Intrinsic Reaction Coordinate Research Articles

Theoretical investigation of isomeric structures of B2O3. Kinetic and thermodynamic study of the transformation of boric oxide to metaboric acid HBO2. Complexation of HBO2: from dimer to hexamer

In this study, Density Functional Theory was adopted. Isomeric structures of boric oxide B 2 O 3 were investigated at B3LYP/6-311G++(d,p), M052X, M062X, M08HX, M11/6-311G++(d,p) levels of theory. For validation of stable states, optimisation was performed using the correlated coupled cluster with single, double, and perturbative triple excitations (CCSD(T)) method in conjunction with the augmented correlation-consistent polarisation valence Double Zeta (aug-cc-pVDZ) (AVDZ) basis sets. Intrinsic Reaction Coordinates (IRCs) calculations were carried out to give kinetics of reactions B 2 O 3 +H 2 O ⇌ 2HBO 2 , B 2 O 3 +HCl ⇌ HBO 2 + OBCl. Complexation of HBO 2 was considered using B3LYP-D3, B97-D, MN15 and wB97X-D dispersion-corrected functionals. Counterpoise-corrected complexation energies as well as frontier orbital HOMO-LUMO energy gaps of (HBO 2 ) n (n = 2, 3, 4, 5, 6) clusters were derived in order to study their stability owed to hydrogen bonds.

Mechanism for Site-Selective Hydroboration of C70 Fullerene with Borane by DFT-D3 Study.

We studied the hydroboration of the C70 fullerene using both B3LYP-D3(BJ)/6-311G(d,p) and M06-2X-D3/6-311G(d,p) levels of theory, incorporating the empirical dispersion interaction, and Fukui index calculations. Potential energy surfaces (PESs) and Gibbs free energy surfaces (GFESs) were calculated for the pathways from four BH3 adducts (located at the AB, CC, D, and E sites) on the C70 to eight products formed by the 1,2-addition of BH3 across the four [6,6]-ring fused bonds (AB, CC, DE, and EE) and across the two [5,6]-ring fused bonds (AA and DD). These pathways are two-step consecutive reactions. We denoted the positions on the fullerene cage as A through E, from the pole to the equator, based on the D5h symmetry of the C70 fullerene. In the first step reaction, the product ratios for the four adduct intermediates should be as the primary intermediate BH3(D), the secondary intermediate BH3(AB), the tertiary intermediate BH3(CC), and the minor intermediate BH3(E), based on the Fukui indices. In addition, in the second step reaction, transition states (TSs) from four adduct intermediates to eight product isomers, namely, BH2(A)H (B) to BH2(E)H (E), were obtained using the QST2 method. The calculated reaction coordinates showed exothermic reactions for all bonds except the EE bond. We also confirmed the transition states by frequency calculations and intrinsic reaction coordinate (IRC) analyses. The PESs and GFESs suggest spontaneous processes for the four isomers, of which the primary products are BH2(A)H (B) and its isomer BH2(B)H (A), the secondary product is BH2(C)H (C), and the tertiary product is BH2(D)H (D), all formed through adduct intermediates. Therefore, through the hydroboration reaction of C70, we could predict and design the site selectivity of C70 by controlling the energy barrier of the transition state in the second step of the reaction. This implies that we could selectively synthesize mainly BH2(B)H (A) isomers across the AB-[6,6]-ring fused bond and also design BH2(D)H(D) isomers across the DD-[5,6]-ring fused bond. Also, the calculations of formation rate constants can well simulate the experimental ratio of two C70H2 isomers by the hydrolysis of BH2(A)H(B), BH2(B)H(A), and BH2(C)H(C) products at room temperature.

Towards a complete description of the reaction mechanisms between nitrenium ions and water.

Nitrenium ions are intermediates in the metabolic routes producing the highly carcinogenic nitrosamines and binding to DNA molecules. The reaction mechanism of nitrenium molecules with explicit water molecules is sensibly dependent on the number of waters: when a second molecule is involved, it acts as a catalyst for the reaction, lowering intrinsic activation barriers regardless of the substituent. For all cases, the reaction force constants and reaction electron flux indicate highly synchronous reactions for . Conversely, for highly non-synchronous reactions are obtained, involving two separate proton transfers happening early and late in the reaction path. As a test case, for the simplest reactions, orbital interactions within the NBO paradigm, bond orders, and their derivatives indicate that each individual proton transfer is highly synchronous. Molecular geometries were optimized and characterized at the B3LYP/6-311++G(d, p) level. Intrinsic reaction coordinates were calculated. CCSD(T) single point energies with the same basis were computed on all stationary points. The reaction force, reaction force constant, and reaction electron flux are used to study the evolution of the reacting systems. Natural bond orbitals are used to understand the primitive changes driving the reaction.

New Quinazolin-4(3H)-One Derivatives Incorporating Isoxazole Moiety as Antioxidant Agents: Synthesis, Structural Characterization, and Theoretical DFT Mechanistic Study.

Background: This research centers on the development and spectroscopic characterization of new quinazolin-4(3H)-one-isoxazole derivatives (5a-e). The aim was to investigate the regioselectivity of the 1,3-dipolar cycloaddition involving arylnitriloxides and N-propargylquinazolin-4(3H)-one, and to assess the antioxidant properties of the synthesized compounds. The synthetic approach started with the alkylation of quinazolin-4(3H)-one using propargyl bromide, followed by a 1,3-dipolar cycloaddition reaction. Methods: The structural identification of the products was performed using various spectroscopic methods, such as IR, 1H, 13C, and HMBC NMR, HRMS, and single-crystal X-ray diffraction. To further examine the regioselectivity of the cycloaddition, Density Functional Theory (DFT) calculations at the B3LYP/6-31G(d) level were employed. Additionally, the antioxidant potential of the compounds was tested in vitro using DPPH (2,2-Diphenyl-1-picrylhydrazyl)radical scavenging assays. The reaction selectively produced 3,5-disubstituted isoxazoles, with the regiochemical outcome being independent of the substituents on the phenyl ring. Results: Theoretical calculations using DFT were in agreement with the experimental results, revealing activation energies of -81.15 kcal/mol for P-1 and -77.32 kcal/mol for P-2, favoring the formation of P-1. An analysis of the Intrinsic Reaction Coordinate (IRC) confirmed that the reaction proceeded via a concerted but asynchronous mechanism. The antioxidant tests demonstrated that the synthesized compounds exhibited significant radical scavenging activity, as shown in the DPPH assay. The 1,3-dipolar cycloaddition of arylnitriloxides with N-propargylquinazolin-4(3H)-one successfully resulted in novel 3,5-disubstituted isoxazoles. Conclusions: The experimental findings were well-supported by theoretical predictions, and the antioxidant assays revealed strong activity, indicating the potential for future biological applications of these compounds.

Deciphering the Two-Step Hydride Mechanism of Monoamine Oxidase Flavoenzymes.

The complete two-step hydride transfer mechanism of amine oxidation involved in the metabolism of monoamine neurotransmitters was scrutinized by DFT calculations. In living organisms, this process is catalyzed by monoamine oxidase enzymes. Herein, we focus on some intriguing aspects of the reaction that may have been previously noticed but have not been clarified to date. The first step of the reaction includes the C-H bond cleavage on the methylene group vicinal to the amino group of the monoamine substrate and the subsequent transfer of hydrogen to the N5 atom of the flavin prosthetic group of the enzyme. We confirmed the nature of this step to be hydride transfer by evaluation of the pertinent HOMO-LUMO gap together with analysis of orbital contours alongside the intrinsic reaction coordinate profile. Next, we investigated the rather peculiar intermediate adduct that may form between the amine substrate and the flavin molecule, featuring an unusually long C-N bond of ∼1.62 Å. Although this bond is quite stable in the gas phase, the presence of just a few explicit water molecules facilitates its dissociation almost without energy input so that the amine-flavin intermediate can form an ionic pair instead. We attribute the existence of the unusual C-N bond to a fragile balance between opposing electronic structure effects, as evaluated by the natural bond orbital analysis. In line with this, the intermediate in the solution or in the enzyme active site can exist in two energetically almost equivalent forms, namely, as a covalently bound complex or as an ion pair, as suggested by previous studies. Finally, we characterized the transformation of the intermediate to the fully reduced flavin and imine products via proton transfer from the amino group to the flavin N1 atom, completing the reductive part of the catalytic cycle. Although we found that explicit solvation substantially boosts the kinetics of this step, the corresponding barrier is significantly lower than that in the hydride transfer step, confirming hydrogen abstraction as the rate-limiting step of amine oxidation and validating the two-step hydride transfer mechanism of monoamine oxidases.

Study of the Torquoselectivity of a Set of Unusual Ring‐Opening Electrocyclic Reactions: Determination of the Electronic Bonding Structure Through the Methodologies of Natural Bond Orbital Analysis and Quantum Theory of Atoms in Molecules, and Analysis of the Electronic Reaction Mechanism Through Bond Reactivity Descriptors

ABSTRACTIn this work, we have studied the torquoselectivity of a set of unusual ring‐opening electrocyclic reactions that have not been successfully rationalized using models based on orbital symmetry nor have they been explained by steric hindrance. Firstly, the corresponding transition states have been obtained, and it has been verified that the intrinsic reaction coordinates associated with these transition states are consistent with the reactants and products of the reactions studied. This has allowed us to theoretically calculate the reaction barriers (with their corresponding thermal corrections) and compare them with the corresponding experimental values. In a second step, we have analyzed the electronic bonding structure using the methodologies of Natural Bond Orbital Analysis and Quantum Theory of Atoms in Molecules, searching for interactions that may significantly stabilize the transition states. Finally, we have analyzed the reactivity using a recent model that has allowed us to calculate the corresponding bond reactivity descriptors.

Non-covalent interactions and charge transfer in the CO activation by low-valent group 14 complexes.

The CO activation by low-valent group 14 catalysts encompasses the rupture of varied covalent bonds in a single transition state through a concerted pathway. The bond between the central main group atom and the hydride in the complex is elongated to trigger the formation of the C-H bond with CO accompanied by the concomitant formation of the E-O bond between the complex and CO to lead the corresponding formate product. Prior studies have established that besides the apolar nature of CO , its initial interaction with the complex is primarily governed by electrostatic interactions. Notably, other stabilizing interactions and the transfer of charge between catalysts and CO during the initial phases of the reaction have been ignored. In this study, we have quantified the non-covalent interactions and charge transfer that facilitate the activation of CO by group 14 main group complex. Our findings indicate that electrostatic interactions predominantly stabilize the complex and CO in the reactant region. However, induction energy becomes the main stabilizing force as the reaction progresses towards the transition state, surpassing electrostatics. Induction contributes about 50% to the stabilization at the transition state, followed by electrostatics (40%) and dispersion interactions (10%). Atomic charges calculated with the minimal basis iterative stockholder (MBIS) method reveal larger charge transfer for the back-side reaction path in which CO approaches the catalysts in contrast to the front-side approach. Notably, it was discovered that a minor initial bending of CO to approximately initiates the charge transfer process for all systems. Furthermore, our investigation of group 14 elements demonstrates a systematic reduction in both activation energies and charge transfer to CO while descending in group 14. All studied reactions were characterized along the reaction coordinate obtained with the intrinsic reaction coordinate (IRC) methodology at the M06-2X/6-31g(d,p) level of theory. Gibbs free energy in toluene was computed using electronic energies at the DLPNO-CCSD(T)/cc-pVTZ-SSD(E) level of theory. Vibrational and translational entropy corrections were applied to provide a more accurate description of the obtained Gibbs free energies. To better characterize the changes in the reaction coordinate for all reactions, the reaction force analysis (RFA) has been employed. It enables the partition of the reaction coordinate into the reactant, transition state, and product regions where different stages of the mechanism occur. A detailed characterization of the main non-covalent driving forces in the initial stages of the activation of CO by low-valent group 14 complexes was performed using symmetry-adapted perturbation theory (SAPT). The SAPT0-CT/def2-SVP method was employed for these computations. Charge transfer descriptors based on atomic population using the MBIS scheme were also obtained to complement the SAPT analyses.

Cooperativity and halonium transfer in the ternary NCI···CH3I···-CN halogen-bonded complex: An ab initio gas phase study.

The strength and nature of the two halogen bonds in the NCI···CH3I···-CN halogen-bonded ternary complex are studied in the gas phase via ab initio calculations. Different indicators of halogen bond strength were employed to examine the interactions including geometries, complexation energies, Natural Bond Order (NBO) Wiberg bond indices, and Atoms in Molecules (AIM)-based charge density topological properties. The results show that the halogen bond is strong and partly covalent in nature when CH3I donates the halogen bond, but weak and noncovalent in nature when CH3I accepts the halogen bond. Significant halogen bond cooperativity emerges in the ternary complex relative to the corresponding heterodimer complexes, NCI···CH3I and CH3I···-CN, respectively. For example, the CCSD(T) complexation energy of the ternary complex (-18.27kcal/mol) is about twice the sum of the complexation energies of the component dimers (-9.54kcal/mol). The halonium transfer reaction that converts the ternary complex into an equivalent one was also investigated. The electronic barrier for the halonium transfer was calculated to be 6.70kcal/mol at the CCSD(T) level. Although the MP2 level underestimates and the MP3 overestimates the barrier, their calculated MP2.5 average barrier (6.44kcal/mol) is close to that of the more robust CCSD(T) level. Insights on the halonium ion transfer reaction was obtained by examining the reaction energy and force profiles along the intrinsic reaction coordinate, IRC. The corresponding evolution of other properties such as bond lengths, Wiberg bond indices, and Mulliken charges provides specific insight on the extent of structural rearrangements and electronic redistribution throughout the entire IRC space. The MP2 method was used for geometry optimizations. Energy calculations were performed using the CCSD(T) method. The aug-cc-pVTZ basis set was employed for all atoms other than iodine for which the aug-cc-pVTZ-PP basis set was used instead.

Surprising Dynamics Phenomena in the Diels-Alder Reaction of C60 Uncovered with AI.

We performed an extensive artificial intelligence-accelerated quasi-classical molecular dynamics investigation of the time-resolved mechanism of the Diels-Alder reaction of fullerene C60 with 2,3-dimethyl-1,3-butadiene. In a substantial fraction (10%) of reactive trajectories, the larger C60 noncovalently attracts the 2,3-dimethyl-1,3-butadiene long before the barrier so that the diene undergoes the series of complex motions including roaming, somersaults, twisting, and twisting somersaults around the fullerene until it aligns itself to pass over the barrier. These complicated processes could be easily missed in typically performed quantum chemical simulations with shorter and fewer trajectories. After the barrier is passed, the bonds take longer to form compared to the simplest prototypical Diels-Alder reaction of ethene with 1,3-butadiene despite high similarities in transition states and barrier widths evaluated with intrinsic reaction coordinate (IRC) calculations. C60 is mainly responsible for these differences as its reaction with 1,3-butadiene is similar to the reaction with 2,3-dimethyl-1,3-butadiene: the only substantial difference being that the extra methyl groups double the probability of the prolonged alignment phase in dynamics. These additional calculations of C60 with 1,3-butadiene could be performed via active learning more easily by reusing the data generated for the other two reactions, showing the potential for larger-scale exploration of the effects of different substrates in the same types of reactions.

On the link between the reaction force constant and conceptual DFT.

The reaction force constant ( ), introduced by Professor Alejandro Toro-Labbé, plays a pivotal role in characterizing the reaction pathway by assessing the curvature of the potential energy profile along the intrinsic reaction coordinate. This study establishes a novel link between and the reactivity descriptors of conceptual density functional theory (c-DFT). Specifically, we derive expressions that relate the reaction force constant to nuclear softness and variations in chemical potential. Our findings indicate that regions of the reaction pathway where is negative match with significant electronic structure rearrangements, while positive regions match mostly with geometric rearrangements. This correlation between and c-DFT reactivity descriptors enhances our understanding of the underlying forces driving chemical reactions and offers new perspectives for analyzing reaction mechanisms. The internal reaction path for the proton transfer in SNOH, chemical potential, and nuclear softness were computed using DFT with B3LYP exchange-correlation functional and 6-311++G(d,2p) basis set.

Multi-Level Protocol for Mechanistic Reaction Studies Using Semi-Local Fitted Potential Energy Surfaces.

In this work, we propose a multi-level protocol for routine theoretical studies of chemical reaction mechanisms. The initial reaction paths of our investigated systems are sampled using the Nudged Elastic Band (NEB) method driven by a cheap electronic structure method. Forces recalculated at the more accurate electronic structure theory for a set of points on the path are fitted with a machine learning technique (in our case symmetric gradient domain machine learning or sGDML) to produce a semi-local reactive potential energy surface (PES), embracing reactants, products and transition state (TS) regions. This approach has been successfully applied to a unimolecular (Bergman cyclization of enediyne) and a bimolecular (SN2 substitution) reaction. In particular, we demonstrate that with only 50 to 150 energy-force evaluations with the accurate reference methods (here complete-active-space self-consistent field, CASSCF, and coupled-cluster singles and doubles, CCSD) it is possible to construct a semi-local PES giving qualitative agreement for stationary-point geometries, intrinsic reaction coordinates and barriers. Furthermore, we find a qualitative agreement in vibrational frequencies and reaction rate coefficients. The key aspect of the method's performance is its multi-level nature, which not only saves computational effort but also allows extracting meaningful information along the reaction path, characterized by zero gradients in all but one direction. Agnostic to the nature of the TS and computationally economic, the protocol can be readily automated and routinely used for mechanistic reaction studies.

Thermal decomposition study of 1,3-dioxolane as a representative of battery solvent

As industrial compounds and organic solvent, 1,3-dioxolane (C3H6O2) is used in lithium-ion batteries arousing extensive interest. The pyrolysis of C3H6O2 at 150 torr pressure was conducted in the temperature range of 743–1013 K. In order to quantify the major products, experimental measurements of the photoionization cross-section (PICS) and photoionization efficiency (PIE) for C3H6O2 were carried out by using synchrotron radiation photoionization mass spectrometry (SR-PIMS). Twenty-three intermediates were detected in pyrolysis of C3H6O2 including the newly observed ketene, acetaldehyde, ethenol, ethanol, dimethyl ether, diacetylene and 2-propen-1-ol which played important roles in developing mechanism. The H-abstraction of C3H6O2 by H, CH3 and OH radicals were studied via high level ab initio calculations. EStokTP code was used to find and calculate optimal geometries, vibration frequencies and intrinsic reaction coordinate (IRC) at the theory level of M06–2X/6–311+G(d,p). Conventional transition state theory (TST) was used and Rice-Ramsperger-Kassel-Marcus/Master Equation (RRKM/ME) was solved to obtain rate coefficients. For H-abstraction by H and CH3, the rates are increasing versus temperature, and rates of H-abstraction by OH show different tendency. These rate parameters were used to update the model of C3H6O2, which could well predict the ignition delay times (IDTs) in shock tube and oxidation data in jet stirred reactor (JSR) from literature. For the pyrolysis, H-abstraction reactions by H, CH3 and OH and unimolecular reactions contribute to solvent decay. Detailed pathways of C3H6O2 decomposition were also given and analyzed through this experiment and previous literature. The findings, including the experimental data and the calculations will assist to better understand pyrolysis characteristics of C3H6O2 as well.

Insights into the variations of kinetic and potential energies in a multi-bond reaction: the reaction electronic flux perspective.

The debate over whether kinetic energy (KE) or potential energy (PE) are the fundamental energy components that contribute to forming covalent bonds has been enduring and stimulating over time. However, the supremacy of these energy components in reactions where multiple bonds are simultaneously formed or broken has yet to be explored. In this study, we use the reaction electronic flux (REF), an effective tool for investigating changes in driving electronic activity when bond formation or dissociation occurs in a chemical reaction, to examine the fluctuations in the KE and PE in a multi-bond reaction. To that end, the activation of CO by low-valent group 14 catalysts through a concerted -bond metathesis mechanism is analyzed. The findings of this preliminary study suggest that the REF can be utilized as a tool to rationalize alterations in the KE and PE in a multi-bond reaction. Specifically, analyses across the reaction coordinate reveal that changes in the KE and PE precede activation in the REF, stimulating the electronic activity where bond formation or dissociation processes dominate. The activation of CO by the low-valent LEH catalysts (L = N,N'-bis(2,6-diisopropyl phenyl)- -diketiminate; E = Si, Ge, Sn, and Pb) was studied along the reaction coordinate at the M06-2X/6-31G(d,p)-LANL2DZ(E) level of theory. The respective minimum energy path calculations were obtained using the intrinsic reaction coordinate (IRC) procedure. The reaction electronic flux (REF) was calculated through the computation of the electronic chemical potential using the frontier molecular orbital approximation. Mayer bond orders along the reaction coordinate have been determined using the NBO 3.1 program in Gaussian16. Most of the reaction coordinate quantities reported in this study (REF, KE, PE, among others) have been determined using the Kudi program and custom Python scripts.

Ab initio investigation on the mechanism of SO2 activation by P/B intermolecular frustrated Lewis pairs.

In silico study investigates the activation of sulfur dioxide by newly designed frustrated Lewis pairs, i.e., [P(tBu)3…B(C2NBSHF2)3], where the Lewis acid part is a super Lewis acid. The activation process involves the making of P-S and B-O bonds, leading to the formation of an FLP-SO2 adduct. The calculated results demonstrate that the activation of SO2 by the FLP is almost barrierless and exothermic. Exploration of the impact of the solvent environment on the feasibility and energetics of the reaction has been investigated. The exothermicity is increasing in nonpolar solvents. This study focuses on understanding the electronic activity of SO2 activation by FLP with the help of the Minnesota 06 functional, M06-2X (global hybrid functional with 54% HF exchange) along with Pople's basis set, 6-311G (d, p). Principal interacting orbital and extended transition state-natural orbitals for chemical valence studies, giving impactful insight into the favorable orbital interaction and electron transfer in this reaction. Furthermore, useful CDFT descriptors such as reaction force constant and reaction electronic flux profiles along the intrinsic reaction coordinate give insights into the synchronicity and total electronic activity of the reaction.

Kinetic Isotope Effects and the Mechanism of CO2 Insertion into the Metal-Hydride Bond of fac-(bpy)Re(CO)3H.

The 1,2-insertion reaction of CO2 into metal-hydride bonds of d6-octahedral complexes to give κ1-O-metal-formate products is the key step in various CO2 reduction schemes and as a result has attracted extensive mechanistic investigations. For many octahedral catalysts, CO2 insertion follows an associative mechanism in which CO2 interacts directly with the coordinated hydride ligand instead of the more classical dissociative mechanism that opens an empty coordination site to bind the substrate to the metal prior to a hydride migration step. To better understand the associative mechanism, we conducted a systematic quantum chemical investigation on the reaction between CO2 and fac-(bpy)Re(CO)3H (1-Re-H; bpy = 2,2'-bipyridine) starting with the gas phase and then moving to THF and other solvents with increased dielectric constants. Detailed analyses of the potential energy surfaces (PESs) and intrinsic reaction coordinates (IRCs) reveal that the reaction is enabled in all media by an initial stage of making a 3c-2e bond between the carbon of CO2 and the metal-hydride bond that is most consistent with an organometallic bridging hydride Re-H-CO2 species. Once CO2 is bent and anchored to the metal-hydride bond, the reaction proceeds by a rotation motion via a cyclic transition state TS2 that interchanges Re-H-CO2 and Re-O-CHO coordination. The combined stages provide an asynchronous-concerted pathway for CO2 insertion on the Gibbs free energy surface with TS2 as the highest energy point. Consideration of TS2 as a rate-determining TS gives activation barriers, inverse KIEs, substituent effects, and solvent effects that agree with the experimental data available in this system. An important new insight revealed by the analyses of the results is that the initial stage of the reaction is not a hydride transfer step as has been assumed in some studies. In fact, the loose vibration of the TS that can be identified for the first stage of the reaction in solution (TS1) does not involve the Re-H stretching vibrational mode. Accordingly, the imaginary frequency of TS1 is insensitive to deuteration, and therefore, TS1 leads to no significant KIE.

3-Pyrazolyl-pyran-2-one: Synthesis, crystal structure, Hirshfeld surface analysis, DFT and ADME studies

Synthesis, crystal structure, Hirshfeld surface analysis, DFT and in-silico studies were carried out for the 4‑hydroxy-6-methyl-3-(1-phenyl-1H-pyrazol-3-yl)-2H-pyran-2-one 2. The reaction efficiency was evaluated performing two conditions to prepare the Vilsmeir-Haack reagent: phosphoryl trichloride in DMF and phosphorus pentachloride in DMF. The molecular structure was confirmed by 1H and 13C NMR, IR spectroscopy and X-ray diffraction analysis. The pyrazole and pyran rings are nearly coplanar. The molecules are connected through C—H···O hydrogen bonds, C—H⋯π and π⋯π stacking interactions, forming layers in the crystal lattice. Hirshfeld surface analysis for crystal packing indicates that the most important contributions are H⋯H (41.6 %), C⋯H/H⋯C (22.6 %), O…H/H…O (20.9 %) interactions. The frontier molecular orbital, Mulliken and QTAIM atomic charge, Molecular Electrostatic Potential, Natural Bond Orbitals were produced using the optimized structure by B3LYP/6–311G(d,p) level of theory. The calculated LUMOHOMO gap (4.261 eV) indicated that the eventual charge transfer and showed chemical reactivity. Intrinsic reaction coordinate (IRC) calculation confirm that the transition state connects the reactants to the products. The experimental geometry parameters of the title compound are compared with the geometry of the optimized molecule in the gas phase and found in good agreement. The crystal structure was further explored to define the interaction energy between the molecular pairs. The ADME profile that pyrazolyl-pyran-2-one 2 is an inhibitor of CYP1A2 one of the five key cytochrome isoforms enzymes involved in drug metabolism.

Understanding the coupling of non-metallic heteroatoms to CO2 from a Conceptual DFT perspective

ContextA Conceptual DFT (CDFT) study has been carry out to analyse the coupling reactions of the simplest amine (CH3NH2), alcohol (CH3OH), and thiol (CH3SH) compounds with CO2 to form the corresponding adducts CH3NHCO2H, CH3OCO2H, and CH3SCO2H. The reaction mechanism takes place in a single step comprising two chemical events: nucleophilic attack of the non-metallic heteroatoms to CO2 followed by hydrogen atom transfer (HAT). According to our calculations, the participation of an additional nucleophilic molecule as HAT assistant entails important decreases in activation electronic energies. In such cases, the formation of a six-membered ring in the transition state (TS) reduces the angular stress with respect to the non-assisted paths, characterised by four-membered ring TSs. Through the analysis of the energy and reaction force profiles along the intrinsic reaction coordinate (IRC), the ratio of structural reorganisation and electronic rearrangement for both activation and relaxation energies has been computed. In addition, the analysis of the electronic chemical potential and reaction electronic flux profiles confirms that the highest electronic activity as well as their changes take place in the TS region. Finally, the distortion/interaction model using an energy decomposition scheme based on the electron density along the reaction coordinate has been carried out and the relative energy gradient (REG) method has been applied to identify the most important components associated to the barriers.MethodsThe theoretical calculation were performed with Gaussian-16 scientific program. The B3LYP-D3(BJ)/aug-cc-pVDZ level was used for optimization of the minima and TSs. IRC calculations has also been carried out connecting the TS with the associated minima. Conceptual-DFT (CDFT) calculations have been carried out with the Eyringpy program and in-house code. The distortion/interaction model along the reaction coordinate have used the decomposition scheme of Mandado et al. and the analysis of the importance of each components have been done with the relative energy gradient (REG) method.

Quantum chemical pathways for the formation of 2,3,7,8-tetrachloro dibenzo-p-dioxin (TCDD) from 2,4,5-trichlorophenol: a mechanistic and thermo-kinetic study.

Dioxins, specifically 2,3,7,8-tetrachlorinated dibenzo-p-dioxin (TCDD), are highly toxic dioxins known for their severe health impacts and persistent environmental pollutants. This study focuses on understanding the formation pathways of TCDD from its precursor molecule 2,4,5-trichlorophenol (2,4,5-TCP). In our exploration of reaction pathways from 2,4,5-trichlorophenol (TCP), we delve into three reaction mechanisms: free-radical, direct condensation, and anionic. Our findings highlight the significance of the radical mechanism, particularly propagated by H radicals, with a notable increase in dioxin formation around 900K. These results are consistent with experimental observations indicating an increase in the conversion of trichlorophenol from 600 to 900K in the non-catalytic gas phase reaction. Thermodynamic parameters (∆H, ∆S, and ∆G), reaction barriers, and rate constants (k) were calculated across a temperature range of 300-1200K to support the findings and provide insights into the optimal temperature range for controlling dioxins during the incineration process. In this study, quantum chemical calculations were conducted using density functional theory (DFT) with the B3LYP functional and the 6-311 + + G(d,p) basis set in Gaussian 16 software. Stationary points, including transition states (TS), were confirmed with frequency calculations. Intrinsic reaction coordinate (IRC) calculations ensured minimum energy paths between TS and products, visualized in GaussView 6.0 Program. Single-point energy calculations utilized a more precise basis set, 6-311 + + G(3df,2p), for enhanced energy accuracy, incorporating zero-point vibrational energy (ZPE) and other energy corrections. These calculations were repeated over a temperature range of 298.15-1200K at 1atm pressure. Finally, rate constant (k) expressions associated with TCDD formation were determined using transition state theory (TST).

Restriction on molecular fluxionality by substitution: A case study for the 1,10-dicyanobullvalene.

We show herein that 1,10-dicyano substitution restricts the paragon fluxionality of bullvalene to just 14 isomers which isomerize along a single cycle. The restricted fluxionality of 1,10-dicyanobullvalene (DCB) is investigated by means of: (i) Bonding analyses of the isomer structures using the adaptive natural density partitioning (AdNDP). (ii) Quantum dynamical simulations of the isomerizations along the cyclic intrinsic reaction coordinate of the potential energy surface (PES). The PES possesses 14 equivalent potential wells supporting 14 isomers which are separated by 14 equivalent potential barriers supporting 14 transition states. Accordingly, at low temperatures, DCB appears as a hindered molecular rotor, without any delocalization of the wavefunction in the 14 potential wells, without any nuclear spin isomers, and with completely negligible tunneling. These results are compared and found to differ from those for molecular boron rotors. (iii) Born-Oppenheimer molecular dynamics (BOMD) simulations of thermally activated isomerizations. (iv) Calculations of the rate constants in the frame of transition state theory (TST) with reasonable agreement achieved with the BOMD results. (v) Simulations of the equilibration dynamics using rate equations for the isomerizations with TST rate coefficients. Accordingly, in the long-time limit, isomerizations of the 14 isomers, each with Cs symmetry, approach the "14 Cs → C7v" thermally averaged structure. This is a superposition of the 14 equally populated isomer structures with an overall C7v symmetry. By extrapolation, the results for DCB yield working hypotheses for so far un-explored properties e.g. for the equilibration dynamics of C10H10.

Concerning for the solvent-polarity-dependent conformational equilibrium and ESIPT mechanism in Pz3HC system: A novel insight

In this report, we propose a new insight into the interaction between the solvent-polarity-dependent conformational equilibrium and excited state intramolecular proton transfer (ESIPT) behavior of Pz3HC system in four different polar solvents (polarity order: ACN > THF > TOL > CYC). Using quantum chemistry method, we first announce a coexistence mechanism between Pz3HC-1 and Pz3HC-3 in the ground state in four solvents based on the Boltzmann distribution. In particular, Pz3HC-1 is the principal configuration in non-polar solvent, but Pz3HC-3 is the principal configuration in polar solvent. In addition, the simulated fluorescence spectra interprets the negative solvatochromism effect of Pz3HC-1 and Pz3HC-3 in four solvents. The evidence from intramolecular hydrogen bonding (IHB) parameters and electronic perspective collectively confirms the light-induced IHB enhancement and intramolecular charge transfer (ICT) properties in Pz3HC-1 and Pz3HC-3, which raises the likelihood of the ESIPT process. Combining the calculation of potential energy curve (PEC) and intrinsic reaction coordinate (IRC), we demonstrate that the ESIPT ease of Pz3HC-1 in different polar solvents obeys the order of CYC > TOL > THF > ACN, while the order of ESIPT ease in Pz3HC-3 is opposite. Notably, the ESIPT process of Pz3HC-3 in CYC solvent is accompanied by the twisted intramolecular charge transfer (TICT) process. In addition, we also reveal that the enol* and keto* fluorescence peaks of Pz3HC-3 in CYC solvent are quenched by ISC and TICT process, respectively. Our work not only provides a satisfactory explanation of the novel dynamics mechanism for Pz3HC system, but also brings light to the design and application of new sensing molecules in the future.