Octanol-water partition coefficient (LogKow), an antioxidant index, helps predict their distribution in hydrophobic polymer matrices. Therefore, this study aimed to investigate the relationship between the structure of DPA derivatives and their antioxidant activities, using machine learning with quantitative structure-activity relationships (QSAR) and quantum mechanics (QM). The structure of DPA derivatives was optimized using Density Functional Theory and analyzed for molecular properties. The QSAR models were trained using important descriptors identified through permutation importance. Among the models developed, the Gradient Boosting Regressor (GBR) showed the best performance, with R2 of 0.983 and root mean square error (RMSE) of 0.642 for the test set. SHAP analysis revealed that molecular weight and electronic properties significantly influenced LogKow predictions. For instance, a higher molecular weight was associated with increased LogKow, and a higher positive charge of C2 correlated with higher LogKow predictions. Consequently, the two potent compounds (D1 and D2) were designed based on QSAR model guidance. The GBR model predicted LogKow values of 9.789 and 7.102 for D1 and D2, respectively, which are higher than the training compounds in the model. To gain molecular insight, the quantum chemical calculations with M062X/6-311++G(d,p)//M062X/6-31G(d,p) were performed to investigate the bond dissociation enthalpy (BDE). The results showed that D1 (79.50 kcal/mol) and D2 (72.43 kcal/mol) exhibited lower BDEs than the reference compounds, suggesting that the designed compounds have the potential for enhanced antioxidant activity. In addition, the antioxidant reaction mechanism was studied by using M062X/6-311++G(d,p)//M062X/6-31G(d,p) which found that the hydrogen atom transfer is the key step, where D1 and D2 showed activation energy barriers of 10.38 and 6.29 kcal/mol, respectively, compared to reference compounds of R3 (10.39 kcal/mol), R1 (10.40 kcal/mol), and R2 (18.26 kcal/mol). Therefore, our findings demonstrate that integrating QSAR with quantum chemical calculations can effectively guide the design of DPA derivatives with improved antioxidant properties.

Photochromic Color Tuning of Copper‐Doped Zinc Sulfide Nanocrystals by Control of Local Dopant Environments

AbstractInorganic photochromic materials offer several advantages over organic compounds, including relatively inexpensive and higher thermal stability. However, tuning their color with the same component has remained a significant challenge. In this study, we demonstrate that the photochromic color of Cu‐doped ZnS nanocrystals (NCs), which is initially pale yellow before light irradiation, can be tuned from gray to brown by adjusting the surface stoichiometry of Zn and S, which is controlled through the use of thiol and non‐thiol ligands. Several experiments and quantum chemical calculations using model clusters revealed that the color change is determined by the distribution of Cu, which significantly contributes to the coloration, specifically whether it resides on the Zn‐rich or S‐rich surface. In contrast, particle size and Cu concentration were found to have little effect on the photochromic color. This study expands the diversity of photochromic responses in inorganic NCs and marks an important step toward the development of further advanced photochromic nanomaterials.

Fragmentation and Isomerization Pathways of Natural and Synthetic Cannabinoids Studied via Higher Collisional Energy Dissociation Profiles

Cannabinoid molecules are the family of molecules that bind to the cannabinoid receptors (CB1 and CB2) of the human body and cause changes in numerous biological functions including motor coordination, emotion, and pain reception. Cannabinoids occur either naturally in the Cannabis Sativa plant or can be produced synthetically in the laboratory. The need for accurate analytical methods for analyzing cannabinoid molecules is of considerable current importance due to demands for detecting illegal cannabinoids and for monitoring the manufacture of popular, non-illegal cannabinoid products. Mass spectrometry has been shown to be an optimum technique for identifying cannabinoids. In this work, we perform Higher Collisional Dissociation (HCD) mass spectrometric measurements on an Orbitrap Fusion Tribrid Mass Spectrometer to measure the collision-energy-dependent molecular fragmentation pathways of a group of key cannabinoids and their metabolites (cannabidiol, Δ9-Tetrahydrocannabinol, 11-Hydroxy-Δ9-tetrahydrocannabinol, 11-nor-9-Carboxy-Δ9-tetrahydrocannabinol, cannabidiolic acid, tetrahydrocannabinolic acid), along with two synthetic cannabinoids (JWH-018 and MDMB-FUBINACA). This is the first time that cannabinoid molecules have been studied using energy-resolved HCD methods. We identified a number of common, primary fragmentation pathways, including loss of water, loss of other small neutral molecule units (e.g., butene), and rupture of the central C-C bond that links the aromatic and alkyl ring groups. Quantum chemical calculations are presented to provide insights into preferred protonation sites and to characterize isomerization of protonated open-ring cannabinoids (e.g., [CBDA + H]+) into closed-ring analogues (e.g., [THCA + H]+). A key result to emerge from our study is that energy-resolved HCD measurements are particularly valuable in identifying isomerization, since the isobaric pairs of molecular ions studied here (e.g., [CBDA + H]+ and [THCA + H]+) are associated with identical HCD profiles indicating that isomerization of one structure into the other has occurred during the electrospray–mass spectrometry process. This is an important result as it will have general applicability to other tautomeric ions and thus demonstrates the application of energy-resolved HCD as a tool for identifying tautomerization proclivity.

Comprehensive Study on Synthesis, Quantum Chemical Calculations, Molecular Modeling Studies, and Cytotoxic Activities of Metal(II) Schiff Base Complexes

ABSTRACTIn this study, mononuclear Ni(II), Cu(II), Zn(II), and Pd(II) complexes of a diimine molecule (H2L) were synthesized, and their structures were elucidated by NMR, FT‐IR, UV–Vis, ICP‐OES, molar conductivity, magnetic susceptibility, and elemental analysis techniques. Stoichiometric and spectroscopic data revealed that the complexes have a metal:ligand ratio of 1:1 and the Schiff base coordinates with the metal(II) ion via nitrogen atoms of two imine groups and oxygen anions of two phenolate moieties and have a square planar geometry. The cytotoxic activity properties of the ligand and its metal complexes were screened in two distinct cancer cell lines: lung (A549) and colon (DLD‐1). The optimized molecular geometries, molecular electrostatic potential diagrams, total density of states plots, and frontier molecular orbitals of the H2L ligand and all metal(II) complexes at the ground level were calculated using density functional theory. The LANL2DZ basis set containing the effective core potentials for transition metals was used for quantum chemical calculations. The calculations supported the square planar geometry of the metal(II) ions in the complexes. The potential of all molecules to inhibit the MLK4 kinase domain (PDB ID: 4UYA) involved in cancer progression was examined by molecular docking study and the best inhibition activity belonged to the H2L molecule with a binding energy of −10.8 kcal/mol. The stability of the H2L–4UYA complex in physiological media was also confirmed by molecular dynamics simulation for 100 ns.

An Accurate Machine-Learned Potential for Krypton under Extreme Conditions.

We have developed two machine-learned pair potentials for krypton based on CCSD(T) quantum chemical calculations on two and three atom clusters. Through extensive testing with molecular dynamics, we find both potentials give good agreement with the experimental equation of state, melting point, and neutron scattering data for the fluid. Compared with the most widely used Lennard-Jones model, our potentials produced similar results in low-pressure melting and equation of state. However, extending the regime to higher pressures of ≤30 GPa showed a remarkable divergence of the Lennard-Jones model from the experimental (solid) equation of state. Our potential showed extremely good agreement, despite having no solid phases in the training set.

Aromatic Polyketides From a Marine-Derived Streptomyces Species.

Three new naphthalene derivatives, strepthalenes A-C (1-3), and the known analogue (S)-DNPA (4), together with six previously reported anthraquinones (5-10), were isolated from the marine-derived Streptomyces sp. OUCMDZ-4182. Their structures were elucidated by detailed spectroscopic analysis and quantum chemical calculations. Strepthalenes B and C showed moderate activity against amyloid-β 42 (Aβ42) aggregation with IC50 values of 47.65 and 24.73µM, respectively.

Anisotropy Factor Spectra for Weakly Allowed Electronic Transitions in Chiral Ketones.

Quantum chemical calculations of one-photon absorption, electronic circular dichroism and anisotropy factor spectra for the A-band transition of fenchone, camphor and 3-methylcyclopentanone (3MCP) are reported. While the only weakly allowed nature of the transition leads to comparatively large anisotropies, a proper theoretical description of the absorption for such a transition requires to account for non-Condon effects. We present experimental data for the anisotropy of 3MCP in the liquid phase and show that corresponding Herzberg-Teller corrections are critical to reproduce the main experimental features. The results obtained with our comprehensive theoretical model highlight the importance of the vibrational degree of freedom, paving the way for a deeper understanding of the dynamics in electronic circular dichroism.

Sesquiterpenes and Lignans From the Branches and Leaves of Wikstroemia micrantha.

One new sesquiterpene wikstromicrol (1), 1 new lignan (7R, 8S, 8'S)-9-acetoxyl (-)-isolariciresinol (8), and 12 known compounds were isolated from the branches and leaves of Wikstroemia micrantha. The structures of new compounds were elucidated by extensive interpretation of spectroscopic data and quantum chemical calculations of electronic circular dichroism spectra. The bioactivity assay showed that compounds 6 and 7 had weak cytotoxicity against MCF-7, HCT-116, and HL-60 cell lines with IC50 values ranging from 33.84 to 49.15µM, whereas compound 8 exhibited moderate cytotoxicity against HCT-116 cell line with an IC50 value of 16.54µM.

Precision Molecular Engineering of Compact Near-Infrared Fluorophores.

Organic fluorophores with near-infrared (NIR) emission and reduced molecular size are crucial for advancing bioimaging and biosensing technologies. Traditional methods, such as conjugation expansion and heteroatom engineering, often fail to reduce fluorophore size without sacrificing NIR emission properties. Addressing this challenge, our study utilized quantum chemical calculations and structure-property relationship analysis to establish an iterative design approach and enable precision engineering for compact, single-benzene-based NIR fluorophores. These newly developed fluorophores exhibit emissions up to 759 nm and maintain molecular weights as low as 192 g/mol, approximately 50% of that of Cy7. Additionally, they display unique environmental sensitivity─nonemissive in aqueous solutions but highly emissive in lipid environments. This property significantly enhances their utility in wash-free imaging of live cells. Our findings mark a substantial breakthrough in fluorophore engineering, paving the way for more efficient and adaptable imaging methodologies.

Novel nanosensors represented by CdS/ZnS quantum dots doped with manganese (II) Ions for detection of vancomycin

Abstract This paper demonstrates potential for analytical nanosensoring offered by core–shell CdS/ZnS and CdS/ZnS quantum dots (QDs) doped with manganese (II) ions for rapid detection of a glycopeptide antibiotic vancomycin (VNC) in aqueous media by luminescence quenching. ‘core–shell’ quantum dots were synthesized by colloidal method and hydrophilized by mercaptopropionic acid (MPA). To reveal the mechanism for luminescence quenching of these nanosensors, we studied spectral characteristics of QDs and VNC and revealed a complex influence of VNC on the luminescence quenching of CdS/ZnS and Cd0.9Mn0.1S/ZnS nanoparticles. We performed quantum chemical calculations of the equilibrium geometry and IR spectra of the VNC-MPA system and the bond energies in the CdS/ZnS–MPA–VNC system. The luminescence quenching of CdS/ZnS QDs by vancomycin was shown to linearly depend on its concentration in the 35–690 μM range with the determination coefficient R2 = 0.988. The luminescence quenching of Cd0.9Mn0.1S/ZnS QDs was linearly sensitive to vancomycin in the narrower concentration range of 0–207 μM with the determination coefficient R2 = 0.999. The detection thresholds of vancomycin were found to be 56.2 μM and 1.9 μM by CdS/ZnS QDs and CdS/ZnS QDs doped with Mn (II) ions, respectively.

Oxygen K-edge inner-shell calculations of polymers in solutions realized by the extraction of local structures from molecular dynamics simulations.

Inner-shell quantum chemical calculations of large molecular systems, such as polymers and soft matter in solution, were performed to understand the phase transition dynamics of these systems using soft x-ray absorption spectroscopy (XAS). The molecular structures of 40-mer poly(N-isopropylacrylamide) (PNIPAM) chains in solutions were obtained using molecular dynamics simulations. The 5-mer PNIPAM chains with terminated H atoms, including the second coordination shells of the solvent methanol and water molecules, were extracted from the 40-mer PNIPAM chains in solutions. The O K-edge inner-shell spectra of the 5-mer PNIPAM chains were obtained by averaging the inner-shell spectra of 9700 extracted polymer structures. This calculation method can be used to precisely evaluate the energy shifts of the C=O π* peaks of PNIPAM caused by the structural changes of the polymer chains, the substitutions of the hydrogen bonds of the C=O groups in PNIPAM from methanol to water molecules, and the increase in the coordination numbers of solvent molecules with the C=O groups, which were observed in the O K-edge XAS experiments.

QeMFi: A Multifidelity Dataset of Quantum Chemical Properties of Diverse Molecules

Progress in both Machine Learning (ML) and Quantum Chemistry (QC) methods have resulted in high accuracy ML models for QC properties. Datasets such as MD17 and WS22 have been used to benchmark these models at a given level of QC method, or fidelity, which refers to the accuracy of the chosen QC method. Multifidelity ML (MFML) methods, where models are trained on data from more than one fidelity, have shown to be effective over single fidelity methods. Much research is progressing in this direction for diverse applications ranging from energy band gaps to excitation energies. One hurdle for effective research here is the lack of a diverse multifidelity dataset for benchmarking. We provide the Quantum chemistry MultiFidelity (QeMFi) dataset consisting of five fidelities calculated with the TD-DFT formalism. The fidelities differ in their basis set choice: STO-3G, 3-21G, 6-31G, def2-SVP, and def2-TZVP. QeMFi offers to the community a variety of QC properties such as vertical excitation properties and molecular dipole moments. Further QeMFi offers QC computation times allowing for a time benefit benchmark of multifidelity models for ML-QC.

Potential impacts of solvents topological aspects, Vanderwal effect, spectral investigation, and biological features of dodecyl 3,4,5-trihydroxybenzoate: anti-viral agent

This work investigates the pharmacological properties of a recently developed pyrimidine compound using computational techniques, including density functional theory and docking of molecules. Quantum chemistry calculations unveil the substance’s persistence and prominent electrophilic character. Utilizing FT-IR, FT-Raman, ultraviolent-visible spectra in experimental and theoretical, the potential compound Dodecyl 3,4,5-trihydroxybenzoate was investigated. The vibrational assignment for various vibration modes, together with the spatial distribution of potential energy. From FMO energies, an energy band gap of 4.848 eV has been predicted, and charge transfer inside the molecules has been verified. DDG exhibits excellent electrophilic properties, with a higher electrophilicity index (ω = 3.064 eV) for DMSO solvent compared to other solvents. Molecular electrostatic potential and Average Local Ionization Energy indicate that electrophiles and nucleophiles can target negative nitrogen and positive hydrogen atoms. Natural bond orbital research offers valuable insights into the relationships between donors and acceptors throughout the molecular structure. The distribution of electrons and holes throughout the molecule exhibited an exchange of charge, and the biological consequences of the molecule were elucidated with the electron localized function and localized orbital locator. The docking molecular studies reveal that it has an excellent affinity (−8.59 kcal/mol) in interaction with 5I5X protein receptors that are involved in antiviral activities. This is corroborated by the low binding energy and inhibition constant of other protein 1I2V. The chemical exhibits significant anti-activity in comparison to conventional medications, indicating its potential as a promising option for the creation of new antiviral treatments.

Effects of pH on the differential absorbance spectra, d-d transition bands and structural properties of copper complexes with humic substances and model compounds.

Interactions between metal cations, notably Cu(II), and humic substances (HS) affect their mobility, bioavailability, and toxicity. This necessitates a molecular-level determination of the nature of HS functional groups binding Cu(II) (Cu-HS) and effects of pH on them. This study investigates the pH effects on the spectroscopic and structural properties of the complexes of Cu(II) with HS and representative model compounds using differential absorbance spectroscopy (DAS), examination of the properties of the d-d transition band characteristic for Cu(II) ions, and quantum chemical (QC) calculations. DAS of Cu-HS show distinct bands at 240, 275, 310 and 400nm, while absorbance features located from 600 to 800nm correspond to the d-d transitions in Cu(II). Similar features appear in copper complexes with the model compounds of salicylic acid (Cu-Sal) and poly(4-styrenesulfonic acid-co-maleic acid) (Cu-PSM). Increasing pH resulted in consistent changes of the DAS and the d-d band of Cu(II) which exhibited a hypsochromic shift and increased intensity. Deconvolution of the d-d bands into discrete Gaussian bands was indicative of transitions between dominant species at increasing pH. Cu-Sal and Cu-PSM structures that were modeled successfully by QC calculations. These results demonstrate the sensitivity of DAS spectra and d-d band to the modes of Cu(II) binding by HS and open a possibility of further elucidation of the functional groups engaged in the binding of heavy metals by HS.

Aggregation Behavior of Asphaltenes in Heavy Oil and Its Influencing Factors: A Multiscale Study Based on Molecular Dynamics Simulations and Quantum Chemical Calculations

Summary Asphaltenes and resins are important and complex components of heavy oils, and their self-aggregation behavior has a profound effect on the oil and gas industry. In this study, based on three classical molecular models of asphaltenes, the aggregation laws of asphaltenes with different structures and their influencing factors were investigated using molecular dynamics (MD) simulations and quantum chemical calculations. By analyzing the equilibrium conformations, interaction energy, radial distribution functions (RDFs), mean square displacements (MSDs), diffusion coefficients, cluster analyses, radii of gyration, electrostatic potentials, and nonbonding interactions, we found that archipelago-type asphaltenes have the strongest interactions, the highest probability of occurrence, and the best stability. In contrast, continental asphaltenes have the strongest diffusion ability in the heavy oil model. Quantum chemical calculations show that the asphaltene association is mainly driven by van der Waals forces initiated by the aromatic core and electrostatic attraction around the heteroatoms, whereas the aggregation behavior is influenced by a variety of factors, such as intermolecular van der Waals forces, hydrogen bonding, and π-π interactions. In addition, external conditions, such as temperature and pressure, considerably affect the aggregation behavior of asphaltenes. This study provides a theoretical basis for exploring the viscosity mechanism of heavy oils and scientific support for the efficient development of oil and gas fields.

Sonochemical Synthesis of Schiff Base of Substituted Benzoxazolone: A Quantum Chemical, Antibacterial Evaluation and Molecular Docking Study

AbstractThe derivatives of benzoxazolone (BOA) have attracted a lot of interest because of their diverse pharmacological potential as therapeutic agents. In this work, we report an environmentally friendly synthetic method based on ultrasonication(US) as well as conventional method to prepare new BOA derivatives (M1–M4). Furthermore, the BOA derivatives were reacted with p‐nitro, p‐chloro, and p‐hydroxy anilines to get Schiff bases compounds (M5–M16). The results demonstrated that, in comparison to traditional approaches, the ultrasonication method had higher reaction kinetics and energy efficiency. Additionally, quantum chemical calculations and molecular docking studies were performed to understand the reaction mechanisms and evaluate the antibacterial potential of the synthesized compounds. The presence of electron‐withdrawing group at the para position of substituted anilines follows the trend ─NO2 > ─Cl > ─OH, leading to higher formation energies of the corresponding products as reflected in the progression of the reactions in the mechanistic studies. Further, the presence of a methyl group in benzoxazolone (BOA) enhances the binding interaction affinity with Escherichia coli, however on the basis of docking scores of nitro group containing (M5, M8, M11, and M14) compounds exhibited stronger interactions with the protein of E. coli, compared to the chlorine and hydroxyl groups. The docking results were also found consistent with in vitro results.

Transition metal complexes of N-furfuryl-N′-benzoylthiourea: A study of synthesis, antibacterial activities, quantum chemical calculations and molecular modeling simulations

Transition metal complexes of N-furfuryl-N′-benzoylthiourea: A study of synthesis, antibacterial activities, quantum chemical calculations and molecular modeling simulations

Structural investigations of benzoyl fluoride and the benzoacyl cation of low-melting compounds and reactive intermediates.

Acyl fluorides and acyl cations represent typical reactive intermediates in organic reactions, such as Friedel-Crafts acylation. However, the comparatively stable phenyl-substituted compounds have not been fully characterized yet, offering a promising backbone. Attempts to isolate the benzoacylium cation have only been carried out starting from the acyl chloride with weaker chloride-based Lewis acids. Therefore, only adducts of 1,4-stabilized acyl cations could be obtained. Due to the low melting point of benzoyl fluoride, together with its volitality and sensitivity toward hydrolysis, the structures of the acyl fluoride and its acylium cation have not been determined. Herein, we report the first crystal structure of benzoyl fluoride, C7H5FO or PhCOF (monoclinic P21/n, Z = 8) and the benzoacylium undecafluorodiarsenate, C7H5O+·As2F11- or [PhCO]+[As2F11]- (monoclinic P21/n, Z = 4). The compounds were characterized by low-temperature vibrational spectroscopy and single-crystal X-ray analysis, and are discussed together with quantum chemical calculations. In addition, their specific π-interactions were elucidated.