Single-point Calculations Research Articles

Discovery of iron-oxo-catalyzed oxidation of fluorophenyl systems to carbonyls or epoxides: reactive intermediates determined mechanism.

Carbonyl and epoxide compounds play crucial roles in organic synthesis, and the utilization of metal catalysis offers distinct advantages. However, the catalysis of their synthesis by high-valent iron-oxo remains a challenge. In this study, we investigated iron-oxo-catalyzed phenyl systems in detail. Our results show that the carbon atoms on the aromatic ring are positively charged by replacing a hydrogen atom with a fluorine atom, which leads to different catalytic mechanisms. Specifically, the cationic intermediate formed via a double-electron transfer in the low-spin (LS) state of a non-fluorinated benzene ring transforms into a radical intermediate via single-electron transfer when fluorine substitution occurs. Further computational investigations revealed that different intermediates in LS drive the formation of different products. The carbocation intermediate strongly favors the generation of carbonyl compounds through the migration of the ipso - hydrogen (known as the "NIH shift"). In contrast, the radical intermediate exhibits kinetic advantages in this pathway, leading to the formation of epoxides. This research provides theoretical support and facilitates the exploration of innovative pathways for carbonyl and epoxide synthesis. Computing was performed via Gaussian 09 software. Geometric optimization, transition state search, and intrinsic reaction coordinate (IRC) analysis were conducted via the hybrid functional B3LYP and the 6-311G(d,p) basis set. Single-point energy calculations were performed via a higher-level basis set, def2-TZVP. Multiwfn 8.0 and VMD 1.9.1 software are utilized for spin density and molecular frontier orbital analysis, as well as for graphically representing key intermediates.

Theoretical Investigation of Bond Dissociation Energies of exo-Polyhedral B–H and B–F Bonds of closo-Borate Anions [BnHn−1X]2− (n = 6, 10, 12; X = H, F)

This paper reports on a theoretical investigation of the bond dissociation energies of B–H and B–F interactions of closo-borate anions [BnHn−1X]2− (n = 6, 10 and 12; X = H and F), in which homolytic and heterolytic bond breaking cases were considered, and the main trends in bond dissociation energy values were analysed. The wB97X-D3/TZVPP level of theory was applied for geometry optimisation of the molecular species under consideration. DLPNO-CCSDT/CBS single-point calculations were made to ensure an accurate estimation of the target systems’ electronic energy. The correlations between the value of the bond dissociation energy and variables such as electron density descriptors of B–H and B–F interactions and frontier orbital energies (HOMO, SOMO and LUMO) were established.

Theoretical study of Ni(0)-catalyzed intermolecular hydroamination of branched 1,3-dienes: reaction mechanism, regioselectivity, enantioselectivity, and prediction of the ligand.

Nickel-catalyzed hydroamination of dienes with phenylmethanamines was studied theoretically to investigate reaction mechanism. These calculated results revealed that Ni-catalyzed hydroamination began with the O - H bond activation of trifluoroethanol, including three important elementary steps: the ligand-to-ligand hydrogen migration, the nucleophilic attack of phenylmethanamine, and hydrogen migration. The nucleophilic attack of phenylmethanamine was the rate-determining step, and the branched product of 3,4-addition with (S)-chirality was the most dominant. The N - H bond activation of phenylmethanamine occurred more difficultly than the O - H bond of trifluoroethanol, because of high ΔG and ΔG≠. In addition, the origin of regioselectivity and enantioselectivity, and prediction of the ligand were also discussed in this text. All computations were performed with Gaussian09 program. All geometries were optimized at the ωB97XD/6-31G(d,p) level (SDD for Ni), and to obtain more accurate potential energy, single-point calculation was carried out at the ωB97XD/cc-pVDZ level (SDD for Ni). The Cramer-Truhlar continuum solvation model (SMD) was used to evaluate solvation effect of mesitylene, and a correction of the translational entropy was made with the procedure of Whitesides group.

High-Level Calculation for Assessing the Atmospheric Reactivity of Pentachlorophenol with Hydroxyl Radical: Mechanism and Kinetics.

This work aims to investigate the reactivity of the pentachlorophenol (PCP) compound, C6Cl5OH, with a hydroxyl (OH) radical in the gas phase. Geometry optimizations and vibrational frequency calculations were performed using DFT-M06-2X/6-311++G(d,p). Single-point energy calculations were carried out using the single-reference coupled cluster method, specifically CCSD(T), and the multiconfigurational CASPT2 level of theory to characterize the atmospheric degradation processes of PCP with OH radicals and to identify which chemical species resulting from their decomposition could remain in the gas phase. The performance of various families of basis sets was tested. The widely used augmented-correlation-consistent basis set family aug-cc-pVXZ-DK (X = D, T, and Q) was compared to the atomic natural orbital basis sets ANO-RCC-VXZP (X = D, T, and Q). The energy profile at 298 K showed that the Cl- and OH-abstractions are not energetically favorable. H-abstraction and OH-addition/Ck (k = 1-6) are characterized by the lowest Gibbs energies of activation and are strongly exothermic. The canonical transition state theory (TST) with a simple Wigner tunneling correction is used to predict the rate constants over the 220-400 K temperature range for each reaction channel. The overall rate constant at 298 K based on our calculations is about 3.25 × 10-13, 3.10 × 10-15, and 2.21 × 10-15 cm3 molecule-1 s-1 at M06-2X, CASPT2/ANO-RCC-VQZP, and CASPT2/aug-cc-pVQZ-DK levels of theory, respectively. The PCP atmospheric lifetime at 298 K is predicted to be in the range from 1 to 12-16 years at 0 km in the presence of variable OH concentration (9.00 × 105 to 1.50 × 107 molecules cm-3) based on CASPT2 data.

Creating Benchmarks for Lithium Clusters and Using Them for Testing and Validation.

Metal clusters often have a variety of possible structures, and they are calculated by a wide range of methods; however, fully converged benchmarks on the energy differences of structures and spin states that could be used to test or validate these methods are rare or nonexistent. Small lithium clusters are good candidates for such benchmarks to test different methods against well-converged relative energetics for qualitatively different structures because they have a small number of electrons. The present study provides fully converged benchmarks for Li4 and Li5 clusters and uses them to test a diverse group of approximation methods. To create a dataset of well-converged single-point energies for Li4 and Li5, stationary structures were optimized by Kohn-Sham density functional theory (KS-DFT) and then single-point energy calculations at these structures were carried out by two quite different beyond-CCSD(T) methods. To test other methods single-point energy calculations at these structures were carried out by KS-DFT, Mo̷ller-Plesset (MP) theory, coupled cluster (CC) theory, five composite methods (Gaussian-4, the Wuhan-Minnesota (WM) composite method, and the W2X, W3X, and W3X-L composite methods of Radom and co-workers), multiconfiguration pair-density functional theory (MC-PDFT), complete active space second-order perturbation theory (CASPT2), and n-electron valence state second-order perturbation theory (NEVPT2). Our results show that rhomboid and trigonal bipyramid (TBP) geometries are the most stable structures for Li4 and Li5, respectively. Using the W3X-L method to obtain our best estimates, the mean unsigned deviations were calculated for other methods for several structures and spin states of both Li4 and Li5. Binding energies and M diagnostics were calculated for all structures. The data in this paper are valuable for assessing the reliability of current electronic structure theories and also developing new density functionals and machine learned models.

Data-Efficient Active Learning for Thermodynamic Integration: Acidity Constants of BiVO4 in Water.

The protonation state of molecules and surfaces is pivotal in various disciplines, including (electro-)catalysis, geochemistry, biochemistry, and pharmaceutics. Accurately and efficiently determining acidity constants is critical yet challenging, particularly when explicitly considering the electronic structure, thermal fluctuations, anharmonic vibrations, and solvation effects. In this research, we employ thermodynamic integration accelerated by committee Neural Network potentials, training a single machine learning model that accurately describes the relevant protonated, deprotonated, and intermediate states. We investigate two deprotonation reactions at the BiVO4 (010)-water interface, a promising candidate for efficient photocatalytic water splitting. Our results illustrate the convergence of the required ensemble averages over simulation time and of the final acidity constant as a function of the Kirkwood coupling parameter. We demonstrate that simulation times on the order of nanoseconds are required for statistical convergence. This time scale is currently unachievable with explicit ab-initio molecular dynamics simulations at the hybrid DFT level of theory. In contrast, our machine learning workflow only requires a few hundred DFT single point calculations for training and testing. Exploiting the extended time scales accessible, we furthermore asses the effect of commonly applied bias potentials. Thus, our study significantly advances calculating free energy differences with ab-initio accuracy.

Catching the π-Stacks: Prediction of Aggregate Structures of Porphyrin.

π-π interactions decisively shape the supramolecular structure and functionality of π-conjugated molecular semiconductor materials. Despite the customizable molecular building blocks, predicting their supramolecular structure remains a challenge. Traditionally, force field methods have been used due to the complexity of these structures, but advances in computational power have enabled ab initio approaches such as density functional theory (DFT). DFT is particularly suitable for finding energetically favorable structures of dye aggregates, which are determined by a large number of different interactions, but a systematic aggregate search can still be very challenging due to the large number of possible geometries. In this work, we show ways to overcome this challenge. We investigate how finely translational and rotational lattices must be structured to identify all energetic minima of π-stack structures, focusing on porphyrins as a prototype challenge. Our approach involves single-point DFT calculations of systematically varied dimer geometries, identification of local energy minima, hierarchical grouping of geometrically similar structures, and optimization of the energetically favorable representatives of each geometric family. This ab initio method provides a general framework for the systematic prediction of aggregate structures and reveals geometrically diverse and energetically favorable dimers.

The molecular structure, electronic properties, and decomposition mechanism of FOX-7 under external electric field were calculated based on density functional theory.

Based on the density functional theory (DFT), we analyzed the changes of the FOX-7 molecule under external electric field (EEF) from multiple perspectives, including molecular structure, electronic structure, decomposition mechanism, frontier molecular orbitals (FMOs), and density of states (DOS). The results revealed that as the intensity of the positive EEF increased, the detonation performance of the FOX-7 molecule was significantly enhanced, while its thermal stability was also improved. This discovery challenges the traditional concept that explosives are inherently dangerous under external electric fields and provides new insights for research in related fields. To further explore the impact of EEF on the thermal stability of FOX-7, we conducted a thorough analysis of the mechanism by which EEF affects the decomposition process. Our findings indicate that applying a positive EEF significantly increases the energy required to overcome intramolecular hydrogen transfer and C-NO2 bond rupture, while having a relatively minor effect on the nitro isomerization process. This observation further demonstrates that the appropriate application of a positive EEF can enhance the detonation performance of FOX-7 without compromising its thermal stability. Further research revealed that as the intensity of the positive EEF increased, the electronegativity of the nitro group gradually enhanced, leading to an increase in the electronegativity of the oxygen atoms within it. This made the oxygen atoms more prone to participating in chemical reactions. This phenomenon also explains why the energy barrier required for nitro isomerization in FOX-7 gradually decreases as the intensity of the positive EEF increases. Based on the density functional theory (DFT), the structural optimizations were performed both under applied EEF and without EEF at the B3LYP/6-311G (d, p) level. All optimized results were converged and exhibited no imaginary frequencies. Based on the optimized structures, single-point energy calculations were further conducted at the B3LYP/def2-TZVPP level. Subsequently, analyses of molecular structure, electronic structure, decomposition mechanism, frontier molecular orbitals, and density of states were carried out.

Structure Determination of Zinc and Cadmium Dication Complexes with Intact and Deprotonated Histidyl Glycine and Glycyl Histidine Dipeptides.

Metalated intact and deprotonated histidyl glycine and glycyl histidine dipeptides were investigated in the gas phase by using infrared multiple photon dissociation (IRMPD) spectroscopy with light from a free-electron laser (FEL). The dipeptides M2+(GlyHis), M2+(HisGly), [M(GlyHis-H)]+, and [M(HisGly-H)]+, where M = Zn and Cd, were probed to elucidate how the His position along the peptide chain and ligand charge state might influence the structures observed in the gas phase. Simulated annealing calculations were performed to determine energetically low-lying conformers and isomers of these structures. Quantum chemical calculations were used to optimize the structures at the B3LYP level of theory using the 6-311+G(d,p) and def2-TZVP basis sets for zinc and cadmium complexes, respectively. IRMPD and calculated linear absorption spectra were compared to evaluate which structures are present. Relative energies of the various species were evaluated using single-point energy calculations for low-lying structures at the B3LYP, B3LYP-GD3BJ, ωB97XD, and MP2(full) levels using the 6-311+G(2d,2p) and def2-TZVPP basis sets. For all species, structures for both metals mirror each other, and those that reproduce the experimental spectrum were determined to be iminol structures for the intact ligands or iminol-like structures for the deprotonated ligands. Additionally, when the spectra of the deprotonated dipeptides are compared to the intact dipeptides, the change in the spectra is correlated to the group that is deprotonated.

QCManyBody: A flexible implementation of the many-body expansion.

While the many-body expansion (MBE) and counterpoise treatments are commonly used to mitigate the high scaling of accurate abinitio methods, researchers may need to piece together tools and scripts if their primary chosen software does not support targeted features. To further modular software in quantum chemistry, the arbitrary-order, multiple-model-chemistry, counterpoise-enabled MBE implementation from Psi4 has been extracted into an independent, lightweight, and open-source Python module, QCManyBody, with new schema underpinning, application programming interface, and software integrations. The package caters to direct users by facilitating single-point and geometry optimization MBE calculations backed by popular quantum chemistry codes through the QCEngine runner and by defining a schema for requesting and reporting many-body computations. It also serves developers and integrators by providing minimal, composable, and extensible interfaces. The design and flexibility of QCManyBody are demonstrated via integrations with geomeTRIC, OptKing, Psi4, QCEngine, and the QCArchive project.

Molecular interaction studies of Gamma-aminobutyric acid (GABA) in an aqueous medium at various temperatures: A comprehensive analysis using volumetric, thermoacoustic and DFT methods

The interaction of Gamma-aminobutyric acid (GABA) in an aqueous medium at various concentrations (0.101–1.086) mol·kg−1 as a function of temperature is being studied using volumetric, viscosity and acoustic analysis. The calculation of apparent molar volume (VΦ), partial molar volume (V∅o), apparent molar isentropic compression (Kϕ) and partial molar isentropic compression (Kϕ0) of GABA in an aqueous medium has been done by measuring the densities and speed of the sound in the temperature range of 298.15–323.15 K. The thermo-acoustic parameters like adiabatic compressibility (βs), acoustic impedance (Z), intermolecular free length (Lf), relative association (RA), relaxation time (τ), internal pressure (πi), enthalpy (ΔH), Gibbs free energy (ΔG), and change in entropy (ΔS) are also computed. The strength of the hydrogen bond interaction of GABA in an aqueous medium and its dipole moment are calculated using single-point energy calculations. These calculations employ IEFPCM and PCM solvation models using DFT/B3LYP and MP2 methods with the 6-311G++ (d, p) basis set. The outcomes are interpreted in terms of hydrogen bond interactions that exist in the mixture.

Zeolites as Solid Solvents: Explaining the Chloromethane Hydrolysis over Metal-Exchanged Zeolite Y by DFT Calculations.

We report a theoretical DFT study of the reaction pathways for chloromethane hydrolysis over metal-exchanged zeolites (Li+, Na+, K+, and Mg2+). A cluster of 78 T atoms (T referring to Si or Al atoms), comprising the zeolite Y super cavity coupled with the sodalite cage and three hexagonal prism units (Si(78-x)Al x O129H54; x = 1 or 2), was used in the calculations. The study was carried out using the ONIOM method. The high layer was computed at M062X/6-31++G(d,p), whereas the low layer was computed at the PM6 level of theory. The energy profile was obtained by single-point calculations at the M062X/6-31++G(d,p) for the entire structure. The first step studied was the adsorption of chloromethane on the zeolite, which involves an ion-dipole interaction between the metal cation and the chlorine atom. Then, two mechanistic pathways were investigated: one via formation of an adsorbed methoxide and the other involving a direct, one-step, nucleophilic attack of the water molecule to the adsorbed chloromethane. In all systems studied, the direct mechanism showed a lower energy of activation than the route involving the methoxide intermediate. The same behavior was also observed for chloromethane methanolysis to afford dimethyl ether on the metal-exchanged zeolites. The theoretical results are in agreement with the experiments of chloromethane hydrolysis over metal-exchanged zeolite Y, explaining the formation of dimethyl ether upon chloromethane methanolysis on zeolites of low or no acidity. The transition state for the direct route resembles a SN2 process assisted by the surface, reinforcing the concept of zeolites as solid solvents, providing a polar nanoenvironment that favors and assists the formation of ionic transition states and intermediates.

Molecular interaction studies of L-proline in water and ethanol at different temperatures using dielectric relaxation, refractive index and DFT methods

The complex dielectric permittivity of L-Proline in water and ethanol solutions with molar concentrations ranging from 0.025 M to 0.15 M was measured by open-ended coaxial probe technique. The measurements were carried out across a frequency span of 0.02 < ν/GHz < 20 and temperatures varying from 298.15 K to 323.15 K. The densities (ρ) and refractive index (nD ) of the L-proline in aqueous and ethanol solutions were also determined to provide insights into the solute-solvent interactions in the system. The Havriliak-Negami equation was employed to compute the dielectric relaxation time of the mixtures. The relaxation time of L-Proline in an ethanol medium was found to be higher than that of L-Proline in an aqueous medium due to the greater degree of self-association of ethanol molecules. Additionally, the relaxation time of the mixtures lengthened with rising molar concentration, which is attributed to the presence of hydrogen bonds among L-Proline and aqueous/ethanol molecules. The strength of the hydrogen bond interaction of L-Proline in both mediums was calculated using single-point energy calculations employing IEFPCM/PCM solvation models through DFT/B3LYP and MP2 approaches with a 6-311 G ++ (d, p) basis set. The results were correlated with the hydrogen bond strength, Gibbs’ free energy of activation parameter, and dipole-dipole interactions. Communicated by Ramaswamy H. Sarma

Quantum Chemistry Dataset with Ground- and Excited-state Properties of 450 Kilo Molecules

Due to rapid advancements in deep learning techniques, the demand for large-volume high-quality datasets grows significantly in chemical research. We developed a quantum-chemistry database that includes 443,106 small organic molecules with sizes up to 10 heavy atoms including C, N, O, and F. Ground-state geometry optimizations and frequency calculations of all compounds were performed at the B3LYP/6-31G* level with the BJD3 dispersion correction, while the excited-state single-point calculations were conducted at the ωB97X-D/6-31G* level. Totally twenty-seven molecular properties, such as geometric, thermodynamic, electronic and energetic properties, were gathered from these calculations. Meanwhile, we also established a comprehensive protocol for the construction of a high-volume quantum-chemistry dataset. Our QCDGE (Quantum Chemistry Dataset with Ground- and Excited-State Properties) dataset contains a substantial volume of data, exhibits high chemical diversity, and most importantly includes excited-state information. This dataset, along with its construction protocol, is expected to have a significant impact on the broad applications of machine learning studies across different fields of chemistry, especially in the area of excited-state research.

Efficient Shift-and-Invert Preconditioning for Multi-GPU Accelerated Density Functional Calculations.

To accelerate the iterative diagonalization of electronic structure calculations, we propose a new inexact shift-and-invert (ISI) preconditioning method. The key idea is to improve shift values in the ISI preconditioning to be closer to the exact eigenvalues, leading to a significant boost in the convergence speed of the iterative diagonalization. Furthermore, we adopted a preconditioned conjugate gradient solver to rapidly evaluate an inversion process. Finally, we accelerated overall processes, including the proposed modification, with state-of-the-art graphical processing units (GPUs) and assessed its parallel efficiency with real-space density functional calculations of 1D, 2D, and 3D periodic systems. Our method attains both fast diagonalization convergence and high multi-GPU parallel efficiency. This is evident from the fact that single-point density functional calculations for hundreds of atom systems can be done in approximately 10 s using 8 GPUs. The proposed method can be generally applied to any electronic structure calculation methods involving large-scale diagonalizations.

Density functional theory guide for copolymerization mechanism between allyl radical with radicalophile: photo-driven radical mediated [3 + 2] cyclization.

The challenge of activating inert allyl monomers for polymerization has persisted, prompting our proposal of the photo-driven radical mediated [3 + 2] cyclization reaction (PRMC). This innovative approach significantly expedites the homopolymerization of multi-allyl monomers, enabling the synthesis of embolic microspheres for hepatocellular carcinoma interventions. PRMC involves allyl monomers to form allylic radicals and then radicals participating in a cycloaddition reaction with unsaturated olefins as radicalophiles to form cyclopentane-based radical products. While extensively studied in the theoretical and experimental homopolymerization, PRMC's application in copolymerization remains unexplored. To address this knowledge gap, we explored the elementary reaction, selecting allyl methyl ether radicals (AMER) and α,β-unsaturated ketones as radicalophiles for copolymerization investigations by density functional theory (DFT) analysis. We quantified energy differences between ground and excited states of reactants, elucidated frontier molecular orbitals, and assessed thermodynamic data for copolymerization feasibility. We also evaluated the electronic properties of reactants, predicting the reactivity of radicalophiles and the interactions of intermolecular reactions. Additionally, we applied transition state theory and interaction/deformation models and conducted a local orbital analysis to comprehensively study excess electron distribution and gyration radius of cyclic radical product. Our findings offer vital insights into PRMC's potential in copolymerization. This research provides a robust theoretical foundation for practical application, enhancing the polymerization field. Based on density functional theory (DFT), the calculations were performed at the M06-2X/6-311 + + G(d,p) level in/by Gaussian 16 package. Subsequently, our analytical results apply time-dependent density-functional theory (TD-DFT) and solvent modeling (SMD). Single-point energy calculations determine the driving force behind the radicals' reaction with radicalophiles. Furthermore, we assessed the electrostatic potential (ESP) of the reactants. The results of the calculations were visualized by the Multiwfn 3.6 and VMD 1.9 programs.

Theoretical kinetics study of key reactions between ammonia and fuel molecules, part II: H-atom abstraction from alcohols and ethers by ṄH2 radicals

Ammonia, as a carbon-free fuel, is expected to be a carbon-neutral alternative fuel to control pollution emissions. However, with lower reactivity, pure ammonia needs to be blended with highly reactive biofuels including alcohols and ethers, for a better combustion performance. Alcohols and ethers can be produced from various sources, including renewable materials and fossil fuels. Therefore, the combination of ammonia with alcohols/ethers is a promising choice for developing carbon-neutral energy solutions. As an important intermediate, ṄH2 radicals can easily be formed during the pyrolysis or oxidation processes for ammonia combustion. The H-atom abstraction reaction between ṄH2 radicals and fuel molecules is vital in determining the blending fuel reactivity. High-level ab initio calculations have been carried out in this study to perform a systematic theoretical chemical kinetic investigation of H-atom abstraction by ṄH2 radicals from C1–C5 alcohols, 2,3-dimethyl-2-butanol, C1–C4 ethers and methyl isobutyl ether with a total of 61 H-atom abstraction reaction channels. The QCISD(T)/CBS//M06–2X/6–311++G(d, p) level of theory was employed to investigate the potential energy surfaces of the title reactions involved. Electronic geometry optimization, frequency analysis, and zero-point energy correction were performed for reactants, transition states and products related to 61 reaction channels at the M06–2X/6–311++G(d, p) level of theory. Single-point energy calculations were performed at the QCISD(T)/cc-pVXZ (X = D, T) and MP2/cc-pVYZ (Y = D, T, Q) level of theory and then extrapolated to the complete basis set. Conventional transition state theory was used to calculate the rate constants for different channels in the temperature range from 500 to 2000 K. The calculated individual and average rate constants for H-atom abstraction from different sites of alcohols and ethers were also obtained to explore the kinetic influence from the functional group. This is the first systematic study providing the rate constants for the title reactions which can be used to develop the combustion kinetic models for ammonia/alcohols and ammonia/ethers blends.

Insight into the interaction between amino acids and SO2: Detailed bonding modes.

Amino acids are a highly effective and environmentally friendly adsorbent for SO2. However, there has been no comprehensive study of the binding modes between amino acids and SO2 at the molecular level. In this paper, the binding modes of three amino acids (Asp, Lys, and Val) with SO2 are studied comprehensively and in detail using quantum chemical calculations. The results indicate that each amino acid has multiple binding modes: 22 for Asp, 49 for Lys, and 10 for Val. Both the amino and carboxyl groups in amino acids, as well as those in side chains, can serve as binding sites for chalcogen bonds. The binding energies range from - 6.42 to - 1.06kcal/mol for Asp, - 12.43 to - 1.63kcal/mol for Lys, and - 7.42 to - 0.60kcal/mol for Val. Chalcogen and hydrogen bonds play a crucial role in the stronger binding modes. The chalcogen bond is the strongest when interacting with an amino group, with an adiabatic force constant of 0.475 mDyn/Å. Energy decomposition analysis indicates that the interaction is primarily electrostatic attraction, with the orbital and dispersive interactions dependent on the binding mode. Amino acids and complexes of amino acids with SO2 were used to do semi-empirical MD using Molclus combined with xtb at the GFN2 level. Optimization and frequency calculations of the structures were conducted using density-functional theory (DFT) B3LYP/6-311G* (with DFT-D3 correction). Single-point energy calculations were performed for all structures using DLPNO-CCSD(T)/aug-cc-pVTZ with tightPNO. Further analysis of the structures was conducted using ESP, AIM, IGMH, and sob-EDA to gain a deeper understanding of the interactions between amino acids and SO2.

Assessing the accuracy and efficacy of multiscale computational methods in predicting reaction mechanisms and kinetics of SN2 reactions and Claisen rearrangement

This study investigates the application of quantum mechanical (QM) and multiscale computational methods in understanding the reaction mechanisms and kinetics of SN2 reactions involving methyl iodide with NH2OH and NH2O−, as well as the Claisen rearrangement of 8-(vinyloxy)dec-9-enoate. Our aim is to evaluate the accuracy and effectiveness of these methods in predicting experimental outcomes for these organic reactions. We achieve this by employing QM-only calculations and several hybrids of QM and molecular mechanics (MM) methods, namely QM/MM, QM1/QM2, and QM1/QM2/MM methodologies. For the SN2 reactions, our results demonstrate the importance of explicitly including solvent effects in the calculations to accurately reproduce the transition state geometry and energetics. The multiscale methods, particularly QM/MM and QM1/QM2, show promising performance in predicting activation energies. Moreover, we observe that the size of the MM active region significantly affects the accuracy of calculated activation energies, highlighting the need for careful consideration during the setup of multiscale calculations. In the case of the Claisen rearrangement, both QM-only and multiscale methods successfully reproduce the proposed reaction mechanism. However, the activation free energies calculated using a continuum solvation model, based on single-point calculations of QM-only structures, fail to account for solvent effects. On the other hand, multiscale methods more accurately capture the impact of solvents on activation free energies, with systematic error correction enhancing the accuracy of the results. Furthermore, we introduce a Python code for setting up multiscale calculations with ORCA, which is available on GitHub at https://github.com/iranimehdi/pdbtoORCA.

Exploration of Free Energy Surface of the Au10 Nanocluster at Finite Temperature.

The first step in comprehending the properties of Au10 clusters is understanding the lowest energy structure at low and high temperatures. Functional materials operate at finite temperatures; however, energy computations employing density functional theory (DFT) methodology are typically carried out at zero temperature, leaving many properties unexplored. This study explored the potential and free energy surface of the neutral Au10 nanocluster at a finite temperature, employing a genetic algorithm coupled with DFT and nanothermodynamics. Furthermore, we computed the thermal population and infrared Boltzmann spectrum at a finite temperature and compared it with the validated experimental data. Moreover, we performed the chemical bonding analysis using the quantum theory of atoms in molecules (QTAIM) approach and the adaptive natural density partitioning method (AdNDP) to shed light on the bonding of Au atoms in the low-energy structures. In the calculations, we take into consideration the relativistic effects through the zero-order regular approximation (ZORA), the dispersion through Grimme's dispersion with Becke-Johnson damping (D3BJ), and we employed nanothermodynamics to consider temperature contributions. Small Au clusters prefer the planar shape, and the transition from 2D to 3D could take place at atomic clusters consisting of ten atoms, which could be affected by temperature, relativistic effects, and dispersion. We analyzed the energetic ordering of structures calculated using DFT with ZORA and single-point energy calculation employing the DLPNO-CCSD(T) methodology. Our findings indicate that the planar lowest energy structure computed with DFT is not the lowest energy structure computed at the DLPN0-CCSD(T) level of theory. The computed thermal population indicates that the 2D elongated hexagon configuration strongly dominates at a temperature range of 50-800 K. Based on the thermal population, at a temperature of 100 K, the computed IR Boltzmann spectrum agrees with the experimental IR spectrum. The chemical bonding analysis on the lowest energy structure indicates that the cluster bond is due only to the electrons of the 6 s orbital, and the Au d orbitals do not participate in the bonding of this system.