DFT calculations in solution systems: solvation energy, dispersion energy and entropy

Carbon-Bromide Bond Activation by Bidentate Halogen, Chalcogen, Pnicogen, and Tetrel Bonds

Halogen, chalcogen, pnictogen, and tetrel bonds in organocatalysis have gained noticeable attention. In this work, carbon-bromide bond activation in the Ritter reaction by bidentate imidazole-type halogen, chalcogen, pnicogen, and tetrel bond donors was studied by density functional theory. All of the above four kinds of catalysts exhibited excellent catalytic performance. σ-hole interactions were formed between the Br atom of the reactant and the halogen, chalcogen, pnicogen, and tetrel bond donors, which elongated the C-Br bond and caused the rearrangement of the electron density of the precomplexes, resulting in the breaking of the C-Br bond and Br abstraction. Notably, the catalytic activity of the chalcogen bond is the best, followed by that of the halogen bond. Although the catalytic activity of pnicogen and tetrel bond catalysts is not as good as that of the halogen bond and chalcogen bond, they can still be used as effective substitutes for the halogen bond and chalcogen bond, providing more choices for noncovalent catalysis. Furthermore, within the same group, the fifth-period atomic catalyst is more effective than the fourth-period one for halogen, chalcogen, pnicogen, and tetrel bond donor catalysts.

Copper(II)-Oxyl Formation in a Biomimetic Complex Activated by Hydrogen Peroxide: The Key Role of Trans-Bis(Hydroxo) Species

Enzymes in nature, such as the copper-based lytic polysaccharide monooxygenases (LPMOs), have gained significant attention for their exceptional performance in C-H activation reactions. The use of H2O2 by LPMOs enzymes has also increased the interest in understanding the oxidation mechanism promoted by this oxidant. While some literature proposes Fenton-like chemistry involving the formation of Cu(II)-OH species and the hydroxyl radical, others contend that Cu(I) activation by H2O2 yields a Cu(II)-oxyl intermediate. In this study, we focused on a bioinspired Cu(I) complex to investigate the reaction mechanism of its oxidation by H2O2 using density functional theory and ab initio molecular dynamics simulations. The latter approach was found to be critical for finding the key Cu intermediates. Our results show that the highly flexible coordination environment of copper strongly influences the nature of the oxidized Cu(II) species. Furthermore, they suggest the favorable formation of trans-Cu(II)-(OH)2 moieties in low-coordinated Cu(II) species. This trans configuration hinders the formation of Cu(II)-oxyl species, facilitating intramolecular H-abstraction reactions in line with experimentally observed ligand oxidation processes.

Reversible CO2 insertion into the silicon-nitrogen σ-bond of an N-heterocyclic iminosilane

The reversible insertion of carbon dioxide into the silicon-nitrogen bond of an N-heterocyclic iminosilane is reported. Solution-phase thermodynamic investigations indicate that this process is thermoneutral and reversible, whereas in the solid-phase CO2 can be stored for extended periods and is only released upon heating to 133 °C.

DFT Investigation on Palladium-Catalyzed [2 + 2 + 1] Spiroannulation between Aryl Halides and Alkynes: Mechanism, Base Additive Role, and Solvent and Ligand Effects

Transition metal-catalyzed spiroannulations are practical strategies for constructing spirocyclic skeletons of pharmaceutical and biological significance, yet the microscopic mechanism still lacks in-depth explorations. Here, the palladium-catalyzed [2 + 2 + 1] spiroannulation between aryl halides and alkynes was studied by employing the density functional theory (DFT) method. Based on comprehensive explorations on a couple of possible reaction pathways, it is found that the reaction probably experiences C-I oxidative addition, alkyne migration insertion, Cs2CO3-assisted aryl C-H activation, C-Br bond oxidative addition, C-C coupling, arene dearomatization and reductive elimination in sequence and leads to the formation of the spiro[4,5]decane pentacyclic product (P) ultimately. Among these, the C-Br bond oxidative addition step acts as the rate-determining step (RDS) of the whole reaction, featuring a practical free energy barrier of 32.4 kcal·mol-1 at 130 °C. Computationally predicted kinetics such as half-life transferred from the RDS step's barrier on the optimal reaction pathway (1.2 × 101 h) coincides well with corresponding experimental results (91% yield of the spiro[4,5]decane pentacyclic product P after reacting 10 h at 130 °C). In addition, theoretical predictions regarding the solvent/ligand effects and base additive role in the reaction, rationalized by distortion-interaction/natural population/noncovalent interaction analyses, are also in good agreement with experimental data and trend. This good agreement between experiment and theory makes sense for new designations and further experimental improvements of such Pd-catalyzed transformations.

Machine learning-guided strategies for reaction conditions design and optimization

This review surveys the recent advances and challenges in predicting and optimizing reaction conditions using machine learning techniques. The paper emphasizes the importance of acquiring and processing large and diverse datasets of chemical reactions, and the use of both global and local models to guide the design of synthetic processes. Global models exploit the information from comprehensive databases to suggest general reaction conditions for new reactions, while local models fine-tune the specific parameters for a given reaction family to improve yield and selectivity. The paper also identifies the current limitations and opportunities in this field, such as the data quality and availability, and the integration of high-throughput experimentation. The paper demonstrates how the combination of chemical engineering, data science, and ML algorithms can enhance the efficiency and effectiveness of reaction conditions design, and enable novel discoveries in synthetic chemistry.

A QSPR Model for Henry's Law Constants of Organic Compounds in Water and Ethanol for Distilled Spirits

Henry's law describes the vapor-liquid equilibrium for dilute gases dissolved in a liquid solvent phase. Descriptions of vapor-liquid equilibrium allow the design of improved separations in the food and beverage industry. The consumer experience of taste and odor are greatly affected by the liquid and vapor phase behavior of organic compounds. This study presents a machine learning (ML) based model that allows quick, accurate predictions of Henry's law constants (kH) for many common organic compounds. Users input only a Simplified Molecular-Input Line-Entry System (SMILES) string or a common English name, and the model returns Henry's law estimates for compounds in water and ethanol. Training was performed on 5,690 compounds. Training data were gathered from an existing database and were supplemented with quantum mechanical (QM) calculations. An extra trees regression model was generated that predicts kH with a mean absolute error of 1.3 in log space and an R2 of 0.98. The model is applied to common flavor and odor compounds in bourbon whiskey as a test case for food and beverage applications.

Dirhodium(II) complex catalyzed dehydrosilylation of styrenes: theoretical investigations on the mechanism, selectivity, and ligand effects

The dirhodium(II) complexes with bridging phosphine and OAc ligands showed high reactivity and selectivities in olefin dehydrosilylation. In order to determine the structure of the actual catalyst which cannot be determined experimentally, the geometries of the dirhodium catalyst, the detailed catalytic mechanism, and the stereo- and chemo-selectivities of the title reaction were studied using DFT calculations. The results showed that one OAc group is monodentate and the other is bidentate in the dirhodium catalyst C'. The determined catalytic cycle consists of four processes: Rh-H bond activation in C', Si-H bond activation in alkoxysilane, alkylene insertion into the Rh-Si bond, followed by β-H elimination or σ-metathesis reaction. Among them, the alkylene insertion process is the rate-determining step. The stereoselectivity of the title reaction is controlled by the steric effect and orbital interactions between the alkyene and dirhodium catalysts in the β-H elimination process. The chemoselectivity is regulated by the presence of the axial ligand in the dirhodium catalyst, when there is an axial ligand coordinated to the Rh atom, E-alkene is the main product, whereas alkane would be obtained in the absence of an axial ligand. Our work determines the structure of the actual catalyst, and provides explanations and predictions for the activity, and chemo- and stereo-selectivity control of olefin dehydrosilylation.

Computation of rate coefficients in solutions based on transition state theory combined with a heuristically corrected polarizable continuum model: intermolecular Diels-Alder reactions as case studies

Transition state theory (TST) based on activation parameters computed using quantum mechanics calculations combined with the polarizable continuum model (QM/PCM) is a fundamental tool for investigating reaction rates in the liquid phase. In conventional QM/PCM methods, thermodynamic data and partition functions for a solute are often derived from a quasi-ideal gas treatment (IGT) widely implemented in commercially available computation packages. This approach tends to overestimate entropy because calculations of thermodynamic parameters in the liquid phase ignore hindered translational and rotational modes in real solutions. The present work formulated partition functions for more realistic solutes hindered by surrounding solvent molecules in conjunction with the basic QM/PCM concept. In addition, a configuration partition function for solute molecules at a standard concentration of 1 mol dm-3 was incorporated using a simple lattice model. The canonical partition function and thermodynamic functions were derived based on statistical thermodynamics for localized systems. Expressions for rate coefficients within TST were also derived with a consistent formalism based on the standard state selected in partition function calculations. The performance of the proposed method was assessed by predicting rate coefficients for three different Diels-Alder reactions and comparing these with experimental results. QM/PCM calculations at the G4//ωB97X-D/6-311++G(d,p)/IEF-PCM level of theory with corrections for the dispersion and repulsion energies were performed to obtain the electronic structures of stationary points on potential energy surfaces as a means of finding activation enthalpy, entropy and Gibbs energy values based on revised partition functions as well as predicting rate coefficients. The activation Gibbs energies obtained from our proposed method were lower than those obtained from the IGT method due to reasonable entropy computations. The proposed method overestimated the rate coefficients by one to two orders of magnitude compared to the experimental values, whereas the IGT method underestimated them by the same amount. This discrepancy arises because the proposed method calculates the partition function from the viewpoint of a localized system, whereas the IGT method calculates it from the viewpoint of a non-localized system. Given that actual liquids exist in a state between non-localized and localized systems, it is essential to formulate the partition function in a way that more accurately represents the liquid state.

Design and Optimization of Molecularly Imprinted Polymer Targeting Epinephrine Molecule: A Theoretical Approach

Molecularly imprinted polymers (MIPs) are a growing highlight in polymer chemistry. They are chemically and thermally stable, may be used in a variety of environments, and fulfill a wide range of applications. Computer-aided studies of MIPs often involve the use of computational techniques to design, analyze, and optimize the production of MIPs. Limited information is available on the computational study of interactions between the epinephrine (EPI) MIP and its target molecule. A rational design for EPI-MIP preparation was performed in this study. First, density functional theory (DFT) and molecular dynamic (MD) simulation were used for the screening of functional monomers suitable for the design of MIPs of EPI in the presence of a crosslinker and a solvent environment. Among the tested functional monomers, acrylic acid (AA) was the most appropriate monomer for EPI-MIP formulation. The trends observed for five out of six DFT functionals assessed confirmed AA as the suitable monomer. The theoretical optimal molar ratio was 1:4 EPI:AA in the presence of ethylene glycol dimethacrylate (EGDMA) and acetonitrile. The effect of temperature was analyzed at this ratio of EPI:AA on mean square displacement, X-ray diffraction, density distribution, specific volume, radius of gyration, and equilibrium energies. The stability observed for all these parameters is much better, ranging from 338 to 353 K. This temperature may determine the processing and operating temperature range of EPI-MIP development using AA as a functional monomer. For cost-effectiveness and to reduce time used to prepare MIPs in the laboratory, these results could serve as a useful template for designing and developing EPI-MIPs.

Thermal Truncation of Heptamethine Cyanine Dyes

Cyanine dyes are a class of organic, usually cationic molecules containing two nitrogen centers linked through conjugated polymethine chains. The synthesis and reactivity of cyanine derivatives have been extensively investigated for decades. Unlike the recently described phototruncation process, the thermal truncation (chain shortening) reaction is a phenomenon that has rarely been reported for these important fluorophores. Here, we present a systematic investigation of the truncation of heptamethine cyanines (Cy7) to pentamethine (Cy5) and trimethine (Cy3) cyanines via homogeneous, acid-base-catalyzed nucleophilic exchange reactions. We demonstrate how different substituents at the C3' and C4' positions of the chain and different heterocyclic end groups, the presence of bases, nucleophiles, and oxygen, solvent properties, and temperature affect the truncation process. The mechanism of chain shortening, studied by various analytical and spectroscopic techniques, was verified by extensive ab initio calculation, implying the necessity to model catalytic reactions by highly correlated wave function-based methods. In this study, we provide critical insight into the reactivity of cyanine polyene chains and elucidate the truncation mechanism and methods to mitigate side processes that can occur during the synthesis of cyanine derivatives. In addition, we offer alternative routes to the preparation of symmetrical and unsymmetrical meso-substituted Cy5 derivatives.

Mechanism of Methyl Transfer Reaction between CH3Co(dmgBF2)2py and PPh3Ni(Triphos)

DFT calculations were performed for the methyl group transfer reaction between CH3Co (dmgBF2)py and PPh3Ni(Triphos). The reaction mechanism and its energetics were investigated. This reaction is relevant to the catalytic mechanism of the enzyme acetyl coenzyme A synthase. BP86 and PBE functionals and dispersion corrections were used. It was found that intermolecular interactions are very important for this reaction. The influence of the solvent on the reaction was studied.

Cationic Hypervalent Chalcogen Bond Catalysis on the Povarov Reaction: Reactivity and Stereoselectivity

Chalcogen bond catalysis, particularly cationic hypervalent chalcogen bond catalysis, is considered to be an effective strategy for organocatalysis. In this work, the cationic hypervalent chalcogen bond catalysis for the Povarov reaction between N-benzylideneaniline and ethyl vinyl ether was investigated by density functional theory (DFT). The catalytic reaction involves the cycloaddition process and the proton transfer process, and the rate-determining step is the cycloaddition process. Cationic hypervalent tellurium derivatives bearing CF3 and F groups exhibit superior catalytic activity. For the rate-determining step, the Gibbs free energy barrier decreases as the positive electrostatic potential of the chalcogen bond catalysts increases. More importantly, the Gibbs free energy barrier has a strong linear correlation with the electrostatic energy of the chalcogen bond in the catalyst-substrate complex. Furthermore, the catalytic reactions include the endo pathway and exo pathway. The C-H⋅⋅⋅π interaction between the substituent of the ethyl vinyl ether and the aryl ring of the N-benzylideneaniline contributes to the endo-selectivity of the reaction. This research contributes to a deeper understanding of chalcogen bond catalysis, providing insights for designing chalcogen bond catalysts with high performance.

Molecular Engineering and Confinement Effect Powered Ultrabright Nanoparticles for Improving Sensitivity of Lateral Flow Immunoassay

The application of traditional lateral flow immunoassay (LFIA)-based gold nanoparticles (AuNPs) to measure traces of target chemicals is usually challenging. In this study, we developed an integrated strategy based on molecular engineering and the spatial confinement of nanoparticles (NPs) to obtain ultrahigh quantum yields (QYs) of aggregation-induced emission (AIE) fluorescence NPs and employed them for the highly sensitive detection of T-2 toxin on the LFIA platform. Tetraethyl-4,4',4″,4‴-(ethene-1,1,2,2-tetrayl)tetrabenzoate (TCPEME), an AIE luminogen, was designed using molecular engineering to lower the energy gap, achieving higher QYs (26.26%) than previous AIEgens (13.02%). Subsequently, TCPEME-doped fluorescence NPs (TFNPs) achieved ultrahigh QYs, up to 84.55%, which were generated from the strong restriction of the NP state, efficiently suppressing nonradiative relaxation channels verified by ultrafast electron dynamics. On the LFIA platform, the sensitivity of the designed TFNP-based LFIA (TFNP-LFIA) was 10.4-fold and 4.3-fold more sensitive than that of the AuNP-LFIA and TPENP-LFIA for detecting the T-2 toxin, respectively. In addition, TFNP-LFIA was used for detecting T-2 toxin in samples and showed satisfactory recoveries (79.5 to 122.0%) with CV (1.49 to 11.75%), which implied excellent application potential for TFNP-LFIA. Overall, dual improvement of the molecule in fluorescence performance originating from the molecular engineering and spatial confinement of NPs could be an efficient tool for promoting the development of high-performance reporters in LFIA.

Chalcogen Bond Catalysis with Telluronium Cations for Bromination Reaction: Importance of Electrostatic and Polarization Effects

Recently, chalcogen bond catalysts with telluronium cations have garnered considerable attention in organic reactions. In this work, chalcogen bond catalysis on the bromination reaction of anisole with N-bromosuccinimide (NBS) with the telluronium cationic catalysts has been explored with density functional theory (DFT). The catalytic reaction is divided into two stages: the bromine transfer step and the proton transfer step. Based on the computational results, one can find the rate-determining step is the bromine transfer step. Moreover, the present study elucidates that a stronger chalcogen bond between catalysts and NBS will give better catalytic performance. Additionally, this work also clarified the importance of the electrostatic and polarization effects in the chalcogen bond between the oxygen atom of NBS and the Te atom of the catalyst in this bromination reaction. The electrostatic and polarization effects are significantly influenced by the electron-withdrawing ability of the substitution groups on the catalysts. Moreover, the structure-property relationship between the strength of chalcogen bond, electrostatic effect, polarization effect and catalytic performance are established for the design of more efficient chalcogen bond catalysts.

DFT Studies on the Mechanisms of Carboamination/Diamination of Unactivated Alkenes Mediated by Pd(IV) Intermediates

Density functional theory (DFT) calculations have been employed to investigate the mechanism of carboamination and diamination of unactivated alkenes mediated by Pd(IV) intermediates. Both reactions share a common Pd(IV) intermediate, serving as the starting point for either the carboamination or the diamination pathway. The formation of this Pd(IV) intermediate encompasses a transition state that substantially impacts the turnover frequency (TOF) of catalytic cycles, with an apparent activation free-energy barrier of 26.1 kcal mol-1. Carboamination of unactivated alkenes proceeds through the coordination of a toluene molecule, C-H activation, inner reductive elimination, and the separation of the carboamination product from this intermediate, while diamination of unactivated alkenes involves the formation of the ion nucleophile, SN2 attack, and the separation of the diamination product. A comparison of the free-energy profiles for carboamination and diamination of unactivated alkenes can elucidate the origin of the chemoselectivity, and Bader's atoms in molecules (AIM) wave function analyses have been performed to analyze the contributions of the outer C-N bonding in the diamination process.

Solvation Plays a Key Role in Antioxidant-Mediated Attenuation of Elevated Creatinine Level: An In Vitro Spectroscopic Investigation

An elevated level of creatinine (CRN) is a mark of kidney ailment, and prolonged retention of such condition could lead to renal failure, associated with severe ischemia. Antioxidants are clinically known to excrete CRN from the body through urine, thereby reducing its level in blood. The molecular mechanism of such an exclusion process is still illusive. As the excretion channel is urine, solvation of the solute is expected to play a pivotal role. Here, we report a detailed time-domain and frequency-domain terahertz (THz) spectroscopic investigation to understand the solvation of CRN in the presence of two model antioxidants, mostly used to treat elevated CRN level: N-Acetyl-l-cysteine (NAC) and ascorbic acid (ASC). FTIR spectroscopy in the mid-infrared region and UV absorption spectroscopy measurements coupled with quantum chemical calculations [at the B3LYP/6-311G++(d,p) level] reveal that both NAC and ASC form HBonded complexes with CRN and rapidly undergo a barrier-less proton transfer process to form creatinium ions. THz measurements provide explicit evidence of the formation of highly solvated complexes compared with bare CRN, which eventually enables its excretion through urine. These observations could provide a foundation for designing more beneficial drugs to resolve kidney diseases..

Iodine(I)-based and iodine(III)-based halogen bond catalysis on the Friedel-Crafts reaction: a theoretical study

Halogen bond catalysis, especially iodine derivatives catalysis, has attracted increasing attention in recent years owing to the advantages of relatively cheap, stable, green, easy to handle, and favorable catalytic activity. To obtain insights into the catalytic mechanism and activity of halogen bond donor catalysts, iodine(I)-based and iodine(III)-based halogen bond catalysis on the Friedel-Crafts reaction were investigated in this study. The entire reaction contains several key steps: carbon-carbon bond coupling, proton transfer, hydroxyl departure, indole addition, and deprotonation process. According to the energetic span model, iodine(III)-based donor catalysts exhibit higher catalytic activity than iodine(I)-based catalysts and double cationic catalysts are more potent than single cationic ones. For halogen bond catalysis, the Gibbs energy barriers have linear relation to the electron density at the halogen bond critical points. Furthermore, the Gibbs energy barriers are also linearly related to the integral charge values of the increased region of electron density outside the oxygen atom of reactants. Therefore, the stronger halogen bond results in lower Gibbs energy barrier, and the stronger polarization further benefits the halogen bond catalysis.